def retro_ts(
respiration_file=None,
cardiac_file=None,
phys_fs=None,
number_of_slices=None,
volume_tr=None,
prefix="Output_File_Name",
slice_offset=0,
slice_major=1,
rvt_shifts=list(range(0, 21, 5)),
respiration_cutoff_frequency=3,
cardiac_cutoff_frequency=3,
interpolation_style="linear",
fir_order=40,
quiet=1,
demo=0,
rvt_out=1,
cardiac_out=1,
respiration_out=1,
slice_order="alt+z",
show_graphs=0,
zero_phase_offset=0,
legacy_transform=0,
phys_file=None,
phys_json=None,
):
"""
:param respiration_file:
:param cardiac_file:
:param phys_fs:
:param number_of_slices:
:param volume_tr:
:param prefix:
:param slice_offset:
:param slice_major:
:param rvt_shifts:
:param respiration_cutoff_frequency:
:param cardiac_cutoff_frequency:
:param interpolation_style: kind : str or int, optional
Specifies the kind of interpolation as a string:
"linear", "nearest", "zero", 'slinear', "quadratic", "cubic",
Where 'slinear', "quadratic" and "cubic" refer to a spline
interpolation of first, second or third order
Or as an integer specifying the order of the spline interpolator to
use. Default is "linear".
:param fir_order:
:param quiet:
:param demo:
:param rvt_out:
:param cardiac_out:
:param respiration_out:
:param slice_order:
:param show_graphs:
:param legacy_transform: Important-this will specify whether you use the original Matlab code's version or the
potentially bug-corrected version for the final phase correction in lib_RetroTS/RVT_from_PeakFinder.py
:param phys_file: IDS formatted physio file in tab separated format. May
be gzipped.
:param phys_json: BIDS formatted physio metadata json file. If not specified
the json corresponding to the phys_file will be loaded.
:return:
"""
if not slice_offset:
slice_offset = zeros((1, number_of_slices))
main_info = {
"respiration_file": respiration_file,
"cardiac_file": cardiac_file,
"phys_fs": phys_fs,
"number_of_slices": number_of_slices,
"volume_tr": volume_tr,
"prefix": prefix,
"slice_offset": slice_offset,
"slice_major": slice_major,
"rvt_shifts": rvt_shifts,
"respiration_cutoff_frequency": respiration_cutoff_frequency,
"cardiac_cutoff_frequency": cardiac_cutoff_frequency,
"interpolation_style":
interpolation_style, # replacement for 'ResamKernel' variable name
"fir_order": fir_order,
"quiet": quiet,
"demo": demo,
"rvt_out": rvt_out,
"cardiac_out": cardiac_out,
"respiration_out": respiration_out,
"slice_order": slice_order,
"show_graphs": show_graphs,
"zero_phase_offset": zero_phase_offset,
"legacy_transform": legacy_transform,
"phys_file": phys_file,
"phsio_json": phys_json,
}
# Determining main_info['slice_offset'] based upon main_info['slice_order'], main_info['volume_tr'],
# and main_info['number_of_slices'].
tt = 0.0 # Default float value to start iterations
dtt = float(main_info["volume_tr"]) / float(
main_info["number_of_slices"]) # Increments for iteration
# init slice_offsets, unless Custom order
# (noted by Jogi Ho on board 27 Dec 2017 [rickr])
if ((main_info["slice_order"] not in ["Custom", "custom"]) or
len(main_info["slice_offset"]) != main_info["number_of_slices"]):
main_info["slice_offset"] = [0] * main_info[
"number_of_slices"] # Initial value for main_info['slice_offset']
slice_file_list = (
[]
) # List for using external file for main_info['slice_offset'] values/
# Indicates if using external file in last loop
if main_info["slice_order"][0:3] == "alt": # Alternating?
for i in range(0, main_info["number_of_slices"], 2):
main_info["slice_offset"][i] = tt
tt += dtt
for i in range(1, main_info["number_of_slices"], 2):
main_info["slice_offset"][i] = tt
tt += dtt
elif main_info["slice_order"][0:3] == "seq": # Sequential?
