imagej/ch.psi.imagej.hdf5
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moved hardcoded strings into static variables

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This commit is contained in:
ebner 2014-03-06 11:57:02 +01:00
parent 8f1b5fc623
commit 42ac035249
2 changed files with 42 additions and 38 deletions
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60
src/main/java/ch/psi/imagej/hdf5/HDF5Config.java
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@ -9,6 +9,10 @@ import java.lang.String;
public class HDF5Config implements PlugIn { public class HDF5Config implements PlugIn {
public static String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName"; public static String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName";
public static String SHOW_UNMATCHED_DATASET_NAMES = "HDF5.showUnmatchedDataSetNames";
public static String GROUP_VARS_BY_NAME_FORMAT_GROUP = "HDF5.groupVarsByNameFormatGroup";
public static String GROUP_VARS_BY_NAME_FORMAT = "HDF5.groupVarsByNameFormat";
public static String DOLLAR_REGEXP_FOR_GROUPING = "HDF5.dollarRegexpForGrouping";
public void run(String arg) { public void run(String arg) {
// set default values // set default values
@ -17,17 +21,17 @@ public class HDF5Config implements PlugIn {
boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME)); boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME));
groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName); groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName);
boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue("HDF5.showUnmatchedDataSetNames")); boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue(SHOW_UNMATCHED_DATASET_NAMES));
showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup = getDefaultValue("HDF5.groupVarsByNameFormatGroup"); String groupVarsByNameFormatGroup = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT_GROUP);
groupVarsByNameFormatGroup = Prefs.get("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
String groupVarsByNameFormat = getDefaultValue("HDF5.groupVarsByNameFormat"); String groupVarsByNameFormat = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
String dollarRegexpForGrouping = getDefaultValue("HDF5.dollarRegexpForGrouping"); String dollarRegexpForGrouping = getDefaultValue(DOLLAR_REGEXP_FOR_GROUPING);
dollarRegexpForGrouping = Prefs.get("HDF5.dollarRegexpForGrouping", dollarRegexpForGrouping); dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
GenericDialog configDiag = new GenericDialog("HDF5 Preferences"); GenericDialog configDiag = new GenericDialog("HDF5 Preferences");
configDiag.addMessage("Reader:"); configDiag.addMessage("Reader:");
@ -93,13 +97,13 @@ public class HDF5Config implements PlugIn {
// all OK and "Save" was pressed, so save it... // all OK and "Save" was pressed, so save it...
Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName); Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName);
Prefs.set("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); Prefs.set(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
Prefs.set("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
Prefs.set("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
// //
// ignore the $ regexp for now, because only numbers work // ignore the $ regexp for now, because only numbers work
// //
Prefs.set("HDF5.dollarRegexpForGrouping", dollarRegexpForGrouping); Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
} }
@ -108,37 +112,37 @@ public class HDF5Config implements PlugIn {
groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName); groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName);
Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName); Prefs.set(GROUP_VARS_BY_NAME, groupVarsByName);
boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue("HDF5.showUnmatchedDataSetNames")); boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue(SHOW_UNMATCHED_DATASET_NAMES));
showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
Prefs.set("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); Prefs.set(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup = getDefaultValue("HDF5.groupVarsByNameFormatGroup"); String groupVarsByNameFormatGroup = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT_GROUP);
groupVarsByNameFormatGroup = Prefs.get("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
Prefs.set("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
String groupVarsByNameFormat = getDefaultValue("HDF5.groupVarsByNameFormat"); String groupVarsByNameFormat = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
Prefs.set("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
String dollarRegexpForGrouping = getDefaultValue("HDF5.dollarRegexpForGrouping"); String dollarRegexpForGrouping = getDefaultValue(DOLLAR_REGEXP_FOR_GROUPING);
