imagej/ch.psi.imagej.hdf5
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added support for reading only every x-th image

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This commit is contained in:
ebner 2015-04-14 11:02:25 +02:00
parent 93885470e4
commit 4aec3a2858
3 changed files with 41 additions and 12 deletions
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8
src/main/java/ch/psi/imagej/hdf5/DatasetSelection.java
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@ -10,6 +10,8 @@ public class DatasetSelection {
private List<Dataset> datasets = new ArrayList<Dataset>(); private List<Dataset> datasets = new ArrayList<Dataset>();
private boolean group = false; private boolean group = false;
private Integer slice; private Integer slice;
// Intervall to read images
private Integer modulo;
public List<Dataset> getDatasets() { public List<Dataset> getDatasets() {
return datasets; return datasets;
@ -29,4 +31,10 @@ public class DatasetSelection {
public Integer getSlice() { public Integer getSlice() {
return slice; return slice;
} }
public void setModulo(Integer modulo) {
this.modulo = modulo;
}
public Integer getModulo() {
return modulo;
}
} }

35
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -10,20 +10,9 @@ import ij.plugin.PlugIn;
import java.io.File; import java.io.File;
import java.lang.reflect.Array; import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.logging.Level; import java.util.logging.Level;
import java.util.logging.Logger; import java.util.logging.Logger;
import java.awt.*;
import javax.swing.BoxLayout;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.ScrollPaneConstants;
import ncsa.hdf.object.*; import ncsa.hdf.object.*;
import ncsa.hdf.object.h5.*; import ncsa.hdf.object.h5.*;
@ -238,6 +227,29 @@ public class HDF5Reader implements PlugIn {
// int startIdx = selectedDatasets.getSlice() * size; // int startIdx = selectedDatasets.getSlice() * size;
addSlice(stack, wholeDataset, 0, size); addSlice(stack, wholeDataset, 0, size);
} }
else if(selectedDatasets.getModulo()!=null){
logger.info("Read every "+selectedDatasets.getModulo()+" image");
// Select what to readout
stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
for(int indexToRead=0;indexToRead<dimensions[0]; indexToRead=indexToRead+selectedDatasets.getModulo()){
long[] selected = var.getSelectedDims();
selected[0] = 1;
selected[1] = dimensions[1];
selected[2] = dimensions[2];
long[] start = var.getStartDims();
start[0] = indexToRead;
Object wholeDataset = var.read();
int size = (int) (dimensions[1] * dimensions[2]);
// int startIdx = selectedDatasets.getSlice() * size;
addSlice(stack, wholeDataset, 0, size);
}
}
else{ else{
// Select what to readout // Select what to readout
long[] selected = var.getSelectedDims(); long[] selected = var.getSelectedDims();
@ -322,6 +334,7 @@ public class HDF5Reader implements PlugIn {
selectedDatasets.setDatasets(panel.getSelectedValues()); selectedDatasets.setDatasets(panel.getSelectedValues());
selectedDatasets.setGroup(panel.groupValues()); selectedDatasets.setGroup(panel.groupValues());
selectedDatasets.setSlice(panel.getSlice()); selectedDatasets.setSlice(panel.getSlice());
selectedDatasets.setModulo(panel.getModulo());
} }
return selectedDatasets; return selectedDatasets;

10
src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java
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@ -89,9 +89,17 @@ public class SelectionPanel extends JPanel {
public Integer getSlice(){ public Integer getSlice(){
String text = textField.getText(); String text = textField.getText();
if(text.matches("[0-9]+")){ if(text.matches("^[0-9]+$")){
return new Integer(text); return new Integer(text);
} }
return null; return null;
} }
public Integer getModulo(){
String text = textField.getText();
if(text.matches("^%[0-9]+$")){
return new Integer(text.replace("%", ""));
}
return null;
}
} }