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Cleanup HDF5Config

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This commit is contained in:
ebner 2014-03-06 14:15:39 +01:00
parent 580c543a5d
commit d5ed374538
4 changed files with 98 additions and 112 deletions
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7
pom.xml
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@ -39,6 +39,13 @@
<artifactId>slf4j-api</artifactId>
<version>1.7.6</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>

117
src/main/java/ch/psi/imagej/hdf5/HDF5Config.java
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@ -12,30 +12,21 @@ public class HDF5Config implements PlugIn {
private static final Logger logger = Logger.getLogger(HDF5Config.class.getName());
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";
private static final String GROUP_VARS_BY_NAME = "HDF5.groupVarsByName";
private static final String SHOW_UNMATCHED_DATASET_NAMES = "HDF5.showUnmatchedDataSetNames";
private static final String GROUP_VARS_BY_NAME_FORMAT_GROUP = "HDF5.groupVarsByNameFormatGroup";
private static final String GROUP_VARS_BY_NAME_FORMAT = "HDF5.groupVarsByNameFormat";
private static final String DOLLAR_REGEXP_FOR_GROUPING = "HDF5.dollarRegexpForGrouping";
// Getting preference or default values
private boolean groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, true);
private boolean showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, true);
private String groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, "/hints");
private String groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, "/t$T/channel$C");
private String dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, "[0-9]+");
public void run(String arg) {
// set default values
setDefaultsIfNoValueExists();
// read ImageJ Preferences
boolean groupVarsByName = Boolean.getBoolean(getDefaultValue(GROUP_VARS_BY_NAME));
groupVarsByName = Prefs.get(GROUP_VARS_BY_NAME, groupVarsByName);
boolean showUnmatchedDataSetNames = Boolean.getBoolean(getDefaultValue(SHOW_UNMATCHED_DATASET_NAMES));
showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT_GROUP);
groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
String groupVarsByNameFormat = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
String dollarRegexpForGrouping = getDefaultValue(DOLLAR_REGEXP_FOR_GROUPING);
dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
GenericDialog configDiag = new GenericDialog("HDF5 Preferences");
configDiag.addMessage("Reader:");
@ -43,45 +34,19 @@ public class HDF5Config implements PlugIn {
configDiag.addCheckbox("Show unmatched data set names in a separate list", showUnmatchedDataSetNames);
configDiag.addStringField("HDF5 group containing pattern " + "for data set grouping: ", groupVarsByNameFormatGroup, 15);
configDiag.addStringField("Pattern for grouping (if no attributes" + " are found): ", groupVarsByNameFormat, 15);
// configDiag.addStringField("$ regexp (ignored because only numbers" +
// " work right now): ",
// dollarRegexpForGrouping,15);
configDiag.addMessage("Writer:");
String yesLabel = "Save";
String noLabel = "Reset";
configDiag.enableYesNoCancel(yesLabel, noLabel);
configDiag.showDialog();
if (configDiag.wasCanceled()) {
// do nothing
return;
}
if (!configDiag.wasOKed()) {
// reset button was pressed
logger.info("reset button was pressed");
// reset all and return a new dialog
configDiag.setVisible(false);
this.run(arg);
return;
}
// get parameters check if they are correct
// Get parameters check if they are correct
groupVarsByName = configDiag.getNextBoolean();
logger.info("groupVarsByName: " + Boolean.toString(groupVarsByName));
showUnmatchedDataSetNames = configDiag.getNextBoolean();
logger.info("showUnmatchedDataSetNames: " + Boolean.toString(showUnmatchedDataSetNames));
groupVarsByNameFormatGroup = configDiag.getNextString();
logger.info("groupVarsByNameFormatGroup: " + groupVarsByNameFormatGroup);
groupVarsByNameFormat = configDiag.getNextString();
logger.info("groupVarsByNameFormat: " + groupVarsByNameFormat);
// dollarRegexpForGrouping = configDiag.getNextString();
// logger.info("dollarRegexpForGrouping: " +
// dollarRegexpForGrouping);
try {
String[] formatTokens = HDF5GroupedVarnames.parseFormatString(groupVarsByNameFormat, dollarRegexpForGrouping);
@ -97,62 +62,32 @@ public class HDF5Config implements PlugIn {
this.run(arg);
return;
}
logger.info("Saving...");
// 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(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
//
// ignore the $ regexp for now, because only numbers work
//
Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
}
public static void setDefaultsIfNoValueExists() {
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(SHOW_UNMATCHED_DATASET_NAMES));
showUnmatchedDataSetNames = Prefs.get(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
Prefs.set(SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT_GROUP);
groupVarsByNameFormatGroup = Prefs.get(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
Prefs.set(GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
String groupVarsByNameFormat = getDefaultValue(GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
Prefs.set(GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
String dollarRegexpForGrouping = getDefaultValue(DOLLAR_REGEXP_FOR_GROUPING);
dollarRegexpForGrouping = Prefs.get(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
Prefs.set(DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
public boolean isGroupVarsByName() {
return groupVarsByName;
}
public static String getDefaultValue(String key) {
if (key.equals(GROUP_VARS_BY_NAME)) {
boolean groupVarsByName = true; // default
return Boolean.toString(groupVarsByName);
} else if (key.equals(SHOW_UNMATCHED_DATASET_NAMES)) {
boolean showUnmatchedDataSetNames = true; // default
return Boolean.toString(showUnmatchedDataSetNames);
} else if (key.equals(GROUP_VARS_BY_NAME_FORMAT_GROUP)) {
String groupVarsByNameFormatGroup = "/hints"; // default
public boolean isShowUnmatchedDataSetNames() {
return showUnmatchedDataSetNames;
}
public String getGroupVarsByNameFormatGroup() {
return groupVarsByNameFormatGroup;
} else if (key.equals(GROUP_VARS_BY_NAME_FORMAT)) {
String groupVarsByNameFormat = "/t$T/channel$C"; // default
}
public String getGroupVarsByNameFormat() {
return groupVarsByNameFormat;
} else if (key.equals(DOLLAR_REGEXP_FOR_GROUPING)) {
String dollarRegexpForGrouping = "[0-9]+"; // default
}
public String getDollarRegexpForGrouping() {
return dollarRegexpForGrouping;
} else {
logger.info("No default value for key: " + key);
return null;
}
}
}

