From b7b9ee7c1327a2561b4ba28d3d12c0a4dbf06cc7 Mon Sep 17 00:00:00 2001
From: Stephane Dallongeville <stephane.dallongeville@pasteur.fr>
Date: Thu, 3 Dec 2020 18:35:10 +0100
Subject: [PATCH] Merged Protocols SDK and Protocols plugins as they were inter
dependant
---
.../adufour/blocks/lang/ArrayLoop.java | 9 +
.../plugins/adufour/blocks/lang/Batch.java | 155 ++
.../plugins/adufour/blocks/lang/Block.java | 33 +
.../adufour/blocks/lang/BlockDescriptor.java | 1121 +++++++++++
.../adufour/blocks/lang/FileBatch.java | 130 ++
.../adufour/blocks/lang/FolderLoop.java | 9 +
.../plugins/adufour/blocks/lang/Link.java | 126 ++
.../plugins/adufour/blocks/lang/Loop.java | 278 +++
.../adufour/blocks/lang/RangeLoop.java | 98 +
.../blocks/lang/SequenceFileBatch.java | 56 +
.../blocks/lang/SequenceSeriesBatch.java | 110 ++
.../plugins/adufour/blocks/lang/WorkFlow.java | 1175 +++++++++++
.../adufour/blocks/tools/Accumulator.java | 142 ++
.../plugins/adufour/blocks/tools/Display.java | 52 +
.../plugins/adufour/blocks/tools/Indexer.java | 61 +
.../adufour/blocks/tools/Iterator.java | 68 +
.../adufour/blocks/tools/ListSize.java | 31 +
.../plugins/adufour/blocks/tools/ReLoop.java | 68 +
.../adufour/blocks/tools/ToolsBlock.java | 8 +
.../adufour/blocks/tools/ij/CallIJMacro.java | 30 +
.../adufour/blocks/tools/ij/CallIJPlugin.java | 61 +
.../adufour/blocks/tools/ij/IJBlock.java | 13 +
.../blocks/tools/ij/ImagePlusToSequence.java | 32 +
.../blocks/tools/ij/SequenceToImagePlus.java | 32 +
.../blocks/tools/ij/ShowImagePlus.java | 28 +
.../adufour/blocks/tools/input/Boolean.java | 24 +
.../adufour/blocks/tools/input/Decimal.java | 29 +
.../adufour/blocks/tools/input/Decimals.java | 29 +
.../adufour/blocks/tools/input/File.java | 34 +
.../adufour/blocks/tools/input/Files.java | 34 +
.../adufour/blocks/tools/input/Folder.java | 34 +
.../adufour/blocks/tools/input/Folders.java | 34 +
.../blocks/tools/input/InputBlock.java | 13 +
.../adufour/blocks/tools/input/Integer.java | 30 +
.../adufour/blocks/tools/input/Integers.java | 29 +
.../adufour/blocks/tools/input/Sequence.java | 36 +
.../adufour/blocks/tools/input/Sequences.java | 30 +
.../adufour/blocks/tools/input/Text.java | 31 +
.../blocks/tools/io/AppendFilePath.java | 58 +
.../adufour/blocks/tools/io/CreateFile.java | 62 +
.../adufour/blocks/tools/io/CreateFolder.java | 57 +
.../adufour/blocks/tools/io/FileToPath.java | 31 +
.../blocks/tools/io/FileToSequence.java | 56 +
.../blocks/tools/io/FilesToSequence.java | 57 +
.../blocks/tools/io/GetSequenceFolder.java | 40 +
.../adufour/blocks/tools/io/IOBlock.java | 14 +
.../adufour/blocks/tools/io/PathToFile.java | 34 +
.../blocks/tools/io/SendToSwimmingPool.java | 47 +
.../blocks/tools/io/SequenceToFile.java | 47 +
.../blocks/tools/roi/AddROIToSequence.java | 56 +
.../blocks/tools/roi/CropSequenceToROI.java | 114 ++
.../adufour/blocks/tools/roi/DilateROI.java | 265 +++
.../adufour/blocks/tools/roi/ErodeROI.java | 259 +++
.../blocks/tools/roi/GetROIFromSequence.java | 72 +
.../adufour/blocks/tools/roi/MergeROI.java | 47 +
.../adufour/blocks/tools/roi/MorphROI.java | 115 ++
.../adufour/blocks/tools/roi/ROIBlock.java | 14 +
.../adufour/blocks/tools/roi/SubtractROI.java | 66 +
.../blocks/tools/roi/TranslateROI.java | 83 +
.../blocks/tools/sequence/SequenceBlock.java | 14 +
.../tools/sequence/SequenceScreenshot.java | 67 +
.../blocks/tools/sequence/ShowSequence.java | 35 +
.../adufour/blocks/tools/text/AppendText.java | 53 +
.../adufour/blocks/util/BlockAnnotations.java | 232 +++
.../adufour/blocks/util/BlockInfo.java | 23 +
.../adufour/blocks/util/BlockListener.java | 20 +
.../adufour/blocks/util/BlocksException.java | 29 +
.../adufour/blocks/util/BlocksFinder.java | 752 +++++++
.../plugins/adufour/blocks/util/BlocksML.java | 1753 +++++++++++++++++
.../blocks/util/BlocksReloadedException.java | 10 +
.../adufour/blocks/util/LinkCutException.java | 10 +
.../adufour/blocks/util/LoopException.java | 18 +
.../adufour/blocks/util/MenuItemListener.java | 7 +
.../blocks/util/NoSuchBlockException.java | 25 +
.../blocks/util/NoSuchLinkException.java | 12 +
.../blocks/util/NoSuchVariableException.java | 24 +
.../adufour/blocks/util/ScopeException.java | 13 +
.../adufour/blocks/util/StopException.java | 10 +
.../plugins/adufour/blocks/util/VarList.java | 334 ++++
.../adufour/blocks/util/VarListListener.java | 10 +
.../blocks/util/VarVisibilityListener.java | 8 +
.../adufour/blocks/util/WorkFlowListener.java | 85 +
.../plugins/adufour/protocols/Protocols.java | 26 +-
.../adufour/protocols/gui/MainFrame.java | 3 +-
.../logo/icysoftware_icon-protocols-sdk.png | Bin 0 -> 6683 bytes
85 files changed, 9469 insertions(+), 11 deletions(-)
create mode 100644 src/main/java/plugins/adufour/blocks/lang/ArrayLoop.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/Batch.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/Block.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/BlockDescriptor.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/FileBatch.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/FolderLoop.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/Link.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/Loop.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/RangeLoop.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/SequenceFileBatch.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/SequenceSeriesBatch.java
create mode 100644 src/main/java/plugins/adufour/blocks/lang/WorkFlow.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/Accumulator.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/Display.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/Indexer.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/Iterator.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ListSize.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ReLoop.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ToolsBlock.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ij/CallIJMacro.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ij/CallIJPlugin.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ij/IJBlock.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ij/ImagePlusToSequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ij/SequenceToImagePlus.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/ij/ShowImagePlus.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Boolean.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Decimal.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Decimals.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/File.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Files.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Folder.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Folders.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/InputBlock.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Integer.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Integers.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Sequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Sequences.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/input/Text.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/AppendFilePath.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/CreateFile.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/CreateFolder.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/FileToPath.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/FileToSequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/FilesToSequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/GetSequenceFolder.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/IOBlock.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/PathToFile.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/SendToSwimmingPool.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/io/SequenceToFile.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/AddROIToSequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/CropSequenceToROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/DilateROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/ErodeROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/GetROIFromSequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/MergeROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/MorphROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/ROIBlock.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/SubtractROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/roi/TranslateROI.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/sequence/SequenceBlock.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/sequence/SequenceScreenshot.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/sequence/ShowSequence.java
create mode 100644 src/main/java/plugins/adufour/blocks/tools/text/AppendText.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlockAnnotations.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlockInfo.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlockListener.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlocksException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlocksFinder.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlocksML.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/BlocksReloadedException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/LinkCutException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/LoopException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/MenuItemListener.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/NoSuchBlockException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/NoSuchLinkException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/NoSuchVariableException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/ScopeException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/StopException.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/VarList.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/VarListListener.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/VarVisibilityListener.java
create mode 100644 src/main/java/plugins/adufour/blocks/util/WorkFlowListener.java
create mode 100644 src/main/resources/logo/icysoftware_icon-protocols-sdk.png
diff --git a/src/main/java/plugins/adufour/blocks/lang/ArrayLoop.java b/src/main/java/plugins/adufour/blocks/lang/ArrayLoop.java
new file mode 100644
index 0000000..e11ef3e
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/ArrayLoop.java
@@ -0,0 +1,9 @@
+package plugins.adufour.blocks.lang;
+
+/**
+ * @deprecated use {@link Batch} instead.
+ * @author Alexandre Dufour
+ */
+@Deprecated
+public class ArrayLoop extends Batch
+{}
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/blocks/lang/Batch.java b/src/main/java/plugins/adufour/blocks/lang/Batch.java
new file mode 100644
index 0000000..fa8ac3f
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/Batch.java
@@ -0,0 +1,155 @@
+package plugins.adufour.blocks.lang;
+
+import java.lang.reflect.Array;
+import java.util.List;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarArray;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarMutableArray;
+import plugins.adufour.vars.util.VarException;
+import plugins.adufour.vars.util.VarListener;
+
+/**
+ * A batch is a particular type of work-flow that will execute repeatedly for every element of a
+ * list of items, allowing to process all list items with a same work-flow. This is the most generic
+ * type of batch available, however there are more user-friendly versions available, such as for
+ * instance a {@link FileBatch File batch} or a {@link SequenceFileBatch Sequence file batch}.
+ *
+ * @author Alexandre Dufour
+ */
+public class Batch extends Loop
+{
+ private VarMutableArray array;
+
+ private VarMutable element;
+
+ /**
+ * Defines the variable used to determine the list of objects to batch process.<br>
+ * By default, this variable is simply a {@link VarArray} containing the elements to process,
+ * but overriding classes may provide special functionalities.
+ *
+ * @see FileBatch#getBatchSource()
+ * @see SequenceFileBatch#getBatchSource()
+ * @see SequenceSeriesBatch#getBatchSource()
+ * @return the variable used to define the contents of the batch
+ */
+ @SuppressWarnings({"unchecked", "rawtypes"})
+ public Var<?> getBatchSource()
+ {
+ if (array == null)
+ {
+ array = new VarMutableArray("array", null);
+ array.addListener(new VarListener()
+ {
+ @Override
+ public void valueChanged(Var source, Object oldValue, Object newValue)
+ {
+ }
+
+ @Override
+ public void referenceChanged(Var source, Var oldReference, Var newReference)
+ {
+ if (oldReference == null)
+ {
+ if (newReference != null)
+ {
+ element.setType(newReference.getType().getComponentType());
+ }
+ }
+ else if (element.isReferenced())
+ {
+ if (newReference != null && newReference.getType() != oldReference.getType())
+ throw new IllegalAccessError("Cannot change the type of a linked mutable variable");
+ }
+ else
+ {
+ if (newReference == null)
+ {
+ element.setType(null);
+ array.setType(null);
+ }
+ else
+ {
+ element.setType(newReference.getType().getComponentType());
+ }
+ }
+ }
+ });
+ }
+ return array;
+ }
+
+ /**
+ * Defines the variable that will contain each element of the batch process, consecutively.
+ *
+ * @see FileBatch#getBatchElement()
+ * @see SequenceFileBatch#getBatchElement()
+ * @see SequenceSeriesBatch#getBatchElement()
+ * @return the inner variable that will contain each element to process
+ */
+ public Var<?> getBatchElement()
+ {
+ if (element == null)
+ {
+ // WARNING: do *not* change the name of this variable
+ // why? see declareInput() below and VarList.add()
+ element = new VarMutable("element", null);
+ }
+
+ return element;
+ }
+
+ @Override
+ public void initializeLoop()
+ {
+ if (array == null || Array.getLength(array.getValue(true)) == 0)
+ throw new VarException(array, "Cannot loop on an empty array");
+ }
+
+ @Override
+ public void beforeIteration()
+ {
+ element.setValue(array.getElementAt(getIterationCounter().getValue()));
+ }
+
+ @Override
+ public boolean isStopConditionReached()
+ {
+ return getIterationCounter().getValue() == Array.getLength(array.getValue());
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ Var<?> batchSource = getBatchSource();
+
+ inputMap.add(batchSource.getName(), getBatchSource());
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ super.declareOutput(outputMap);
+
+ Var<?> batchElement = getBatchElement();
+
+ outputMap.add(batchElement.getName(), batchElement);
+ }
+
+ /**
+ * {@inheritDoc} <br>
+ * <br>
+ * The implementation provided in this class automatically declares the source and element of
+ * the batch as loop variables, therefore they don't need to be declared by overriding classes
+ */
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ loopVariables.add(getBatchSource());
+ loopVariables.add(getBatchElement());
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/Block.java b/src/main/java/plugins/adufour/blocks/lang/Block.java
new file mode 100644
index 0000000..55a27de
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/Block.java
@@ -0,0 +1,33 @@
+package plugins.adufour.blocks.lang;
+
+import plugins.adufour.blocks.util.VarList;
+
+/**
+ * Interface indicating that implementing classes can be used in a block programming context
+ *
+ * @see WorkFlow
+ * @author Alexandre Dufour
+ */
+public interface Block extends Runnable
+{
+ /**
+ * Fills the specified map with all the necessary input variables
+ *
+ * @param inputMap
+ * the list of input variables to fill
+ */
+ void declareInput(final VarList inputMap);
+
+ /**
+ * Fills the specified map with all the necessary output variables
+ *
+ * @param outputMap
+ * the list of output variables to fill
+ */
+ void declareOutput(final VarList outputMap);
+
+ /**
+ * Main method
+ */
+ void run();
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/BlockDescriptor.java b/src/main/java/plugins/adufour/blocks/lang/BlockDescriptor.java
new file mode 100644
index 0000000..b1b284f
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/BlockDescriptor.java
@@ -0,0 +1,1121 @@
+package plugins.adufour.blocks.lang;
+
+import java.awt.Dimension;
+import java.awt.Point;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+
+import icy.file.xml.XMLPersistent;
+import icy.gui.plugin.PluginErrorReport;
+import icy.network.NetworkUtil;
+import icy.plugin.PluginDescriptor;
+import icy.plugin.PluginInstaller;
+import icy.plugin.PluginLoader;
+import icy.plugin.PluginRepositoryLoader;
+import icy.plugin.abstract_.Plugin;
+import icy.util.ClassUtil;
+import icy.util.StringUtil;
+import icy.util.XMLUtil;
+import plugins.adufour.blocks.tools.Display;
+import plugins.adufour.blocks.tools.input.InputBlock;
+import plugins.adufour.blocks.util.*;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarMutableArray;
+import plugins.adufour.vars.util.MutableType;
+import plugins.adufour.vars.util.VarListener;
+
+/**
+ * Class defining all the metadata associated to a {@link Block}.
+ *
+ * @author Alexandre Dufour
+ */
+@SuppressWarnings("rawtypes")
+public class BlockDescriptor implements Runnable, VarListener, VarListListener, XMLPersistent
+{
+ public static enum BlockStatus
+ {
+ /**
+ * The result is not up-to-date. This status is active at startup and whenever a variable is
+ * changed
+ */
+ DIRTY("This block is ready to run"),
+ /**
+ * The block is currently running
+ */
+ RUNNING("This block is currently running..."),
+ /**
+ * The result is up-to-date and need not be recomputed (unless explicitly required)
+ */
+ READY("This block is up to date"),
+ /**
+ * There was an error while running this block
+ */
+ ERROR("This block did not run properly");
+
+ public final String defaultErrorMessage;
+
+ private String optionalUserMessage = "";
+
+ private BlockStatus(String message)
+ {
+ defaultErrorMessage = message;
+ }
+
+ public String getUserMessage()
+ {
+ return optionalUserMessage;
+ }
+
+ public void setUserMessage(String message)
+ {
+ optionalUserMessage = (message != null ? message : "");
+ }
+
+ @Override
+ public String toString()
+ {
+ return defaultErrorMessage + (optionalUserMessage.isEmpty() ? "" : ":\n" + optionalUserMessage);
+ }
+ }
+
+ private Integer id = hashCode();
+
+ private Block block;
+
+ private WorkFlow container;
+
+ private final HashSet<BlockListener> listeners = new HashSet<BlockListener>();
+
+ /**
+ * The input variables of this descriptor's block
+ */
+ public final VarList inputVars;
+
+ /**
+ * The output variables of this descriptor's block
+ */
+ public final VarList outputVars;
+
+ private final Point location = new Point();
+
+ private final Dimension dimension = new Dimension(0, 0);
+
+ private boolean collapsed = false;
+
+ private BlockStatus status = BlockStatus.DIRTY;
+
+ private boolean finalBlock;
+
+ private String definedName = null;
+
+ private boolean keepResults = true;
+
+ /** Command-line ID (used only for input blocks) */
+ private String commandLineID = "";
+
+ public BlockDescriptor()
+ {
+ this.inputVars = new VarList();
+ this.inputVars.addVarListListener(this);
+ this.outputVars = new VarList();
+ this.outputVars.addVarListListener(this);
+ }
+
+ public BlockDescriptor(int ID, Block block)
+ {
+ this();
+
+ this.block = block;
+
+ try
+ {
+ block.declareInput(inputVars);
+
+ block.declareOutput(outputVars);
+ }
+ catch (RuntimeException e)
+ {
+ String blockName = block.getClass().getName();
+
+ String devId = blockName.substring("plugins.".length());
+ devId = devId.substring(0, devId.indexOf('.'));
+
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw);
+ pw.write("Unable to insert block: " + block.getClass().getName() + "\n");
+ pw.write("Reason: " + e.getClass().getName() + ": " + e.getMessage() + "\n");
+ pw.write("Stack trace:\n");
+ e.printStackTrace(pw);
+
+ PluginErrorReport.report(null, devId, sw.toString());
+ }
+
+ if (ID != -1)
+ id = ID;
+ }
+
+ /**
+ * @deprecated use {@link #BlockDescriptor(int, Block)} instead
+ * @param ID
+ * Identifier
+ * @param block
+ * Block template instance.
+ * @param owner
+ * Workflow containing the new block.
+ * @param location
+ * Position of the new block.
+ */
+ @Deprecated
+ public BlockDescriptor(int ID, Block block, WorkFlow owner, Point location)
+ {
+ this(ID, block);
+
+ this.container = owner;
+ setLocation(location.x, location.y);
+ }
+
+ /**
+ * Adds a new input variable to this block <u>after</u> it has been initialized. This method is
+ * called when the block is embedded inside another work flow, such that the block variables can
+ * be later exposed (and linked) outside the work flow.
+ * <p>
+ * NB: default (startup) block variables are not added here, they are automatically created in
+ * {@link #BlockDescriptor(int, Block)} via {@link Block#declareInput(VarList)} and
+ * {@link Block#declareOutput(VarList)}.
+ *
+ * @param uid
+ * a unique identifier for the variable
+ * @param variable
+ * the variable to add
+ * @throws IllegalArgumentException
+ * if a variable with same unique ID exists
+ */
+ public void addInput(String uid, Var<?> variable) throws IllegalArgumentException
+ {
+ inputVars.add(uid, variable);
+ }
+
+ /**
+ * Adds a new input variable to this block <u>after</u> it has been initialized. This method is
+ * called when the block is embedded inside another work flow, such that the block variables can
+ * be later exposed (and linked) outside the work flow.
+ * <p>
+ * NB: default (startup) block variables are not added here, they are automatically created in
+ * {@link #BlockDescriptor(int, Block)} via {@link Block#declareInput(VarList)} and
+ * {@link Block#declareOutput(VarList)}.
+ *
+ * @param uid
+ * a unique identifier for the variable
+ * @param variable
+ * the variable to add
+ * @throws IllegalArgumentException
+ * if a variable with same unique ID exists
+ */
+ public void addOutput(String uid, Var<?> variable) throws IllegalArgumentException
+ {
+ outputVars.add(uid, variable);
+ }
+
+ public void addBlockListener(BlockListener listener)
+ {
+ listeners.add(listener);
+ }
+
+ public void addBlockPanelListener(BlockListener listener)
+ {
+ listeners.add(listener);
+ }
+
+ public void removeBlockListener(BlockListener listener)
+ {
+ listeners.remove(listener);
+ }
+
+ public void removeBlockPanelListener(BlockListener listener)
+ {
+ listeners.remove(listener);
+ }
+
+ public Block getBlock()
+ {
+ return block;
+ }
+
+ public WorkFlow getContainer()
+ {
+ return container;
+ }
+
+ public Dimension getDimension()
+ {
+ return dimension;
+ }
+
+ public Integer getID()
+ {
+ return id;
+ }
+
+ /**
+ * @return the location of the block in the work flow (use only in graphical mode)
+ */
+ public Point getLocation()
+ {
+ return location;
+ }
+
+ /**
+ * @return The name of the block
+ */
+ public String getName()
+ {
+ String blockName = block.getClass().getSimpleName();
+
+ if (block instanceof Plugin && ((Plugin) block).getDescriptor() != null)
+ {
+ String pluginName = ((Plugin) block).getDescriptor().getName();
+
+ if (!pluginName.equalsIgnoreCase(blockName))
+ return pluginName;
+ }
+
+ if (blockName.endsWith("block"))
+ {
+ blockName = blockName.substring(0, blockName.lastIndexOf("block"));
+ }
+ else if (blockName.endsWith("Block"))
+ {
+ blockName = blockName.substring(0, blockName.lastIndexOf("Block"));
+ }
+
+ return BlocksFinder.getFlattened(blockName);
+ }
+
+ public BlockStatus getStatus()
+ {
+ return status;
+ }
+
+ /**
+ * Retrieves the unique ID of this variable. This method first searches in the list of input
+ * variables, and then in the list of output variables if necessary.
+ *
+ * @param variable
+ * The variable to retrieve.
+ * @return Identifier of the given variable.
+ * @throws NoSuchVariableException
+ * If the variable cannot be found in this block's input or output.
+ */
+ public String getVarID(Var<?> variable) throws NoSuchVariableException
+ {
+ if (inputVars.contains(variable))
+ {
+ String varID = inputVars.getID(variable);
+
+ if (!isWorkFlow() || varID.contains(":"))
+ return varID;
+
+ return ((WorkFlow) block).getInputVarID(variable);
+ }
+
+ String varID = outputVars.getID(variable);
+
+ if (!isWorkFlow() || varID.contains(":"))
+ return varID;
+
+ return ((WorkFlow) block).getOutputVarID(variable);
+ }
+
+ public boolean isCollapsed()
+ {
+ return collapsed;
+ }
+
+ /**
+ * @return true if this block is the last block to execute in the work flow. If true, then the
+ * execution of the top-level work flow will stop after execution of this block.
+ */
+ public boolean isFinalBlock()
+ {
+ return finalBlock;
+ }
+
+ public boolean isLoop()
+ {
+ return block instanceof Loop;
+ }
+
+ public boolean isSingleBlock()
+ {
+ return block instanceof Display || block instanceof InputBlock;
+ }
+
+ public boolean isWorkFlow()
+ {
+ return block instanceof WorkFlow;
+ }
+
+ public boolean isTopLevelWorkFlow()
+ {
+ // Stephane FIX: properly detect top level workflow
+ return isWorkFlow() && ((WorkFlow) block).isTopLevel();
+ // return isWorkFlow() && container == null;
+ }
+
+ public void setCollapsed(boolean collapsed)
+ {
+ if (this.collapsed == collapsed)
+ return;
+
+ this.collapsed = collapsed;
+
+ for (BlockListener l : listeners)
+ l.blockCollapsed(this, collapsed);
+ }
+
+ public void setContainer(WorkFlow container)
+ {
+ this.container = container;
+ }
+
+ /**
+ * Sets whether this block is the last block to execute in the work flow. If true, then the
+ * execution of the top-level work flow will stop after execution of this block. Note that if
+ * multiple blocks are marked as final, the execution will stop after the first block marked
+ * final, in order of execution.
+ *
+ * @param finalBlock
+ * true to stop the work flow after running this block, false otherwise.
+ */
+ public void setFinalBlock(boolean finalBlock)
+ {
+ this.finalBlock = finalBlock;
+ }
+
+ /**
+ * Sets the dimension of this block.
+ *
+ * @param width
+ * Width of the block in pixels.
+ * @param height
+ * Height of the block in pixels.
+ */
+ public void setDimension(int width, int height)
+ {
+ if (dimension.width == width && dimension.height == height)
+ return;
+
+ dimension.setSize(width, height);
+
+ for (BlockListener l : listeners)
+ l.blockDimensionChanged(this, width, height);
+ }
+
+ /**
+ * Sets the ID of this block.
+ *
+ * @param id
+ * Block unique identifier.
+ */
+ public void setID(int id)
+ {
+ this.id = id;
+ }
+
+ /**
+ * Sets the value of the specified input variable
+ *
+ * @param <T>
+ * Type of the value of the variable being set.
+ * @param varID
+ * The unique ID of the input variable to set.
+ * @param value
+ * The new variable value.
+ * @throws NoSuchVariableException
+ * If the variable is not in this block.
+ */
+ public <T> void setInput(String varID, T value) throws NoSuchVariableException
+ {
+ Var<T> input = inputVars.get(varID);
+ if (input == null)
+ throw new NoSuchVariableException(this, varID);
+
+ input.setValue(value);
+ }
+
+ /**
+ * Stores the location of the block and notifies listeners.
+ *
+ * @param x
+ * X-axis position in pixels.
+ * @param y
+ * Y-axis position in pixels.
+ */
+ public void setLocation(int x, int y)
+ {
+ if (location.x == x && location.y == y)
+ return;
+
+ location.move(x, y);
+ for (BlockListener l : listeners)
+ l.blockLocationChanged(this, x, y);
+ }
+
+ /**
+ * Sets the value of the specified output variable
+ *
+ * @param <T>
+ * Type of the value in the variable being set.
+ * @param varID
+ * the unique ID of the output variable to set
+ * @param value
+ * the new variable value
+ * @throws NoSuchVariableException
+ * if the variable is not in this block
+ */
+ public <T> void setOutput(String varID, T value) throws NoSuchVariableException
+ {
+ Var<T> output = outputVars.get(varID);
+ if (output == null)
+ throw new NoSuchVariableException(this, varID);
+
+ output.setValue(value);
+ }
+
+ public void setStatus(BlockStatus newStatus)
+ {
+ if (this.status == newStatus)
+ return;
+
+ this.status = newStatus;
+ for (BlockListener listener : listeners)
+ listener.blockStatusChanged(this, status);
+
+ if (status == BlockStatus.DIRTY && container != null)
+ {
+ // propagate dirty status to the container (if it is not running)
+ BlockDescriptor wfDescriptor = container.getBlockDescriptor();
+
+ if (wfDescriptor.getStatus() != BlockStatus.RUNNING)
+ {
+ wfDescriptor.setStatus(BlockStatus.DIRTY);
+ }
+ }
+ }
+
+ /**
+ * Removes the specified variable from the list of inputs
+ *
+ * @param inputVar
+ * Variable to be removed from the input variable list.
+ */
+ public void removeInput(Var<?> inputVar)
+ {
+ if (!inputVars.contains(inputVar))
+ return;
+
+ inputVars.setVisible(inputVar, false);
+ inputVars.remove(inputVar);
+ }
+
+ /**
+ * Removes the specified variable from the list of outputs
+ *
+ * @param outputVar
+ * Variable to be removed from the output variable list.
+ */
+ public void removeOutput(Var<?> outputVar)
+ {
+ if (!outputVars.contains(outputVar))
+ return;
+
+ outputVars.setVisible(outputVar, false);
+ outputVars.remove(outputVar);
+ }
+
+ /**
+ * Resets all output variables in this block to their default value
+ */
+ @SuppressWarnings("unchecked")
+ public void reset()
+ {
+ setStatus(BlockStatus.DIRTY);
+
+ for (Var var : outputVars)
+ var.setValue(var.getDefaultValue());
+
+ if (isWorkFlow())
+ ((WorkFlow) block).reset();
+ }
+
+ public void run()
+ {
+ if (keepResults && status == BlockStatus.READY)
+ return;
+
+ setStatus(BlockStatus.RUNNING);
+
+ try
+ {
+ block.run();
+ setStatus(keepResults ? BlockStatus.READY : BlockStatus.DIRTY);
+ }
+ catch (RuntimeException e)
+ {
+ BlockStatus error = BlockStatus.ERROR;
+
+ error.setUserMessage(e.getMessage());
+
+ setStatus(error);
+ throw e;
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void valueChanged(Var source, Object oldValue, Object newValue)
+ {
+ if (inputVars.contains(source))
+ setStatus(BlockStatus.DIRTY);
+
+ for (BlockListener listener : listeners)
+ listener.blockVariableChanged(this, source, newValue);
+ }
+
+ @Override
+ public void referenceChanged(Var source, Var oldReference, Var newReference)
+ {
+ setStatus(BlockStatus.DIRTY);
+ }
+
+ @Override
+ public String toString()
+ {
+ return getContainer().getBlockDescriptor().getName() + "." + getName();
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void variableAdded(VarList list, Var<?> variable)
+ {
+ variable.addListener(this);
+
+ for (BlockListener listener : listeners)
+ listener.blockVariableAdded(this, variable);
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void variableRemoved(VarList list, Var<?> variable)
+ {
+ variable.removeListener(this);
+
+ // although we removed a variable, there is no "removed" notifier
+ // use the "added" notifier just for the sake of refreshing the GUI
+ for (BlockListener listener : listeners)
+ listener.blockVariableAdded(this, variable);
+ }
+
+ /**
+ * Goes online, downloads and installs the plug-in containing the specified block
+ *
+ * @param blockType
+ * @return
+ * @throws ClassNotFoundException
+ */
+ @SuppressWarnings("unchecked")
+ private Class<? extends Block> installRequiredBlock(String pluginClassName, String blockType)
+ throws ClassNotFoundException
+ {
+ Class<?> clazz = null;
+
+ // check if the class exists, otherwise try downloading it (if online)
+ try
+ {
+ clazz = ClassUtil.findClass(blockType);
+ }
+ catch (ClassNotFoundException e)
+ {
+ if (!NetworkUtil.hasInternetAccess() || getClass().getClassLoader() == ClassLoader.getSystemClassLoader())
+ {
+ throw new BlocksException("Plugin " + blockType
+ + " is missing, but no internet connection is available.\nTry again later", true);
+ }
+
+ // String simpleName =
+ // ClassUtil.getSimpleClassName(ClassUtil.getBaseClassName(blockType));
+
+ // status.setValue("Downloading " + simpleName + "...");
+
+ PluginDescriptor pd = PluginRepositoryLoader.getPlugin(pluginClassName);
+
+ if (pd == null)
+ {
+ // status.setValue("Couldn't find plugin online !");
+ throw e;
+ }
+
+ // status.setValue("Installing " + simpleName + "...");
+
+ PluginInstaller.install(pd, false);
+
+ throw new BlocksReloadedException();
+ }
+
+ return (Class<? extends Block>) clazz;
+ }
+
+ @Override
+ public boolean loadFromXML(Node node)
+ {
+ boolean noWarnings = true;
+
+ Element blockNode = (Element) node;
+
+ String blockType = XMLUtil.getAttributeValue(blockNode, "blockType", null);
+
+ try
+ {
+ Class<? extends Block> blockClass = installRequiredBlock(
+ XMLUtil.getAttributeValue(blockNode, "className", null), blockType);
+
+ block = blockClass.newInstance();
+
+ if (block == null)
+ throw new BlocksException("Couldn't create block from class " + blockClass.getName(), true);
+
+ block.declareInput(inputVars);
+ block.declareOutput(outputVars);
+
+ setID(XMLUtil.getAttributeIntValue(blockNode, "ID", -1));
+
+ int width = XMLUtil.getAttributeIntValue(blockNode, "width", 500);
+ int height = XMLUtil.getAttributeIntValue(blockNode, "height", 500);
+ setDimension(width, height);
+
+ int xPos = XMLUtil.getAttributeIntValue(blockNode, "xLocation", -1);
+ int yPos = XMLUtil.getAttributeIntValue(blockNode, "yLocation", -1);
+ setLocation(xPos, yPos);
+
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = inputVars.get(uid);
+
+ if (var == null)
+ {
+ if (noWarnings)
+ {
+ System.err.println("Error(s) while loading protocol:");
+ noWarnings = false;
+ }
+ System.err.println(new NoSuchVariableException(this, uid).getMessage());
+ continue;
+ }
+
+ if (var instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ Class<?> mutableType = BlocksML.getPrimitiveType(type);
+
+ if (mutableType == null)
+ mutableType = Class.forName(type);
+
+ ((MutableType) var).setType(mutableType);
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+
+ var.loadFromXML(varNode);
+
+ inputVars.setVisible(var, XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+ }
+
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = outputVars.get(uid);
+
+ if (var == null)
+ {
+ if (noWarnings)
+ {
+ System.err.println("Error(s) while loading protocol:");
+ noWarnings = false;
+ }
+ System.err.println(new NoSuchVariableException(this, uid).getMessage());
+ continue;
+ }
+
+ outputVars.setVisible(var, XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+
+ if (var instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ Class<?> mutableType = BlocksML.getPrimitiveType(type);
+ ((MutableType) var).setType(mutableType != null ? mutableType : Class.forName(type));
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+ }
+
+ }
+ catch (ClassNotFoundException e1)
+ {
+ throw new BlocksException("Cannot create block (" + e1.getMessage() + ") => class not found", true);
+ }
+ catch (InstantiationException e)
+ {
+ e.printStackTrace();
+ }
+ catch (IllegalAccessException e)
+ {
+ e.printStackTrace();
+ }
+
+ return noWarnings;
+ }
+
+ @Override
+ public boolean saveToXML(Node node)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ public void setDefinedName(String s)
+ {
+ definedName = s;
+ }
+
+ public String getDefinedName()
+ {
+ if (definedName == null || definedName.isEmpty())
+ return getName();
+
+ return definedName;
+ }
+
+ private BlockDescriptor getBlockDescriptor(int blockId, Set<BlockDescriptor> bds)
+ {
+ for (BlockDescriptor bd : bds)
+ if (bd.getID().intValue() == blockId)
+ return bd;
+
+ return null;
+ }
+
+ private String getNewVarId(String oldVarId, Map<BlockDescriptor, BlockDescriptor> copies)
+ {
+ // search for workflow shadow exposed variable
+ final int index = oldVarId.indexOf(":");
+
+ // direct variable id ? --> return it
+ if (index == -1)
+ return oldVarId;
+
+ String result = "";
+
+ // get block Id
+ final int blockId = StringUtil.parseInt(oldVarId.substring(0, index), 0);
+ // get block descriptor from id
+ final BlockDescriptor bd = getBlockDescriptor(blockId, copies.keySet());
+ // get corresponding new block
+ final BlockDescriptor nbd = copies.get(bd);
+
+ if (nbd != null)
+ result = nbd.getID().toString();
+
+ // remaining var id
+ return result + ":" + getNewVarId(oldVarId.substring(index + 1), copies);
+ }
+
+ public BlockDescriptor clone(boolean embedding)
+ {
+ return clone(embedding, new HashMap<BlockDescriptor, BlockDescriptor>());
+ }
+
+ @SuppressWarnings("unchecked")
+ public BlockDescriptor clone(boolean embedding, Map<BlockDescriptor, BlockDescriptor> copies)
+ {
+ Class<? extends Block> blockClass = PluginLoader.getPlugin(getBlock().getClass().getName()).getPluginClass()
+ .asSubclass(Block.class);
+ WorkFlow wf = null;
+ WorkFlow wfCpy = null;
+ BlockDescriptor cpy = null;
+ Block newBlock = null;
+
+ try
+ {
+ newBlock = blockClass.newInstance();
+ }
+ catch (InstantiationException e1)
+ {
+ e1.printStackTrace();
+ }
+ catch (IllegalAccessException e1)
+ {
+ e1.printStackTrace();
+ }
+
+ cpy = (newBlock instanceof WorkFlow ? ((WorkFlow) newBlock).getBlockDescriptor()
+ : new BlockDescriptor(-1, newBlock));
+
+ cpy.setDefinedName(getDefinedName());
+ cpy.setLocation(getLocation().x + 12, getLocation().y + 12);
+ cpy.setDimension(getDimension().width, getDimension().height);
+ cpy.setCollapsed(isCollapsed());
+
+ // Clone input variables
+ for (Var oldVar : inputVars)
+ {
+ final String oldID = inputVars.getID(oldVar);
+
+ // FIX: shadow exposed variable from workflow ? --> don't copy it for now (Stephane)
+ if (oldID.contains(":") && (getBlock() instanceof WorkFlow))
+ continue;
+
+ Var newVar = cpy.inputVars.get(oldID);
+ // If newVar is null, then oldVar was a runtime variable
+ if (newVar == null)
+ {
+ newVar = new VarMutable(oldVar.getName(), oldVar.getType());
+ cpy.inputVars.addRuntimeVariable(oldID, (VarMutable) newVar);
+ }
+ else
+ {
+ if (newVar instanceof VarMutable)
+ ((VarMutable) newVar).setType(oldVar.getType());
+ newVar.setValue(oldVar.getValue());
+ }
+
+ // FIX: preserve visibility information (Stephane)
+ cpy.inputVars.setVisible(newVar, inputVars.isVisible(oldVar));
+ }
+
+ // Clone output variables
+ for (Var oldVar : outputVars)
+ {
+ final String oldID = outputVars.getID(oldVar);
+
+ // FIX: shadow exposed variable from workflow ? --> don't copy it for now (Stephane)
+ if (oldID.contains(":") && (getBlock() instanceof WorkFlow))
+ continue;
+
+ Var newVar = cpy.outputVars.get(oldID);
+ // If newVar is null, then oldVar was a runtime variable
+ if (newVar == null)
+ {
+ newVar = new VarMutable(oldVar.getName(), oldVar.getType());
+ cpy.outputVars.addRuntimeVariable(oldID, (VarMutable) newVar);
+ }
+ else
+ {
+ if (newVar instanceof VarMutable)
+ ((VarMutable) newVar).setType(oldVar.getType());
+ newVar.setValue(oldVar.getValue());
+ }
+
+ // FIX: preserve visibility information (Stephane)
+ cpy.outputVars.setVisible(newVar, outputVars.isVisible(oldVar));
+ }
+
+ if (getBlock() instanceof WorkFlow)
+ {
+ wf = (WorkFlow) getBlock();
+ wfCpy = (WorkFlow) cpy.getBlock();
+
+ BlockDescriptor tmp;
+ if (wf.getBlockSelection().isEmpty() || embedding)
+ {
+ for (BlockDescriptor bd : wf)
+ {
+ tmp = bd.clone(true, copies);
+ copies.put(bd, tmp);
+ wfCpy.addBlock(tmp);
+ wfCpy.selectBlock(tmp);
+ }
+ cloneLinks(wf.getLinksIterator(), copies, wfCpy);
+ }
+ else
+ {
+ for (BlockDescriptor bd : wf.getBlockSelection())
+ {
+ tmp = bd.clone(true, copies);
+ copies.put(bd, tmp);
+ wfCpy.addBlock(tmp);
+ wfCpy.selectBlock(tmp);
+ }
+ cloneLinks(wf.getLinkSelection(), copies, wfCpy);
+ }
+
+ for (Var oldVar : inputVars)
+ {
+ final String oldID = inputVars.getID(oldVar);
+ final int index = oldID.indexOf(":");
+
+ // shadow exposed variable ? --> try to recover it
+ if (index != -1)
+ {
+ // get block ID
+ final int blockID = StringUtil.parseInt(oldID.substring(0, index), 0);
+ // get var ID
+ final String varID = oldID.substring(index + 1);
+ // get new var ID
+ final String newVarID = getNewVarId(varID, copies);
+ // get block descriptor from ID
+ final BlockDescriptor bd = wf.getBlockByID(blockID);
+ // get corresponding new block
+ final BlockDescriptor nbd = copies.get(bd);
+ // get corresponding var for this block
+ final Var<Object> inputVar = nbd.inputVars.get(newVarID);
+
+ // finally add the shadow exposed variable if not already done (can be done in WorkFlow.addBlock(..) method) !
