imagej/ch.psi.imagej.hdf5
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Merge pull request #1 in IM/ch.psi.imagej.hdf5 from slice_selection to master

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# By ebner
# Via ebner
* commit 'dfa00c8dc45a6dec5f6255bf4074f930a0a5589a':
  updated readme
  added support for reading only every x-th image
  Added support for slice / tested
  externalized Panel for dialog
  added gradle build file
This commit is contained in:
ebner 2015-04-14 11:08:53 +02:00
commit 2464a795d1
10 changed files with 483 additions and 58 deletions
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2
.gitignore vendored
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@ -1 +1,3 @@
/target /target
.gradle
build

4
Readme.md
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@ -2,7 +2,9 @@
ImageJ plugin for reading and writing HDF5 files. ImageJ plugin for reading and writing HDF5 files.
For 3D datasets an individual slice can be selected for visualization.
Also, especially for very big datasets only every x-th slice can be selected
for visualization. This can be done by either specifying a number, e.g. `10` (for the slice 10) or a number with a preceding %, e.g. `%10` (for every 10th image). Indexing starts at 0.
# Usage # Usage

30
build.gradle Normal file
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@ -0,0 +1,30 @@
apply plugin: 'java'
apply plugin: 'maven'
group = 'ch.psi'
version = '0.8.0'
description = """"""
sourceCompatibility = 1.7
targetCompatibility = 1.7
repositories {
mavenCentral()
maven { url "http://slsyoke4.psi.ch:8081/artifactory/libs-releases" }
}
dependencies {
compile group: 'hdf5', name: 'hdf', version:'2.10.0'
compile group: 'hdf5', name: 'hdfobj', version:'2.10.0'
compile group: 'hdf5', name: 'hdf5', version:'2.10.0'
compile group: 'hdf5', name: 'hdf5obj', version:'2.10.0'
compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.6'
testCompile group: 'junit', name: 'junit', version:'4.11'
compile(group: 'gov.nih.imagej', name: 'imagej', version:'1.46') {
/* This dependency was originally in the Maven provided scope, but the project was not of type war.
This behavior is not yet supported by Gradle, so this dependency has been converted to a compile dependency.
Please review and delete this closure when resolved. */
}
}

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gradle/wrapper/gradle-wrapper.jar vendored Normal file
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gradle/wrapper/gradle-wrapper.properties vendored Normal file
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@ -0,0 +1,6 @@
#Tue Apr 14 08:25:23 CEST 2015
distributionBase=GRADLE_USER_HOME
distributionPath=wrapper/dists
zipStoreBase=GRADLE_USER_HOME
zipStorePath=wrapper/dists
distributionUrl=https\://services.gradle.org/distributions/gradle-2.3-bin.zip

