mirror of
https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5.git
synced 2025-06-04 01:30:40 +02:00
replaced System.outs with log messages
This commit is contained in:
parent
a5d175bd2e
commit
580c543a5d
@ -3,10 +3,14 @@ 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.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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public static String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName";
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public static String SHOW_UNMATCHED_DATASET_NAMES = "HDF5.showUnmatchedDataSetNames";
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@ -55,7 +59,7 @@ public class HDF5Config implements PlugIn {
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}
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if (!configDiag.wasOKed()) {
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// reset button was pressed
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System.out.println("reset button was pressed");
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logger.info("reset button was pressed");
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// reset all and return a new dialog
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configDiag.setVisible(false);
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this.run(arg);
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@ -64,36 +68,36 @@ public class HDF5Config implements PlugIn {
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// get parameters check if they are correct
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groupVarsByName = configDiag.getNextBoolean();
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System.out.println("groupVarsByName: " + Boolean.toString(groupVarsByName));
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logger.info("groupVarsByName: " + Boolean.toString(groupVarsByName));
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showUnmatchedDataSetNames = configDiag.getNextBoolean();
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System.out.println("showUnmatchedDataSetNames: " + Boolean.toString(showUnmatchedDataSetNames));
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logger.info("showUnmatchedDataSetNames: " + Boolean.toString(showUnmatchedDataSetNames));
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groupVarsByNameFormatGroup = configDiag.getNextString();
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System.out.println("groupVarsByNameFormatGroup: " + groupVarsByNameFormatGroup);
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logger.info("groupVarsByNameFormatGroup: " + groupVarsByNameFormatGroup);
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groupVarsByNameFormat = configDiag.getNextString();
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System.out.println("groupVarsByNameFormat: " + groupVarsByNameFormat);
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logger.info("groupVarsByNameFormat: " + groupVarsByNameFormat);
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// dollarRegexpForGrouping = configDiag.getNextString();
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// System.out.println("dollarRegexpForGrouping: " +
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// logger.info("dollarRegexpForGrouping: " +
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// dollarRegexpForGrouping);
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try {
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String[] formatTokens = HDF5GroupedVarnames.parseFormatString(groupVarsByNameFormat, dollarRegexpForGrouping);
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for (int i = 0; i < formatTokens.length; i++) {
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System.out.println("tok " + Integer.toString(i) + " : " + formatTokens[i]);
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logger.info("tok " + Integer.toString(i) + " : " + formatTokens[i]);
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}
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} catch (PatternSyntaxException e) {
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// produce an error dialog an start over
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String errMsg = e.getMessage();
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System.out.println(errMsg);
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logger.info(errMsg);
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// reset all and return a new dialog
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configDiag.setVisible(false);
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this.run(arg);
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return;
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}
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System.out.println("Saving...");
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logger.info("Saving...");
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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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@ -146,7 +150,7 @@ public class HDF5Config implements PlugIn {
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String dollarRegexpForGrouping = "[0-9]+"; // default
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return dollarRegexpForGrouping;
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} else {
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System.out.println("No default value for key: " + key);
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logger.info("No default value for key: " + key);
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return null;
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}
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}
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@ -1,5 +1,6 @@
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package ch.psi.imagej.hdf5;
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import java.util.logging.Logger;
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import java.util.regex.*;
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import java.util.ArrayList;
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import java.util.Arrays;
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@ -8,6 +9,8 @@ import java.util.List;
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public class HDF5GroupedVarnames {
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private static final Logger logger = Logger.getLogger(HDF5GroupedVarnames.class.getName());
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private final List<String> matchedVarNames = new ArrayList<String>();
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private final List<String> unMatchedVarNames = new ArrayList<String>();
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private final List<TimeFrame> frameList = new ArrayList<TimeFrame>();
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@ -26,7 +29,7 @@ public class HDF5GroupedVarnames {
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boolean rightOrderOfFormatVars = groupVarsByNameFormat.indexOf("$T") < groupVarsByNameFormat.indexOf("$C");
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for (int i = 0; i < formatTokens.length; i++) {
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System.out.println("tok " + Integer.toString(i) + " : " + formatTokens[i]);
