def recon_visit(visit, databin, shallow_recon=False):
'shallow_recon will NOT check the individual files to see if they exist. Shallow Recon will stop if the top level folder exists'
dcm2nii_object = dcm2nii(args_list=[
'-a', 'N', '-d', 'N', '-e', 'N', '-g', 'N', '-i', 'N', '-n', 'Y', '-p',
'N', '-m', 'N', '-r', 'N', '-v', 'Y', '-x', 'N'
])
could_not_recon_list = []
#remove garbage in quarantine
for dicom in visit.dicomlist:
dicom.series_folder_list.sort(key=lambda x: x.SeriesNumber
) # to ensure that 0 entry removed first
folders_to_check = [
x for x in dicom.series_folder_list
if x.bad == False and x.manual_recon == False
]
num_folders_to_check = len(folders_to_check)
skip_check = False
for series_folder in folders_to_check:
series_info = databin.dicom_series_read.merged_series[
visit.subject.subid][visit.visid][
series_folder.SeriesInstanceUID]
dicom_series_type = series_info.DICOMseries_types.itervalues(
).next()
folder_name = dicom_series_type.folder #folder inside visit dir
expected_image_quantity = dicom_series_type.expected_image_quantity #number of niftis we expect
if series_info.series == 'DTI_1' or series_info.series == 'DTI_2':
folder_name = series_info.series
if shallow_recon and folder_name in visit.niftis: #i
print "SHALLOW SKIPPING"
continue
if num_folders_to_check == 1:
skip_check = True
if databin.dicom_series_read.merged_series[visit.subject.subid][
visit.visid][
series_folder.
SeriesInstanceUID].Modality == 'PR': #skip PR visits
num_folders_to_check = num_folders_to_check - 1
continue
elif skip_check:
check_recon_dicom_folder(series_folder, dcm2nii_object,
folder_name, expected_image_quantity)
if expected_image_quantity >= 0: #not -1, the default
generated_nifti_paths = gen_nifti_basename_fullpaths(
series_folder, folder_name, expected_image_quantity)
if all([nifti_exists(x) for x in generated_nifti_paths]):
break
else:
could_not_recon_list.append(
"subid:{0.visit.subject.subid} visid: {0.visit.visid} series: {0.series}"
.format(dicom))
misc.set_permissions(visit.path)
return could_not_recon_list
def check_recon_dicom_folder(series_folder, dcm2nii_object, folder_name,
expected_image_quantity):
reconstructed_image_quantity = -1
number_paths_to_generate = expected_image_quantity
if expected_image_quantity < 0:
reconstructed_image_quantity = recon_into_quarantine(
series_folder, dcm2nii_object)
number_paths_to_generate = reconstructed_image_quantity
generated_nifti_paths = gen_nifti_basename_fullpaths(
series_folder, folder_name, number_paths_to_generate)
#if all niftis exist, delete all files in quarantine and exit
niftis_exist = [nifti_exists(x) for x in generated_nifti_paths]
if all(niftis_exist):
visit = series_folder.image.visit
quar_dir = os.path.join(visit.path, 'Quarantine')
if os.path.exists(quar_dir):
shutil.rmtree(quar_dir)
os.mkdir(quar_dir)
return
#reconstruct into nifti if we havn't already
elif reconstructed_image_quantity < 0: #not reconstructed into quarantine before
reconstructed_image_quantity = recon_into_quarantine(
series_folder, dcm2nii_object)
#check that number of reconstructed images matches number expected
if expected_image_quantity > 0 and expected_image_quantity != reconstructed_image_quantity:
visit = series_folder.image.visit
quar_dir = os.path.join(visit.path, 'Quarantine')
reconed_files = os.listdir(quar_dir)
reconstructed_niftis = [x for x in reconed_files if is_nifti(x)]
quar_dir = os.path.join(visit.path, 'Quarantine')
raise Wrong_Number_Of_Files_Error(
quar_dir,
"Unexpected number niftis produced by reconstruction. Expected:{0} Reconstructed:{1}\nReconstructedPaths\n{2}\nExpectedBasenames\n{3}"
.format(expected_image_quantity, reconstructed_image_quantity,
'\n'.join(reconstructed_niftis),
'\n'.join(generated_nifti_paths)))
move_niftis(series_folder, folder_name, generated_nifti_paths)
move_non_niftis(series_folder, folder_name)
