mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-04-20 05:00:03 +02:00
Removed unused stuff
This commit is contained in:
parent
84cceda936
commit
82a69ebf36
13
Readme.md
13
Readme.md
@ -1,3 +1,16 @@
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# Usage
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To open a HDF5 file use:
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```
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File > Import > HDF5...
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```
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To save to an HDF5 file use:
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```
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File > SaveAs > HDF5
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```
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# Installation
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# Installation
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* Download latest HDF5 ImageJ plugin from [here](http://slsyoke4.psi.ch:8081/artifactory/releases/HDF5_Viewer-0.2.0.zip).
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* Download latest HDF5 ImageJ plugin from [here](http://slsyoke4.psi.ch:8081/artifactory/releases/HDF5_Viewer-0.2.0.zip).
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2
pom.xml
2
pom.xml
@ -3,7 +3,7 @@
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<modelVersion>4.0.0</modelVersion>
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<modelVersion>4.0.0</modelVersion>
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<groupId>ch.psi</groupId>
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<groupId>ch.psi</groupId>
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<artifactId>imagej.hdf5</artifactId>
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<artifactId>imagej.hdf5</artifactId>
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<version>0.3.0</version>
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<version>0.5.0</version>
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<dependencies>
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<dependencies>
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<dependency>
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<dependency>
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@ -1,87 +0,0 @@
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package ch.psi.imagej.hdf5;
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import ij.Prefs;
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import ij.gui.GenericDialog;
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import ij.plugin.PlugIn;
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import java.util.logging.Level;
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import java.util.logging.Logger;
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import java.util.regex.*;
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import java.lang.String;
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public class HDF5Config implements PlugIn {
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private static final Logger logger = Logger.getLogger(HDF5Config.class.getName());
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private static final String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName";
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private static final String SHOW_UNMATCHED_DATASET_NAMES = "HDF5.showUnmatchedDataSetNames";
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private static final String GROUP_VARS_BY_NAME_FORMAT_GROUP = "HDF5.groupVarsByNameFormatGroup";
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private static final String GROUP_VARS_BY_NAME_FORMAT = "HDF5.groupVarsByNameFormat";
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private static final String DOLLAR_REGEXP_FOR_GROUPING = "HDF5.dollarRegexpForGrouping";
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// Getting preference or default values
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private boolean groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, true);
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private boolean showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, true);
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private String groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, "/hints");
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private String groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, "/t$T/channel$C");
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private String dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, "[0-9]+");
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public void run(String arg) {
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GenericDialog configDiag = new GenericDialog("HDF5 Preferences");
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configDiag.addMessage("Reader:");
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configDiag.addCheckbox("Group data set names instead of showing a list " + "of data set names.", groupVarsByName);
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configDiag.addCheckbox("Show unmatched data set names in a separate list", showUnmatchedDataSetNames);
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configDiag.addStringField("HDF5 group containing pattern " + "for data set grouping: ", groupVarsByNameFormatGroup, 15);
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configDiag.addStringField("Pattern for grouping (if no attributes" + " are found): ", groupVarsByNameFormat, 15);
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configDiag.showDialog();
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if (configDiag.wasCanceled()) {
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return;
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}
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// Get parameters check if they are correct
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groupVarsByName = configDiag.getNextBoolean();
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showUnmatchedDataSetNames = configDiag.getNextBoolean();
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groupVarsByNameFormatGroup = configDiag.getNextString();
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groupVarsByNameFormat = configDiag.getNextString();
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try {
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HDF5GroupedVarnames.parseFormatString(groupVarsByNameFormat, dollarRegexpForGrouping);
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} catch (PatternSyntaxException e) {
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logger.log(Level.WARNING, "", e);
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this.run(arg);
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return;
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}
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logger.info("Saving configuration ...");
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// All OK and "Save" was pressed, so save it...
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Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName);
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Prefs.set(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
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Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
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Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
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Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
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}
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public boolean isGroupVarsByName() {
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return groupVarsByName;
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}
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public boolean isShowUnmatchedDataSetNames() {
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return showUnmatchedDataSetNames;
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}
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public String getGroupVarsByNameFormatGroup() {
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return groupVarsByNameFormatGroup;
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}
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public String getGroupVarsByNameFormat() {
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return groupVarsByNameFormat;
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}
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public String getDollarRegexpForGrouping() {
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return dollarRegexpForGrouping;
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}
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}
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@ -86,95 +86,13 @@ public class HDF5Reader implements PlugIn {
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IJ.showStatus("Loading HDF5 File: " + directory + name);
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IJ.showStatus("Loading HDF5 File: " + directory + name);
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// Read HDF5 file
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H5File inFile = null;
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H5File inFile = null;
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// define grouping class
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HDF5GroupedVarnames groupedVarnames = new HDF5GroupedVarnames();
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boolean loadGroupedVarNames = true;
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try {
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try {
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inFile = new H5File(directory + name, H5File.READ);
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inFile = new H5File(directory + name, H5File.READ);
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inFile.open();
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inFile.open();
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/*-------------------------------------------------------------------
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* read HDF5_Config prefs
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*-------------------------------------------------------------------*/
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HDF5Config config = new HDF5Config();
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boolean groupVarsByName = config.isGroupVarsByName();
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boolean showUnmatchedDataSetNames = config.isShowUnmatchedDataSetNames();
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String groupVarsByNameFormatGroup = config.getGroupVarsByNameFormatGroup();
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String dollarRegexpForGrouping = config.getDollarRegexpForGrouping();
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// TODO: try to read attribute containing format String
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String groupVarsByNameFormat = null;
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try {
