Skip to content

GitLab

Commit c21fde40 authored by Stephane Dallongeville's avatar Stephane Dallongeville
Browse files

removed ols sources files

parent d50a75b6
Hide whitespace changes
Inline Side-by-side
src/plugins/stef/roi/bloc/op/FilterROI.java deleted 100644 → 0
View file @ d50a75b6
/**
*
*/
package plugins.stef.roi.bloc.op;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import icy.roi.ROI;
import icy.roi.ROIDescriptor;
import icy.sequence.Sequence;
import icy.system.IcyExceptionHandler;
import icy.type.collection.CollectionUtil;
import icy.util.StringUtil;
import icy.util.StringUtil.AlphanumComparator;
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.gui.model.ValueSelectionModel;
import plugins.adufour.vars.lang.VarEnum;
import plugins.adufour.vars.lang.VarROIArray;
import plugins.adufour.vars.lang.VarSequence;
import plugins.adufour.vars.lang.VarString;
import plugins.adufour.vars.util.VarException;
import plugins.kernel.roi.descriptor.measure.ROIInteriorDescriptor;
import plugins.kernel.roi.descriptor.property.ROIColorDescriptor;
import plugins.stef.roi.bloc.RoiBlocks;
/**
* Block to filter a set of ROIs using a specific descriptor.
*
* @author Stephane
*/
public class FilterROI extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
{
public static enum CompareOperator
{
EQUAL
{
@Override
public String toString()
{
return "Equal to";
}
},
NOT_EQUAL
{
@Override
public String toString()
{
return "Not equal to";
}
},
LOWER
{
@Override
public String toString()
{
return "Lower than";
}
},
LOWER_OR_EQUAL
{
@Override
public String toString()
{
return "Lower or equal than";
}
},
GREATER
{
@Override
public String toString()
{
return "Greater than";
}
},
GREATER_OR_EQUAL
{
@Override
public String toString()
{
return "Greater or equal than";
}
}
}
private static final AlphanumComparator comp = new AlphanumComparator();
protected final VarROIArray roiSet = new VarROIArray("ROI(s)", null);
protected final VarSequence sequence = new VarSequence("Sequence", null);
protected final VarString descriptors = new VarString("Filter on", "");
protected final VarEnum<CompareOperator> operator = new VarEnum<CompareOperator>("Accept if",
CompareOperator.EQUAL);
protected final VarString value = new VarString("Value", "0.0");
// protected final VarDouble value = new VarDouble("Value", 0d);
protected final VarROIArray output = new VarROIArray("Filtered ROI(s)");
@Override
public void run()
{
try
{
final List<ROI> result = filterROIs(CollectionUtil.asList(roiSet.getValue()), sequence.getValue(),
descriptors.getValue(), operator.getValue(), value.getValue());
output.setValue(result.toArray(new ROI[result.size()]));
}
catch (IllegalArgumentException e)
{
throw new VarException(descriptors, e.getMessage());
}
}
@Override
public void declareInput(VarList inputMap)
{
final List<ROIDescriptor> roiDescriptors = new ArrayList<ROIDescriptor>(
ROIDescriptor.getDescriptors().keySet());
// build list of descriptor id
final List<String> descriptorsId = new ArrayList<String>();
String sizeDescriptorId = null;
for (ROIDescriptor descriptor : roiDescriptors)
{
final String id = descriptor.getId();
// keep trace of size descriptor
if (StringUtil.equals(ROIInteriorDescriptor.ID, id))
sizeDescriptorId = id;
descriptorsId.add(id);
}
// alpha sort
Collections.sort(descriptorsId);
// initialize descriptors field
descriptors.setDefaultEditorModel(new ValueSelectionModel<String>(
descriptorsId.toArray(new String[descriptorsId.size()]), sizeDescriptorId, false));
inputMap.add("roi", roiSet);
inputMap.add("sequence", sequence);
inputMap.add("descriptors", descriptors);
inputMap.add("operator", operator);
inputMap.add("value", value);
}
@Override
public void declareOutput(VarList outputMap)
{
outputMap.add("out", output);
}
@Override
public String getMainPluginClassName()
{
return RoiBlocks.class.getName();
}
private static Object getTypedValue(String value)
{
try
{
return Double.valueOf(Double.parseDouble(value.replace(',', '.')));
}
catch (NumberFormatException e1)
{
try
{
return Double.valueOf(Float.parseFloat(value.replace('.', ',')));
}
catch (NumberFormatException e2)
{
try
{
return Long.valueOf(Long.parseLong(value));
}
catch (NumberFormatException e4)
{
// probably not a number then...