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logger.info("tok " + Integer.toString(i) + " : " + formatTokens[i]);
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}
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if (formatTokens.length < 2 || !containsFormatVars || !rightOrderOfFormatVars) {
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throw new PatternSyntaxException("Your format string has errors. " + "You must provide $T and $C and " + "also in correct order!", groupVarsByNameFormat, -1);
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@ -34,7 +37,7 @@ public class HDF5GroupedVarnames {
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String regexp = groupVarsByNameFormat;
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regexp = regexp.replace("$T", dollarRegexpForGrouping);
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regexp = regexp.replace("$C", dollarRegexpForGrouping);
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System.out.println(regexp);
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logger.info(regexp);
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// check if we have a regexp;
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Pattern.compile(regexp);
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return formatTokens;
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@ -48,14 +51,14 @@ public class HDF5GroupedVarnames {
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} catch (PatternSyntaxException e) {
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// produce an error dialog an start over
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String errMsg = e.getMessage();
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System.out.println(errMsg);
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logger.info(errMsg);
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return;
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}
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String regexp = groupVarsByNameFormat;
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regexp = regexp.replace("$T", dollarRegexpForGrouping);
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regexp = regexp.replace("$C", dollarRegexpForGrouping);
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System.out.println(regexp);
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logger.info(regexp);
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// check if we have a regexp;
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Pattern p = null;
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p = Pattern.compile(regexp);
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@ -66,7 +69,7 @@ public class HDF5GroupedVarnames {
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Matcher m = p.matcher(varNames[i]);
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boolean b = m.matches();
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if (b) {
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System.out.println(varNames[i]);
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logger.info(varNames[i]);
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matchedVarNames.add(varNames[i]);
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} else {
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unMatchedVarNames.add(varNames[i]);
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@ -101,14 +104,14 @@ public class HDF5GroupedVarnames {
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}
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if (tokens.length < 2 || tokens.length > 3) {
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System.out.println("Error parsing varname!");
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logger.info("Error parsing varname!");
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} else {
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Integer channelIndex = new Integer(tokens[1]);
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System.out.println("channelIndex: " + channelIndex.toString());
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System.out.println("left token: " + tokens[0]);
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logger.info("channelIndex: " + channelIndex.toString());
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logger.info("left token: " + tokens[0]);
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tokens = tokens[0].split("/t");
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Integer frameIndex = new Integer(tokens[1]);
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System.out.println("frameIndex: " + frameIndex.toString());
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logger.info("frameIndex: " + frameIndex.toString());
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if (minFrameIndex == -1)
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minFrameIndex = frameIndex.intValue();
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@ -135,7 +138,7 @@ public class HDF5GroupedVarnames {
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frame.addChannel(channelIndex.intValue());
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frameList.add(frame);
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}
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// System.out.println(frame.toString());
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// logger.info(frame.toString());
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}
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}
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}
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@ -212,8 +215,8 @@ public class HDF5GroupedVarnames {
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}
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public void setFrameAndChannelRange(int minFrame, int skipFrame, int maxFrame, int minChannel, int skipChannel, int maxChannel) {
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System.out.println("Setting frame range: " + Integer.toString(minFrame) + ":" + Integer.toString(skipFrame) + ":" + Integer.toString(maxFrame));
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System.out.println("Setting channel range: " + Integer.toString(minChannel) + ":" + Integer.toString(skipChannel) + ":" + Integer.toString(maxChannel));
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logger.info("Setting frame range: " + Integer.toString(minFrame) + ":" + Integer.toString(skipFrame) + ":" + Integer.toString(maxFrame));
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logger.info("Setting channel range: " + Integer.toString(minChannel) + ":" + Integer.toString(skipChannel) + ":" + Integer.toString(maxChannel));
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if (hasAllFramesInRange()) {
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// copy frames
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List<TimeFrame> completeFrameList = new ArrayList<TimeFrame>(frameList);
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@ -225,7 +228,7 @@ public class HDF5GroupedVarnames {
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TimeFrame frame = new TimeFrame(frameAllChannels.getFrameIndex());
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// TODO remove unwanted channels
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for (int c = minChannel; c < maxChannel + 1; c += skipChannel) {
