Add Frame Group information to DICOM

src/cli/bruker2dicom

@@ -45,10 +45,15 @@ def main():
         default="ImplicitVRLittleEndian",
         help="Transfer syntax of the output files"
     )
-    convert_parser.add_argument(
-        "--multiframe", "-m", action="store_true",
-        help="Generate multiframe dicom files"
-    )
+    # Disabled in order to correctly store the Frame Group index: since some
+    # frame groups are empty (i.e. in VisuFGOrderDesc one where the last value 
+    # is 0), we store the Frame Group index in Contributing Equipment Sequence;
+    # however, this is per-instance and no frame-level element exist to match 
+    # this.
+    # convert_parser.add_argument(
+    #     "--multiframe", "-m", action="store_true",
+    #     help="Generate multiframe dicom files"
+    # )
     convert_parser.add_argument(
         "--dicomdir", "-d", action="store_true", help="Create a DICOMDIR")
     convert_parser.add_argument(
@@ -57,6 +62,7 @@ def main():
     convert_parser.set_defaults(function=convert)
 
     arguments = vars(parser.parse_args())
+    arguments["multiframe"] = False # cf. previous comment
 
     if "function" not in arguments:
         parser.error("too few arguments")

src/python/dicomifier/bruker_to_dicom/frame_index_generator.py

@@ -63,7 +63,12 @@ def _get_frame_groups(data_set):
         frame_groups = []
         for description in data_set.get("VisuFGOrderDesc", []):
             frame_count, name, _, begin, fields_count = description
-            fields = [x[0] for x in data_set["VisuGroupDepVals"][begin:begin+fields_count]]
+            if fields_count == 0:
+                fields = []
+            else:
+                fields = [
+                    x[0] for x in 
+                    data_set["VisuGroupDepVals"][begin:begin+fields_count]]
             frame_groups.append([frame_count, name]+[fields])
         # CAUTION: the frame groups are listed in innermost-to-outermost
         # order, while FrameIndexGenerator uses outermost-to-innermost order.

src/python/dicomifier/bruker_to_dicom/image.py

@@ -7,6 +7,7 @@
 #########################################################################
 
 import datetime
+import json
 import re
 
 import numpy
@@ -192,6 +193,23 @@ def _get_geometry_of_kSpace_traversal(data_set, generator, frame_index):
     else:
         return None
 
+def _get_frame_index(bruker_data_set, generator, frame_index):
+    purpose = odil.DataSet()
+    purpose.add("CodeValue", ["109102"])
+    purpose.add("CodingSchemeDesignator", ["DCM"])
+    purpose.add("CodeMeaning", ["Processing Equipment"])
+
+    data_set = odil.DataSet()
+    data_set.add("PurposeOfReferenceCodeSequence", [purpose])
+    data_set.add("Manufacturer", ["Dicomifier"])
+    data_set.add("ManufacturerModelName", ["Bruker Frame Group index"])
+    contribution = [
+        [fg[1], frame_index[i]]
+        for i, fg in enumerate(generator.frame_groups) 
+        if fg[1] != 'FG_SLICE']
+    data_set.add("ContributionDescription", [json.dumps(contribution)])
+
+    return data_set
 
 GeneralImage = [ # http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.6.html#sect_C.7.6.1
     (None, "InstanceNumber", 2, lambda d,g,i: [1+g.get_linear_index(i)], None),
@@ -355,12 +373,13 @@ def _get_geometry_of_kSpace_traversal(data_set, generator, frame_index):
 ]
 
 SOPCommon = [ # http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.12.html#sect_C.12.1
-    # Will be add further in the converting function (mr_image_storage or enhanced_mr_image_storage)
-    # (None, "SOPClassUID", 1, lambda d,g,i: [odil.registry.MRImageStorage], None),
     (None, "SOPInstanceUID", 1, lambda d,g,i: [odil.generate_uid()], None),
     #SpecificCharacterSet
     (None, "InstanceCreationDate", 3, lambda d,g,i: [str(datetime.datetime.now())], None),
     (None, "InstanceCreationTime", 3, lambda d,g,i: [str(datetime.datetime.now())], None),
+    (
+        None, "ContributingEquipmentSequence", 3, 
+        lambda d,g,i: [_get_frame_index(d,g,i)], None)
 ]