def load_file(self, file, default=False):
if default:
return load_json(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
f'{file}.json'))
else:
return load_json(
os.path.join(self.credentials_home, f'{file}.json'))
def set_project(self, location):
if path.exists(path.join(self.credentials_home, 'projects.json')):
projects = load_json(
path.join(self.credentials_home, 'projects.json'))
projects['LOCATION'].append(location)
save_json(projects,
path.join(self.credentials_home, 'projects.json'))
# self.save_json('projects.json', projects, self.credentials_home)
new_loc = load_json(
path.join(self.credentials_home, 'remote1.json'))
new_loc['USER']['user'] = self.username
save_json(new_loc,
path.join(self.credentials_home, location + '.json'))
def chk_if_processed(self, abs_path2mr):
"""Check if any unconverted,
- if not converted, update config file based on sidecar params (update_config())
- redo run() up to repeat_lim
"""
ls_niigz_files = [
i for i in os.listdir(self.sub_SUBJDIR_tmp) if '.nii.gz' in i
]
if ls_niigz_files:
print(f'{" " *12}> remaining nii in {self.sub_SUBJDIR_tmp}')
if self.repeat_updating < self.repeat_lim:
self.update = False
for niigz_f in ls_niigz_files:
f_name = niigz_f.replace('.nii.gz', '')
sidecar = f'{f_name}.json'
self.sidecar_content = load_json(
os.path.join(self.sub_SUBJDIR_tmp, sidecar))
self.update_config()
if self.update:
print(f'{" " *12}removing folder: {self.sub_SUBJDIR_tmp}')
self.repeat_updating += 1
self.rm_dir(self.sub_SUBJDIR_tmp)
print(f'{" " *12}re-renning dcm2bids')
self.run_dcm2bids(abs_path2mr)
print(f'{" " *12}looping to another chk_if_processed')
self.chk_if_processed(abs_path2mr)
else:
self.populate_bids_classifed()
self.cleaning_after_conversion(abs_path2mr)
def chk_if_processed(self):
"""Check if any unconverted,
- if not converted, update config file based on sidecar params (update_config())
- redo run() up to repeat_lim
"""
ls_niigz_files = [
i for i in os.listdir(self.sub_SUBJDIR) if '.nii.gz' in i
]
if ls_niigz_files:
print(" remaining nii in ", self.sub_SUBJDIR)
if self.repeat_updating < self.repeat_lim:
self.update = False
for niigz_f in ls_niigz_files:
f_name = niigz_f.replace('.nii.gz', '')
sidecar = f'{f_name}.json'
self.sidecar_content = load_json(
os.path.join(self.sub_SUBJDIR, sidecar))
self.update_config()
if self.update:
print(' removing folder: ', self.sub_SUBJDIR)
self.repeat_updating += 1
self.rm_dir(self.sub_SUBJDIR)
print(' re-renning dcm2bids')
self.run_dcm2bids()
print(' looping to another chk_if_processed')
self.chk_if_processed()
else:
print(' dcm2bids conversion DONE')
if os.path.exists(self.sub_SUBJDIR):
self.rm_dir(self.sub_SUBJDIR)
def get_subjects(self):
# subjects = self.db_nl.get_db()
new_subjects_f_name = DEFAULT.app_files[self.app]["new_subjects"]
new_subjects_f_path = os.path.join(self.NIMB_tmp, new_subjects_f_name)
if os.path.isfile(new_subjects_f_path):
print(' reading new subjects to process')
new_subj = load_json(new_subjects_f_path)
self.db_nl = new_subj
def get_subjects(self):
new_subjects_f_name = DEFAULT.app_files[self.app]["new_subjects"]
new_subjects_f_path = os.path.join(self.NIMB_tmp, new_subjects_f_name)
if os.path.isfile(new_subjects_f_path):
print(f'{LogLVL.lvl1}reading new subjects to process')
new_subj = load_json(new_subjects_f_path)
self.db_dp = new_subj
else:
print(f'{LogLVL.lvl1}ERR: file with subjects is MISSING')
def run(self, nimb_id='none', ses='none', nimb_classified_per_id=dict()):
#run dcm2bids:
'''
if nimb_classified.json[nimb_id][archived]:
extract from archive specific subject_session
start dcm2bids for subject_session
Return:
self.bids_classified =
{'bids_id':
{'anat':
{'t1': ['local',