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// System.out.println("Adding channels: " +
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// logger.info("Adding channels: " +
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// Integer.toString(c));
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frame.addChannel(c);
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}
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@ -235,9 +238,9 @@ public class HDF5GroupedVarnames {
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}
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// TODO update min/max of frames/channels
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nChannels = ((maxChannel - minChannel) / skipChannel) + 1;
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System.out.println("Adding nChannels: " + Integer.toString(nChannels));
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logger.info("Adding nChannels: " + Integer.toString(nChannels));
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} else {
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System.out.println("-------------------------\n" + "hasAllFramesInRange==false\n" + "-------------------------");
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logger.info("-------------------------\n" + "hasAllFramesInRange==false\n" + "-------------------------");
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// copy frames
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List<TimeFrame> completeFrameList = new ArrayList<TimeFrame>(frameList);
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// clear frames
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@ -246,12 +249,12 @@ public class HDF5GroupedVarnames {
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for (int f = minFrame; f < maxFrame + 1; f += skipFrame) {
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TimeFrame frame = new TimeFrame(f);
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int idx = completeFrameList.indexOf(frame);
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// System.out.println("index of frame in list: " +
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// logger.info("index of frame in list: " +
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// Integer.toString(idx));
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if (idx != -1) {
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// TODO remove unwanted channels
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for (int c = minChannel; c < maxChannel + 1; c += skipChannel) {
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// System.out.println("Adding channels: " +
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// logger.info("Adding channels: " +
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// Integer.toString(c));
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frame.addChannel(c);
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}
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@ -259,12 +262,12 @@ public class HDF5GroupedVarnames {
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// nChannels = frame.getNChannels();
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frameList.add(frame);
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} else {
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System.out.println("Timestep " + Integer.toString(f) + " is missing!");
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logger.info("Timestep " + Integer.toString(f) + " is missing!");
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}
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}
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// TODO update min/max of frames/channels
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nChannels = ((maxChannel - minChannel) / skipChannel) + 1;
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System.out.println("Adding nChannels: " + Integer.toString(nChannels));
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logger.info("Adding nChannels: " + Integer.toString(nChannels));
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}
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}
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}
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@ -134,18 +134,18 @@ public class HDF5Reader implements PlugIn {
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attrName = attrSelecD.getNextChoice();
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}
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System.out.println("Reading attribute");
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logger.info("Reading attribute");
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Attribute attr = getAttribute(gr, attrName);
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System.out.println("Reading attribute is ok");
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logger.info("Reading attribute is ok");
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if (attr != null)
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System.out.println("attr is not null");
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System.out.println("attr.getName(): " + attr.getName());
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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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System.out.println(dType.getDatatypeDescription());
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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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System.out.println("get value is ok");
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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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@ -156,14 +156,14 @@ public class HDF5Reader implements PlugIn {
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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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System.out.println("File has format string for grouping: " + groupVarsByNameFormat);
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logger.info("File has format string for grouping: " + groupVarsByNameFormat);
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} else {
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System.out.println("File has no format string for grouping" + ", using default");
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logger.info("File has no format string for grouping" + ", using default");
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groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
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groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
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}
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} catch (Exception e) {
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System.out.println("Error occured read format string " + "for grouping, using default");
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logger.info("Error occured read format string " + "for grouping, using default");
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groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
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groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
