Merge pull request #3925 from melissalinkert/vsi-blob-files-develop

Olympus .vsi: only read pixels from frame_*.ets files
ome · Jan 27, 2023 · 3493350 · 3493350
2 parents d3be809 + c46deeb
commit 3493350
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Showing 2 changed files with 34 additions and 4 deletions.
diff --git a/components/formats-gpl/src/loci/formats/in/CellSensReader.java b/components/formats-gpl/src/loci/formats/in/CellSensReader.java
@@ -376,6 +376,8 @@ public class CellSensReader extends FormatReader {
   // -- Fields --
 
   private String[] usedFiles;
+  // non-pixels files that are included in the directory (e.g. "blobs")
+  private ArrayList<String> extraFiles = new ArrayList<String>();
   private HashMap<Integer, String> fileMap = new HashMap<Integer, String>();
 
   private TiffParser parser;
@@ -451,7 +453,15 @@ public String[] getSeriesUsedFiles(boolean noPixels) {
     FormatTools.assertId(currentId, true, 1);
 
     // all files contain pixels
-    return noPixels ? null : usedFiles;
+    if (noPixels) {
+      return extraFiles.toArray(new String[extraFiles.size()]);
+    }
+    String[] allFiles = new String[extraFiles.size() + usedFiles.length];
+    System.arraycopy(usedFiles, 0, allFiles, 0, usedFiles.length);
+    for (int i=0; i<extraFiles.size(); i++) {
+      allFiles[usedFiles.length + i] = extraFiles.get(i);
+    }
+    return allFiles;
   }
 
   /* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@@ -591,6 +601,7 @@ public void close(boolean fileOnly) throws IOException {
       parser = null;
       ifds = null;
       usedFiles = null;
+      extraFiles.clear();
       fileMap.clear();
       tileOffsets.clear();
       jpeg = false;
@@ -673,9 +684,12 @@ protected void initFile(String id) throws FormatException, IOException {
         if (pixelsFiles != null) {
           Arrays.sort(pixelsFiles);
           for (String pixelsFile : pixelsFiles) {
-            if (checkSuffix(pixelsFile, "ets")) {
+            if (checkSuffix(pixelsFile, "ets") && pixelsFile.startsWith("frame_")) {
               files.add(new Location(stackDir, pixelsFile).getAbsolutePath());
             }
+            else {
+              extraFiles.add(new Location(stackDir, pixelsFile).getAbsolutePath());
+            }
           }
         }
       }

diff --git a/components/test-suite/src/loci/tests/testng/FormatReaderTest.java b/components/test-suite/src/loci/tests/testng/FormatReaderTest.java
@@ -2010,7 +2010,15 @@ else if (success) {
           {
             continue;
           }
-
+
+          // .vsi datasets can only be detected with .vsi and frame*.ets
+          if (reader.getFormat().equals("CellSens VSI") &&
+            ((!base[i].toLowerCase().endsWith(".vsi") && !base[i].toLowerCase().endsWith(".ets")) ||
+            (base[i].toLowerCase().endsWith(".ets") && !base[i].toLowerCase().startsWith("frame"))))
+          {
+            continue;
+          }
+
           // XLef datasets not detected from xlif/lof file
           if (reader.getFormat().equals("Extended leica file") &&
             (base[i].toLowerCase().endsWith("xlif") || base[i].toLowerCase().endsWith("lof") 
@@ -2801,7 +2809,15 @@ else if (!result && r instanceof OlympusTileReader &&
             {
               continue;
             }
-
+
+            // .vsi data can only be detected from .vsi and frame*.ets
+            if (!result && r instanceof CellSensReader &&
+              ((!used[i].endsWith(".vsi") && !used[i].endsWith(".ets")) ||
+              (used[i].endsWith(".ets") && !used[i].startsWith("frame"))))
+            {
+              continue;
+            }
+
             // XLEF data can only be detected from xlef file
             if (!result && readers[j] instanceof XLEFReader &&
                 (used[i].endsWith(".xlif") || used[i].endsWith(".xlcf") ||