Remove matlab

.appveyor.yml

@@ -12,8 +12,6 @@ environment:
     - java: 1.8
       build: ant
       ant_version: 1.10.1
-    - java: 1.7
-      build: maven
 
 cache:
   - '%AV_BF_M2% -> appveyor.yml'
@@ -27,7 +25,6 @@ init:
   - git config --global core.autocrlf input
   - if [%build%] == [ant] appveyor-retry cinst -y ant --version %ant_version%
   - refreshenv
-  - 'if [%java%] == [1.7] set "JAVA_HOME=C:\Program Files\Java\jdk1.7.0"'
   - 'if [%java%] == [1.8] set "JAVA_HOME=C:\Program Files\Java\jdk1.8.0"'
   - 'if [%java%] == [10] set "JAVA_HOME=C:\Program Files\Java\jdk10"'
   - PATH=%JAVA_HOME%\bin;%PATH%
@@ -36,12 +33,3 @@ init:
 
 build_script:
   - tools\test-build %build%
-
-#artifacts:
-#  - path: 'components\bundles\bioformats_package\target\*.zip'
-#  - path: 'components\bundles\bioformats_package\target\*.jar'
-#  - path: 'components\bundles\bioformats_package\target\*.tar.*'
-#  - path: 'artifacts\bioformats_package.jar'
-#  - path: 'artifacts\bftools.zip'
-#  - path: 'artifacts\bfmatlab.zip'
-#  - path: 'artifacts\bioformats-octave*.tar.*'

ant/java.xml

@@ -251,7 +251,7 @@ your FindBugs installation's lib directory. E.g.:
       <doctitle><![CDATA[<h1>Bio-Formats</h1>]]></doctitle>
       <bottom><![CDATA[${copyright.begin} ${YEAR} ${copyright.end}]]></bottom>
       <link href="http://docs.oracle.com/javase/7/docs/api/"/>
-      <link href="http://rsbweb.nih.gov/ij/developer/api/"/>
+      <link href="https://imagej.nih.gov/ij/developer/api/"/>
       <link href="http://www.ssec.wisc.edu/visad-docs/javadoc/"/>
       <!--<link href="http://www.jdocs.com/formlayout/1.0.4/api/"/>-->
       <!--<link href="http://www.jdocs.com/looks/1.2.2/api/"/>-->

ant/toplevel.xml

@@ -353,49 +353,6 @@ Type "ant -p" for a list of targets.
     <ant dir="components/bundles/bioformats_package" target="bftools"/>
   </target>
 
-  <!-- Matlab -->
-  <target name="dist-matlab"
-    description="generate a zip bundle of the Matlab toolbox">
-    <echo>----------=========== bfmatlab ===========----------</echo>
-    <ant dir="components/bundles/bioformats_package" target="bfmatlab"/>
-  </target>
-
-  <target name="test-matlab" description="run Matlab tests" depends="tools">
-    <property environment="env"/>
-    <exec executable="matlab">
-      <env key="MATLABPATH" value="${env.MATLABPATH}:${root.dir}/components/bio-formats/matlab:${artifact.dir}"/>
-      <arg value="-nodesktop"/>
-      <arg value="-nosplash"/>
-      <arg value="-r"/>
-      <arg value="runtests ${root.dir}/components/formats-gpl/test/matlab"/>
-    </exec>
-  </target>
-
-  <!-- Octave -->
-  <target name="dist-octave" description="generate an Octave package">
-    <echo>-------=========== Octave package ===========-------</echo>
-
-    <tempfile property="temp.file" destDir="${java.io.tmpdir}"/>
-    <copy file="${root.dir}/components/formats-gpl/octave/DESCRIPTION.in"
-          toFile="${temp.file}">
-      <filterset begintoken="$${" endtoken ="}" >
-        <filter token="release.version" value="${release.version}"/>
-        <filter token="DATE" value="${date}"/>
-      </filterset>
-    </copy>
-
-    <tar destfile="${artifact.dir}/bioformats-octave-${release.version}.tar.gz"
-         compression="gzip">
-      <tarfileset dir="${root.dir}/components/formats-gpl/octave"
-                  prefix="bioformats/" excludes="DESCRIPTION.in"/>
-      <tarfileset file="${temp.file}" fullpath="bioformats/DESCRIPTION"/>
-      <tarfileset file="${root.dir}/LICENSE.txt" fullpath="bioformats/COPYING"/>
-      <tarfileset dir="${root.dir}/components/formats-gpl/matlab"
-                  prefix="bioformats/inst/"/>
-    </tar>
-    <delete file="${temp.file}"/>
-  </target>
-
   <!-- Internal targets -->
 