+ if (inputVar != null)
+ {
+ if (!cpy.inputVars.contains(inputVar))
+ cpy.addInput(wfCpy.getInputVarID(inputVar), inputVar);
+ // and preserve visibility (very important)
+ cpy.inputVars.setVisible(inputVar, inputVars.isVisible(oldVar));
+ }
+ }
+ }
+
+ for (Var oldVar : outputVars)
+ {
+ final String oldID = outputVars.getID(oldVar);
+ final int index = oldID.indexOf(":");
+
+ // shadow exposed variable ? --> try to recover it
+ if (index != -1)
+ {
+ // get block ID
+ final int blockID = StringUtil.parseInt(oldID.substring(0, index), 0);
+ // get var ID
+ final String varID = oldID.substring(index + 1);
+ // get new var ID
+ final String newVarID = getNewVarId(varID, copies);
+ // get block descriptor from ID
+ final BlockDescriptor bd = wf.getBlockByID(blockID);
+ // get corresponding new block
+ final BlockDescriptor nbd = copies.get(bd);
+ // get corresponding var for this block
+ final Var<Object> outputVar = nbd.outputVars.get(newVarID);
+
+ // finally add the shadow exposed variable if not already done (can be done in WorkFlow.addBlock(..) method) !
+ if (outputVar != null)
+ {
+ if (!cpy.outputVars.contains(outputVar))
+ cpy.addOutput(wfCpy.getInputVarID(outputVar), outputVar);
+ // and preserve visibility (very important)
+ cpy.outputVars.setVisible(outputVar, outputVars.isVisible(oldVar));
+ }
+ }
+ }
+ }
+
+ return cpy;
+ }
+
+ private static void cloneLinks(Iterable<Link<?>> iterable, Map<BlockDescriptor, BlockDescriptor> copies,
+ WorkFlow dest)
+ {
+ for (Link<?> l : iterable)
+ {
+ if (l.srcBlock.getBlock() instanceof Loop || l.dstBlock.getBlock() instanceof Loop)
+ {
+ System.err.println("Warning : cannot copy a link to a loop variable");
+ continue;
+ }
+ if (l.srcBlock.getBlock() instanceof WorkFlow || l.dstBlock.getBlock() instanceof WorkFlow)
+ {
+ System.err.println("Warning : cannot copy a link to an exposed variable");
+ continue;
+ }
+ try
+ {
+ dest.addLink(copies.get(l.srcBlock),
+ copies.get(l.srcBlock).inputVars.get(l.srcBlock.inputVars.getID(l.srcVar)),
+ copies.get(l.dstBlock),
+ copies.get(l.dstBlock).inputVars.get(l.dstBlock.inputVars.getID(l.dstVar)));
+ }
+ catch (NoSuchVariableException nsve)
+ {
+ dest.addLink(copies.get(l.srcBlock),
+ copies.get(l.srcBlock).outputVars.get(l.srcBlock.outputVars.getID(l.srcVar)),
+ copies.get(l.dstBlock),
+ copies.get(l.dstBlock).inputVars.get(l.dstBlock.inputVars.getID(l.dstVar)));
+ }
+ }
+ }
+
+ /**
+ * @return <code>true</code> if the block keeps results in memory, <code>false</code> otherwise
+ */
+ public boolean keepsResults()
+ {
+ return keepResults;
+ }
+
+ /**
+ * Sets whether the block should keep results in memory (and not need to recalculate it unless a
+ * parameter has changed)
+ *
+ * @param keep
+ * Flag to keep results in memory.
+ */
+ public void keepResults(boolean keep)
+ {
+ this.keepResults = keep;
+ }
+
+ /**
+ * (This method is used only if the block implements {@link InputBlock})
+ *
+ * @return the command-line identifier for the input block's variable
+ */
+ public String getCommandLineID()
+ {
+ return commandLineID;
+ }
+
+ /**
+ * (This method is used only if the block implements {@link InputBlock})
+ * Sets the command line identifier for this input block's variable
+ *
+ * @param id
+ * Block identifier when using the command line.
+ */
+ public void setCommandLineID(String id)
+ {
+ commandLineID = id;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/FileBatch.java b/src/main/java/plugins/adufour/blocks/lang/FileBatch.java
new file mode 100644
index 0000000..827bb51
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/FileBatch.java
@@ -0,0 +1,130 @@
+package plugins.adufour.blocks.lang;
+
+import java.io.File;
+import java.io.FileFilter;
+import java.util.List;
+
+import icy.file.FileUtil;
+import icy.gui.frame.progress.AnnounceFrame;
+import icy.main.Icy;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarString;
+import plugins.adufour.vars.util.VarException;
+
+/**
+ * A file batch is a work-flow that will execute repeatedly on every file of a
+ * user-selected folder. Files can be retrieved from sub-folders if necessary,
+ * and filtered by extension. Note however that the files are given "as-is": it
+ * is up to the user to indicate inside the work-flow how these files should be
+ * read (for the particular case of image files, use the
+ * {@link SequenceFileBatch Sequence file batch} instead).
+ *
+ * @author Alexandre Dufour
+ */
+public class FileBatch extends Batch implements FileFilter
+{
+ // loop variables //
+
+ private VarFile element;
+
+ private VarFile folder;
+
+ private VarString extension;
+
+ private VarBoolean includeSubFolders;
+
+ // local variables //
+
+ /**
+ * The list of files containing the elements to process
+ */
+ protected File[] files;
+
+ @Override
+ public Var<?> getBatchSource()
+ {
+ if (folder == null)
+ {
+ // WARNING: do *not* change the name of this variable
+ // why? see declareInput() and VarList.add()
+ folder = new VarFile("folder", null);
+ folder.setDefaultEditorModel(new FileTypeModel(null, FileMode.FOLDERS, null, false));
+ }
+ return folder;
+ }
+
+ @Override
+ public boolean accept(File f)
+ {
+ String ext = extension.getValue();
+ return f.isDirectory() || ext.isEmpty() || f.getPath().toLowerCase().endsWith(ext.toLowerCase());
+ }
+
+ @Override
+ public Var<?> getBatchElement()
+ {
+ if (element == null)
+ {
+ // WARNING: do *not* change the name of this variable
+ // why? see declareInput() and VarList.add()
+ element = new VarFile("file", null);
+ }
+ return element;
+ }
+
+ @Override
+ public void initializeLoop()
+ {
+ if (folder.getValue() == null)
+ throw new VarException(folder, "No folder indicated");
+
+ File file = folder.getValue();
+ if (!file.isDirectory())
+ throw new VarException(folder, file.getAbsolutePath() + " is not a folder");
+
+ AnnounceFrame process = null;
+
+ if (!Icy.getMainInterface().isHeadLess())
+ process = new AnnounceFrame("Listing files...");
+
+ files = FileUtil.getFiles(file, this, includeSubFolders.getValue(), false, false);
+
+ if (process != null)
+ process.close();
+ }
+
+ @Override
+ public void beforeIteration()
+ {
+ element.setValue(files[getIterationCounter().getValue()]);
+ }
+
+ @Override
+ public boolean isStopConditionReached()
+ {
+ return getIterationCounter().getValue() == files.length;
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ inputMap.add("extension", extension = new VarString("extension", ""));
+ inputMap.add("Include sub-folders", includeSubFolders = new VarBoolean("Include sub-folders", true));
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ super.declareLoopVariables(loopVariables);
+
+ loopVariables.add(extension);
+ loopVariables.add(includeSubFolders);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/FolderLoop.java b/src/main/java/plugins/adufour/blocks/lang/FolderLoop.java
new file mode 100644
index 0000000..c02f5d3
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/FolderLoop.java
@@ -0,0 +1,9 @@
+package plugins.adufour.blocks.lang;
+
+/**
+ * @deprecated use {@link FileBatch} instead.
+ * @author Alexandre Dufour
+ */
+@Deprecated
+public class FolderLoop extends FileBatch
+{}
diff --git a/src/main/java/plugins/adufour/blocks/lang/Link.java b/src/main/java/plugins/adufour/blocks/lang/Link.java
new file mode 100644
index 0000000..26cb755
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/Link.java
@@ -0,0 +1,126 @@
+package plugins.adufour.blocks.lang;
+
+import icy.file.xml.XMLPersistent;
+import icy.util.XMLUtil;
+
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+
+import plugins.adufour.blocks.util.BlocksException;
+import plugins.adufour.blocks.util.BlocksML;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarMutableArray;
+import plugins.adufour.vars.util.MutableType;
+
+/**
+ * Class describing a link between two variables within a work flow
+ *
+ * @author Alexandre Dufour
+ */
+public class Link<T> implements XMLPersistent
+{
+ private final WorkFlow workFlow;
+
+ public BlockDescriptor srcBlock;
+
+ public Var<T> srcVar;
+
+ public BlockDescriptor dstBlock;
+
+ public Var<T> dstVar;
+
+ /**
+ * Creates a new (empty) link in the specified work flow. This constructor is generally followed
+ * by a call to {@link #loadFromXML(Node)} to restore the link status from a previously saved
+ * state (e.g. XML file)
+ *
+ * @param workFlow
+ * Workflow containing the new link.
+ */
+ public Link(WorkFlow workFlow)
+ {
+ this.workFlow = workFlow;
+ }
+
+ public Link(WorkFlow workFlow, final BlockDescriptor srcBlock, final Var<T> output, final BlockDescriptor dstBlock,
+ final Var<T> input)
+ {
+ this(workFlow);
+
+ this.srcBlock = srcBlock;
+ this.srcVar = output;
+ this.dstBlock = dstBlock;
+ this.dstVar = input;
+ }
+
+ public Class<?> getType()
+ {
+ return srcVar.getType();
+ }
+
+ @SuppressWarnings({"unchecked", "rawtypes"})
+ @Override
+ public boolean loadFromXML(Node node)
+ {
+ Element linkNode = (Element) node;
+
+ int srcBlockID = XMLUtil.getAttributeIntValue(linkNode, "srcBlockID", -1);
+ String srcVarID = XMLUtil.getAttributeValue(linkNode, "srcVarID", null);
+ int dstBlockID = XMLUtil.getAttributeIntValue(linkNode, "dstBlockID", -1);
+ String dstVarID = XMLUtil.getAttributeValue(linkNode, "dstVarID", null);
+
+ // load the source variable
+ BlockDescriptor theSrcBlock = workFlow.getBlockByID(srcBlockID);
+ Var theSrcVar = theSrcBlock.outputVars.get(srcVarID);
+ if (theSrcVar == null)
+ theSrcVar = theSrcBlock.inputVars.get(srcVarID);
+
+ if (theSrcVar == null)
+ {
+ System.err.println("Cannot create a link from variable " + srcVarID + " (from block " + theSrcBlock + ")");
+ return false;
+ }
+
+ if (theSrcVar instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(linkNode, "srcVarType", null);
+ if (type != null)
+ {
+ try
+ {
+ if (theSrcVar instanceof VarMutable)
+ {
+ Class<?> mutableType = BlocksML.getPrimitiveType(type);
+ ((MutableType) theSrcVar).setType(mutableType != null ? mutableType : Class.forName(type));
+ }
+ else if (theSrcVar instanceof VarMutableArray)
+ {
+ type = "[L" + type + ";";
+ ((MutableType) theSrcVar).setType(Class.forName(type));
+ }
+ }
+ catch (ClassNotFoundException e1)
+ {
+ throw new BlocksException("Cannot create link: unknown type " + type, true);
+ }
+ }
+ }
+
+ // load the destination variable
+ BlockDescriptor theDstBlock = workFlow.getBlockByID(dstBlockID);
+
+ Var theDstVar = theDstBlock.inputVars.get(dstVarID);
+
+ workFlow.addLink(theSrcBlock, theSrcVar, theDstBlock, theDstVar);
+
+ return true;
+ }
+
+ @Override
+ public boolean saveToXML(Node node)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/Loop.java b/src/main/java/plugins/adufour/blocks/lang/Loop.java
new file mode 100644
index 0000000..b3edd5b
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/Loop.java
@@ -0,0 +1,278 @@
+package plugins.adufour.blocks.lang;
+
+import icy.system.IcyHandledException;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import plugins.adufour.blocks.lang.BlockDescriptor.BlockStatus;
+import plugins.adufour.blocks.tools.ReLoop;
+import plugins.adufour.blocks.util.BlocksException;
+import plugins.adufour.blocks.util.LoopException;
+import plugins.adufour.blocks.util.ScopeException;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarInteger;
+
+/**
+ * Special work flow that will repeat its contents forever until is it manually stopped by the user.
+ *
+ * @see Batch
+ * @see RangeLoop
+ * @see FileBatch
+ * @see SequenceFileBatch
+ * @see SequenceSeriesBatch
+ * @author Alexandre Dufour
+ */
+public class Loop extends WorkFlow
+{
+ private final ArrayList<Var<?>> loopVariables = new ArrayList<Var<?>>();
+
+ private VarInteger iterationCounter;
+
+ public final VarBoolean stopOnFirstError = new VarBoolean("Stop on first error", false);
+
+ public Loop()
+ {
+ super(false);
+
+ declareLoopVariables(loopVariables);
+
+ // always add the iteration counter in last position
+ loopVariables.add(iterationCounter);
+ }
+
+ @Override
+ public BlockDescriptor getBlock(int blockID)
+ {
+ if (blockID == -1)
+ return getBlockDescriptor();
+
+ return super.getBlock(blockID);
+ }
+
+ @Override
+ public BlockDescriptor getInputOwner(Var<?> var)
+ {
+ return loopVariables.contains(var) ? getBlockDescriptor() : super.getInputOwner(var);
+ }
+
+ @Override
+ public BlockDescriptor getOutputOwner(Var<?> var)
+ {
+ return loopVariables.contains(var) ? getBlockDescriptor() : super.getOutputOwner(var);
+ }
+
+ public String getInputVarID(Var<?> variable)
+ {
+ for (Var<?> innerVar : loopVariables)
+ if (variable == innerVar)
+ {
+ return getBlockDescriptor().inputVars.getID(variable);
+ }
+
+ return super.getInputVarID(variable);
+ }
+
+ public String getOutputVarID(Var<?> variable)
+ {
+ for (Var<?> innerVar : loopVariables)
+ if (variable == innerVar)
+ {
+ return getBlockDescriptor().outputVars.getID(variable);
+ }
+
+ return super.getOutputVarID(variable);
+ }
+
+ public VarInteger getIterationCounter()
+ {
+ return iterationCounter;
+ }
+
+ /**
+ * Adds the specified variable to the list of inner loop variables, i.e., variables describing
+ * the parameters of the loop, which can be referenced from inside the loop by other blocks.
+ *
+ * @deprecated The process of declaring loop variables has changed. Override
+ * {@link #declareLoopVariables(List)} instead.
+ * @param loopVar
+ * the variable to register
+ */
+ @Deprecated
+ protected void addLoopVariable(Var<?> loopVar)
+ {
+ loopVariables.add(loopVar);
+ }
+
+ /**
+ * @param var
+ * the variable to look for
+ * @return true if <code>var</code> is a loop variable, false otherwise
+ */
+ public boolean isLoopVariable(Var<?> var)
+ {
+ return loopVariables.contains(var);
+ }
+
+ public List<Var<?>> getLoopVariables()
+ {
+ return loopVariables;
+ }
+
+ @Override
+ public void run()
+ {
+ iterationCounter.setValue(0);
+ initializeLoop();
+
+ List<IcyHandledException> exceptions = new ArrayList<IcyHandledException>();
+
+ while (!Thread.currentThread().isInterrupted() && !isStopConditionReached())
+ {
+ // FIXED (Stephane)
+ // we need to reset to dirty state for all contained blocks before the iteration
+ // as we never expect any contained block to keep value from previous iteration
+ final Iterator<BlockDescriptor> blockIt = iterator();
+
+ while (blockIt.hasNext())
+ {
+ final BlockDescriptor block = blockIt.next();
+ // put block back in dirty state
+ if (block.getStatus() == BlockStatus.READY)
+ block.setStatus(BlockStatus.DIRTY);
+ }
+
+ beforeIteration();
+
+ try
+ {
+ super.run();
+ }
+ catch (IcyHandledException e)
+ {
+ exceptions.add(e);
+ if (stopOnFirstError.getValue())
+ break;
+ }
+
+ iterationCounter.setValue(iterationCounter.getValue() + 1);
+ afterIteration();
+ }
+
+ if (exceptions.size() > 0)
+ {
+ String message = "The following errors occurred during the loop:\n\n";
+ for (Exception e : exceptions)
+ message += " - " + e.getMessage() + "\n";
+ throw new BlocksException(message, true);
+ }
+ }
+
+ /**
+ * Initializes (or resets) internal loop structures such as iterators or counters. This method
+ * is called once before actually starting the loop. Note that the iteration counter is already
+ * reset before calling this method.
+ */
+ public void initializeLoop()
+ {
+ // nothing to do in an infinite loop
+ }
+
+ /**
+ * Called before the current iteration takes place (i.e. before calling the {@link #run()}
+ * method. This method is typically used to fetch array or iterator values necessary for the
+ * core code execution.
+ */
+ public void beforeIteration()
+ {
+ // nothing to do in an infinite loop
+ }
+
+ /**
+ * Notifies that the current iteration has finished, allowing the loop to handle custom
+ * increments or iterators to move forward before executing the next iteration. Note that the
+ * iteration counter is automatically increased before calling this method.
+ */
+ public void afterIteration()
+ {
+ // release other threads for a very short time
+ // (especially the AWT, to receive user interruption and display stuff)
+ Thread.yield();
+
+ }
+
+ /**
+ * NB: this method must be called by overriding methods to ensure that the loop can be
+ * interrupted correctly upon request
+ *
+ * @return true if the stopping condition is reached, false otherwise.
+ */
+ public boolean isStopConditionReached()
+ {
+ // infinite loop
+ return false;
+ }
+
+ @Override
+ protected <T> void checkScope(Link<T> link) throws ScopeException
+ {
+ try
+ {
+ super.checkScope(link);
+ }
+ catch (ScopeException e)
+ {
+ // authorize links coming from variable loops
+ if (!loopVariables.contains(link.srcVar))
+ throw e;
+ }
+ }
+
+ @Override
+ protected <T> void checkLoop(Link<T> link) throws LoopException
+ {
+ try
+ {
+ super.checkLoop(link);
+ }
+ catch (LoopException e)
+ {
+ // authorize loops only if the destination is a "ReLoop" block
+ if (link.dstBlock.getBlock() instanceof ReLoop)
+ {
+ ReLoop reLoop = (ReLoop) link.dstBlock.getBlock();
+
+ if (link.dstVar == reLoop.reloopValue)
+ return;
+ }
+
+ throw e;
+ }
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ super.declareOutput(outputMap);
+
+ iterationCounter = new VarInteger("iteration", 0);
+ iterationCounter.setEnabled(false);
+ outputMap.add("iteration", iterationCounter);
+ }
+
+ /**
+ * Declares the necessary loop variables by adding them to the specified list. Loop variables
+ * describe the parameters of the loop, which can be referenced from inside the loop by other
+ * blocks.
+ *
+ * @param loopVars
+ * the variable to register
+ */
+ public void declareLoopVariables(List<Var<?>> loopVars)
+ {
+ // a loop has no inner variable
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/RangeLoop.java b/src/main/java/plugins/adufour/blocks/lang/RangeLoop.java
new file mode 100644
index 0000000..cf75e20
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/RangeLoop.java
@@ -0,0 +1,98 @@
+package plugins.adufour.blocks.lang;
+
+import java.util.List;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarInteger;
+
+/**
+ * Particular type of loop that will repeats its contents for every number within the provided range
+ * of values
+ *
+ * @author Alexandre Dufour
+ */
+public class RangeLoop extends Loop
+{
+ private VarInteger startIndex;
+ private VarInteger endIndex;
+ private VarInteger step;
+ private VarInteger index;
+
+ public VarInteger getEndIndex()
+ {
+ return endIndex;
+ }
+
+ public VarInteger getIndex()
+ {
+ return index;
+ }
+
+ public VarInteger getStartIndex()
+ {
+ return startIndex;
+ }
+
+ public VarInteger getStep()
+ {
+ return step;
+ }
+
+ @Override
+ public void initializeLoop()
+ {
+ index.setValue(startIndex.getValue());
+ }
+
+ @Override
+ public void beforeIteration()
+ {
+ // nothing to do here
+ }
+
+ @Override
+ public void afterIteration()
+ {
+ index.setValue(index.getValue() + step.getValue());
+ }
+
+ @Override
+ public boolean isStopConditionReached()
+ {
+ if (super.isStopConditionReached()) return true;
+
+ if (step.getValue() > 0) return index.getValue() >= endIndex.getValue();
+
+ return index.getValue() <= endIndex.getValue();
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ super.declareInput(inputMap);
+
+ inputMap.add("start", startIndex = new VarInteger("start", 0));
+ inputMap.add("step", step = new VarInteger("step", 1));
+ inputMap.add("end", endIndex = new VarInteger("end", 10));
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ super.declareOutput(outputMap);
+
+ outputMap.add("index", index = new VarInteger("index", startIndex.getDefaultValue().intValue()));
+ }
+
+ @Override
+ public void declareLoopVariables(List<Var<?>> loopVariables)
+ {
+ loopVariables.add(startIndex);
+ loopVariables.add(endIndex);
+ loopVariables.add(step);
+ loopVariables.add(index);
+
+ super.declareLoopVariables(loopVariables);
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/blocks/lang/SequenceFileBatch.java b/src/main/java/plugins/adufour/blocks/lang/SequenceFileBatch.java
new file mode 100644
index 0000000..c58c047
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/SequenceFileBatch.java
@@ -0,0 +1,56 @@
+package plugins.adufour.blocks.lang;
+
+import java.io.File;
+
+import icy.file.Loader;
+import plugins.adufour.vars.lang.VarSequence;
+
+/**
+ * Similar to the {@link FileBatch File batch}, a Sequence file batch will read
+ * all files of a user-defined folder, and additionally load and give access to
+ * the sequence contained within these files (non-imaging files will be
+ * skipped).<br>
+ * Note for multi-series imaging files (e.g. Leica .lif): when loading
+ * multi-series files, a dialog box will appear to let the user select the
+ * series to process. However only the first selected series will be loaded. To
+ * batch process entire multi-series files, use the {@link SequenceSeriesBatch
+ * Sequence series batch} instead.
+ *
+ * @author Alexandre Dufour
+ */
+public class SequenceFileBatch extends FileBatch
+{
+ VarSequence element;
+
+ @Override
+ public VarSequence getBatchElement()
+ {
+ if (element == null)
+ {
+ // WARNING: do *not* change the name of this variable
+ // why? see declareInput() and VarList.add()
+ element = new VarSequence("Sequence", null);
+ }
+ return element;
+ }
+
+ @Override
+ public boolean accept(File f)
+ {
+ return f.isDirectory() || super.accept(f) && Loader.isSupportedImageFile(f.getPath());
+ }
+
+ @Override
+ public void beforeIteration()
+ {
+ try
+ {
+ element.setValue(Loader.loadSequence(files[getIterationCounter().getValue()].getPath(), -1, false));
+ Thread.yield();
+ }
+ catch (Exception e)
+ {
+ Thread.currentThread().interrupt();
+ }
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/SequenceSeriesBatch.java b/src/main/java/plugins/adufour/blocks/lang/SequenceSeriesBatch.java
new file mode 100644
index 0000000..3b549f5
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/SequenceSeriesBatch.java
@@ -0,0 +1,110 @@
+package plugins.adufour.blocks.lang;
+
+import java.io.File;
+import java.io.IOException;
+
+import icy.common.exception.UnsupportedFormatException;
+import icy.file.Loader;
+import icy.file.SequenceFileImporter;
+import icy.sequence.MetaDataUtil;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.util.VarException;
+import plugins.kernel.importer.LociImporterPlugin;
+
+/**
+ * A Sequence series batch will iteratively load all series contained in a multi-series (e.g. Leica
+ * .lif) file, allowing to process all the series with a single work-flow. It can be used in
+ * combination with the {@link FileBatch File batch} to batch process entire folders of multi-series
+ * files.
+ *
+ * @author Alexandre Dufour
+ */
+public class SequenceSeriesBatch extends Batch
+{
+ private VarFile multiSeriesFile;
+
+ private int nbSeries;
+
+ private VarSequence element;
+
+ @Override
+ public VarFile getBatchSource()
+ {
+ if (multiSeriesFile == null)
+ {
+ // WARNING: do *not* change the name of this variable
+ // why? see declareInput() and VarList.add()
+ multiSeriesFile = new VarFile("Series file", null);
+ multiSeriesFile.setDefaultEditorModel(new FileTypeModel(null, FileMode.FILES, null, false));
+ }
+
+ return multiSeriesFile;
+ }
+
+ @Override
+ public VarSequence getBatchElement()
+ {
+ if (element == null)
+ {
+ // WARNING: do *not* change the name of this variable
+ // why? see declareInput() and VarList.add()
+ element = new VarSequence("Sequence", null);
+ }
+
+ return element;
+ }
+
+ @Override
+ public void initializeLoop()
+ {
+ if (multiSeriesFile.getValue() == null)
+ throw new VarException(multiSeriesFile, "No file indicated");
+
+ File f = multiSeriesFile.getValue();
+ if (f.isDirectory())
+ throw new VarException(multiSeriesFile, f.getAbsolutePath() + " is not a file");
+
+ String path = f.getPath();
+
+ try
+ {
+ final SequenceFileImporter importer = Loader.getSequenceFileImporter(path, true);
+
+ // FIX: force un-grouping to get number of series (Stephane)
+ if (importer instanceof LociImporterPlugin)
+ ((LociImporterPlugin) importer).setGroupFiles(false);
+
+ nbSeries = MetaDataUtil.getNumSeries(Loader.getOMEXMLMetaData(importer, path));
+ }
+ catch (UnsupportedFormatException e)
+ {
+ throw new VarException(multiSeriesFile, path + " is not an imaging file");
+ }
+ catch (IOException e)
+ {
+ throw new VarException(multiSeriesFile, "Unable to read " + path);
+ }
+ }
+
+ @Override
+ public void beforeIteration()
+ {
+ final String path = multiSeriesFile.getValue().getPath();
+ final SequenceFileImporter importer = Loader.getSequenceFileImporter(path, true);
+
+ // FIX: force un-grouping as we iterate over series (Stephane)
+ if (importer instanceof LociImporterPlugin)
+ ((LociImporterPlugin) importer).setGroupFiles(false);
+
+ element.setValue(Loader.loadSequence(importer, path, getIterationCounter().getValue(), true));
+ }
+
+ @Override
+ public boolean isStopConditionReached()
+ {
+ return getIterationCounter().getValue() == nbSeries;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/lang/WorkFlow.java b/src/main/java/plugins/adufour/blocks/lang/WorkFlow.java
new file mode 100644
index 0000000..499ac7d
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/lang/WorkFlow.java
@@ -0,0 +1,1175 @@
+package plugins.adufour.blocks.lang;
+
+import java.awt.Point;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
+
+import icy.gui.dialog.ConfirmDialog;
+import icy.main.Icy;
+import icy.math.UnitUtil;
+import icy.plugin.abstract_.Plugin;
+import icy.system.IcyHandledException;
+import icy.system.thread.ThreadUtil;
+import icy.util.StringUtil;
+import plugins.adufour.blocks.lang.BlockDescriptor.BlockStatus;
+import plugins.adufour.blocks.util.BlockListener;
+import plugins.adufour.blocks.util.BlocksException;
+import plugins.adufour.blocks.util.LinkCutException;
+import plugins.adufour.blocks.util.LoopException;
+import plugins.adufour.blocks.util.NoSuchBlockException;
+import plugins.adufour.blocks.util.NoSuchLinkException;
+import plugins.adufour.blocks.util.NoSuchVariableException;
+import plugins.adufour.blocks.util.ScopeException;
+import plugins.adufour.blocks.util.StopException;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.blocks.util.VarListListener;
+import plugins.adufour.blocks.util.WorkFlowListener;
+import plugins.adufour.protocols.gui.MainFrame;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarObject;
+import plugins.adufour.vars.util.VarException;
+
+public class WorkFlow extends Plugin implements Block, Iterable<BlockDescriptor>, BlockListener, WorkFlowListener
+{
+ private final BlockDescriptor descriptor = new BlockDescriptor(-1, this);
+
+ private final HashSet<WorkFlowListener> listeners = new HashSet<WorkFlowListener>();
+
+ private final ArrayList<BlockDescriptor> orderedBlocks = new ArrayList<BlockDescriptor>();
+
+ private final boolean topLevel;
+
+ private final ArrayList<Link<?>> links = new ArrayList<Link<?>>();
+
+ private final VarListListener inputVarListener = new VarListListener()
+ {
+ @Override
+ public void variableAdded(VarList list, Var<?> variable)
+ {
+ descriptor.addInput(getInputVarID(variable), variable);
+ }
+
+ @Override
+ public void variableRemoved(VarList list, Var<?> variable)
+ {
+ descriptor.removeInput(variable);
+ }
+ };
+
+ private final VarListListener outputVarListener = new VarListListener()
+ {
+ @Override
+ public void variableAdded(VarList list, Var<?> variable)
+ {
+ descriptor.addOutput(getOutputVarID(variable), variable);
+ }
+
+ @Override
+ public void variableRemoved(VarList list, Var<?> variable)
+ {
+ descriptor.removeOutput(variable);
+ }
+ };
+
+ private Thread executionThread;
+
+ private boolean userInterruption = false;
+
+ private ArrayList<BlockDescriptor> blockSelection = new ArrayList<BlockDescriptor>();
+ private ArrayList<Link<?>> linkSelection = new ArrayList<Link<?>>();
+
+ private static final OutputStream nullStream = new OutputStream()
+ {
+ @Override
+ public void write(int b) throws IOException
+ {
+ }
+ };
+
+ /**
+ * The stream where the execution log is sent.