for i in range(0, main_info["number_of_slices"]):
main_info["slice_offset"][i] = tt
tt += dtt
elif main_info["slice_order"] in [
"Custom", "custom"
]: # Does nothing, unsure of it's purpose
pass
else: # Open external file specified in argument line,
# fill SliceFileList with values, then load into main_info['slice_offset']
with open(main_info["slice_order"], "r") as f:
for i in f.readlines():
slice_file_list.append(int(i))
if len(slice_file_list) != main_info["number_of_slices"]:
print("Could not read enough slice offsets from file")
print(
"File should have as many offsets as number_of_slices")
quit()
main_info["slice_offset"] = slice_file_list
if (main_info["slice_order"][3] == "-"
and slice_file_list == []): # Check for a minus to indicate
# a reversed offset list
main_info["slice_offset"].reverse()
if (
main_info["quiet"] != 1
): # Show the slice timing (P.S. Printing is very time consuming in python)
print("Slice timing: %s" % main_info["slice_offset"])
# Create information copy for each type of signal
respiration_info = dict(main_info)
respiration_info["frequency_cutoff"] = main_info[
"respiration_cutoff_frequency"]
# Amplitude-based phase for respiration
respiration_info["amp_phase"] = 1
# respiration_info['as_percover'] = 50 # Percent overlap of windows for fft
# respiration_info['as_windwidth'] = 0 # Window width in seconds for fft, 0 for full window
# respiration_info['as_fftwin'] = 0 # 1 == hamming window. 0 == no windowing
cardiac_info = dict(main_info)
cardiac_info["frequency_cutoff"] = main_info["cardiac_cutoff_frequency"]
# Time-based phase for cardiac signal
cardiac_info["amp_phase"] = 0
# Handle file inputs
if (((phys_file is not None) and (respiration_file is not None))
or ((phys_file is not None) and (cardiac_file is not None))):
raise ValueError('You should not pass a BIDS style phsyio file'
' and respiration or cardiac files.')
# Get the peaks for respiration_info and cardiac_info
if phys_file:
if phys_json is None:
phys_json = phys_file.replace(".gz", "").replace(".tsv", ".json")
with open(phys_json, 'rt') as h:
phys_meta = json.load(h)
phys_ending = phys_file.split(".")[-1]
if phys_ending == 'gz':
opener = gzip.open
else:
opener = open
phys_dat = {k: [] for k in phys_meta['Columns']}
with opener(phys_file, 'rt') as h:
for pl in h.readlines():
pls = pl.split("\t")
for k, v in zip(phys_meta['Columns'], pls):
phys_dat[k].append(float(v))
for k in phys_meta['Columns']:
phys_dat[k] = array(phys_dat[k])
if k.lower() == 'respiratory':
if not main_info['phys_fs']:
respiration_info['phys_fs'] = phys_meta[
'SamplingFrequency']
respiration_peak, error = peak_finder(respiration_info,
v=phys_dat[k])
if error:
print("Died in respiratory PeakFinder")
return
elif k.lower() == 'cardiac':
if not main_info['phys_fs']:
cardiac_info['phys_fs'] = phys_meta['SamplingFrequency']
cardiac_peak, error = peak_finder(cardiac_info, v=phys_dat[k])
if error:
print("Died in cardiac PeakFinder")
return
else:
Warning('phys data contains a {s} column, but RetroTS will'
' only handle cardiac or reipiratory data.')
else:
if respiration_file:
respiration_peak, error = peak_finder(respiration_info,
respiration_file)
if error:
print("Died in respiratory PeakFinder")
return
else:
respiration_peak = {}
if cardiac_file:
cardiac_peak, error = peak_finder(cardiac_info, cardiac_file)
if error:
print("Died in cardiac PeakFinder")
return
else:
cardiac_peak = {}
main_info["resp_peak"] = respiration_peak
main_info["card_peak"] = cardiac_peak
respiration_info.update(respiration_peak)
cardiac_info.update(cardiac_peak)
# Get the phase
if respiration_peak:
print("Estimating phase for respiration_info")
respiration_phased = phase_estimator(respiration_info["amp_phase"],
respiration_info)
else:
respiration_phased = {}
if cardiac_peak:
print("Estimating phase for cardiac_info")