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}
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@ -208,7 +208,7 @@ public class HDF5Reader implements PlugIn {
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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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System.out.println(groupedVarnames.toString());
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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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@ -249,7 +249,7 @@ public class HDF5Reader implements PlugIn {
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varSelections[i] = title;
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defaultValues[i] = false;
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}
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System.out.println("addcheckboxgroup with " + unmatchedVarNames.size() + " rows");
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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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@ -282,7 +282,7 @@ public class HDF5Reader implements PlugIn {
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if (frameRangeToks.length == 1) {
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// single frame
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try {
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System.out.println("single frame");
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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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@ -292,7 +292,7 @@ public class HDF5Reader implements PlugIn {
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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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System.out.println("frame range with skipFrameIndex=1");
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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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@ -302,7 +302,7 @@ public class HDF5Reader implements PlugIn {
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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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System.out.println("frame range with skipFrameIndex");
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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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@ -312,7 +312,7 @@ public class HDF5Reader implements PlugIn {
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}
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} else {
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// wrong format
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System.out.println("wrong format");
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logger.info("wrong format");
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wrongFrameRange = true;
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}
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@ -352,7 +352,7 @@ public class HDF5Reader implements PlugIn {
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}
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if (wrongFrameRange || wrongChannelRange) {
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// show dialog again
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System.out.println("show dialog again");
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logger.info("show dialog again");
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// TODO reset dialog when possible
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gd = new GenericDialog("Range Selection");
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gd.addMessage("Select frames and channels you want to read");
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@ -363,7 +363,7 @@ public class HDF5Reader implements PlugIn {
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gd.addStringField("Channel selection (start:[step:]end): ",
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Integer.toString(minChannelIndex) + ":" + Integer.toString(skipChannelIndex) + ":" + Integer.toString(maxChannelIndex));
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gd.showDialog();
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System.out.println("read ranges again");
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logger.info("read ranges again");
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frameRange = gd.getNextString();
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channelRange = gd.getNextString();
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@ -385,7 +385,7 @@ public class HDF5Reader implements PlugIn {
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varList.add((Dataset) ds);
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}
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} catch (Exception e) {
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System.out.println("The file does not contain a variable " + "with name " + "`" + dsName + "`!");
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logger.info("The file does not contain a variable " + "with name " + "`" + dsName + "`!");
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}
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}
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} else {
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@ -395,11 +395,11 @@ public class HDF5Reader implements PlugIn {
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} else if (varList.size() > 1000) {
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System.out.println("#######");
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logger.info("#######");
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for(Dataset d: varList){
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System.out.println(d.getFullName());
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logger.info(d.getFullName());
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}
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System.out.println("#######");
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logger.info("#######");
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/*-----------------------------------------------------------------
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* FIXME: quick an dirty hack for files with more than 1000
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@ -448,7 +448,7 @@ public class HDF5Reader implements PlugIn {
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varSelections[i] = title;
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defaultValues[i] = false;
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}
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System.out.println("addcheckboxgroup with " + varList.size() + " rows");
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logger.info("addcheckboxgroup with " + varList.size() + " rows");
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gd.addCheckboxGroup(varList.size(), 1, varSelections, defaultValues);
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addScrollBars(gd);
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gd.showDialog();
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@ -478,12 +478,12 @@ public class HDF5Reader implements PlugIn {
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try {
