def main():
logger = logging.getLogger()
logger.setLevel(logLevel)
logging.info('amygActivation: 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')
args = argParser.parse_args()
# Initialize the RPC connection to the projectInterface
# This will give us a dataInterface for retrieving files and
# a subjectInterface for giving feedback
clientInterface = ClientInterface()
dataInterface = clientInterface.dataInterface
subjInterface = clientInterface.subjInterface
webInterface = clientInterface.webInterface
args.dataRemote = dataInterface.isRunningRemote()
cfg = utils.loadConfigFile(args.config)
cfg = initialize(cfg, args)
# DELETE ALL FILES IF FLAGGED (DEFAULT) #
if args.deleteTmpNifti == '1':
deleteTmpFiles(cfg, args)
else:
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
print('NOT DELETING NIFTIS IN tmp/convertedNiftis')
print('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
createTmpFolder(cfg, args)
#### MAIN PROCESSING ###
nRuns = len(cfg.runNum)
for runIndex in np.arange(nRuns):
# Steps that we have to do:
# 1. load run regressor X - ** make run regressor that has TRs -
# 2. find the happy 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)
runNum = cfg.runNum[
runIndex] # this will be 1-based now!! it will be the actual run number in case it's out of order
runId = makeRunHeader(cfg, args, runIndex)
run = cfg.runNum[runIndex]
# create run folder
runFolder = createRunFolder(cfg, args, runNum)
scanNum = cfg.scanNum[runIndex]
regressor = makeRunReg(cfg,
args,
dataInterface,
runNum,
runFolder,
saveMat=1)
# intialize data stream
dicomScanNamePattern = utils.stringPartialFormat(
cfg.dicomNamePattern, 'SCAN', scanNum)
streamId = dataInterface.initScannerStream(cfg.dicomDir,
dicomScanNamePattern,
cfg.minExpectedDicomSize)
happy_TRs = findConditionTR(regressor, int(cfg.HAPPY))
happy_TRs_shifted = happy_TRs + cfg.nTR_shift
happy_TRs_shifted_filenum = happy_TRs_shifted + cfg.nTR_skip # to account for first 10 files that we're skipping
happy_blocks = list(split_tol(happy_TRs_shifted, 1))
TR_per_block = cfg.nTR_block
fixation_TRs = findConditionTR(regressor, int(cfg.REST))
fixation_TRs_shifted = fixation_TRs + cfg.nTR_shift
fixation_blocks = list(split_tol(fixation_TRs_shifted, 1))
runData = StructDict()
runData.all_data = np.zeros(
(cfg.nVox[cfg.useMask], 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([])
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()
dicomFilename = dicomScanNamePattern.format(TR=TRFilenum)
print(f'Get Dicom: {dicomFilename}')
dicomData = dataInterface.getImageData(streamId, int(TRFilenum),
timeout_file)
if dicomData is None:
print('Error: getImageData returned None')
return
full_nifti_name = convertToNifti(cfg, args, TRFilenum, scanNum,
dicomData)
print(full_nifti_name)
print(cfg.MASK_transformed[cfg.useMask])
maskedData = apply_mask(full_nifti_name,
cfg.MASK_transformed[cfg.useMask])
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 take previous fixation block for z scoring
this_block = [
b for b in np.arange(4) if TRindex in happy_blocks[b]
][0]
fixation_this_block = fixation_blocks[this_block]
avg_activity, runData = getAvgSignal(fixation_this_block,
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,
TRFilenum) # save as the actual file number, not index
# now we want to always send this back to the local computer running the display
full_file_name_to_save = os.path.join(
cfg.local.subject_full_day_path, runId, file_name_to_save)
# Send classification result back to the console computer
try:
dataInterface.putFile(full_file_name_to_save, text_to_save)
except Exception as err:
print('Error putFile: ' + str(err))
return
# JUST TO PLOT ON WEB SERVER
subjInterface.setResult(run, int(TRFilenum),
float(runData.percent_change[TRindex]))
webInterface.plotDataPoint(
run, int(TRFilenum),
float(runData.percent_change[TRindex]))
TRheader = makeTRHeader(cfg, runIndex, TRFilenum, TRindex,
runData.percent_change[TRindex])
TRindex += 1
# SAVE OVER RUN
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(runFolder, run_filename)
sio.savemat(full_run_filename_to_save, runData, appendmat=False)
sys.exit(0)
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)