'PATH_TO_rawdata/bids_id_label/bids_id_session/modality/bids_label_ses-xx_run-xx_T1w.nii.gz']},
},
{'dwi':
{'dwi': ['local',
'PATH_TO_rawdata/bids_id_label/bids_id_session/modality/bids_label_ses-xx_run-xx_dwi.nii.gz'],
'bval': ['local',
'PATH_TO_rawdata/bids_id_label/bids_id_session/modality/bids_label_ses-xx_run-xx_dwi.bval'],
'bvec': ['local',
'PATH_TO_rawdata/bids_id_label/bids_id_session/modality/bids_label_ses-xx_run-xx_dwi.bvec']}
}
}
'''
self.id_classified = nimb_classified_per_id
self.bids_classified = dict()
print(f'{" " *8}folder with subjects is: {self.DICOM_DIR}')
if self.id_classified:
self.nimb_id = nimb_id
self.ses = ses
self.bids_id, self.bids_id_dir = self.make_bids_id(
self.nimb_id, self.ses)
self.start_stepwise_choice()
else:
self.nimb_classified = dict()
try:
self.nimb_classified = load_json(
os.path.join(self.DICOM_DIR, DEFAULT.f_nimb_classified))
except Exception as e:
print(
f'{" " *12} could not load the nimb_classified file at: {self.DICOM_DIR}'
)
sys.exit(0)
if self.nimb_classified:
self.nimb_ids = list(self.nimb_classified.keys())
for self.nimb_id in self.nimb_ids:
self.id_classified = self.nimb_classified[self.nimb_id]
for self.ses in [
i for i in self.id_classified
if i not in ('archived', )
]:
self.bids_id, self.bids_id_dir = self.make_bids_id(
self.nimb_id, self.ses)
self.start_stepwise_choice()
return self.bids_classified, self.bids_id
def read_fdr_images(self):
img = load_json(self.param.sig_fdr_json)
ls_img = list(img.keys())
for sig in img:
analysis_name = img[sig]['analysis_name']
glmdir = path.join(self.param.PATH_img, analysis_name)
self.make_images_results_fdr(img[sig]['hemi'], glmdir,
analysis_name,
img[sig]['fsgd_type_contrast'])
print(
f" \n\n\n{len(ls_img[ls_img.index(sig):])} images LEFT for extraction"
)
def read_mc_images(self):
img = load_json(self.param.sig_mc_json)
ls_img = list(img.keys())
for sig in img:
analysis_name = img[sig]['analysis_name']
contrast = img[sig]['contrast']
cwsig_mc_f = path.join(self.param.PATH_img, img[sig]['cwsig_mc_f'])
oannot_mc_f = path.join(self.param.PATH_img,
img[sig]['oannot_mc_f'])
self.make_images_results_mc(img[sig]['hemi'], analysis_name,
contrast, img[sig]['direction'],
cwsig_mc_f, oannot_mc_f)
print(
f" \n\n\n{len(ls_img[ls_img.index(sig):])} images LEFT for extraction"
)
def get_dict_4classification(self, dir_abspath):
main = dict()
self.f_nimb_classified = os.path.join(self.MAIN_DIR,
DEFAULT.f_nimb_classified)
# remove nimb_classified file from list of files in MAIN_DIR
if self.f_nimb_classified in self.dir_2classify:
self.dir_2classify.remove(self.f_nimb_classified)
# update the existing file ?
if os.path.exists(self.f_nimb_classified):
if self.update:
print('updating file with ids')
main = load_json(self.f_nimb_classified)
os.remove(self.f_nimb_classified)
return main
def update_config(self):
"""....."""
self.add_criterion = False
self.config = load_json(self.config_file)
criterion1 = 'SeriesDescription'
sidecar_crit1 = self.sidecar_content[criterion1]
list_criteria = list()
for des in self.config['descriptions']:
if des['dataType'] == self.data_Type and \
des["modalityLabel"] == self.modalityLabel:
list_criteria.append(des)
if len(list_criteria) > 0:
print(
f'{" " *12}> there is at least one configuration with dataType: {self.data_Type}'
)
for des in list_criteria[::-1]:
if criterion1 in des['criteria']:
if des['criteria'][criterion1] == sidecar_crit1:
print(
f'{" " *12} sidecar is present in the config file. Add another sidecar criterion in the dcm2bids_helper.py script'
)
self.add_criterion = True
sys.exit(0)
else:
list_criteria.remove(des)
if len(list_criteria) > 0:
print(
f'{" " *12}> cannot find a correct sidecar location. Please add more parameters.'