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TimeFrame f = groupedVarnames.getFrame(0);
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if (f == null)
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System.out.println("frame is null");
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logger.info("frame is null");
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if (formatTokens.length == 2)
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dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[0]);
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else if (formatTokens.length == 3)
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dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[0]) + formatTokens[2];
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System.out.println("VarName: " + dsName);
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logger.info("VarName: " + dsName);
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HObject ds = inFile.get(dsName);
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if (ds != null && ds instanceof Dataset) {
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var = (Dataset) ds;
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@ -511,7 +511,7 @@ public class HDF5Reader implements PlugIn {
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elem_sizes[1] = 1.0;
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elem_sizes[2] = 1.0;
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} else {
|
||||
System.out.println("Reading element_size_um");
|
||||
logger.info("Reading element_size_um");
|
||||
float[] tmp = null;
|
||||
try {
|
||||
tmp = ((float[]) elemsize_att.getValue());
|
||||
@ -558,7 +558,7 @@ public class HDF5Reader implements PlugIn {
|
||||
|
||||
// create a new image stack and fill in the data
|
||||
ImageStack stack = new ImageStack(nCols, nRows, nFrames * nSlices * nChannels);
|
||||
System.out.println("stackSize: " + Integer.toString(stack.getSize()));
|
||||
logger.info("stackSize: " + Integer.toString(stack.getSize()));
|
||||
|
||||
ImagePlus imp = new ImagePlus();
|
||||
// to get getFrameIndex() working
|
||||
@ -575,7 +575,7 @@ public class HDF5Reader implements PlugIn {
|
||||
// get current frame
|
||||
TimeFrame f = groupedVarnames.getFrame(fIdx);
|
||||
if (f == null)
|
||||
System.out.println("frame is null");
|
||||
logger.info("frame is null");
|
||||
// get channel indices
|
||||
|
||||
// TODO: check if frame has same parameters as first,
|
||||
@ -588,7 +588,7 @@ public class HDF5Reader implements PlugIn {
|
||||
else if (formatTokens.length == 3)
|
||||
dsName = formatTokens[0] + Integer.toString(f.getFrameIndex()) + formatTokens[1] + Integer.toString(f.getChannelIndices()[cIdx]) + formatTokens[2];
|
||||
|
||||
System.out.println("VarName: " + dsName);
|
||||
logger.info("VarName: " + dsName);
|
||||
|
||||
HObject ds = inFile.get(dsName);
|
||||
if (ds != null && ds instanceof Dataset) {
|
||||
@ -648,7 +648,7 @@ public class HDF5Reader implements PlugIn {
|
||||
short[] tmp = (short[]) extractSubarray(wholeDataset, startIdx, numElements);
|
||||
stack.setPixels(tmp, imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
||||
} else if (wholeDataset instanceof int[]) {
|
||||
System.out.println("Datatype `int` is not supported. " + "Skipping whole frame!");
|
||||
logger.info("Datatype `int` is not supported. " + "Skipping whole frame!");
|
||||
// int[] tmp = (int[])
|
||||
// extractSubarray(wholeDataset,
|
||||
// startIdx,
|
||||
@ -666,7 +666,7 @@ public class HDF5Reader implements PlugIn {
|
||||
// imp.getStackIndex(cIdx+1,lev+1,fIdx+1));
|
||||
// }
|
||||
} else if (wholeDataset instanceof long[]) {
|
||||
System.out.println("Datatype `long` is not supported. " + "Skipping whole frame!");
|
||||
logger.info("Datatype `long` is not supported. " + "Skipping whole frame!");
|
||||
// long[] tmp = (long[])
|
||||
// extractSubarray(wholeDataset,
|
||||
// startIdx,
|
||||
@ -687,7 +687,7 @@ public class HDF5Reader implements PlugIn {
|
||||
float[] tmp = (float[]) extractSubarray(wholeDataset, startIdx, numElements);
|
||||
stack.setPixels(tmp, imp.getStackIndex(cIdx + 1, lev + 1, fIdx + 1));
|
||||
} else if (wholeDataset instanceof double[]) {
|
||||
System.out.println("Datatype `double` is not supported. " + "Converting whole frame to `float`!");
|
||||
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 {
|
||||
@ -699,32 +699,32 @@ public class HDF5Reader implements PlugIn {
|
||||
}
|
||||
IJ.showProgress(1.f);
|
||||
|
||||
System.out.println("Creating image plus");
|
||||
logger.info("Creating image plus");
|
||||
// stack.trim();
|
||||
imp = new ImagePlus(directory + name + ": " + groupedVarnames.getFormatString(), stack);
|
||||
|
||||
imp.setDimensions(nChannels, nSlices, nFrames);
|
||||
|
||||
if (nChannels > 1) {
|
||||
System.out.println("Creating composite hyperstack with " + Integer.toString(nChannels) + " channels.");
|
||||
logger.info("Creating composite hyperstack with " + Integer.toString(nChannels) + " channels.");
|
||||
imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
|
||||
} else {
|
||||
System.out.println("Creating grayscale hyperstack.");
|
||||
logger.info("Creating grayscale hyperstack.");
|
||||
// imp = new CompositeImage(imp,
|
||||
// CompositeImage.GRAYSCALE);
|
||||
}
|
||||
|
||||
System.out.println("nFrames: " + Integer.toString(nFrames));
|
||||
System.out.println("nSlices: " + Integer.toString(nSlices));
|
||||
logger.info("nFrames: " + Integer.toString(nFrames));
|
||||
logger.info("nSlices: " + Integer.toString(nSlices));
|
||||
|
||||
System.out.println("stackSize: " + Integer.toString(stack.getSize()));
|
||||
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];
|
||||
|
||||
// System.out.println(" Min = " + minMaxVal[0] +
|
||||
// logger.info(" Min = " + minMaxVal[0] +
|
||||
// ", Max = " + minMaxVal[1]);
|
||||
// imp.setDisplayRange(1.5*minMaxVal[0], 0.5*minMaxVal[1]);
|
||||
// imp.resetDisplayRange();
|
||||
@ -735,12 +735,12 @@ public class HDF5Reader implements PlugIn {
|
||||
// channelsIJ[c]);
|
||||
// imp.setSlice(c+1);
|
||||
imp.setPosition(c + 1, 1, 1);
|
||||
System.out.println("Current channel: " + Integer.toString(imp.getChannel() - 1));
|
||||
logger.info("Current channel: " + Integer.toString(imp.getChannel() - 1));
|
||||
|
||||
imp.setDisplayRange(minValChannel[c], maxValChannel[c]);
|
||||
// ,
|
||||
// channelsIJ[c]);
|
||||
System.out.println("Setting display range for channel " + Integer.toString(c) + " (ij idx: " + Integer.toString(channelsIJ[c]) + "): \n\t" + Double.toString(minValChannel[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]));
|
||||
}
|
||||
|
||||
@ -763,12 +763,12 @@ public class HDF5Reader implements PlugIn {
|
||||
Datatype datatypeIfUnsupported = null;
|
||||
long[] extent = var.getDims();
|
||||
|
||||
System.out.println("Reading Variable: " + var.getName());
|
||||
System.out.println(" Rank = " + rank + ", Data-type = " + datatype.getDatatypeDescription());
|
||||
logger.info("Reading Variable: " + var.getName());
|
||||
logger.info(" Rank = " + rank + ", Data-type = " + datatype.getDatatypeDescription());
|
||||
System.out.print(" Extent in px (level,row,col):");
|
||||
for (int d = 0; d < rank; ++d)
|
||||
System.out.print(" " + extent[d]);
|
||||
System.out.println("");
|
||||
logger.info("");
|
||||
IJ.showStatus("Reading Variable: " + var.getName() + " (" + extent[0] + " slices)");
|
||||
|
||||
Attribute elemsize_att = getAttribute(var, "element_size_um");