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HObject gr = inFile.get(groupVarsByNameFormatGroup);
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String attrName = ""; // this will throw an error
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if (gr != null) {
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// get the attr list and make a selection dialog if
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// necessary
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List<Attribute> hintsAttrList = getAttrList(gr);
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if (hintsAttrList.size() == 1)
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attrName = hintsAttrList.get(0).getName();
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else if (hintsAttrList.size() > 1) {
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String[] hintsAttrNames = new String[hintsAttrList.size()];
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for (int a = 0; a < hintsAttrList.size(); a++)
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hintsAttrNames[a] = hintsAttrList.get(a).getName();
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GenericDialog attrSelecD = new GenericDialog("Format string selector");
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attrSelecD.addChoice("Select format string", hintsAttrNames, hintsAttrNames[0]);
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attrSelecD.showDialog();
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if (attrSelecD.wasCanceled())
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return;
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else
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attrName = attrSelecD.getNextChoice();
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}
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logger.info("Reading attribute");
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Attribute attr = getAttribute(gr, attrName);
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logger.info("Reading attribute is ok");
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if (attr != null)
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logger.info("attr is not null");
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logger.info("attr.getName(): " + attr.getName());
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Datatype dType = attr.getType();
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logger.info(dType.getDatatypeDescription());
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Object tmp = attr.getValue();
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if (tmp != null)
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logger.info("get value is ok");
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if (tmp instanceof String) {
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// we have a string
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groupVarsByNameFormat = (String) tmp;
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} else if (tmp instanceof String[]) {
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// we have a cstring
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String[] sTmp = (String[]) tmp;
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groupVarsByNameFormat = "";
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for (int i = 0; i < sTmp.length; i++)
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groupVarsByNameFormat = groupVarsByNameFormat + sTmp[i];
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}
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logger.info("File has format string for grouping: " + groupVarsByNameFormat);
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} else {
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logger.info("File has no format string for grouping" + ", using default");
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groupVarsByNameFormat = config.getGroupVarsByNameFormat();
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}
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} catch (Exception e) {
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logger.info("Error occured read format string " + "for grouping, using default");
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groupVarsByNameFormat = config.getGroupVarsByNameFormat();
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}
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/*-------------------------------------------------------------------
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* init the frame and channel ranges
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*-------------------------------------------------------------------*/
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int minFrameIndex = -1;
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int maxFrameIndex = -1;
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int skipFrameIndex = 1;
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int minChannelIndex = -1;
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int maxChannelIndex = -1;
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int skipChannelIndex = 1;
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/*-------------------------------------------------------------------
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/*-------------------------------------------------------------------
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* parse the file
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* parse the file
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@ -190,203 +108,6 @@ public class HDF5Reader implements PlugIn {
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IJ.error("The file did not contain variables. (broken?)");
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IJ.error("The file did not contain variables. (broken?)");
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inFile.close();
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inFile.close();
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return;
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return;
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}
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// else if (varList.size() < 2)
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// {
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// gd.addCheckbox("single variable", true);
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// }
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else if (groupVarsByName) {
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// parse file structure
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String[] varNames = new String[varList.size()];
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for (int i = 0; i < varList.size(); i++) {
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varNames[i] = varList.get(i).getFullName();
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}
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groupedVarnames.parseVarNames(varNames, groupVarsByNameFormat, dollarRegexpForGrouping);
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logger.info(groupedVarnames.toString());
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// make the data set selection dialog
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minFrameIndex = groupedVarnames.getMinFrameIndex();
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maxFrameIndex = groupedVarnames.getMaxFrameIndex();
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minChannelIndex = groupedVarnames.getMinChannelIndex();
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maxChannelIndex = groupedVarnames.getMaxChannelIndex();
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gd = new GenericDialog("Variable Name Selection");
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// check if we have matched var names
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if (groupedVarnames.getNFrames() > 0) {
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gd.addCheckbox("Load grouped data sets", loadGroupedVarNames);
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gd.addMessage("Select frames and channels you want to read");
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gd.addMessage("Frame selection (start/step/end): ");
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gd.addStringField("Frame selection (start:[step:]end): ", Integer.toString(minFrameIndex) + ":" + Integer.toString(skipFrameIndex) + ":" + Integer.toString(maxFrameIndex));
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gd.addStringField("Channel selection (start:[step:]end): ", Integer.toString(minChannelIndex) + ":" + Integer.toString(skipChannelIndex) + ":" + Integer.toString(maxChannelIndex));
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}
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// get unmatched names
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List<String> unmatchedVarNames = groupedVarnames.getUnmatchedVarNames();
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if (showUnmatchedDataSetNames) {
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// add all unmatched data set names to the dialog
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String[] varSelections = new String[unmatchedVarNames.size()];
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boolean[] defaultValues = new boolean[unmatchedVarNames.size()];
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for (int i = 0; i < unmatchedVarNames.size(); i++) {
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Dataset var = (Dataset) inFile.get(unmatchedVarNames.get(i));
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int rank = var.getRank();
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String title = rank + "D: " + var.getFullName() + " " + var.getDatatype().getDatatypeDescription() + "( ";
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long[] extent = var.getDims();
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for (int d = 0; d < rank; ++d) {
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if (d != 0)
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title += "x";
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title += extent[d];
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}
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title += ")";
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varSelections[i] = title;
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defaultValues[i] = false;
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}
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logger.info("addcheckboxgroup with " + unmatchedVarNames.size() + " rows");
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gd.addCheckboxGroup(unmatchedVarNames.size(), 1, varSelections, defaultValues);
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addScrollBars(gd);
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}
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gd.showDialog();
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if (gd.wasCanceled()) {
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return;
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}
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// load grouped var names ?