   <target name="init"/>

components/bio-formats-plugins/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/bio-formats-plugins/src/loci/plugins/out/Exporter.java

@@ -568,9 +568,9 @@ else if (cal.frameInterval != 0.0 && cal.getTimeUnit().equals("sec")) {
                 String ext = outfile.substring(dot);
 
                 int nextFile = 0;
-                for (int z=0; z<(splitZ ? sizeZ : 1); z++) {
-                    for (int c=0; c<(splitC ? sizeC : 1); c++) {
-                        for (int t=0; t<(splitT ? sizeT : 1); t++) {
+                for (int t=0; t<(splitT ? sizeT : 1); t++) {
+                    for (int z=0; z<(splitZ ? sizeZ : 1); z++) {
+                        for (int c=0; c<(splitC ? sizeC : 1); c++) {
                             int index = FormatTools.getIndex(ORDER, sizeZ, sizeC, sizeT, sizeZ*sizeC*sizeT, z, c, t);
                             String pattern = base + (splitZ ? "_Z%z" : "") + (splitC ? "_C%c" : "") + (splitT ? "_T%t" : "") + ext;
                             outputFiles[nextFile++] = FormatTools.getFilename(0, index, store, pattern, padded);

components/bio-formats-tools/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/bio-formats-tools/src/loci/formats/tools/GenerateCache.java

@@ -0,0 +1,127 @@
+/*
+ * #%L
+ * Bio-Formats command line tools for reading and converting files
+ * %%
+ * Copyright (C) 2018 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package loci.formats.tools;
+
+import java.io.File;
+import java.io.IOException;
+
+import loci.common.DataTools;
+import loci.formats.Memoizer;
+
+/**
+ * Generate cache file(s) for a specified file or directory.
+ */
+public class GenerateCache {
+
+  /**
+   * Use the given Memoizer to initialize the given file
+   * and attempt to generate a memo file.
+   * Prints a message if the memo file could not be saved.
+   */
+  private static void generateMemo(Memoizer reader, String path) {
+    boolean success = false;
+    try {
+      success = reader.generateMemo(path);
+    }
+    catch (IOException e) {
+      e.printStackTrace();
+    }
+    if (!success) {
+      System.out.println("Memo file not saved for " + path);
+    }
+  }
+
+  /**
+   * Recursively scan the given directory and generate a memo file
+   * for each found file.
+   * Delegates to #generateMemo(Memoizer, String) to perform the actual
+   * memo file generation.
+   */
+  private static void processDirectory(Memoizer reader, File dir) {
+    String[] list = dir.list();
+    for (String f : list) {
+      File file = new File(dir, f);
+      if (file.isDirectory()) {
+        processDirectory(reader, file);
+      }
+      else {
+        generateMemo(reader, file.getAbsolutePath());
+      }
+    }
+  }
+
+  public static void main(String[] args) {
+    CommandLineTools.runUpgradeCheck(args);
+
+    if (args.length < 2) {
+      System.out.println("Usage:");
+      System.out.println(
+        "cachegen [-list] fileOrDir cacheFileDir");
+      System.out.println();
+      System.out.println("If '-list' is specified, then 'fileOrDir' is a text file with one file per line.");
+      return;
+    }
+
+    boolean fileList = args.length >= 3 && args[0].equals("-list");
+    String input = args[args.length - 2];
+    String outputDir = args[args.length - 1];
+
+    Memoizer reader = new Memoizer(0, new File(outputDir));
+    File inputFile = new File(input);
+
+    if (!inputFile.isDirectory()) {
+      if (fileList) {
+        String[] files = null;
+        try {
+          files = DataTools.readFile(inputFile.getAbsolutePath()).split("\n");
+        }
+        catch (IOException e) {
+          System.out.println("Could not read file list from " + inputFile);
+          e.printStackTrace();
+        }
+        if (files != null) {
+          for (String f : files) {
+            generateMemo(reader, f);
+          }
+        }
+      }
+      else {
+        generateMemo(reader, inputFile.getAbsolutePath());
+      }
+    }
+    else {
+      processDirectory(reader, inputFile);
+    }
+  }
+
+}

