def test_rapidtide2x_phase3(debug=False):
recalculate = True
if recalculate:
# create outputdir if it doesn't exist
create_dir(get_test_temp_path())
# trigger the usage function
rapidtide2x_workflow.usage()
# and launch the processing
theargs = ['rapidtide2x']
theargs += [os.path.join(get_examples_path(), 'fmri.nii.gz')]
theargs += [
os.path.join(get_test_temp_path(), 'rapidtide2x_phase3output')
]
theargs += ['--nowindow']
theargs += ['--windowfunc=hamming']
theargs += ['--liang', '--eckart', '--phat']
theargs += ['--usesp']
theargs += ['--preservefiltering']
theargs += ['--corrmaskthresh=0.25']
theargs += ['-I', '-B', '-a', '-M', '-m']
theargs += ['-C', '-R', '-L', '-V', '-F', '0.01,0.08']
theargs += ['-v', '--debug']
theargs += ['--globalmaskmethod=mean']
theargs += ['--mklthreads=1']
theargs += ['--nosharedmem']
theargs += ['-S']
rapidtide2x_workflow.rapidtide_main(theargs)
assert True
def test_rapidtide2x_phase3(debug=False):
recalculate = True
if recalculate:
# create outputdir if it doesn't exist
create_dir(get_test_temp_path())
# trigger the usage function
rapidtide2x_workflow.usage()
# and launch the processing
theargs = ["rapidtide2x"]
theargs += [os.path.join(get_examples_path(), "fmri.nii.gz")]
theargs += [
os.path.join(get_test_temp_path(), "rapidtide2x_phase3output")
]
theargs += ["--nowindow"]
theargs += ["--windowfunc=hamming"]
theargs += ["--liang", "--eckart", "--phat"]
theargs += ["--usesp"]
theargs += ["--preservefiltering"]
theargs += ["--corrmaskthresh=0.25"]
theargs += ["-I", "-B", "-a", "-M", "-m"]
theargs += ["-C", "-R", "-L", "-V", "-F", "0.01,0.08"]
theargs += ["-v", "--debug"]
theargs += ["--globalmaskmethod=mean"]
theargs += ["--mklthreads=1"]
theargs += ["--nosharedmem"]
theargs += ["-S"]
rapidtide2x_workflow.rapidtide_main(theargs)
assert True
def test_rapidtide2x(debug=False):
recalculate = True
if recalculate:
# create outputdir if it doesn't exist
create_dir(get_test_temp_path())
# and launch the processing
theargs = ["rapidtide2x"]
theargs += [os.path.join(get_examples_path(), "fmri.nii.gz")]
theargs += [
os.path.join(get_test_temp_path(), "rapidtide2x_phase2output")
]
theargs += [
"--regressor=" +
os.path.join(get_test_data_path(),
"rapidtide2x_phase1target_reference_fmrires.txt")
]
theargs += ["--regressortstep=1.5"]
theargs += ["--limitoutput"]
theargs += ["-s", "25.0"]
theargs += ["-L"]
theargs += ["-r", "-20,20"]
theargs += ["-f", "2"]
theargs += ["--passes=3"]
theargs += ["--refineoffset"]
theargs += ["--despecklepasses=4"]
theargs += ["--accheck"]
theargs += ["--nprocs=2"]
theargs += ["--saveoptionsasjson"]
theargs += ["--detrendorder=3"]
theargs += ["--pickleft"]
theargs += [
"--corrmask=" +
os.path.join(get_examples_path(), "quartermask.nii.gz")
]
theargs += ["--noglm"]
rapidtide2x_workflow.rapidtide_main(theargs)
diffmaps = tide_util.comparerapidtideruns(
os.path.join(get_test_temp_path(), "rapidtide2x_phase2output"),
os.path.join(get_test_target_path(), "rapidtide2x_phase2target"),
)
for mapname, maps in diffmaps.items():
print("checking", mapname)
print("\trelmindiff", maps["relmindiff"])
print("\trelmaxdiff", maps["relmaxdiff"])
print("\trelmeandiff", maps["relmeandiff"])
print("\trelmse", maps["relmse"])
assert maps["relmindiff"] < 1e2
assert maps["relmaxdiff"] < 1e2
assert maps["relmeandiff"] < 1e-2
assert maps["relmse"] < 1e2
def test_rapidtide2x(debug=False):
recalculate = True
if recalculate:
# create outputdir if it doesn't exist
create_dir(get_test_temp_path())
# and launch the processing
theargs = ['rapidtide2x']
theargs += [os.path.join(get_examples_path(), 'fmri.nii.gz')]
theargs += [os.path.join(get_test_temp_path(), 'rapidtide2x_phase2output')]
theargs += ['--regressor=' + os.path.join(get_test_data_path(), 'rapidtide2x_phase1target_reference_fmrires.txt')]
theargs += ['--regressortstep=1.5']
theargs += ['--limitoutput']
theargs += ['-s', '25.0']
theargs += ['-L']
theargs += ['-r', '-20,20']
theargs += ['-f', '2']
theargs += ['--passes=3']
theargs += ['--refineoffset']
theargs += ['--despecklepasses=4']
theargs += ['--accheck']
theargs += ['--nprocs=2']
theargs += ['--saveoptionsasjson']
theargs += ['--detrendorder=3']
theargs += ['--pickleft']
theargs += ['--corrmask=' + os.path.join(get_examples_path(), 'quartermask.nii.gz')]
theargs += ['--noglm']
rapidtide2x_workflow.rapidtide_main(theargs)
diffmaps = tide_util.comparerapidtideruns(os.path.join(get_test_temp_path(), 'rapidtide2x_phase2output'), os.path.join(get_test_target_path(), 'rapidtide2x_phase2target'))
for mapname, maps in diffmaps.items():
print('checking', mapname)
print('\trelmindiff', maps['relmindiff'])
print('\trelmaxdiff', maps['relmaxdiff'])
print('\trelmeandiff', maps['relmeandiff'])
print('\trelmse', maps['relmse'])
assert maps['relmindiff'] < 1e2
assert maps['relmaxdiff'] < 1e2
assert maps['relmeandiff'] < 1e-2
assert maps['relmse'] < 1e2