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if (groupedVarnames.getNFrames() > 0)
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loadGroupedVarNames = gd.getNextBoolean();
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// read range selections if we have matched varnames
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String frameRange = null;
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String channelRange = null;
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if (groupedVarnames.getNFrames() > 0) {
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frameRange = gd.getNextString();
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channelRange = gd.getNextString();
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}
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// parse the range selection
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String[] frameRangeToks = null;
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String[] channelRangeToks = null;
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boolean wrongFrameRange = true;
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boolean wrongChannelRange = true;
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// check if the parsed values are in range
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if (groupedVarnames.getNFrames() > 0 && loadGroupedVarNames)
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while (wrongFrameRange || wrongChannelRange) {
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// check frame range
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frameRangeToks = frameRange.split(":");
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if (frameRangeToks.length == 1) {
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// single frame
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try {
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logger.info("single frame");
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minFrameIndex = Integer.parseInt(frameRangeToks[0]);
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maxFrameIndex = minFrameIndex;
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wrongFrameRange = false;
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} catch (Exception e) {
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wrongFrameRange = true;
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}
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} else if (frameRangeToks.length == 2) {
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// frame range with skipFrameIndex=1
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try {
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logger.info("frame range with skipFrameIndex=1");
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minFrameIndex = Integer.parseInt(frameRangeToks[0]);
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maxFrameIndex = Integer.parseInt(frameRangeToks[1]);
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wrongFrameRange = false;
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} catch (Exception e) {
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wrongFrameRange = true;
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}
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} else if (frameRangeToks.length == 3) {
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// frame range with skipFrameIndex
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try {
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logger.info("frame range with skipFrameIndex");
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minFrameIndex = Integer.parseInt(frameRangeToks[0]);
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skipFrameIndex = Integer.parseInt(frameRangeToks[1]);
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maxFrameIndex = Integer.parseInt(frameRangeToks[2]);
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wrongFrameRange = false;
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} catch (Exception e) {
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wrongFrameRange = true;
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}
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} else {
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// wrong format
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logger.info("wrong format");
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wrongFrameRange = true;
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}
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// check channel range
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channelRangeToks = channelRange.split(":");
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if (channelRangeToks.length == 1) {
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// single channel
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try {
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minChannelIndex = Integer.parseInt(channelRangeToks[0]);
