Fix for true single well plates, add one more test for multiple direc…

…tories
glencoesoftware · Jul 21, 2024 · b7d3286 · b7d3286
1 parent 411a030
commit b7d3286
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Showing 2 changed files with 35 additions and 8 deletions.
diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/BioTekReader.java b/src/main/java/com/glencoesoftware/bioformats2raw/BioTekReader.java
@@ -240,18 +240,31 @@ protected void initFile(String id) throws FormatException, IOException {
       LOGGER.debug("plate directory = {}", plateDir);
       String[] wellDirs = plateDir.list(true);
       ArrayList<String> allFiles = new ArrayList<String>();
+      boolean multipleDirs = true;
       for (String well : wellDirs) {
         Location wellDir = new Location(plateDir, well).getAbsoluteFile();
         LOGGER.debug("looking in well directory = {}", wellDir);
-        String[] f = wellDir.list(true);
-        for (String file : f) {
-          LOGGER.debug("  adding well file {}", file);
-          allFiles.add(new Location(wellDir, file).getAbsolutePath());
+        if (wellDir == null) {
+          multipleDirs = false;
         }
+        else {
+          String[] f = wellDir.list(true);
+          if (f == null) {
+            multipleDirs = false;
+          }
+          else {
+            for (String file : f) {
+              LOGGER.debug("  adding well file {}", file);
+              allFiles.add(new Location(wellDir, file).getAbsolutePath());
+            }
+          }
+        }
+      }
+      if (multipleDirs) {
+        LOGGER.debug("found files = {}", allFiles);
+        files = allFiles.toArray(new String[allFiles.size()]);
+        Arrays.sort(files);
       }
-      LOGGER.debug("found files = {}", allFiles);
-      files = allFiles.toArray(new String[allFiles.size()]);
-      Arrays.sort(files);
     }
 
     Pattern regexA = Pattern.compile(TIFF_REGEX_A);

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/BioTekTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/BioTekTest.java
@@ -224,7 +224,21 @@ static Stream<Arguments> getTestCases() {
       Arguments.of(new String[] {
         "B2/B2_1_Bright Field_1_001_02.tif",
         "D3/D3_1_Bright Field_1_001_02.tif",
-      }, new int[] {1, 3}, new int[] {1, 2}, 1, 1, 1, 1)
+      }, new int[] {1, 3}, new int[] {1, 2}, 1, 1, 1, 1),
+      Arguments.of(new String[] {
+        "ID_A9 info/A9_-1_1_1_Phase Contrast_001.tif",
+        "ID_A9 info/A9_-1_2_1_GFP_001.tif",
+        "ID_A9 info/A9_-1_3_1_DAPI_001.tif",
+        "ID_A10 info/A10_-1_1_1_Phase Contrast_001.tif",
+        "ID_A10 info/A10_-1_2_1_GFP_001.tif",
+        "ID_A10 info/A10_-1_3_1_DAPI_001.tif",
+        "ID_E9 info/E9_-1_1_1_Phase Contrast_001.tif",
+        "ID_E9 info/E9_-1_2_1_GFP_001.tif",
+        "ID_E9 info/E9_-1_3_1_DAPI_001.tif",
+        "ID_E10 info/E10_-1_1_1_Phase Contrast_001.tif",
+        "ID_E10 info/E10_-1_2_1_GFP_001.tif",
+        "ID_E10 info/E10_-1_3_1_DAPI_001.tif",
+      }, new int[] {0, 0, 4, 4}, new int[] {8, 9, 8, 9}, 1, 1, 3, 1)
     );
   }