|
||||
@ -778,7 +778,7 @@ public class HDF5Reader implements PlugIn {
|
||||
elem_sizes[1] = 1.0;
|
||||
elem_sizes[2] = 1.0;
|
||||
} else {
|
||||
System.out.println("Reading element_size_um");
|
||||
logger.info("Reading element_size_um");
|
||||
Object tmp = elemsize_att.getValue();
|
||||
if (tmp instanceof float[]) {
|
||||
elem_sizes[0] = ((float[]) tmp)[0];
|
||||
@ -797,7 +797,7 @@ public class HDF5Reader implements PlugIn {
|
||||
elem_sizes[2] = 1.0;
|
||||
}
|
||||
}
|
||||
System.out.println(" Element-Size in um (level,row,col): " + elem_sizes[0] + ", " + elem_sizes[1] + ", " + elem_sizes[2]);
|
||||
logger.info(" Element-Size in um (level,row,col): " + elem_sizes[0] + ", " + elem_sizes[1] + ", " + elem_sizes[2]);
|
||||
|
||||
// nice gadget to update the progress bar
|
||||
long progressDivisor = extent[0] / 50; // we assume 50 process steps
|
||||
@ -806,7 +806,7 @@ public class HDF5Reader implements PlugIn {
|
||||
|
||||
// check if we have an unsupported datatype
|
||||
if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) {
|
||||
System.out.println("Datatype not supported by ImageJ");
|
||||
logger.info("Datatype not supported by ImageJ");
|
||||
GenericDialog typeSelDiag = new GenericDialog("Datatype Selection");
|
||||
typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n");
|
||||
typeSelDiag.addMessage("Please select your wanted datatype.\n");
|
||||
@ -821,11 +821,11 @@ public class HDF5Reader implements PlugIn {
|
||||
}
|
||||
int selection = typeSelDiag.getNextChoiceIndex();
|
||||
if (selection == 0) {
|
||||
System.out.println("float selected");
|
||||
logger.info("float selected");
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
}
|
||||
if (selection == 1) {
|
||||
System.out.println("short selected");
|
||||
logger.info("short selected");
|
||||
int typeSizeInByte = 2;
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, -1);
|
||||
}
|
||||
@ -833,7 +833,7 @@ public class HDF5Reader implements PlugIn {
|
||||
|
||||
// read dataset
|
||||
if (rank == 5 && extent[4] == 3) {
|
||||
System.out.println(" Detected HyperVolume (type RGB).");
|
||||
logger.info(" Detected HyperVolume (type RGB).");
|
||||
|
||||
// create a new image stack and fill in the data
|
||||
ImageStack stack = new ImageStack((int) extent[3], (int) extent[2]);
|
||||
@ -1044,10 +1044,10 @@ public class HDF5Reader implements PlugIn {
|
||||
int nChannels = 3;
|
||||
int nSlices = (int) extent[1];
|
||||
int nFrames = (int) extent[0];
|
||||
System.out.println("nFrames: " + Integer.toString(nFrames));
|
||||
System.out.println("nSlices: " + Integer.toString(nSlices));
|
||||
logger.info("nFrames: " + Integer.toString(nFrames));
|
||||
logger.info("nSlices: " + Integer.toString(nSlices));
|
||||
|
||||
System.out.println("stackSize: " + Integer.toString(stack.getSize()));
|
||||
logger.info("stackSize: " + Integer.toString(stack.getSize()));
|
||||
|
||||
imp.setDimensions(nChannels, nSlices, nFrames);
|
||||
imp = new CompositeImage(imp, CompositeImage.COMPOSITE);
|
||||
@ -1068,7 +1068,7 @@ public class HDF5Reader implements PlugIn {
|
||||
imp.show();
|
||||
} else if (rank == 4) {
|
||||
if (extent[3] == 3) {
|
||||
System.out.println(" Detected color Image (type RGB).");
|
||||
logger.info(" Detected color Image (type RGB).");
|
||||
|
||||
// create a new image stack and fill in the data
|
||||
ImageStack stack = new ImageStack((int) extent[2], (int) extent[1]);
|
||||
@ -1245,7 +1245,7 @@ public class HDF5Reader implements PlugIn {
|
||||
imp.updateStatusbarValue();
|
||||
} else // we have a HyperVolume
|
||||
{
|
||||
System.out.println(" Detected HyperVolume (type GREYSCALE).");
|
||||
logger.info(" Detected HyperVolume (type GREYSCALE).");
|
||||
|
||||
// create a new image stack and fill in the data
|
||||
ImageStack stack = new ImageStack((int) extent[3], (int) extent[2]);
|
||||
@ -1342,11 +1342,11 @@ public class HDF5Reader implements PlugIn {
|
||||
int nFrames = (int) extent[0];
|
||||
Integer nFramesI = new Integer(nFrames);
|
||||
Integer nSlicesI = new Integer(nSlices);
|
||||
System.out.println("nFrames: " + nFramesI.toString());
|
||||
System.out.println("nSlices: " + nSlicesI.toString());
|
||||
logger.info("nFrames: " + nFramesI.toString());
|
||||
logger.info("nSlices: " + nSlicesI.toString());
|
||||
|
||||
Integer myStackSize = new Integer(stack.getSize());
|
||||
System.out.println("stackSize: " + myStackSize.toString());
|
||||
logger.info("stackSize: " + myStackSize.toString());
|
||||
|
||||
imp.setDimensions(nChannels, nSlices, nFrames);
|
||||
imp.setOpenAsHyperStack(true);
|
||||
@ -1360,7 +1360,7 @@ public class HDF5Reader implements PlugIn {
|
||||
imp.show();
|
||||
}
|
||||
} else if (rank == 3 && extent[2] == 3) {
|
||||
System.out.println("This is an rgb image");
|
||||
logger.info("This is an rgb image");
|
||||
// create a new image stack and fill in the data
|
||||
ImageStack stack = new ImageStack((int) extent[1], (int) extent[0]);
|
||||
|
||||
@ -1515,7 +1515,7 @@ public class HDF5Reader implements PlugIn {
|
||||
imp.show();
|
||||
imp.updateStatusbarValue();
|
||||
} else if (rank == 3) {
|
||||
System.out.println("Rank is 3");
|
||||
logger.info("Rank is 3");
|
||||
|
||||
// create a new image stack and fill in the data
|
||||
ImageStack stack = new ImageStack((int) extent[2], (int) extent[1]);
|
||||
@ -1605,7 +1605,7 @@ public class HDF5Reader implements PlugIn {
|
||||
|
||||
// check if we have an unsupported datatype
|
||||
if (datatype.getDatatypeClass() == Datatype.CLASS_INTEGER && (datatype.getDatatypeSize() == 4 || datatype.getDatatypeSize() == 8)) {
|
||||
System.out.println("Datatype not supported by ImageJ");
|
||||
logger.info("Datatype not supported by ImageJ");
|
||||
GenericDialog typeSelDiag = new GenericDialog("Datatype Selection");
|
||||
typeSelDiag.addMessage("The datatype `" + datatype.getDatatypeDescription() + "` is not supported by ImageJ.\n\n");
|
||||
typeSelDiag.addMessage("Please select your wanted datatype.\n");
|
||||
@ -1620,11 +1620,11 @@ public class HDF5Reader implements PlugIn {
|
||||
}
|
||||
int selection = typeSelDiag.getNextChoiceIndex();
|
||||
if (selection == 0) {
|
||||
System.out.println("float selected");
|
||||
logger.info("float selected");
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
}
|
||||
if (selection == 1) {
|
||||
System.out.println("short selected");
|
||||
logger.info("short selected");
|
||||
int typeSizeInByte = 2;
|
||||
datatypeIfUnsupported = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, -1);
|
||||
}
|
||||
@ -1693,7 +1693,7 @@ public class HDF5Reader implements PlugIn {
|
||||
double imgMax = ips.getMax();
|
||||
double imgMin = ips.getMin();
|
||||
|
||||
System.out.println(" Min = " + imgMin + ", Max = " + imgMax);
|
||||
logger.info(" Min = " + imgMin + ", Max = " + imgMax);
|
||||
ips.setMinAndMax(imgMin, imgMax);
|
||||
imp.updateAndDraw();
|
||||
imp.show();
|
||||
@ -1927,7 +1927,7 @@ public class HDF5Reader implements PlugIn {
|
||||
} else if (unsignedConvSelec == 1) {
|
||||
// convert to float
|
||||
if (dataIn instanceof short[]) {
|
||||
System.out.println("Converting to float");
|
||||
logger.info("Converting to float");
|
||||
short[] tmpIn = (short[]) dataIn;
|
||||
float[] tmp = new float[tmpIn.length];
|
||||
for (int i = 0; i < tmp.length; i++)
|
||||
|
||||
@ -25,9 +25,11 @@ import ij.io.*;
|
||||
import ij.plugin.filter.PlugInFilter;
|
||||
import ij.process.*;
|
||||