}
}
}
// ok so this is probably just a String
return value;
}
private static String colorToString(Color color)
{
return StringUtil.toHexaString(color.getAlpha(), 2) + StringUtil.toHexaString(color.getRed(), 2)
+ StringUtil.toHexaString(color.getGreen(), 2) + StringUtil.toHexaString(color.getBlue(), 2);
}
private static boolean compareNumber(CompareOperator op, double value1, double value2)
{
// compute comparison
final int compResult = Double.compare(value1, value2);
switch (op)
{
default:
case EQUAL:
return compResult == 0;
case NOT_EQUAL:
return compResult != 0;
case LOWER:
return compResult < 0;
case LOWER_OR_EQUAL:
return compResult <= 0;
case GREATER:
return compResult > 0;
case GREATER_OR_EQUAL:
return compResult >= 0;
}
}
private static boolean compareString(CompareOperator op, String value1, String value2, String value2Regex)
{
switch (op)
{
default:
case EQUAL:
return value1.matches(value2Regex);
case NOT_EQUAL:
return !value1.matches(value2Regex);
case LOWER:
return comp.compare(value1, value2) < 0;
case LOWER_OR_EQUAL:
return comp.compare(value1, value2) <= 0;
case GREATER:
return comp.compare(value1, value2) > 0;
case GREATER_OR_EQUAL:
return comp.compare(value1, value2) >= 0;
}
}
/**
* Filter a set of ROIs using a specific descriptor and the compare operation (keep ROIS where result of comparison is true).
*
* @param rois
* input ROIS to filter
* @param sequence
* input sequence used for ROI descriptor computation (can be null if not required)
* @param descriptorId
* the {@link ROIDescriptor} id to use for filtering
* @param op
* Compare operation to use
* @param value
* the value for the comparison (can be a Number or just a String)
* @return filtered list of ROIS
* @throws IllegalArgumentException
* if given ROI descriptor id is not found
*/
public static List<ROI> filterROIs(Collection<ROI> rois, Sequence sequence, String descriptorId, CompareOperator op,
String value) throws IllegalArgumentException
{
final List<ROI> result = new ArrayList<ROI>();
final ROIDescriptor roiDescriptor = ROIDescriptor.getDescriptor(ROIDescriptor.getDescriptors().keySet(),
descriptorId);
if (roiDescriptor == null)
throw new IllegalArgumentException("Cannot found '" + descriptorId + "' ROI descriptor !");
// try to get the type behind
final Object typedValue = getTypedValue(value);
// get regex from String
final String regexValue;
if (roiDescriptor instanceof ROIColorDescriptor)
{
regexValue = StringUtil.wildcardToRegex(value.toLowerCase());
value = value.toLowerCase();
}
else
{
regexValue = StringUtil.wildcardToRegex(value);
}
// number comparison
if (typedValue instanceof Number)
{
final double doubleValue = ((Number) typedValue).doubleValue();
for (ROI roi : rois)
{
if (roi != null)
{
try
{
final Object res = roiDescriptor.compute(roi, sequence);
final boolean accepted;
// get double value if possible
if (res instanceof Number)
accepted = compareNumber(op, ((Number) res).doubleValue(), doubleValue);
else if (res instanceof Color)
accepted = compareNumber(op, ((Color) res).getRGB(), doubleValue);
// can't filter --> show error message
else if (res instanceof String)
accepted = compareString(op, (String) res, value, regexValue);
else if (res != null)
accepted = compareString(op, res.toString(), value, regexValue);
else
// don't accept when result is null
accepted = false;
// throw new VarException(null,
// "Descriptor result is null, can't apply filtering criterion !");
if (accepted)
result.add(roi);
}
catch (VarException e1)
{
throw e1;
}
catch (Exception e2)
{
IcyExceptionHandler.showErrorMessage(e2, false, true);
// if we can't compute the descriptor we accept the ROI by default...