22
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -21,7 +21,6 @@ package ch.psi.imagej.hdf5;
*/
import ij.IJ;
import ij.Prefs;
import ij.ImagePlus;
import ij.CompositeImage;
import ij.ImageStack;
@ -100,14 +99,12 @@ public class HDF5Reader implements PlugIn {
/*-------------------------------------------------------------------
* read HDF5_Config prefs
*-------------------------------------------------------------------*/
boolean groupVarsByName = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME));
groupVarsByName = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME, groupVarsByName);
HDF5Config config = new HDF5Config();
boolean groupVarsByName = config.isGroupVarsByName();
boolean showUnmatchedDataSetNames = config.isShowUnmatchedDataSetNames();
String groupVarsByNameFormatGroup = config.getGroupVarsByNameFormatGroup();
String dollarRegexpForGrouping = config.getDollarRegexpForGrouping();
boolean showUnmatchedDataSetNames = Boolean.getBoolean(HDF5Config.getDefaultValue(HDF5Config.SHOW_UNMATCHED_DATASET_NAMES));
showUnmatchedDataSetNames = Prefs.get(HDF5Config.SHOW_UNMATCHED_DATASET_NAMES, showUnmatchedDataSetNames);
String groupVarsByNameFormatGroup = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT_GROUP);
groupVarsByNameFormatGroup = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT_GROUP, groupVarsByNameFormatGroup);
// TODO: try to read attribute containing format String
String groupVarsByNameFormat = null;
@ -159,17 +156,14 @@ public class HDF5Reader implements PlugIn {
logger.info("File has format string for grouping: " + groupVarsByNameFormat);
} else {
logger.info("File has no format string for grouping" + ", using default");
groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
groupVarsByNameFormat = config.getGroupVarsByNameFormat();
}
} catch (Exception e) {
logger.info("Error occured read format string " + "for grouping, using default");
groupVarsByNameFormat = HDF5Config.getDefaultValue(HDF5Config.GROUP_VARS_BY_NAME_FORMAT);
groupVarsByNameFormat = Prefs.get(HDF5Config.GROUP_VARS_BY_NAME_FORMAT, groupVarsByNameFormat);
groupVarsByNameFormat = config.getGroupVarsByNameFormat();
}
String dollarRegexpForGrouping = HDF5Config.getDefaultValue(HDF5Config.DOLLAR_REGEXP_FOR_GROUPING);
dollarRegexpForGrouping = Prefs.get(HDF5Config.DOLLAR_REGEXP_FOR_GROUPING, dollarRegexpForGrouping);
/*-------------------------------------------------------------------
* init the frame and channel ranges

50
src/test/java/ch/psi/imagej/hdf5/HDF5ConfigTest.java Normal file
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@ -0,0 +1,50 @@
/**
*
* Copyright 2014 Paul Scherrer Institute. All rights reserved.
*
* This code is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* This code is distributed in the hope that it will be useful, but without any
* warranty; without even the implied warranty of merchantability or fitness for
* a particular purpose. See the GNU Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this code. If not, see <http://www.gnu.org/licenses/>.
*
*/
package ch.psi.imagej.hdf5;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
/**
*
*/
public class HDF5ConfigTest {
/**
* @throws java.lang.Exception
*/
@Before
public void setUp() throws Exception {
}
/**
* @throws java.lang.Exception
*/
@After
public void tearDown() throws Exception {
}
@Test
public void test() {
HDF5Config config = new HDF5Config();
config.run("");
}
}