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maxChannelIndex = minChannelIndex;
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wrongChannelRange = false;
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} catch (Exception e) {
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wrongChannelRange = true;
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}
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} else if (channelRangeToks.length == 2) {
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// channel range with skipChannelIndex=1
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try {
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minChannelIndex = Integer.parseInt(channelRangeToks[0]);
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maxChannelIndex = Integer.parseInt(channelRangeToks[1]);
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wrongChannelRange = false;
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} catch (Exception e) {
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wrongChannelRange = true;
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}
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} else if (channelRangeToks.length == 3) {
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// channel range with skipChannelIndex
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|
||||||
try {
|
|
||||||
minChannelIndex = Integer.parseInt(channelRangeToks[0]);
|
|
||||||
skipChannelIndex = Integer.parseInt(channelRangeToks[1]);
|
|
||||||
maxChannelIndex = Integer.parseInt(channelRangeToks[2]);
|
|
||||||
wrongChannelRange = false;
|
|
||||||
} catch (Exception e) {
|
|
||||||
wrongChannelRange = true;
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
// wrong format
|
|
||||||
wrongChannelRange = true;
|
|
||||||
}
|
|
||||||
if (wrongFrameRange || wrongChannelRange) {
|
|
||||||
// show dialog again
|
|
||||||
logger.info("show dialog again");
|
|
||||||
// TODO reset dialog when possible
|
|
||||||
gd = new GenericDialog("Range Selection");
|
|
||||||
gd.addMessage("Select frames and channels you want to read");
|
|
||||||
gd.addMessage("Frame selection (start/step/end): ");
|
|
||||||
|
|
||||||
gd.addStringField("Frame selection (start:[step:]end): ", Integer.toString(minFrameIndex) + ":" + Integer.toString(skipFrameIndex) + ":" + Integer.toString(maxFrameIndex));
|
|
||||||
|
|
||||||
gd.addStringField("Channel selection (start:[step:]end): ",
|
|
||||||
Integer.toString(minChannelIndex) + ":" + Integer.toString(skipChannelIndex) + ":" + Integer.toString(maxChannelIndex));
|
|
||||||
gd.showDialog();
|
|
||||||
logger.info("read ranges again");
|
|
||||||
frameRange = gd.getNextString();
|
|
||||||
channelRange = gd.getNextString();
|
|
||||||
|
|
||||||
}
|
|
||||||
if (gd.wasCanceled()) {
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
// the parameters for the range have correct format
|
|
||||||
}
|
|
||||||
|
|
||||||
if (showUnmatchedDataSetNames) {
|
|
||||||
varList = new ArrayList<Dataset>();
|
|
||||||
// fill varList with unmatched var names
|
|
||||||
for (int i = 0; i < unmatchedVarNames.size(); i++) {
|
|
||||||
String dsName = unmatchedVarNames.get(i);
|
|
||||||
try {
|
|
||||||
HObject ds = inFile.get(dsName);
|
|
||||||
if (ds != null && ds instanceof Dataset) {
|
|
||||||
varList.add((Dataset) ds);
|
|
||||||
}
|
|
||||||
} catch (Exception e) {
|
|
||||||
logger.info("The file does not contain a variable " + "with name " + "`" + dsName + "`!");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
// set varList=empty if we dont want unmatched var names
|
|
||||||
varList = new ArrayList<Dataset>();
|
|
||||||
}
|
|
||||||
|
|
||||||
} else if (varList.size() > 1000) {
|
} else if (varList.size() > 1000) {
|
||||||
|
|
||||||
logger.info("#######");
|
logger.info("#######");
|
||||||
@ -451,301 +172,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
/*-------------------------------------------------------------------
|
|
||||||
* now reading data sets
|
|
||||||
*-------------------------------------------------------------------*/
|
|
||||||
if (groupVarsByName && groupedVarnames.getNFrames() > 0 && loadGroupedVarNames) {
|
|
||||||
groupedVarnames.setFrameAndChannelRange(minFrameIndex, skipFrameIndex, maxFrameIndex, minChannelIndex, skipChannelIndex, maxChannelIndex);
|
|
||||||
// TODO implement hyperstack reading
|
|
||||||
int nFrames = groupedVarnames.getNFrames();
|
|
||||||
int nChannels = groupedVarnames.getNChannels();
|
|
||||||
|
|
||||||
// get extents of first data set
|
|
||||||
long[] extent = null;
|
|
||||||
int rank = -1;
|
|
||||||
double[] elem_sizes = new double[3];
|
|
||||||
String dsName = "";
|
|
||||||
String[] formatTokens = groupedVarnames.getFormatTokens();
|
|
||||||
Dataset var = null;
|
|
||||||
boolean isSigned16Bit = false;
|
|
||||||
int unsignedConvSelec = 0; // cut off values
|
|
||||||
try {
|
|
||||||
TimeFrame f = groupedVarnames.getFrame(0);
|
|
||||||
if (f == null)
|
|
||||||
logger.info("frame is null");
|
|
||||||
if (formatTokens.length == 2)
|
|
||||||
dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[0]);
|
|
