def main():
"""py_pRF_mapping entry point."""
# Get list of input arguments (without first one, which is the path to the
# function that is called): --NOTE: This is another way of accessing
# input arguments, but since we use 'argparse' it is redundant.
# lstArgs = sys.argv[1:]
strWelcome = 'PyPRF ' + __version__
strDec = '=' * len(strWelcome)
print(strDec + '\n' + strWelcome + '\n' + strDec)
# Create parser object:
objParser = argparse.ArgumentParser()
# Add argument to namespace - config file path:
objParser.add_argument('-config',
metavar='config.csv',
help='Absolute file path of config file with \
parameters for pRF analysis. Ignored if in \
testing mode.')
# # Add argument to namespace - test flag:
# objParser.add_argument('-test',
# action='store_true',
# help='Whether to run a test with pytest.'
# )
# Namespace object containign arguments and values:
objNspc = objParser.parse_args()
# # Get test flag from argument parser ('True' if the '-test' flag is
# # provided, otherwise 'False'):
# lgcTest = objNspc.test
# if lgcTest:
# print('Test mode initiated...')
# # Path of config file for tests:
# strCsvCnfg = (strDir + '/testing/config_testing.csv')
# # Signal test mode to lower functions:
# lgcTest = True
# else:
# Get path of config file from argument parser:
strCsvCnfg = objNspc.config
# Print info if no config argument is provided.
if strCsvCnfg is None:
print('Please provide the file path to a config file, e.g.:')
print(' pyprf -config /path/to/my_config_file.csv')
else:
# Signal non-test mode to lower functions (needed for pytest):
lgcTest = False
# Call to main function, to invoke pRF analysis:
pyprf(strCsvCnfg, lgcTest)
def test_main():
"""Run main pyprf function and compare results with template."""
# --------------------------------------------------------------------------
# *** Preparations
# Decimal places to round before comparing template and test results:
varRnd = 3
# Load template result:
aryTmplR2, _, _ = util.load_nii((strDir + '/exmpl_data_results_R2.nii.gz'))
# Round template reults:
aryTmplR2 = np.around(aryTmplR2.astype(np.float32), decimals=varRnd)
# --------------------------------------------------------------------------
# --------------------------------------------------------------------------
# *** Test numpy version
# Path of config file for tests:
strCsvCnfgNp = (strDir + '/config_testing_numpy.csv')
# Call main pyprf function:
pyprf_main.pyprf(strCsvCnfgNp, lgcTest=True)
# Load result:
aryTestNpR2, _, _ = util.load_nii(
(strDir + '/result/' + 'pRF_test_results_np_R2.nii.gz'))
# Round test results:
aryTestNpR2 = np.around(aryTestNpR2.astype(np.float32), decimals=varRnd)
# Test whether the template and test results correspond:
lgcTestNp = np.all(np.equal(aryTmplR2, aryTestNpR2))
# --------------------------------------------------------------------------
# --------------------------------------------------------------------------
# *** Test cython version
# Path of config file for tests:
strCsvCnfgCy = (strDir + '/config_testing_cython.csv')
# Call main pyprf function:
pyprf_main.pyprf(strCsvCnfgCy, lgcTest=True)
# Load result:
aryTestCyR2, _, _ = util.load_nii(
(strDir + '/result/' + 'pRF_test_results_cy_R2.nii.gz'))
# Round test results:
aryTestCyR2 = np.around(aryTestCyR2.astype(np.float32), decimals=varRnd)
# Test whether the template and test results correspond:
lgcTestCy = np.all(np.equal(aryTmplR2, aryTestCyR2))
# --------------------------------------------------------------------------
# --------------------------------------------------------------------------
# *** Test tensorflow version
# Path of config file for tests:
strCsvCnfgTf = (strDir + '/config_testing_tensorflow.csv')
# Call main pyprf function:
pyprf_main.pyprf(strCsvCnfgTf, lgcTest=True)
# Load result:
aryTestTfR2, _, _ = util.load_nii(
(strDir + '/result/' + 'pRF_test_results_tf_R2.nii.gz'))
# Round test results:
aryTestTfR2 = np.around(aryTestTfR2.astype(np.float32), decimals=varRnd)
# Test whether the template and test results correspond:
lgcTestTf = np.all(np.equal(aryTmplR2, aryTestTfR2))
# --------------------------------------------------------------------------
# --------------------------------------------------------------------------
# *** Clean up
# Path of directory with results:
strDirRes = strDir + '/result/'
# Get list of files in results directory:
lstFls = [f for f in os.listdir(strDirRes) if isfile(join(strDirRes, f))]
# Delete results of test:
for strTmp in lstFls:
if '.nii' in strTmp:
# print(strTmp)
os.remove((strDirRes + '/' + strTmp))
elif '.npy' in strTmp:
# print(strTmp)
os.remove((strDirRes + '/' + strTmp))
# --------------------------------------------------------------------------
assert (lgcTestNp and lgcTestCy and lgcTestTf)
def test_main():
"""Run main pyprf function and compare results with template."""
