def test_readDicom():
dicomDir = os.path.join(os.path.dirname(__file__), 'test_input')
dicomFile = os.path.join(dicomDir, test_dicomFile)
dicomImg1 = rd.readDicomFromFile(dicomFile)
vol1 = rd.parseDicomVolume(dicomImg1, 64)
assert vol1 is not None
with open(dicomFile, 'rb') as fp:
data = fp.read()
dicomImg2 = rd.readDicomFromBuffer(data)
vol2 = rd.parseDicomVolume(dicomImg2, 64)
assert vol2 is not None
assert (vol1 == vol2).all()
fileInterface = FileInterface()
fileInterface.initWatch(dicomDir, '*.dcm', 0)
dicomImg3 = rd.readRetryDicomFromFileInterface(fileInterface, dicomFile)
vol3 = rd.parseDicomVolume(dicomImg3, 64)
assert vol3 is not None
assert (vol1 == vol3).all()
# read in a truncated file, should fail and return None.
trucatedDicomFile = os.path.join(dicomDir, test_dicomTruncFile)
dicomImg4 = rd.readRetryDicomFromFileInterface(fileInterface,
trucatedDicomFile)
assert dicomImg4 is None
# Test convert to nifti
niftiObject = dicomreaders.mosaic_to_nii(dicomImg3)
assert niftiObject is not None
fileInterface.fileWatcher.__del__()
fileInterface.fileWatcher = None
def main():
logger = logging.getLogger()
logger.setLevel(logLevel)
logging.info('GREEN EYES: first log message!')
argParser = argparse.ArgumentParser()
argParser.add_argument('--config', '-c', default=defaultConfig, type=str,
help='experiment config file (.json or .toml)')
argParser.add_argument('--runs', '-r', default='', type=str,
help='Comma separated list of run numbers')
argParser.add_argument('--scans', '-s', default='', type=str,
help='Comma separated list of scan number')
argParser.add_argument('--deleteTmpNifti', '-d', default='1', type=str,
help='Set to 0 if rerunning during a single scanning after error')
# creates pipe communication link to send/request responses through pipe
argParser.add_argument('--commpipe', '-q', default=None, type=str,
help='Named pipe to communicate with projectInterface')
argParser.add_argument('--filesremote', '-x', default=False, action='store_true',
help='dicom files retrieved from remote server')
args = argParser.parse_args()
print(args)
cfg = initializeGreenEyes(args.config,args)
# DELETE ALL FILES IF FLAGGED TO #
if args.deleteTmpNifti == '1':
deleteTmpFiles(cfg)
else:
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
print('NOT DELETING NIFTIS IN tmp/convertedNiftis')
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
# DELETE ALL FILES IF FLAGGED TO #
# comm pipe
projComm = projUtils.initProjectComm(args.commpipe,args.filesremote)
# initialize file interface class -- for now only local
fileInterface = FileInterface(filesremote=args.filesremote, commPipes=projComm)
# intialize watching in particular directory
fileInterface.initWatch(cfg.dicomDir, cfg.dicomNamePattern, cfg.minExpectedDicomSize)
story_TRs = cfg.story_TR_2 - cfg.story_TR_1 + 1
#### MAIN PROCESSING ###
nRuns = len(cfg.runNum)
for runIndex in np.arange(nRuns):
runData = StructDict()
runData.cheating_probability = np.zeros((cfg.nStations,))
runData.zTransferred = np.zeros((cfg.nStations,))
runData.correct_prob = np.zeros((cfg.nStations,))
runData.interpretation = getSubjectInterpretation(cfg)
runData.badVoxels = {}
runData.dataForClassification = {}
all_data = np.zeros((cfg.nVox,cfg.nTR_run + 1)) # adding 1 because we're not starting at 0 with the indexing
runData.story_data = np.zeros((cfg.nVox,story_TRs))
makeRunHeader(cfg,runIndex)
run = cfg.runNum[runIndex]
scanNum = cfg.scanNum[runIndex]
storyTRCount = 0
stationInd=0
for TRFilenum in np.arange(cfg.nTR_skip+1,cfg.nTR_run+1):
# for TRFilenum in np.arange(11,54):
if TRFilenum == cfg.nTR_skip+1: # wait until run starts
timeout_file = 180
else:
timeout_file = 5
A = time.time()
dicomData = readRetryDicomFromFileInterface(fileInterface, getDicomFileName(cfg, scanNum, TRFilenum), timeout=timeout_file)
full_nifti_name = convertToNifti(TRFilenum,scanNum,cfg,dicomData)
registeredFileName = registerNewNiftiToMNI(cfg,full_nifti_name)
maskedData = apply_mask(registeredFileName,cfg.mask_filename)