+ */
+ private PrintStream logStream = new PrintStream(nullStream);
+
+ public void setLogStream(PrintStream logStream)
+ {
+ this.logStream = logStream;
+ }
+
+ /**
+ * Searches recursively for the top-level stream where the execution log will be sent
+ *
+ * @return The top-level stream where the log is sent
+ */
+ public PrintStream getLogStream()
+ {
+ return descriptor.getContainer() == null ? logStream : descriptor.getContainer().getLogStream();
+ }
+
+ public WorkFlow()
+ {
+ this(false);
+ }
+
+ public WorkFlow(boolean topLevel)
+ {
+ super();
+
+ this.topLevel = topLevel;
+ }
+
+ public void addBlock(BlockDescriptor blockInfo)
+ {
+ blockInfo.setContainer(this);
+
+ orderedBlocks.add(blockInfo);
+ blockInfo.addBlockListener(this);
+
+ if (blockInfo.isWorkFlow())
+ ((WorkFlow) blockInfo.getBlock()).addListener(this);
+
+ // FIX: sometime getContainer() isn't yet initialized even for internal workflow (Stephane)
+ // if (descriptor.getContainer() != null)
+ if (!descriptor.isTopLevelWorkFlow())
+ {
+ // Add the variables from the block to the work flow itself
+ // this is to allow variable exposing
+
+ // Retrieve input variables
+ for (Var<?> inputVar : blockInfo.inputVars)
+ {
+ // FIX: avoid to duplicate variable (Stephane)
+ if (!descriptor.inputVars.contains(inputVar))
+ descriptor.addInput(getInputVarID(inputVar), inputVar);
+ }
+ // Retrieve output variables
+ for (Var<?> outputVar : blockInfo.outputVars)
+ {
+ // FIX: avoid to duplicate variable (Stephane)
+ if (!descriptor.outputVars.contains(outputVar))
+ descriptor.addOutput(getOutputVarID(outputVar), outputVar);
+ }
+
+ blockInfo.inputVars.addVarListListener(inputVarListener);
+ blockInfo.outputVars.addVarListListener(outputVarListener);
+ }
+
+ blockAdded(this, blockInfo);
+ }
+
+ /**
+ * @deprecated Use {@link #addBlock(BlockDescriptor)} instead.
+ * @param block
+ * Block to add.
+ * @return Descriptor relative to this workflow of the added block.
+ */
+ @Deprecated
+ public BlockDescriptor addBlock(Block block)
+ {
+ return addBlock(-1, block, new Point());
+ }
+
+ /**
+ * @deprecated Use {@link #addBlock(BlockDescriptor)} instead.
+ * @param ID
+ * Block identifier.
+ * @param block
+ * Block to be added.
+ * @param location
+ * Position to put the block at.
+ * @return Descriptor relative to this workflow of the added block.
+ */
+ @SuppressWarnings("deprecation")
+ @Deprecated
+ public BlockDescriptor addBlock(int ID, Block block, Point location)
+ {
+ BlockDescriptor blockDescriptor;
+
+ if (block instanceof WorkFlow)
+ {
+ blockDescriptor = ((WorkFlow) block).descriptor;
+ blockDescriptor.setContainer(this);
+ blockDescriptor.setLocation(location.x, location.y);
+ }
+ else
+ {
+ blockDescriptor = new BlockDescriptor(ID, block, this, location);
+ }
+
+ addBlock(blockDescriptor);
+
+ return blockDescriptor;
+ }
+
+ /**
+ * Links the specified variables
+ *
+ * @param <T>
+ * Type of the variable to be linked.
+ * @param srcBlock
+ * the source block
+ * @param srcArgID
+ * the unique ID of the source (output) variable
+ * @param dstBlock
+ * the destination block
+ * @param dstArgID
+ * the unique ID of the destination (input) variable
+ * @return the newly created link
+ * @throws NoSuchBlockException
+ * if either the source or destination block is not in this work flow
+ * @throws NoSuchVariableException
+ * if either the source or destination variable is not in the corresponding block
+ */
+ public <T> Link<T> addLink(BlockDescriptor srcBlock, String srcArgID, BlockDescriptor dstBlock, String dstArgID)
+ throws NoSuchBlockException, NoSuchVariableException, ClassCastException
+ {
+ if (!orderedBlocks.contains(srcBlock))
+ throw new NoSuchBlockException(srcBlock);
+ if (!orderedBlocks.contains(dstBlock))
+ throw new NoSuchBlockException(dstBlock);
+
+ Var<T> srcVar = srcBlock.outputVars.get(srcArgID);
+ if (srcVar == null)
+ throw new NoSuchVariableException(srcBlock, srcArgID);
+
+ Var<T> dstVar = dstBlock.inputVars.get(dstArgID);
+ if (dstVar == null)
+ throw new NoSuchVariableException(dstBlock, dstArgID);
+
+ return addLink(srcBlock, srcVar, dstBlock, dstVar);
+ }
+
+ /**
+ * Creates a link between the given variables and re-schedules the blocks accordingly
+ *
+ * @param <T>
+ * Type of the value of the link that is generated.
+ * @param srcBlock
+ * Start-point block descriptor of the link.
+ * @param srcVar
+ * Start-point variable instance of the link.
+ * @param dstBlock
+ * End-point block descriptor of the link.
+ * @param dstVar
+ * End-point variable instance of the link.
+ * @return Link instance connecting source and destination blocks.
+ * @throws LoopException
+ * if a loop is detected in the current scope
+ * @throws NoSuchVariableException
+ * if the variable cannot be found in the current scope
+ * @throws ClassCastException
+ * If the link is not valid, meaning that the two specified variables are of
+ * incompatible types.
+ */
+ public <T> Link<T> addLink(BlockDescriptor srcBlock, Var<T> srcVar, BlockDescriptor dstBlock, Var<T> dstVar)
+ throws LoopException, ClassCastException
+ {
+ Link<T> link = checkLink(srcBlock, srcVar, dstBlock, dstVar);
+
+ dstVar.setReference(srcVar);
+
+ // re-order the boxes to make sure srcBlock runs before dstBlock
+ if (orderedBlocks.indexOf(link.srcBlock) > orderedBlocks.indexOf(link.dstBlock))
+ reOrder(link.srcBlock, link.dstBlock);
+
+ links.add(link);
+
+ for (WorkFlowListener listener : listeners)
+ {
+ listener.linkAdded(this, link);
+ }
+
+ return link;
+ }
+
+ public void addListener(WorkFlowListener listener)
+ {
+ listeners.add(listener);
+ }
+
+ public boolean isTopLevel()
+ {
+ return topLevel;
+ }
+
+ public boolean contains(BlockDescriptor dstBlock)
+ {
+ return orderedBlocks.contains(dstBlock);
+ }
+
+ /**
+ * Checks whether the specified variables can be linked, and if so returns the pair of
+ * {@link Block} objects to link
+ *
+ * @param <T>
+ * Type of value being transported through the link.
+ * @param srcBlock
+ * the {@link Block} to link from
+ * @param srcVar
+ * the {@link Var}iable to link from
+ * @param dstBlock
+ * the {@link Block} to link to
+ * @param dstVar
+ * the {@link Var}iable to link to
+ * @return The link instance connecting source and destination variables.
+ * @throws ClassCastException
+ * if the link is not valid, meaning that the two specified variables are of
+ * incompatible types
+ */
+ public <T> Link<T> checkLink(final BlockDescriptor srcBlock, Var<T> srcVar, final BlockDescriptor dstBlock,
+ Var<T> dstVar) throws ClassCastException
+ {
+ Link<T> link = new Link<T>(this, srcBlock, srcVar, dstBlock, dstVar);
+
+ checkScope(link);
+
+ checkLoop(link);
+
+ checkType(link);
+
+ return link;
+ }
+
+ protected <T> void checkScope(Link<T> link) throws ScopeException
+ {
+ if (contains(link.srcBlock) != contains(link.dstBlock))
+ throw new ScopeException();
+
+ // special case: inner loop variables should not link to outside the loop
+ if (link.srcBlock.isLoop() && ((Loop) link.srcBlock.getBlock()).isLoopVariable(link.srcVar))
+ throw new ScopeException();
+ }
+
+ protected <T> void checkLoop(Link<T> link) throws LoopException
+ {
+ if (link.srcBlock.equals(link.dstBlock) || depends(link.srcBlock, link.dstBlock))
+ throw new LoopException();
+ }
+
+ protected <T> void checkType(Link<T> link) throws ClassCastException
+ {
+ // filter all valid cases
+
+ if (link.dstVar.isAssignableFrom(link.srcVar))
+ return;
+
+ if (link.srcVar instanceof VarObject)
+ return;
+
+ if (link.dstVar instanceof VarMutable)
+ return;
+ // {
+ // VarMutable dst = (VarMutable) link.dstVar;
+ // dst.setType(link.srcVar.getType());
+ // return;
+ // }
+
+ throw new ClassCastException("<html><h4>Variables \"" + link.dstVar.getName() + "\" and \""
+ + link.srcVar.getName() + "\" are of different type and cannot be linked</h4></html>");
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+ private boolean depends(BlockDescriptor srcBlock, BlockDescriptor dstBlock)
+ {
+ boolean srcDependsOnDst = false;
+
+ for (Link<?> link : links)
+ {
+ if (link.dstBlock == srcBlock)
+ {
+ // link points to srcBlock.
+ if (link.srcBlock == dstBlock)
+ return true;
+
+ // else
+ srcDependsOnDst |= depends(link.srcBlock, dstBlock);
+
+ // exit ASAP
+ if (srcDependsOnDst)
+ return true;
+ }
+ }
+
+ return srcDependsOnDst;
+ }
+
+ public BlockDescriptor getBlock(int index)
+ {
+ return orderedBlocks.get(index);
+ }
+
+ public BlockDescriptor getBlockByID(int blockID) throws NoSuchBlockException
+ {
+ if (blockID == descriptor.getID())
+ return descriptor;
+
+ for (BlockDescriptor bd : orderedBlocks)
+ if (bd.getID() == blockID)
+ return bd;
+
+ throw new NoSuchBlockException(blockID, this);
+ }
+
+ /**
+ * @param variable
+ * The input variable to retrieve.
+ * @return A unique ID for the variable within this work flow (used for XML loading/saving).
+ */
+ public String getInputVarID(Var<?> variable)
+ {
+ BlockDescriptor owner = getInputOwner(variable);
+
+ return owner.getID() + ":" + owner.getVarID(variable);
+ }
+
+ /**
+ * @param variable
+ * The input variable to retrieve.
+ * @return A unique ID for the variable within this work flow (used for XML loading/saving).
+ */
+ public String getOutputVarID(Var<?> variable)
+ {
+ BlockDescriptor owner = getOutputOwner(variable);
+
+ return owner.getID() + ":" + owner.getVarID(variable);
+ }
+
+ public BlockDescriptor getBlockDescriptor()
+ {
+ return descriptor;
+ }
+
+ public BlockDescriptor getInputOwner(Var<?> var)
+ {
+ for (BlockDescriptor blockInfo : orderedBlocks)
+ for (Var<?> inputVar : blockInfo.inputVars)
+ if (inputVar.equals(var))
+ return blockInfo;
+
+ return null;
+ }
+
+ public BlockDescriptor getOutputOwner(Var<?> var)
+ {
+ for (BlockDescriptor blockInfo : orderedBlocks)
+ for (Var<?> outputVar : blockInfo.outputVars)
+ if (outputVar.equals(var))
+ return blockInfo;
+
+ return null;
+ }
+
+ public Iterable<Link<?>> getLinksIterator()
+ {
+ return new Iterable<Link<?>>()
+ {
+ @Override
+ public Iterator<Link<?>> iterator()
+ {
+ return links.iterator();
+ }
+ };
+ }
+
+ public int indexOf(BlockDescriptor blockInfo)
+ {
+ if (blockInfo == null)
+ return -1;
+
+ return orderedBlocks.indexOf(blockInfo);
+ }
+
+ @Override
+ public Iterator<BlockDescriptor> iterator()
+ {
+ // return orderedBlocks.iterator();
+ return new Iterator<BlockDescriptor>()
+ {
+ private final Iterator<BlockDescriptor> orderedBlocksIt = orderedBlocks.iterator();
+
+ @Override
+ public boolean hasNext()
+ {
+ return orderedBlocksIt.hasNext();
+ }
+
+ @Override
+ public BlockDescriptor next()
+ {
+ return orderedBlocksIt.next();
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ };
+ }
+
+ /**
+ * Give the highest priority to the specified block, by placing giving it the smallest possible
+ * index in the list (i.e. after its direct dependencies). This method reorganizes the block execution order.
+ *
+ * @param blockDesc
+ * Descriptor of the block to be prioritized.
+ */
+ public void prioritize(BlockDescriptor blockDesc)
+ {
+ // retrieve the current order
+ int currentOrder = indexOf(blockDesc);
+ // assume we can give the block maximum priority
+ int targetOrder = 0;
+
+ // find its dependencies
+ HashSet<BlockDescriptor> dependencies = new HashSet<BlockDescriptor>();
+
+ for (Link<?> link : links)
+ if (link.dstBlock == blockDesc && contains(link.srcBlock))
+ dependencies.add(link.srcBlock);
+
+ // give piority to the dependencies first
+ for (BlockDescriptor dependency : dependencies)
+ prioritize(dependency);
+
+ // calculate the final order
+ for (BlockDescriptor dependency : dependencies)
+ {
+ int order = indexOf(dependency) + 1;
+ if (order > targetOrder)
+ targetOrder = order;
+ }
+
+ // assign the final order
+
+ if (targetOrder != currentOrder)
+ {
+ orderedBlocks.add(targetOrder, orderedBlocks.remove(currentOrder));
+ for (WorkFlowListener listener : listeners)
+ listener.workFlowReordered(this);
+ }
+ }
+
+ /**
+ * Re-orders the specified blocks to ensure that prevBlock will execute before nextBlock.<br>
+ * NOTE: this method assumes that the specified blocks belong to the current work flow. If this
+ * is not the case, see the {@link #reOrder(Link)} method instead.
+ *
+ * @param prevBlock
+ * The block that should be executed right before this instance.
+ * @param nextBlock
+ * The block that should be executed right after this instance.
+ */
+ private void reOrder(BlockDescriptor prevBlock, BlockDescriptor nextBlock)
+ {
+ orderedBlocks.remove(prevBlock);
+ orderedBlocks.add(orderedBlocks.indexOf(nextBlock), prevBlock);
+
+ for (Link<?> link : links)
+ if (link.dstBlock == prevBlock && orderedBlocks.indexOf(link.srcBlock) > orderedBlocks.indexOf(prevBlock))
+ {
+ reOrder(link.srcBlock, prevBlock);
+ break; // only do it once, even if multiple links exist
+ }
+
+ for (WorkFlowListener listener : listeners)
+ listener.workFlowReordered(this);
+ }
+
+ public void removeBlock(BlockDescriptor blockInfo, boolean checkSelection)
+ {
+ // pops out workflows' selections
+ if (blockInfo.getBlock() instanceof WorkFlow)
+ {
+ WorkFlow wf = ((WorkFlow) blockInfo.getBlock());
+ if (checkSelection && !wf.getBlockSelection().isEmpty())
+ try
+ {
+ // use location in main container instead of in the inner workflow
+ // avoids jumping toward the top left
+ for (BlockDescriptor bd : wf)
+ {
+ Point contLoc = bd.getContainer().getBlockDescriptor().getLocation();
+ Point loc = bd.getLocation();
+ bd.setLocation(contLoc.x + loc.x, contLoc.y + loc.y);
+ }
+ MainFrame.copySelection(wf, true);
+ MainFrame.pasteSelection(this, true);
+ }
+ catch (LinkCutException e)
+ {
+ if (ConfirmDialog.confirm("Warning", e.getMessage(), ConfirmDialog.OK_CANCEL_OPTION))
+ {
+ MainFrame.pasteSelection(this, true);
+ }
+ else
+ return;
+ }
+ else
+ {
+ checkSelection = false;
+ }
+ }
+
+ // 1) remove all links to/from this block
+ // this must be done first for self-adjusting blocks
+ // example: Accumulator may remove some variables as soon as they get unlinked
+
+ // 1.a) links from this block elsewhere
+ for (int i = 0; i < links.size(); i++)
+ {
+ Link<?> link = links.get(i);
+
+ if (blockInfo == link.srcBlock)
+ {
+ link.dstVar.setReference(null);
+ links.remove(i--);
+
+ for (WorkFlowListener listener : listeners)
+ listener.linkRemoved(this, link);
+ }
+ }
+
+ // 1.b) links from elsewhere to this block
+ for (int i = 0; i < links.size(); i++)
+ {
+ Link<?> link = links.get(i);
+
+ if (blockInfo == link.dstBlock)
+ {
+ link.dstVar.setReference(null);
+ links.remove(i--);
+
+ for (WorkFlowListener listener : listeners)
+ listener.linkRemoved(this, link);
+ }
+ }
+
+ // 2) remove the block variables (this removes their exposure as well)
+
+ // a work flow does not have variables of its own => nothing to remove
+ if (!blockInfo.isWorkFlow())
+ {
+ // Remove input variables
+ for (Var<?> inputVar : blockInfo.inputVars)
+ this.descriptor.removeInput(inputVar);
+
+ // Remove output variables
+ for (Var<?> outputVar : blockInfo.outputVars)
+ this.descriptor.removeOutput(outputVar);
+ }
+
+ // 3) if the block is a work flow, remove its inner blocks
+
+ // if (blockInfo.isWorkFlow())
+ // {
+ // WorkFlow innerFlow = (WorkFlow) blockInfo.getBlock();
+ // while (innerFlow.size() > 0)
+ // innerFlow.removeBlock(innerFlow.getBlock(0), checkSelection);
+ // }
+
+ // 4) remove the block itself
+
+ orderedBlocks.remove(blockInfo);
+
+ blockInfo.removeBlockListener(this);
+
+ // 5) Notify listeners...
+
+ for (WorkFlowListener listener : listeners)
+ {
+ listener.blockRemoved(this, blockInfo);
+ listener.workFlowReordered(this);
+ }
+
+ blockInfo.inputVars.removeVarListListener(inputVarListener);
+ blockInfo.outputVars.removeVarListListener(outputVarListener);
+
+ blockSelection.remove(blockInfo);
+ }
+
+ /**
+ * @param var
+ * the variable (input or output) to look for
+ * @return true if the specified variable is linked to another block, false otherwise
+ */
+ public boolean isLinked(Var<?> var)
+ {
+ for (Link<?> link : links)
+ if (link.dstVar == var || link.srcVar == var)
+ return true;
+ return false;
+ }
+
+ /**
+ * Removes the link to the specified variable, and returns false if this variable wasn't linked
+ *
+ * @param dstVar
+ * the destination variable of the link to remove
+ */
+ public void removeLink(Var<?> dstVar)
+ {
+ for (Link<?> link : links)
+ if (link.dstVar == dstVar && links.remove(link))
+ {
+ link.dstVar.setReference(null);
+
+ for (WorkFlowListener listener : listeners)
+ listener.linkRemoved(this, link);
+
+ return;
+ }
+
+ // if code runs here, no link was found
+ // => check in the parent work flow for links to an "exposed" variable
+
+ if (descriptor.getContainer() != null)
+ {
+ descriptor.getContainer().removeLink(dstVar);
+ }
+ else
+ {
+ throw new NoSuchLinkException("In method WorkFlow.removeLink():\nNo link points to "
+ + getInputOwner(dstVar).getName() + " > " + dstVar.getName());
+ }
+ }
+
+ public void removeListener(WorkFlowListener listener)
+ {
+ listeners.remove(listener);
+ }
+
+ /**
+ * Resets all output variables of each block in this work flow to their default value
+ */
+ public void reset()
+ {
+ for (BlockDescriptor block : orderedBlocks)
+ block.reset();
+ }
+
+ /**
+ * Resets and runs this work flow in an independent thread.
+ */
+ public void runWorkFlow()
+ {
+ runWorkFlow(false);
+ }
+
+ /**
+ * Resets and runs this work flow in an independent thread.
+ *
+ * @param waitForCompletion
+ * <code>true</code> if this method should wait for the work flow to finish before
+ * returning, or <code>false</code> if the method should return immediately (in this
+ * case, the status of the work flow can be accessed via {@link #getDescriptor()}
+ * {@link BlockDescriptor#getStatus() .getStatus()})
+ */
+ public void runWorkFlow(boolean waitForCompletion)
+ {
+ // this is the top-level work flow
+ // force it "dirty" to run it
+ this.descriptor.setStatus(BlockStatus.DIRTY);
+ executionThread = new Thread(this.descriptor, "Workflow");
+ executionThread.start();
+
+ if (waitForCompletion)
+ {
+ while (descriptor.getStatus() == BlockStatus.RUNNING)
+ ThreadUtil.sleep(100);
+ }
+ }
+
+ public void interrupt()
+ {
+ if (executionThread != null)
+ {
+ executionThread.interrupt();
+ userInterruption = true;
+ }
+ else
+ {
+ // this is not the top-level workflow
+ // => look for it
+ descriptor.getContainer().interrupt();
+ }
+ }
+
+ private boolean isInterrupted()
+ {
+ if (Icy.getMainInterface().isHeadLess())
+ return false;
+
+ if (descriptor.getContainer() != null)
+ return descriptor.getContainer().isInterrupted();
+
+ return userInterruption || executionThread.isInterrupted();
+ }
+
+ /**
+ * DO NOT CALL DIRECTLY FROM CLIENT CODE: this method assumes running in its own thread, and may
+ * behave inconsistently if interrupted. Use the {@link #runWorkFlow()} method instead
+ */
+ public void run()
+ {
+ if (orderedBlocks.size() == 0)
+ return;
+
+ descriptor.setStatus(BlockStatus.RUNNING);
+
+ BlockDescriptor runningBlock = null;
+
+ String finalStatus = "";
+ userInterruption = false;
+
+ long startTime = 0, endTime = 0;
+ try
+ {
+ startTime = System.nanoTime();
+
+ String statusPrefix = getBlockDescriptor().getContainer() == null ? ""
+ : "\"" + getBlockDescriptor().getContainer().descriptor.getName() + "\"" + " => ";
+
+ // get the log stream recursively to ensure it is always the top-level one
+ PrintStream log = getLogStream();
+
+ for (int blockIndex = 0; blockIndex < orderedBlocks.size(); blockIndex++)
+ {
+ if (isInterrupted())
+ throw new StopException();
+
+ BlockDescriptor blockDescriptor = orderedBlocks.get(blockIndex);
+
+ if (blockDescriptor.getStatus() != BlockStatus.READY)
+ {
+ runningBlock = blockDescriptor;
+
+ String blockLog = "block #" + (blockIndex + 1) + " [" + blockDescriptor.getDefinedName() + "]";
+
+ // Adjust status
+ statusChanged(this, "Running block " + statusPrefix + "\"" + blockDescriptor.getDefinedName()
+ + "\" (#" + (blockIndex + 1) + ")...");
+
+ // Log should be indented
+ String indentation = "";
+ // indent as many times as we go deep in the tree
+ WorkFlow container = this.descriptor.getContainer();
+ while (container != null)
+ {
+ indentation += " ";
+ container = container.descriptor.getContainer();
+ }
+ log.print(indentation + "Running " + blockLog);
+
+ if (blockDescriptor.inputVars.size() > 0)
+ {
+ log.println(" with the following parameters:");
+ for (Var<?> var : blockDescriptor.inputVars)
+ {
+ if (!blockDescriptor.inputVars.isVisible(var))
+ continue;
+
+ log.print(indentation + "- " + var.getName() + ": " + var.getValueAsString(true));
+
+ // If this variable points to another one, say so
+ Var<?> reference = var.getReference();
+ if (reference != null)
+ {
+ // The owner of the reference is either...
+
+ // 1) an output variable...
+ BlockDescriptor owner = getOutputOwner(reference);
+ // 2) a pass-through input...
+ if (owner == null)
+ owner = getInputOwner(reference);
+ // 3) a variable outside the work flow
+ if (owner == null)
+ {
+ log.println(" (from variable \"" + reference.getName()
+ + "\" defined outside this workflow)");
+ }
+ else if (owner == this.descriptor)
+ {
+ log.println(" (from local loop or batch variable \"" + reference.getName() + "\")");
+ }
+ else
+ {
+ log.println(" (from variable \"" + reference.getName() + "\" of block #"
+ + (indexOf(owner) + 1) + " [" + owner.getDefinedName() + "])");
+ }
+ }
+ else
+ log.println();
+ }
+ }
+
+ // THIS IS WHERE IT HAPPENS
+ long tic = System.nanoTime();
+ blockDescriptor.run();
+ long tac = System.nanoTime();
+
+ String time = UnitUtil.displayTimeAsStringWithUnits((tac - tic) / 1000000, false);
+ log.println(indentation + "Finished " + blockLog + " in " + (time.isEmpty() ? "0 ms" : time));
+
+ runningBlock = null;
+
+ if (blockDescriptor.isFinalBlock())
+ {
+ blockDescriptor.setFinalBlock(false);
+ interrupt();
+ }
+ }
+ }
+
+ if (descriptor.getContainer() != null)
+ log.println();
+
+ finalStatus = "The workflow executed successfully";
+ }
+ catch (StopException e)
+ {
+ // push the exception upstairs
+ if (descriptor.getContainer() != null)
+ throw e;
+
+ finalStatus = "The workflow was interrupted";
+ }
+ catch (RuntimeException e)
+ {
+ finalStatus = "The workflow did not execute properly";
+
+ boolean catchException = false;
+
+ if (e instanceof IcyHandledException || e instanceof VarException)
+ {
+ catchException = true;
+ }
+ else if (e instanceof BlocksException)
+ {
+ catchException = ((BlocksException) e).catchException;
+ }
+
+ if (catchException)
+ {
+ String blockName = runningBlock.getDefinedName();
+ int blockID = indexOf(runningBlock) + 1;
+ throw new IcyHandledException(
+ "While running block \"" + blockName + "\" (" + blockID + "):\n" + e.getMessage());
+ }
+
+ // it's probably a real problem, re-throw
+ throw e;
+ }
+ finally
+ {
+ descriptor.setStatus(BlockStatus.READY);
+ endTime = System.nanoTime();
+ double time = endTime - startTime;
+ finalStatus += " (total running time: " + StringUtil.toString(time / 1e9, 2) + " seconds)";
+ statusChanged(this, finalStatus);
+ }
+ }
+
+ public void setLocation(BlockDescriptor blockInfo, Point point)
+ {
+ blockInfo.setLocation(point.x, point.y);
+ }
+
+ /**
+ * @return the number of blocks in this work flow
+ */
+ public int size()
+ {
+ return orderedBlocks.size();
+ }
+
+ @Override
+ public void blockStatusChanged(BlockDescriptor blockInfo, BlockStatus status)
+ {
+ if (status == BlockStatus.DIRTY)
+ {
+ // "dirty-fy" following blocks
+ for (Link<?> link : links)
+ if (link.srcBlock == blockInfo)
+ link.dstBlock.setStatus(BlockStatus.DIRTY);
+ }
+ }
+
+ @Override
+ public void blockVariableAdded(BlockDescriptor block, Var<?> variable)
+ {
+
+ }
+
+ @Override
+ public <T> void blockVariableChanged(BlockDescriptor block, Var<T> variable, T newValue)
+ {
+ blockVariableChanged(this, block, variable, newValue);
+ }
+
+ @Override
+ public void blockCollapsed(BlockDescriptor block, boolean collapsed)
+ {
+
+ }
+
+ @Override
+ public void blockDimensionChanged(BlockDescriptor block, int newWidth, int newHeight)
+ {
+ blockDimensionChanged(this, block, newWidth, newHeight);
+ }
+
+ @Override
+ public void blockLocationChanged(BlockDescriptor block, int newX, int newY)
+ {
+ blockLocationChanged(this, block, newX, newY);
+ }
+
+ @Override
+ public void blockAdded(WorkFlow source, BlockDescriptor addedBlock)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockAdded(source, addedBlock);
+ }
+
+ @Override
+ public void blockRemoved(WorkFlow source, BlockDescriptor removedBlock)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockRemoved(source, removedBlock);
+ }
+
+ @Override
+ public void linkAdded(WorkFlow source, Link<?> addedLink)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.linkAdded(source, addedLink);
+ }
+
+ @Override
+ public void linkRemoved(WorkFlow source, Link<?> removedLink)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.linkRemoved(source, removedLink);
+ }
+
+ @Override
+ public void workFlowReordered(WorkFlow source)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.workFlowReordered(source);
+ }
+
+ @Override
+ public void blockCollapsed(WorkFlow source, BlockDescriptor block, boolean collapsed)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockCollapsed(source, block, collapsed);
+ }
+
+ @Override
+ public void blockDimensionChanged(WorkFlow source, BlockDescriptor block, int newWidth, int newHeight)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockDimensionChanged(this, block, newWidth, newHeight);
+ }
+
+ @Override
+ public void blockLocationChanged(WorkFlow source, BlockDescriptor block, int newX, int newY)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockLocationChanged(this, block, newX, newY);
+ }
+
+ @Override
+ public void blockStatusChanged(WorkFlow source, BlockDescriptor block, BlockStatus status)
+ {
+ // no need to propagate this event
+ }
+
+ @Override
+ public void blockVariableAdded(WorkFlow source, BlockDescriptor block, Var<?> variable)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockVariableAdded(this, block, variable);
+ }
+
+ @Override
+ public <T> void blockVariableChanged(WorkFlow source, BlockDescriptor block, Var<T> variable, T newValue)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.blockVariableChanged(this, block, variable, newValue);
+ }
+
+ @Override
+ public void statusChanged(WorkFlow source, String message)
+ {
+ for (WorkFlowListener listener : listeners)
+ listener.statusChanged(source, message);
+ }
+
+ public void newSelection()
+ {
+ blockSelection = new ArrayList<BlockDescriptor>();
+ linkSelection = new ArrayList<Link<?>>();
+ }
+
+ public boolean isBlockSelected(BlockDescriptor bd)
+ {
+ return blockSelection.contains(bd);
+ }
+
+ public boolean isLinkSelected(Link<?> l)
+ {
+ return linkSelection.contains(l);
+ }
+
+ public void selectBlock(BlockDescriptor bd)
+ {
+ if (!isBlockSelected(bd))
+ blockSelection.add(bd);
+ }
+
+ public void selectLink(Link<?> l)
+ {
+ if (!isLinkSelected(l))
+ linkSelection.add(l);
+ }
+
+ public void unselectBlock(BlockDescriptor bd)
+ {
+ if (isBlockSelected(bd))
+ blockSelection.remove(bd);
+ }
+
+ public void unselectLink(Link<?> l)
+ {
+ if (isLinkSelected(l))
+ linkSelection.remove(l);
+ }
+
+ public ArrayList<BlockDescriptor> getBlockSelection()
+ {
+ return blockSelection;
+ }
+
+ public ArrayList<Link<?>> getLinkSelection()
+ {
+ return linkSelection;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/Accumulator.java b/src/main/java/plugins/adufour/blocks/tools/Accumulator.java
new file mode 100644
index 0000000..01809e5
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/Accumulator.java
@@ -0,0 +1,142 @@
+package plugins.adufour.blocks.tools;
+
+import java.lang.reflect.Array;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.blocks.util.VarListListener;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarTrigger;
+import plugins.adufour.vars.util.TypeChangeListener;
+import plugins.adufour.vars.util.VarReferencingPolicy;
+
+public class Accumulator extends Plugin implements ToolsBlock, TypeChangeListener
+{
+ Class<?> type = null;
+
+ VarList inputMap;
+
+ VarMutable output = new VarMutable("output", null);
+
+ @Override
+ public void run()
+ {
+ int arrayLength = 0;
+
+ for (Var<?> var : inputMap)
+ {
+ if (var.getValue() == null || var instanceof VarTrigger) continue;
+
+ if (var.getValue().getClass().isArray())
+ {
+ arrayLength += Array.getLength(var.getValue());
+ }
+ else arrayLength++;
+ }
+
+ Object array = Array.newInstance(type.getComponentType(), arrayLength);
+
+ int i = 0;
+ for (Var<?> var : inputMap)
+ {
+ if (var.getValue() == null || var instanceof VarTrigger) continue;
+
+ if (var.getValue().getClass().isArray())
+ {
+ int length = Array.getLength(var.getValue());
+ System.arraycopy(var.getValue(), 0, array, i, length);
+ i += length;
+ }
+ else Array.set(array, i++, var.getValue());
+ }
+
+ output.setValue(array);
+ }
+
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ @Override
+ public void declareInput(final VarList theInputMap)
+ {
+ if (this.inputMap == null)
+ {
+ this.inputMap = theInputMap;
+ VarTrigger trigger = new VarTrigger("Add variable", new VarTrigger.TriggerListener()
+ {
+ @Override
+ public void valueChanged(Var<Integer> source, Integer oldValue, Integer newValue)
+ {
+
+ }
+
+ @Override
+ public void referenceChanged(Var<Integer> source, Var<? extends Integer> oldReference, Var<? extends Integer> newReference)
+ {
+
+ }
+
+ @Override
+ public void triggered(VarTrigger source)
+ {
+ final VarMutable var = new VarMutable("input", type)
+ {
+ public boolean isAssignableFrom(Var aVariable)
+ {
+ if (this.type == null) return true;
+
+ if (super.isAssignableFrom(aVariable)) return true;
+
+ return type.getComponentType().isAssignableFrom(aVariable.getType());
+ };
+ };
+ var.addTypeChangeListener(Accumulator.this);
+ theInputMap.addRuntimeVariable("" + var.hashCode(), var);
+ }
+ });
+
+ trigger.setReferencingPolicy(VarReferencingPolicy.NONE);
+
+ theInputMap.add("Add variable", trigger);
+
+ theInputMap.addVarListListener(new VarListListener()
+ {
+ @Override
+ public void variableRemoved(VarList list, Var variable)
+ {
+ }
+
+ @Override
+ public void variableAdded(VarList list, Var variable)
+ {
+ if (variable instanceof VarMutable)
+ {
+ ((VarMutable) variable).addTypeChangeListener(Accumulator.this);
+ }
+ }
+ });
+ }
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output", output);
+ }
+
+ @Override
+ public void typeChanged(Object source, Class<?> oldType, Class<?> newType)
+ {
+ if (type == null)
+ {
+ this.type = (newType.isArray() ? newType : Array.newInstance(newType, 0).getClass());
+
+ output.setType(type);
+
+ for (Var<?> var : inputMap)
+ {
+ if (var instanceof VarMutable) ((VarMutable) var).setType(type);
+ }
+ }
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/Display.java b/src/main/java/plugins/adufour/blocks/tools/Display.java
new file mode 100644
index 0000000..f77cbd1
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/Display.java
@@ -0,0 +1,52 @@
+package plugins.adufour.blocks.tools;
+
+import icy.main.Icy;
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.util.VarListener;
+
+public class Display extends Plugin implements Block
+{
+ private VarMutable object = new VarMutable("object", null);
+
+ @Override
+ public void run()
+ {
+ if (Icy.getMainInterface().isHeadLess())
+ {
+ // Print to the standard output stream
+ System.out.println(object.getValueAsString());
+ }
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("object", object);
+
+ object.addListener(new VarListener<Object>()
+ {
+ @Override
+ public void referenceChanged(Var<Object> source, Var<? extends Object> oldReference, Var<? extends Object> newReference)
+ {
+ if (newReference == null && !object.isReferenced()) object.setType(null);
+ }
+
+ @Override
+ public void valueChanged(Var<Object> source, Object oldValue, Object newValue)
+ {
+
+ }
+ });
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/Indexer.java b/src/main/java/plugins/adufour/blocks/tools/Indexer.java
new file mode 100644
index 0000000..c88d8d2
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/Indexer.java
@@ -0,0 +1,61 @@
+package plugins.adufour.blocks.tools;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarMutableArray;
+import plugins.adufour.vars.util.VarException;
+import plugins.adufour.vars.util.VarListener;
+
+/**
+ * Utility block reading the specified index of an input array. This block uses mutable types to
+ * receive any type of input and adjust the output accordingly
+ *
+ * @author Alexandre Dufour
+ */
+public class Indexer extends Plugin implements ToolsBlock
+{
+ VarMutableArray array = new VarMutableArray("array", null);
+ VarInteger index = new VarInteger("index", 0);
+
+ VarMutable element = new VarMutable("element", null);
+
+ @Override
+ public void run()
+ {
+ if (index.getValue() >= array.size()) throw new VarException(index, "Index " + index.getValueAsString() + " does not exist (array size: " + array.size() + ")");
+
+ element.setValue(array.getElementAt(index.getValue()));
+ }
+
+ @SuppressWarnings({ "unchecked", "rawtypes" })
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("array", array);
+ inputMap.add("index", index);
+
+ array.addListener(new VarListener()
+ {
+ @Override
+ public void valueChanged(Var source, Object oldValue, Object newValue)
+ {
+ }
+
+ @Override
