Changeset 7075

Timestamp:

10/14/10 18:23:51 (9 years ago)

Author:

melissa

Message:

• Fixed various file stitching bugs.
• Removed debugging statement.

Location:

trunk/components

Files:

• bio-formats/src/loci/formats/FilePattern.java (modified) (3 diffs)
• bio-formats/src/loci/formats/FileStitcher.java (modified) (3 diffs)
• bio-formats/src/loci/formats/in/BioRadReader.java (modified) (1 diff)
• test-suite/src/loci/tests/testng/FormatReaderTest.java (modified) (2 diffs)

trunk/components/bio-formats/src/loci/formats/FilePattern.java

@@ -161 +161 @@
     buildFiles("", num, fileList);
     files = fileList.toArray(new String[0]);
+
+    if (files.length == 0 && new Location(pattern).exists()) {
+      files = new String[] {pattern};
+    }
 
     valid = true;
@@ -448 +452 @@
   {
     String baseSuffix = base.substring(base.lastIndexOf(File.separator) + 1);
-    baseSuffix = baseSuffix.substring(baseSuffix.indexOf(".") + 1);
+    int dot = baseSuffix.indexOf(".");
+    if (dot < 0) baseSuffix = "";
+    else baseSuffix = baseSuffix.substring(dot + 1);
 
     ArrayList<String> patterns = new ArrayList<String>();
@@ -457 +463 @@
       if (start < 0) start = 0;
       String patternSuffix = pattern.substring(start);
-      patternSuffix = patternSuffix.substring(patternSuffix.indexOf(".") + 1);
+      dot = patternSuffix.indexOf(".");
+      if (dot < 0) patternSuffix = "";
+      else patternSuffix = patternSuffix.substring(dot + 1);
+
+      String checkPattern = findPattern(name, dir, nameList);
+      String[] checkFiles = new FilePattern(checkPattern).getFiles();
 
       if (!patterns.contains(pattern) && (!new Location(pattern).exists() ||
-        base.equals(pattern)) && patternSuffix.equals(baseSuffix))
+        base.equals(pattern)) && patternSuffix.equals(baseSuffix) &&
+        DataTools.indexOf(checkFiles, base) >= 0)
       {
         patterns.add(pattern);

trunk/components/bio-formats/src/loci/formats/FileStitcher.java

@@ -708 +708 @@
     LOGGER.debug("initFile: {}", id);
 
-    String[] patterns = findPatterns(id);
-    externals = new ExternalSeries[patterns.length];
-
-    for (int i=0; i<externals.length; i++) {
-      externals[i] = new ExternalSeries(new FilePattern(patterns[i]));
-    }
-
-    FilePattern fp = new FilePattern(patterns[0]);
+    FilePattern fp = new FilePattern(id);
 
     boolean mustGroup = false;
@@ -735 +728 @@
       return;
     }
+
+    String[] patterns = findPatterns(id);
+    if (patterns.length == 0) patterns = new String[] {id};
+    externals = new ExternalSeries[patterns.length];
+
+    for (int i=0; i<externals.length; i++) {
+      externals[i] = new ExternalSeries(new FilePattern(patterns[i]));
+    }
+    fp = new FilePattern(patterns[0]);
+
     reader.close();
     reader.setGroupFiles(false);
@@ -854 +857 @@
     store = reader.getMetadataStore();
     // don't overwrite pixel info if files aren't actually grouped
-    if (!noStitch && externals.length > 1) {
+    if (!noStitch) {
       MetadataTools.populatePixels(store, this);
       for (int i=0; i<getSeriesCount(); i++) {

trunk/components/bio-formats/src/loci/formats/in/BioRadReader.java

@@ -278 +278 @@
     in = new RandomAccessInputStream(id);
     in.order(true);
-
-    /* debug */ System.out.println("initializing .pic file: " + id);
 
     offset = new Vector<Double>();

trunk/components/test-suite/src/loci/tests/testng/FormatReaderTest.java

@@ -942 +942 @@
   private boolean initFile() {
     if (skip) throw new SkipException(SKIP_MESSAGE);
+
+    // initialize configuration tree
+    if (config != null) config.setId(id);
+
     if (reader == null) {
-      reader = new BufferedImageReader(new FileStitcher());
+      if (config.noStitching()) {
+        reader = new BufferedImageReader();
+      }
+      else {
+        reader = new BufferedImageReader(new FileStitcher());
+      }
       reader.setNormalized(true);
       reader.setMetadataFiltered(true);
@@ -985 +994 @@
         LOGGER.error("Used files list does not include base file");
       }
-
-      // initialize configuration tree
-      if (config != null) config.setId(id);
     }
     catch (Throwable t) {