mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-06-06 10:30:43 +02:00
Merge pull request #1 in IM/ch.psi.imagej.hdf5 from slice_selection to master
# 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:
commit
2464a795d1
2
.gitignore
vendored
2
.gitignore
vendored
@ -1 +1,3 @@
|
||||
/target
|
||||
.gradle
|
||||
build
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||||
|
||||
@ -2,7 +2,9 @@
|
||||
|
||||
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.
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||||
|
||||
# Usage
|
||||
|
||||
|
||||
30
build.gradle
Normal file
30
build.gradle
Normal file
@ -0,0 +1,30 @@
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||||
apply plugin: 'java'
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||||
apply plugin: 'maven'
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||||
|
||||
group = 'ch.psi'
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||||
version = '0.8.0'
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||||
|
||||
description = """"""
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||||
|
||||
sourceCompatibility = 1.7
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||||
targetCompatibility = 1.7
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||||
|
||||
|
||||
|
||||
repositories {
|
||||
mavenCentral()
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||||
maven { url "http://slsyoke4.psi.ch:8081/artifactory/libs-releases" }
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||||
}
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||||
dependencies {
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compile group: 'hdf5', name: 'hdf', version:'2.10.0'
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compile group: 'hdf5', name: 'hdfobj', version:'2.10.0'
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compile group: 'hdf5', name: 'hdf5', version:'2.10.0'
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||||
compile group: 'hdf5', name: 'hdf5obj', version:'2.10.0'
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||||
compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.6'
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||||
testCompile group: 'junit', name: 'junit', version:'4.11'
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||||
compile(group: 'gov.nih.imagej', name: 'imagej', version:'1.46') {
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||||
/* This dependency was originally in the Maven provided scope, but the project was not of type war.
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||||
This behavior is not yet supported by Gradle, so this dependency has been converted to a compile dependency.
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||||
Please review and delete this closure when resolved. */
|
||||
}
|
||||
}
|
||||
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
BIN
gradle/wrapper/gradle-wrapper.jar
vendored
Normal file
Binary file not shown.
6
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
6
gradle/wrapper/gradle-wrapper.properties
vendored
Normal file
@ -0,0 +1,6 @@
|
||||
#Tue Apr 14 08:25:23 CEST 2015
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||||
distributionBase=GRADLE_USER_HOME
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||||
distributionPath=wrapper/dists
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||||
zipStoreBase=GRADLE_USER_HOME
|
||||
zipStorePath=wrapper/dists
|
||||
distributionUrl=https\://services.gradle.org/distributions/gradle-2.3-bin.zip
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||||
164
gradlew
vendored
Executable file
164
gradlew
vendored
Executable file
@ -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 "$@"
|
||||
90
gradlew.bat
vendored
Normal file
90
gradlew.bat
vendored
Normal file
@ -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
|
||||
@ -5,10 +5,13 @@ import java.util.List;
|
||||
|
||||
import ncsa.hdf.object.Dataset;
|
||||
|
||||
public class SelectedDatasets {
|
||||
public class DatasetSelection {
|
||||
|
||||
private List<Dataset> datasets = new ArrayList<Dataset>();
|
||||
private boolean group = false;
|
||||
private Integer slice;
|
||||
// Intervall to read images
|
||||
private Integer modulo;
|
||||
|
||||
public List<Dataset> getDatasets() {
|
||||
return datasets;
|
||||
@ -22,5 +25,16 @@ public class SelectedDatasets {
|
||||
public void setGroup(boolean 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;
|
||||
}
|
||||
}
|
||||
@ -10,20 +10,9 @@ import ij.plugin.PlugIn;
|
||||
|
||||
import java.io.File;
|
||||
import java.lang.reflect.Array;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.logging.Level;
|
||||
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.h5.*;
|
||||
@ -68,7 +57,7 @@ public class HDF5Reader implements PlugIn {
|
||||
file.open();
|
||||
|
||||
List<Dataset> datasets = HDF5Utilities.getDatasets(file);
|
||||
SelectedDatasets selectedDatasets = selectDatasets(datasets);
|
||||
DatasetSelection selectedDatasets = selectDatasets(datasets);
|
||||
|
||||
|
||||
// TODO Remove
|
||||
@ -217,19 +206,67 @@ public class HDF5Reader implements PlugIn {
|
||||
} else if (numberOfDimensions == 3) {
|
||||
logger.info("3D Image");
|
||||
|
||||
// Select what to readout
|
||||
long[] selected = var.getSelectedDims();
|
||||
selected[0] = dimensions[0];
|
||||
selected[1] = dimensions[1];
|
||||
selected[2] = dimensions[2];
|
||||
ImageStack stack;
|
||||
|
||||
if(selectedDatasets.getSlice()!=null){
|
||||
|
||||
// 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]);
|
||||
for (int lev = 0; lev < dimensions[0]; ++lev) {
|
||||
int startIdx = lev * size;
|
||||
addSlice(stack, wholeDataset, startIdx, size);
|
||||
|
||||
Object wholeDataset = var.read();
|
||||
|
||||
stack = new ImageStack((int) dimensions[2], (int) dimensions[1]);
|
||||
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);
|
||||
@ -279,39 +316,12 @@ public class HDF5Reader implements PlugIn {
|
||||
* @return List of datasets to visualize. If nothing selected the list will be empty
|
||||
* @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");
|
||||
gd.addMessage("Please select variables to be loaded.\n");
|
||||
|
||||
// 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);
|
||||
}
|
||||
}
|
||||
|
||||
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);
|
||||
SelectionPanel panel = new SelectionPanel(datasets);
|
||||
|
||||
gd = new GenericDialog("Variable Name Selection");
|
||||
gd.add(panel);
|
||||
@ -319,10 +329,12 @@ public class HDF5Reader implements PlugIn {
|
||||
gd.pack();
|
||||
gd.showDialog();
|
||||
|
||||
SelectedDatasets selectedDatasets = new SelectedDatasets();
|
||||
DatasetSelection selectedDatasets = new DatasetSelection();
|
||||
if (!gd.wasCanceled()) {
|
||||
selectedDatasets.setDatasets(list.getSelectedValuesList());
|
||||
selectedDatasets.setGroup(checkbox.isSelected());
|
||||
selectedDatasets.setDatasets(panel.getSelectedValues());
|
||||
selectedDatasets.setGroup(panel.groupValues());
|
||||
selectedDatasets.setSlice(panel.getSlice());
|
||||
selectedDatasets.setModulo(panel.getModulo());
|
||||
}
|
||||
|
||||
return selectedDatasets;
|
||||
|
||||
105
src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java
Normal file
105
src/main/java/ch/psi/imagej/hdf5/SelectionPanel.java
Normal file
@ -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;
|
||||
}
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user