+ public void referenceChanged(Var source, Var oldReference, Var newReference)
+ {
+ element.setType(newReference == null ? null : newReference.getType().getComponentType());
+ }
+ });
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("element", element);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/Iterator.java b/src/main/java/plugins/adufour/blocks/tools/Iterator.java
new file mode 100644
index 0000000..9e0c05f
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/Iterator.java
@@ -0,0 +1,68 @@
+package plugins.adufour.blocks.tools;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarMutableArray;
+import plugins.adufour.vars.util.VarListener;
+
+/**
+ * Utility block reading the specified index of an input array. This block uses mutable types to
+ * receive any type of input and adjust the output accordingly
+ *
+ * @author Alexandre Dufour
+ */
+public class Iterator extends Plugin implements ToolsBlock
+{
+ VarMutableArray array = new VarMutableArray("array", null);
+ VarInteger index = new VarInteger("index", 0);
+ VarBoolean end = new VarBoolean("end", false);
+ VarMutable element = new VarMutable("element", null);
+
+ @Override
+ public void run()
+ {
+ if (array.getValue() != null && index.getValue() < array.size())
+ {
+ element.setValue(array.getElementAt(index.getValue()));
+ index.setValue(index.getValue() + 1);
+ }
+ else
+ {
+ end.setValue(true);
+ }
+ }
+
+ @SuppressWarnings({ "rawtypes", "unchecked" })
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("array", array);
+
+ array.addListener(new VarListener()
+ {
+ @Override
+ public void valueChanged(Var source, Object oldValue, Object newValue)
+ {
+ }
+
+ @Override
+ public void referenceChanged(Var source, Var oldReference, Var newReference)
+ {
+ element.setType(newReference == null ? null : newReference.getType().getComponentType());
+ }
+ });
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("element", element);
+ outputMap.add("index", index);
+ outputMap.add("end", end);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ListSize.java b/src/main/java/plugins/adufour/blocks/tools/ListSize.java
new file mode 100644
index 0000000..998273c
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ListSize.java
@@ -0,0 +1,31 @@
+package plugins.adufour.blocks.tools;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarMutableArray;
+
+public class ListSize extends Plugin implements ToolsBlock
+{
+ private final VarMutableArray list = new VarMutableArray("List", null);
+
+ private final VarInteger size = new VarInteger("Size", 0);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("list", list);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("size", size);
+ }
+
+ @Override
+ public void run()
+ {
+ size.setValue(list.size());
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ReLoop.java b/src/main/java/plugins/adufour/blocks/tools/ReLoop.java
new file mode 100644
index 0000000..f8bbee0
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ReLoop.java
@@ -0,0 +1,68 @@
+package plugins.adufour.blocks.tools;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.util.TypeChangeListener;
+
+public class ReLoop extends Plugin implements ToolsBlock
+{
+ public final VarMutable initValue = new VarMutable("init", null);
+
+ public final VarMutable reloopValue = new VarMutable("reloop", null);
+
+ public final VarMutable output = new VarMutable("output", null);
+
+ @Override
+ public void run()
+ {
+ // first run: output is null
+ if (output.getValue() == null)
+ {
+ output.setValue(initValue.getValue());
+ }
+ else
+ {
+ output.setValue(reloopValue.getValue());
+ }
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("init", initValue);
+ inputMap.add("reloop", reloopValue);
+
+ initValue.addTypeChangeListener(new TypeChangeListener()
+ {
+ @Override
+ public void typeChanged(Object source, Class<?> oldType, Class<?> newType)
+ {
+ if (newType != null)
+ {
+ reloopValue.setType(newType);
+ output.setType(newType);
+ }
+ }
+ });
+
+ reloopValue.addTypeChangeListener(new TypeChangeListener()
+ {
+ @Override
+ public void typeChanged(Object source, Class<?> oldType, Class<?> newType)
+ {
+ if (newType != null)
+ {
+ initValue.setType(newType);
+ output.setType(newType);
+ }
+ }
+ });
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output", output);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ToolsBlock.java b/src/main/java/plugins/adufour/blocks/tools/ToolsBlock.java
new file mode 100644
index 0000000..f447b96
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ToolsBlock.java
@@ -0,0 +1,8 @@
+package plugins.adufour.blocks.tools;
+
+import plugins.adufour.blocks.lang.Block;
+
+public interface ToolsBlock extends Block
+{
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ij/CallIJMacro.java b/src/main/java/plugins/adufour/blocks/tools/ij/CallIJMacro.java
new file mode 100644
index 0000000..fc5262f
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ij/CallIJMacro.java
@@ -0,0 +1,30 @@
+package plugins.adufour.blocks.tools.ij;
+
+import icy.plugin.abstract_.Plugin;
+import ij.IJ;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarFile;
+
+public class CallIJMacro extends Plugin implements IJBlock
+{
+ VarFile macroFile = new VarFile("Macro file", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("Macro file", macroFile);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+
+ }
+
+ @Override
+ public void run()
+ {
+ IJ.runMacroFile(macroFile.getValue(true).getPath());
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ij/CallIJPlugin.java b/src/main/java/plugins/adufour/blocks/tools/ij/CallIJPlugin.java
new file mode 100644
index 0000000..31330e0
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ij/CallIJPlugin.java
@@ -0,0 +1,61 @@
+package plugins.adufour.blocks.tools.ij;
+
+import icy.plugin.abstract_.Plugin;
+import icy.system.IcyHandledException;
+import ij.IJ;
+import ij.ImagePlus;
+import ij.WindowManager;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarImagePlus;
+import plugins.adufour.vars.lang.VarString;
+
+public class CallIJPlugin extends Plugin implements IJBlock
+{
+ VarImagePlus varIp = new VarImagePlus("Input ImagePlus", null);
+
+ VarString pluginName = new VarString("plug-in name", "");
+
+ VarString pluginParams = new VarString("parameters", "");
+
+ VarImagePlus varActiveIP = new VarImagePlus("Output (active) ImagePlus", null);
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ IJ.run(varIp.getValue(true), pluginName.getValue(true), pluginParams.getValue(true));
+ // Set the output image (if available) with the following priority
+ ImagePlus output = WindowManager.getCurrentImage();
+ if (output == null)
+ {
+ // Default to the current "temporary" image (if any)
+ output = WindowManager.getTempCurrentImage();
+ }
+ if (output == null)
+ {
+ // Default to the input image (may have been modified "in-place"
+ output = varIp.getValue();
+ }
+ varActiveIP.setValue(output);
+ }
+ catch (RuntimeException e)
+ {
+ throw new IcyHandledException(e.getLocalizedMessage());
+ }
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("Input ImagePlus", varIp);
+ inputMap.add("ImageJ plug-in name", pluginName);
+ inputMap.add("ImageJ plug-in parameters", pluginParams);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("Output ImagePlus", varActiveIP);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ij/IJBlock.java b/src/main/java/plugins/adufour/blocks/tools/ij/IJBlock.java
new file mode 100644
index 0000000..39c20dc
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ij/IJBlock.java
@@ -0,0 +1,13 @@
+package plugins.adufour.blocks.tools.ij;
+
+import plugins.adufour.blocks.lang.Block;
+
+/**
+ * Interface used to flag ImageJ-related blocks
+ *
+ * @author Alexandre Dufour
+ *
+ */
+public interface IJBlock extends Block
+{
+}
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/blocks/tools/ij/ImagePlusToSequence.java b/src/main/java/plugins/adufour/blocks/tools/ij/ImagePlusToSequence.java
new file mode 100644
index 0000000..ef66688
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ij/ImagePlusToSequence.java
@@ -0,0 +1,32 @@
+package plugins.adufour.blocks.tools.ij;
+
+import icy.imagej.ImageJUtil;
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarImagePlus;
+import plugins.adufour.vars.lang.VarSequence;
+
+public class ImagePlusToSequence extends Plugin implements IJBlock
+{
+ VarImagePlus vip = new VarImagePlus("IJ ImagePlus", null);
+ VarSequence vs = new VarSequence("Icy Sequence", null);
+
+ @Override
+ public void run()
+ {
+ vs.setValue(ImageJUtil.convertToIcySequence(vip.getValue(true), null));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("IJ ImagePlus", vip);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("Icy Sequence", vs);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ij/SequenceToImagePlus.java b/src/main/java/plugins/adufour/blocks/tools/ij/SequenceToImagePlus.java
new file mode 100644
index 0000000..57e5ff0
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ij/SequenceToImagePlus.java
@@ -0,0 +1,32 @@
+package plugins.adufour.blocks.tools.ij;
+
+import icy.imagej.ImageJUtil;
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarImagePlus;
+import plugins.adufour.vars.lang.VarSequence;
+
+public class SequenceToImagePlus extends Plugin implements IJBlock
+{
+ VarSequence vs = new VarSequence("Icy Sequence", null);
+ VarImagePlus vip = new VarImagePlus("ImagePlus", null);
+
+ @Override
+ public void run()
+ {
+ vip.setValue(ImageJUtil.convertToImageJImage(vs.getValue(true), null));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("Icy Sequence", vs);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("IJ ImagePlus", vip);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/ij/ShowImagePlus.java b/src/main/java/plugins/adufour/blocks/tools/ij/ShowImagePlus.java
new file mode 100644
index 0000000..f18b07c
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/ij/ShowImagePlus.java
@@ -0,0 +1,28 @@
+package plugins.adufour.blocks.tools.ij;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarImagePlus;
+
+public class ShowImagePlus extends Plugin implements IJBlock
+{
+ VarImagePlus ip = new VarImagePlus("ImagePlus", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("ImagePlus", ip);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+ @Override
+ public void run()
+ {
+ ip.getValue(true).show();
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Boolean.java b/src/main/java/plugins/adufour/blocks/tools/input/Boolean.java
new file mode 100644
index 0000000..4eff08b
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Boolean.java
@@ -0,0 +1,24 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarBoolean;
+
+public class Boolean extends Plugin implements InputBlock
+{
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("boolean", new VarBoolean("Boolean", false));
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+ @Override
+ public void run()
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Decimal.java b/src/main/java/plugins/adufour/blocks/tools/input/Decimal.java
new file mode 100644
index 0000000..9e345aa
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Decimal.java
@@ -0,0 +1,29 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarDouble;
+
+/**
+ * Input block reading a 64-bit double-precision floating-point value
+ *
+ * @author Alexandre Dufour
+ */
+public class Decimal extends Plugin implements InputBlock
+{
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("decimal", new VarDouble("decimal", 0.0));
+ }
+
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Decimals.java b/src/main/java/plugins/adufour/blocks/tools/input/Decimals.java
new file mode 100644
index 0000000..1ab76db
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Decimals.java
@@ -0,0 +1,29 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarDoubleArrayNative;
+
+/**
+ * Utility block reading an array of double-precision floating-point values
+ *
+ * @author Alexandre Dufour
+ */
+public class Decimals extends Plugin implements InputBlock
+{
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("decimals", new VarDoubleArrayNative("decimals", new double[0]));
+ }
+
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/File.java b/src/main/java/plugins/adufour/blocks/tools/input/File.java
new file mode 100644
index 0000000..141604a
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/File.java
@@ -0,0 +1,34 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.VarFile;
+
+/**
+ * Input block reading a file
+ *
+ * @author Alexandre Dufour
+ */
+public class File extends Plugin implements InputBlock
+{
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ VarFile vf = new VarFile("file", null);
+ vf.setDefaultEditorModel(new FileTypeModel("", FileMode.FILES, null, false));
+ inputMap.add("file", vf);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Files.java b/src/main/java/plugins/adufour/blocks/tools/input/Files.java
new file mode 100644
index 0000000..38592b4
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Files.java
@@ -0,0 +1,34 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeListModel;
+import plugins.adufour.vars.lang.VarFileArray;
+
+/**
+ * Input block reading a list of files
+ *
+ * @author Alexandre Dufour
+ */
+public class Files extends Plugin implements InputBlock
+{
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ VarFileArray vf = new VarFileArray("files", new java.io.File[0]);
+ vf.setDefaultEditorModel(new FileTypeListModel("", FileMode.FILES, null, false));
+ inputMap.add("files", vf);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Folder.java b/src/main/java/plugins/adufour/blocks/tools/input/Folder.java
new file mode 100644
index 0000000..af38bad
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Folder.java
@@ -0,0 +1,34 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.VarFile;
+
+/**
+ * Input block reading a folder
+ *
+ * @author Alexandre Dufour
+ */
+public class Folder extends Plugin implements InputBlock
+{
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ VarFile vf = new VarFile("folder", null);
+ vf.setDefaultEditorModel(new FileTypeModel("", FileMode.FOLDERS, null, false));
+ inputMap.add("folder", vf);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Folders.java b/src/main/java/plugins/adufour/blocks/tools/input/Folders.java
new file mode 100644
index 0000000..038676e
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Folders.java
@@ -0,0 +1,34 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeListModel;
+import plugins.adufour.vars.lang.VarFileArray;
+
+/**
+ * Input block reading a list of folders
+ *
+ * @author Alexandre Dufour
+ */
+public class Folders extends Plugin implements InputBlock
+{
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ VarFileArray vf = new VarFileArray("folders", new java.io.File[0]);
+ vf.setDefaultEditorModel(new FileTypeListModel("", FileMode.FOLDERS, null, false));
+ inputMap.add("folders", vf);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/InputBlock.java b/src/main/java/plugins/adufour/blocks/tools/input/InputBlock.java
new file mode 100644
index 0000000..a43653e
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/InputBlock.java
@@ -0,0 +1,13 @@
+package plugins.adufour.blocks.tools.input;
+
+import plugins.adufour.blocks.lang.Block;
+
+/**
+ * Interface used to flag pure input blocks
+ *
+ * @author Alexandre Dufour
+ *
+ */
+public interface InputBlock extends Block
+{
+}
\ No newline at end of file
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Integer.java b/src/main/java/plugins/adufour/blocks/tools/input/Integer.java
new file mode 100644
index 0000000..514ca1e
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Integer.java
@@ -0,0 +1,30 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarInteger;
+
+/**
+ * Utility block reading a 32-bit integer value
+ *
+ * @author Alexandre Dufour
+ */
+public class Integer extends Plugin implements InputBlock
+{
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ VarInteger vi = new VarInteger("integer", 0);
+ inputMap.add("integer", vi);
+ }
+
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Integers.java b/src/main/java/plugins/adufour/blocks/tools/input/Integers.java
new file mode 100644
index 0000000..acae7c2
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Integers.java
@@ -0,0 +1,29 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarIntegerArrayNative;
+
+/**
+ * Utility block reading an array of 32-bit integer values
+ *
+ * @author Alexandre Dufour
+ */
+public class Integers extends Plugin implements InputBlock
+{
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("integers", new VarIntegerArrayNative("integers", new int[0]));
+ }
+
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Sequence.java b/src/main/java/plugins/adufour/blocks/tools/input/Sequence.java
new file mode 100644
index 0000000..bd2ab20
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Sequence.java
@@ -0,0 +1,36 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarSequence;
+
+/**
+ * Utility block reading a {@link icy.sequence.Sequence} object
+ *
+ * @author Alexandre Dufour
+ */
+public class Sequence extends Plugin implements InputBlock
+{
+ private final VarSequence vs = new VarSequence("sequence", null);
+
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input sequence", vs);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+ public VarSequence getVariable()
+ {
+ return vs;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Sequences.java b/src/main/java/plugins/adufour/blocks/tools/input/Sequences.java
new file mode 100644
index 0000000..bf5d484
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Sequences.java
@@ -0,0 +1,30 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarSequenceArray;
+
+/**
+ * Utility block reading a list of {@link icy.sequence.Sequence} objects
+ *
+ * @author Alexandre Dufour
+ */
+public class Sequences extends Plugin implements InputBlock
+{
+ @Override
+ public void run()
+ {
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ VarSequenceArray vsa = new VarSequenceArray("sequence");
+ inputMap.add("input sequence", vsa);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/input/Text.java b/src/main/java/plugins/adufour/blocks/tools/input/Text.java
new file mode 100644
index 0000000..8ced613
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/input/Text.java
@@ -0,0 +1,31 @@
+package plugins.adufour.blocks.tools.input;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarString;
+
+/**
+ * Text input
+ *
+ * @author Alexandre Dufour
+ */
+public class Text extends Plugin implements InputBlock
+{
+ @Override
+ public void run()
+ {
+
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("text", new VarString("text", ""));
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/AppendFilePath.java b/src/main/java/plugins/adufour/blocks/tools/io/AppendFilePath.java
new file mode 100644
index 0000000..9cb77e3
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/AppendFilePath.java
@@ -0,0 +1,58 @@
+package plugins.adufour.blocks.tools.io;
+
+import java.io.File;
+
+import icy.file.FileUtil;
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarString;
+
+public class AppendFilePath extends Plugin implements IOBlock
+{
+ VarMutable in = new VarMutable("Current file", null);
+
+ VarFile out = new VarFile("New file", null);
+
+ VarBoolean removeExt = new VarBoolean("Remove extension", false);
+
+ VarString suffix = new VarString("Add suffix", "");
+
+ @Override
+ public void run()
+ {
+ Object input = in.getValue(true);
+ String newPath = "";
+
+ if (input instanceof File)
+ newPath = ((File)input).getAbsolutePath();
+ else newPath = input.toString();
+
+ if (removeExt.getValue())
+ {
+ String fileName = FileUtil.getFileName(newPath, false);
+ newPath = FileUtil.getDirectory(newPath) + fileName;
+ }
+
+ newPath += suffix.getValue();
+
+ out.setValue(new File(newPath));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input file", in);
+ inputMap.add("remove ext.", removeExt);
+ inputMap.add("suffix", suffix);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output file", out);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/CreateFile.java b/src/main/java/plugins/adufour/blocks/tools/io/CreateFile.java
new file mode 100644
index 0000000..f327782
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/CreateFile.java
@@ -0,0 +1,62 @@
+package plugins.adufour.blocks.tools.io;
+
+import java.io.File;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarString;
+import plugins.adufour.vars.util.VarException;
+import icy.file.FileUtil;
+import icy.plugin.abstract_.Plugin;
+
+public class CreateFile extends Plugin implements IOBlock
+{
+ VarFile parentFolder = new VarFile("Base folder", new File(System.getProperty("user.home")));
+
+ VarString fileName = new VarString("File name", "newFile");
+
+ VarFile file = new VarFile("New file", null);
+
+ VarBoolean overwrite = new VarBoolean("Overwrite", false);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ parentFolder.setDefaultEditorModel(new FileTypeModel(parentFolder.getValue().getPath(), FileMode.FOLDERS, null, true));
+ inputMap.add("parent folder", parentFolder);
+ inputMap.add("file name", fileName);
+ inputMap.add("overwrite", overwrite);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("new file", file);
+ }
+
+ @Override
+ public void run()
+ {
+ File parent = parentFolder.getValue();
+
+ if (parent == null || !parent.exists() || !parent.isDirectory()) throw new VarException(parentFolder, "The parent folder does not exist or is not a folder");
+
+ if (fileName.getValue().isEmpty()) throw new VarException(fileName, "The name of the file cannot be empty");
+
+ File newFile = new File(parentFolder + File.separator + fileName.getValue());
+
+ if (!newFile.exists())
+ {
+ FileUtil.createFile(newFile);
+ }
+ else if (!newFile.isDirectory() && !overwrite.getValue())
+ {
+ throw new VarException(fileName, "Cannot create file " + newFile.getPath() + "\n=> A file with this name already exists");
+ }
+
+ file.setValue(newFile);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/CreateFolder.java b/src/main/java/plugins/adufour/blocks/tools/io/CreateFolder.java
new file mode 100644
index 0000000..e0efdc0
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/CreateFolder.java
@@ -0,0 +1,57 @@
+package plugins.adufour.blocks.tools.io;
+
+import icy.file.FileUtil;
+import icy.plugin.abstract_.Plugin;
+
+import java.io.File;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarString;
+import plugins.adufour.vars.util.VarException;
+
+public class CreateFolder extends Plugin implements IOBlock
+{
+ VarFile parentFolder = new VarFile("Base folder", new File(System.getProperty("user.home")));
+
+ VarString folderName = new VarString("Folder name", "myFolder");
+
+ VarFile folder = new VarFile("New folder", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ parentFolder.setDefaultEditorModel(new FileTypeModel(parentFolder.getValue().getPath(), FileMode.FOLDERS, null, true));
+ inputMap.add("parent folder", parentFolder);
+ inputMap.add("folder name", folderName);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("new folder", folder);
+ }
+
+ @Override
+ public void run()
+ {
+ File parent = parentFolder.getValue();
+
+ if (parent == null || !parent.exists() || !parent.isDirectory()) throw new VarException(parentFolder, "The parent folder does not exist or is not a folder");
+
+ if (folderName.getValue().isEmpty()) throw new VarException(folderName, "The name of the folder cannot be empty");
+
+ File newFolder = new File(parentFolder + File.separator + folderName.getValue());
+
+ if (newFolder.exists() && !newFolder.isDirectory())
+ {
+ throw new VarException(folderName, "Cannot create folder " + newFolder.getPath() + "\n=> A file with this name already exists");
+ }
+
+ FileUtil.createDir(newFolder);
+
+ folder.setValue(newFolder);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/FileToPath.java b/src/main/java/plugins/adufour/blocks/tools/io/FileToPath.java
new file mode 100644
index 0000000..e38996e
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/FileToPath.java
@@ -0,0 +1,31 @@
+package plugins.adufour.blocks.tools.io;
+
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarString;
+
+public class FileToPath extends Plugin implements IOBlock
+{
+ VarString path = new VarString("path", "", 1);
+
+ VarFile file = new VarFile("file", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input file", file);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output path", path);
+ }
+
+ @Override
+ public void run()
+ {
+ path.setValue(file.getValue() == null ? null : file.getValue().getPath());
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/FileToSequence.java b/src/main/java/plugins/adufour/blocks/tools/io/FileToSequence.java
new file mode 100644
index 0000000..93c386a
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/FileToSequence.java
@@ -0,0 +1,56 @@
+package plugins.adufour.blocks.tools.io;
+
+import icy.file.Loader;
+import icy.plugin.abstract_.Plugin;
+import icy.sequence.Sequence;
+
+import java.io.File;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.util.VarException;
+
+/**
+ * Utility block that reads a file from disk
+ *
+ * @author Alexandre Dufour
+ */
+public class FileToSequence extends Plugin implements IOBlock
+{
+ VarFile inputFile = new VarFile("input file", null);
+ VarSequence outputSequence = new VarSequence("sequence", null);
+ VarInteger series = new VarInteger("Series", 0);
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ File file = inputFile.getValue(true);
+ Sequence sequence = Loader.loadSequence(file.getPath(), series.getValue(), false);
+ if (sequence == null) throw new VarException(inputFile, "Cannot read " + file.getPath() + " into a sequence");
+ outputSequence.setValue(sequence);
+ }
+ catch (Exception e)
+ {
+ File file = inputFile.getValue(true);
+ throw new VarException(inputFile, "unable to read file " + file.getAbsolutePath());
+ }
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input file", inputFile);
+ inputMap.add("Series", series);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("sequence", outputSequence);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/FilesToSequence.java b/src/main/java/plugins/adufour/blocks/tools/io/FilesToSequence.java
new file mode 100644
index 0000000..3dc196d
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/FilesToSequence.java
@@ -0,0 +1,57 @@
+package plugins.adufour.blocks.tools.io;
+
+import icy.file.Loader;
+import icy.plugin.abstract_.Plugin;
+import icy.sequence.Sequence;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarFileArray;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.util.VarException;
+
+/**
+ * Utility block that reads multiple image files from disk into a {@link Sequence}
+ *
+ * @author Alexandre Dufour
+ */
+public class FilesToSequence extends Plugin implements IOBlock
+{
+ VarFileArray inputFiles = new VarFileArray("input file", new File[] {});
+ VarSequence outputSequence = new VarSequence("sequence", null);
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ File[] files = inputFiles.getValue(true);
+ List<String> paths = new ArrayList<String>(files.length);
+
+ for (int i = 0; i < files.length; i++)
+ if (files[i] != null) paths.add(files[i].getPath());
+
+ outputSequence.setValue(Loader.loadSequence(paths, false));
+ }
+ catch (Exception e)
+ {
+ throw new VarException(inputFiles, "unable to read files");
+ }
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input file", inputFiles);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("sequence", outputSequence);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/GetSequenceFolder.java b/src/main/java/plugins/adufour/blocks/tools/io/GetSequenceFolder.java
new file mode 100644
index 0000000..5cfbf86
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/GetSequenceFolder.java
@@ -0,0 +1,40 @@
+package plugins.adufour.blocks.tools.io;
+
+import java.io.File;
+
+import icy.file.FileUtil;
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.tools.sequence.SequenceBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.util.VarException;
+
+public class GetSequenceFolder extends Plugin implements SequenceBlock, IOBlock
+{
+ VarSequence sequence = new VarSequence("Sequence", null);
+
+ VarFile folder = new VarFile("Folder", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("Sequence", sequence);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("Folder", folder);
+ }
+
+ @Override
+ public void run()
+ {
+ String filePath = sequence.getValue(true).getFilename();
+ if (filePath == null) throw new VarException(sequence, "[Get sequence folder]: the selected sequence has not been saved on disk");
+
+ String folderPath = FileUtil.getDirectory(filePath);
+ folder.setValue(new File(folderPath));
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/IOBlock.java b/src/main/java/plugins/adufour/blocks/tools/io/IOBlock.java
new file mode 100644
index 0000000..2c8eab2
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/IOBlock.java
@@ -0,0 +1,14 @@
+package plugins.adufour.blocks.tools.io;
+
+import plugins.adufour.blocks.lang.Block;
+
+/**
+ * Interface used to mark blocks as I/O blocks (and appear in the appropriate menu)
+ *
+ * @author Alexandre Dufour
+ *
+ */
+public interface IOBlock extends Block
+{
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/PathToFile.java b/src/main/java/plugins/adufour/blocks/tools/io/PathToFile.java
new file mode 100644
index 0000000..e1a1155
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/PathToFile.java
@@ -0,0 +1,34 @@
+package plugins.adufour.blocks.tools.io;
+
+import icy.plugin.abstract_.Plugin;
+
+import java.io.File;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarString;
+
+public class PathToFile extends Plugin implements IOBlock
+{
+ VarString path = new VarString("path", "", 1);
+
+ VarFile file = new VarFile("file", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input path", path);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output file", file);
+ }
+
+ @Override
+ public void run()
+ {
+ file.setValue(new File(path.getValue(true)));
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/SendToSwimmingPool.java b/src/main/java/plugins/adufour/blocks/tools/io/SendToSwimmingPool.java
new file mode 100644
index 0000000..7ebfcd0
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/SendToSwimmingPool.java
@@ -0,0 +1,47 @@
+package plugins.adufour.blocks.tools.io;
+
+import javax.swing.SwingUtilities;
+
+import icy.main.Icy;
+import icy.plugin.abstract_.Plugin;
+import icy.swimmingPool.SwimmingObject;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarMutable;
+
+/**
+ * Sends any data to the swimming pool
+ *
+ * @author Alexandre Dufour
+ */
+public class SendToSwimmingPool extends Plugin implements Block
+{
+ private VarMutable data = new VarMutable("Data", null);
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("Data", data);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+ @Override
+ public void run()
+ {
+ if (data.getValue() == null) return;
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Icy.getMainInterface().getSwimmingPool().add(new SwimmingObject(data.getValue(), data.getReference().getName()));
+ }
+ });
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/io/SequenceToFile.java b/src/main/java/plugins/adufour/blocks/tools/io/SequenceToFile.java
new file mode 100644
index 0000000..f3c4a87
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/io/SequenceToFile.java
@@ -0,0 +1,47 @@
+package plugins.adufour.blocks.tools.io;
+
+import icy.file.Saver;
+import icy.plugin.abstract_.Plugin;
+
+import java.io.File;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.FileMode;
+import plugins.adufour.vars.gui.model.FileTypeModel;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarSequence;
+
+/**
+ * Utility block that saves a sequence to disk
+ *
+ * @author Alexandre Dufour
+ */
+public class SequenceToFile extends Plugin implements IOBlock
+{
+ private VarFile folder = new VarFile("File or folder", null);
+ private VarSequence sequence = new VarSequence("sequence", null);
+
+ @Override
+ public void run()
+ {
+ File f = new File(folder.getValue(true).getAbsolutePath());
+ if (f.isDirectory())
+ {
+ f = new File(f.getAbsolutePath() + File.separator + sequence.getValue(true) + ".tif");
+ }
+ Saver.save(sequence.getValue(true), f, false, false);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ folder.setDefaultEditorModel(new FileTypeModel("", FileMode.FOLDERS, null, false));
+ inputMap.add("folder", folder);
+ inputMap.add("sequence", sequence);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/AddROIToSequence.java b/src/main/java/plugins/adufour/blocks/tools/roi/AddROIToSequence.java
new file mode 100644
index 0000000..231821d
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/AddROIToSequence.java
@@ -0,0 +1,56 @@
+package plugins.adufour.blocks.tools.roi;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import icy.sequence.Sequence;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+
+/**
+ * (Deprecated: Use plugins.tprovoost.sequenceblocks.add.AddRois instead)
+ * Block to add one or several {@link ROI} to a Sequence.
