def initialize(cfg, args):
""" purpose: load information and add to config """
if cfg.sessionId in (None, '') or cfg.useSessionTimestamp is True:
cfg.useSessionTimestamp = True
cfg.sessionId = utils.dateStr30(time.localtime())
else:
cfg.useSessionTimestamp = False
# MERGE WITH PARAMS
if args.runs != '' and args.scans != '':
# use the run and scan numbers passed in as parameters
cfg.runNum = [int(x) for x in args.runs.split(',')]
cfg.scanNum = [int(x) for x in args.scans.split(',')]
else: # when you're not specifying on the command line it's already in a list
cfg.runNum = [int(x) for x in cfg.runNum]
cfg.scanNum = [int(x) for x in cfg.scanNum]
# GET DICOM DIRECTORY
if cfg.buildImgPath:
imgDirDate = datetime.now()
dateStr = cfg.date.lower()
if dateStr != 'now' and dateStr != 'today':
try:
imgDirDate = parser.parse(cfg.date)
except ValueError as err:
raise RequestError('Unable to parse date string {} {}'.format(cfg.date, err))
datestr = imgDirDate.strftime("%Y%m%d")
imgDirName = "{}.{}.{}".format(datestr, cfg.subjectName, cfg.subjectName)
cfg.dicomDir = os.path.join(cfg.local.dicomDir,imgDirName)
else:
cfg.dicomDir = cfg.local.dicomDir # then the whole path was supplied
########
cfg.bids_id = 'sub-{0:03d}'.format(cfg.subjectNum)
cfg.ses_id = 'ses-{0:02d}'.format(cfg.subjectDay)
# specify local directories
cfg.local.codeDir = os.path.join(cfg.local.rtcloudDir, 'projects', cfg.projectName)
cfg.local.dataDir = os.path.join(cfg.local.codeDir, 'data')
cfg.local.subject_full_day_path = os.path.join(cfg.local.dataDir, cfg.bids_id, cfg.ses_id)
cfg.local.subject_reg_dir = os.path.join(cfg.local.subject_full_day_path, 'registration_outputs')
cfg.local.wf_dir = os.path.join(cfg.local.dataDir, cfg.bids_id, 'ses-01', 'registration')
cfg.local.maskDir = os.path.join(cfg.local.codeDir, 'ROI')
cfg.subject_reg_dir = cfg.local.subject_reg_dir
cfg.wf_dir = cfg.local.wf_dir
cfg.n_masks = len(cfg.MASK)
if args.filesremote: # here we will need to specify separate paths for processing
cfg.server.codeDir = os.path.join(cfg.server.rtcloudDir, 'projects', cfg.projectName)
cfg.server.dataDir = os.path.join(cfg.server.codeDir, cfg.server.serverDataDir)
cfg.server.subject_full_day_path = os.path.join(cfg.server.dataDir, cfg.bids_id, cfg.ses_id)
cfg.server.subject_reg_dir = os.path.join(cfg.server.subject_full_day_path, 'registration_outputs')
cfg.server.wf_dir = os.path.join(cfg.server.dataDir, cfg.bids_id, 'ses-01', 'registration')
cfg.server.maskDir = os.path.join(cfg.server.codeDir, 'ROI')
cfg.subject_reg_dir = cfg.server.subject_reg_dir
cfg.wf_dir = cfg.server.wf_dir
cfg.ref_BOLD = os.path.join(cfg.wf_dir,'ref_image.nii.gz')
cfg.MNI_ref_filename = os.path.join(cfg.wf_dir, cfg.MNI_ref_BOLD)
cfg.T1_to_BOLD = os.path.join(cfg.wf_dir, 'affine.txt')
cfg.MNI_to_T1 = os.path.join(cfg.wf_dir, 'ants_t1_to_mniInverseComposite.h5')
cfg.MASK_transformed = [''] * cfg.n_masks
cfg.local_MASK_transformed = [''] * cfg.n_masks
for m in np.arange(cfg.n_masks):
mask_name = cfg.MASK[m].split('.')[0] + '_space-native.nii.gz'
cfg.MASK_transformed[m] = os.path.join(cfg.subject_reg_dir, mask_name)
cfg.local_MASK_transformed[m] = os.path.join(cfg.local.subject_reg_dir, mask_name)
# get conversion to flip dicom to nifti files
cfg.axesTransform = getTransform(('L', 'A', 'S'),('P', 'L', 'S'))
return cfg
def initializeGreenEyes(configFile,args):