import ij.gui.*;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.logging.Logger;
|
||||
|
||||
import javax.swing.tree.DefaultMutableTreeNode;
|
||||
|
||||
@ -36,6 +38,9 @@ import ncsa.hdf.object.h5.*; // the HDF5 implementation
|
||||
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
|
||||
|
||||
public class HDF5Writer implements PlugInFilter {
|
||||
|
||||
private static final Logger logger = Logger.getLogger(HDF5Writer.class.getName());
|
||||
|
||||
private Boolean _batchMode = false;
|
||||
private String _batchFileName = null;
|
||||
|
||||
@ -96,7 +101,7 @@ public class HDF5Writer implements PlugInFilter {
|
||||
|
||||
// check for hyperstack
|
||||
if (imp.getOpenAsHyperStack() || imp.isHyperStack()) {
|
||||
System.out.println("This is a hyperstack");
|
||||
logger.info("This is a hyperstack");
|
||||
boolean splitChannels = true;
|
||||
gd.addCheckbox("Split frames and channels", splitChannels);
|
||||
gd.addStringField(imp.getTitle(), "/t$T/channel$C");
|
||||
@ -108,14 +113,14 @@ public class HDF5Writer implements PlugInFilter {
|
||||
int nRows = imp.getHeight();
|
||||
int nCols = imp.getWidth();
|
||||
boolean isComposite = imp.isComposite();
|
||||
System.out.println("isComposite: " + Boolean.toString(isComposite));
|
||||
System.out.println("Saving image \"" + title + "\"");
|
||||
System.out.println("nDims: " + Integer.toString(nDims));
|
||||
System.out.println("nFrames: " + Integer.toString(nFrames));
|
||||
System.out.println("nChannels: " + Integer.toString(nChannels));
|
||||
System.out.println("nSlices: " + Integer.toString(nLevs));
|
||||
System.out.println("nRows: " + Integer.toString(nRows));
|
||||
System.out.println("nCols: " + Integer.toString(nCols));
|
||||
logger.info("isComposite: " + Boolean.toString(isComposite));
|
||||
logger.info("Saving image \"" + title + "\"");
|
||||
logger.info("nDims: " + Integer.toString(nDims));
|
||||
logger.info("nFrames: " + Integer.toString(nFrames));
|
||||
logger.info("nChannels: " + Integer.toString(nChannels));
|
||||
logger.info("nSlices: " + Integer.toString(nLevs));
|
||||
logger.info("nRows: " + Integer.toString(nRows));
|
||||
logger.info("nCols: " + Integer.toString(nCols));
|
||||
gd.showDialog();
|
||||
if (gd.wasCanceled()) {
|
||||
IJ.error("Plugin canceled!");
|
||||
@ -123,22 +128,22 @@ public class HDF5Writer implements PlugInFilter {
|
||||
}
|
||||
splitChannels = gd.getNextBoolean();
|
||||
String formatString = gd.getNextString();
|
||||
System.out.println("formatString: " + formatString);
|
||||
System.out.println("Bitdepth: " + imp.getBitDepth());
|
||||
System.out.println("Saving HDF5 File: " + filename);
|
||||
logger.info("formatString: " + formatString);
|
||||
logger.info("Bitdepth: " + imp.getBitDepth());
|
||||
logger.info("Saving HDF5 File: " + filename);
|
||||
|
||||
int imgColorDepth = imp.getBitDepth();
|
||||
int imgColorType = imp.getType();
|
||||
Datatype type = null;
|
||||
if (imgColorType == ImagePlus.GRAY8) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: GRAY8");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY16) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: GRAY16");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
|
||||
int typeSizeInByte = 2;
|
||||
type = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY32) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: GRAY32");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
|
||||
// int typeSizeInByte = 4;
|
||||
type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
}
|
||||
@ -176,9 +181,9 @@ public class HDF5Writer implements PlugInFilter {
|
||||
for (int c = 0; c < nChannels; c++) {
|
||||
String fullName = makeDataSetName(formatTokens, f, c);
|
||||
String dataSetName = getDataSetDescriptor(fullName);
|
||||
System.out.println("dataset name: " + dataSetName);
|
||||
logger.info("dataset name: " + dataSetName);
|
||||
String groupName = getGroupDescriptor(fullName);
|
||||
System.out.println("group name: " + groupName);
|
||||
logger.info("group name: " + groupName);
|
||||
// ensure group exists
|
||||
Group group = createGroupRecursive(groupName, null, outFile);
|
||||
// create data set
|
||||
@ -208,14 +213,14 @@ public class HDF5Writer implements PlugInFilter {
|
||||
// dataet
|
||||
// write levels
|
||||
|
||||
System.out.println("selected.length: " + Integer.toString(selected.length));
|
||||
System.out.println("channelDims.length: " + Integer.toString(channelDims.length));
|
||||
logger.info("selected.length: " + Integer.toString(selected.length));
|
||||
logger.info("channelDims.length: " + Integer.toString(channelDims.length));
|
||||
if (nLevs == 1) {
|
||||
for (int d = 0; d < selected.length; d++) {
|
||||
selected[d] = channelDims[d];
|
||||
}
|
||||
int stackIndex = imp.getStackIndex(c + 1, 1, f + 1);
|
||||
System.out.println("Stackindex: " + Integer.toString(stackIndex));
|
||||
logger.info("Stackindex: " + Integer.toString(stackIndex));
|
||||
// get raw data
|
||||
Object slice = stack.getPixels(stackIndex);
|
||||
assert (slice != null);
|
||||
@ -263,7 +268,7 @@ public class HDF5Writer implements PlugInFilter {
|
||||
return;
|
||||
}
|
||||
} else {
|
||||
System.out.println("This is NO hyperstack");
|
||||
logger.info("This is NO hyperstack");
|
||||
// String title = imp.getTitle();
|
||||
// int nDims = imp.getNDimensions();
|
||||
// int nFrames = imp.getNFrames();
|
||||
@ -272,14 +277,14 @@ public class HDF5Writer implements PlugInFilter {
|
||||
// int nRows = imp.getHeight();
|
||||
// int nCols = imp.getWidth();
|
||||
// boolean isComposite = imp.isComposite() ;
|
||||
// System.out.println("isComposite: "+Boolean.toString(isComposite));
|
||||
// System.out.println("Saving image \""+title+"\"");
|
||||
// System.out.println("nDims: "+Integer.toString(nDims));
|
||||
// System.out.println("nFrames: "+Integer.toString(nFrames));
|
||||
// System.out.println("nChannels: "+Integer.toString(nChannels));
|
||||
// System.out.println("nSlices: "+Integer.toString(nLevs));
|
||||
// System.out.println("nRows: "+Integer.toString(nRows));
|
||||
// System.out.println("nCols: "+Integer.toString(nCols));
|
||||
// logger.info("isComposite: "+Boolean.toString(isComposite));
|
||||
// logger.info("Saving image \""+title+"\"");
|
||||
// logger.info("nDims: "+Integer.toString(nDims));
|
||||
// logger.info("nFrames: "+Integer.toString(nFrames));
|
||||
// logger.info("nChannels: "+Integer.toString(nChannels));
|
||||
// logger.info("nSlices: "+Integer.toString(nLevs));
|
||||
// logger.info("nRows: "+Integer.toString(nRows));
|
||||
// logger.info("nCols: "+Integer.toString(nCols));
|
||||
|
||||
gd.addStringField(imp.getTitle(), "");
|
||||
gd.showDialog();
|
||||
@ -314,12 +319,12 @@ public class HDF5Writer implements PlugInFilter {
|
||||
int imgColorDepth;
|
||||
int imgColorType;
|
||||
|
||||
System.out.println("writing data to variable: " + varName);
|
||||
logger.info("writing data to variable: " + varName);
|
||||
|
||||
String dataSetName = getDataSetDescriptor(varName);
|
||||
System.out.println("dataset name: " + dataSetName);
|
||||
logger.info("dataset name: " + dataSetName);
|
||||
String groupName = getGroupDescriptor(varName);
|
||||
System.out.println("group name: " + groupName);
|
||||
logger.info("group name: " + groupName);
|
||||
|
||||
// ensure group exists
|
||||
Group group = createGroupRecursive(groupName, null, outFile);
|
||||
@ -342,7 +347,7 @@ public class HDF5Writer implements PlugInFilter {
|
||||
} else {
|
||||
// color images have 4 dimensions, grey value images
|
||||
// have 3.