||||||
else if (formatTokens.length == 3)
|
|
||||||
dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[0]) + formatTokens[2];
|
|
||||||
logger.info("VarName: " + dsName);
|
|
||||||
HObject ds = inFile.get(dsName);
|
|
||||||
if (ds != null && ds instanceof Dataset) {
|
|
||||||
var = (Dataset) ds;
|
|
||||||
Datatype dType = var.getDatatype();
|
|
||||||
isSigned16Bit = !dType.isUnsigned() && (dType.getDatatypeClass() == Datatype.CLASS_INTEGER) && (dType.getDatatypeSize() == 2);
|
|
||||||
if (isSigned16Bit) {
|
|
||||||
GenericDialog convDiag = new GenericDialog("Unsigned to signed conversion");
|
|
||||||
convDiag.addMessage("Detected unsigned datatype, which " + "is not supported.");
|
|
||||||
String[] convOptions = new String[2];
|
|
||||||
convOptions[0] = "cut off values";
|
|
||||||
convOptions[1] = "convert to float";
|
|
||||||
convDiag.addChoice("Please select an conversion option:", convOptions, convOptions[0]);
|
|
||||||
convDiag.showDialog();
|
|
||||||
if (convDiag.wasCanceled())
|
|
||||||
return;
|
|
||||||
unsignedConvSelec = convDiag.getNextChoiceIndex();
|
|
||||||
}
|
|
||||||
// TODO check for unsupported datatypes int,long
|
|
||||||
rank = var.getRank();
|
|
||||||
extent = var.getDims();
|
|
||||||
Attribute elemsize_att = getAttribute(var, "element_size_um");
|
|
||||||
|
|
||||||
if (elemsize_att == null) {
|
|
||||||
elem_sizes[0] = 1.0;
|
|
||||||
elem_sizes[1] = 1.0;
|
|
||||||
elem_sizes[2] = 1.0;
|
|
||||||
} else {
|
|
||||||
logger.info("Reading element_size_um");
|
|
||||||
float[] tmp = null;
|
|
||||||
try {
|
|
||||||
tmp = ((float[]) elemsize_att.getValue());
|
|
||||||
elem_sizes[0] = tmp[0];
|
|
||||||
elem_sizes[1] = tmp[1];
|
|
||||||
elem_sizes[2] = tmp[2];
|
|
||||||
} catch (java.lang.ClassCastException e) {
|
|
||||||
String title = "Error Reading Element Size";
|
|
||||||
String msg = "The element_size_um attribute " + "has wrong format!\n";
|
|
||||||
msg += "Setting to default size of (1,1,1)...";
|
|
||||||
new ij.gui.MessageDialog(null, title, msg);
|
|
||||||
elem_sizes[0] = 1;
|
|
||||||
elem_sizes[1] = 1;
|
|
||||||
elem_sizes[2] = 1;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
IJ.error("The file does not contain a variable with name " + "`" + dsName + "`!");
|
|
||||||
inFile.close();
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
} catch (Exception e) {
|
|
||||||
IJ.error("The file does not contain a variable with name " + "`" + dsName + "`!");
|
|
||||||
inFile.close();
|
|
||||||
return;
|
|
||||||
}
|
|
||||||
// String title = rank + "D: " + var.getFullName() +
|
|
||||||
// " "
|
|
||||||
// + var.getDatatype().getDatatypeDescription() + "( ";
|
|
||||||
|
|
||||||
// read 3D or 2D dataset
|
|
||||||
if (rank == 3 || rank == 2) {
|
|
||||||
int nRows = -1; // height
|
|
||||||
int nCols = -1; // width
|
|
||||||
int nSlices = 1; // if rank == 2
|
|
||||||
if (rank == 3) {
|
|
||||||
nSlices = (int) extent[0];
|
|
||||||
nRows = (int) extent[1];
|
|
||||||
nCols = (int) extent[2];
|
|
||||||
} else {
|
|
||||||
nRows = (int) extent[0];
|
|
||||||
nCols = (int) extent[1];
|
|
||||||
}
|
|
||||||
|
|
||||||
// create a new image stack and fill in the data
|
|
||||||
ImageStack stack = new ImageStack(nCols, nRows, nFrames * nSlices * nChannels);
|
|
||||||
logger.info("stackSize: " + Integer.toString(stack.getSize()));
|
|
||||||
|
|
||||||
ImagePlus imp = new ImagePlus();
|
|
||||||
// to get getFrameIndex() working
|
|
||||||
imp.setDimensions(nChannels, nSlices, nFrames);
|
|
||||||
|
|
||||||
long stackSize = nCols * nRows;
|
|
||||||
// global min max values of all data sets
|
|
||||||
double[] minValChannel = new double[nChannels];
|
|
||||||
double[] maxValChannel = new double[nChannels];
|
|
||||||
|
|
||||||
// TODO implement frame and channel ranges
|
|
||||||
// now read frame by frame
|
|
||||||
for (int fIdx = 0; fIdx < nFrames; fIdx++) {
|
|
||||||
// get current frame
|
|
||||||
TimeFrame f = groupedVarnames.getFrame(fIdx);
|
|
||||||
if (f == null)
|
|
||||||
logger.info("frame is null");
|
|
||||||
// get channel indices
|
|
||||||
|
|
||||||
// TODO: check if frame has same parameters as first,
|
|
||||||
// skip otherwise
|
|
||||||
|
|
||||||
// now read channel by channel of frame
|
|
||||||
for (int cIdx = 0; cIdx < nChannels; cIdx++) {
|
|
||||||
if (formatTokens.length == 2)
|
|
||||||
dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[cIdx]);
|
|
||||||
else if (formatTokens.length == 3)
|
|
||||||
dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[cIdx]) + formatTokens[2];
|
|
||||||
|
|
||||||
logger.info("VarName: " + dsName);
|
|
||||||
|
|
||||||
HObject ds = inFile.get(dsName);
|
|
||||||
if (ds != null && ds instanceof Dataset) {
|
|
||||||
var = (Dataset) ds;
|
|
||||||
rank = var.getRank();
|
|
||||||
extent = var.getDims();
|
|
||||||
}
|
|
||||||
|
|
||||||
// TODO: check if dataset has same parameters as
|
|
||||||
// first,
|
|
||||||
// skip otherwise
|
|
||||||
|
|
||||||
long[] selected = var.getSelectedDims(); // the
|
|
||||||
// selected
|
|
||||||
// size of
|
|
||||||
// the
|
|
||||||
// dataet
|
|
||||||