+ *
+ * class: plugins.adufour.blacks.tools.roi.AddROIToSequence
+ *
+ * @author Alexandre Dufour
+ */
+@Deprecated
+public class AddROIToSequence extends Plugin implements ROIBlock
+{
+ VarROIArray rois = new VarROIArray("ROI to add");
+
+ VarSequence sequence = new VarSequence("Source", null);
+
+ VarBoolean replace = new VarBoolean("Overwrite", false);
+
+ @Override
+ public void run()
+ {
+ Sequence s = sequence.getValue(true);
+
+ if (replace.getValue()) s.removeAllROI();
+
+ s.beginUpdate();
+ for (ROI roi : rois.getValue(true))
+ s.addROI(roi);
+ s.endUpdate();
+
+ s.saveXMLData();
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("target sequence", sequence);
+ inputMap.add("input rois", rois);
+ inputMap.add("replace existing", replace);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/CropSequenceToROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/CropSequenceToROI.java
new file mode 100644
index 0000000..fa22cb8
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/CropSequenceToROI.java
@@ -0,0 +1,114 @@
+package plugins.adufour.blocks.tools.roi;
+
+import icy.image.IcyBufferedImage;
+import icy.image.IcyBufferedImageUtil;
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import icy.sequence.Sequence;
+import icy.type.rectangle.Rectangle5D;
+import icy.util.OMEUtil;
+import icy.util.StringUtil;
+
+import java.awt.Rectangle;
+import java.util.ArrayList;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarGenericArray;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+
+public class CropSequenceToROI extends Plugin implements ROIBlock
+{
+ VarSequence input = new VarSequence("Sequence to crop", null);
+
+ VarROIArray rois = new VarROIArray("List of ROI");
+
+ VarGenericArray<Sequence[]> output = new VarGenericArray<Sequence[]>("List of crops", Sequence[].class, new Sequence[] {});
+
+ @Override
+ public void run()
+ {
+ Sequence seq = input.getValue(true);
+
+ int nbROIs = rois.getValue(true).length;
+
+ ArrayList<Sequence> crops = new ArrayList<Sequence>(nbROIs);
+
+ int cpt = 1;
+ int digitSize = 1 + (int) Math.log10(nbROIs);
+
+ for (ROI roi : rois.getValue())
+ {
+ final Sequence result = new Sequence(OMEUtil.createOMEXMLMetadata(seq.getOMEXMLMetadata()));
+
+ Rectangle5D.Integer region = roi.getBounds5D().toInteger();
+
+ final Rectangle region2d = region.toRectangle2D().getBounds();
+ final int startZ;
+ final int endZ;
+ final int startT;
+ final int endT;
+
+ if (region.isInfiniteZ())
+ {
+ startZ = 0;
+ endZ = seq.getSizeZ();
+ }
+ else
+ {
+ startZ = Math.max(0, region.z);
+ endZ = Math.min(seq.getSizeZ(), region.z + region.sizeZ);
+ }
+ if (region.isInfiniteT())
+ {
+ startT = 0;
+ endT = seq.getSizeT();
+ }
+ else
+ {
+ startT = Math.max(0, region.t);
+ endT = (int) Math.min(seq.getSizeT(), (long) region.t + (long) region.sizeT);
+ }
+
+ result.beginUpdate();
+ try
+ {
+ for (int t = startT; t < endT; t++)
+ {
+ for (int z = startZ; z < endZ; z++)
+ {
+ IcyBufferedImage img = seq.getImage(t, z);
+
+ if (img != null) img = IcyBufferedImageUtil.getSubImage(img, region2d, region.c, region.sizeC);
+
+ result.setImage(t - startT, z - startZ, img);
+ }
+ }
+ }
+ finally
+ {
+ result.endUpdate();
+ }
+
+ result.setName(seq.getName() + "_crop" + StringUtil.toString(cpt, digitSize));
+ crops.add(result);
+ cpt++;
+ }
+
+ output.setValue(crops.toArray(new Sequence[crops.size()]));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("sequence to crop", input);
+ inputMap.add("list of ROI", rois);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("list of crops", output);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/DilateROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/DilateROI.java
new file mode 100644
index 0000000..1a984cd
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/DilateROI.java
@@ -0,0 +1,265 @@
+package plugins.adufour.blocks.tools.roi;
+
+import java.awt.Point;
+import java.util.ArrayList;
+
+import icy.roi.BooleanMask2D;
+import icy.roi.BooleanMask3D;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import icy.roi.ROI3D;
+import icy.type.point.Point3D;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.util.VarException;
+import plugins.kernel.roi.roi2d.ROI2DArea;
+import plugins.kernel.roi.roi3d.ROI3DArea;
+
+public class DilateROI extends MorphROI
+{
+ public DilateROI()
+ {
+ roiOUT = new VarROIArray("Dilated ROI");
+ }
+
+ @Override
+ public void run()
+ {
+ switch (unit.getValue())
+ {
+ case PIXELS:
+ roiOUT.setValue(dilateROI(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+ break;
+ case PERCENTAGE:
+ roiOUT.setValue(dilateROIByPercentage(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+ break;
+ default:
+ throw new VarException(unit, "Unsupported unit");
+ }
+ }
+
+ /**
+ * Perform a morphological dilation on the specified set of ROI by the given amount in each
+ * dimension
+ *
+ * @param inputRoi
+ * The ROI to dilate
+ * @param xRadius
+ * the radius (in pixels) along X
+ * @param yRadius
+ * the radius (in pixels) along X
+ * @param zRadius
+ * the radius (in pixels) along Z (not used if <code>roi</code> is 2D)
+ * @return a new set of dilated ROI of type "area"
+ */
+ public static ROI[] dilateROI(ROI[] inputRoi, int xRadius, int yRadius, int zRadius)
+ {
+ ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
+
+ for (ROI roi : inputRoi)
+ {
+ if (Thread.currentThread().isInterrupted())
+ break;
+
+ ROI dilated = dilateROI(roi, xRadius, yRadius, zRadius);
+ if (dilated != null)
+ out.add(dilated);
+ }
+
+ return out.toArray(new ROI[out.size()]);
+ }
+
+ /**
+ * Perform a morphological dilation on the specified set of ROI by the given percentage in each
+ * dimension
+ *
+ * @param inputRoi
+ * the ROI to dilate
+ * @param xPct
+ * the percentage (from 0 to 100) to dilate along X
+ * @param yPct
+ * the percentage (from 0 to 100) to dilate along Y
+ * @param zPct
+ * the percentage (from 0 to 100) to dilate along Z (not used in 2D)
+ * @return a new set of dilated ROI of type "area"
+ */
+ public static ROI[] dilateROIByPercentage(ROI[] inputRoi, int xPct, int yPct, int zPct)
+ {
+ ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
+
+ for (ROI roi : inputRoi)
+ {
+ if (Thread.currentThread().isInterrupted())
+ break;
+
+ ROI dilated = dilateROIByPercentage(roi, xPct, yPct, zPct);
+ if (dilated != null)
+ out.add(dilated);
+ }
+
+ return out.toArray(new ROI[out.size()]);
+ }
+
+ /**
+ * Perform a morphological dilation on the specified ROI by the given percentage in each
+ * dimension
+ *
+ * @author Joel Rogers, Alexandre Dufour
+ * @param roi
+ * the ROI to dilate
+ * @param xPct
+ * the percentage (from 0 to 100) to dilate along X
+ * @param yPct
+ * the percentage (from 0 to 100) to dilate along Y
+ * @param zPct
+ * the percentage (from 0 to 100) to dilate along Z (not used in 2D)
+ * @return a new, dilated ROI of type "area"
+ */
+ public static ROI dilateROIByPercentage(ROI roi, int xPct, int yPct, int zPct)
+ {
+ int xRadius = percentageToRadiusX(roi, xPct);
+ int yRadius = percentageToRadiusY(roi, yPct);
+ int zRadius = percentageToRadiusZ(roi, zPct);
+
+ return dilateROI(roi, xRadius, yRadius, zRadius);
+ }
+
+ /**
+ * Perform a morphological dilation on the specified ROI by the given radius in each dimension
+ *
+ * @param roi
+ * the ROI to dilate
+ * @param xRadius
+ * the radius in pixels along X
+ * @param yRadius
+ * the radius in pixels along X
+ * @param zRadius
+ * the radius in pixels along Z (not used if <code>roi</code> is 2D)
+ * @return a new, dilated ROI of type "area"
+ */
+ public static ROI dilateROI(ROI roi, int xRadius, int yRadius, int zRadius)
+ {
+ int rx = xRadius, rrx = rx * rx;
+ int ry = yRadius, rry = ry * ry;
+ int rz = zRadius, rrz = rz * rz;
+
+ if (roi instanceof ROI2D)
+ {
+ BooleanMask2D m2 = ((ROI2D) roi).getBooleanMask(true);
+ ROI2DArea r2 = new ROI2DArea(m2);
+ r2.setC(((ROI2D) roi).getC());
+ r2.setZ(((ROI2D) roi).getZ());
+ r2.setT(((ROI2D) roi).getT());
+ r2.setName(roi.getName() + " dilated[" + xRadius + "," + yRadius + "]");
+
+ r2.beginUpdate();
+
+ for (Point p : m2.getContourPoints())
+ {
+ // Brute force
+ for (int y = -ry; y <= ry; y++)
+ for (int x = -rx; x <= rx; x++)
+ {
+ double xr2 = rrx == 0 ? 0 : x * x / rrx;
+ double yr2 = rry == 0 ? 0 : y * y / rry;
+
+ if (xr2 + yr2 <= 1.0)
+ {
+ if (!m2.contains(p.x + x, p.y + y))
+ r2.addPoint(p.x + x, p.y + y);
+ }
+ }
+
+ // Bresenham style
+ // int x = r;
+ // int y = 0;
+ // int xChange = 1 - (r << 1);
+ // int yChange = 0;
+ // int radiusError = 0;
+ //
+ // while (x >= y)
+ // {
+ // for (int i = p.x - x; i <= p.x + x; i++)
+ // {
+ // if (!m2.contains(i, p.y + y)) r2.addPoint(i, p.y + y);
+ // if (!m2.contains(i, p.y - y)) r2.addPoint(i, p.y - y);
+ // }
+ // for (int i = p.x - y; i <= p.x + y; i++)
+ // {
+ // if (!m2.contains(i, p.y + x)) r2.addPoint(i, p.y + x);
+ // if (!m2.contains(i, p.y - x)) r2.addPoint(i, p.y - x);
+ // }
+ //
+ // y++;
+ // radiusError += yChange;
+ // yChange += 2;
+ // if (((radiusError << 1) + xChange) > 0)
+ // {
+ // x--;
+ // radiusError += xChange;
+ // xChange += 2;
+ // }
+ // }
+ }
+ r2.endUpdate();
+
+ return r2;
+ }
+ else if (roi instanceof ROI3D)
+ {
+ ROI3D roi3D = (ROI3D) roi;
+
+ BooleanMask3D m3 = roi3D.getBooleanMask(true);
+
+ ROI3DArea r3 = new ROI3DArea(m3);
+ r3.setC(((ROI3D) roi).getC());
+ r3.setT(((ROI3D) roi).getT());
+ r3.setName(roi.getName() + " dilated[" + xRadius + "," + yRadius + "," + zRadius + "]");
+
+ r3.beginUpdate();
+
+ for (Point3D.Integer p : m3.getContourPoints())
+ { // Brute force
+
+ if (rrz == 0)
+ {
+ int z = 0;
+ for (int y = -ry; y <= ry; y++)
+ for (int x = -rx; x <= rx; x++)
+ {
+ double xr2 = rrx == 0 ? 0 : x * x / rrx;
+ double yr2 = rry == 0 ? 0 : y * y / rry;
+
+ if (xr2 + yr2 <= 1.0)
+ {
+ if (!m3.contains(p.x + x, p.y + y, p.z + z))
+ r3.addPoint(p.x + x, p.y + y, p.z + z);
+ }
+ }
+ }
+ else
+ {
+ for (int z = -rz; z <= rz; z++)
+ for (int y = -ry; y <= ry; y++)
+ for (int x = -rx; x <= rx; x++)
+ {
+ double xr2 = rrx == 0 ? 0 : x * x / rrx;
+ double yr2 = rry == 0 ? 0 : y * y / rry;
+ double zr2 = rrz == 0 ? 0 : z * z / rrz;
+
+ if (xr2 + yr2 + zr2 <= 1.0)
+ {
+ if (!m3.contains(p.x + x, p.y + y, p.z + z))
+ r3.addPoint(p.x + x, p.y + y, p.z + z);
+ }
+ }
+ }
+ }
+ r3.endUpdate();
+ r3.optimizeBounds();
+ return r3;
+ }
+
+ System.out.println("[Dilate ROI] Warning: unsupported ROI: " + roi.getName());
+ return null;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/ErodeROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/ErodeROI.java
new file mode 100644
index 0000000..aa0fc7d
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/ErodeROI.java
@@ -0,0 +1,259 @@
+package plugins.adufour.blocks.tools.roi;
+
+import java.awt.Point;
+import java.util.ArrayList;
+
+import icy.roi.BooleanMask2D;
+import icy.roi.BooleanMask3D;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import icy.roi.ROI3D;
+import icy.type.point.Point3D;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.util.VarException;
+import plugins.kernel.roi.roi2d.ROI2DArea;
+import plugins.kernel.roi.roi3d.ROI3DArea;
+
+public class ErodeROI extends MorphROI
+{
+ public ErodeROI()
+ {
+ roiOUT = new VarROIArray("Eroded ROI");
+ }
+
+ @Override
+ public void run()
+ {
+ switch (unit.getValue())
+ {
+ case PIXELS:
+ roiOUT.setValue(erodeROI(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+ break;
+ case PERCENTAGE:
+ roiOUT.setValue(erodeROIByPercentage(roiIN.getValue(), x.getValue(), y.getValue(), z.getValue()));
+ break;
+ default:
+ throw new VarException(unit, "Unsupported unit");
+ }
+ }
+
+ /**
+ * Perform a morphological erosion on the specified set of ROI by the given radius in each
+ * dimension
+ *
+ * @param inputRoi
+ * the ROI to erode
+ * @param xRadius
+ * the radius (in pixels) along X
+ * @param yRadius
+ * the radius (in pixels) along Y
+ * @param zRadius
+ * the radius (in pixels) along Z (not used if <code>roi</code> is 2D)
+ * @return a new set of eroded ROI of type "area"
+ */
+ public static ROI[] erodeROI(ROI[] inputRoi, int xRadius, int yRadius, int zRadius)
+ {
+ ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
+
+ for (ROI roi : inputRoi)
+ {
+ if (Thread.currentThread().isInterrupted())
+ break;
+
+ ROI eroded = erodeROI(roi, xRadius, yRadius, zRadius);
+ if (eroded != null)
+ out.add(eroded);
+ }
+
+ return out.toArray(new ROI[out.size()]);
+ }
+
+ /**
+ * Perform a morphological erosion on the specified set of ROI by the given scale factor in each
+ * dimension
+ *
+ * @param inputRoi
+ * the ROI to erode
+ * @param xPct
+ * the percentage (from 0 to 100) to erode along X
+ * @param yPct
+ * the percentage (from 0 to 100) to erode along Y
+ * @param zPct
+ * the percentage (from 0 to 100) to erode along Z (not used in 2D)
+ * @return a new set of eroded ROI of type "area"
+ */
+ public static ROI[] erodeROIByPercentage(ROI[] inputRoi, int xPct, int yPct, int zPct)
+ {
+ ArrayList<ROI> out = new ArrayList<ROI>(inputRoi.length);
+
+ for (ROI roi : inputRoi)
+ {
+ if (Thread.currentThread().isInterrupted())
+ break;
+
+ ROI eroded = erodeROIByPercentage(roi, xPct, yPct, zPct);
+ if (eroded != null)
+ out.add(eroded);
+ }
+
+ return out.toArray(new ROI[out.size()]);
+ }
+
+ /**
+ * Perform a morphological erosion on the specified ROI by the given scale factor in each
+ * dimension
+ *
+ * @author Joel Rogers, Alexandre Dufour
+ * @param roi
+ * the ROI to erode
+ * @param xPct
+ * the percentage (from 0 to 100) to dilate along X
+ * @param yPct
+ * the percentage (from 0 to 100) to dilate along Y
+ * @param zPct
+ * the percentage (from 0 to 100) to dilate along Z (not used in 2D)
+ * @return a new, dilated ROI of type "area"
+ */
+ public static ROI erodeROIByPercentage(ROI roi, int xPct, int yPct, int zPct)
+ {
+ int xRadius = percentageToRadiusX(roi, xPct);
+ int yRadius = percentageToRadiusY(roi, yPct);
+ int zRadius = percentageToRadiusZ(roi, zPct);
+
+ return erodeROI(roi, xRadius, yRadius, zRadius);
+ }
+
+ /**
+ * Perform a morphological erosion on the specified ROI by the given radius in each dimension
+ *
+ * @param roi
+ * the ROI to erode
+ * @param xRadius
+ * the radius in pixels along X
+ * @param yRadius
+ * the radius in pixels along X
+ * @param zRadius
+ * the radius in pixels along Z (not used if <code>roi</code> is 2D)
+ * @return a new, eroded ROI of type "area"
+ */
+ public static ROI erodeROI(ROI roi, int xRadius, int yRadius, int zRadius)
+ {
+ // The basis of this erosion operator is to remove all pixels within a distance of "radius"
+ // from the border. Since we have easy access to the contour points of the ROI, we will
+ // start from there and instead use a radius of "radius - 1" when searching for pixels to
+ // erase, so as to be consistent with the dual dilation operator, such that openings
+ // (erosion + dilation) and closings (dilation + erosion) preserve the global ROI size
+
+ int rx = Math.max(0, xRadius - 1), rrx = rx * rx;
+ int ry = Math.max(0, yRadius - 1), rry = ry * ry;
+ int rz = Math.max(0, zRadius - 1), rrz = rz * rz;
+
+ if (roi instanceof ROI2D)
+ {
+ BooleanMask2D m2 = ((ROI2D) roi).getBooleanMask(true);
+ ROI2DArea r2 = new ROI2DArea(m2);
+ r2.setC(((ROI2D) roi).getC());
+ r2.setZ(((ROI2D) roi).getZ());
+ r2.setT(((ROI2D) roi).getT());
+ r2.setName(roi.getName() + " eroded[" + xRadius + "," + yRadius + "]");
+
+ r2.beginUpdate();
+
+ for (Point p : m2.getContourPoints())
+ {
+ // Brute force
+ for (int y = -ry; y <= ry; y++)
+ for (int x = -rx; x <= rx; x++)
+ {
+ double xr2 = rrx == 0 ? 0 : x * x / rrx;
+ double yr2 = rry == 0 ? 0 : y * y / rry;
+
+ // correct the sphere equation to include the outer rim for each pixel
+ if (xr2 + yr2 <= 2.0)
+ {
+ if (m2.contains(p.x + x, p.y + y))
+ r2.removePoint(p.x + x, p.y + y);
+ }
+ }
+ }
+ r2.endUpdate();
+
+ return r2.getNumberOfPoints() > 0 ? r2 : null;
+ }
+ else if (roi instanceof ROI3D)
+ {
+ ROI3D roi3D = (ROI3D) roi;
+
+ BooleanMask3D m3 = roi3D.getBooleanMask(true);
+
+ ROI3DArea r3 = new ROI3DArea(m3);
+ r3.setC(((ROI3D) roi).getC());
+ r3.setT(((ROI3D) roi).getT());
+ r3.setName(roi.getName() + " eroded[" + xRadius + "," + yRadius + "," + zRadius + "]");
+
+ r3.beginUpdate();
+
+ for (Point3D.Integer p : m3.getContourPoints())
+ { // Brute force
+
+ if (rrz == 0)
+ {
+ int z = 0;
+ for (int y = -ry; y <= ry; y++)
+ for (int x = -rx; x <= rx; x++)
+ {
+ double xr2 = rrx == 0 ? 0 : x * x / rrx;
+ double yr2 = rry == 0 ? 0 : y * y / rry;
+
+ // correct the sphere equation to include the outer rim for each pixel
+ if (xr2 + yr2 <= 2.0)
+ {
+ if (m3.contains(p.x + x, p.y + y, p.z + z))
+ try
+ {
+ r3.removePoint(p.x + x, p.y + y, p.z + z);
+ }
+ catch (ArrayIndexOutOfBoundsException aioobe)
+ {
+ // FIXME @Stephane, what's wrong here?!
+ }
+ }
+ }
+ }
+ else
+ {
+ for (int z = -rz; z <= rz; z++)
+ for (int y = -ry; y <= ry; y++)
+ for (int x = -rx; x <= rx; x++)
+ {
+ double xr2 = rrx == 0 ? 0 : x * x / rrx;
+ double yr2 = rry == 0 ? 0 : y * y / rry;
+ double zr2 = rrz == 0 ? 0 : z * z / rrz;
+
+ // correct the sphere equation to include the outer rim for each
+ // pixel
+ if (xr2 + yr2 + zr2 <= 2.0)
+ {
+ if (m3.contains(p.x + x, p.y + y, p.z + z))
+ try
+ {
+ r3.removePoint(p.x + x, p.y + y, p.z + z);
+ }
+ catch (ArrayIndexOutOfBoundsException aioobe)
+ {
+ // FIXME @Stephane, what's wrong here?!
+ }
+ }
+ }
+ }
+ }
+ r3.endUpdate();
+ r3.optimizeBounds();
+
+ return r3.getNumberOfPoints() > 0 ? r3 : null;
+ }
+
+ System.out.println("[Erode ROI] Warning: unsupported ROI: " + roi.getName());
+ return null;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/GetROIFromSequence.java b/src/main/java/plugins/adufour/blocks/tools/roi/GetROIFromSequence.java
new file mode 100644
index 0000000..29024d6
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/GetROIFromSequence.java
@@ -0,0 +1,72 @@
+package plugins.adufour.blocks.tools.roi;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import icy.sequence.Sequence;
+
+import java.util.ArrayList;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarEnum;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.adufour.vars.lang.VarSequence;
+
+public class GetROIFromSequence extends Plugin implements ROIBlock
+{
+ public enum ROIFilter
+ {
+ SELECTED, NON_SELECTED, ALL
+ }
+
+ VarEnum<ROIFilter> filter = new VarEnum<ROIFilter>("ROI to get", ROIFilter.ALL);
+
+ VarROIArray rois = new VarROIArray("List of ROI");
+
+ VarSequence sequence = new VarSequence("Source", null);
+
+ @Override
+ public void run()
+ {
+ Sequence s = sequence.getValue();
+
+ if (s == null)
+ {
+ rois.setValue(new ROI[] {});
+ return;
+ }
+
+ ArrayList<ROI> inputROI = s.getROIs();
+
+ switch (filter.getValue())
+ {
+ case SELECTED:
+ for (int i = 0; i < inputROI.size(); i++)
+ if (!inputROI.get(i).isSelected()) inputROI.remove(i--);
+ break;
+ case NON_SELECTED:
+ for (int i = 0; i < inputROI.size(); i++)
+ if (inputROI.get(i).isSelected()) inputROI.remove(i--);
+ break;
+ case ALL:
+ break;
+
+ default:
+ throw new UnsupportedOperationException("Unknown ROI selection option: " + filter.getValueAsString());
+ }
+
+ rois.setValue(inputROI.toArray(new ROI[inputROI.size()]));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input sequence", sequence);
+ inputMap.add("selection state of ROI to extract", filter);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("extracted rois", rois);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/MergeROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/MergeROI.java
new file mode 100644
index 0000000..07c51d5
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/MergeROI.java
@@ -0,0 +1,47 @@
+package plugins.adufour.blocks.tools.roi;
+
+import java.util.Arrays;
+import java.util.List;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import icy.roi.ROIUtil;
+import icy.util.ShapeUtil.BooleanOperator;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarEnum;
+import plugins.adufour.vars.lang.VarROIArray;
+
+public class MergeROI extends Plugin implements ROIBlock
+{
+ VarEnum<BooleanOperator> operation = new VarEnum<BooleanOperator>("Merge operation", BooleanOperator.AND);
+
+ VarROIArray roiIn = new VarROIArray("List of ROI");
+
+ VarROIArray roiOut = new VarROIArray("Merged ROI");
+
+ @Override
+ public void run()
+ {
+ roiOut.setValue(new ROI[0]);
+
+ List<ROI> rois = Arrays.asList(roiIn.getValue());
+
+ ROI merge = ROIUtil.merge(rois, operation.getValue());
+
+ if (merge != null) roiOut.add(merge);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("List of ROI", roiIn);
+ inputMap.add("Merge operation", operation);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("Merged ROI", roiOut);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/MorphROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/MorphROI.java
new file mode 100644
index 0000000..8f5ee8d
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/MorphROI.java
@@ -0,0 +1,115 @@
+package plugins.adufour.blocks.tools.roi;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.gui.model.IntegerRangeModel;
+import plugins.adufour.vars.lang.VarEnum;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarROIArray;
+
+abstract class MorphROI extends Plugin implements ROIBlock
+{
+ protected enum MorphUnit
+ {
+ PIXELS("Radius (px)"), PERCENTAGE("Scale (%)");
+
+ private final String displayText;
+
+ private MorphUnit(String displayText)
+ {
+ this.displayText = displayText;
+ }
+
+ @Override
+ public String toString()
+ {
+ return displayText;
+ }
+ }
+
+ VarROIArray roiIN = new VarROIArray("List of ROI");
+ VarInteger x = new VarInteger("Along X", 1);
+ VarInteger y = new VarInteger("Along Y", 1);
+ VarInteger z = new VarInteger("Along Z", 1);
+
+ VarEnum<MorphUnit> unit = new VarEnum<MorphUnit>("Unit", MorphUnit.PIXELS);
+
+ VarROIArray roiOUT;
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ x.setDefaultEditorModel(new IntegerRangeModel(1, 0, 100, 1));
+ y.setDefaultEditorModel(new IntegerRangeModel(1, 0, 100, 1));
+ z.setDefaultEditorModel(new IntegerRangeModel(1, 0, 100, 1));
+ inputMap.add("input ROI", roiIN);
+ inputMap.add("X radius", x);
+ inputMap.add("Y radius", y);
+ inputMap.add("Z radius", z);
+ inputMap.add("unit", unit);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output ROI", roiOUT);
+ }
+
+ /**
+ * Converts a scaling factor to a corresponding radius along the X axis (to the nearest pixel)
+ *
+ * @author Joel Rogers, Alexandre Dufour
+ * @param roi
+ * the ROI to scale
+ * @param pct
+ * the percentage factor
+ * @return a radius that is directly usable with the
+ * {@link ErodeROI#erodeROI(ROI, int, int, int)} and
+ * {@link DilateROI#dilateROI(ROI, int, int, int)} methods
+ */
+ static int percentageToRadiusX(ROI roi, int pct)
+ {
+ double size = roi.getBounds5D().getSizeX();
+ double diff = (size * pct / 100);
+ return (int) Math.round(diff * 0.5);
+ }
+
+ /**
+ * Converts a scaling factor to a corresponding radius along the Y axis (to the nearest pixel)
+ *
+ * @author Joel Rogers, Alexandre Dufour
+ * @param roi
+ * the ROI to rescale
+ * @param pct
+ * the percentage factor
+ * @return a radius that is directly usable with the
+ * {@link ErodeROI#erodeROI(ROI, int, int, int)} and
+ * {@link DilateROI#dilateROI(ROI, int, int, int)} methods
+ */
+ static int percentageToRadiusY(ROI roi, int pct)
+ {
+ double size = roi.getBounds5D().getSizeY();
+ double diff = (size * pct / 100);
+ return (int) Math.round(diff * 0.5);
+ }
+
+ /**
+ * Converts a scaling factor to a corresponding radius along the Z axis (to the nearest pixel)
+ *
+ * @author Joel Rogers, Alexandre Dufour
+ * @param roi
+ * the ROI to rescale
+ * @param pct
+ * the percentage factor
+ * @return a radius that is directly usable with the
+ * {@link ErodeROI#erodeROI(ROI, int, int, int)} and
+ * {@link DilateROI#dilateROI(ROI, int, int, int)} methods
+ */
+ static int percentageToRadiusZ(ROI roi, int pct)
+ {
+ double size = roi.getBounds5D().getSizeZ();
+ double diff = (size * pct / 100);
+ return (int) Math.round(diff * 0.5);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/ROIBlock.java b/src/main/java/plugins/adufour/blocks/tools/roi/ROIBlock.java
new file mode 100644
index 0000000..56b43f2
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/ROIBlock.java
@@ -0,0 +1,14 @@
+package plugins.adufour.blocks.tools.roi;
+
+import plugins.adufour.blocks.lang.Block;
+
+/**
+ * Interface used to flag ROI-related blocks
+ *
+ * @author Alexandre Dufour
+ *
+ */
+public interface ROIBlock extends Block
+{
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/SubtractROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/SubtractROI.java
new file mode 100644
index 0000000..3529353
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/SubtractROI.java
@@ -0,0 +1,66 @@
+package plugins.adufour.blocks.tools.roi;
+
+import java.util.ArrayList;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarROIArray;
+
+public class SubtractROI extends Plugin implements ROIBlock
+{
+ VarROIArray roiA = new VarROIArray("List of ROI #1");
+
+ VarROIArray roiB = new VarROIArray("List of ROI #2");
+
+ VarROIArray roiOut = new VarROIArray("Subtracted ROI");
+
+ @Override
+ public void run()
+ {
+ roiOut.setValue(subtractROI(roiA.getValue(true), roiB.getValue(true)));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("List of ROI #1", roiA);
+ inputMap.add("List of ROI #2", roiB);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("subtraction output ROI", roiOut);
+ }
+
+ /**
+ * Subtracts a set of ROI from another
+ *
+ * @param roiA
+ * ROIs to be subtracted from.
+ * @param roiB
+ * ROIs subtracted from the first group of ROIs.
+ * @return A - B. The group of ROIs resulting from the subtraction from the each element of the group A and each element of the group B.
+ */
+ public static ROI[] subtractROI(ROI[] roiA, ROI[] roiB)
+ {
+ ArrayList<ROI> out = new ArrayList<ROI>(roiA.length);
+
+ for (ROI a : roiA)
+ {
+ ROI subtraction = a.getCopy();
+
+ for (ROI b : roiB)
+ subtraction = subtraction.getSubtraction(b);
+
+ if (subtraction == null || subtraction.isEmpty())
+ continue;
+
+ if (!subtraction.getBounds5D().isEmpty())
+ out.add(subtraction);
+ }
+
+ return out.toArray(new ROI[out.size()]);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/roi/TranslateROI.java b/src/main/java/plugins/adufour/blocks/tools/roi/TranslateROI.java
new file mode 100644
index 0000000..8d20cf4
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/roi/TranslateROI.java
@@ -0,0 +1,83 @@
+package plugins.adufour.blocks.tools.roi;
+
+import icy.plugin.abstract_.Plugin;
+import icy.roi.ROI;
+import icy.type.point.Point5D;
+
+import java.awt.geom.Point2D;
+
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.kernel.roi.roi2d.ROI2DArea;
+import plugins.kernel.roi.roi3d.ROI3DArea;
+
+public class TranslateROI extends Plugin implements ROIBlock
+{
+ VarROIArray inputROI = new VarROIArray("Input ROI");
+
+ VarInteger xShift = new VarInteger("X shift", 0);
+ VarInteger yShift = new VarInteger("Y shift", 0);
+ VarInteger zShift = new VarInteger("Z shift", 0);
+
+ VarROIArray outputROI = new VarROIArray("Translated ROI");
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input ROI", inputROI);
+ inputMap.add("X shift", xShift);
+ inputMap.add("Y shift", yShift);
+ inputMap.add("Z shift", zShift);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output ROI", outputROI);
+ }
+
+ @Override
+ public void run()
+ {
+ outputROI.setValue(new ROI[0]);
+
+ for (ROI roi : inputROI)
+ {
+ if (Thread.currentThread().isInterrupted()) break;
+
+ if (roi.canSetPosition())
+ {
+ ROI shiftedROI = roi.getCopy();
+ Point5D pos = shiftedROI.getPosition5D();
+ pos.setX(pos.getX() + xShift.getValue());
+ pos.setY(pos.getY() + yShift.getValue());
+ pos.setZ(pos.getZ() + zShift.getValue());
+ shiftedROI.setPosition5D(pos);
+ outputROI.add(shiftedROI);
+ }
+ else
+ {
+ if (roi instanceof ROI3DArea)
+ {
+ ROI3DArea shiftedROI = new ROI3DArea();
+
+ for (ROI2DArea slice : (ROI3DArea) roi)
+ {
+ ROI2DArea sliceCopy = (ROI2DArea) slice.getCopy();
+
+ Point2D p2 = slice.getPosition2D();
+ p2.setLocation(p2.getX() + xShift.getValue(), p2.getY() + yShift.getValue());
+ sliceCopy.setPosition2D(p2);
+
+ shiftedROI.setSlice(slice.getZ() + zShift.getValue(), sliceCopy);
+ }
+
+ outputROI.add(shiftedROI);
+ }
+ }
+
+ }
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/sequence/SequenceBlock.java b/src/main/java/plugins/adufour/blocks/tools/sequence/SequenceBlock.java
new file mode 100644
index 0000000..bbc1f14
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/sequence/SequenceBlock.java
@@ -0,0 +1,14 @@
+package plugins.adufour.blocks.tools.sequence;
+
+import plugins.adufour.blocks.lang.Block;
+
+/**
+ * Interface used to flag Sequence-related blocks
+ *
+ * @author Alexandre Dufour
+ *
+ */
+public interface SequenceBlock extends Block
+{
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/sequence/SequenceScreenshot.java b/src/main/java/plugins/adufour/blocks/tools/sequence/SequenceScreenshot.java
new file mode 100644
index 0000000..f5ae733
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/sequence/SequenceScreenshot.java
@@ -0,0 +1,67 @@
+package plugins.adufour.blocks.tools.sequence;
+
+import icy.canvas.Canvas2D;
+import icy.gui.viewer.Viewer;
+import icy.plugin.abstract_.Plugin;
+import icy.sequence.Sequence;
+import icy.system.thread.ThreadUtil;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarSequence;
+
+public class SequenceScreenshot extends Plugin implements SequenceBlock
+{
+ private VarSequence seq = new VarSequence("Sequence", null);
+
+ private VarSequence seqOut = new VarSequence("Screenshot", null);
+
+ @Override
+ public void run()
+ {
+ final Sequence in = seq.getValue();
+ final int time = in.getSizeT();
+ final int depth = in.getSizeZ();
+ final Sequence out = new Sequence("Screenshot of " + in.getName());
+
+ final Viewer viewer = new Viewer(in, false);
+ final Canvas2D[] canvas2DP = new Canvas2D[1];
+
+ // init
+ canvas2DP[0] = null;
+ // force completion of SWING EDT tasks
+ ThreadUtil.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ canvas2DP[0] = (Canvas2D) viewer.getCanvas();
+ }
+ });
+
+ final long startTime = System.currentTimeMillis();
+ // wait 2 seconds max for initialization
+ while ((canvas2DP[0] == null) && ((System.currentTimeMillis() - startTime) < 2000L))
+ ThreadUtil.sleep(10);
+
+ final Canvas2D canvas2D = canvas2DP[0];
+
+ for (int t = 0; t < time; t++)
+ for (int z = 0; z < depth; z++)
+ out.setImage(t, z, canvas2D.getRenderedImage(t, z, -1, false));
+
+ viewer.close();
+
+ seqOut.setValue(out);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input sequence", seq);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("screenshot", seqOut);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/sequence/ShowSequence.java b/src/main/java/plugins/adufour/blocks/tools/sequence/ShowSequence.java
new file mode 100644
index 0000000..8689351
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/sequence/ShowSequence.java
@@ -0,0 +1,35 @@
+package plugins.adufour.blocks.tools.sequence;
+
+import icy.main.Icy;
+import icy.plugin.abstract_.Plugin;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.vars.lang.VarSequence;
+
+//@BlockSearchAnnotation(
+// name="show sequence",
+// category="sequence",
+// description="",
+// author="adufour"
+//)
+public class ShowSequence extends Plugin implements SequenceBlock
+{
+ VarSequence sequence = new VarSequence("sequence", null);
+
+ @Override
+ public void run()
+ {
+ if (sequence.getValue() != null) Icy.getMainInterface().addSequence(sequence.getValue());
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("sequence", sequence);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/tools/text/AppendText.java b/src/main/java/plugins/adufour/blocks/tools/text/AppendText.java
new file mode 100644
index 0000000..dd9ed78
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/tools/text/AppendText.java
@@ -0,0 +1,53 @@
+package plugins.adufour.blocks.tools.text;
+
+import icy.plugin.abstract_.Plugin;
+import icy.plugin.interface_.PluginBundled;
+import icy.sequence.Sequence;
+import plugins.adufour.blocks.tools.ToolsBlock;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.protocols.Protocols;
+import plugins.adufour.vars.lang.VarObject;
+import plugins.adufour.vars.lang.VarString;
+
+public class AppendText extends Plugin implements ToolsBlock, PluginBundled
+{
+ VarObject in = new VarObject("input", null);
+ VarString separator = new VarString("Separator", "_");
+ VarObject suffix = new VarObject("Suffix", "");
+
+ VarString out = new VarString("output", "");
+
+ @Override
+ public void run()
+ {
+ Object i = in.getValue();
+
+ Object o = suffix.getValue();
+
+ String prefix = i == null ? "" : i.toString();
+
+ if (i instanceof Sequence) prefix = ((Sequence) i).getName();
+
+ out.setValue(prefix + separator.getValue() + (o == null ? "" : o));
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ inputMap.add("input", in);
+ inputMap.add("Separator", separator);
+ inputMap.add("Suffix", suffix);
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ outputMap.add("output", out);
+ }
+
+ @Override
+ public String getMainPluginClassName()
+ {
+ return Protocols.class.getName();
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlockAnnotations.java b/src/main/java/plugins/adufour/blocks/util/BlockAnnotations.java
new file mode 100644
index 0000000..05c98c8
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlockAnnotations.java
@@ -0,0 +1,232 @@
+package plugins.adufour.blocks.util;
+
+import icy.plugin.abstract_.Plugin;
+import icy.sequence.Sequence;
+
+import java.io.File;
+import java.lang.annotation.Annotation;
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.Method;
+import java.lang.reflect.Modifier;
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarBoolean;
+import plugins.adufour.vars.lang.VarDouble;
+import plugins.adufour.vars.lang.VarFile;
+import plugins.adufour.vars.lang.VarFloat;
+import plugins.adufour.vars.lang.VarInteger;
+import plugins.adufour.vars.lang.VarSequence;
+import plugins.adufour.vars.lang.VarString;
+
+/**
+ * Utility class that parses block annotations and generates blocks from valid methods
+ *
+ * @author Alexandre Dufour
+ * @see BlockInput
+ * @see BlockMethod
+ */
+public class BlockAnnotations
+{
+ /**
+ * Annotation used to mark a method as block-compatible
+ *
+ * @author Alexandre Dufour
+ * @see BlockAnnotations
+ */
+ @Retention(RetentionPolicy.RUNTIME)
+ @Target(ElementType.METHOD)
+ @interface BlockMethod
+ {
+ /**
+ * @return The method's description
+ */
+ String value();
+ }
+
+ /**
+ * Annotation used to mark a method parameter as a block input parameter
+ *
+ * @author Alexandre Dufour
+ * @see BlockAnnotations
+ */
+ @Retention(RetentionPolicy.RUNTIME)
+ @Target(ElementType.PARAMETER)
+ @interface BlockInput
+ {
+ String value();
+ }
+
+ public static Class<?> getInnerType(Class<? extends Var<?>> variableClass)
+ {
+ if (variableClass == VarInteger.class) return Integer.class;
+
+ if (variableClass == VarDouble.class) return Double.class;
+
+ if (variableClass == VarFloat.class) return Float.class;
+
+ if (variableClass == VarBoolean.class) return Boolean.class;
+
+ if (variableClass == VarFile.class) return File.class;
+
+ if (variableClass == VarSequence.class) return Sequence.class;
+
+ if (variableClass == VarString.class) return String.class;
+
+ throw new UnsupportedOperationException("Unsupported type: " + variableClass.getSimpleName());
+ }
+
+ public static Class<? extends Var<?>> getVariableType(Class<?> clazz)
+ {
+ if (clazz == Integer.class) return VarInteger.class;
+
+ if (clazz == Double.class) return VarDouble.class;
+
+ if (clazz == Float.class) return VarFloat.class;
+
+ if (clazz == Boolean.class) return VarBoolean.class;
+
+ if (clazz == File.class) return VarFile.class;
+
+ if (clazz == Sequence.class) return VarSequence.class;
+
+ if (clazz == String.class) return VarString.class;
+
+ throw new UnsupportedOperationException("Unsupported type: " + clazz.getSimpleName());
+ }
+
+ public static ArrayList<BlockAnnotations> findBlockMethods(Class<? extends Plugin> clazz)
+ {
+ final ArrayList<BlockAnnotations> blockDescriptors = new ArrayList<BlockAnnotations>();
+
+ Method[] methods = clazz.getDeclaredMethods();
+
+ for (final Method method : methods)
+ {
+ // make sure the method is static and annotated
+
+ if (!Modifier.isStatic(method.getModifiers())) continue;
+
+ BlockMethod blockFunction = method.getAnnotation(BlockMethod.class);
+ if (blockFunction == null) continue;
+
+ blockDescriptors.add(new BlockAnnotations(method));
+ }
+
+ return blockDescriptors;
+ }
+
+ private final Method method;
+
+ public BlockAnnotations(Method method)
+ {
+ this.method = method;
+ }
+
+ public String getDescription()
+ {
+ return method.getAnnotation(BlockMethod.class).value();
+ }
+
+ public Block createBlock()
+ {
+ return new Block()
+ {
+ @SuppressWarnings("rawtypes")
+ private Var outputVariable;
+
+ private VarList inputMap;
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public void run()
+ {
+ try
+ {
+ Object[] arguments = new Object[inputMap.size()];
+ Iterator<Var<?>> inputIterator = inputMap.iterator();
+
+ for (int i = 0; i < arguments.length; i++)
+ arguments[i] = inputIterator.next().getValue();
+
+ Object result = method.invoke(null, arguments);
+
+ if (outputVariable != null) outputVariable.setValue(result);
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ try
+ {
+ Class<?> returnType = method.getReturnType();
+ if (returnType == Void.TYPE)
+ {
+ outputVariable = null;
+ }
+ else
+ {
+ Class<? extends Var<?>> outputVarClass = getVariableType(returnType);
+ Constructor<? extends Var<?>> outputConstructor = outputVarClass.getDeclaredConstructor(String.class, returnType);
+ outputVariable = outputConstructor.newInstance("output (" + returnType.getSimpleName() + ")", null);
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ if (outputVariable != null) outputMap.add("output", outputVariable);
+ }
+
+ @Override
+ public void declareInput(VarList theInputMap)
+ {
+ this.inputMap = theInputMap;
+
+ try
+ {
+ Class<?>[] types = method.getParameterTypes();
+ Annotation[][] annotations = method.getParameterAnnotations();
+
+ for (int i = 0; i < types.length; i++)
+ {
+ Class<?> parameterClass = types[i];
+ String parameterName = parameterClass.getSimpleName();
+
+ for (Annotation annotation : annotations[i])
+ if (annotation.annotationType() == BlockInput.class)
+ {
+ parameterName = ((BlockInput) annotation).value();
+ }
+
+ Class<? extends Var<?>> inputVarClass = getVariableType(parameterClass);
+ Constructor<? extends Var<?>> inputConstructor = inputVarClass.getDeclaredConstructor(String.class, parameterClass);
+ Var<?> instance = inputConstructor.newInstance(parameterName, null);
+ theInputMap.add(instance.getName(), instance);
+ }
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ };
+ }
+
+ public String getName()
+ {
+ return method.getName();
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlockInfo.java b/src/main/java/plugins/adufour/blocks/util/BlockInfo.java
new file mode 100644
index 0000000..6614cc5
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlockInfo.java
@@ -0,0 +1,23 @@
+package plugins.adufour.blocks.util;
+
+/**
+ * @deprecated Using this interface is no longer recommended, as the information provided here can
+ * not be parsed either online or via the plug-in installer. Block information (name and
+ * description) will soon appear on the Icy web site (and the plug-in loader).
