actually implement the documented groupfiles option

bioformats/formatreader.py

@@ -538,7 +538,7 @@ class ImageReader(object):
 
     '''
 
-    def __init__(self, path=None, url=None, perform_init=True):
+    def __init__(self, path=None, url=None, perform_init=True, groupFiles=False):
         self.stream = None
         file_scheme = "file:"
         self.url = url
@@ -561,7 +561,7 @@ def __init__(self, path=None, url=None, perform_init=True):
                         self.rdr = get_omero_reader()
                         self.path = url
                         if perform_init:
-                            self.init_reader()
+                            self.init_reader(groupFiles)
                         return
                     except jutil.JavaException, e:
                         je = e.throwable
@@ -666,7 +666,7 @@ def __init__(self, path=None, url=None, perform_init=True):
         self.rdr = IFormatReader()
         self.rdr.o = jrdr
         if perform_init:
-            self.init_reader()
+            self.init_reader(groupFiles)
 
     def __enter__(self):
         return self
@@ -690,10 +690,10 @@ def close(self):
         #
         jutil.static_call("java/lang/System", "gc","()V")
 
-    def init_reader(self):
+    def init_reader(self, groupFiles=False):
         mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
         self.rdr.setMetadataOptions(mdoptions)
-        self.rdr.setGroupFiles(False)
+        self.rdr.setGroupFiles(groupFiles)
         self.metadata = metadatatools.createOMEXMLMetadata()
         self.rdr.setMetadataStore(self.metadata)
         try:
@@ -943,7 +943,7 @@ def load_using_bioformats(path, c=None, z=0, t=0, series=None, index=None,
         return rdr.read(c, z, t, series, index, rescale, wants_max_intensity,
                         channel_names)
 
-def get_omexml_metadata(path=None, url=None):
+def get_omexml_metadata(path=None, url=None, groupfiles=False):
     '''Read the OME metadata from a file using Bio-formats
 
     :param path: path to the file
@@ -954,6 +954,8 @@ def get_omexml_metadata(path=None, url=None):
     :returns: the metdata as XML.
 
     '''
+    if not isinstance(groupfiles, bool):
+        groupfiles = False
     with ImageReader(path=path, url=url, perform_init=False) as rdr:
         #
         # Below, "in" is a keyword and Rhino's parser is just a little wonky I fear.
@@ -966,7 +968,7 @@ def get_omexml_metadata(path=None, url=None):
                     Packages.loci.formats.services.OMEXMLService,
                     Packages.loci.formats['in'].DefaultMetadataOptions,
                     Packages.loci.formats['in'].MetadataLevel);
-        reader.setGroupFiles(false);
+        reader.setGroupFiles(""" + str(groupfiles).lower() + """);
         reader.setOriginalMetadataPopulated(true);
         var service = new ServiceFactory().getInstance(OMEXMLService);
         var metadata = service.createOMEXMLMetadata();