improve 4D dicom writing and add lookup table for GE isotope names and dicom radio nuclide codes

Author: gschramm

pymirc/fileio/radioPharmaceuticalInfoSequence.py

@@ -2,6 +2,47 @@
 
 import warnings
 
+def GE_PET_nuclide_code_dict():
+  d = {
+  '11C':'C-105A1',
+  '13N':'C-107A1',
+  '14O':'C-1018C',
+  '15O':'C-B1038',
+  '18F':'C-111A1',
+  '22Na':'C-155A1',
+  '38K':'C-135A4',
+  '43Sc':'126605',
+  '44Sc':'126600',
+  '45Ti':'C-166A2',
+  '51Mn':'126601',
+  '52Fe':'C-130A1',
+  '52Mn':'C-149A1',
+  '52mMn':'126607',
+  '60Cu':'C-127A4',
+  '61Cu':'C-127A1',
+  '62Cu':'C-127A5',
+  '62Zn':'C-141A1',
+  '64Cu':'C-127A2',
+  '66Ga':'C-131A1',
+  '68Ga':'C-131A3',
+  '68Ge':'C-128A2',
+  '70As': '126602',
+  '72As':'C-115A2',
+  '73Se':'C-116A2',
+  '75Br':'C-113A1',
+  '76Br':'C-113A2',
+  '77Br':'C-113A3',
+  '82Rb':'C-159A2',
+  '86Y':'C-162A3',
+  '89Zr':'C-168A4',
+  '90Nb':'126603',
+  '90Y':'C-162A7',
+  '94mTc':'C-163AA',
+  '124I':'C-114A5',
+  '152Tb':'126606'}
+
+  return d
+
 def radioPharmaceuticalDict():
   rpd = {
    '126752'   : ['28H1 ^89^Zr'                                      ,'DCM'],

pymirc/fileio/write_dicom.py

@@ -417,9 +417,12 @@ def write_4d_dicom(vol_lps,
   """
   numFrames = vol_lps.shape[0]
 
-  StudyInstanceUID    = dicom.uid.generate_uid(uid_base) 
   SeriesInstanceUID   = dicom.uid.generate_uid(uid_base)
-  FrameOfReferenceUID = dicom.uid.generate_uid(uid_base)
+
+  if not 'StudyInstanceUID' in kwargs:
+    kwargs['StudyInstanceUID'] = dicom.uid.generate_uid(uid_base) 
+  if not 'FrameOfReferenceUID' in kwargs:
+    kwargs['FrameOfReferenceUID'] = dicom.uid.generate_uid(uid_base)
 
   numSlices = vol_lps.shape[-1]
 
@@ -441,9 +444,7 @@ def write_4d_dicom(vol_lps,
                                         uid_base                   = uid_base,
                                         TemporalPositionIdentifier = i + 1,
                                         NumberOfTemporalPositions  = numFrames,
-                                        StudyInstanceUID           = StudyInstanceUID,   
                                         SeriesInstanceUID          = SeriesInstanceUID,  
-                                        FrameOfReferenceUID        = FrameOfReferenceUID,
                                         SeriesType                 = SeriesType,
                                         frm                        = frm,
                                         **kw))