164
gradlew vendored Executable file
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@ -0,0 +1,164 @@
#!/usr/bin/env bash
##############################################################################
##
## Gradle start up script for UN*X
##
##############################################################################
# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
DEFAULT_JVM_OPTS=""
APP_NAME="Gradle"
APP_BASE_NAME=`basename "$0"`
# Use the maximum available, or set MAX_FD != -1 to use that value.
MAX_FD="maximum"
warn ( ) {
echo "$*"
}
die ( ) {
echo
echo "$*"
echo
exit 1
}
# OS specific support (must be 'true' or 'false').
cygwin=false
msys=false
darwin=false
case "`uname`" in
CYGWIN* )
cygwin=true
;;
Darwin* )
darwin=true
;;
MINGW* )
msys=true
;;
esac
# For Cygwin, ensure paths are in UNIX format before anything is touched.
if $cygwin ; then
[ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
fi
# Attempt to set APP_HOME
# Resolve links: $0 may be a link
PRG="$0"
# Need this for relative symlinks.
while [ -h "$PRG" ] ; do
ls=`ls -ld "$PRG"`
link=`expr "$ls" : '.*-> \(.*\)$'`
if expr "$link" : '/.*' > /dev/null; then
PRG="$link"
else
PRG=`dirname "$PRG"`"/$link"
fi
done
SAVED="`pwd`"
cd "`dirname \"$PRG\"`/" >&-
APP_HOME="`pwd -P`"
cd "$SAVED" >&-
CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
# Determine the Java command to use to start the JVM.
if [ -n "$JAVA_HOME" ] ; then
if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
# IBM's JDK on AIX uses strange locations for the executables
JAVACMD="$JAVA_HOME/jre/sh/java"
else
JAVACMD="$JAVA_HOME/bin/java"
fi
if [ ! -x "$JAVACMD" ] ; then
die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
else
JAVACMD="java"
which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
Please set the JAVA_HOME variable in your environment to match the
location of your Java installation."
fi
# Increase the maximum file descriptors if we can.
if [ "$cygwin" = "false" -a "$darwin" = "false" ] ; then
MAX_FD_LIMIT=`ulimit -H -n`
if [ $? -eq 0 ] ; then
if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
MAX_FD="$MAX_FD_LIMIT"
fi
ulimit -n $MAX_FD
if [ $? -ne 0 ] ; then
warn "Could not set maximum file descriptor limit: $MAX_FD"
fi
else
warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
fi
fi
# For Darwin, add options to specify how the application appears in the dock
if $darwin; then
GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
fi
# For Cygwin, switch paths to Windows format before running java
if $cygwin ; then
APP_HOME=`cygpath --path --mixed "$APP_HOME"`
CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
# We build the pattern for arguments to be converted via cygpath
ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
SEP=""
for dir in $ROOTDIRSRAW ; do
ROOTDIRS="$ROOTDIRS$SEP$dir"
SEP="|"
done
OURCYGPATTERN="(^($ROOTDIRS))"
# Add a user-defined pattern to the cygpath arguments
if [ "$GRADLE_CYGPATTERN" != "" ] ; then
OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
fi
# Now convert the arguments - kludge to limit ourselves to /bin/sh
i=0
for arg in "$@" ; do
CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option
if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition
eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
else
eval `echo args$i`="\"$arg\""
fi
i=$((i+1))
done
case $i in
(0) set -- ;;
(1) set -- "$args0" ;;
(2) set -- "$args0" "$args1" ;;
(3) set -- "$args0" "$args1" "$args2" ;;
(4) set -- "$args0" "$args1" "$args2" "$args3" ;;
(5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
(6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
(7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
(8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
(9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
esac
fi
# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
function splitJvmOpts() {
JVM_OPTS=("$@")
}
eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"

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gradlew.bat vendored Normal file
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@ -0,0 +1,90 @@
@if "%DEBUG%" == "" @echo off
@rem ##########################################################################
@rem
@rem Gradle startup script for Windows
@rem
@rem ##########################################################################
@rem Set local scope for the variables with windows NT shell
if "%OS%"=="Windows_NT" setlocal
@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
set DEFAULT_JVM_OPTS=
set DIRNAME=%~dp0
if "%DIRNAME%" == "" set DIRNAME=.
set APP_BASE_NAME=%~n0
set APP_HOME=%DIRNAME%
@rem Find java.exe
if defined JAVA_HOME goto findJavaFromJavaHome
set JAVA_EXE=java.exe
%JAVA_EXE% -version >NUL 2>&1
if "%ERRORLEVEL%" == "0" goto init
echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.
goto fail
:findJavaFromJavaHome
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe
if exist "%JAVA_EXE%" goto init
echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.
goto fail
:init
@rem Get command-line arguments, handling Windowz variants
if not "%OS%" == "Windows_NT" goto win9xME_args
if "%@eval[2+2]" == "4" goto 4NT_args
:win9xME_args
@rem Slurp the command line arguments.
set CMD_LINE_ARGS=
set _SKIP=2
:win9xME_args_slurp
if "x%~1" == "x" goto execute
set CMD_LINE_ARGS=%*
goto execute
:4NT_args
@rem Get arguments from the 4NT Shell from JP Software
set CMD_LINE_ARGS=%$
:execute
@rem Setup the command line
set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
@rem Execute Gradle
"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
:end
@rem End local scope for the variables with windows NT shell
if "%ERRORLEVEL%"=="0" goto mainEnd
:fail
rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
rem the _cmd.exe /c_ return code!
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
exit /b 1
:mainEnd
if "%OS%"=="Windows_NT" endlocal
:omega