selected[0] = extent[0];
|
|
||||||
selected[1] = extent[1];
|
|
||||||
if (selected.length > 2)
|
|
||||||
selected[2] = extent[2];
|
|
||||||
|
|
||||||
Object wholeDataset = var.read();
|
|
||||||
if (isSigned16Bit)
|
|
||||||
wholeDataset = convertToUnsigned(wholeDataset, unsignedConvSelec);
|
|
||||||
|
|
||||||
long wholeDatasetSize = 1;
|
|
||||||
for (int d = 0; d < extent.length; d++)
|
|
||||||
wholeDatasetSize *= extent[d];
|
|
||||||
|
|
||||||
if (fIdx == 0) {
|
|
||||||
// init min/max
|
|
||||||
double[] minMaxVal = getMinMax(wholeDataset, wholeDatasetSize);
|
|
||||||
minValChannel[cIdx] = minMaxVal[0];
|
|
||||||
maxValChannel[cIdx] = minMaxVal[1];
|
|
||||||
} else {
|
|
||||||
// update minMaxVal
|
|
||||||
double[] minMaxVal = getMinMax(wholeDataset, wholeDatasetSize);
|
|
||||||
minValChannel[cIdx] = Math.min(minMaxVal[0], minValChannel[cIdx]);
|
|
||||||
maxValChannel[cIdx] = Math.max(minMaxVal[1], maxValChannel[cIdx]);
|
|
||||||
}
|
|
||||||
|
|
||||||
for (int lev = 0; lev < nSlices; ++lev) {
|
|
||||||
// if ((lev % progressDivisor) == 0)
|
|
||||||
// IJ.showProgress((float) lev / (float)
|
|
||||||
// extent[0]);
|
|
||||||
// select hyperslab for lev
|
|
||||||
// start[0] = lev;
|
|
||||||
// Object slice = var.read();
|
|
||||||
|
|
||||||
long startIdx = lev * stackSize;
|
|
||||||
long numElements = stackSize;
|
|
||||||
if (wholeDataset instanceof byte[]) {
|
|
||||||
byte[] tmp = (byte[]) extractSubarray(wholeDataset, startIdx, numElements);
|
|
||||||
stack.setPixels(tmp, imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
|
||||||
} else if (wholeDataset instanceof short[]) {
|
|
||||||
short[] tmp = (short[]) extractSubarray(wholeDataset, startIdx, numElements);
|
|
||||||
stack.setPixels(tmp, imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
|
||||||
} else if (wholeDataset instanceof int[]) {
|
|
||||||
logger.info("Datatype `int` is not supported. " + "Skipping whole frame!");
|
|
||||||
// int[] tmp = (int[])
|
|
||||||
// extractSubarray(wholeDataset,
|
|
||||||
// startIdx,
|
|
||||||
// numElements);
|
|
||||||
// if(datatypeIfUnsupported.getDatatypeClass()
|
|
||||||
// == Datatype.CLASS_FLOAT)
|
|
||||||
// {
|
|
||||||
// stack.setPixels(convertInt32ToFloat(tmp),
|
|
||||||
// imp.getStackIndex(cIdx+1,lev+1,fIdx+1));
|
|
||||||
// }
|
|
||||||
// if(datatypeIfUnsupported.getDatatypeClass()
|
|
||||||
// == Datatype.CLASS_INTEGER)
|
|
||||||
// {
|
|
||||||
// stack.setPixels(convertInt32ToShort(tmp),
|
|
||||||
// imp.getStackIndex(cIdx+1,lev+1,fIdx+1));
|
|
||||||
// }
|
|
||||||
} else if (wholeDataset instanceof long[]) {
|
|
||||||
logger.info("Datatype `long` is not supported. " + "Skipping whole frame!");
|
|
||||||
// long[] tmp = (long[])
|
|
||||||
// extractSubarray(wholeDataset,
|
|
||||||
// startIdx,
|
|
||||||
// numElements);
|
|
||||||
// if(datatypeIfUnsupported.getDatatypeClass()
|
|
||||||
// == Datatype.CLASS_FLOAT)
|
|
||||||
// {
|
|
||||||
// stack.setPixels(convertInt64ToFloat(tmp),
|
|
||||||
// imp.getStackIndex(cIdx+1,lev+1,fIdx+1));
|
|
||||||
// }
|
|
||||||
// if(datatypeIfUnsupported.getDatatypeClass()
|
|
||||||
// == Datatype.CLASS_INTEGER)
|
|
||||||
// {
|
|
||||||
// stack.setPixels(convertInt64ToShort(tmp),
|
|
||||||
// imp.getStackIndex(cIdx+1,lev+1,fIdx+1));
|
|
||||||
// }
|
|
||||||
} else if (wholeDataset instanceof float[]) {
|
|
||||||
float[] tmp = (float[]) extractSubarray(wholeDataset, startIdx, numElements);
|
|
||||||
stack.setPixels(tmp, imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
|
||||||
} else if (wholeDataset instanceof double[]) {
|
|
||||||
logger.info("Datatype `double` is not supported. " + "Converting whole frame to `float`!");
|
|
||||||
float[] tmp = convertDoubleToFloat((double[]) extractSubarray(wholeDataset, startIdx, numElements));
|
|
||||||
stack.setPixels(tmp, imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
|
||||||
} else {
|
|
||||||
// try to put pixels on stack
|
|
||||||
stack.setPixels(extractSubarray(wholeDataset, startIdx, numElements), imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
IJ.showProgress(1.f);
|
|
||||||
|
|
||||||
logger.info("Creating image plus");
|
|
||||||
// stack.trim();
|
|
||||||
imp = new ImagePlus(directory + name + ": " + groupedVarnames.getFormatString(), stack);
|
|
||||||
|
|
||||||
imp.setDimensions(nChannels, nSlices, nFrames);
|
|
||||||
|
|
||||||
if (nChannels > 1) {
|
|
||||||
logger.info("Creating composite hyperstack with " + Integer.toString(nChannels) + " channels.");
|
|
||||||
imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
|
|
||||||
} else {
|
|
||||||
logger.info("Creating grayscale hyperstack.");
|
|
||||||
// imp = new CompositeImage(imp,
|
|
||||||
// CompositeImage.GRAYSCALE);
|
|
||||||
}
|
|
||||||
|
|
||||||
logger.info("nFrames: " + Integer.toString(nFrames));
|
|
||||||
logger.info("nSlices: " + Integer.toString(nSlices));
|
|
||||||
|
|
||||||
logger.info("stackSize: " + Integer.toString(stack.getSize()));
|
|
||||||
|
|
||||||
// set element_size_um
|
|
||||||
imp.getCalibration().pixelDepth = elem_sizes[0];
|
|
||||||