print(cardiac_info["v"])
cardiac_phased = phase_estimator(cardiac_info["amp_phase"],
cardiac_info)
else:
cardiac_phased = {}
respiration_info.update(respiration_phased)
cardiac_info.update(cardiac_phased)
if respiration_phased:
print("Computing RVT from peaks")
print(respiration_info["p_trace_r"])
rvt = rvt_from_peakfinder(respiration_phased)
respiration_info.update(rvt)
# Show some results
if show_graphs:
if respiration_info:
print("Showing RVT Peaks for R\n")
show_rvt_peak(respiration_info, 1)
"""
# Not sure if this code is necessary, 'if 0' is never run in MATLAB
# Show RVT graphs goes here, currently not important though
if 0:
# Write retroicor regressors
for i in range(0, opt['main_info['number_of_slices']']):
fname = '%s.RetroCard.slc%02d.1D' % (opt['Prefix'], i)
#wryte3(cardiac_phased['phase_slice_reg'][:,:,i], fname, 1);
savetxt(fname, cardiac_phased['phase_slice_reg'][:,:,i], fmt="%12.6G")
fname = sprintf('%s.RetroResp.slc%02d.1D', Opt.Prefix, i);
# wryte3(respiration_info.phase_slice_reg(:,:,i), fname, 1);
savetxt(fname, respiration_phased['phase_slice_reg'][:,:,i], fmt="%12.6G")
# And write the RVT puppy, plus or minus a few seconds delay
fname = '%s.RetroRVT.1D' % opt['Prefix']
# wryte3(respiration_info.rvtrs_slc, fname, 1);
savetxt(fname, rvt['rvtrs_slc'], fmt="%12.6G")
"""
# also generate files as 3dREMLfit likes them
n_n = 0
n_r_v = 0
n_r_p = 0
n_e = 0
if "time_series_time" in respiration_info:
n_n = len(respiration_info["time_series_time"])
n_r_p = size(respiration_info["phase_slice_reg"], 1)
n_r_v = size(respiration_info["rvtrs_slc"], 0)
if "time_series_time" in cardiac_info: # must have cardiac_info
n_n = len(
cardiac_phased["time_series_time"]
) # ok to overwrite len(respiration_info.tst), should be same.
n_e = size(cardiac_phased["phase_slice_reg"], 1)
if (main_info["cardiac_out"] == 0 and main_info["respiration_out"] == 0
and main_info["rvt_out"] == 0):
print(
"Options cardiac_out, respiration_out, and RVT_out all 0.\nNo output required.\n"
)
return
temp_y_axis = main_info["number_of_slices"] * (
(main_info["rvt_out"]) * int(n_r_v) +
(main_info["respiration_out"]) * int(n_r_p) +
(main_info["cardiac_out"]) * int(n_e))
main_info["reml_out"] = zeros((n_n, temp_y_axis))
cnt = 0
head = ("<RetroTSout\n"
'ni_type = "%d*double"\n'
'ni_dimen = "%d"\n'
'ColumnLabels = "' %
(size(main_info["reml_out"], 1), size(main_info["reml_out"], 0)))
tail = '"\n>'
tailclose = "</RetroTSout>"
label = head
main_info["reml_out"] = []
if main_info["slice_major"] == 0: # old approach, not handy for 3dREMLfit
# RVT
if main_info["rvt_out"] != 0:
for j in range(0, size(respiration_info["rvtrs_slc"], 2)):
for i in range(0, main_info["number_of_slices"]):
cnt += 1
main_info["reml_out"][:, cnt] = respiration_info[
"rvtrs_slc"][:, j] # same for each slice
label = "%s s%d.RVT%d ;" % (label, i, j)
# Resp
if main_info["respiration_out"] != 0:
for j in range(0, size(respiration_info["phase_slice_reg"], 2)):
for i in range(0, main_info["number_of_slices"]):
cnt += 1
main_info["reml_out"][:, cnt] = respiration_info[
"phase_slice_reg"][:, j, i]
label = "%s s%d.Resp%d ;" % (label, i, j)
# Card
if main_info["Card_out"] != 0:
for j in range(0, size(cardiac_info["phase_slice_reg"], 2)):
for i in range(0, main_info["number_of_slices"]):
cnt += 1
main_info["reml_out"][:, cnt] = cardiac_info[
"phase_slice_reg"][:, j, i]
label = "%s s%d.Card%d ;" % (label, i, j)
fid = open(("%s.retrots.1D", main_info["prefix"]), "w")
else:
for i in range(0, main_info["number_of_slices"]):
if main_info["rvt_out"] != 0:
# RVT
for j in range(0, shape(respiration_info["rvtrs_slc"])[0]):
cnt += 1
main_info["reml_out"].append(
respiration_info["rvtrs_slc"]
[j]) # same regressor for each slice
label = "%s s%d.RVT%d ;" % (label, i, j)
if main_info["respiration_out"] != 0:
# Resp
for j in range(0,
shape(respiration_info["phase_slice_reg"])[1]):
cnt += 1
main_info["reml_out"].append(
respiration_info["phase_slice_reg"][:, j, i])
label = "%s s%d.Resp%d ;" % (label, i, j)
if main_info["cardiac_out"] != 0:
# Card
for j in range(0, shape(cardiac_info["phase_slice_reg"])[1]):
cnt += 1
main_info["reml_out"].append(
cardiac_info["phase_slice_reg"][:, j, i])
label = "%s s%d.Card%d ;" % (label, i, j)
fid = open(("%s.slibase.1D" % main_info["prefix"]), "w")
# remove very last ';'
label = label[1:-2]
savetxt(
"%s.slibase.1D" % main_info["prefix"],
column_stack(main_info["reml_out"]),
fmt="%.4f",
delimiter=" ",
newline="\n",
header=("%s%s" % (label, tail)),
footer=("%s" % tailclose),
)
"""
fid.write('%s', label)
fid.write('%s ', tail)
for i in range(0, len(main_info['reml_out'])):
fid.write('%s ', main_info['reml_out'][i, :])
fprintf(fid, '\n ')
fprintf(fid, '%s', tailclose)
fclose(fid)
"""
main_info["error"] = 0
return main_info
def retro_ts(respiration_file,
cardiac_file,
phys_fs,
number_of_slices,
volume_tr,
prefix='Output_File_Name',
slice_offset=0,
slice_major=1,
rvt_shifts=range(0, 21, 5),
respiration_cutoff_frequency=3,
cardiac_cutoff_frequency=3,
interpolation_style='linear',
fir_order=40,
quiet=1,
demo=0,
rvt_out=1,
cardiac_out=1,
respiration_out=1,
slice_order='alt+z',
show_graphs=0,
zero_phase_offset=0,
legacy_transform=0):
"""
:param respiration_file:
:param cardiac_file:
:param phys_fs:
:param number_of_slices:
:param volume_tr:
:param prefix:
:param slice_offset:
:param slice_major:
:param rvt_shifts:
:param respiration_cutoff_frequency:
:param cardiac_cutoff_frequency:
:param interpolation_style: kind : str or int, optional
Specifies the kind of interpolation as a string:
"linear", "nearest", "zero", 'slinear', "quadratic", "cubic",
Where 'slinear', "quadratic" and "cubic" refer to a spline
interpolation of first, second or third order
Or as an integer specifying the order of the spline interpolator to
use. Default is "linear".
:param fir_order:
:param quiet:
:param demo:
:param rvt_out:
:param cardiac_out:
:param respiration_out:
:param slice_order:
:param show_graphs:
:param legacy_transform: Important-this will specify whether you use the original Matlab code's version or the
potentially bug-corrected version for the final phase correction in lib_RetroTS/RVT_from_PeakFinder.py
:return:
"""
if not slice_offset:
slice_offset = zeros((1, number_of_slices))
main_info = {
'respiration_file': respiration_file,
'cardiac_file': cardiac_file,
'phys_fs': phys_fs,
'number_of_slices': number_of_slices,
'volume_tr': volume_tr,
'prefix': prefix,
'slice_offset': slice_offset,
'slice_major': slice_major,
'rvt_shifts': rvt_shifts,
'respiration_cutoff_frequency': respiration_cutoff_frequency,
'cardiac_cutoff_frequency': cardiac_cutoff_frequency,
'interpolation_style':
interpolation_style, # replacement for 'ResamKernel' variable name
'fir_order': fir_order,
'quiet': quiet,
'demo': demo,
'rvt_out': rvt_out,
'cardiac_out': cardiac_out,
'respiration_out': respiration_out,
'slice_order': slice_order,
'show_graphs': show_graphs,
'zero_phase_offset': zero_phase_offset,
'legacy_transform': legacy_transform
}
# Determining main_info['slice_offset'] based upon main_info['slice_order'], main_info['volume_tr'],
# and main_info['number_of_slices'].
tt = 0.0 # Default float value to start iterations
dtt = float(main_info['volume_tr']) / float(
main_info['number_of_slices']) # Increments for iteration
main_info['slice_offset'] = [0] * main_info[
'number_of_slices'] # Initial value for main_info['slice_offset']
slice_file_list = [
] # List for using external file for main_info['slice_offset'] values/
# Indicates if using external file in last loop
if main_info['slice_order'][0:3] == 'alt': # Alternating?