18
src/main/java/ch/psi/imagej/hdf5/SelectedDatasets.java → src/main/java/ch/psi/imagej/hdf5/DatasetSelection.java
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@ -5,10 +5,13 @@ import java.util.List;
import ncsa.hdf.object.Dataset; import ncsa.hdf.object.Dataset;
public class SelectedDatasets { 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;
// Intervall to read images
private Integer modulo;
public List<Dataset> getDatasets() { public List<Dataset> getDatasets() {
return datasets; return datasets;
@ -22,5 +25,16 @@ public class SelectedDatasets {
public void setGroup(boolean group) { public void setGroup(boolean group) {
this.group = group; this.group = group;
} }
public void setSlice(Integer slice) {
this.slice = slice;
}
public Integer getSlice() {
return slice;
}
public void setModulo(Integer modulo) {
this.modulo = modulo;
}
public Integer getModulo() {
return modulo;
}
} }

122
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.*;
@ -68,7 +57,7 @@ public class HDF5Reader implements PlugIn {
file.open(); file.open();
List<Dataset> datasets = HDF5Utilities.getDatasets(file); List<Dataset> datasets = HDF5Utilities.getDatasets(file);
SelectedDatasets selectedDatasets = selectDatasets(datasets); DatasetSelection selectedDatasets = selectDatasets(datasets);
// TODO Remove // TODO Remove
@ -217,19 +206,67 @@ public class HDF5Reader implements PlugIn {
} else if (numberOfDimensions == 3) { } else if (numberOfDimensions == 3) {
logger.info("3D Image"); logger.info("3D Image");
// Select what to readout ImageStack stack;
long[] selected = var.getSelectedDims();
selected[0] = dimensions[0]; if(selectedDatasets.getSlice()!=null){
selected[1] = dimensions[1];
selected[2] = dimensions[2]; // Select what to readout
long[] selected = var.getSelectedDims();
selected[0] = 1;
selected[1] = dimensions[1];
selected[2] = dimensions[2];
long[] start = var.getStartDims();
start[0] = selectedDatasets.getSlice();
Object wholeDataset = var.read(); Object wholeDataset = var.read();
stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
int size = (int) (dimensions[1] * dimensions[2]);
// int startIdx = selectedDatasets.getSlice() * 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{
// Select what to readout
long[] selected = var.getSelectedDims();
selected[0] = dimensions[0];
selected[1] = dimensions[1];
selected[2] = dimensions[2];
ImageStack stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
int size = (int) (dimensions[1] * dimensions[2]); Object wholeDataset = var.read();
for (int lev = 0; lev < dimensions[0]; ++lev) {
int startIdx = lev * size; stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
addSlice(stack, wholeDataset, startIdx, size); int size = (int) (dimensions[1] * dimensions[2]);
for (int lev = 0; lev < dimensions[0]; ++lev) {
int startIdx = lev * size;
addSlice(stack, wholeDataset, startIdx, size);
}
} }
ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack); ImagePlus imp = new ImagePlus(filename + " " + datasetName, stack);
@ -279,39 +316,12 @@ public class HDF5Reader implements PlugIn {
* @return List of datasets to visualize. If nothing selected the list will be empty * @return List of datasets to visualize. If nothing selected the list will be empty
* @throws HDF5Exception * @throws HDF5Exception
*/ */
private SelectedDatasets selectDatasets(List<Dataset> datasets) throws HDF5Exception { private DatasetSelection selectDatasets(List<Dataset> datasets) throws HDF5Exception {
GenericDialog gd = new GenericDialog("Variable Name Selection"); GenericDialog gd = new GenericDialog("Variable Name Selection");
gd.addMessage("Please select variables to be loaded.\n"); gd.addMessage("Please select variables to be loaded.\n");
// Filter datasets that are not potential images / that cannot be displayed SelectionPanel panel = new SelectionPanel(datasets);
List<Dataset> fdatasets = new ArrayList<Dataset>();
for(Dataset d: datasets){
if(d.getRank()>=2 && d.getRank()<=5){
fdatasets.add(d);
}
}
JList<Dataset> list = new JList<>(fdatasets.toArray(new Dataset[fdatasets.size()]));
list.setCellRenderer(new DefaultListCellRenderer() {
private static final long serialVersionUID = 1L;
public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
JLabel label = (JLabel) super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
final Dataset d = ((Dataset) value);
label.setText(d.getFullName()+" ("+d.getRank()+"D)");
return label;
}
});
JScrollPane scroll = new JScrollPane(list);
scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel,BoxLayout.Y_AXIS));
panel.add(scroll);
JCheckBox checkbox = new JCheckBox("Group Datasets (2D datasets only)");
panel.add(checkbox);
gd = new GenericDialog("Variable Name Selection"); gd = new GenericDialog("Variable Name Selection");
gd.add(panel); gd.add(panel);
@ -319,10 +329,12 @@ public class HDF5Reader implements PlugIn {
gd.pack(); gd.pack();
gd.showDialog(); gd.showDialog();
SelectedDatasets selectedDatasets = new SelectedDatasets(); DatasetSelection selectedDatasets = new DatasetSelection();
if (!gd.wasCanceled()) { if (!gd.wasCanceled()) {
selectedDatasets.setDatasets(list.getSelectedValuesList()); selectedDatasets.setDatasets(panel.getSelectedValues());
selectedDatasets.setGroup(checkbox.isSelected()); selectedDatasets.setGroup(panel.groupValues());
selectedDatasets.setSlice(panel.getSlice());
selectedDatasets.setModulo(panel.getModulo());
} }
return selectedDatasets; return selectedDatasets;