)
if len(list_criteria) == 0:
print(f'{" " *12}> updating config with value: {sidecar_crit1}')
new_des = {
'dataType': self.data_Type,
'modalityLabel': self.modalityLabel,
'criteria': {
criterion1: sidecar_crit1
}
}
self.config['descriptions'].append(new_des)
self.update = True
if self.update:
self.run_stt = 0
save_json(self.config, self.config_file, print_space=12)
else:
print(f'{" " *12}criterion {criterion1} present in config file')
def set_projects(self):
"""retrieve projects_ids"""
file = os.path.join(self.credentials_home, 'projects.json')
default = False
if not self.chk_if_defined('projects'):
self.define_credentials()
default = True
shutil.copy(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'projects.json'), file)
shutil.copy(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'stats.json'),
os.path.join(self.credentials_home, 'stats.json'))
print(
f' CHECK PROJECTS AND VARIABLES in: {self.credentials_home}'
)
self.projects = self.load_file('projects', default=default)
self.stats_vars = load_json(
path.join(self.credentials_home, 'stats.json'))
self.project_ids = self.get_projects_ids()
def run(self, nimb_id='none', ses='none'):
#run dcm2bids:
'''
if nimb_classified.json[nimb_id][archived]:
extract from archive specific subject_session
start dcm2bids for subject_session
'''
print(f' folder with subjects is: {self.DICOM_DIR}')
self.nimb_id = nimb_id
self.ses = ses
self.bids_id = f'sub-{self.nimb_id}_{self.ses}'
if self.id_classified:
self.start_stepwise_choice()
else:
self.nimb_classified = dict()
try:
self.nimb_classified = load_json(
os.path.join(self.DICOM_DIR, DEFAULT.f_nimb_classified))
except Exception as e:
print(
f' could not load the nimb_classified file at: {self.DICOM_DIR}'
)
sys.exit(0)
if self.nimb_classified:
self.nimb_ids = list(self.nimb_classified.keys())
for self.nimb_id in self.nimb_ids:
self.id_classified = self.nimb_classified[self.nimb_id]
for self.ses in [
i for i in self.id_classified
if i not in ('archived', )
]:
self.start_stepwise_choice()
if nimb_id != 'none':
return self.bids_id
else:
return 'none'
def __init__(self,
all_vars,
PATHglm,
sig_fdr_thresh = 3.0):
'''
sig_fdr_thresh at 3.0 corresponds to p = 0.001;
for p=0.05 use value 1.3,
but it should be used ONLY for visualisation.
'''
vars_fs = all_vars.location_vars['local']["FREESURFER"]
self.FREESURFER_HOME = vars_fs["FREESURFER_HOME"]
self.SUBJECTS_DIR = vars_fs["SUBJECTS_DIR"]
self.measurements = vars_fs["GLM_measurements"]
self.thresholds = vars_fs["GLM_thresholds"]
self.mc_cache_thresh = vars_fs["GLM_MCz_cache"]
param = fs_definitions.FSGLMParams(PATHglm)
self.PATHglm = PATHglm
self.sig_fdr_thresh = sig_fdr_thresh
self.PATHglm_glm = param.PATHglm_glm
self.PATH_img = param.PATH_img
self.PATHglm_results = param.PATHglm_results
self.sig_fdr_json = param.sig_fdr_json
self.sig_mc_json = param.sig_mc_json
self.err_mris_preproc_file = param.err_mris_preproc_file
self.mcz_sim_direction = param.mcz_sim_direction
self.hemispheres = fs_definitions.hemi
self.GLM_sim_fwhm4csd = param.GLM_sim_fwhm4csd
self.GLM_MCz_meas_codes = param.GLM_MCz_meas_codes
self.cluster_stats = param.cluster_stats
self.cluster_stats_2csv = param.cluster_stats_2csv
self.sig_contrasts = param.sig_contrasts
RUN = True
# get files_glm.
try:
files_glm = load_json(param.files_for_glm)
print(f' successfully uploaded file: {param.files_for_glm}')
except ImportError as e:
print(e)
print(f' file {param.files_for_glm} is missing')
RUN = False
# get file with subjects per group
try:
subjects_per_group = load_json(param.subjects_per_group)
print(f' successfully uploaded file: {param.subjects_per_group}')
except Exception as e:
print(e)
print(f' file {param.subjects_per_group} is missing')
RUN = False
# checking that all subjects are present
print(' subjects are located in: {}'.format(self.SUBJECTS_DIR))
for group in subjects_per_group:
for subject in subjects_per_group[group]:
if subject not in os.listdir(self.SUBJECTS_DIR):
print(f' subject is missing from FreeSurfer Subjects folder: {subject}')
RUN = False
break
for subdir in (self.PATHglm_glm, self.PATHglm_results, self.PATH_img):
if not os.path.isdir(subdir): os.makedirs(subdir)
if not os.path.isfile(self.sig_contrasts):
open(self.sig_contrasts,'w').close()
if RUN:
self.err_preproc = list()
self.sig_fdr_data = dict()
self.sig_mc_data = dict()
self.run_loop(files_glm)
if self.err_preproc:
save_json(self.err_preproc, self.err_mris_preproc_file)
if self.sig_fdr_data:
save_json(self.sig_fdr_data, self.sig_fdr_json)
if self.sig_mc_data:
save_json(self.sig_mc_data, self.sig_mc_json)
if os.path.exists(self.cluster_stats):
ClusterFile2CSV(self.cluster_stats,
self.cluster_stats_2csv)
print('\n\nGLM DONE')
else:
sys.exit('some ERRORS were found. Cannot perform FreeSurfer GLM')