for i in range(0, main_info['number_of_slices'], 2):
main_info['slice_offset'][i] = tt
tt += dtt
for i in range(1, main_info['number_of_slices'], 2):
main_info['slice_offset'][i] = tt
tt += dtt
elif main_info['slice_order'][0:3] == 'seq': #Sequential?
for i in range(0, main_info['number_of_slices']):
main_info['slice_offset'][i] = tt
tt += dtt
elif main_info[
'slice_order'] == 'Custom': #Does nothing, unsure of it's purpose
pass
else: # Open external file specified in argument line,
# fill SliceFileList with values, then load into main_info['slice_offset']
with open(main_info['slice_order'], 'r') as f:
for i in f.readlines():
slice_file_list.append(int(i))
if len(slice_file_list) != main_info['number_of_slices']:
print 'Could not read enough slice offsets from file'
print 'File should have as many offsets as number_of_slices'
quit()
main_info['slice_offset'] = slice_file_list
if main_info['slice_order'][
3] == '-' and slice_file_list == []: # Check for a minus to indicate
# a reversed offset list
main_info['slice_offset'].reverse()
if main_info[
'quiet'] != 1: # Show the slice timing (P.S. Printing is very time consuming in python)
print 'Slice timing:', main_info['slice_offset']
# Create information copy for each type of signal
respiration_info = dict(main_info)
respiration_info['frequency_cutoff'] = main_info[
'respiration_cutoff_frequency']
# Amplitude-based phase for respiration
respiration_info['amp_phase'] = 1
# respiration_info['as_percover'] = 50 # Percent overlap of windows for fft
# respiration_info['as_windwidth'] = 0 # Window width in seconds for fft, 0 for full window
# respiration_info['as_fftwin'] = 0 # 1 == hamming window. 0 == no windowing
cardiac_info = dict(main_info)
cardiac_info['frequency_cutoff'] = main_info['cardiac_cutoff_frequency']
# Time-based phase for cardiac signal
cardiac_info['amp_phase'] = 0
# Get the peaks for respiration_info and cardiac_info
if respiration_file:
respiration_peak, error = peak_finder(respiration_info,
respiration_file)
if error:
print 'Died in PeakFinder'
return
else:
respiration_peak = {}
if cardiac_file:
cardiac_peak, error = peak_finder(cardiac_info, cardiac_file)
if error:
print 'Died in PeakFinder'
return
else:
cardiac_peak = {}
main_info['resp_peak'] = respiration_peak
main_info['card_peak'] = cardiac_peak
respiration_info.update(respiration_peak)
cardiac_info.update(cardiac_peak)
# Get the phase
if respiration_peak:
print 'Estimating phase for respiration_info'
respiration_phased = phase_estimator(respiration_info['amp_phase'],
respiration_info)
else:
respiration_phased = {}
if cardiac_peak:
print 'Estimating phase for cardiac_info'
print cardiac_info['v']
cardiac_phased = phase_estimator(cardiac_info['amp_phase'],
cardiac_info)
else:
cardiac_phased = {}
respiration_info.update(respiration_phased)
cardiac_info.update(cardiac_phased)
if respiration_phased:
print "Computing RVT from peaks"
print respiration_info['p_trace_r']
rvt = rvt_from_peakfinder(respiration_phased)
respiration_info.update(rvt)
# Show some results
if show_graphs:
if respiration_info:
print 'Showing RVT Peaks for R\n'
show_rvt_peak(respiration_info, 1)
"""
# Not sure if this code is necessary, 'if 0' is never run in MATLAB
# Show RVT graphs goes here, currently not important though
if 0:
# Write retroicor regressors
for i in range(0, opt['main_info['number_of_slices']']):
fname = '%s.RetroCard.slc%02d.1D' % (opt['Prefix'], i)
#wryte3(cardiac_phased['phase_slice_reg'][:,:,i], fname, 1);
savetxt(fname, cardiac_phased['phase_slice_reg'][:,:,i], fmt="%12.6G")
fname = sprintf('%s.RetroResp.slc%02d.1D', Opt.Prefix, i);
# wryte3(respiration_info.phase_slice_reg(:,:,i), fname, 1);
savetxt(fname, respiration_phased['phase_slice_reg'][:,:,i], fmt="%12.6G")
# And write the RVT puppy, plus or minus a few seconds delay
fname = '%s.RetroRVT.1D' % opt['Prefix']
# wryte3(respiration_info.rvtrs_slc, fname, 1);
savetxt(fname, rvt['rvtrs_slc'], fmt="%12.6G")
"""
# also generate files as 3dREMLfit likes them
n_n = 0
n_r_v = 0
n_r_p = 0
n_e = 0
if respiration_info:
n_n = len(respiration_info['time_series_time'])
n_r_p = size(respiration_info['phase_slice_reg'], 1)
n_r_v = size(respiration_info['rvtrs_slc'], 0)
if cardiac_info: # must have cardiac_info
n_n = len(
cardiac_phased['time_series_time']
) # ok to overwrite len(respiration_info.tst), should be same.