all_data[:,TRFilenum] = maskedData
B = time.time()
print('read to mask time: {:5f}'.format(B-A))
if TRFilenum >= cfg.fileNum_story_TR_1 and TRFilenum <= cfg.fileNum_story_TR_2: # we're at a story TR now
runData.story_data[:,storyTRCount] = maskedData
if np.any(storyTRCount == cfg.last_tr_in_station.astype(int)):
# NOW PREPROCESS AND CLASSIFY
stationInd = np.argwhere(storyTRCount == cfg.last_tr_in_station.astype(int))[0][0]
A = time.time()
runData = preprocessAndPredict(cfg,runData,storyTRCount)
B = time.time()
print('preprocessAndPredict time: {:5f}'.format(B-A))
text_to_save = '{0:05f}'.format(runData.correct_prob[stationInd])
file_name_to_save = getStationClassoutputFilename(run, stationInd)
if cfg.mode == 'cloud':
full_filename_to_save = os.path.join(cfg.intelrt.subject_full_day_path,file_name_to_save)
else:
full_filename_to_save = os.path.join(cfg.subject_full_day_path,file_name_to_save)
fileInterface.putTextFile(full_filename_to_save,text_to_save)
if args.commpipe:
# JUST TO PLOT ON WEB SERVER
projUtils.sendResultToWeb(projComm, run,int(stationInd) ,runData.correct_prob[stationInd] )
storyTRCount += 1
TRheader = makeTRHeader(cfg,runIndex,TRFilenum,storyTRCount-1,stationInd,runData.correct_prob[stationInd])
# SAVE OVER RUN NP FILE
runData.scanNum = scanNum # save scanning number
runData.subjectName = cfg.subjectName
runData.dicomDir = cfg.dicomDir
run_filename = getRunFilename(cfg.sessionId, run)
full_run_filename_to_save = os.path.join(cfg.subject_full_day_path,run_filename)
#try:
sio.savemat(full_run_filename_to_save, runData, appendmat=False)
#except Exception as err:
# errorReply = self.createReplyMessage(msg, MsgResult.Errsor)
# errorReply.data = "Error: Unable to save blkGrpFile %s: %r" % (blkGrpFilename, err)
# return errorReply
# DELETE ALL FILES IF FLAGGED TO #
# REPEAT AT THE END OF THE RUN AS WELL
if args.deleteTmpNifti == '1':
deleteTmpFiles(cfg)
else:
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
print('NOT DELETING NIFTIS IN tmp/convertedNiftis')
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
# DELETE ALL FILES IF FLAGGED TO #
sys.exit(0)
def getLocalDicomData(cfg, fullpath):
projComm = projUtils.initProjectComm(None, False)
fileInterface = FileInterface(filesremote=False, commPipes=projComm)
fileInterface.initWatch(cfg.dicomDir, cfg.dicomNamePattern, 300000)
dicomData = readRetryDicomFromFileInterface(fileInterface, fullpath)
return dicomData
def main():
logger = logging.getLogger()
logger.setLevel(logLevel)
logging.info('Face matching: first log message!')
argParser = argparse.ArgumentParser()
argParser.add_argument('--config',
'-c',
default=defaultConfig,
type=str,
help='experiment config file (.json or .toml)')
argParser.add_argument('--runs',
'-r',
default='',
type=str,
help='Comma separated list of run numbers')
argParser.add_argument('--scans',
'-s',
default='',
type=str,
help='Comma separated list of scan number')
argParser.add_argument(
'--deleteTmpNifti',
'-d',
default='1',
type=str,
help='Set to 0 if rerunning during a single scanning after error')
# creates pipe communication link to send/request responses through web pipe
argParser.add_argument(
'--commpipe',
'-q',
default=None,
type=str,
help='Named pipe to communicate with projectInterface')
argParser.add_argument('--filesremote',
'-x',
default=False,
action='store_true',
help='dicom files retrieved from remote server')
args = argParser.parse_args()
print(args)
cfg = initializeFaceMatching(args.config, args)
# DELETE ALL FILES IF FLAGGED TO #
if args.deleteTmpNifti == '1':
deleteTmpFiles(cfg)
else:
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
print('NOT DELETING NIFTIS IN tmp/convertedNiftis')
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
# DELETE ALL FILES IF FLAGGED TO #
# comm pipe
projComm = projUtils.initProjectComm(args.commpipe, args.filesremote)
fileInterface = FileInterface(filesremote=args.filesremote,
commPipes=projComm)