# load subject information
# create directories for new niftis
# randomize which category they'll be attending to and save that
# purpose: load information and add to configuration things that you won't want to do each time a new file comes in
# TO RUN AT THE START OF EACH RUN
cfg = loadConfigFile(configFile)
if cfg.sessionId in (None, '') or cfg.useSessionTimestamp is True:
cfg.useSessionTimestamp = True
cfg.sessionId = dateStr30(time.localtime())
else:
cfg.useSessionTimestamp = False
# MERGE WITH PARAMS
if args.runs != '' and args.scans != '':
# use the run and scan numbers passed in as parameters
cfg.runNum = [int(x) for x in args.runs.split(',')]
cfg.scanNum = [int(x) for x in args.scans.split(',')]
else: # when you're not specifying on the command line it's already in a list
cfg.runNum = [int(x) for x in cfg.runNum]
cfg.scanNum = [int(x) for x in cfg.scanNum]
# GET DICOM DIRECTORY
if cfg.mode != 'debug':
if cfg.buildImgPath:
imgDirDate = datetime.datetime.now()
dateStr = cfg.date.lower()
if dateStr != 'now' and dateStr != 'today':
try:
imgDirDate = parser.parse(cfg.date)
except ValueError as err:
raise RequestError('Unable to parse date string {} {}'.format(cfg.date, err))
datestr = imgDirDate.strftime("%Y%m%d")
imgDirName = "{}.{}.{}".format(datestr, cfg.subjectName, cfg.subjectName)
cfg.dicomDir = os.path.join(cfg.intelrt.imgDir, imgDirName)
else:
cfg.dicomDir = cfg.intelrt.imgDir # then the whole path was supplied
cfg.dicomNamePattern = cfg.intelrt.dicomNamePattern
else:
cfg.dicomDir = glob.glob(cfg.cluster.imgDir.format(cfg.subjectName))[0]
cfg.dicomNamePattern = cfg.cluster.dicomNamePattern
#cfg.commPipe = args.commPipe
#cfg.webfilesremote = args.filesremote # FLAG FOR REMOTE OR LOCAL
########
cfg.bids_id = 'sub-{0:03d}'.format(cfg.subjectNum)
cfg.ses_id = 'ses-{0:02d}'.format(cfg.subjectDay)
if cfg.mode == 'local':
# then all processing is happening on linux too
cfg.dataDir = cfg.intelrt.codeDir + 'data'
cfg.classifierDir = cfg.intelrt.classifierDir
cfg.mask_filename = os.path.join(cfg.intelrt.maskDir, cfg.MASK)
cfg.MNI_ref_filename = os.path.join(cfg.intelrt.maskDir, cfg.MNI_ref_BOLD)
elif cfg.mode == 'cloud':
cfg.dataDir = cfg.cloud.codeDir + 'data'
cfg.classifierDir = cfg.cloud.classifierDir
cfg.mask_filename = os.path.join(cfg.cloud.maskDir, cfg.MASK)
cfg.MNI_ref_filename = os.path.join(cfg.cloud.maskDir, cfg.MNI_ref_BOLD)
cfg.intelrt.subject_full_day_path = '{0}/data/{1}/{2}'.format(cfg.intelrt.codeDir,cfg.bids_id,cfg.ses_id)
elif cfg.mode == 'debug':
cfg.dataDir = cfg.cluster.codeDir + 'data'
cfg.classifierDir = cfg.cluster.classifierDir
cfg.mask_filename = cfg.cluster.maskDir + cfg.MASK
cfg.MNI_ref_filename = cfg.cluster.maskDir + cfg.MNI_ref_BOLD
cfg.station_stats = cfg.classifierDir + 'station_stats.npz'
cfg.subject_full_day_path = '{0}/{1}/{2}'.format(cfg.dataDir,cfg.bids_id,cfg.ses_id)
cfg.temp_nifti_dir = '{0}/converted_niftis/'.format(cfg.subject_full_day_path)
cfg.subject_reg_dir = '{0}/registration_outputs/'.format(cfg.subject_full_day_path)
cfg.nStations, cfg.stationsDict, cfg.last_tr_in_station, cfg.all_station_TRs = getStationInformation(cfg)
# REGISTRATION THINGS
cfg.wf_dir = '{0}/{1}/ses-{2:02d}/registration/'.format(cfg.dataDir,cfg.bids_id,1)
cfg.BOLD_to_T1= cfg.wf_dir + 'affine.txt'
cfg.T1_to_MNI= cfg.wf_dir + 'ants_t1_to_mniComposite.h5'
cfg.ref_BOLD=cfg.wf_dir + 'ref_image.nii.gz'
# GET CONVERSION FOR HOW TO FLIP MATRICES
cfg.axesTransform = getTransform()
###### BUILD SUBJECT FOLDERS #######
return cfg