dollarRegexpForGrouping = Prefs.get("HDF5.dollarRegexpForGrouping", dollarRegexpForGrouping); dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
Prefs.set("HDF5.dollarRegexpForGrouping", dollarRegexpForGrouping); Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
} }
public static String getDefaultValue(String key) { public static String getDefaultValue(String key) {
if (key.equals(GROUP_VARS_BY_NAME)) { if (key.equals(GROUP_VARS_BY_NAME)) {
boolean groupVarsByName = true; // default boolean groupVarsByName = true; // default
return Boolean.toString(groupVarsByName); return Boolean.toString(groupVarsByName);
} else if (key.equals("HDF5.showUnmatchedDataSetNames")) { } else if (key.equals(SHOW_UNMATCHED_DATASET_NAMES)) {
boolean showUnmatchedDataSetNames = true; // default boolean showUnmatchedDataSetNames = true; // default
return Boolean.toString(showUnmatchedDataSetNames); return Boolean.toString(showUnmatchedDataSetNames);
} else if (key.equals("HDF5.groupVarsByNameFormatGroup")) { } else if (key.equals(GROUP_VARS_BY_NAME_FORMAT_GROUP)) {
String groupVarsByNameFormatGroup = "/hints"; // default String groupVarsByNameFormatGroup = "/hints"; // default
return groupVarsByNameFormatGroup; return groupVarsByNameFormatGroup;
} else if (key.equals("HDF5.groupVarsByNameFormat")) { } else if (key.equals(GROUP_VARS_BY_NAME_FORMAT)) {
String groupVarsByNameFormat = "/t$T/channel$C"; // default String groupVarsByNameFormat = "/t$T/channel$C"; // default
return groupVarsByNameFormat; return groupVarsByNameFormat;
} else if (key.equals("HDF5.dollarRegexpForGrouping")) { } else if (key.equals(DOLLAR_REGEXP_FOR_GROUPING)) {
String dollarRegexpForGrouping = "[0-9]+"; // default String dollarRegexpForGrouping = "[0-9]+"; // default
return dollarRegexpForGrouping; return dollarRegexpForGrouping;
} else { } else {

20
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -103,11 +103,11 @@ public class HDF5Reader implements PlugIn {
boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME)); boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME));
groupVarsByName = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME, groupVarsByName); groupVarsByName = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME, groupVarsByName);
boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5Config.getDefaultValue("HDF5.showUnmatchedDataSetNames")); boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.SHOW_UNMATCHED_DATASET_NAMES));
showUnmatchedDataSetNames = Prefs.get("HDF5.showUnmatchedDataSetNames", showUnmatchedDataSetNames); showUnmatchedDataSetNames = Prefs.get(HDF5Config.SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup = HDF5Config.getDefaultValue("HDF5.groupVarsByNameFormatGroup"); String groupVarsByNameFormatGroup = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT_GROUP);
groupVarsByNameFormatGroup = Prefs.get("HDF5.groupVarsByNameFormatGroup", groupVarsByNameFormatGroup); groupVarsByNameFormatGroup = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
// TODO: try to read attribute containing format String // TODO: try to read attribute containing format String
String groupVarsByNameFormat = null; String groupVarsByNameFormat = null;
@ -159,17 +159,17 @@ public class HDF5Reader implements PlugIn {
System.out.println("File has format string for grouping: " + groupVarsByNameFormat); System.out.println("File has format string for grouping: " + groupVarsByNameFormat);
} else { } else {
System.out.println("File has no format string for grouping" + ", using default"); System.out.println("File has no format string for grouping" + ", using default");
groupVarsByNameFormat = HDF5Config.getDefaultValue("HDF5.groupVarsByNameFormat"); groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
} }
} catch (Exception e) { } catch (Exception e) {
System.out.println("Error occured read format string " + "for grouping, using default"); System.out.println("Error occured read format string " + "for grouping, using default");
groupVarsByNameFormat = HDF5Config.getDefaultValue("HDF5.groupVarsByNameFormat"); groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get("HDF5.groupVarsByNameFormat", groupVarsByNameFormat); groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
} }
String dollarRegexpForGrouping = HDF5Config.getDefaultValue("HDF5.dollarRegexpForGrouping"); String dollarRegexpForGrouping = HDF5Config.getDefaultValue(HDF5Config.DOLLAR_REGEXP_FOR_GROUPING);
dollarRegexpForGrouping = Prefs.get("HDF5.dollarRegexpForGrouping", dollarRegexpForGrouping); dollarRegexpForGrouping = Prefs.get(HDF5Config.DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
/*------------------------------------------------------------------- /*-------------------------------------------------------------------
* init the frame and channel ranges * init the frame and channel ranges