imp.getCalibration().pixelHeight = elem_sizes[1];
|
|
||||||
imp.getCalibration().pixelWidth = elem_sizes[2];
|
|
||||||
|
|
||||||
// logger.info(" Min = " + minMaxVal[0] +
|
|
||||||
// ", Max = " + minMaxVal[1]);
|
|
||||||
// imp.setDisplayRange(1.5*minMaxVal[0], 0.5*minMaxVal[1]);
|
|
||||||
// imp.resetDisplayRange();
|
|
||||||
int[] channelsIJ = { 4, 2, 1 };
|
|
||||||
for (int c = 0; c < nChannels; c++) {
|
|
||||||
// imp.setDisplayRange(minValChannel[c],
|
|
||||||
// maxValChannel[c],
|
|
||||||
// channelsIJ[c]);
|
|
||||||
// imp.setSlice(c+1);
|
|
||||||
imp.setPosition(c + 1, 1, 1);
|
|
||||||
logger.info("Current channel: " + Integer.toString(imp.getChannel() - 1));
|
|
||||||
|
|
||||||
imp.setDisplayRange(minValChannel[c], maxValChannel[c]);
|
|
||||||
// ,
|
|
||||||
// channelsIJ[c]);
|
|
||||||
logger.info("Setting display range for channel " + Integer.toString(c) + " (ij idx: " + Integer.toString(channelsIJ[c]) + "): \n\t" + Double.toString(minValChannel[c])
|
|
||||||
+ "/" + Double.toString(maxValChannel[c]));
|
|
||||||
}
|
|
||||||
|
|
||||||
imp.show();
|
|
||||||
imp.updateStatusbarValue();
|
|
||||||
imp.setOpenAsHyperStack(true);
|
|
||||||
} else {
|
|
||||||
// not supported format
|
|
||||||
IJ.error("The file does not contain a supported data set structure!" + "\nChannels have to be 2D or 3D scalar data sets!");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// varList should have size=0 if only grouping is wanted
|
// varList should have size=0 if only grouping is wanted
|
||||||
// use old style
|
// use old style
|
||||||
@ -1767,101 +1193,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private static Attribute getAttribute(HObject ds, String attrName) throws Exception {
|
|
||||||
for(Attribute a: getAttrList(ds)){
|
|
||||||
if (a.getName().equals(attrName)) {
|
|
||||||
return a;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return null;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Find min and maximum of array
|
|
||||||
* @param data
|
|
||||||
* @param stackSize
|
|
||||||
* @return
|
|
||||||
*/
|
|
||||||
private double[] getMinMax(Object data, long stackSize) {
|
|
||||||
double[] minmax = new double[2];
|
|
||||||
|
|
||||||
if (data instanceof byte[]) {
|
|
||||||
byte[] tmp = (byte[]) data;
|
|
||||||
minmax[0] = tmp[0];
|
|
||||||
minmax[1] = tmp[0];
|
|
||||||
for (int i = 1; i < stackSize; i++) {
|
|
||||||
double val = (double) tmp[i];
|
|
||||||
// we only support unsigned
|
|
||||||
if (tmp[i] < 0)
|
|
||||||
val = (float) Byte.MAX_VALUE - (float) Byte.MIN_VALUE + (float) tmp[i] + 1;
|
|
||||||
|
|
||||||
if (val < minmax[0])
|
|
||||||
minmax[0] = val;
|
|
||||||
if (val > minmax[1])
|
|
||||||
minmax[1] = val;
|
|
||||||
}
|
|
||||||
} else if (data instanceof short[]) {
|
|
||||||
short[] tmp = (short[]) data;
|
|
||||||
minmax[0] = tmp[0];
|
|
||||||
minmax[1] = tmp[0];
|
|
||||||
for (int i = 1; i < stackSize; i++) {
|
|
||||||
double val = (double) tmp[i];
|
|
||||||
// we only support unsigned
|
|
||||||
if (tmp[i] < 0)
|
|
||||||
val = (float) Short.MAX_VALUE - (float) Short.MIN_VALUE + (float) tmp[i] + 1;
|
|
||||||
|
|
||||||
if (val < minmax[0])
|
|
||||||
minmax[0] = val;
|
|
||||||
if (val > minmax[1])
|
|
||||||
minmax[1] = val;
|
|
||||||
}
|
|
||||||
} else if (data instanceof int[]) {
|
|
||||||
int[] tmp = (int[]) data;
|
|
||||||
minmax[0] = tmp[0];
|
|
||||||
minmax[1] = tmp[0];
|
|
||||||
for (int i = 1; i < stackSize; i++) {
|
|
||||||
if (tmp[i] < minmax[0])
|
|
||||||
minmax[0] = tmp[i];
|
|
||||||
if (tmp[i] > minmax[1])
|
|
||||||
minmax[1] = tmp[i];
|
|
||||||
}
|
|
||||||
} else if (data instanceof long[]) {
|
|
||||||
long[] tmp = (long[]) data;
|
|
||||||
minmax[0] = tmp[0];
|
|
||||||
minmax[1] = tmp[0];
|
|
||||||
for (int i = 1; i < stackSize; i++) {
|
|
||||||
if (tmp[i] < minmax[0])
|
|
||||||
minmax[0] = tmp[i];
|
|
||||||
if (tmp[i] > minmax[1])
|
|
||||||
minmax[1] = tmp[i];
|
|
||||||
}
|
|
||||||
} else if (data instanceof float[]) {
|
|
||||||
float[] tmp = (float[]) data;
|
|
||||||
minmax[0] = tmp[0];
|
|
||||||
minmax[1] = tmp[0];
|
|
||||||
for (int i = 1; i < stackSize; i++) {
|
|
||||||
if (tmp[i] < minmax[0])
|
|
||||||
minmax[0] = tmp[i];
|
|
||||||
if (tmp[i] > minmax[1])
|
|
||||||
minmax[1] = tmp[i];
|
|
||||||
}
|
|
||||||
} else if (data instanceof double[]) {
|
|
||||||
double[] tmp = (double[]) data;
|
|
||||||
minmax[0] = tmp[0];
|
|
||||||
minmax[1] = tmp[0];
|
|
||||||
for (int i = 1; i < stackSize; i++) {
|
|
||||||
if (tmp[i] < minmax[0])
|
|
||||||
minmax[0] = tmp[i];
|
|
||||||
if (tmp[i] > minmax[1])
|
|
||||||
minmax[1] = tmp[i];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
logger.info("min: " + minmax[0] + ", max: " + minmax[1]);
|
|
||||||
return minmax;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
private float[] convertDoubleToFloat(double[] dataIn) {
|
private float[] convertDoubleToFloat(double[] dataIn) {
|
||||||
float[] dataOut = new float[dataIn.length];
|
float[] dataOut = new float[dataIn.length];
|
||||||
for (int index = 0; index < dataIn.length; index++) {
|