|
||||
System.out.println("adding 4 dimensions");
|
||||
logger.info("adding 4 dimensions");
|
||||
dims = new long[4];
|
||||
dims[0] = nLevels;
|
||||
dims[1] = nRows;
|
||||
@ -356,7 +361,7 @@ public class HDF5Writer implements PlugInFilter {
|
||||
dims[0] = nRows;
|
||||
dims[1] = nCols;
|
||||
} else {
|
||||
System.out.println("adding 3 dimensions");
|
||||
logger.info("adding 3 dimensions");
|
||||
dims = new long[3];
|
||||
dims[0] = nLevels;
|
||||
dims[1] = nRows;
|
||||
@ -386,23 +391,23 @@ public class HDF5Writer implements PlugInFilter {
|
||||
// supported data types
|
||||
// FIXME: set the right signed and precision stuff
|
||||
if (imgColorType == ImagePlus.GRAY8) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: GRAY8");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY8");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY16) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: GRAY16");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY16");
|
||||
int typeSizeInByte = 2;
|
||||
type = new H5Datatype(Datatype.CLASS_INTEGER, typeSizeInByte, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.GRAY32) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: GRAY32");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: GRAY32");
|
||||
// int typeSizeInByte = 4;
|
||||
type = new H5Datatype(Datatype.CLASS_FLOAT, Datatype.NATIVE, Datatype.NATIVE, -1);
|
||||
} else if (imgColorType == ImagePlus.COLOR_RGB) {
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: COLOR_RGB");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_RGB");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
} else if (imgColorType == ImagePlus.COLOR_256) {
|
||||
// FIXME: not supported yet
|
||||
System.out.println(" bit depth: " + imgColorDepth + ", type: COLOR_256");
|
||||
System.out.println(" ERROR: untested, this might fail.");
|
||||
logger.info(" bit depth: " + imgColorDepth + ", type: COLOR_256");
|
||||
logger.info(" ERROR: untested, this might fail.");
|
||||
type = new H5Datatype(Datatype.CLASS_CHAR, Datatype.NATIVE, Datatype.NATIVE, Datatype.SIGN_NONE);
|
||||
}
|
||||
|
||||
@ -465,7 +470,7 @@ public class HDF5Writer implements PlugInFilter {
|
||||
}
|
||||
// get pixel sizes
|
||||
ij.measure.Calibration cal = imp.getCalibration();
|
||||
System.out.println(" Element-Size in um (level,row,col): " + cal.pixelDepth + ", " + cal.pixelHeight + ", " + cal.pixelWidth);
|
||||
logger.info(" Element-Size in um (level,row,col): " + cal.pixelDepth + ", " + cal.pixelHeight + ", " + cal.pixelWidth);
|
||||
|
||||
float[] element_sizes = new float[3];
|
||||
element_sizes[0] = (float) cal.pixelDepth;
|
||||
@ -545,8 +550,8 @@ public class HDF5Writer implements PlugInFilter {
|
||||
} else {
|
||||
String subgroupRelativName = groupRelativName.substring(posOfSlash);
|
||||
String currentGroup = groupRelativName.substring(0, posOfSlash);
|
||||
System.out.println("Create: " + currentGroup);
|
||||
System.out.println("Call back for: " + subgroupRelativName);
|
||||
logger.info("Create: " + currentGroup);
|
||||
logger.info("Call back for: " + subgroupRelativName);
|
||||
try {
|
||||
Group newGroup;
|
||||
String newGroupName;
|
||||
@ -555,7 +560,7 @@ public class HDF5Writer implements PlugInFilter {
|
||||
else
|
||||
newGroupName = group.getFullName() + "/" + currentGroup;
|
||||
|
||||
System.out.println("try opening: " + newGroupName);
|
||||
logger.info("try opening: " + newGroupName);
|
||||
newGroup = (Group) file.get(newGroupName);
|
||||
|
||||
if (newGroup == null)
|
||||
@ -632,11 +637,11 @@ public class HDF5Writer implements PlugInFilter {
|
||||
obj = (Metadata) members.get(i);
|
||||
if (obj instanceof Attribute) {
|
||||
try {
|
||||
System.out.println(((Attribute) obj).getName());
|
||||
logger.info(((Attribute) obj).getName());
|
||||
attributes.add((Attribute) obj);
|
||||
} catch (java.lang.UnsupportedOperationException e) {
|
||||
System.out.println("Caught UnsupportedOperationException datasets2.add((Dataset) obj)");
|
||||
System.out.println(e.getMessage());
|
||||
logger.info("Caught UnsupportedOperationException datasets2.add((Dataset) obj)");
|
||||
logger.info(e.getMessage());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user