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Implement multi-slice data support in DICOM export #17

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Implement multi-slice data support in DICOM export #17

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50 changes: 38 additions & 12 deletions mrd2dicom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,9 +107,11 @@ def main(args):
print("RGB data not yet supported")
continue
else:
if (mrdImg.data.shape[1] != 1):
print("Multi-slice data not yet supported")
continue
# Test for multi slice data
DataIsMultiSlice = False
if (mrdImg.data.shape[1] > 1):
DataIsMultiSlice = True
print(" Image %d is a 3D volume with %d slices" % (imgNum, mrdImg.data.shape[1]))

if (mrdImg.data.shape[0] != 1):
print("Multi-channel data not yet supported")
Expand All @@ -120,7 +122,7 @@ def main(args):
dicomDset = pydicom.dataset.Dataset.from_json(base64.b64decode(meta['DicomJson']))
else:
dicomDset = pydicom.dataset.Dataset()
dicomDset = pydicom.dataset.Dataset()
# dicomDset = pydicom.dataset.Dataset() # Double, already executed if no JSON header exists

# Enforce explicit little endian for written DICOM files
dicomDset.file_meta = pydicom.dataset.FileMetaDataset()
Expand Down Expand Up @@ -183,11 +185,6 @@ def main(args):
except:
print("Error setting header information from MRD header's acquisitionSystemInformation section")

# Set mrdImg pixel data from MRD mrdImg
dicomDset.PixelData = np.squeeze(mrdImg.data).tobytes() # mrdImg.data is [cha z y x] -- squeeze to [y x] for [row col]
dicomDset.Rows = mrdImg.data.shape[2]
dicomDset.Columns = mrdImg.data.shape[3]

if (mrdImg.data.dtype == 'uint16') or (mrdImg.data.dtype == 'int16'):
dicomDset.BitsAllocated = 16
dicomDset.BitsStored = 16
Expand All @@ -203,9 +200,6 @@ def main(args):
else:
print("Unsupported data type: ", mrdImg.data.dtype)

dicomDset.SeriesNumber = mrdImg.image_series_index
dicomDset.InstanceNumber = mrdImg.image_index

# ----- Set some mandatory default values -----
if not 'SamplesPerPixel' in dicomDset:
dicomDset.SamplesPerPixel = 1
Expand Down Expand Up @@ -280,6 +274,38 @@ def main(args):
# LUTFileName
# ROI

if DataIsMultiSlice:

# Loop over slices
for sli in range(mrdImg.data.shape[1]):

# Set mrdImg pixel data from MRD mrdImg
dicomDset.PixelData = np.squeeze(mrdImg.data[:,sli,:,:]).tobytes() # mrdImg.data is [cha z y x] -- squeeze to [y x] for [row col]
dicomDset.Rows = mrdImg.data.shape[2]
dicomDset.Columns = mrdImg.data.shape[3]
dicomDset.SeriesNumber = mrdImg.image_series_index
dicomDset.InstanceNumber = mrdImg.image_index + sli

# Create folder for each group
Groupfolder = os.path.join(args.out_folder, group)
if not os.path.exists(Groupfolder):
os.makedirs(Groupfolder)

# Write DICOM files
fileName = "%02.0f_%s_%03.0f.dcm" % (dicomDset.SeriesNumber, dicomDset.SeriesDescription, dicomDset.InstanceNumber)
# print(" Writing file %s" % fileName)
dicomDset.save_as(os.path.join(Groupfolder, fileName), enforce_file_format=True)
filesWritten += 1

else:

# Set mrdImg pixel data from MRD mrdImg
dicomDset.PixelData = np.squeeze(mrdImg.data).tobytes() # mrdImg.data is [cha z y x] -- squeeze to [y x] for [row col]
dicomDset.Rows = mrdImg.data.shape[2]
dicomDset.Columns = mrdImg.data.shape[3]
dicomDset.SeriesNumber = mrdImg.image_series_index
dicomDset.InstanceNumber = mrdImg.image_index

# Write DICOM files
fileName = "%02.0f_%s_%03.0f.dcm" % (dicomDset.SeriesNumber, dicomDset.SeriesDescription, dicomDset.InstanceNumber)
print(" Writing file %s" % fileName)
Expand Down