Merge branch 'master' into s3

glencoesoftware · Jun 29, 2021 · b435320 · b435320
2 parents f6ac52b + 382ad05
commit b435320
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Showing 3 changed files with 73 additions and 21 deletions.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -340,6 +340,13 @@ public class Converter implements Callable<Void> {
   )
   private volatile boolean noHCS = false;
 
+  @Option(
+          names = "--no-ome-meta-export",
+          description = "Turn off OME metadata exporting " +
+                        "[Will break compatibility with raw2ometiff]"
+  )
+  private volatile boolean noOMEMeta = false;
+
   @Option(
           names = "--no-root-group",
           description = "Turn off creation of root group and corresponding " +
@@ -523,7 +530,7 @@ public void convert()
         memoizer.setMetadataOptions(options);
       }
 
-      memoizer.setOriginalMetadataPopulated(true);
+      memoizer.setOriginalMetadataPopulated(!noOMEMeta);
       memoizer.setFlattenedResolutions(false);
       memoizer.setMetadataFiltered(true);
       memoizer.setMetadataStore(createMetadata());
@@ -601,16 +608,17 @@ public void convert()
           }
         }
 
-        String xml = getService().getOMEXML(meta);
+        if (!noOMEMeta) {
+          String xml = getService().getOMEXML(meta);
 
-        // write the original OME-XML to a file
-        Path metadataPath = getRootPath().resolve("OME");
-        if (!Files.exists(metadataPath)) {
-          Files.createDirectories(metadataPath);
+          // write the original OME-XML to a file
+          Path metadataPath = getRootPath().resolve("OME");
+          if (!Files.exists(metadataPath)) {
+            Files.createDirectories(metadataPath);
+          }
+          Path omexmlFile = metadataPath.resolve(METADATA_FILE);
+          Files.write(omexmlFile, xml.getBytes(Constants.ENCODING));
         }
-
-        Path omexmlFile = metadataPath.resolve(METADATA_FILE);
-        Files.write(omexmlFile, xml.getBytes(Constants.ENCODING));
       }
       catch (ServiceException se) {
         LOGGER.error("Could not retrieve OME-XML", se);

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/MiraxReader.java b/src/main/java/com/glencoesoftware/bioformats2raw/MiraxReader.java
@@ -137,14 +137,25 @@ public class MiraxReader extends FormatReader {
 
   /** Constructs a new Mirax reader. */
   public MiraxReader() {
-    super("Mirax", "mrxs");
+    super("Mirax", new String[] {"mrxs", "ini"});
     domains = new String[] {FormatTools.HISTOLOGY_DOMAIN};
-    datasetDescription = "One .vms file plus several .jpg files";
+    datasetDescription =
+      "A directory of .ini and .dat files, and an optional .mrxs file";
     suffixNecessary = true;
+    suffixSufficient = false;
   }
 
   // -- IFormatReader API methods --
 
+  /* @see loci.formats.IFormatReader#isThisType(String, boolean) */
+  @Override
+  public boolean isThisType(String name, boolean open) {
+    if (checkSuffix(name, "mrxs")) {
+      return true;
+    }
+    return new Location(name).getName().equals(SLIDE_DATA);
+  }
+
   /* @see loci.formats.IFormatReader#getOptimalTileWidth() */
   @Override
   public int getOptimalTileWidth() {
@@ -172,7 +183,9 @@ public String[] getSeriesUsedFiles(boolean noPixels) {
 
     ArrayList<String> f = new ArrayList<String>();
     f.add(currentId);
-    f.add(iniPath);
+    if (!iniPath.equals(currentId)) {
+      f.add(iniPath);
+    }
     for (String file : files) {
       if (!checkSuffix(file, "dat") || !noPixels) {
         f.add(file);
@@ -366,13 +379,21 @@ public void reopenFile() throws IOException {
   protected void initFile(String id) throws FormatException, IOException {
     super.initFile(id);
 
-    offsets = new TreeMap<TilePointer, List<TilePointer>>();
+    Location slideDirectory = null;
 
-    Location dir = new Location(id.substring(0, id.lastIndexOf(".")));
-    Location slideData = new Location(dir, SLIDE_DATA);
-    iniPath = slideData.getAbsolutePath();
+    if (checkSuffix(id, "mrxs")) {
+      slideDirectory = new Location(id.substring(0, id.lastIndexOf(".")));
+      Location slideData = new Location(slideDirectory, SLIDE_DATA);
+      iniPath = slideData.getAbsolutePath();
+    }
+    else {
+      slideDirectory = new Location(id).getParentFile();
+      iniPath = new Location(id).getAbsolutePath();
+    }
+
+    offsets = new TreeMap<TilePointer, List<TilePointer>>();
 
-    String ini = DataTools.readFile(slideData.getAbsolutePath());
+    String ini = DataTools.readFile(iniPath);
     ini = ini.substring(ini.indexOf("["));
     IniParser parser = new IniParser();
     IniList data = parser.parseINI(new BufferedReader(new StringReader(ini)));
@@ -394,7 +415,7 @@ protected void initFile(String id) throws FormatException, IOException {
     }
 
     String indexFile = hierarchy.get("INDEXFILE");
-    Location index = new Location(dir, indexFile);
+    Location index = new Location(slideDirectory, indexFile);
     if (!index.exists()) {
       throw new IOException(
         "Index file " + index.getAbsolutePath() + " missing");
@@ -424,7 +445,7 @@ protected void initFile(String id) throws FormatException, IOException {
     int nFiles = Integer.parseInt(fileTable.get("FILE_COUNT"));
 
     for (int i=0; i<nFiles; i++) {
-      Location f = new Location(dir, fileTable.get("FILE_" + i));
+      Location f = new Location(slideDirectory, fileTable.get("FILE_" + i));
       if (!f.exists()) {
         throw new IOException("Data file " + f.getAbsolutePath() + " missing");
       }

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -91,8 +91,6 @@ void assertTool(String...additionalArgs) throws IOException {
     try {
       converter = new Converter();
       CommandLine.call(converter, args.toArray(new String[]{}));
-      assertTrue(Files.exists(
-        output.resolve("OME").resolve("METADATA.ome.xml")));
     }
     catch (RuntimeException rt) {
       throw rt;
@@ -1053,6 +1051,31 @@ public void testNoRootGroupOption() throws Exception {
     assertTrue(!Files.exists(output.resolve(".zgroup")));
   }
 
+  /**
+   * Check that a OME metadata is exported.
+   */
+  @Test
+  public void testOmeMetaExportOption() throws Exception {
+    input = fake();
+    assertTool();
+
+    assertTrue(Files.exists(
+      output.resolve("OME").resolve("METADATA.ome.xml")));
+  }
+
+  /**
+   * Convert with the --no-ome-meta-export option.  Conversion should succeed,
+   * but no OME metadata should be exported.
+   */
+  @Test
+  public void testNoOmeMetaExportOption() throws Exception {
+    input = fake();
+    assertTool("--no-ome-meta-export");
+
+    assertTrue(!Files.exists(
+      output.resolve("OME").resolve("METADATA.ome.xml")));
+  }
+
   /**
    * Convert with the --use-existing-resolutions option.  Conversion should
    * produce multiscales matching the input resolution numbers and scale.