def check_recon_dicom_folder(series_folder, dcm2nii_object, folder_name, expected_image_quantity):
reconstructed_image_quantity = -1
number_paths_to_generate = expected_image_quantity
if expected_image_quantity < 0:
reconstructed_image_quantity = recon_into_quarantine(series_folder, dcm2nii_object)
number_paths_to_generate = reconstructed_image_quantity
generated_nifti_paths = gen_nifti_basename_fullpaths(series_folder, folder_name, number_paths_to_generate)
#if all niftis exist, delete all files in quarantine and exit
niftis_exist = [nifti_exists(x) for x in generated_nifti_paths]
if all(niftis_exist):
visit = series_folder.image.visit
quar_dir = os.path.join(visit.path, 'Quarantine')
if os.path.exists(quar_dir):
shutil.rmtree(quar_dir)
os.mkdir(quar_dir)
return
#reconstruct into nifti if we havn't already
elif reconstructed_image_quantity < 0: #not reconstructed into quarantine before
reconstructed_image_quantity = recon_into_quarantine(series_folder, dcm2nii_object)
#check that number of reconstructed images matches number expected
if expected_image_quantity > 0 and expected_image_quantity != reconstructed_image_quantity:
visit = series_folder.image.visit
quar_dir = os.path.join(visit.path, 'Quarantine')
reconed_files = os.listdir(quar_dir)
reconstructed_niftis = [x for x in reconed_files if is_nifti(x)]
quar_dir = os.path.join(visit.path, 'Quarantine')
raise Wrong_Number_Of_Files_Error(quar_dir, "Unexpected number niftis produced by reconstruction. Expected:{0} Reconstructed:{1}\nReconstructedPaths\n{2}\nExpectedBasenames\n{3}".format(
expected_image_quantity,
reconstructed_image_quantity,
'\n'.join(reconstructed_niftis),
'\n'.join(generated_nifti_paths)
))
move_niftis(series_folder, folder_name, generated_nifti_paths)
move_non_niftis(series_folder, folder_name)
def recon_visit(visit, databin, shallow_recon=False):
'shallow_recon will NOT check the individual files to see if they exist. Shallow Recon will stop if the top level folder exists'
dcm2nii_object = dcm2nii(args_list=['-a', 'N', '-d', 'N', '-e', 'N', '-g', 'N', '-i', 'N', '-n', 'Y', '-p', 'N', '-m', 'N', '-r', 'N', '-v', 'Y', '-x', 'N'])
could_not_recon_list = []
#remove garbage in quarantine
for dicom in visit.dicomlist:
dicom.series_folder_list.sort(key=lambda x: x.SeriesNumber) # to ensure that 0 entry removed first
folders_to_check = [x for x in dicom.series_folder_list if x.bad == False and x.manual_recon == False]
num_folders_to_check = len(folders_to_check)
skip_check = False
for series_folder in folders_to_check:
series_info = databin.dicom_series_read.merged_series[visit.subject.subid][visit.visid][series_folder.SeriesInstanceUID]
dicom_series_type = series_info.DICOMseries_types.itervalues().next()
folder_name = dicom_series_type.folder #folder inside visit dir
expected_image_quantity = dicom_series_type.expected_image_quantity #number of niftis we expect
if series_info.series == 'DTI_1' or series_info.series == 'DTI_2':
folder_name = series_info.series
if shallow_recon and folder_name in visit.niftis: #i
print "SHALLOW SKIPPING"
continue
if num_folders_to_check == 1:
skip_check = True
if databin.dicom_series_read.merged_series[visit.subject.subid][visit.visid][series_folder.SeriesInstanceUID].Modality == 'PR': #skip PR visits
num_folders_to_check = num_folders_to_check - 1
continue
elif skip_check:
check_recon_dicom_folder(series_folder, dcm2nii_object, folder_name, expected_image_quantity)
if expected_image_quantity >= 0: #not -1, the default
generated_nifti_paths = gen_nifti_basename_fullpaths(series_folder, folder_name, expected_image_quantity)
if all([nifti_exists(x) for x in generated_nifti_paths]):
break
else:
could_not_recon_list.append("subid:{0.visit.subject.subid} visid: {0.visit.visid} series: {0.series}".format(dicom))
misc.set_permissions(visit.path)
return could_not_recon_list
