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Commit ab714727 authored by danyfel80's avatar danyfel80
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added new code

parent f9f0737c
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WellPlateReader/src/main/java/plugins/adufour/hcs/WellPlateImporter.java
View file @ ab714727
......@@ -21,6 +21,7 @@ import plugins.adufour.hcs.data.WellPlate;
import plugins.adufour.hcs.gui.WellPlateViewer;
import plugins.adufour.hcs.io.WellPlateReader;
import plugins.adufour.hcs.io.WellPlateReader_Opera;
import plugins.adufour.hcs.io.WellPlateReader_OperaColumbusNew;
public class WellPlateImporter extends PluginActionable {
private static final Set<WellPlateReader> availableReaders = new HashSet<WellPlateReader>();
......@@ -36,6 +37,7 @@ public class WellPlateImporter extends PluginActionable {
if (importers.isEmpty()) {
// Probably debugging within Eclipse => add one (known) entry manually
importers.add((Class<WellPlateReader>) WellPlateReader_Opera.class.asSubclass(WellPlateReader.class));
importers.add((Class<WellPlateReader>) WellPlateReader_OperaColumbusNew.class.asSubclass(WellPlateReader.class));
}
// Add available file filters
......@@ -83,7 +85,8 @@ public class WellPlateImporter extends PluginActionable {
try {
File selection = jfc.getSelectedFile();
CancelableProgressFrame loadingProgress = new CancelableProgressFrame("Loading plate " + selection.getName());
CancelableProgressFrame loadingProgress = new CancelableProgressFrame(
"Loading plate " + selection.getName());
getPreferencesRoot().put("lastUsedDirectory", selection.getPath());
......@@ -106,8 +109,7 @@ public class WellPlateImporter extends PluginActionable {
}
/**
* @param path
* Path to check.
* @param path Path to check.
* @return <code>true</code> if at least one reader accepts the given file
*/
public static boolean isValid(File path) {
......@@ -121,11 +123,9 @@ public class WellPlateImporter extends PluginActionable {
}
/**
* Looks for an appropriate readed of the files contained in the provided
* path.
* Looks for an appropriate readed of the files contained in the provided path.
*
* @param file
* Path of the folder containing the files to read.
* @param file Path of the folder containing the files to read.
* @return The appropriate reader for the files.
*/
public static WellPlateReader getReaderFor(File file) {
......
WellPlateReader/src/main/java/plugins/adufour/hcs/data/IChannel.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.awt.Color;
public interface IChannel {
long getId();
String getName();
Color getColor();
double getExcitationWavelength();
double getEmissionWavelength();
IImage getImage();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/IField.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.awt.geom.Point2D;
import java.util.Map;
public interface IField {
long getId();
Point2D getPosition();
Map<Long, ? extends IPlane> getPlanes();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/IImage.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.awt.Color;
import java.util.Date;
public interface IImage {
public String getVersion();
public String getId();
public String getState();
public long getBufferNumber();
public String getUrl();
public long getRow();
public long getColumn();
public long getFieldId();
public long getPlaneId();
public long getTimepointId();
public long getChannelId();
public Color getChannelColor();
public String getChannelType();
public String getAcquisitionType();
public double getResolutionX();
public double getResolutionY();
public long getSizeX();
public long getSizeY();
public double getPositionX();
public double getPositionY();
public double getAbsPositionZ();
public double getPositionZ();
public double getTime();
public Date getDate();
public double getExcitationWavelength();
public double getEmissionWavelength();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/IPlane.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.util.Map;
public interface IPlane {
long getId();
double getPositionZ();
public Map<Long, ? extends ITimepoint> getTimepoints();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/IPlate.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.awt.Dimension;
import java.util.Map;
public interface IPlate {
String getId();
String getName();
String getType();
Dimension getDimension();
Map<Long, ? extends IWell> getWells();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/ITimepoint.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.util.Map;
public interface ITimepoint {
long getId();
public Map<Long, ? extends IChannel> getChannels();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/IWell.java 0 → 100644
View file @ ab714727
package plugins.adufour.hcs.data;
import java.awt.Point;
import java.util.Map;
public interface IWell {
long getId();
Point getPositionInPlate();
Map<Long, ? extends IField> getFields();
}
WellPlateReader/src/main/java/plugins/adufour/hcs/data/Well.java
View file @ ab714727
......@@ -8,25 +8,57 @@ import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.Map;
import icy.type.dimension.Dimension2D;
import icy.util.StringUtil;
public class Well {
public enum Shape {
Circle(new Ellipse2D.Double()),
Square(new Rectangle2D.Double()),
Rectangle(new Rectangle2D.Double());
public static class Shape {
public static Shape newCircle() {
return new Shape(new Ellipse2D.Double(0, 0, 1, 1));
}
public static Shape newSquare() {
return new Shape(new Rectangle2D.Double(0, 0, 1, 1));
}
public static Shape newRectangle() {
return new Shape(new Rectangle2D.Double(0, 0, 2, 1));
}
public final RectangularShape wellShape;
private Shape(RectangularShape shape) {
this.wellShape = shape;
// Assign default values in case none are available
shape.setFrame(0, 0, 5000, 5000);
}
public void setDimension(double width, double height) {
wellShape.setFrame(0, 0, width, height);
}
public RectangularShape getShape() {
return wellShape;
}
public Dimension2D getDimension() {
return new Dimension2D.Double(wellShape.getWidth(), wellShape.getHeight());
}
public static Shape valueOf(String shape) {
Shape s;
switch (shape.toLowerCase()) {
case "circle":
s = newCircle();
break;
case "square":
s = newSquare();
break;
default: // rectangle
s = newRectangle();
break;
}
return s;
}
}
/**
......
