Replace dictionary by MetaData class

src/cli/dicom2nifti

@@ -58,20 +58,20 @@ def convert(dicom, destination, dtype, pretty_print, zip):
     nifti_data = dicomifier.dicom_to_nifti.convert(dicom_data_sets, dtype)
 
     stacks_count = {}
-    for nifti_image, nifti_meta_data in nifti_data:
-        series_instance_uid = nifti_meta_data["SeriesInstanceUID"][0]
+    for image, meta_data in nifti_data:
+        series_instance_uid = meta_data["SeriesInstanceUID"][0]
 
         stacks_count.setdefault(series_instance_uid, 0)
         stacks_count[series_instance_uid] += 1
 
     directories = {}
 
-    for nifti_image, nifti_meta_data in nifti_data:
-        study_instance_uid = nifti_meta_data["StudyInstanceUID"]
-        series_instance_uid = nifti_meta_data["SeriesInstanceUID"][0]
+    for image, meta_data in nifti_data:
+        study_instance_uid = meta_data["StudyInstanceUID"][0]
+        series_instance_uid = meta_data["SeriesInstanceUID"][0]
 
-        study_description = nifti_meta_data.get("StudyDescription", "")
-        series_description = nifti_meta_data.get("SeriesDescription", "")
+        study_description = meta_data.get("StudyDescription", [""])[0]
+        series_description = meta_data.get("SeriesDescription", [""])[0]
 
         study_directory, _ = directories.setdefault(
             study_instance_uid, [1+len(directories), {}])
@@ -99,12 +99,14 @@ def convert(dicom, destination, dtype, pretty_print, zip):
         suffix = ".nii"
         if zip:
             suffix += ".gz"
-        nifti_image.save(destination_root+suffix)
+        image.save(destination_root+suffix)
 
         kwargs = {}
         if pretty_print:
             kwargs = {"sort_keys": True, "indent": 4}
-        json.dump(nifti_meta_data, open(destination_root+".json", "w"), **kwargs)
+        json.dump(
+            meta_data, open(destination_root+".json", "w"), 
+            cls=dicomifier.MetaData.JSONEncoder, **kwargs)
 
 if __name__ == "__main__":
     sys.exit(main())

src/python/dicomifier/dicom_to_nifti/convert.py

@@ -1,4 +1,4 @@
-from __future__ import print_function
+import logging
 import itertools
 
 import numpy
@@ -11,11 +11,13 @@ def convert(dicom_data_sets, dtype, pretty_print=False):
     nifti_data = []
 
     stacks = get_stacks(dicom_data_sets)
+    logging.info(
+        "Found {} stack{}".format(len(stacks), "s" if len(stacks)>1 else ""))
     for key, data_sets in stacks.items():
         sort(data_sets)
 
-        nifti_image = image.get_nifti_image(data_sets, dtype)
-        nifti_meta_data = meta_data.get_nifti_meta_data(data_sets, key)
+        nifti_image = image.get_image(data_sets, dtype)
+        nifti_meta_data = meta_data.get_meta_data(data_sets, key)
 
         nifti_data.append((nifti_image, nifti_meta_data))
 

src/python/dicomifier/dicom_to_nifti/image.py

@@ -13,7 +13,7 @@
 import numpy
 import odil
 
-def get_nifti_image(data_sets, dtype):
+def get_image(data_sets, dtype):
     pixel_data = [get_pixel_data(data_set) for data_set in data_sets]
     pixel_data = numpy.asarray(pixel_data, dtype=dtype)
 

src/python/dicomifier/dicom_to_nifti/meta_data.py

@@ -8,9 +8,18 @@
 
 import itertools
 
+import numpy
 import odil
 
-def get_nifti_meta_data(data_sets, key):
+from .. import MetaData
+
+def get_meta_data(data_sets, key):
+    """ Return the merged meta-data from the DICOM data sets in the NIfTI+JSON
+        format: a dictionary keyed by the DICOM keyword (or the string 
+        representation of the tag if no keyword is found) and valued by the 
+        Value (or InlineBinary) of the DICOM elements.
+    """
+
     meta_data = [convert_meta_data(x) for x in data_sets]
 
     named_key = []
@@ -21,18 +30,26 @@ def get_nifti_meta_data(data_sets, key):
         except odil.Exception as e:
             pass
         named_key.append(name)
-            
+
     return merge_meta_data(meta_data, named_key)
 
 def convert_meta_data(data_set):
+    """ Convert the meta-data from DICOM data sets to the NIfTI+JSON format.
+    """
+
     meta_data = {}
 
     skipped = [
+        # Stored in the NIfTI image
         "Rows", "Columns", 
         "ImageOrientationPatient", "ImagePositionPatient", "PixelSpacing",
+        # Useless in the NIfTI world (?)
         "SOPInstanceUID", 
+        # Implicit with the NIfTI data type
         "PixelRepresentation", "HighBit", "BitsStored", "BitsAllocated",
+        # Stored in the NIfTI image
         "PixelData",
+        # PixelValueTransformation sequence is applied on the image
         "PixelValueTransformationSequence",
         "SmallestImagePixelValue", "LargestImagePixelValue",
     ]
@@ -64,34 +81,24 @@ def convert_meta_data(data_set):
     return meta_data
 
 def merge_meta_data(data_sets, key):
+    """ Merge the meta-data of DICOM data sets if they are equal.
+    """
+
     merged = {}
 
     tags = set(itertools.chain(*[x.keys() for x in data_sets]))
     for tag in tags:
-        multiplicity = "unknown"
-        try:
-            multiplicity = odil.registry.public_dictionary[
-                getattr(odil.registry, tag)].vm
-        except:
-            # Nothing is known about the multiplicity
-            pass
-
         merged_value = None
         if tag in key:
-            if multiplicity == "1":
-                merged_value = data_sets[0][tag]
-            else:
-                merged_value = data_sets[0][tag]
+            merged_value = data_sets[0][tag]
         else:
             merged_value = []
             for data_set in data_sets:
                 value = data_set.get(tag, None)
-                if value is not None and multiplicity == "1":
-                    value = value[0]
                 merged_value.append(value)
 
             if all(x == merged_value[0] for x in merged_value):
                 merged_value = merged_value[0]
         merged[tag] = merged_value
 
-    return merged
+    return MetaData(merged)