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fix SM conversion and add metadata for op and SM
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@jomasator2
jomasator2 committed Oct 23, 2023
1 parent 3d76de6 commit 6c5760b
Showing 1 changed file with 43 additions and 51 deletions.
94 changes: 43 additions & 51 deletions xnat2mids/mids_conversion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -103,20 +103,20 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part, debug_le
procedure_class_light = LightProcedure()
procedure_class_radiology = RadiologyProcedure()
for subject_xnat_path in tqdm(xnat_data_path.iterdir()):
if "_S" not in subject_xnat_path.name:continue
# if "_S" not in subject_xnat_path.name:continue
# num_sessions = len(list(subject_xnat_path.glob('*/')))
procedure_class_mr.reset_indexes()
procedure_class_light.reset_indexes()
for sessions_xnat_path in subject_xnat_path.iterdir():
if "_E" not in sessions_xnat_path.name: continue
# if "_E" not in sessions_xnat_path.name: continue


print(sessions_xnat_path)
findings = re.search(subses_pattern, str(sessions_xnat_path), re.X)
#print('subject,', findings.group('prefix_sub'), findings.group('suffix_sub'))
#print('session,', findings.group('prefix_ses'), findings.group('suffix_ses'))
subject_name = f"sub-{findings.group('prefix_sub')}S{findings.group('suffix_sub')}"
session_name = f"ses-{findings.group('prefix_ses')}E{findings.group('suffix_ses')}"
subject_name = f"sub-{subject_xnat_path.stem}" #f"sub-{findings.group('prefix_sub')}S{findings.group('suffix_sub')}"
session_name = f"ses-{sessions_xnat_path.stem}" #f"ses-{findings.group('prefix_ses')}E{findings.group('suffix_ses')}"

mids_session_path = mids_data_path.joinpath(subject_name, session_name)
xml_session_rois = list(sessions_xnat_path.rglob('*.xml'))
Expand Down Expand Up @@ -227,15 +227,12 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part, debug_le

if modality in ["OP", "SC", "XC", "OT", "SM"]:

try:
folder_conversion = dicom2png(path_dicoms) #.joinpath("resources")
except RuntimeError as e:
continue
modality_ = ("op" if modality in ["OP", "SC", "XC", "OT"] else "BF")
mim = ("mim-ligth" if modality in ["OP", "SC", "XC", "OT"] else "micr")

folder_conversion = dicom2png(path_dicoms) #.joinpath("resources")
modality_, mim= (("op", "mim-ligth/op") if modality in ["OP", "SC", "XC", "OT"] else ("BF", "micr"))
laterality = dict_json.get("Laterality")
acq = "" if "ORIGINAL" in image_type else "opacitysubstract"
# print(laterality, acq)

print("!"*79)
print(modality, mids_session_path.joinpath(mim))
print("!"*79)
Expand Down Expand Up @@ -273,12 +270,14 @@ def create_directory_mids_v1(xnat_data_path, mids_data_path, body_part, debug_le
session_header = ['session_id','session_pseudo_id', 'acquisition_date_Time','radiology_report']
sessions_keys = ['AccessionNumber', 'AcquisitionDateTime']
scans_header = [
'scan_file','BodyPart',
'Manufacturer','ManufacturersModelName','DeviceSerialNumber',
'scan_file','BodyPart','SeriesNumber','AccessionNumber',
'Manufacturer','ManufacturerModelName',
'MagneticFieldStrength','ReceiveCoilName','PulseSequenceType',
'ScanningSequence','SequenceVariant','ScanOptions','SequenceName','PulseSequenceDetails','MRAcquisitionType',
'EchoTime','InversionTime','SliceTiming','SliceEncodingDirection','FlipAngle'
]
scans_header_micr = ['scan_file','BodyPart','SeriesNumber','AccessionNumber','Manufacturer','ManufacturerModelName','Modality', 'Columns','Rows','PhotometricInterpretation','ImagedVolumeHeight', 'ImagedVolumeHeight']
scans_header_op = ['scan_file','BodyPart','SeriesNumber','AccessionNumber','Manufacturer','ManufacturerModelName','Modality', 'Columns','Rows','PhotometricInterpretation', 'Laterality']

def create_tsvs(xnat_data_path, mids_data_path, body_part_aux):
"""
Expand All @@ -290,20 +289,13 @@ def create_tsvs(xnat_data_path, mids_data_path, body_part_aux):
for subject_path in mids_data_path.glob('*/'):
if not subject_path.match("sub-*"): continue
subject = subject_path.parts[-1]

old_subject = "_".join([
subject.split("-")[-1].split("S")[0],
"S"+subject.split("-")[-1].split("S")[1]
])
old_subject =subject.split("-")[-1]
list_sessions_information = []
for session_path in subject_path.glob('*/'):
if not session_path.match("ses-*"): continue
session = session_path.parts[-1]

old_sesion = "_".join([
session.split("-")[-1].split("E")[0],
"E"+session.split("-")[-1].split("E")[1]
])
old_sesion = session.split("-")[-1]

modalities = []
body_parts = []
Expand Down Expand Up @@ -401,35 +393,6 @@ def create_tsvs(xnat_data_path, mids_data_path, body_part_aux):
except AttributeError as e:
print("error de formato:", acquisition_date_time)


# if (acquisition_date != "n/a") and acquisition_time != "n/a":
# acquisition_date_time = str(acquisition_date) + str(acquisition_time)
# acquisition_date_time_check = aquisition_date_pattern_comp.search(acquisition_date_time)
# else:
# if acquisition_date_time == "n/a":
# acquisition_date_time_correct = "n/a"
# else:
# acquisition_date_time_check = aquisition_date_pattern_comp.search(acquisition_date_time)
# try:
# time_values = list(int (x) for x in acquisition_date_time_check.groups())
# except AttributeError as e:
# print("error de formato")

# # acquisition_date_time_check = aquisition_date_pattern_comp.search(json_file[participants_keys[5]])

# try:
# time_values = list(int (x) for x in acquisition_date_time_check.groups())
# except AttributeError as e:
# continue
# acquisition_date_time_correct = f"\
# {time_values[0]:04d}-\
# {time_values[1]:02d}-\
# {time_values[2]:02d}T\
# {time_values[3]:02d}:\
# {time_values[4]:02d}:\
# {time_values[5]:02d}.\
# {time_values[6]:06d}\
# "
adquisition_date_time = datetime.fromisoformat(acquisition_date_time_correct)
# adquisition_date_time = datetime.fromisoformat(json_file[participants_keys[5]].split('T')[0])
if patient_birthday != "n/a":
Expand All @@ -448,6 +411,35 @@ def create_tsvs(xnat_data_path, mids_data_path, body_part_aux):
)


})
if json_file[participants_keys[1]] in ["OP", "SC", "XC", "OT"]:
list_scan_information.append({
key:value
for nifti in list_nifties for key, value in zip(
scans_header_op,
[
str(Path(".").joinpath(*nifti.parts[-2:])),
body_parts[-1],
*[json_file.get(key, "n/a") for key in scans_header_op[2:]]
]
)


})
if json_file[participants_keys[1]] in ["SM"]:
print("estoy en SM")
list_scan_information.append({
key:value
for nifti in list_nifties for key, value in zip(
scans_header_micr,
[
str(Path(".").joinpath(*nifti.parts[-2:])),
body_parts[-1],
*[json_file.get(key, "n/a") for key in scans_header_micr[2:]]
]
)


})
#print(list_scan_information)
# if json_file[participants_keys[1]] in ["OP", "SC", "XC", "OT", "SM"]:
Expand Down

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