+ * @author Alexandre Dufour
+ *
+ */
+@Deprecated
+public interface BlockInfo
+{
+ /**
+ * @return The title of the block (displays on the graphical interface)
+ */
+ String getName();
+
+ /**
+ * @return A short description of the block (will appear as a tool tip text when hovering on the
+ * block title)
+ */
+ String getDescription();
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlockListener.java b/src/main/java/plugins/adufour/blocks/util/BlockListener.java
new file mode 100644
index 0000000..5c8085e
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlockListener.java
@@ -0,0 +1,20 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.blocks.lang.BlockDescriptor;
+import plugins.adufour.blocks.lang.BlockDescriptor.BlockStatus;
+import plugins.adufour.vars.lang.Var;
+
+public interface BlockListener
+{
+ void blockCollapsed(BlockDescriptor block, boolean collapsed);
+
+ void blockDimensionChanged(BlockDescriptor block, int newWidth, int newHeight);
+
+ void blockLocationChanged(BlockDescriptor block, int newX, int newY);
+
+ void blockStatusChanged(BlockDescriptor block, BlockStatus status);
+
+ <T> void blockVariableChanged(BlockDescriptor block, Var<T> variable, T newValue);
+
+ void blockVariableAdded(BlockDescriptor block, Var<?> variable);
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlocksException.java b/src/main/java/plugins/adufour/blocks/util/BlocksException.java
new file mode 100644
index 0000000..8c45f68
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlocksException.java
@@ -0,0 +1,29 @@
+package plugins.adufour.blocks.util;
+
+/**
+ * Convenience class for the Blocks framework that allows optimizing bug finding / reporting /
+ * fixing.
+ *
+ * @author Alexandre Dufour
+ */
+public class BlocksException extends RuntimeException
+{
+ private static final long serialVersionUID = 666L;
+
+ public final boolean catchException;
+
+ /**
+ * Creates a new exception with the specified message and catching behavior.
+ *
+ * @param message
+ * the error message bound the current exception
+ * @param catchException
+ * true if the exception should be caught within the EzPlug layer, false to let the
+ * exception pass to the global exception manager
+ */
+ public BlocksException(String message, boolean catchException)
+ {
+ super(message);
+ this.catchException = catchException;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlocksFinder.java b/src/main/java/plugins/adufour/blocks/util/BlocksFinder.java
new file mode 100644
index 0000000..73c13ac
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlocksFinder.java
@@ -0,0 +1,752 @@
+package plugins.adufour.blocks.util;
+
+import icy.gui.menu.PluginMenuItem;
+import icy.image.ImageUtil;
+import icy.plugin.PluginDescriptor;
+import icy.plugin.PluginLoader;
+import icy.plugin.abstract_.Plugin;
+import icy.resource.ResourceUtil;
+import icy.resource.icon.IcyIcon;
+import icy.system.SystemUtil;
+import icy.util.ClassUtil;
+
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Point;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DragGestureEvent;
+import java.awt.dnd.DragGestureListener;
+import java.awt.dnd.DragSource;
+import java.awt.dnd.DragSourceDragEvent;
+import java.awt.dnd.DragSourceDropEvent;
+import java.awt.dnd.DragSourceEvent;
+import java.awt.dnd.DragSourceListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.JComponent;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.TransferHandler;
+
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.lang.BlockDescriptor;
+import plugins.adufour.blocks.lang.Loop;
+import plugins.adufour.blocks.lang.WorkFlow;
+import plugins.adufour.blocks.tools.Display;
+import plugins.adufour.blocks.tools.ReLoop;
+import plugins.adufour.blocks.tools.ToolsBlock;
+import plugins.adufour.blocks.tools.ij.IJBlock;
+import plugins.adufour.blocks.tools.input.InputBlock;
+import plugins.adufour.blocks.tools.io.IOBlock;
+import plugins.adufour.blocks.tools.roi.ROIBlock;
+import plugins.adufour.blocks.tools.sequence.SequenceBlock;
+import plugins.adufour.protocols.gui.BlockSearchPanel;
+import plugins.adufour.protocols.gui.block.WorkFlowContainer;
+
+public class BlocksFinder
+{
+ /**
+ * Indicates whether annotated methods should be parsed and made available as
+ * blocks
+ */
+ public final boolean parseAnnotations = false;
+
+ /**
+ * class for handling Drag and Drop on the menu items
+ *
+ * @author Ludovic Laborde, Alexandre Dufour
+ */
+ @SuppressWarnings("serial")
+ public class DND_MenuItem extends PluginMenuItem
+ implements MouseListener, Transferable, DragSourceListener, DragGestureListener
+ {
+ private DragSource source;
+ private TransferHandler handler;
+ private PluginDescriptor descriptor;
+
+ private List<MenuItemListener> menuItemListeners;
+
+ public DND_MenuItem(final PluginDescriptor d)
+ {
+ super(d);
+ setOpaque(false);
+
+ for (MouseListener listener : getMouseListeners())
+ removeMouseListener(listener);
+
+ descriptor = d;
+ menuItemListeners = new ArrayList<MenuItemListener>();
+
+ handler = new TransferHandler()
+ {
+ public Transferable createTransferable(JComponent c)
+ {
+ return new DND_MenuItem(descriptor);
+ }
+ };
+
+ source = new DragSource();
+ source.createDefaultDragGestureRecognizer(this, DnDConstants.ACTION_COPY, this);
+
+ setTransferHandler(handler);
+ addMouseListener(this);
+ }
+
+ public PluginDescriptor getDescriptor()
+ {
+ return descriptor;
+ }
+
+ @Override
+ public void dragGestureRecognized(DragGestureEvent dge)
+ {
+ source.startDrag(dge, DragSource.DefaultMoveDrop, new DND_MenuItem(descriptor), this);
+ }
+
+ @Override
+ public Object getTransferData(DataFlavor flavor) throws UnsupportedFlavorException, IOException
+ {
+ return this;
+ }
+
+ @Override
+ public DataFlavor[] getTransferDataFlavors()
+ {
+ try
+ {
+ return new DataFlavor[] {
+ new DataFlavor(DataFlavor.javaJVMLocalObjectMimeType + ";class=java.util.ArrayList")};
+ }
+ catch (ClassNotFoundException e)
+ {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ @Override
+ public boolean isDataFlavorSupported(DataFlavor flavor)
+ {
+ return true;
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent arg0)
+ {
+ setBackground(Color.GRAY);
+ notifyListeners();
+ }
+
+ public void addMenuItemListener(MenuItemListener l)
+ {
+ menuItemListeners.add(l);
+ }
+
+ // updates the search panel
+ private void notifyListeners()
+ {
+ for (MenuItemListener l : menuItemListeners)
+ l.displayDoc(descriptor);
+ }
+
+ @Override
+ public void dragDropEnd(DragSourceDropEvent dsde)
+ {
+ setBackground(Color.GRAY);
+ notifyListeners();
+ }
+
+ @Override
+ public void dragEnter(DragSourceDragEvent dsde)
+ {
+ }
+
+ @Override
+ public void dragExit(DragSourceEvent dse)
+ {
+ }
+
+ @Override
+ public void dragOver(DragSourceDragEvent dsde)
+ {
+ }
+
+ @Override
+ public void dropActionChanged(DragSourceDragEvent dsde)
+ {
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent arg0)
+ {
+ }
+
+ @Override
+ public void mouseExited(MouseEvent arg0)
+ {
+ }
+
+ @Override
+ public void mousePressed(MouseEvent arg0)
+ {
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent arg0)
+ {
+ }
+ }
+
+ /**
+ * Searches for a block using the specified search text, and populates the
+ * specified search panel with the search results
+ *
+ * @param menuContainer BlockSearchPanel
+ * @param searchText String
+ */
+ public void createSearchMenu(BlockSearchPanel menuContainer, String searchText)
+ {
+ ArrayList<PluginDescriptor> plugins = PluginLoader.getPlugins(Block.class, true, false, false);
+
+ if (plugins.size() == 0)
+ {
+ JMenuItem item = new JMenuItem(
+ "The plug-in list has been updated.\nPlease close and re-open the Protocols editor.");
+ item.setFont(item.getFont().deriveFont(Font.ITALIC));
+ menuContainer.add(item);
+ return;
+ }
+
+ for (PluginDescriptor descriptor : plugins)
+ {
+
+ Class<? extends Plugin> _class = descriptor.getPluginClass();
+ final Class<? extends Block> blockClass = _class.asSubclass(Block.class);
+
+ if (ClassUtil.isAbstract(blockClass))
+ continue;
+ if (ClassUtil.isPrivate(blockClass))
+ continue;
+
+ // ALEX (2014-06-17): removing annotations for now
+ // // handle default annotated blocks defined in protocols
+ // if (blockClass.isAnnotationPresent(BlockSearchAnnotation.class))
+ // {
+ // Annotation annotation =
+ // blockClass.getAnnotation(BlockSearchAnnotation.class);
+ // BlockSearchAnnotation blockSearchAnnotation = (BlockSearchAnnotation)
+ // annotation;
+ //
+ // // search conditions
+ // if
+ // (!(blockSearchAnnotation.name().toLowerCase().contains(searchText.toLowerCase())
+ // ||
+ // blockSearchAnnotation.category().toLowerCase().contains(searchText.toLowerCase())
+ // || blockSearchAnnotation.description().toLowerCase()
+ // .contains(searchText.toLowerCase()))) continue;
+ // }
+
+ // handle other external plugins
+ // search conditions
+
+ String testString = "block";
+ testString += descriptor.getName();
+ testString += blockClass.getSimpleName();
+ testString += descriptor.getDescription();
+ testString += descriptor.getAuthor();
+ testString = testString.toLowerCase();
+
+ searchText = searchText.trim().toLowerCase();
+ String searchTextNoSpaces = searchText.replace(" ", "");
+
+ if (testString.contains(searchText) || testString.contains(searchTextNoSpaces))
+ {
+ DND_MenuItem menuItem = new DND_MenuItem(descriptor);
+ menuItem.addMenuItemListener(menuContainer);
+ menuItem.setMaximumSize(new Dimension(Integer.MAX_VALUE, 35));
+ menuItem.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+ String name = blockClass.getSimpleName();
+ name = descriptor.getName().equalsIgnoreCase(name) ? getFlattened(name) : descriptor.getName();
+
+ // Remove the "block" word at the end of the class name
+ if (name.toLowerCase().endsWith("block"))
+ name = name.substring(0, name.length() - 5);
+
+ if (blockClass.isAnnotationPresent(Deprecated.class))
+ {
+ name = "(deprecated) " + name;
+ }
+ menuItem.setText(name);
+ menuContainer.add(menuItem);
+ }
+ }
+ }
+
+ /**
+ * Create a JMenu component with all existing classes implementing {@link Block}
+ *
+ * @param menuContainer Container
+ * @param workFlowPane WorkFlowContainer
+ * @param location Point
+ */
+ public final void createJMenu(Container menuContainer, final WorkFlowContainer workFlowPane, final Point location)
+ {
+ JMenu mnBlocks = new JMenu("Blocks...");
+ mnBlocks.setIcon(new IcyIcon(ResourceUtil.getAlphaIconAsImage("box.png"), 22));
+
+ JMenu mnInput = new JMenu("Read...");
+ mnInput.setIcon(new IcyIcon(ResourceUtil.ICON_REDO, 22));
+
+ JMenu mnIO = new JMenu("I/O...");
+ mnIO.setIcon(new IcyIcon(ResourceUtil.ICON_SAVE, 22));
+
+ JMenu mnSeq = new JMenu("Sequence...");
+ mnSeq.setIcon(new IcyIcon(ResourceUtil.ICON_PHOTO, 22));
+
+ JMenu mnROI = new JMenu("ROI...");
+ mnROI.setIcon(new IcyIcon(ResourceUtil.ICON_ROI_POLYGON, 22));
+
+ JMenu mnImageJ = new JMenu("ImageJ...");
+ mnImageJ.setIcon(new IcyIcon(ResourceUtil.ICON_TOIJ, 22));
+
+ JMenu mnLoops = new JMenu("Loop / Batch...");
+ mnLoops.setIcon(new IcyIcon(ResourceUtil.ICON_RELOAD, 22));
+
+ JMenu mnTools = new JMenu("Tools...");
+ mnTools.setIcon(new IcyIcon(ResourceUtil.ICON_TOOLS, 22));
+
+ ArrayList<PluginDescriptor> plugins = PluginLoader.getPlugins(Block.class, true, false, false);
+
+ if (plugins.size() == 0)
+ {
+ JMenuItem item = new JMenuItem(
+ "The plug-in list has been updated.\nPlease close and re-open the Protocols editor.");
+ item.setFont(item.getFont().deriveFont(Font.ITALIC));
+ menuContainer.add(item);
+ return;
+ }
+
+ for (PluginDescriptor descriptor : plugins)
+ {
+ Class<? extends Plugin> clazz = descriptor.getPluginClass();
+ try
+ {
+ final Class<? extends Block> blockClass = clazz.asSubclass(Block.class);
+
+ if (ClassUtil.isAbstract(blockClass))
+ continue;
+ if (ClassUtil.isPrivate(blockClass))
+ continue;
+ if (blockClass.isAnnotationPresent(Deprecated.class))
+ continue;
+
+ // create the menu item
+ PluginMenuItem menuItem = new PluginMenuItem(descriptor);
+
+ // remove the internal action listener
+ menuItem.removeActionListener(menuItem);
+
+ String name = blockClass.getSimpleName();
+
+ name = descriptor.getName().equalsIgnoreCase(name) ? getFlattened(name) : descriptor.getName();
+
+ // Remove the "block" word at the end of the class name
+ if (name.toLowerCase().endsWith("block"))
+ name = name.substring(0, name.length() - 5);
+
+ menuItem.setText(name);
+
+ if (!descriptor.getDescription().isEmpty())
+ {
+ menuItem.setToolTipText(
+ "<html>" + descriptor.getDescription().replaceAll("\n", "<br/>") + "</html>");
+ }
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ try
+ {
+ addBlock(workFlowPane, blockClass.newInstance(), location);
+ }
+ catch (InstantiationException e1)
+ {
+ e1.printStackTrace();
+ }
+ catch (IllegalAccessException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+
+ // place the menu item where appropriate
+
+ if (blockClass == Display.class)
+ {
+ // will be dealt with outside this loop
+ continue;
+ }
+ else if (ClassUtil.isSubClass(blockClass, Loop.class)
+ && !blockClass.isAnnotationPresent(Deprecated.class))
+ {
+ final JMenuItem item = new JMenuItem(getFlattened(blockClass.getSimpleName()));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ try
+ {
+ addBlock(workFlowPane, blockClass.newInstance(), location);
+ }
+ catch (InstantiationException e1)
+ {
+ e1.printStackTrace();
+ }
+ catch (IllegalAccessException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ mnLoops.add(item);
+ }
+ else if (InputBlock.class.isAssignableFrom(blockClass))
+ {
+ mnInput.add(menuItem);
+ }
+ else if (SequenceBlock.class.isAssignableFrom(blockClass))
+ {
+ mnSeq.add(menuItem);
+ }
+ else if (IOBlock.class.isAssignableFrom(blockClass))
+ {
+ mnIO.add(menuItem);
+ }
+ else if (ROIBlock.class.isAssignableFrom(blockClass))
+ {
+ mnROI.add(menuItem);
+ }
+ else if (IJBlock.class.isAssignableFrom(blockClass))
+ {
+ mnImageJ.add(menuItem);
+ }
+ else if (ToolsBlock.class.isAssignableFrom(blockClass))
+ {
+ if (blockClass == ReLoop.class)
+ continue; // TODO
+
+ mnTools.add(menuItem);
+ }
+ else
+ {
+ // default case: put the rest in the "Blocks" menu
+ mnBlocks.add(menuItem);
+ }
+
+ if (parseAnnotations)
+ {
+ // find annotated methods
+ ArrayList<BlockAnnotations> blocks = BlockAnnotations.findBlockMethods(clazz);
+
+ for (final BlockAnnotations annotatedMethod : blocks)
+ {
+ JMenuItem item2 = new JMenuItem(clazz.getSimpleName() + "." + annotatedMethod.getName());
+ item2.setToolTipText(annotatedMethod.getDescription());
+ item2.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addBlock(workFlowPane, annotatedMethod.createBlock(), location);
+ }
+ });
+ mnBlocks.add(item2);
+ }
+ }
+ }
+ catch (ClassCastException e1)
+ {
+ }
+ }
+
+ splitLongMenus(mnBlocks, 15);
+ splitLongMenus(mnInput, 15);
+ splitLongMenus(mnSeq, 15);
+ splitLongMenus(mnROI, 15);
+ splitLongMenus(mnIO, 15);
+ splitLongMenus(mnImageJ, 15);
+ splitLongMenus(mnLoops, 15);
+ splitLongMenus(mnTools, 15);
+
+ menuContainer.add(mnBlocks);
+ menuContainer.add(mnInput);
+ menuContainer.add(mnSeq);
+ menuContainer.add(mnROI);
+ menuContainer.add(mnIO);
+ menuContainer.add(mnImageJ);
+ menuContainer.add(mnLoops);
+ menuContainer.add(mnTools);
+
+ // and add the Display block last
+
+ JMenuItem mnDisp = new JMenuItem("Display");
+ mnDisp.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ try
+ {
+ addBlock(workFlowPane, Display.class.newInstance(), location);
+ }
+ catch (InstantiationException e1)
+ {
+ e1.printStackTrace();
+ }
+ catch (IllegalAccessException e1)
+ {
+ e1.printStackTrace();
+ }
+ }
+ });
+ mnDisp.setIcon(new IcyIcon(ImageUtil.scaleQuality(ResourceUtil.getAlphaIconAsImage("eye_open.png"), 22, 22)));
+ menuContainer.add(mnDisp);
+
+ // // 3rd-party block providers (very soon...)
+ //
+ // JMenu mnOthers = new JMenu("Others...");
+ // mnOthers.setIcon(new IcyIcon(ResourceUtil.getAlphaIconAsImage("box.png"),
+ // 22));
+ //
+ // for (PluginDescriptor providerPlugin :
+ // PluginLoader.getPlugins(BlockProvider.class, true,
+ // false, false))
+ // {
+ // try
+ // {
+ // BlockProvider provider =
+ // providerPlugin.getPluginClass().asSubclass(BlockProvider.class).newInstance();
+ //
+ // Map<String, Block> blocks = provider.getBlocks();
+ //
+ // for(String blockName : blocks.keySet())
+ // {
+ // final Block block = blocks.get(blockName);
+ // final JMenuItem item = new JMenuItem(blockName);
+ // item.addActionListener(new ActionListener()
+ // {
+ // @Override
+ // public void actionPerformed(ActionEvent arg0)
+ // {
+ // try
+ // {
+ // addBlock(workFlowPane, block.getClass().newInstance(), location);
+ // }
+ // catch (InstantiationException e1)
+ // {
+ // e1.printStackTrace();
+ // }
+ // catch (IllegalAccessException e1)
+ // {
+ // e1.printStackTrace();
+ // }
+ // }
+ // });
+ // mnOthers.add(item);
+ // }
+ // }
+ // catch (Exception e)
+ // {
+ // // TODO Auto-generated catch block
+ // e.printStackTrace();
+ // }
+ // }
+ // splitLongMenus(mnOthers, 15);
+ // menuContainer.add(mnOthers);
+ }
+
+ /**
+ * Create a JMenu component with all existing classes implementing {@link Block}
+ *
+ * @param menuContainer Container
+ * @param workFlowPane WorkFlowContainer
+ */
+ public static void createEmbedJMenu(final Container menuContainer, final WorkFlowContainer workFlowPane)
+ {
+ // One day, when Java 8 rules...
+ // PluginLoader.getPlugins(WorkFlow.class).stream()
+ // // get the plug-in class
+ // .map(PluginDescriptor::getPluginClass)
+ // // Create a menu item for each element
+ // .forEach(enclosure -> {
+ // String menuName = getFlattened(enclosure.getSimpleName());
+ // JMenuItem menuItem = new JMenuItem(menuName);
+ // menuItem.addActionListener(a -> {
+ // try
+ // {
+ // workFlowPane.embedWorkFlow((Class<? extends WorkFlow>) enclosure);
+ // }
+ // catch (Exception e)
+ // {
+ // throw new RuntimeException(e);
+ // }
+ // });
+ // menuContainer.add(menuItem);
+ // });
+
+ // In the meantime...
+ for (PluginDescriptor plugin : PluginLoader.getPlugins(WorkFlow.class))
+ {
+ JMenuItem menuItem = new JMenuItem(getFlattened(plugin.getName()));
+ final PluginDescriptor pf = plugin;
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ try
+ {
+ workFlowPane.embedWorkFlow(pf.getPluginClass().asSubclass(WorkFlow.class));
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ });
+ menuContainer.add(menuItem);
+ }
+ }
+
+ private static void addBlock(WorkFlowContainer workFlowPane, Block block, Point location)
+ {
+ BlockDescriptor blockDesc = (block instanceof WorkFlow ? ((WorkFlow) block).getBlockDescriptor()
+ : new BlockDescriptor(-1, block));
+
+ blockDesc.setLocation(location.x, location.y);
+
+ workFlowPane.getWorkFlow().addBlock(blockDesc);
+ }
+
+ /**
+ * Breaks the list of items in the specified menu, by creating sub-menus
+ * containing the specified number of items, and a "More..." menu to access
+ * subsequent items.
+ *
+ * @param menu
+ * the menu to break into smaller sub-menus
+ * @param maxItemsPerMenu
+ * the maximum number of items to display in each sub-menu
+ */
+ private void splitLongMenus(JMenu menu, int maxItemsPerMenu)
+ {
+ ArrayList<Component> components = new ArrayList<Component>(Arrays.asList(menu.getPopupMenu().getComponents()));
+
+ if (components.size() > maxItemsPerMenu)
+ {
+ menu.removeAll();
+
+ JMenu currentMenu = menu;
+
+ while (components.size() > 0)
+ {
+ int n = Math.min(components.size(), maxItemsPerMenu - 1);
+
+ for (int i = 0; i < n; i++)
+ currentMenu.add(components.remove(0));
+
+ if (components.size() > 0)
+ currentMenu = (JMenu) currentMenu.add(new JMenu("More..."));
+ }
+
+ if (components.size() > 0)
+ throw new RuntimeException("Error while splitting menus: " + components.size() + " are remaining.");
+ }
+
+ // do this recursively for sub-menus
+ for (Component component : menu.getPopupMenu().getComponents())
+ {
+ if (component instanceof JMenu)
+ splitLongMenus((JMenu) component, maxItemsPerMenu);
+ }
+ }
+
+ /**
+ * Creates a flattened version of the provided String. The flattening operation
+ * splits the string by inserting spaces between words starting with an upper
+ * case letter, and converts upper case letters to lower case (with the
+ * exception of the first word). Note that <b>consecutive upper case letters</b>
+ * <b>will remain grouped</b>, as they are considered to represent an acronym.<br>
+ * <br>
+ * <u>NOTE:</u> This method is optimized for class names that follow the Java
+ * naming convention. <br>
+ * Examples:<br>
+ * MyGreatClass -< "My great class"<br>
+ * MyXYZClass -< "My XYZ class"
+ *
+ * @param string
+ * the string to flatten
+ * @return a flattened (i.e. pretty-printed) String based on the name of the
+ * string
+ */
+ public static String getFlattened(String string)
+ {
+ String[] words = string.split("(?=[A-Z])");
+
+ String output = words[0];
+ if (words.length > 1)
+ {
+ int nextWordIndex = 1;
+
+ final int javaVersion = (int) SystemUtil.getJavaVersionAsNumber();
+ if (javaVersion < 8)
+ {
+ output = words[1];
+ nextWordIndex++;
+ }
+
+ for (int i = nextWordIndex; i < words.length; i++)
+ {
+ String word = words[i];
+ if (word.length() == 1)
+ {
+ // single letter
+ if (words[i - 1].length() == 1)
+ {
+ // append to the previous letter (acronym)
+ output += word;
+ }
+ else
+ {
+ // new isolated letter or acronym
+ output += " " + word;
+ }
+ }
+ else
+ output += " " + word.toLowerCase();
+ }
+ }
+
+ return output;
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlocksML.java b/src/main/java/plugins/adufour/blocks/util/BlocksML.java
new file mode 100644
index 0000000..c77a0ac
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlocksML.java
@@ -0,0 +1,1753 @@
+package plugins.adufour.blocks.util;
+
+import java.awt.Point;
+import java.io.File;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.concurrent.Callable;
+
+import javax.swing.filechooser.FileFilter;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.DocumentType;
+import org.w3c.dom.Element;
+
+import icy.gui.frame.progress.AnnounceFrame;
+import icy.main.Icy;
+import icy.network.NetworkUtil;
+import icy.plugin.PluginDescriptor;
+import icy.plugin.PluginInstaller;
+import icy.plugin.PluginLoader;
+import icy.plugin.PluginRepositoryLoader;
+import icy.plugin.PluginUpdater;
+import icy.plugin.interface_.PluginBundled;
+import icy.system.IcyExceptionHandler;
+import icy.system.IcyHandledException;
+import icy.system.thread.ThreadUtil;
+import icy.util.ClassUtil;
+import icy.util.XMLUtil;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.lang.BlockDescriptor;
+import plugins.adufour.blocks.lang.Link;
+import plugins.adufour.blocks.lang.WorkFlow;
+import plugins.adufour.blocks.tools.input.InputBlock;
+import plugins.adufour.protocols.Protocols;
+import plugins.adufour.vars.gui.model.TypeSelectionModel;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+import plugins.adufour.vars.lang.VarMutableArray;
+import plugins.adufour.vars.lang.VarString;
+import plugins.adufour.vars.util.MutableType;
+import plugins.adufour.vars.util.VarListener;
+
+public class BlocksML
+{
+ private static final String RUNTIME = "runtime";
+
+ private static BlocksML instance = new BlocksML();
+
+ public static BlocksML getInstance()
+ {
+ return instance;
+ }
+
+ public static final int CURRENT_VERSION = 4;
+
+ public static final FileFilter XML_FILE_FILTER = new FileFilter()
+ {
+ @Override
+ public String getDescription()
+ {
+ return "Icy protocols (.xml | .protocol)";
+ }
+
+ @Override
+ public boolean accept(File f)
+ {
+ return f.isDirectory() || f.getPath().toLowerCase().endsWith(".xml")
+ || f.getPath().toLowerCase().endsWith(".protocol");
+ }
+ };
+
+ private Transformer transformer;
+
+ private VarString status = new VarString("status", "");
+
+ private BlocksML()
+ {
+ try
+ {
+ transformer = TransformerFactory.newInstance().newTransformer();
+ transformer.setOutputProperty(OutputKeys.METHOD, "xml");
+ transformer.setOutputProperty(OutputKeys.ENCODING, "ISO-8859-1");
+ transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
+ transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "no");
+ transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+ }
+ catch (Exception e)
+ {
+ }
+ }
+
+ public void addStatusListener(VarListener<String> listener)
+ {
+ status.addListener(listener);
+ }
+
+ public void removeStatusListener(VarListener<String> listener)
+ {
+ status.removeListener(listener);
+ }
+
+ /**
+ * Generates the XML representation of this work flow as a String object.
+ *
+ * @param workFlow
+ * Target workflow instance.
+ * @return A XML representation of this work flow as a String object
+ * @throws TransformerException
+ * If an unrecoverable error occurs during the course of the transformation.
+ */
+ public synchronized String toString(WorkFlow workFlow) throws TransformerException
+ {
+ return toString(toXML(workFlow));
+ }
+
+ /**
+ * Converts an XML document to its string representation.
+ *
+ * @param xml
+ * The target xml document to transform into string.
+ * @return A XML representation of this work flow as a String object
+ * @throws TransformerException
+ * If an unrecoverable error occurs during the course of the transformation.
+ */
+ public synchronized String toString(Document xml) throws TransformerException
+ {
+ xml.normalizeDocument();
+
+ DocumentType doctype = xml.getDoctype();
+ DOMSource domSource = new DOMSource(xml);
+ StringWriter string = new StringWriter();
+ StreamResult streamResult = new StreamResult(string);
+
+ if (doctype != null)
+ {
+ transformer.setOutputProperty(OutputKeys.DOCTYPE_PUBLIC, doctype.getPublicId());
+ transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, doctype.getSystemId());
+ }
+
+ transformer.transform(domSource, streamResult);
+
+ return string.toString();
+ }
+
+ /**
+ * Creates a XML document representing the specified work flow.
+ *
+ * @param workFlow
+ * The work flow to save.
+ * @return The XML document representing the target workflow.
+ */
+ public synchronized Document toXML(WorkFlow workFlow)
+ {
+ Document xml = XMLUtil.createDocument(false);
+ Element workSpaceRoot = XMLUtil.createRootElement(xml, "protocol");
+
+ XMLUtil.setAttributeIntValue(workSpaceRoot, "VERSION", CURRENT_VERSION);
+
+ switch (CURRENT_VERSION)
+ {
+ case 1:
+ saveWorkFlow_V1(workFlow, workSpaceRoot);
+ break;
+ case 2:
+ saveWorkFlow_V2(workFlow, workSpaceRoot);
+ break;
+ case 3:
+ saveWorkFlow_V3(workFlow, workSpaceRoot);
+ break;
+ case 4:
+ saveWorkFlow_V4(workFlow, workSpaceRoot);
+ break;
+ default:
+ throw new UnsupportedOperationException("Cannot save Blocks ML version " + CURRENT_VERSION);
+ }
+
+ return xml;
+ }
+
+ /**
+ * Saves the specified work flow into the specified file in XML format.
+ *
+ * @param workFlow
+ * The work flow to save.
+ * @param f
+ * The file to write (or overwrite).
+ * @throws BlocksException
+ * If the file could not be saved.
+ * @throws IOException
+ * If an error occurs when saving the workflow in the file.
+ */
+ public synchronized void saveWorkFlow(WorkFlow workFlow, File f) throws BlocksException, IOException
+ {
+ Document xml = toXML(workFlow);
+
+ if (!XMLUtil.saveDocument(xml, f))
+ throw new IOException(
+ "Unable to save the protocol.\nDo you have write permissions to the destination folder.");
+ }
+
+ /**
+ * @deprecated Legacy method, use {@link #saveWorkFlow_V4(WorkFlow, Element)} instead.