components/bundles/bioformats_package/build.xml

@@ -31,7 +31,7 @@ Type "ant -p" for a list of targets.
       <doctitle><![CDATA[<h1>Bio-Formats</h1>]]></doctitle>
       <bottom><![CDATA[${copyright.begin} ${YEAR} ${copyright.end}]]></bottom>
       <link href="http://docs.oracle.com/javase/7/docs/api/"/>
-      <link href="http://rsbweb.nih.gov/ij/developer/api/"/>
+      <link href="https://imagej.nih.gov/ij/developer/api/"/>
       <!--<link href="http://www.jdocs.com/formlayout/1.0.4/api/"/>-->
       <!--<link href="http://www.jdocs.com/looks/1.2.2/api/"/>-->
     </javadoc>
@@ -50,13 +50,4 @@ Type "ant -p" for a list of targets.
       <zipfileset file="${artifact.dir}/${bundle.jar}" prefix="bftools"/>
     </zip>
   </target>
-
-  <target name="bfmatlab"
-    description="generate the a zip bundle of the MATLAB toolbox">
-    <zip destfile="${artifact.dir}/bfmatlab.zip">
-      <zipfileset dir="${root.dir}/components/formats-gpl/matlab"
-        includes="**/*" prefix="bfmatlab"/>
-      <zipfileset file="${artifact.dir}/${bundle.jar}" prefix="bfmatlab"/>
-    </zip>
-  </target>
 </project>

components/bundles/bioformats_package/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../../../</relativePath>
   </parent>
 

components/bundles/loci_tools/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../../../</relativePath>
   </parent>
 

components/forks/turbojpeg/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../../../</relativePath>
   </parent>
 

components/formats-api/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/formats-api/src/loci/formats/IFormatReader.java

@@ -341,23 +341,48 @@ Object openPlane(int no, int x, int y, int w, int h)
    */
   int fileGroupOption(String id) throws FormatException, IOException;
 
-  /** Returns an array of filenames needed to open this dataset. */
+  /**
+   * Returns an array of filenames needed to open this dataset.
+   * The first element in the array is expected to be the path passed to
+   * {@link #setId(String)}.  The remaining elements are expected to be in a
+   * consistent order; if a directory listing is necessary to build the list
+   * then it should be sorted first.
+   */
   String[] getUsedFiles();
 
   /**
    * Returns an array of filenames needed to open this dataset.
    * If the 'noPixels' flag is set, then only files that do not contain
    * pixel data will be returned.
+   *
+   * The first element in the array is expected to be the path passed to
+   * {@link #setId(String)}, if appropriate based upon 'noPixels'.
+   * The remaining elements are expected to be in a consistent order;
+   * if a directory listing is necessary to build the list then it should
+   * be sorted first.
    */
   String[] getUsedFiles(boolean noPixels);
 
-  /** Returns an array of filenames needed to open the current series. */
+  /**
+   * Returns an array of filenames needed to open the current series.
+   *
+   * The first element in the array is expected to be the path passed to
+   * {@link #setId(String)}.  The remaining elements are expected to be in a
+   * consistent order; if a directory listing is necessary to build the list
+   * then it should be sorted first.
+   */
   String[] getSeriesUsedFiles();
 
   /**
    * Returns an array of filenames needed to open the current series.
    * If the 'noPixels' flag is set, then only files that do not contain
    * pixel data will be returned.
+   *
+   * The first element in the array is expected to be the path passed to
+   * {@link #setId(String)}, if appropriate based upon 'noPixels'.
+   * The remaining elements are expected to be in a consistent order;
+   * if a directory listing is necessary to build the list then it should
+   * be sorted first.
    */
   String[] getSeriesUsedFiles(boolean noPixels);
 

components/formats-bsd/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>5.9.0-SNAPSHOT</version>
+    <version>5.10.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>