Merge pull request #3019 from ctrueden/bf-file-pattern-ids

Add setFilePatternIds method to ImporterOptions
ome · Jan 18, 2018 · 801f12c · 801f12c
2 parents e514c57 + b8bfad5
commit 801f12c
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Showing 2 changed files with 11 additions and 2 deletions.
diff --git a/components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java b/components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java
@@ -48,6 +48,7 @@
 import loci.formats.ChannelSeparator;
 import loci.formats.ClassList;
 import loci.formats.DimensionSwapper;
+import loci.formats.FilePattern;
 import loci.formats.FileStitcher;
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
@@ -495,7 +496,8 @@ private void initializeFile() throws FormatException, IOException {
       baseReader.getMetadataOptions().setMetadataLevel(
           MetadataLevel.NO_OVERLAYS);
     }
-    baseReader.setId(options.getId());
+    baseReader.setId(options.isUsingPatternIds() ?
+      new FilePattern(options.getId()).getFiles()[0] : options.getId());
 
     boolean mustGroup = baseReader.fileGroupOption(options.getId()) == FormatTools.MUST_GROUP;
     options.setMustGroup(mustGroup);
@@ -615,7 +617,8 @@ private void createBaseReader() throws FormatException, IOException {
     if (options.isLocal() || options.isHTTP()) {
       BF.status(options.isQuiet(), "Identifying " + idName);
       imageReader = LociPrefs.makeImageReader();
-      baseReader = imageReader.getReader(options.getId());
+      baseReader = imageReader.getReader(options.isUsingPatternIds() ?
+        new FilePattern(options.getId()).getFiles()[0] : options.getId());
     }
     else if (options.isOMERO()) {
       BF.status(options.isQuiet(), "Establishing server connection");

diff --git a/components/bio-formats-plugins/src/loci/plugins/in/ImporterOptions.java b/components/bio-formats-plugins/src/loci/plugins/in/ImporterOptions.java
@@ -154,6 +154,9 @@ public class ImporterOptions extends OptionsList {
   private List<List<DoubleOption>> customColors =
     new ArrayList<List<DoubleOption>>();
 
+  // whether to treat the given id as a file pattern directly
+  private boolean usePatternIds;
+
   // -- Constructor --
 
   public ImporterOptions() throws IOException {
@@ -510,6 +513,9 @@ public String getCustomColorKey(int s, int c) {
     return s + "_" + c;
   }
 
+  public boolean isUsingPatternIds() { return usePatternIds; }
+  public void setUsingPatternIds(boolean b) { usePatternIds = b; }
+
   // -- Helper methods --
 
   private <T extends Object> void set(List<T> list,