+ * @param workFlow
+ * The workflow to save.
+ * @param workFlowRoot
+ * Root element where elements are to be inserted.
+ */
+ @SuppressWarnings("deprecation")
+ @Deprecated
+ public synchronized void saveWorkFlow_V1(WorkFlow workFlow, Element workFlowRoot)
+ {
+ Element blocksNode = XMLUtil.addElement(workFlowRoot, "blocks");
+
+ for (BlockDescriptor blockData : workFlow)
+ {
+ Element blockNode;
+ Block block = blockData.getBlock();
+
+ if (block instanceof WorkFlow)
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "workflow");
+ }
+ else
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "block");
+ }
+
+ XMLUtil.setAttributeValue(blockNode, "type", block.getClass().getCanonicalName());
+ XMLUtil.setAttributeIntValue(blockNode, "ID", workFlow.indexOf(blockData));
+ XMLUtil.setAttributeIntValue(blockNode, "xLocation", blockData.getLocation().x);
+ XMLUtil.setAttributeIntValue(blockNode, "yLocation", blockData.getLocation().y);
+
+ if (block instanceof WorkFlow)
+ {
+ WorkFlow innerWorkFlow = (WorkFlow) block;
+
+ saveWorkFlow_V1(innerWorkFlow, blockNode);
+
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ BlockDescriptor owner = innerWorkFlow.getInputOwner(var);
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeIntValue(varNode, "ID", blockData.inputVars.indexOf(var));
+ XMLUtil.setAttributeIntValue(varNode, "blockID", innerWorkFlow.indexOf(owner));
+ XMLUtil.setAttributeIntValue(varNode, "varID", owner.inputVars.indexOf(var));
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ BlockDescriptor owner = innerWorkFlow.getOutputOwner(var);
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeIntValue(varNode, "ID", blockData.outputVars.indexOf(var));
+ XMLUtil.setAttributeIntValue(varNode, "blockID", innerWorkFlow.indexOf(owner));
+ XMLUtil.setAttributeIntValue(varNode, "varID", owner.outputVars.indexOf(var));
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ }
+ }
+ else
+ {
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeIntValue(varNode, Var.XML_KEY_ID, blockData.inputVars.indexOf(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeIntValue(varNode, Var.XML_KEY_ID, blockData.outputVars.indexOf(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ }
+ }
+ }
+
+ Element linkRoot = XMLUtil.addElement(workFlowRoot, "links");
+
+ for (Link<?> link : workFlow.getLinksIterator())
+ {
+ Element linkNode = XMLUtil.addElement(linkRoot, "link");
+
+ XMLUtil.setAttributeIntValue(linkNode, "srcBlockID", workFlow.indexOf(link.srcBlock));
+ XMLUtil.setAttributeIntValue(linkNode, "srcVarID", link.srcBlock.outputVars.indexOf(link.srcVar));
+ XMLUtil.setAttributeIntValue(linkNode, "dstBlockID", workFlow.indexOf(link.dstBlock));
+ XMLUtil.setAttributeIntValue(linkNode, "dstVarID", link.dstBlock.inputVars.indexOf(link.dstVar));
+ }
+ }
+
+ /**
+ * @deprecated Legacy method, use {@link #saveWorkFlow_V4(WorkFlow, Element)} instead.
+ * @param workFlow
+ * The workflow to save.
+ * @param workFlowRoot
+ * Root element where elements are to be inserted.
+ */
+ @Deprecated
+ public synchronized void saveWorkFlow_V2(WorkFlow workFlow, Element workFlowRoot)
+ {
+ Element blocksNode = XMLUtil.addElement(workFlowRoot, "blocks");
+
+ for (BlockDescriptor blockData : workFlow)
+ {
+ Element blockNode;
+ Block block = blockData.getBlock();
+
+ if (block instanceof WorkFlow)
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "workflow");
+ XMLUtil.setAttributeBooleanValue(blockNode, "collapsed", blockData.isCollapsed());
+ }
+ else
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "block");
+ }
+
+ XMLUtil.setAttributeValue(blockNode, "type", block.getClass().getCanonicalName());
+ XMLUtil.setAttributeIntValue(blockNode, "ID", workFlow.indexOf(blockData));
+ XMLUtil.setAttributeIntValue(blockNode, "xLocation", blockData.getLocation().x);
+ XMLUtil.setAttributeIntValue(blockNode, "yLocation", blockData.getLocation().y);
+
+ if (blockData.isWorkFlow())
+ {
+ WorkFlow innerWorkFlow = (WorkFlow) block;
+
+ saveWorkFlow_V2(innerWorkFlow, blockNode);
+
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ BlockDescriptor owner = innerWorkFlow.getInputOwner(var);
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, "ID", blockData.inputVars.getID(var));
+ XMLUtil.setAttributeIntValue(varNode, "blockID", innerWorkFlow.indexOf(owner));
+ XMLUtil.setAttributeValue(varNode, "varID", owner.inputVars.getID(var));
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ BlockDescriptor owner = innerWorkFlow.getOutputOwner(var);
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, "ID", blockData.outputVars.getID(var));
+ XMLUtil.setAttributeIntValue(varNode, "blockID", innerWorkFlow.indexOf(owner));
+ XMLUtil.setAttributeValue(varNode, "varID", owner.outputVars.getID(var));
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ }
+ }
+ else
+ {
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, Var.XML_KEY_ID, blockData.inputVars.getID(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ if (var instanceof VarMutable && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getCanonicalName());
+ }
+ else if (var instanceof VarMutableArray && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getComponentType().getCanonicalName());
+ }
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, Var.XML_KEY_ID, blockData.outputVars.getID(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ if (var instanceof VarMutable && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getCanonicalName());
+ }
+ else if (var instanceof VarMutableArray && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getComponentType().getCanonicalName());
+ }
+ }
+ }
+ }
+
+ Element linkRoot = XMLUtil.addElement(workFlowRoot, "links");
+
+ for (Link<?> link : workFlow.getLinksIterator())
+ {
+ Element linkNode = XMLUtil.addElement(linkRoot, "link");
+
+ XMLUtil.setAttributeIntValue(linkNode, "srcBlockID", workFlow.indexOf(link.srcBlock));
+ XMLUtil.setAttributeValue(linkNode, "srcVarID", link.srcBlock.getVarID(link.srcVar));
+ XMLUtil.setAttributeIntValue(linkNode, "dstBlockID", workFlow.indexOf(link.dstBlock));
+ XMLUtil.setAttributeValue(linkNode, "dstVarID", link.dstBlock.getVarID(link.dstVar));
+ }
+ }
+
+ /**
+ * @deprecated Legacy method, use {@link #saveWorkFlow_V4(WorkFlow, Element)} instead.
+ * @param workFlow
+ * The workflow to save.
+ * @param workFlowRoot
+ * Root element where elements are to be inserted.
+ */
+ @Deprecated
+ public synchronized void saveWorkFlow_V3(WorkFlow workFlow, Element workFlowRoot)
+ {
+ Element blocksNode = XMLUtil.addElement(workFlowRoot, "blocks");
+
+ for (BlockDescriptor blockData : workFlow)
+ {
+ Element blockNode;
+ Block block = blockData.getBlock();
+
+ if (block instanceof WorkFlow)
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "workflow");
+ XMLUtil.setAttributeBooleanValue(blockNode, "collapsed", blockData.isCollapsed());
+ XMLUtil.setAttributeIntValue(blockNode, "width", blockData.getDimension().width);
+ XMLUtil.setAttributeIntValue(blockNode, "height", blockData.getDimension().height);
+ }
+ else
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "block");
+ }
+
+ String blockClass = block.getClass().getCanonicalName();
+ String mainClass = block instanceof PluginBundled ? ((PluginBundled) block).getMainPluginClassName()
+ : blockClass;
+
+ XMLUtil.setAttributeValue(blockNode, "className", mainClass);
+ XMLUtil.setAttributeValue(blockNode, "blockType", blockClass);
+ XMLUtil.setAttributeIntValue(blockNode, "ID", workFlow.indexOf(blockData));
+ XMLUtil.setAttributeIntValue(blockNode, "xLocation", blockData.getLocation().x);
+ XMLUtil.setAttributeIntValue(blockNode, "yLocation", blockData.getLocation().y);
+
+ if (blockData.isWorkFlow())
+ {
+ WorkFlow innerWorkFlow = (WorkFlow) block;
+
+ saveWorkFlow_V3(innerWorkFlow, blockNode);
+
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, "ID", innerWorkFlow.getInputVarID(var));
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, "ID", innerWorkFlow.getOutputVarID(var));
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ }
+ }
+ else
+ {
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, Var.XML_KEY_ID, blockData.inputVars.getID(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ if (var instanceof VarMutable && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getCanonicalName());
+ }
+ else if (var instanceof VarMutableArray && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getComponentType().getCanonicalName());
+ }
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, Var.XML_KEY_ID, blockData.outputVars.getID(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ if (var instanceof VarMutable && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getCanonicalName());
+ }
+ else if (var instanceof VarMutableArray && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getComponentType().getCanonicalName());
+ }
+ }
+ }
+ }
+
+ Element linkRoot = XMLUtil.addElement(workFlowRoot, "links");
+
+ for (Link<?> link : workFlow.getLinksIterator())
+ {
+ Element linkNode = XMLUtil.addElement(linkRoot, "link");
+
+ XMLUtil.setAttributeIntValue(linkNode, "srcBlockID", workFlow.indexOf(link.srcBlock));
+ XMLUtil.setAttributeValue(linkNode, "srcVarID", link.srcBlock.getVarID(link.srcVar));
+ XMLUtil.setAttributeIntValue(linkNode, "dstBlockID", workFlow.indexOf(link.dstBlock));
+ XMLUtil.setAttributeValue(linkNode, "dstVarID", link.dstBlock.getVarID(link.dstVar));
+ }
+ }
+
+ /**
+ * @param workFlow
+ * The workflow to save.
+ * @param workFlowRoot
+ * Root element where elements are to be inserted.
+ */
+ public synchronized void saveWorkFlow_V4(WorkFlow workFlow, Element workFlowRoot)
+ {
+ Element blocksNode = XMLUtil.addElement(workFlowRoot, "blocks");
+
+ for (BlockDescriptor blockData : workFlow)
+ {
+ Element blockNode;
+ Block block = blockData.getBlock();
+
+ if (block instanceof WorkFlow)
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "workflow");
+ XMLUtil.setAttributeBooleanValue(blockNode, "collapsed", blockData.isCollapsed());
+ }
+ else
+ {
+ blockNode = XMLUtil.addElement(blocksNode, "block");
+ }
+
+ String blockClass = block.getClass().getName();
+ String mainClass = block instanceof PluginBundled ? ((PluginBundled) block).getMainPluginClassName()
+ : blockClass;
+
+ XMLUtil.setAttributeValue(blockNode, "className", mainClass);
+ XMLUtil.setAttributeValue(blockNode, "blockType", blockClass);
+ XMLUtil.setAttributeIntValue(blockNode, "ID", blockData.getID());
+ XMLUtil.setAttributeIntValue(blockNode, "xLocation", blockData.getLocation().x);
+ XMLUtil.setAttributeIntValue(blockNode, "yLocation", blockData.getLocation().y);
+ XMLUtil.setAttributeIntValue(blockNode, "width", blockData.getDimension().width);
+ XMLUtil.setAttributeIntValue(blockNode, "height", blockData.getDimension().height);
+ XMLUtil.setAttributeBooleanValue(blockNode, "collapsed", blockData.isCollapsed());
+ XMLUtil.setAttributeValue(blockNode, "definedName", blockData.getDefinedName());
+ XMLUtil.setAttributeBooleanValue(blockNode, "keepsResults", blockData.keepsResults());
+
+ if (block instanceof InputBlock)
+ XMLUtil.setAttributeValue(blockNode, "CommandLineID", blockData.getCommandLineID());
+
+ if (blockData.isWorkFlow())
+ {
+ WorkFlow innerWorkFlow = (WorkFlow) block;
+
+ saveWorkFlow_V4(innerWorkFlow, blockNode);
+
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ BlockDescriptor owner = innerWorkFlow.getInputOwner(var);
+ if (owner == null)
+ {
+ System.err
+ .println("Warning: could not find owner for input variable: \"" + var + "\", skipping");
+ continue;
+ }
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, "ID", blockData.getVarID(var));
+ XMLUtil.setAttributeIntValue(varNode, "blockID", owner.getID());
+ var.saveToXML(varNode);
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ BlockDescriptor owner = innerWorkFlow.getOutputOwner(var);
+ if (owner == null)
+ {
+ System.err.println(
+ "Warning: could not find owner for output variable: \"" + var + "\", skipping");
+ continue;
+ }
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, "ID", blockData.getVarID(var));
+ XMLUtil.setAttributeIntValue(varNode, "blockID", owner.getID());
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ }
+ }
+ else
+ {
+ Element varRoot = XMLUtil.addElement(blockNode, "variables");
+
+ Element inputVarRoot = XMLUtil.addElement(varRoot, "input");
+
+ for (Var<?> var : blockData.inputVars)
+ {
+ Element varNode = XMLUtil.addElement(inputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, Var.XML_KEY_ID, blockData.getVarID(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+
+ // only save user values (linked values are stored or generated elsewhere)
+ if (var.getReference() == null)
+ var.saveToXML(varNode);
+
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.inputVars.isVisible(var));
+ if (var instanceof MutableType)
+ {
+ if (var instanceof VarMutable && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getName());
+ }
+ else if (var instanceof VarMutableArray && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getComponentType().getName());
+ }
+ }
+ XMLUtil.setAttributeBooleanValue(varNode, RUNTIME, blockData.inputVars.isRuntimeVariable(var));
+ }
+
+ Element outputVarRoot = XMLUtil.addElement(varRoot, "output");
+
+ for (Var<?> var : blockData.outputVars)
+ {
+ Element varNode = XMLUtil.addElement(outputVarRoot, "variable");
+ XMLUtil.setAttributeValue(varNode, Var.XML_KEY_ID, blockData.getVarID(var));
+ XMLUtil.setAttributeValue(varNode, "name", var.getName());
+ XMLUtil.setAttributeBooleanValue(varNode, "visible", blockData.outputVars.isVisible(var));
+ if (var instanceof MutableType)
+ {
+ if (var instanceof VarMutable && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getName());
+ }
+ else if (var instanceof VarMutableArray && var.getType() != null)
+ {
+ XMLUtil.setAttributeValue(varNode, "type", var.getType().getComponentType().getName());
+ }
+ }
+ XMLUtil.setAttributeBooleanValue(varNode, RUNTIME, blockData.outputVars.isRuntimeVariable(var));
+ }
+ }
+ }
+
+ Element linkRoot = XMLUtil.addElement(workFlowRoot, "links");
+
+ for (Link<?> link : workFlow.getLinksIterator())
+ {
+ Element linkNode = XMLUtil.addElement(linkRoot, "link");
+
+ XMLUtil.setAttributeIntValue(linkNode, "srcBlockID", link.srcBlock.getID());
+ XMLUtil.setAttributeValue(linkNode, "srcVarID", link.srcBlock.getVarID(link.srcVar));
+ if (link.srcVar instanceof MutableType)
+ {
+ if (link.srcVar instanceof VarMutable && link.srcVar.getType() != null)
+ {
+ XMLUtil.setAttributeValue(linkNode, "srcVarType", link.srcVar.getType().getName());
+ }
+ else if (link.srcVar instanceof VarMutableArray && link.srcVar.getType() != null)
+ {
+ XMLUtil.setAttributeValue(linkNode, "srcVarType",
+ link.srcVar.getType().getComponentType().getName());
+ }
+ }
+ XMLUtil.setAttributeIntValue(linkNode, "dstBlockID", link.dstBlock.getID());
+ XMLUtil.setAttributeValue(linkNode, "dstVarID", link.dstBlock.getVarID(link.dstVar));
+ }
+ }
+
+ /**
+ * @param xml
+ * The xml document to load.
+ * @param targetWorkFlow
+ * The workflow where elements generated from the xml document are to be inserted.
+ * @return true if the loaded file is at the latest BlocksML version, false otherwise.
+ */
+ public synchronized boolean loadWorkFlow(Document xml, WorkFlow targetWorkFlow)
+ {
+ Element xmlRoot = XMLUtil.getRootElement(xml);
+
+ String rootName = xmlRoot.getNodeName();
+
+ if (!rootName.equalsIgnoreCase("protocol") && !rootName.equalsIgnoreCase("workspace"))
+ {
+ throw new IcyHandledException("The selected file is not an Icy protocol");
+ }
+
+ int fileVersion = XMLUtil.getAttributeIntValue(xmlRoot, "VERSION", -1);
+
+ // scan the protocol for missing plugins
+ Set<String> missingPlugins = getMissingPlugins(xmlRoot, fileVersion);
+
+ if (missingPlugins.size() > 0)
+ {
+ // Are we connected to the internet?
+ if (!NetworkUtil.hasInternetAccess())
+ throw new IcyHandledException(
+ "Some plugins required by this protocol are missing, but no internet connection is available");
+
+ // Are we using Icy's plug-in loader (and not Eclipse)?
+ if (getClass().getClassLoader() == ClassLoader.getSystemClassLoader())
+ throw new IcyHandledException(
+ "Cannot install missing blocks while using Icy4Eclipse in \"Debug\" or \"Run\" modes");
+
+ // we are live!
+ String message = "[Protocols] Installing required plugins...";
+ System.out.println(message);
+ AnnounceFrame announcement = null;
+
+ if (!Icy.getMainInterface().isHeadLess())
+ announcement = new AnnounceFrame(message);
+
+ Set<PluginDescriptor> descriptors = new HashSet<PluginDescriptor>(missingPlugins.size());
+
+ for (String className : missingPlugins)
+ {
+ PluginDescriptor pDesc = PluginRepositoryLoader.getPlugin(className);
+ if (pDesc == null)
+ {
+ // sadly, I believe the plugin loader could be reloaded at anytime...
+ // double check that for every plugin, just to be safe
+ if (PluginLoader.getPlugins(Block.class, true, false, false).size() == 0)
+ throw new BlocksReloadedException();
+
+ throw new BlocksException(
+ "Couldn't find plugin " + ClassUtil.getSimpleClassName(className) + " online", true);
+ }
+ descriptors.add(pDesc);
+ }
+
+ for (PluginDescriptor pDesc : descriptors)
+ PluginInstaller.install(pDesc, false);
+
+ PluginInstaller.waitInstall();
+ PluginLoader.waitWhileLoading();
+
+ System.out.println("[Protocols] Plugins installed successfully.");
+ if (announcement != null)
+ announcement.close();
+
+ // reload the whole mother!
+ throw new BlocksReloadedException();
+ }
+
+ switch (fileVersion)
+ {
+ case 1:
+ loadWorkFlow_V1(xmlRoot, targetWorkFlow);
+ break;
+ case 2:
+ loadWorkFlow_V2(xmlRoot, targetWorkFlow);
+ break;
+ case 3:
+ loadWorkFlow_V3(xmlRoot, targetWorkFlow);
+ break;
+ case 4:
+ loadWorkFlow_V4(xmlRoot, targetWorkFlow);
+ break;
+ default:
+ throw new UnsupportedOperationException("Unknown Protocol version: " + fileVersion);
+ }
+
+ return fileVersion == CURRENT_VERSION;
+ }
+
+ private Set<String> getMissingPlugins(Element workFlowRoot, int fileVersion)
+ {
+ Set<String> missingPlugins = new HashSet<String>();
+
+ Element blocksRoot = XMLUtil.getElement(workFlowRoot, "blocks");
+
+ // we are not in a node that has blocks => stop the recursion
+ if (blocksRoot == null)
+ return missingPlugins;
+
+ ArrayList<Element> blocksNode = XMLUtil.getElements(blocksRoot);
+
+ for (Element blockNode : blocksNode)
+ {
+ // the class name of the block to find
+ String blockTag = (fileVersion <= 2) ? "type" : "blockType";
+ String blockType = XMLUtil.getAttributeValue(blockNode, blockTag, null);
+ // the class name of the plugin providing this block (may be the same)
+ String pluginClassName = XMLUtil.getAttributeValue(blockNode, "className", blockType);
+
+ try
+ {
+ ClassUtil.findClass(blockType);
+ }
+ catch (ClassNotFoundException e)
+ {
+ // the block appears to be missing
+ // => is the corresponding plug-in missing or out-dated?
+ PluginDescriptor mainPlugin = PluginLoader.getPlugin(pluginClassName);
+ if (mainPlugin == null || PluginUpdater.getUpdate(mainPlugin) != null)
+ {
+ // store the class name of the missing plug-in
+ missingPlugins.add(pluginClassName);
+ }
+ else
+ {
+ // The block is definitely missing, stop everything!
+ IcyExceptionHandler.handleException(mainPlugin, e, false);
+ }
+ }
+ finally
+ {
+ // whether the current block is missing or not,
+ // perhaps it's a work flow and has more blocks within
+ missingPlugins.addAll(getMissingPlugins(blockNode, fileVersion));
+ }
+ }
+
+ return missingPlugins;
+ }
+
+ /**
+ * @deprecated legacy method. Use {@link #loadWorkFlow_V4(Element, WorkFlow)} instead.
+ * @param workFlowRoot
+ * XML element of the workflow root to be loaded.
+ * @param workFlow
+ * Target workflow to add elements from document.
+ */
+ @Deprecated
+ @SuppressWarnings({"unchecked", "deprecation"})
+ public synchronized void loadWorkFlow_V1(Element workFlowRoot, WorkFlow workFlow)
+ {
+ Element blocksRoot = XMLUtil.getElement(workFlowRoot, "blocks");
+
+ ArrayList<Element> blocksNode = XMLUtil.getElements(blocksRoot);
+
+ for (Element blockNode : blocksNode)
+ {
+ String className = XMLUtil.getAttributeValue(blockNode, "type", null);
+
+ int xPos = XMLUtil.getAttributeIntValue(blockNode, "xLocation", 0);
+ int yPos = XMLUtil.getAttributeIntValue(blockNode, "yLocation", 0);
+
+ try
+ {
+ Class<? extends Block> blockClass = (Class<? extends Block>) ClassUtil.findClass(className);
+
+ Block block = blockClass.newInstance();
+
+ if (block == null)
+ throw new BlocksException("Couldn't create block from class " + blockClass.getName(), true);
+
+ if (block instanceof WorkFlow)
+ {
+ // load the inner work flow
+ loadWorkFlow_V1(blockNode, (WorkFlow) block);
+
+ BlockDescriptor blockInfo = workFlow.addBlock(-1, block, new Point(xPos, yPos));
+
+ // adjust visibility triggers
+ {
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ int id = XMLUtil.getAttributeIntValue(varNode, "ID", -1);
+ Var<?> var = blockInfo.inputVars.get(id);
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ blockInfo.inputVars.setVisible(var, visible);
+ }
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ int id = XMLUtil.getAttributeIntValue(varNode, "ID", -1);
+ Var<?> var = blockInfo.outputVars.get(id);
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ blockInfo.outputVars.setVisible(var, visible);
+ }
+ }
+ }
+ else
+ {
+ BlockDescriptor blockInfo = workFlow.addBlock(-1, block, new Point(xPos, yPos));
+
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ int id = XMLUtil.getAttributeIntValue(varNode, Var.XML_KEY_ID, -1);
+ Var<?> var = blockInfo.inputVars.get(id);
+ var.loadFromXML(varNode);
+ blockInfo.inputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+ }
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ int id = XMLUtil.getAttributeIntValue(varNode, Var.XML_KEY_ID, -1);
+ Var<?> var = blockInfo.outputVars.get(id);
+ var.loadFromXML(varNode);
+ blockInfo.outputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+ }
+ }
+ }
+ catch (Exception e1)
+ {
+ throw new BlocksException("Cannot create block (" + e1.getMessage() + ")", true);
+ }
+ }
+
+ Element linkRoot = XMLUtil.getElement(workFlowRoot, "links");
+
+ for (Element linkNode : XMLUtil.getElements(linkRoot))
+ {
+ int srcBlockID = XMLUtil.getAttributeIntValue(linkNode, "srcBlockID", -1);
+ int srcVarID = XMLUtil.getAttributeIntValue(linkNode, "srcVarID", -1);
+ int dstBlockID = XMLUtil.getAttributeIntValue(linkNode, "dstBlockID", -1);
+ int dstVarID = XMLUtil.getAttributeIntValue(linkNode, "dstVarID", -1);
+
+ BlockDescriptor srcBlock = workFlow.getBlock(srcBlockID);
+ @SuppressWarnings("rawtypes")
+ // this is assumed correct
+ Var srcVar = srcBlock.outputVars.get(srcVarID);
+
+ BlockDescriptor dstBlock = workFlow.getBlock(dstBlockID);
+ @SuppressWarnings("rawtypes")
+ // this is assumed correct
+ Var dstVar = dstBlock.inputVars.get(dstVarID);
+
+ workFlow.addLink(srcBlock, srcVar, dstBlock, dstVar);
+ }
+ }
+
+ /**
+ * @deprecated legacy method. Use {@link #loadWorkFlow_V4(Element, WorkFlow)} instead.
+ * @param workFlowRoot
+ * XML element of the workflow root to be loaded.
+ * @param workFlow
+ * Target workflow to add elements from document.
+ */
+ @Deprecated
+ @SuppressWarnings({"unchecked", "rawtypes", "deprecation"})
+ public synchronized void loadWorkFlow_V2(Element workFlowRoot, WorkFlow workFlow)
+ {
+ Element blocksRoot = XMLUtil.getElement(workFlowRoot, "blocks");
+
+ ArrayList<Element> blocksNode = XMLUtil.getElements(blocksRoot);
+
+ for (Element blockNode : blocksNode)
+ {
+ String className = XMLUtil.getAttributeValue(blockNode, "type", null);
+
+ int xPos = XMLUtil.getAttributeIntValue(blockNode, "xLocation", -1);
+ int yPos = XMLUtil.getAttributeIntValue(blockNode, "yLocation", -1);
+
+ try
+ {
+ Class<? extends Block> blockClass = (Class<? extends Block>) ClassUtil.findClass(className);
+
+ Block block = blockClass.newInstance();
+
+ if (block == null)
+ throw new BlocksException("Couldn't create block from class " + blockClass.getName(), true);
+
+ if (block instanceof WorkFlow)
+ {
+ BlockDescriptor blockInfo = workFlow.addBlock(-1, block, new Point(xPos, yPos));
+
+ // load the inner work flow
+ loadWorkFlow_V2(blockNode, (WorkFlow) block);
+
+ // adjust visibility triggers
+ {
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.inputVars.get(uid);
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ blockInfo.inputVars.setVisible(var, visible);
+ }
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.outputVars.get(uid);
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ blockInfo.outputVars.setVisible(var, visible);
+ }
+ }
+ }
+ else
+ {
+ BlockDescriptor blockInfo = workFlow.addBlock(-1, block, new Point(xPos, yPos));
+
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.inputVars.get(uid);
+ var.loadFromXML(varNode);
+ blockInfo.inputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+
+ if (var instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ ((MutableType) var).setType(Class.forName(type));
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+ }
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.outputVars.get(uid);
+ var.loadFromXML(varNode);
+ blockInfo.outputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+
+ if (var instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ ((MutableType) var).setType(Class.forName(type));
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+ }
+ }
+ }
+ catch (Exception e1)
+ {
+ throw new BlocksException("Cannot create block (" + e1.getMessage() + ")", true);
+ }
+ }
+
+ Element linkRoot = XMLUtil.getElement(workFlowRoot, "links");
+
+ for (Element linkNode : XMLUtil.getElements(linkRoot))
+ {
+ int srcBlockID = XMLUtil.getAttributeIntValue(linkNode, "srcBlockID", -1);
+ String srcVarID = XMLUtil.getAttributeValue(linkNode, "srcVarID", null);
+ int dstBlockID = XMLUtil.getAttributeIntValue(linkNode, "dstBlockID", -1);
+ String dstVarID = XMLUtil.getAttributeValue(linkNode, "dstVarID", null);
+
+ BlockDescriptor srcBlock = workFlow.getBlock(srcBlockID);
+ Var srcVar = srcBlock.outputVars.get(srcVarID);
+ if (srcVar == null)
+ srcVar = srcBlock.inputVars.get(srcVarID);
+
+ BlockDescriptor dstBlock = workFlow.getBlock(dstBlockID);
+ Var dstVar = dstBlock.inputVars.get(dstVarID);
+
+ workFlow.addLink(srcBlock, srcVar, dstBlock, dstVar);
+ }
+ }
+
+ /**
+ * @deprecated legacy method. Use {@link #loadWorkFlow_V4(Element, WorkFlow)} instead.
+ * @param workFlowRoot
+ * XML element of the workflow root to be loaded.
+ * @param workFlow
+ * Target workflow to add elements from document.
+ */
+ @Deprecated
+ @SuppressWarnings({"unchecked", "rawtypes", "deprecation"})
+ public synchronized void loadWorkFlow_V3(Element workFlowRoot, WorkFlow workFlow)
+ {
+ Element blocksRoot = XMLUtil.getElement(workFlowRoot, "blocks");
+
+ ArrayList<Element> blocksNode = XMLUtil.getElements(blocksRoot);
+
+ for (Element blockNode : blocksNode)
+ {
+ String blockType = XMLUtil.getAttributeValue(blockNode, "blockType", null);
+
+ int xPos = XMLUtil.getAttributeIntValue(blockNode, "xLocation", -1);
+ int yPos = XMLUtil.getAttributeIntValue(blockNode, "yLocation", -1);
+
+ try
+ {
+ Class<? extends Block> blockClass = (Class<? extends Block>) ClassUtil.findClass(blockType);
+
+ Block block = blockClass.newInstance();
+
+ if (block == null)
+ throw new BlocksException("Couldn't create block from class " + blockClass.getName(), true);
+
+ if (block instanceof WorkFlow)
+ {
+ int width = XMLUtil.getAttributeIntValue(blockNode, "width", 500);
+ int height = XMLUtil.getAttributeIntValue(blockNode, "height", 500);
+ ((WorkFlow) block).getBlockDescriptor().setDimension(width, height);
+
+ BlockDescriptor blockInfo = workFlow.addBlock(-1, block, new Point(xPos, yPos));
+
+ // load the inner work flow
+ loadWorkFlow_V3(blockNode, (WorkFlow) block);
+
+ // adjust visibility triggers
+ {
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.inputVars.get(uid);
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ blockInfo.inputVars.setVisible(var, visible);
+ }
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.outputVars.get(uid);
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ blockInfo.outputVars.setVisible(var, visible);
+ }
+ }
+ }
+ else
+ {
+ BlockDescriptor blockInfo = workFlow.addBlock(-1, block, new Point(xPos, yPos));
+
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+ for (Element varNode : XMLUtil.getElements(inVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.inputVars.get(uid);
+ var.loadFromXML(varNode);
+ blockInfo.inputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+
+ if (var instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ ((MutableType) var).setType(Class.forName(type));
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+ }
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+ for (Element varNode : XMLUtil.getElements(outVarRoot))
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockInfo.outputVars.get(uid);
+ var.loadFromXML(varNode);
+ blockInfo.outputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+
+ if (var instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ ((MutableType) var).setType(Class.forName(type));
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+ }
+ }
+ }
+ catch (Exception e1)
+ {
+ throw new BlocksException("Cannot create block (" + e1.getMessage() + ")", true);
+ }
+ }
+
+ Element linkRoot = XMLUtil.getElement(workFlowRoot, "links");
+
+ for (Element linkNode : XMLUtil.getElements(linkRoot))
+ {
+ int srcBlockID = XMLUtil.getAttributeIntValue(linkNode, "srcBlockID", -1);
+ String srcVarID = XMLUtil.getAttributeValue(linkNode, "srcVarID", null);
+ int dstBlockID = XMLUtil.getAttributeIntValue(linkNode, "dstBlockID", -1);
+ String dstVarID = XMLUtil.getAttributeValue(linkNode, "dstVarID", null);
+
+ BlockDescriptor srcBlock = workFlow.getBlock(srcBlockID);
+ Var srcVar = srcBlock.outputVars.get(srcVarID);
+ if (srcVar == null)
+ srcVar = srcBlock.inputVars.get(srcVarID);
+
+ BlockDescriptor dstBlock = workFlow.getBlock(dstBlockID);
+ Var dstVar = dstBlock.inputVars.get(dstVarID);
+
+ workFlow.addLink(srcBlock, srcVar, dstBlock, dstVar);
+ }
+ }
+
+ /**
+ * @param workFlowRoot
+ * XML element of the workflow root to be loaded.
+ * @param workFlow
+ * Target workflow to add elements from document.
+ * @throws BlocksException
+ * If an error occurs while loading the workflow.
