diff --git a/.classpath b/.classpath index 426add3..bd7877d 100644 --- a/.classpath +++ b/.classpath @@ -12,14 +12,14 @@ - - - + + + - + diff --git a/.settings/org.eclipse.core.resources.prefs b/.settings/org.eclipse.core.resources.prefs new file mode 100644 index 0000000..5b781ec --- /dev/null +++ b/.settings/org.eclipse.core.resources.prefs @@ -0,0 +1,3 @@ +eclipse.preferences.version=1 +encoding//src/main/java=UTF-8 +encoding//src/test/java=UTF-8 diff --git a/.settings/org.eclipse.jdt.core.prefs b/.settings/org.eclipse.jdt.core.prefs index abec6ca..ec4300d 100644 --- a/.settings/org.eclipse.jdt.core.prefs +++ b/.settings/org.eclipse.jdt.core.prefs @@ -1,5 +1,5 @@ eclipse.preferences.version=1 -org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5 -org.eclipse.jdt.core.compiler.compliance=1.5 +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.compliance=1.7 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning -org.eclipse.jdt.core.compiler.source=1.5 +org.eclipse.jdt.core.compiler.source=1.7 diff --git a/pom.xml b/pom.xml index 7009e99..a208b45 100644 --- a/pom.xml +++ b/pom.xml @@ -3,7 +3,7 @@ 4.0.0 ch.psi imagej.hdf5 - 0.0.1 + 0.2.0 @@ -12,39 +12,61 @@ 1.46 provided - + hdf5 jhdf 1.0.0 - hdf5 jhdfobj 1.0.0 - hdf5 jhdf5 1.0.0 - hdf5 jhdf5obj 1.0.0 - + + + + maven-compiler-plugin + 2.3.2 + + UTF-8 + 1.7 + 1.7 + + maven-assembly-plugin 2.4 diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5Config.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Config.java index f565b0f..1a3da70 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5Config.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Config.java @@ -8,12 +8,14 @@ import java.lang.String; public class HDF5Config implements PlugIn { + public static String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName"; + public void run(String arg) { // set default values setDefaultsIfNoValueExists(); // read ImageJ Preferences - boolean groupVarsByName = Boolean.getBoolean(getDefaultValue("HDF5.groupVarsByName")); - groupVarsByName = Prefs.get("HDF5.groupVarsByName", groupVarsByName); + boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME)); + groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName); boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue("HDF5.showUnmatchedDataSetNames")); showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); @@ -90,7 +92,7 @@ public class HDF5Config implements PlugIn { System.out.println("Saving..."); // all OK and "Save" was pressed, so save it... - Prefs.set("HDF5.groupVarsByName", groupVarsByName); + Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName); Prefs.set("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); Prefs.set("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); Prefs.set("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); @@ -102,9 +104,9 @@ public class HDF5Config implements PlugIn { } public static void setDefaultsIfNoValueExists() { - boolean groupVarsByName = Boolean.getBoolean(getDefaultValue("HDF5.groupVarsByName")); - groupVarsByName = Prefs.get("HDF5.groupVarsByName", groupVarsByName); - Prefs.set("HDF5.groupVarsByName", groupVarsByName); + boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME)); + groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName); + Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName); boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue("HDF5.showUnmatchedDataSetNames")); showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); @@ -124,7 +126,7 @@ public class HDF5Config implements PlugIn { } public static String getDefaultValue(String key) { - if (key.equals("HDF5.groupVarsByName")) { + if (key.equals(GROUP_VARS_BY_NAME)) { boolean groupVarsByName = true; // default return Boolean.toString(groupVarsByName); } else if (key.equals("HDF5.showUnmatchedDataSetNames")) { diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java index 0e066f1..3f4230b 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java @@ -32,16 +32,20 @@ import ij.process.ImageProcessor; import java.io.File; import java.util.ArrayList; -import java.util.Iterator; import java.util.List; +import java.util.logging.Level; +import java.util.logging.Logger; import java.awt.*; -import ncsa.hdf.object.*; // the common object package -import ncsa.hdf.object.h5.*; // the HDF5 implementation +import ncsa.hdf.object.*; +import ncsa.hdf.object.h5.*; import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; -import ncsa.hdf.hdflib.HDFException; public class HDF5Reader implements PlugIn { + + + private static final Logger logger = Logger.getLogger(HDF5Reader.class.getName()); + public void run(String arg) { // make sure default values for config are written // HDF5_Config.setDefaultsIfNoValueExists(); @@ -91,8 +95,8 @@ public class HDF5Reader implements PlugIn { /*------------------------------------------------------------------- * read HDF5_Config prefs *-------------------------------------------------------------------*/ - boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue("HDF5.groupVarsByName")); - groupVarsByName = Prefs.get("HDF5.groupVarsByName", groupVarsByName); + boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME)); + groupVarsByName = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME, groupVarsByName); boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5Config.getDefaultValue("HDF5.showUnmatchedDataSetNames")); showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); @@ -385,6 +389,13 @@ public class HDF5Reader implements PlugIn { } } else if (varList.size() > 1000) { + + System.out.println("#######"); + for(Dataset d: varList){ + System.out.println(d.getFullName()); + } + System.out.println("#######"); + /*----------------------------------------------------------------- * FIXME: quick an dirty hack for files with more than 1000 * datasets @@ -784,7 +795,7 @@ public class HDF5Reader implements