def initializeFaceMatching(configFile, args):
# load subject information
# create directories for new niftis
# purpose: load information and add to configuration things that you won't want to do each time a new file comes in
# TO RUN AT THE START OF EACH RUN
cfg = loadConfigFile(configFile)
if cfg.sessionId in (None, '') or cfg.useSessionTimestamp is True:
cfg.useSessionTimestamp = True
cfg.sessionId = dateStr30(time.localtime())
else:
cfg.useSessionTimestamp = False
# MERGE WITH PARAMS
if args.runs != '' and args.scans != '':
# use the run and scan numbers passed in as parameters
cfg.runNum = [int(x) for x in args.runs.split(',')]
cfg.scanNum = [int(x) for x in args.scans.split(',')]
else: # when you're not specifying on the command line it's already in a list
cfg.runNum = [int(x) for x in cfg.runNum]
cfg.scanNum = [int(x) for x in cfg.scanNum]
# GET DICOM DIRECTORY
if cfg.buildImgPath:
imgDirDate = datetime.datetime.now()
dateStr = cfg.date.lower()
if dateStr != 'now' and dateStr != 'today':
try:
imgDirDate = parser.parse(cfg.date)
except ValueError as err:
raise RequestError('Unable to parse date string {} {}'.format(
cfg.date, err))
datestr = imgDirDate.strftime("%Y%m%d")
imgDirName = "{}.{}.{}".format(datestr, cfg.subjectName,
cfg.subjectName)
if cfg.mode != 'debug':
cfg.dicomDir = os.path.join(cfg.intelrt.imgDir, imgDirName)
cfg.dicomNamePattern = cfg.intelrt.dicomNamePattern
else:
cfg.dicomDir = os.path.join(cfg.cluster.imgDir, imgDirName)
cfg.dicomNamePattern = cfg.cluster.dicomNamePattern
else: # if you're naming the full folder directly
if cfg.mode != 'debug':
cfg.dicomDir = cfg.intelrt.imgDir # then the whole path was supplied
cfg.dicomNamePattern = cfg.intelrt.dicomNamePattern
else:
cfg.dicomDir = cfg.cluster.imgDir
cfg.dicomNamePattern = cfg.cluster.dicomNamePattern
########
cfg.bids_id = 'sub-{0:03d}'.format(cfg.subjectNum)
cfg.ses_id = 'ses-{0:02d}'.format(cfg.subjectDay)
if cfg.mode == 'local':
# then all processing is happening on linux too
cfg.dataDir = cfg.intelrt.codeDir + 'data'
cfg.mask_filename = os.path.join(cfg.intelrt.maskDir, cfg.MASK)
cfg.MNI_ref_filename = os.path.join(cfg.intelrt.maskDir,
cfg.MNI_ref_BOLD)
elif cfg.mode == 'cloud':
cfg.dataDir = cfg.cloud.codeDir + 'data'
cfg.mask_filename = os.path.join(cfg.cloud.maskDir, cfg.MASK)
cfg.MNI_ref_filename = os.path.join(cfg.cloud.maskDir,
cfg.MNI_ref_BOLD)
cfg.intelrt.subject_full_day_path = '{0}/data/{1}/{2}'.format(
cfg.intelrt.codeDir, cfg.bids_id, cfg.ses_id)
elif cfg.mode == 'debug':
cfg.dataDir = cfg.cluster.codeDir + '/data'
cfg.mask_filename = os.path.join(cfg.cluster.maskDir, cfg.MASK)
cfg.MNI_ref_filename = os.path.join(cfg.cluster.maskDir,
cfg.MNI_ref_BOLD)
cfg.subject_full_day_path = '{0}/{1}/{2}'.format(cfg.dataDir, cfg.bids_id,
cfg.ses_id)
cfg.subject_reg_dir = '{0}/registration_outputs/'.format(
cfg.subject_full_day_path)
# check that this directory exists
if not os.path.exists(cfg.subject_reg_dir):
os.mkdir(cfg.subject_reg_dir)
print('CREATING REGISTRATION DIRECTORY %s' % cfg.subject_reg_dir)
# REGISTRATION THINGS
cfg.wf_dir = '{0}/{1}/ses-{2:02d}/registration/'.format(
cfg.dataDir, cfg.bids_id, 1)
cfg.BOLD_to_T1 = cfg.wf_dir + 'affine.txt'
cfg.T1_to_MNI = cfg.wf_dir + 'ants_t1_to_mniComposite.h5'
cfg.ref_BOLD = cfg.wf_dir + 'ref_image.nii.gz'
# GET CONVERSION FOR HOW TO FLIP MATRICES
cfg.axesTransform = getTransform()
###### BUILD SUBJECT FOLDERS #######
return cfg