result.add(roi);
}
}
}
}
else if (typedValue instanceof String)
{
for (ROI roi : rois)
{
if (roi != null)
{
try
{
final Object res = roiDescriptor.compute(roi, sequence);
final String stringRes;
// not really safe to compare number with a String here
if (res instanceof Number)
throw new VarException(null,
"Can't apply filtering criterion, you need to provide a valid number in 'Value' field.");
// stringRes = ((Number) res).toString();
else if (res instanceof String)
stringRes = (String) res;
else if (res instanceof Color)
stringRes = colorToString((Color) res).toLowerCase();
else if (res != null)
stringRes = res.toString();
else
stringRes = "";
if (compareString(op, stringRes, value, regexValue))
result.add(roi);
}
catch (VarException e1)
{
throw e1;
}
catch (Exception e2)
{
IcyExceptionHandler.showErrorMessage(e2, false, true);
// if we can't compute the descriptor we accept the ROI by default...
result.add(roi);
}
}
}
}
return result;
}
/**
* Filter a set of ROIs using a specific descriptor and the compare operation (keep ROIS where result of comparison is true).
*
* @param rois
* input ROIS to filter
* @param sequence
* input sequence used for ROI descriptor computation (can be null if not required)
* @param descriptorId
* the {@link ROIDescriptor} id to use for filtering
* @param op
* Compare operation to use
* @param value
* the value for the comparison
* @return filtered list of ROIS
* @throws IllegalArgumentException
* if given ROI descriptor id is not found
*/
public static List<ROI> filterROIs(Collection<ROI> rois, Sequence sequence, String descriptorId, CompareOperator op,
double value) throws IllegalArgumentException
{
return filterROIs(rois, sequence, descriptorId, op, Double.toString(value));
}
}
\ No newline at end of file
src/plugins/stef/roi/bloc/property/GetROIPosition.java deleted 100644 → 0
View file @ d50a75b6
package plugins.stef.roi.bloc.property;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import icy.roi.ROI;
import icy.type.rectangle.Rectangle5D;
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarDouble;
import plugins.adufour.vars.lang.VarROIArray;
import plugins.stef.roi.bloc.RoiBlocks;
/**
* Block to get the position of a ROI
*
* @author Stephane
*/
public class GetROIPosition extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
{
// we use ROI array for convenience here but only the first ROI is considered
protected VarROIArray roiSet = new VarROIArray("ROI", null);
protected VarDouble posX = new VarDouble("position X", 0d);
protected VarDouble posY = new VarDouble("position Y", 0d);
protected VarDouble posZ = new VarDouble("position Z", 0d);
protected VarDouble posT = new VarDouble("position T", 0d);
protected VarDouble posC = new VarDouble("position C", 0d);
protected VarDouble posXCenter = new VarDouble("position X(center)", 0d);
protected VarDouble posYCenter = new VarDouble("position Y(center)", 0d);
protected VarDouble posZCenter = new VarDouble("position Z(center)", 0d);
@Override
public void run()
{
for (ROI roi : roiSet)
{
if (roi != null)
{
final Rectangle5D bounds = roi.getBounds5D();
posX.setValue(Double.valueOf(bounds.getX()));
posY.setValue(Double.valueOf(bounds.getY()));
posZ.setValue(Double.valueOf(bounds.getZ()));