# intialize watching in particular directory
fileInterface.initWatch(cfg.dicomDir, cfg.dicomNamePattern,
cfg.minExpectedDicomSize)
#### MAIN PROCESSING ###
nRuns = len(cfg.runNum)
for runIndex in np.arange(nRuns):
# Steps that we have to do:
# 1. load run regressor X
# 2. find the emotional face trials (happy) X
# 3. find the rest TRs right before each one X
# At every TR --> register to MNI, mask, etc
# 4. zscore previous rest data (convert + register like before)
# 5. calculate percent signal change over ROI
# 6. save as a text file (Every TR-- display can smooth it)
# LOAD RUN REGRESSOR
runNum = runIndex + 1
regressor = getRegressorMatrix(cfg, runNum)
happy_TRs = findConditionTR(regressor,
int(cfg.HAPPY)) # 3 blocks 12 TRs each
happy_TRs_shifted = happy_TRs + cfg.nTR_shift
happy_TRs_shifted_filenum = happy_TRs_shifted + cfg.nTR_skip # to account for first 2 files that we're skipping
neutral_TRs = findConditionTR(regressor, int(cfg.NEUTRAL))
neutral_TRs_shifted = neutral_TRs + cfg.nTR_shift
object_TRs = findConditionTR(regressor, int(cfg.OBJECT))
object_TRs_shifted = object_TRs + cfg.nTR_shift
nBlocks = np.shape(happy_TRs)[0]
nTR_per_block = np.shape(happy_TRs)[1]
fixation_TRs, fixation_blocks = findFixationTR(regressor)
fixation_TRs_shifted = fixation_TRs + cfg.nTR_shift
fixation_blocks_shifted = fixation_blocks + cfg.nTR_shift
all_other_categories_shifted = np.concatenate(
(neutral_TRs_shifted, object_TRs_shifted, fixation_blocks_shifted),
axis=0).flatten()
runData = StructDict()
runData.all_data = np.zeros((cfg.nVox, cfg.nTR_run - cfg.nTR_skip))
runData.percent_change = np.zeros((cfg.nTR_run - cfg.nTR_skip, ))
runData.percent_change[:] = np.nan
runData.badVoxels = np.array([])
makeRunHeader(cfg, runIndex)
run = cfg.runNum[runIndex]
scanNum = cfg.scanNum[runIndex]
TRindex = 0
for TRFilenum in np.arange(cfg.nTR_skip + 1,
cfg.nTR_run + 1): # iterate through all TRs
if TRFilenum == cfg.nTR_skip + 1: # wait until run starts
timeout_file = 180
else:
timeout_file = 5
A = time.time()
dicomData = readRetryDicomFromFileInterface(fileInterface,
getDicomFileName(
cfg, scanNum,
TRFilenum),
timeout=timeout_file)
full_nifti_name = convertToNifti(TRFilenum, scanNum, cfg,
dicomData)
registeredFileName = registerNewNiftiToMNI(cfg, full_nifti_name)
maskedData = apply_mask(registeredFileName, cfg.mask_filename)
runData.all_data[:, TRindex] = maskedData
B = time.time()
print('read to mask time: {:5f}'.format(B - A))
if TRindex in happy_TRs_shifted: # we're at a happy block
# now get TRs to use for zscoring
TRs_to_use_other_categories = np.sort(
all_other_categories_shifted[
all_other_categories_shifted < TRindex])
avg_activity, runData = getAvgSignal(
TRs_to_use_other_categories, runData, TRindex, cfg)
runData.percent_change[TRindex] = calculatePercentChange(
avg_activity, runData.all_data[:, TRindex])
text_to_save = '{0:05f}'.format(
runData.percent_change[TRindex])
file_name_to_save = getOutputFilename(run, TRindex)
if cfg.mode == 'cloud':
full_filename_to_save = os.path.join(
cfg.intelrt.subject_full_day_path, file_name_to_save)
else:
full_filename_to_save = os.path.join(
cfg.subject_full_day_path, file_name_to_save)
fileInterface.putTextFile(full_filename_to_save, text_to_save)
if args.commpipe:
# JUST TO PLOT ON WEB SERVER
projUtils.sendResultToWeb(projComm, run, int(TRindex),
runData.percent_change[TRindex])
TRheader = makeTRHeader(cfg, runIndex, TRFilenum, TRindex,
runData.percent_change[TRindex])
TRindex += 1
# SAVE OVER RUN NP FILE
runData.scanNum = scanNum # save scanning number
runData.subjectName = cfg.subjectName
runData.dicomDir = cfg.dicomDir
run_filename = getRunFilename(cfg.sessionId, run)
full_run_filename_to_save = os.path.join(cfg.subject_full_day_path,
run_filename)
#try:
sio.savemat(full_run_filename_to_save, runData, appendmat=False)
#except Exception as err:
# errorReply = self.createReplyMessage(msg, MsgResult.Errsor)
# errorReply.data = "Error: Unable to save blkGrpFile %s: %r" % (blkGrpFilename, err)
# return errorReply
sys.exit(0)