+ */
+ @SuppressWarnings({"unchecked", "rawtypes"})
+ public synchronized void loadWorkFlow_V4(Element workFlowRoot, final WorkFlow workFlow) throws BlocksException
+ {
+ boolean hasWarnings = false;
+
+ // Prepare a list of blocks to collapse after loading
+ ArrayList<BlockDescriptor> blocksToCollapse = new ArrayList<BlockDescriptor>();
+
+ // 1) Load blocks and inner work flows
+
+ Element blocksRoot = XMLUtil.getElement(workFlowRoot, "blocks");
+
+ ArrayList<Element> blocksNode = XMLUtil.getElements(blocksRoot);
+
+ for (final Element blockNode : blocksNode)
+ {
+ final String blockType = XMLUtil.getAttributeValue(blockNode, "blockType", null);
+
+ Block block = null;
+
+ try
+ {
+ block = ThreadUtil.invokeNow(new Callable<Block>()
+ {
+ @Override
+ public Block call() throws Exception
+ {
+ return (Block) ClassUtil.findClass(blockType).newInstance();
+ }
+ });
+ }
+ catch (Exception e)
+ {
+ String message = "Couldn't create block from class \"" + blockType + "\".\n";
+ message += "Reason: " + e.getClass().getName() + " (" + e.getMessage() + ")";
+
+ throw new BlocksException(message, true);
+ }
+
+ int blockID = XMLUtil.getAttributeIntValue(blockNode, "ID", -1);
+
+ final BlockDescriptor blockDescriptor;
+
+ if (block instanceof WorkFlow)
+ {
+ blockDescriptor = ((WorkFlow) block).getBlockDescriptor();
+ blockDescriptor.setID(blockID);
+ }
+ else
+ {
+ blockDescriptor = new BlockDescriptor(blockID, block);
+ }
+
+ int xPos = XMLUtil.getAttributeIntValue(blockNode, "xLocation", -1);
+ int yPos = XMLUtil.getAttributeIntValue(blockNode, "yLocation", -1);
+ blockDescriptor.setLocation(xPos, yPos);
+
+ int width = XMLUtil.getAttributeIntValue(blockNode, "width", 0);
+ int height = XMLUtil.getAttributeIntValue(blockNode, "height", 0);
+
+ // set the block's dimension, but don't collapse just now
+ // => wait for all the drawing to be done
+ blockDescriptor.setDimension(width, height);
+
+ String definedName = XMLUtil.getAttributeValue(blockNode, "definedName", null);
+ blockDescriptor.setDefinedName(definedName);
+
+ blockDescriptor.keepResults(XMLUtil.getAttributeBooleanValue(blockNode, "keepsResults", true));
+
+ if (block instanceof InputBlock)
+ blockDescriptor.setCommandLineID(XMLUtil.getAttributeValue(blockNode, "CommandLineID", ""));
+
+ workFlow.addBlock(blockDescriptor);
+
+ if (block instanceof WorkFlow)
+ {
+ // load the inner work flow
+ loadWorkFlow_V4(blockNode, (WorkFlow) block);
+
+ // adjust visibility triggers
+
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+ final ArrayList<Element> inVarNodes = XMLUtil.getElements(inVarRoot);
+
+ synchronized (blockDescriptor.inputVars)
+ {
+ for (Element varNode : inVarNodes)
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockDescriptor.inputVars.get(uid);
+
+ if (var == null)
+ {
+ System.err.println(new NoSuchVariableException(blockDescriptor, uid).getMessage());
+ continue;
+ }
+
+ if (var.getReference() == null)
+ {
+ var.loadFromXML(varNode);
+
+ // adjust visibility
+
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ try
+ {
+ blockDescriptor.inputVars.setVisible(var, visible);
+ }
+ catch (NoSuchVariableException e)
+ {
+ if (!hasWarnings)
+ {
+ System.err.println("Error(s) while loading protocol:");
+ hasWarnings = true;
+ }
+ System.err.println(new NoSuchVariableException(blockDescriptor, uid).getMessage());
+ }
+ }
+ }
+ }
+
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+ final ArrayList<Element> outVarNodes = XMLUtil.getElements(outVarRoot);
+
+ synchronized (blockDescriptor.outputVars)
+ {
+ for (Element varNode : outVarNodes)
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockDescriptor.outputVars.get(uid);
+
+ // adjust visibility
+
+ boolean visible = XMLUtil.getAttributeBooleanValue(varNode, "visible", false);
+ try
+ {
+ blockDescriptor.outputVars.setVisible(var, visible);
+ }
+ catch (NoSuchVariableException e)
+ {
+ if (!hasWarnings)
+ {
+ System.err.println("Error(s) while loading protocol:");
+ hasWarnings = true;
+ }
+ System.err.println(new NoSuchVariableException(blockDescriptor, uid).getMessage());
+ // throw new NoSuchVariableException(blockInfo, uid);
+ }
+ }
+ }
+ }
+ else
+ {
+ Element varRoot = XMLUtil.getElement(blockNode, "variables");
+ Element inVarRoot = XMLUtil.getElement(varRoot, "input");
+ final ArrayList<Element> inVarNodes = XMLUtil.getElements(inVarRoot);
+
+ synchronized (blockDescriptor.inputVars)
+ {
+ for (Element varNode : inVarNodes)
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockDescriptor.inputVars.get(uid);
+
+ boolean isDynamicVariable = XMLUtil.getAttributeBooleanValue(varNode, RUNTIME, false);
+
+ if (var == null)
+ {
+ if (isDynamicVariable)
+ {
+ var = new VarMutable(XMLUtil.getAttributeValue(varNode, "name", "input"), null);
+ ((VarMutable) var).setDefaultEditorModel(new TypeSelectionModel());
+ blockDescriptor.inputVars.addRuntimeVariable(uid, (VarMutable) var);
+ }
+ else
+ {
+ if (!hasWarnings)
+ {
+ System.err.println("Error(s) while loading protocol:");
+ hasWarnings = true;
+ }
+ System.err.println(new NoSuchVariableException(blockDescriptor, uid).getMessage());
+ continue;
+ // throw new NoSuchVariableException(blockInfo, uid);
+ }
+ }
+
+ try
+ {
+ if (var instanceof MutableType)
+ {
+ Class<?> mutableType = null;
+
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ mutableType = getPrimitiveType(type);
+
+ if (mutableType == null)
+ mutableType = Class.forName(type);
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ mutableType = Class.forName("[L" + type + ";");
+ }
+
+ ((MutableType) var).setType(mutableType);
+ }
+ }
+
+ var.loadFromXML(varNode);
+
+ // Input blocks can have their values set from command line
+ if (block instanceof InputBlock)
+ {
+ String clID = blockDescriptor.getCommandLineID();
+ if (!clID.isEmpty())
+ {
+ Map<String, String> map = Protocols.getCommandLineArguments();
+ if (map.containsKey(clID))
+ {
+ // Set the value of the first (and only) block variable
+ var.setValueAsString(map.get(clID));
+ }
+ }
+ }
+ }
+ catch (Exception e)
+ {
+ String message = "Unable to read input variable \"" + var.getName() + "\" in block \""
+ + blockDescriptor.getDefinedName() + "\".\n";
+ message += "Reason: " + e.getClass().getName() + " (" + e.getMessage() + ")";
+ throw new BlocksException(message, true);
+ }
+ blockDescriptor.inputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+ }
+ }
+
+ Element outVarRoot = XMLUtil.getElement(varRoot, "output");
+ final ArrayList<Element> outVarNodes = XMLUtil.getElements(outVarRoot);
+
+ synchronized (blockDescriptor.outputVars)
+ {
+ for (Element varNode : outVarNodes)
+ {
+ String uid = XMLUtil.getAttributeValue(varNode, "ID", null);
+ Var<?> var = blockDescriptor.outputVars.get(uid);
+
+ boolean isDynamicVariable = XMLUtil.getAttributeBooleanValue(varNode, RUNTIME, false);
+
+ if (var == null)
+ {
+ if (isDynamicVariable)
+ {
+ var = new VarMutable(XMLUtil.getAttributeValue(varNode, "name", "output"), null);
+ ((VarMutable) var).setDefaultEditorModel(new TypeSelectionModel());
+ blockDescriptor.outputVars.addRuntimeVariable(uid, (VarMutable) var);
+ }
+ else
+ {
+ if (!hasWarnings)
+ {
+ System.err.println("Error(s) while loading protocol:");
+ hasWarnings = true;
+ }
+ System.err.println(new NoSuchVariableException(blockDescriptor, uid).getMessage());
+ continue;
+ // throw new NoSuchVariableException(blockInfo, uid);
+ }
+ }
+
+ blockDescriptor.outputVars.setVisible(var,
+ XMLUtil.getAttributeBooleanValue(varNode, "visible", false));
+
+ if (var instanceof MutableType)
+ try
+ {
+ String type = XMLUtil.getAttributeValue(varNode, "type", null);
+ if (type != null)
+ {
+ if (var instanceof VarMutable)
+ {
+ Class<?> mutableType = getPrimitiveType(type);
+ ((MutableType) var)
+ .setType(mutableType != null ? mutableType : Class.forName(type));
+ }
+ else if (var instanceof VarMutableArray)
+ {
+ ((MutableType) var).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ }
+ catch (ClassNotFoundException e)
+ {
+ String message = "Unable to read output variable \"" + var.getName() + "\" in block \""
+ + blockDescriptor.getDefinedName() + "\".\n";
+ message += "Reason: " + e.getClass().getName() + " (" + e.getMessage() + ")";
+ throw new BlocksException(message, true);
+ }
+ }
+ }
+ }
+
+ // prepare to collapse the block if necessary
+ if (XMLUtil.getAttributeBooleanValue(blockNode, "collapsed", false))
+ blocksToCollapse.add(blockDescriptor);
+ }
+
+ // 2) Load links
+
+ Element linkRoot = XMLUtil.getElement(workFlowRoot, "links");
+
+ ArrayList<Element> links = XMLUtil.getElements(linkRoot);
+ Collections.sort(links, new Comparator<Element>()
+ {
+ @Override
+ public int compare(Element link1, Element link2)
+ {
+ int srcBlock1 = XMLUtil.getAttributeIntValue(link1, "srcBlockID", -1);
+ int srcBlock2 = XMLUtil.getAttributeIntValue(link2, "srcBlockID", -1);
+
+ int i1 = workFlow.indexOf(workFlow.getBlockByID(srcBlock1));
+ int i2 = workFlow.indexOf(workFlow.getBlockByID(srcBlock2));
+
+ return i1 < i2 ? -1 : i1 > i2 ? 1 : 0;
+ }
+ });
+
+ for (Element linkNode : links)
+ {
+ int srcBlockID = XMLUtil.getAttributeIntValue(linkNode, "srcBlockID", -1);
+ String srcVarID = XMLUtil.getAttributeValue(linkNode, "srcVarID", null);
+ int dstBlockID = XMLUtil.getAttributeIntValue(linkNode, "dstBlockID", -1);
+ String dstVarID = XMLUtil.getAttributeValue(linkNode, "dstVarID", null);
+
+ // load the source variable
+ BlockDescriptor srcBlock = workFlow.getBlockByID(srcBlockID);
+ Var srcVar = srcBlock.outputVars.get(srcVarID);
+ if (srcVar == null)
+ srcVar = srcBlock.inputVars.get(srcVarID);
+
+ if (srcVar == null)
+ {
+ System.err.println("Cannot create a link from variable " + srcVarID + " (from block " + srcBlock
+ + "). It may have been removed or renamed.");
+ continue;
+ }
+
+ if (srcVar instanceof MutableType)
+ {
+ String type = XMLUtil.getAttributeValue(linkNode, "srcVarType", null);
+ if (type != null)
+ {
+ try
+ {
+ if (srcVar instanceof VarMutable)
+ {
+ Class<?> mutableType = getPrimitiveType(type);
+ ((MutableType) srcVar).setType(mutableType != null ? mutableType : Class.forName(type));
+ }
+ else if (srcVar instanceof VarMutableArray)
+ {
+ ((MutableType) srcVar).setType(Class.forName("[L" + type + ";"));
+ }
+ }
+ catch (ClassNotFoundException e1)
+ {
+ throw new BlocksException("Cannot create block (" + e1.getMessage() + ") => class not found",
+ true);
+ }
+ }
+ }
+
+ // load the destination variable
+ BlockDescriptor dstBlock = workFlow.getBlockByID(dstBlockID);
+
+ Var dstVar = dstBlock.inputVars.get(dstVarID);
+
+ if (dstVar == null)
+ {
+ System.err.println("Cannot link to variable " + dstVarID + " (from block " + dstBlock
+ + "). It may have been removed or renamed.");
+ continue;
+ }
+
+ workFlow.addLink(srcBlock, srcVar, dstBlock, dstVar);
+ }
+
+ // 3) Collapse necessary blocks
+ for (BlockDescriptor block : blocksToCollapse)
+ block.setCollapsed(true);
+
+ if (hasWarnings)
+ System.err.println("--");
+ }
+
+ public synchronized void loadWorkFlow_V5(Element workFlowRoot, WorkFlow workFlow, WorkFlow parentFlow)
+ throws BlocksException
+ {
+ boolean noWarnings = true;
+
+ Element blocksRoot = XMLUtil.getElement(workFlowRoot, "blocks");
+
+ ArrayList<Element> blocksNode = XMLUtil.getElements(blocksRoot);
+
+ for (Element blockNode : blocksNode)
+ {
+ BlockDescriptor blockDesc = new BlockDescriptor();
+ noWarnings &= blockDesc.loadFromXML(blockNode);
+ workFlow.addBlock(blockDesc);
+ }
+
+ Element linkRoot = XMLUtil.getElement(workFlowRoot, "links");
+
+ for (Element linkNode : XMLUtil.getElements(linkRoot))
+ {
+ @SuppressWarnings("rawtypes")
+ Link link = new Link(workFlow);
+ link.loadFromXML(linkNode);
+ }
+
+ if (!noWarnings)
+ System.err.println("--");
+ }
+
+ /**
+ * @param primitiveName
+ * The string representation of the primitive type.
+ * @return The Java primitive type represented by the given name, or null if the given name does
+ * not represent a primitive type
+ */
+ public static Class<?> getPrimitiveType(String primitiveName)
+ {
+ if (primitiveName.equals("byte"))
+ return byte.class;
+ if (primitiveName.equals("short"))
+ return short.class;
+ if (primitiveName.equals("int"))
+ return int.class;
+ if (primitiveName.equals("long"))
+ return long.class;
+ if (primitiveName.equals("char"))
+ return char.class;
+ if (primitiveName.equals("float"))
+ return float.class;
+ if (primitiveName.equals("double"))
+ return double.class;
+ if (primitiveName.equals("boolean"))
+ return boolean.class;
+ if (primitiveName.equals("void"))
+ return void.class;
+
+ return null;
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/BlocksReloadedException.java b/src/main/java/plugins/adufour/blocks/util/BlocksReloadedException.java
new file mode 100644
index 0000000..70a13c0
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/BlocksReloadedException.java
@@ -0,0 +1,10 @@
+package plugins.adufour.blocks.util;
+
+@SuppressWarnings("serial")
+public class BlocksReloadedException extends BlocksException
+{
+ public BlocksReloadedException()
+ {
+ super("The plugin list has been updated", true);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/LinkCutException.java b/src/main/java/plugins/adufour/blocks/util/LinkCutException.java
new file mode 100644
index 0000000..16dafea
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/LinkCutException.java
@@ -0,0 +1,10 @@
+package plugins.adufour.blocks.util;
+
+@SuppressWarnings("serial")
+public class LinkCutException extends BlocksException
+{
+ public LinkCutException(String s)
+ {
+ super(s, true);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/LoopException.java b/src/main/java/plugins/adufour/blocks/util/LoopException.java
new file mode 100644
index 0000000..6336d78
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/LoopException.java
@@ -0,0 +1,18 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.blocks.lang.WorkFlow;
+
+/**
+ * Exception raised whenever a loop is detected in an {@link WorkFlow}
+ *
+ * @author Alexandre Dufour
+ */
+public class LoopException extends BlocksException
+{
+ private static final long serialVersionUID = 1L;
+
+ public LoopException()
+ {
+ super("Cannot create loops inside a workflow", true);
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/MenuItemListener.java b/src/main/java/plugins/adufour/blocks/util/MenuItemListener.java
new file mode 100644
index 0000000..1a51723
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/MenuItemListener.java
@@ -0,0 +1,7 @@
+package plugins.adufour.blocks.util;
+
+import icy.plugin.PluginDescriptor;
+
+public interface MenuItemListener {
+ public void displayDoc(PluginDescriptor d);
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/NoSuchBlockException.java b/src/main/java/plugins/adufour/blocks/util/NoSuchBlockException.java
new file mode 100644
index 0000000..19eab99
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/NoSuchBlockException.java
@@ -0,0 +1,25 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.blocks.lang.BlockDescriptor;
+import plugins.adufour.blocks.lang.WorkFlow;
+
+public class NoSuchBlockException extends BlocksException
+{
+ private static final long serialVersionUID = 1L;
+
+ public NoSuchBlockException(BlockDescriptor block)
+ {
+ super("Cannot find block '" + (block == null ? "null" : block.getName()) + "'", false);
+ }
+
+ public NoSuchBlockException(int ID)
+ {
+ super("Cannot find block with ID '" + ID + "'", false);
+ }
+
+ public NoSuchBlockException(int ID, WorkFlow container)
+ {
+ super("Cannot find block with ID '" + ID + "' in workflow '" + container.getBlockDescriptor().getName() + "'", false);
+
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/NoSuchLinkException.java b/src/main/java/plugins/adufour/blocks/util/NoSuchLinkException.java
new file mode 100644
index 0000000..68fc762
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/NoSuchLinkException.java
@@ -0,0 +1,12 @@
+package plugins.adufour.blocks.util;
+
+public class NoSuchLinkException extends BlocksException
+{
+ private static final long serialVersionUID = 1L;
+
+ public NoSuchLinkException(String message)
+ {
+ super(message, false);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/NoSuchVariableException.java b/src/main/java/plugins/adufour/blocks/util/NoSuchVariableException.java
new file mode 100644
index 0000000..5b60c7c
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/NoSuchVariableException.java
@@ -0,0 +1,24 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.blocks.lang.BlockDescriptor;
+import plugins.adufour.vars.lang.Var;
+
+public class NoSuchVariableException extends BlocksException
+{
+ private static final long serialVersionUID = 1L;
+
+ public NoSuchVariableException(String varName)
+ {
+ super("Variable not found: '" + varName + "'", false);
+ }
+
+ public NoSuchVariableException(BlockDescriptor blockInfo, String varName)
+ {
+ super("Variable '" + varName + "' not found in block '" + blockInfo.getName() + "'. It may have been removed or renamed.", false);
+ }
+
+ public NoSuchVariableException(Var<?> src)
+ {
+ this(src == null ? null : src.getName());
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/ScopeException.java b/src/main/java/plugins/adufour/blocks/util/ScopeException.java
new file mode 100644
index 0000000..d7488a3
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/ScopeException.java
@@ -0,0 +1,13 @@
+package plugins.adufour.blocks.util;
+
+public class ScopeException extends BlocksException
+{
+ private static final long serialVersionUID = 1L;
+
+ public ScopeException()
+ {
+ super("Two variables located in different loops or workflows cannot be directly linked.\n"
+ + "Expose the inner-most variable(s) by right-clicking on them and select \"expose variable\"", true);
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/StopException.java b/src/main/java/plugins/adufour/blocks/util/StopException.java
new file mode 100644
index 0000000..8bcce2b
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/StopException.java
@@ -0,0 +1,10 @@
+package plugins.adufour.blocks.util;
+
+@SuppressWarnings("serial")
+public class StopException extends RuntimeException
+{
+ public StopException()
+ {
+ super("This workflow was interrupted prematurely");
+ }
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/VarList.java b/src/main/java/plugins/adufour/blocks/util/VarList.java
new file mode 100644
index 0000000..a484a3b
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/VarList.java
@@ -0,0 +1,334 @@
+package plugins.adufour.blocks.util;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.vars.lang.Var;
+import plugins.adufour.vars.lang.VarMutable;
+
+/**
+ * Class defining a map of variables using a {@link java.util.HashMap} dictionary
+ *
+ * @author Alexandre Dufour
+ */
+public class VarList implements Iterable<Var<?>>
+{
+ private final LinkedHashMap<String, Var<?>> varMap = new LinkedHashMap<String, Var<?>>();
+
+ private final HashMap<Var<?>, Boolean> visibilityMap = new HashMap<Var<?>, Boolean>();
+
+ private final HashMap<Var<?>, Boolean> runtimeVariableMap = new HashMap<Var<?>, Boolean>();
+
+ private final ArrayList<VarVisibilityListener> visibilityListeners = new ArrayList<VarVisibilityListener>();
+
+ private final ArrayList<VarListListener> varListListeners = new ArrayList<VarListListener>();
+
+ /**
+ * Adds the specified variable to this variable list. Each variable is given a unique
+ * identifier, which is here the variable's name. Adding another variable with the same name
+ * using this method will throw a {@link IllegalArgumentException}. Instead, use the
+ * {@link #add(String, Var)} method to specify a unique identifier for each variable.
+ *
+ * @param variable
+ * The variable to add
+ * @throws IllegalArgumentException
+ * if the variable already exists, or if a variable with same unique ID exists
+ * @deprecated Changing the name of a variable will also change the default UID, and protocols
+ * containing an older version of this block (with the old name) will not reload
+ * properly. Use {@link #add(String, Var)} to specify a unique identifier (and make
+ * sure this identifier never changes across versions!)<br>
+ * NB: for the same reason, when migrating to {@link #add(String, Var)}, use the
+ * current name of the variable as unique identifier
+ */
+ @Deprecated
+ public void add(Var<?> variable)
+ {
+ add(variable.getName(), variable);
+ }
+
+ /**
+ * Adds the given variable to this list with the specified unique ID. If a variable with same
+ * unique ID already exists, an {@link IllegalArgumentException} is thrown.
+ *
+ * @param uid
+ * the unique ID of the variable (within this list)
+ * @param variable
+ * The variable to add
+ * @throws IllegalArgumentException
+ * if the variable already exists, or if a variable with same unique ID exists
+ */
+ public void add(String uid, Var<?> variable)
+ {
+ add(uid, variable, false);
+ }
+
+ /**
+ * Add a runtime variable to this list (see {@link #isRuntimeVariable(Var)} for more details).
+ * Runtime variables are limited to {@link VarMutable} for reloading purposes. <br>
+ * WARNING: Do *not* add a runtime variable from within {@link Block#declareInput(VarList)} or
+ * {@link Block#declareOutput(VarList)} with no particular runtime condition.
+ *
+ * @param uid
+ * the unique ID of the variable (within this list)
+ * @param variable
+ * The variable to add
+ */
+ public void addRuntimeVariable(String uid, VarMutable variable)
+ {
+ add(uid, variable, true);
+ }
+
+ /**
+ * Adds the given variable to this list with the specified unique ID. Note that if a variable
+ * with same unique ID already exists, an {@link IllegalArgumentException} is thrown. <br/>
+ * <br/>
+ * WARNING: Do *not* mark a variable as dynamic if it is created and added from within
+ * {@link Block#declareInput(VarList)} or {@link Block#declareOutput(VarList)} with no
+ * particular runtime condition.
+ *
+ * @param uid
+ * the unique ID of the variable (within this list)
+ * @param variable
+ * The variable to add
+ * @param isRuntimeVariable
+ * <code>true</code> is the variable is dynamic (see {@link #isRuntimeVariable(Var)})
+ * for more details.
+ * @throws IllegalArgumentException
+ * if the variable already exists, or if a variable with same unique ID exists
+ */
+ private void add(String uid, Var<?> variable, boolean isRuntimeVariable)
+ {
+ if (varMap.containsKey(uid))
+ throw new IllegalArgumentException("A variable with same unique ID (" + uid + ") exists in the map");
+
+ varMap.put(uid, variable);
+
+ // By default, all block variables are visible
+ // However, variables from embedded blocks should not be visible
+ // (and should remain so until they are exposed by the user)
+ visibilityMap.put(variable, !uid.contains(":"));
+
+ runtimeVariableMap.put(variable, isRuntimeVariable);
+
+ for (VarListListener l : varListListeners)
+ l.variableAdded(this, variable);
+ }
+
+ /**
+ * Registers a new listener to receive events when a variable is added to this list
+ *
+ * @param listener
+ * Variable list listener to be added.
+ */
+ public void addVarListListener(VarListListener listener)
+ {
+ varListListeners.add(listener);
+ }
+
+ /**
+ * Registers a new listener to receive events when variables in this list change visibility
+ *
+ * @param listener
+ * Variable list listener to be added.
+ */
+ public void addVisibilityListener(VarVisibilityListener listener)
+ {
+ visibilityListeners.add(listener);
+ }
+
+ public void clear()
+ {
+ // remove elements one by one to notify listeners properly
+ ArrayList<Var<?>> vars = new ArrayList<Var<?>>(varMap.values());
+
+ for (Var<?> var : vars)
+ remove(var);
+
+ // FIXME this code does not remove links in the enclosing work flow...
+ }
+
+ public boolean contains(Var<?> variable)
+ {
+ return varMap.containsValue(variable);
+ }
+
+ /**
+ * @deprecated Legacy method (used to load old XML work flows).
+ * @param <T>
+ * Type of the variable value.
+ * @param varID
+ * Variable identifier.
+ * @return The stored variable.
+ * @throws NoSuchVariableException
+ * If no variable is not found with the given identifier
+ */
+ @Deprecated
+ @SuppressWarnings("unchecked")
+ public <T> Var<T> get(int varID) throws NoSuchVariableException
+ {
+ int id = 0;
+ for (Var<?> var : this)
+ {
+ if (id == varID)
+ return (Var<T>) var;
+ id++;
+ }
+ throw new NoSuchVariableException("No variable with ID " + varID);
+ }
+
+ /**
+ * Generic access method to retrieve a variable from the map. This method uses generic types to
+ * prevent unchecked conversion warning in higher-level code.
+ *
+ * @param <T>
+ * Type of the variable value.
+ * @param uid
+ * The unique ID of the variable to retrieve.
+ * @return The stored variable, or null if this name isn't in the map.
+ */
+ @SuppressWarnings("unchecked")
+ public <T> Var<T> get(String uid)
+ {
+ Var<?> var = varMap.get(uid);
+ return var == null ? null : (Var<T>) var;
+ }
+
+ /**
+ * Returns the unique ID of the specified variable. Although the underlying structure
+ *
+ * @param var
+ * Target variable
+ * @return Identifier of the given variable.
+ * @throws NoSuchVariableException
+ * If given variable is not present in this variable list.
+ */
+ public String getID(Var<?> var) throws NoSuchVariableException
+ {
+ for (String uid : varMap.keySet())
+ if (varMap.get(uid) == var)
+ return uid;
+
+ throw new NoSuchVariableException("Variable " + var.getName() + " does not exist in this list");
+ }
+
+ /**
+ * @deprecated Variable index should not be used to refer to a variable
+ * @param variable
+ * Target variable.
+ * @return The index of the list where the given variable is stored.
+ * @throws NoSuchVariableException
+ * If the variable is not found in this variable list.
+ */
+ @Deprecated
+ public int indexOf(Var<?> variable) throws NoSuchVariableException
+ {
+ // throw new UnsupportedOperationException("Cannot retrieve the index of a variable");
+ // return varMap.indexOf(variable);
+ int index = 0;
+ for (Var<?> var : this)
+ {
+ if (variable == var)
+ return index;
+ index++;
+ }
+ throw new NoSuchVariableException(variable.getName());
+ }
+
+ /**
+ * Indicates whether the specified variable is dynamic.<br>
+ * A variable is considered dynamic if it has been added to the list at "design-time" (e.g. via
+ * the graphical user interface) rather than at "compile-time" (i.e. via
+ * {@link Block#declareInput(VarList)} or {@link Block#declareOutput(VarList)}). <br>
+ * A dynamic variable is marked with an additional attribute when stored in XML, such that it
+ * can be restored properly (via {@link VarMutable} objects) when the variable is reloaded from
+ * XML.
+ *
+ * @param var
+ * Variable to be checked.
+ * @return true if the variable is of type runtime.
+ */
+ public boolean isRuntimeVariable(Var<?> var)
+ {
+ return runtimeVariableMap.get(var);
+ }
+
+ public boolean isVisible(Var<?> var)
+ {
+ return visibilityMap.get(var);
+ }
+
+ @Override
+ public Iterator<Var<?>> iterator()
+ {
+ return varMap.values().iterator();
+ }
+
+ public void remove(Var<?> var)
+ {
+ if (var.getReference() != null)
+ {
+ var.setReference(null);
+ return;
+ }
+
+ varMap.remove(getID(var));
+ visibilityMap.remove(var);
+ runtimeVariableMap.remove(var);
+
+ for (VarListListener l : varListListeners)
+ l.variableRemoved(this, var);
+ }
+
+ /**
+ * Registers a new listener to receive events when a variable is removed from this list.
+ *
+ * @param listener
+ * Listener to remove.
+ */
+ public void removeVarListListener(VarListListener listener)
+ {
+ varListListeners.remove(listener);
+ }
+
+ /**
+ * Registers a new listener to receive events when variables in this list change visibility.
+ *
+ * @param listener
+ * Listener to remove.
+ */
+ public void removeVisibilityListener(VarVisibilityListener listener)
+ {
+ visibilityListeners.remove(listener);
+ }
+
+ /**
+ * Adjusts the visibility of the given variable outside the enclosing work flow.
+ *
+ * @param var
+ * Variable to set visibility.
+ * @param visible
+ * true if the variable is to be visible. false otherwise.
+ */
+ public void setVisible(Var<?> var, boolean visible)
+ {
+ if (!visibilityMap.containsKey(var))
+ return;// throw new NoSuchVariableException(var);
+
+ if (visibilityMap.get(var) != visible)
+ {
+ visibilityMap.put(var, visible);
+
+ for (VarVisibilityListener l : visibilityListeners)
+ l.visibilityChanged(var, visible);
+ }
+ }
+
+ public int size()
+ {
+ return varMap.size();
+ }
+
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/VarListListener.java b/src/main/java/plugins/adufour/blocks/util/VarListListener.java
new file mode 100644
index 0000000..d9f1cdd
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/VarListListener.java
@@ -0,0 +1,10 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.vars.lang.Var;
+
+public interface VarListListener
+{
+ void variableAdded(VarList list, Var<?> variable);
+
+ void variableRemoved(VarList list, Var<?> variable);
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/VarVisibilityListener.java b/src/main/java/plugins/adufour/blocks/util/VarVisibilityListener.java
new file mode 100644
index 0000000..2df7f3a
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/VarVisibilityListener.java
@@ -0,0 +1,8 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.vars.lang.Var;
+
+public interface VarVisibilityListener
+{
+ void visibilityChanged(Var<?> source, boolean isVisible);
+}
diff --git a/src/main/java/plugins/adufour/blocks/util/WorkFlowListener.java b/src/main/java/plugins/adufour/blocks/util/WorkFlowListener.java
new file mode 100644
index 0000000..29f431f
--- /dev/null
+++ b/src/main/java/plugins/adufour/blocks/util/WorkFlowListener.java
@@ -0,0 +1,85 @@
+package plugins.adufour.blocks.util;
+
+import plugins.adufour.blocks.lang.BlockDescriptor;
+import plugins.adufour.blocks.lang.Link;
+import plugins.adufour.blocks.lang.WorkFlow;
+import plugins.adufour.blocks.lang.BlockDescriptor.BlockStatus;
+import plugins.adufour.vars.lang.Var;
+
+public interface WorkFlowListener
+{
+ static final String WORKFLOW_MODIFIED = "WORKFLOW_MODIFIED";
+
+ static final String WORKFLOW_REPLACED = "WORKFLOW_REPLACED";
+
+ /**
+ * Called when a block has been added to a work flow
+ *
+ * @param source
+ * The workflow on which the block has been added.
+ * @param addedBlock
+ * The block that has been added.
+ */
+ void blockAdded(WorkFlow source, BlockDescriptor addedBlock);
+
+ void blockCollapsed(WorkFlow source, BlockDescriptor block, boolean collapsed);
+
+ void blockDimensionChanged(WorkFlow source, BlockDescriptor block, int newWidth, int newHeight);
+
+ void blockLocationChanged(WorkFlow source, BlockDescriptor block, int newX, int newY);
+
+ void blockStatusChanged(WorkFlow source, BlockDescriptor block, BlockStatus status);
+
+ void blockVariableAdded(WorkFlow source, BlockDescriptor block, Var<?> variable);
+
+ <T> void blockVariableChanged(WorkFlow source, BlockDescriptor block, Var<T> variable, T newValue);
+
+ /**
+ * Called when a block has been removed from a work flow
+ *
+ * @param source
+ * The workflow on which the block has been removed.
+ * @param removedBlock
+ * The block that has been removed.
+ */
+ void blockRemoved(WorkFlow source, BlockDescriptor removedBlock);
+
+ /**
+ * Called when a link has been added to a work flow
+ *
+ * @param source
+ * The workflow to which the link has been added.
+ * @param addedLink
+ * The link that has been added to the workflow.
+ */
+ void linkAdded(WorkFlow source, Link<?> addedLink);
+
+ /**
+ * Called when a link has been removed from a work flow
+ *
+ * @param source
+ * The workflow to which the link has been removed.
+ * @param removedLink
+ * The link that has been added to the workflow.
+ */
+ void linkRemoved(WorkFlow source, Link<?> removedLink);
+
+ /**
+ * Called when the order of the blocks in the work flow has changed
+ *
+ * @param source
+ * The workflow that has been reordered.
+ */
+ void workFlowReordered(WorkFlow source);
+
+ /**
+ * Called when the work flow changes status (useful to display messages to the user via a status
+ * bar)
+ *
+ * @param source
+ * The workflow which its status has been changed.
+ * @param message
+ * The message describing the change.
+ */
+ void statusChanged(WorkFlow source, String message);
+}
diff --git a/src/main/java/plugins/adufour/protocols/Protocols.java b/src/main/java/plugins/adufour/protocols/Protocols.java
index 202cd32..056e59a 100644
--- a/src/main/java/plugins/adufour/protocols/Protocols.java
+++ b/src/main/java/plugins/adufour/protocols/Protocols.java
@@ -20,6 +20,7 @@ import org.w3c.dom.Document;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
+import icy.common.Version;
import icy.file.FileUtil;
import icy.main.Icy;
import icy.plugin.PluginLoader;
@@ -93,14 +94,14 @@ public class Protocols extends PluginActionable
}
/**
- * Saves the current state of the Protocols interface and restarts it.
- * <p>
- * This method is useful when plug-ins have been modified (via the plug-in
- * loader) and requires Protocols to restart to take into account the new
- * changes
- *
- * @throws TransformerFactoryConfigurationError
- */
+ * Saves the current state of the Protocols interface and restarts it.
+ * <p>
+ * This method is useful when plug-ins have been modified (via the plug-in
+ * loader) and requires Protocols to restart to take into account the new
+ * changes
+ *
+ * @throws TransformerFactoryConfigurationError
+ */
public void reload(final Document reloadingXML, final String reloadingPath)
{
// 0) avoid silly situations...
@@ -154,7 +155,7 @@ public class Protocols extends PluginActionable
ThreadUtil.invokeLater(new Runnable()
{
@Override
- public void run()
+ public void run()
{
// 3) launch a new instance of the Protocols plug-in
try
@@ -388,4 +389,11 @@ public class Protocols extends PluginActionable
if (mainFrame != null)
mainFrame.getContentPane().dispatchEvent(key);
}
+
+ public String getFriendlyVersion()
+ {
+ Version v = getDescriptor().getVersion();
+ return "Blocks engine v." + v.getMajor() + "." + v.getMinor();
+ }
+
}
diff --git a/src/main/java/plugins/adufour/protocols/gui/MainFrame.java b/src/main/java/plugins/adufour/protocols/gui/MainFrame.java
index ffff065..2049c11 100644
--- a/src/main/java/plugins/adufour/protocols/gui/MainFrame.java
+++ b/src/main/java/plugins/adufour/protocols/gui/MainFrame.java
@@ -53,7 +53,6 @@ import icy.system.IcyExceptionHandler;
import icy.system.IcyHandledException;
import icy.system.thread.ThreadUtil;
import icy.util.XMLUtil;
-import plugins.adufour.blocks.Blocks;
import plugins.adufour.blocks.lang.Block;
import plugins.adufour.blocks.lang.BlockDescriptor;
import plugins.adufour.blocks.lang.BlockDescriptor.BlockStatus;
@@ -107,7 +106,7 @@ public class MainFrame extends IcyFrame implements IcyFrameListener, ActionListe
public MainFrame(Protocols pluginInstance)
{
- super("Protocols editor (" + new Blocks().getFriendlyVersion() + ")", true, true, true, true, true);
+ super("Protocols editor (" + pluginInstance.getFriendlyVersion() + ")", true, true, true, true, true);
this.pluginInstance = pluginInstance;
diff --git a/src/main/resources/logo/icysoftware_icon-protocols-sdk.png b/src/main/resources/logo/icysoftware_icon-protocols-sdk.png
new file mode 100644
index 0000000000000000000000000000000000000000..21eb08f98fbf3e02dd68e1c96e5f2e435a1ecaaa
GIT binary patch
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literal 0
HcmV?d00001
--
GitLab