n_e = size(cardiac_phased['phase_slice_reg'], 1)
if main_info['cardiac_out'] == 0 and main_info[
'respiration_out'] == 0 and main_info['rvt_out'] == 0:
print 'Options cardiac_out, respiration_out, and RVT_out all 0.\nNo output required.\n'
return
temp_y_axis = main_info['number_of_slices'] * \
((main_info['rvt_out']) * int(n_r_v) +
(main_info['respiration_out']) * int(n_r_p) +
(main_info['cardiac_out']) * int(n_e))
main_info['reml_out'] = zeros((n_n, temp_y_axis))
cnt = 0
head = '<RetroTSout\n' \
'ni_type = "%d*double"\n' \
'ni_dimen = "%d"\n' \
'ColumnLabels = "'\
% (size(main_info['reml_out'], 1), size(main_info['reml_out'], 0))
tail = '"\n>'
tailclose = '</RetroTSout>'
label = head
main_info['reml_out'] = []
if main_info['slice_major'] == 0: # old approach, not handy for 3dREMLfit
# RVT
if main_info['rvt_out'] != 0:
for j in range(0, size(respiration_info['rvtrs_slc'], 2)):
for i in range(0, main_info['number_of_slices']):
cnt += 1
main_info['reml_out'][:, cnt] = respiration_info[
'rvtrs_slc'][:, j] # same for each slice
label = '%s s%d.RVT%d ;' % (label, i, j)
# Resp
if main_info['respiration_out'] != 0:
for j in range(0, size(respiration_info['phase_slice_reg'], 2)):
for i in range(0, main_info['number_of_slices']):
cnt += 1
main_info['reml_out'][:, cnt] = respiration_info[
'phase_slice_reg'][:, j, i]
label = '%s s%d.Resp%d ;' % (label, i, j)
# Card
if main_info['Card_out'] != 0:
for j in range(0, size(cardiac_info['phase_slice_reg'], 2)):
for i in range(0, main_info['number_of_slices']):
cnt += 1
main_info['reml_out'][:, cnt] = cardiac_info[
'phase_slice_reg'][:, j, i]
label = '%s s%d.Card%d ;' % (label, i, j)
fid = open(('%s.retrots.1D', main_info['prefix']), 'w')
else:
for i in range(0, main_info['number_of_slices']):
if main_info['rvt_out'] != 0:
# RVT
for j in range(0, shape(respiration_info['rvtrs_slc'])[0]):
cnt += 1
main_info['reml_out'].append(
respiration_info['rvtrs_slc']
[j]) # same regressor for each slice
label = '%s s%d.RVT%d ;' % (label, i, j)
if main_info['respiration_out'] != 0:
# Resp
for j in range(0,
shape(respiration_info['phase_slice_reg'])[1]):
cnt += 1
main_info['reml_out'].append(
respiration_info['phase_slice_reg'][:, j, i])
label = '%s s%d.Resp%d ;' % (label, i, j)
if main_info['cardiac_out'] != 0:
# Card
for j in range(0, shape(cardiac_info['phase_slice_reg'])[1]):
cnt += 1
main_info['reml_out'].append(
cardiac_info['phase_slice_reg'][:, j, i])
label = '%s s%d.Card%d ;' % (label, i, j)
fid = open(('%s.slibase.1D' % main_info['prefix']), 'w')
# remove very last ';'
label = label[1:-2]
savetxt('%s.slibase.1D' % main_info['prefix'],
column_stack(main_info['reml_out']),
fmt='%.4f',
delimiter=' ',
newline='\n',
header=('%s%s' % (label, tail)),
footer=('%s' % tailclose))
"""
fid.write('%s', label)
fid.write('%s ', tail)
for i in range(0, len(main_info['reml_out'])):
fid.write('%s ', main_info['reml_out'][i, :])
fprintf(fid, '\n ')
fprintf(fid, '%s', tailclose)
fclose(fid)
"""
main_info['error'] = 0
return main_info