posT.setValue(Double.valueOf(bounds.getT()));
posC.setValue(Double.valueOf(bounds.getC()));
posXCenter.setValue(Double.valueOf(bounds.getCenterX()));
posYCenter.setValue(Double.valueOf(bounds.getCenterY()));
posZCenter.setValue(Double.valueOf(bounds.getCenterZ()));
// stop here
break;
}
}
}
@Override
public void declareInput(VarList inputMap)
{
inputMap.add("roi", roiSet);
}
@Override
public void declareOutput(VarList outputMap)
{
outputMap.add("posX", posX);
outputMap.add("posY", posY);
outputMap.add("posZ", posZ);
outputMap.add("posT", posT);
outputMap.add("posC", posC);
outputMap.add("posXCenter", posXCenter);
outputMap.add("posYCenter", posYCenter);
outputMap.add("posZCenter", posZCenter);
}
@Override
public String getMainPluginClassName()
{
return RoiBlocks.class.getName();
}
}
\ No newline at end of file
src/plugins/stef/roi/bloc/property/SetROIPosition.java deleted 100644 → 0
View file @ d50a75b6
/**
*
*/
package plugins.stef.roi.bloc.property;
import icy.plugin.abstract_.Plugin;
import icy.plugin.interface_.PluginBundled;
import icy.plugin.interface_.PluginLibrary;
import icy.roi.ROI;
import icy.type.point.Point5D;
import icy.type.point.Point5D.Double;
import icy.type.rectangle.Rectangle5D;
import plugins.adufour.blocks.tools.roi.ROIBlock;
import plugins.adufour.blocks.util.VarList;
import plugins.adufour.vars.lang.VarBoolean;
import plugins.adufour.vars.lang.VarDouble;
import plugins.adufour.vars.lang.VarROIArray;
import plugins.stef.roi.bloc.RoiBlocks;
/**
* Block to set the position of a ROI set
*
* @author Stephane
*/
public class SetROIPosition extends Plugin implements ROIBlock, PluginLibrary, PluginBundled
{
protected VarROIArray roiSet = new VarROIArray("ROI(s)", null);
protected VarDouble posX = new VarDouble("position X", 0d);
protected VarDouble posY = new VarDouble("position Y", 0d);
protected VarDouble posZ = new VarDouble("position Z", -1d);
protected VarDouble posT = new VarDouble("position T", -1d);
protected VarDouble posC = new VarDouble("position C", -1d);
protected VarBoolean useCenter = new VarBoolean("Set XYZ Center", false);
@Override
public void run()
{
final Point5D.Double pos = new Point5D.Double(posX.getValue().doubleValue(), posY.getValue().doubleValue(),
posZ.getValue().doubleValue(), posT.getValue().doubleValue(), posC.getValue().doubleValue());
for (ROI roi : roiSet)
{
if ((roi != null) && roi.canSetPosition())
{
if (useCenter.getValue())
{
Rectangle5D bounds = roi.getBounds5D();
Point5D.Double newPos = (Double) pos.clone();
newPos.setX(pos.getX() - bounds.getSizeX() / 2);
newPos.setY(pos.getY() - bounds.getSizeY() / 2);
newPos.setZ(pos.getZ() - bounds.getSizeZ() / 2);
roi.setPosition5D(newPos);
}
else
{
roi.setPosition5D(pos);
}
}
}
}
@Override
public void declareInput(VarList inputMap)
{
inputMap.add("rois", roiSet);
inputMap.add("posX", posX);
inputMap.add("posY", posY);
inputMap.add("posZ", posZ);
inputMap.add("posT", posT);
inputMap.add("posC", posC);
inputMap.add("useXYZCenter", useCenter);
}
@Override
public void declareOutput(VarList outputMap)
{
//
}
@Override
public String getMainPluginClassName()
{
return RoiBlocks.class.getName();
}
}
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment