diff --git a/.classpath b/.classpath index ce86f24..426add3 100644 --- a/.classpath +++ b/.classpath @@ -24,9 +24,5 @@ - - - - diff --git a/hdf-java/Readme.md b/hdf-java/Readme.md new file mode 100644 index 0000000..9d6f7b3 --- /dev/null +++ b/hdf-java/Readme.md @@ -0,0 +1 @@ +jar files where uploaded to http://yoke.psi.ch/artifactory \ No newline at end of file diff --git a/pom.xml b/pom.xml index c93bf77..7009e99 100644 --- a/pom.xml +++ b/pom.xml @@ -12,8 +12,37 @@ 1.46 provided + + + hdf5 + jhdf + 1.0.0 + + + + hdf5 + jhdfobj + 1.0.0 + + + + hdf5 + jhdf5 + 1.0.0 + + + + hdf5 + jhdf5obj + 1.0.0 + + - + diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5_Config.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Config.java similarity index 97% rename from src/main/java/ch/psi/imagej/hdf5/HDF5_Config.java rename to src/main/java/ch/psi/imagej/hdf5/HDF5Config.java index 3a8a3cc..f565b0f 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5_Config.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Config.java @@ -6,7 +6,7 @@ import ij.plugin.PlugIn; import java.util.regex.*; import java.lang.String; -public class HDF5_Config implements PlugIn { +public class HDF5Config implements PlugIn { public void run(String arg) { // set default values @@ -74,7 +74,7 @@ public class HDF5_Config implements PlugIn { // dollarRegexpForGrouping); try { - String[] formatTokens = HDF5_GroupedVarnames.parseFormatString(groupVarsByNameFormat, dollarRegexpForGrouping); + String[] formatTokens = HDF5GroupedVarnames.parseFormatString(groupVarsByNameFormat, dollarRegexpForGrouping); for (int i = 0; i < formatTokens.length; i++) { System.out.println("tok " + Integer.toString(i) + " : " + formatTokens[i]); } diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5_GroupedVarnames.java b/src/main/java/ch/psi/imagej/hdf5/HDF5GroupedVarnames.java similarity index 99% rename from src/main/java/ch/psi/imagej/hdf5/HDF5_GroupedVarnames.java rename to src/main/java/ch/psi/imagej/hdf5/HDF5GroupedVarnames.java index ce700af..74dc385 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5_GroupedVarnames.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5GroupedVarnames.java @@ -6,7 +6,7 @@ import java.util.Arrays; import java.util.Iterator; import java.util.List; -public class HDF5_GroupedVarnames { +public class HDF5GroupedVarnames { private final List matchedVarNames = new ArrayList(); private final List unMatchedVarNames = new ArrayList(); diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5_Reader_.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java similarity index 99% rename from src/main/java/ch/psi/imagej/hdf5/HDF5_Reader_.java rename to src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java index fe85783..0e066f1 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5_Reader_.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java @@ -41,7 +41,7 @@ import ncsa.hdf.object.h5.*; // the HDF5 implementation import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; import ncsa.hdf.hdflib.HDFException; -public class HDF5_Reader_ implements PlugIn { +public class HDF5Reader implements PlugIn { public void run(String arg) { // make sure default values for config are written // HDF5_Config.setDefaultsIfNoValueExists(); @@ -81,7 +81,7 @@ public class HDF5_Reader_ implements PlugIn { H5File inFile = null; // define grouping class - HDF5_GroupedVarnames groupedVarnames = new HDF5_GroupedVarnames(); + HDF5GroupedVarnames groupedVarnames = new HDF5GroupedVarnames(); boolean loadGroupedVarNames = true; try { @@ -91,13 +91,13 @@ public class HDF5_Reader_ implements PlugIn { /*------------------------------------------------------------------- * read HDF5_Config prefs *-------------------------------------------------------------------*/ - boolean groupVarsByName = Boolean.getBoolean(HDF5_Config.getDefaultValue("HDF5.groupVarsByName")); + boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue("HDF5.groupVarsByName")); groupVarsByName = Prefs.get("HDF5.groupVarsByName", groupVarsByName); - boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5_Config.getDefaultValue("HDF5.showUnmatchedDataSetNames")); + boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5Config.getDefaultValue("HDF5.showUnmatchedDataSetNames")); showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); - String groupVarsByNameFormatGroup = HDF5_Config.getDefaultValue("HDF5.groupVarsByNameFormatGroup"); + String groupVarsByNameFormatGroup = HDF5Config.getDefaultValue("HDF5.groupVarsByNameFormatGroup"); groupVarsByNameFormatGroup = Prefs.get("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); // TODO: try to read attribute containing format String @@ -150,16 +150,16 @@ public class HDF5_Reader_ implements PlugIn { System.out.println("File has format string for grouping: " + groupVarsByNameFormat); } else { System.out.println("File has no format string for grouping" + ", using default"); - groupVarsByNameFormat = HDF5_Config.getDefaultValue("HDF5.groupVarsByNameFormat"); + groupVarsByNameFormat = HDF5Config.getDefaultValue("HDF5.groupVarsByNameFormat"); groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); } } catch (Exception e) { System.out.println("Error occured read format string " + "for grouping, using default"); - groupVarsByNameFormat = HDF5_Config.getDefaultValue("HDF5.groupVarsByNameFormat"); + groupVarsByNameFormat = HDF5Config.getDefaultValue("HDF5.groupVarsByNameFormat"); groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); } - String dollarRegexpForGrouping = HDF5_Config.getDefaultValue("HDF5.dollarRegexpForGrouping"); + String dollarRegexpForGrouping = HDF5Config.getDefaultValue("HDF5.dollarRegexpForGrouping"); dollarRegexpForGrouping = Prefs.get("HDF5.dollarRegexpForGrouping", dollarRegexpForGrouping); /*------------------------------------------------------------------- diff --git a/src/main/java/ch/psi/imagej/hdf5/HDF5_Writer_.java b/src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java similarity index 99% rename from src/main/java/ch/psi/imagej/hdf5/HDF5_Writer_.java rename to src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java index 428ce76..8064bd0 100644 --- a/src/main/java/ch/psi/imagej/hdf5/HDF5_Writer_.java +++ b/src/main/java/ch/psi/imagej/hdf5/HDF5Writer.java @@ -35,7 +35,7 @@ import ncsa.hdf.object.*; // the common object package import ncsa.hdf.object.h5.*; // the HDF5 implementation import ncsa.hdf.hdf5lib.exceptions.HDF5Exception; -public class HDF5_Writer_ implements PlugInFilter { +public class HDF5Writer implements PlugInFilter { private Boolean _batchMode = false; private String _batchFileName = null; @@ -156,7 +156,7 @@ public class HDF5_Writer_ implements PlugInFilter { if (splitChannels) { // parse format string - String[] formatTokens = HDF5_GroupedVarnames.parseFormatString(formatString, "[0-9]+"); // dummy + String[] formatTokens = HDF5GroupedVarnames.parseFormatString(formatString, "[0-9]+"); // dummy // regexp long[] channelDims = null; if (nLevs > 1) { diff --git a/src/main/resources/plugins.config b/src/main/resources/plugins.config index 8da272a..2ea34aa 100644 --- a/src/main/resources/plugins.config +++ b/src/main/resources/plugins.config @@ -1,5 +1,5 @@ -File>Import, "HDF5...", ch.psi.imageJ.hdf5.HDF5_Reader_ -File>Save As, "HDF5", ch.psi.imageJ.hdf5.HDF5_Writer_ -Plugins>HDF5, "Load HDF5 File", ch.psi.imageJ.hdf5.HDF5_Reader_ -Plugins>HDF5, "Save HDF5 File", ch.psi.imageJ.hdf5.HDF5_Writer_ -Plugins>HDF5, "HDF5 Preferences", ch.psi.imageJ.hdf5.HDF5_Config +File>Import, "HDF5...", ch.psi.imagej.hdf5.HDF5Reader +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 \ No newline at end of file