WellPlateReader/src/main/java/plugins/adufour/hcs/data/WellPlate.java
View file @ ab714727
......@@ -5,207 +5,208 @@ import java.util.Iterator;
import org.xml.sax.SAXException;
import com.drew.imaging.tiff.TiffProcessingException;
import icy.sequence.Sequence;
import ome.xml.meta.OMEXMLMetadata;
import plugins.adufour.hcs.io.WellPlateReader;
public class WellPlate
{
private final WellPlateReader wellPlateReader;
private final OMEXMLMetadata metadata;
private final Sequence sequence;
/**
* Linearized 2D array containing all wells
*/
private final Well[] wells;
/**
* @param reader
* the reader that creates this well plate (will be used to load individual fields)
* @param metadata
* the well plate metadata containing the plate layout
* @param shape
* the shape of the wells in this plate
*/
public WellPlate(WellPlateReader reader, OMEXMLMetadata metadata, Well.Shape shape)
{
this.wellPlateReader = reader;
this.metadata = metadata;
this.sequence = new Sequence(metadata);
// Initialize the wells (even if they contain no image)
int nbRows = getNbRows();
int nbCols = getNbCols();
wells = new Well[nbRows * nbCols];
for (int row = 0; row < nbRows; row++)
for (int col = 0; col < nbCols; col++)
wells[row * nbCols + col] = new Well(shape, row, col);
}
/**
* @return The number of rows in this well plate
*/
public int getNbRows()
{
return metadata.getPlateRows(0).getValue();
}
/**
* @return The number of columns in this well plate
*/
public int getNbCols()
{
return metadata.getPlateColumns(0).getValue();
}
public Well getWellAt(int row, int col)
{
return wells[row * getNbCols() + col];
}
public OMEXMLMetadata getMetaData()
{
return metadata;
}
@Override
public String toString()
{
String plateID = metadata.getPlateID(0);
String plateType = metadata.getPlateName(0);
return plateID + " (" + plateType + ")";
}
public Sequence loadField(Field field) throws IOException, SAXException, TiffProcessingException
{
wellPlateReader.loadField(field, sequence);
if (field != null) sequence.setName(field.getWell().getAlphanumericID());
return sequence;
}
/**
* @return A well iterator that automatically skips empty wells
*/
public Iterator<Well> wellIterator()
{
return wellIterator(null);
}
/**
* @return A well iterator that automatically skips empty wells
* @param filters
* one or more templates (separated by spaces) used to select only a subset of wells,
* e.g.:
* <ul>
* <li><code>"A"</code> will select all wells in row A</li>
* <li><code>"A 03 B12"</code> will select all wells in row A, column 03, and well
* B12</li>
* <li>etc.</li>
* </ul>
*/
public Iterator<Well> wellIterator(final String filters)
{
return new Iterator<Well>()
{
int currentWellIndex = -1;
int nextWellIndex = 0;
Well nextWell = null;
@Override
public Well next()
{
currentWellIndex = nextWellIndex;
return nextWell;
}
@Override
public boolean hasNext()
{
for (int newWell = currentWellIndex + 1; newWell < wells.length; newWell++)
{
Well candidateWell = wells[newWell];
if (candidateWell.isEmpty()) continue;
// the well is automatically valid if there are no filters
boolean isValidWell = (filters == null);
if (filters != null)
{
for (String filter : filters.split("\\s+"))
if (candidateWell.getAlphanumericID().contains(filter))
{
isValidWell = true;
break;
}
}
if (isValidWell)
{
nextWell = wells[newWell];
nextWellIndex = newWell;
return true;
}
}
return false;
}
};
}
/**
* @return A field iterator that automatically skips empty wells
*/
public Iterator<Field> fieldIterator()
{
return fieldIterator(null);
}
/**
* @return A field iterator that automatically skips empty wells
* @param templates
* one or more templates (separated by spaces) used to select only a subset of wells,
* e.g.:
* <ul>
* <li><code>"A"</code> will select all wells in row A</li>
* <li><code>"A 03 B12"</code> will select all wells in row A, column 03, and well
* B12</li>
* <li>etc.</li>
* </ul>
*/
public Iterator<Field> fieldIterator(final String templates)
{
return new Iterator<Field>()
{
Iterator<Well> wellIterator = wellIterator(templates);
Iterator<Field> currentFieldIterator = null;
@Override
public Field next()
{
return currentFieldIterator.next();
}
@Override
public boolean hasNext()
{
// Are there more fields remaining?
