def __init__(self, atlasobj, title, outfilepath, plot_config=None):
if plot_config is None:
plot_config = {}
self.atlasobj = atlasobj
if plot_config.get('draw_RSN', False):
self.brainparts = BrainParts(
self.atlasobj.get_brainparts_config(
'RSN')) # circosparts.json file in each atlas's folder
else:
self.brainparts = BrainParts(self.atlasobj.get_brainparts_config(
)) # circosparts.json file in each atlas's folder
self.title = title
if outfilepath[-4:] == '.png':
outfilepath = outfilepath[:-4]
self.outfilepath = outfilepath
self.outfolder, self.outfilename = os.path.split(outfilepath)
self.circosfolder = os.path.join(self.outfolder, 'circosdata',
self.outfilename)
path.makedirs(self.circosfolder)
self.circosConfigFile = CircosConfigFile()
self.circoslinks = []
self.circos_directed_links = []
self.circosvalues = []
self.ideogram_radius = None
self.colorlist = None
if atlasobj.name == 'bnatlas':
plot_config['region_tick_size'] = '20p'
plot_config['link_thickness'] = '10p'
elif atlasobj.name == 'aicha':
plot_config['region_tick_size'] = '10p'
plot_config['link_thickness'] = '5p'
self.customizeSize(plot_config)
def convert_dicom_to_nifti(infolder, outfolder):
"""
Convert DICOM to raw NIFTI.
The infolder should be the DICOM folder.
The outfolder will be the converted NIFTI folder.
the ret is the conversion program return value. 0 typically indicates success.
"""
path.rmtree(outfolder)
path.makedirs(outfolder)
gen_scan_info(infolder, outfolder)
ret = subprocess.call(
[rootconfig.path.dcm2nii, '-z', 'y', '-o', outfolder, infolder],
cwd=os.path.dirname(rootconfig.path.dcm2nii))
print(outfolder, ret)
return ret
def calc_binary_density(img, atlasobj, atlasimg):
timg = atlasimg
data = img.get_data()
tdata = timg.get_data()
threshold = 0.5
data[data <= threshold * 255] = 0
path.makedirs('t1mean')
nib.save(img, 't1mean/thres_{}.nii.gz'.format(threshold))
data[data > threshold] = 1
res = np.empty(atlasobj.count)
for i, region in enumerate(atlasobj.regions):
regiondots = data[tdata == region]
regioncount = regiondots.shape[0]
ndots = np.sum(regiondots)
res[i] = ndots / regioncount
return res
def copy_one_nifti(self, mriscan):
"""Copy all modals for one mriscan."""
infolder = os.path.join(self.inMainFolder, mriscan)
outfolder = os.path.join(self.outMainFolder, mriscan)
path.makedirs(outfolder)
niftigetter = self.cls_niftigetter(infolder)
modalities_coverage = [False, False, False, False]
modalities_coverage[0] = self.copy_one_nifti_modal(
outfolder, niftigetter.get_T1, 'T1.nii.gz')
modalities_coverage[1] = self.copy_one_nifti_modal(
outfolder, niftigetter.get_T2, 'T2.nii.gz')
modalities_coverage[2] = self.copy_one_nifti_modal(
outfolder, niftigetter.get_BOLD, 'BOLD.nii.gz')
modalities_coverage[3] = self.copy_one_nifti_modal(
outfolder, niftigetter.get_DWI, 'DWI')
self.copy_one_nifti_modal(outfolder, niftigetter.get_ScanInfo,
'scan_info.json')
return modalities_coverage
def run(self):
"""Run the para.
finalfolders is the constructed folder in which to run the job in parallel,
Or sequential if configured that way.
Env MMDPS_NEWLIST_TXT will override folderlist.
Env MMDPS_SECONDLIST_TXT will override secondlist.
"""
if self.folderlist == 'listdir':
originalfolders = path.clean_listdir(self.mainfolder)
else:
originalfolders = loadsave.load_txt(
path.env_override(self.folderlist, 'MMDPS_NEWLIST_TXT'))
folders = [os.path.join(self.mainfolder, f) for f in originalfolders]
if self.bsecond:
finalfolders = []
if type(self.secondlist) is list:
secondfolders = self.secondlist
elif self.secondlist == 'all':
secondfolders = loadsave.load_txt(
os.path.join(rootconfig.path.atlas, 'atlas_list.txt'))
else:
secondfolders = loadsave.load_txt(
path.env_override(self.secondlist, 'MMDPS_SECONDLIST_TXT'))
for folder in folders:
for secondfolder in secondfolders:
newfolder = os.path.join(folder, secondfolder)
path.makedirs(newfolder)
finalfolders.append(newfolder)
else:
finalfolders = folders
currentJob = job.create_from_dict(
loadsave.load_json(path.fullfile(self.jobconfig)))
if self.runmode == 'FirstOnly':
return self.run_seq(currentJob, finalfolders[0:1])
if self.runmode == 'Parallel':
return self.run_para(currentJob, finalfolders)
if self.runmode == 'Sequential':
return self.run_seq(currentJob, finalfolders)
else:
print('Error: no such runmode as', self.runmode)
return None
def convert_dicom_to_nifti(infolder, outfolder):
"""
Convert DICOM to raw NIFTI.
The infolder should be the DICOM folder.
The outfolder will be the converted NIFTI folder.
the ret is the conversion program return value. 0 typically indicates success.
"""
if os.path.isdir(outfolder):
print('Output path %s is not empty. Continue anyway...' % outfolder)
else:
path.makedirs(outfolder)
try:
# try to generate scan info, processing date-time etc
# will fail on non-Changgung data folder structure
gen_scan_info(infolder, outfolder)
except Exception:
pass
ret = subprocess.call(
[rootconfig.path.dcm2nii, '-z', 'y', '-o', outfolder, infolder],
cwd=os.path.dirname(rootconfig.path.dcm2nii))
print('Conversion finished. Return value: %d. Data saved at: %s' %
(ret, outfolder))
return ret
def genlogfilename(info=''):
"""Generate a log file name base on current time and supplied info."""
path.makedirs('log')
timestr = clock.now()
return 'log/log_{}_{}.txt'.format(timestr, info)