PlugIn { System.out.println(" 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] / progressSteps; + long progressDivisor = extent[0] / 50; // we assume 50 process steps if (progressDivisor < 1) progressDivisor = 1; @@ -1689,21 +1700,8 @@ public class HDF5Reader implements PlugIn { } } - } catch (java.io.IOException err) { - System.err.println("Error while opening '" + directory + name + "'"); - System.err.println(err); - IJ.showStatus("Error opening file."); - } catch (HDFException err) { - System.err.println("Error while opening '" + directory + name + "'"); - System.err.println(err); - IJ.showStatus("Error opening file."); - } catch (HDF5Exception err) { - System.err.println("Error while opening '" + directory + name + "'"); - System.err.println(err); - IJ.showStatus("Error opening file."); - } catch (Exception err) { - System.err.println("Error while opening '" + directory + name + "'"); - System.err.println(err); + } catch (Exception e) { + logger.log(Level.WARNING, "Error while opening '" + directory + name + "'", e); IJ.showStatus("Error opening file."); } catch (OutOfMemoryError o) { IJ.outOfMemory("Load HDF5"); @@ -1722,18 +1720,7 @@ public class HDF5Reader implements PlugIn { IJ.showProgress(1.0); } - // int byteToUnsignedByte(int n) - // { - // if (n < 0) - // return (256 + n); - // return n; - // } - - private int progressSteps = 50; - - /*----------------------------------------------------------------------- - * helpers for hdf5 library - *-----------------------------------------------------------------------*/ + private static List getDataSetList(Group g, List datasets) throws Exception { if (g == null){ return datasets; @@ -1744,7 +1731,6 @@ public class HDF5Reader implements PlugIn { if (obj instanceof Dataset) { ((Dataset) obj).init(); datasets.add((Dataset) obj); - // System.out.println(obj.getFullName()); } else if (obj instanceof Group) { datasets = (getDataSetList((Group) obj, datasets)); } @@ -1752,9 +1738,11 @@ public class HDF5Reader implements PlugIn { return datasets; } + private static List getAttrList(HObject ds) throws Exception { - if (ds == null) + if (ds == null){ return null; + } List attributes = new ArrayList(); List members = ds.getMetadata(); @@ -1763,48 +1751,39 @@ public class HDF5Reader implements PlugIn { for (int i = 0; i < n; i++) { obj = (Metadata) members.get(i); if (obj instanceof Attribute) { - try { - System.out.println(((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()); - } } } return attributes; } + private static Attribute getAttribute(Dataset ds, String attrName) throws Exception { - List attrList = getAttrList((HObject) ds); - Iterator attrIter = attrList.iterator(); - - while (attrIter.hasNext()) { - Attribute attr = attrIter.next(); - if (attr.getName().equals(attrName)) { - return attr; + for(Attribute a: getAttrList((HObject) ds)){ + if (a.getName().equals(attrName)) { + return a; } } return null; } + private static Attribute getAttribute(HObject ds, String attrName) throws Exception { - List attrList = getAttrList(ds); - Iterator attrIter = attrList.iterator(); - - while (attrIter.hasNext()) { - Attribute attr = attrIter.next(); - System.out.println(attr.getName()); - if (attr.getName().equals(attrName)) { - return attr; + for(Attribute a: getAttrList(ds)){ + if (a.getName().equals(attrName)) { + return a; } } return null; } - /*----------------------------------------------------------------------- - * minmax of array - *-----------------------------------------------------------------------*/ + + /** + * Find min and maximum of array + * @param data + * @param stackSize + * @return + */ private double[] getMinMax(Object data, long stackSize) { double[] minmax = new double[2]; @@ -1879,13 +1858,11 @@ public class HDF5Reader implements PlugIn { minmax[1] = tmp[i]; } } - System.out.println("min: " + minmax[0] + ", max: " + minmax[1]); + logger.info("min: " + minmax[0] + ", max: " + minmax[1]); return minmax; } - /*----------------------------------------------------------------------- - * converter functions - *-----------------------------------------------------------------------*/ + private float[] convertDoubleToFloat(double[] dataIn) { float[] dataOut = new float[dataIn.length]; for (int index = 0; index < dataIn.length; index++) { @@ -1894,6 +1871,7 @@ public class HDF5Reader implements PlugIn { return dataOut; } + private float[] convertInt32ToFloat(int[] dataIn) { float[] dataOut = new float[dataIn.length]; for (int index = 0; index < dataIn.length; index++) { @@ -1902,6 +1880,7 @@ public class HDF5Reader implements PlugIn { return dataOut; } + private short[] convertInt32ToShort(int[] dataIn) { short[] dataOut = new short[dataIn.length]; for (int index = 0; index < dataIn.length; index++) { @@ -1910,6 +1889,7 @@ public class HDF5Reader implements PlugIn { return dataOut; } + private float[] convertInt64ToFloat(long[] dataIn) { float[] dataOut = new float[dataIn.length]; for (int index = 0; index < dataIn.length; index++) { @@ -1918,6 +1898,7 @@ public class HDF5Reader implements PlugIn { return dataOut; } + private short[] convertInt64ToShort(long[] dataIn) { short[] dataOut = new short[dataIn.length]; for (int index = 0; index < dataIn.length; index++) { @@ -1926,6 +1907,7 @@ public class HDF5Reader implements PlugIn { return dataOut; } + private Object convertToUnsigned(Object dataIn, int unsignedConvSelec) { Object dataOut = null; if (unsignedConvSelec == 0) { @@ -1951,10 +1933,8 @@ public class HDF5Reader implements PlugIn { return dataOut; } - /*----------------------------------------------------------------------- - * extract subarrays - *-----------------------------------------------------------------------*/ - Object extractSubarray(Object data, long startIdx, long numElements) { + + private Object extractSubarray(Object data, long startIdx, long numElements) { Object subarray = null; if (data instanceof byte[]) {