if (currentFieldIterator != null && currentFieldIterator.hasNext()) return true;
// If not, a new well perhaps?
if (wellIterator.hasNext())
{
currentFieldIterator = wellIterator.next().fieldIterator();
return currentFieldIterator.hasNext();
}
return false;
}
};
}
public class WellPlate {
private final WellPlateReader wellPlateReader;
private final OMEXMLMetadata metadata;
private final Sequence sequence;
/**
* Linearized 2D array containing all wells
*/
private final Well[] wells;
/**
* @param reader the reader that creates this well plate (will be used to load
* individual fields)
* @param metadata the well plate metadata containing the plate layout
* @param shape the shape of the wells in this plate
*/
public WellPlate(WellPlateReader reader, OMEXMLMetadata metadata, Well.Shape shape) {
this.wellPlateReader = reader;
this.metadata = metadata;
this.sequence = new Sequence(metadata);
// Initialize the wells (even if they contain no image)
int nbRows = getNbRows();
int nbCols = getNbCols();
wells = new Well[nbRows * nbCols];
for (int row = 0; row < nbRows; row++)
for (int col = 0; col < nbCols; col++)
wells[row * nbCols + col] = new Well(shape, row, col);
}
/**
* Builds a well plate considering the metadata and the array of wells (already
* prepared before calling this constructor).
*
* @param reader the reader that creates this well plate (will be used to load
* @param metadata the well plate metadata containing the plate layout
* @param wells The wells contained in the plate. Make sure to use the same
* size as in the metadata.
* @throws IllegalArgumentException If the size of the wells array is not
* equivalent to the size specified in the
* metadata.
*/
public WellPlate(WellPlateReader reader, OMEXMLMetadata metadata, Well[] wells) {
this.wellPlateReader = reader;
this.metadata = metadata;
this.sequence = new Sequence(metadata);
// Initialize the wells with parameter
int nbRows = getNbRows();
int nbCols = getNbCols();
if (nbRows * nbCols == wells.length)
this.wells = wells;
else
throw new IllegalArgumentException("The size of the wells array (" + wells.length
+ ") is not compatible with the metadata (" + nbRows + ", " + nbCols + ")");
}
/**
* @return The number of rows in this well plate
*/
public int getNbRows() {
return metadata.getPlateRows(0).getValue();
}
/**
* @return The number of columns in this well plate
*/
public int getNbCols() {
return metadata.getPlateColumns(0).getValue();
}
public Well getWellAt(int row, int col) {
return wells[row * getNbCols() + col];
}
public OMEXMLMetadata getMetaData() {
return metadata;
}
@Override
public String toString() {
String plateID = metadata.getPlateID(0);
String plateType = metadata.getPlateName(0);
return plateID + " (" + plateType + ")";
}
public Sequence loadField(Field field) throws IOException, SAXException {
wellPlateReader.loadField(field, sequence);
if (field != null)
sequence.setName(field.getWell().getAlphanumericID());
return sequence;
}
/**
* @return A well iterator that automatically skips empty wells
*/
public Iterator<Well> wellIterator() {
return wellIterator(null);
}
/**
* @return A well iterator that automatically skips empty wells
* @param filters one or more templates (separated by spaces) used to select
* only a subset of wells, e.g.:
* <ul>
* <li><code>"A"</code> will select all wells in row A</li>
* <li><code>"A 03 B12"</code> will select all wells in row A,
* column 03, and well B12</li>
* <li>etc.</li>
* </ul>
*/
public Iterator<Well> wellIterator(final String filters) {
return new Iterator<Well>() {
int currentWellIndex = -1;
int nextWellIndex = 0;
Well nextWell = null;
@Override
public Well next() {
currentWellIndex = nextWellIndex;