for (int index = 0; index < dataIn.length; index++) {
|
||||||
@ -1870,7 +1201,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return dataOut;
|
return dataOut;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private float[] convertInt32ToFloat(int[] dataIn) {
|
private float[] convertInt32ToFloat(int[] dataIn) {
|
||||||
float[] dataOut = new float[dataIn.length];
|
float[] dataOut = new float[dataIn.length];
|
||||||
for (int index = 0; index < dataIn.length; index++) {
|
for (int index = 0; index < dataIn.length; index++) {
|
||||||
@ -1879,7 +1209,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return dataOut;
|
return dataOut;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private short[] convertInt32ToShort(int[] dataIn) {
|
private short[] convertInt32ToShort(int[] dataIn) {
|
||||||
short[] dataOut = new short[dataIn.length];
|
short[] dataOut = new short[dataIn.length];
|
||||||
for (int index = 0; index < dataIn.length; index++) {
|
for (int index = 0; index < dataIn.length; index++) {
|
||||||
@ -1888,7 +1217,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return dataOut;
|
return dataOut;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private float[] convertInt64ToFloat(long[] dataIn) {
|
private float[] convertInt64ToFloat(long[] dataIn) {
|
||||||
float[] dataOut = new float[dataIn.length];
|
float[] dataOut = new float[dataIn.length];
|
||||||
for (int index = 0; index < dataIn.length; index++) {
|
for (int index = 0; index < dataIn.length; index++) {
|
||||||
@ -1897,7 +1225,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return dataOut;
|
return dataOut;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private short[] convertInt64ToShort(long[] dataIn) {
|
private short[] convertInt64ToShort(long[] dataIn) {
|
||||||
short[] dataOut = new short[dataIn.length];
|
short[] dataOut = new short[dataIn.length];
|
||||||
for (int index = 0; index < dataIn.length; index++) {
|
for (int index = 0; index < dataIn.length; index++) {
|
||||||
@ -1906,7 +1233,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return dataOut;
|
return dataOut;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private Object convertToUnsigned(Object dataIn, int unsignedConvSelec) {
|
private Object convertToUnsigned(Object dataIn, int unsignedConvSelec) {
|
||||||
Object dataOut = null;
|
Object dataOut = null;
|
||||||
if (unsignedConvSelec == 0) {
|
if (unsignedConvSelec == 0) {
|
||||||
@ -1932,7 +1258,6 @@ public class HDF5Reader implements PlugIn {
|
|||||||
return dataOut;
|
return dataOut;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
private Object extractSubarray(Object data, long startIdx, long numElements) {
|
private Object extractSubarray(Object data, long startIdx, long numElements) {
|
||||||
Object subarray = null;
|
Object subarray = null;
|
||||||
|
|
||||||
|
|||||||
@ -1,5 +1,2 @@
|
|||||||
File>Import, "HDF5...", ch.psi.imagej.hdf5.HDF5Reader
|
File>Import, "HDF5...", ch.psi.imagej.hdf5.HDF5Reader
|
||||||
File>Save As, "HDF5", ch.psi.imagej.hdf5.HDF5Writer
|
File>Save As, "HDF5", ch.psi.imagej.hdf5.HDF5Writer
|
||||||
Plugins>HDF5, "Load HDF5 File", ch.psi.imagej.hdf5.HDF5Reader
|
|
||||||
Plugins>HDF5, "Save HDF5 File", ch.psi.imagej.hdf5.HDF5Writer
|
|
||||||
Plugins>HDF5, "HDF5 Preferences", ch.psi.imagej.hdf5.HDF5Config
|
|
||||||
@ -1,50 +0,0 @@
|
|||||||
/**
|
|
||||||
*
|
|
||||||
* Copyright 2014 Paul Scherrer Institute. All rights reserved.
|
|
||||||
*
|
|
||||||
* This code is free software: you can redistribute it and/or modify it under
|
|
||||||
* the terms of the GNU Lesser General Public License as published by the Free
|
|
||||||
* Software Foundation, either version 3 of the License, or (at your option) any
|
|
||||||
* later version.
|
|
||||||
*
|
|
||||||
* This code is distributed in the hope that it will be useful, but without any
|
|
||||||
* warranty; without even the implied warranty of merchantability or fitness for
|
|
||||||
* a particular purpose. See the GNU Lesser General Public License for more
|
|
||||||
* details.
|
|
||||||
*
|
|
||||||
* You should have received a copy of the GNU Lesser General Public License
|
|
||||||
* along with this code. If not, see <http://www.gnu.org/licenses/>.
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
package ch.psi.imagej.hdf5;
|
|
||||||
|
|
||||||
import org.junit.After;
|
|
||||||
import org.junit.Before;
|
|
||||||
import org.junit.Test;
|
|
||||||
|
|
||||||
/**
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
public class HDF5ConfigTest {
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @throws java.lang.Exception
|
|
||||||
*/
|
|
||||||
@Before
|
|
||||||
public void setUp() throws Exception {
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @throws java.lang.Exception
|
|
||||||
*/
|
|
||||||
@After
|
|
||||||
public void tearDown() throws Exception {
|
|
||||||
}
|
|
||||||
|
|
||||||
@Test
|
|
||||||
public void test() {
|
|
||||||
HDF5Config config = new HDF5Config();
|
|
||||||
config.run("");
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
Loading…
x
Reference in New Issue
Block a user