105
src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java Normal file
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@ -0,0 +1,105 @@
package ch.psi.imagej.hdf5;
import java.awt.Component;
import java.util.ArrayList;
import java.util.List;
import javax.swing.BoxLayout;
import javax.swing.DefaultListCellRenderer;
import javax.swing.DefaultListModel;
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.Dataset;
import javax.swing.JTextField;
import java.awt.FlowLayout;
public class SelectionPanel extends JPanel {
private static final long serialVersionUID = 1L;
private final JList<Dataset> list;
private JCheckBox checkbox;
private JCheckBox chckbxNewCheckBox;
private JLabel lblSlice;
private JPanel panel;
private JTextField textField;
public SelectionPanel(){
this(new ArrayList<Dataset>());
}
public SelectionPanel(List<Dataset> datasets){
// Filter datasets that are not potential images / that cannot be displayed
List<Dataset> fdatasets = new ArrayList<Dataset>();
for(Dataset d: datasets){
if(d.getRank()>=2 && d.getRank()<=5){
fdatasets.add(d);
}
}
list = new JList<>(new DefaultListModel<Dataset>());
list.setListData(fdatasets.toArray(new Dataset[fdatasets.size()]));
list.setCellRenderer(new DefaultListCellRenderer() {
private static final long serialVersionUID = 1L;
public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
JLabel label = (JLabel) super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
final Dataset d = ((Dataset) value);
label.setText(d.getFullName()+" ("+d.getRank()+"D)");
return label;
}
});
JScrollPane scroll = new JScrollPane(list);
scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS);
setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
add(scroll);
checkbox = new JCheckBox("Group Datasets (2D datasets only)");
add(checkbox);
chckbxNewCheckBox = new JCheckBox("Virtual Stack");
add(chckbxNewCheckBox);
panel = new JPanel();
FlowLayout flowLayout = (FlowLayout) panel.getLayout();
flowLayout.setAlignment(FlowLayout.LEFT);
add(panel);
lblSlice = new JLabel("Slice (3D only):");
panel.add(lblSlice);
textField = new JTextField();
panel.add(textField);
textField.setColumns(10);
}
public List<Dataset> getSelectedValues(){
return list.getSelectedValuesList();
}
public boolean groupValues(){
return checkbox.isSelected();
}
public Integer getSlice(){
String text = textField.getText();
if(text.matches("^[0-9]+$")){
return new Integer(text);
}
return null;
}
public Integer getModulo(){
String text = textField.getText();
if(text.matches("^%[0-9]+$")){
return new Integer(text.replace("%", ""));
}
return null;
}
}