# -------------------------------------------------------------------------
# *** Preparations
# Decimal places to round before comparing template and test results:
varRnd = 3
# Load template result - R2:
aryTmplR2, _, _ = util.load_nii((strDir + '/exmpl_data_results_R2.nii.gz'))
# Load template result - eccentricity:
aryTmplEcc, _, _ = util.load_nii(
(strDir + '/exmpl_data_results_eccentricity.nii.gz'))
# Load template result - polar angle:
aryTmplPol, _, _ = util.load_nii(
(strDir + '/exmpl_data_results_polar_angle.nii.gz'))
# Load template result - SD:
aryTmplSd, _, _ = util.load_nii((strDir + '/exmpl_data_results_SD.nii.gz'))
# Load template result - parameter estimate condition 1:
aryTmplPe01, _, _ = util.load_nii(
(strDir + '/exmpl_data_results_PE_01.nii.gz'))
# Load template result - parameter estimate condition 2:
aryTmplPe02, _, _ = util.load_nii(
(strDir + '/exmpl_data_results_PE_02.nii.gz'))
# Round template reults:
aryTmplR2 = np.around(aryTmplR2, decimals=varRnd).astype(np.float32)
aryTmplEcc = np.around(aryTmplEcc, decimals=varRnd).astype(np.float32)
aryTmplPol = np.around(aryTmplPol, decimals=varRnd).astype(np.float32)
aryTmplSd = np.around(aryTmplSd, decimals=varRnd).astype(np.float32)
aryTmplPe01 = np.around(aryTmplPe01, decimals=varRnd).astype(np.float32)
aryTmplPe02 = np.around(aryTmplPe02, decimals=varRnd).astype(np.float32)
# -------------------------------------------------------------------------
# *** Test pyprf main pipeline
# Test numpy, cython, and tensorflow version. List with version
# abbreviations:
lstVrsn = ['np', 'cy', 'cy_hdf5'] # 'np_hdf5'
# Path of config file for tests (version abbreviation left open):
strCsvCnfg = (strDir + '/config_testing_{}.csv')
for strVrsn in lstVrsn:
# Call main pyprf function:
pyprf_main.pyprf(strCsvCnfg.format(strVrsn), lgcTest=True)
# Load result - R2:
aryTestR2, _, _ = util.load_nii(
(strDir + '/result/' +
'pRF_test_results_{}_R2.nii.gz'.format(strVrsn)))
# Load result - eccentricity:
aryTestEcc, _, _ = util.load_nii(
(strDir + '/result/' +
'pRF_test_results_{}_eccentricity.nii.gz'.format(strVrsn)))
# Load result - polar angle:
aryTestPol, _, _ = util.load_nii(
(strDir + '/result/' +
'pRF_test_results_{}_polar_angle.nii.gz'.format(strVrsn)))
# Load result - SD:
aryTestSd, _, _ = util.load_nii(
(strDir + '/result/' +
'pRF_test_results_{}_SD.nii.gz'.format(strVrsn)))
# Load result - parameter estimate condition 1:
aryTestlPe01, _, _ = util.load_nii(
(strDir + '/result/' +
'pRF_test_results_{}_PE_01.nii.gz'.format(strVrsn)))
# Load result - parameter estimate condition 2:
aryTestlPe02, _, _ = util.load_nii(
(strDir + '/result/' +
'pRF_test_results_{}_PE_02.nii.gz'.format(strVrsn)))
# Round test results:
aryTestR2 = np.around(aryTestR2, decimals=varRnd).astype(np.float32)
aryTestEcc = np.around(aryTestEcc, decimals=varRnd).astype(np.float32)
aryTestPol = np.around(aryTestPol, decimals=varRnd).astype(np.float32)
aryTestSd = np.around(aryTestSd, decimals=varRnd).astype(np.float32)
aryTestlPe01 = np.around(aryTestlPe01,
decimals=varRnd).astype(np.float32)
aryTestlPe02 = np.around(aryTestlPe02,
decimals=varRnd).astype(np.float32)
# Test whether the template and test results correspond:
# print('np.max(np.abs(np.subtract(aryTmplR2, aryTestR2)))')
# print(np.max(np.abs(np.subtract(aryTmplR2, aryTestR2))))
lgcTestR2 = np.all(np.equal(aryTmplR2, aryTestR2))
lgcTestEcc = np.all(np.equal(aryTmplEcc, aryTestEcc))
lgcTestPol = np.all(np.equal(aryTmplPol, aryTestPol))
lgcTestSd = np.all(np.equal(aryTmplSd, aryTestSd))
lgcTestPe01 = np.all(np.equal(aryTmplPe01, aryTestlPe01))
lgcTestPe02 = np.all(np.equal(aryTmplPe02, aryTestlPe02))
# Did version pass the test?
assert lgcTestR2
assert lgcTestEcc
assert lgcTestPol
assert lgcTestSd
assert lgcTestPe01
assert lgcTestPe02
# -------------------------------------------------------------------------
# *** Clean up testing results
# Path of directory with results:
strDirRes = strDir + '/result/'
# Get list of files in results directory:
lstFls = [f for f in os.listdir(strDirRes) if isfile(join(strDirRes, f))]
# Delete results of test:
for strTmp in lstFls:
if '.nii' in strTmp:
# print(strTmp)
os.remove((strDirRes + '/' + strTmp))
elif '.npy' in strTmp:
# print(strTmp)
os.remove((strDirRes + '/' + strTmp))
elif '.hdf5' in strTmp:
# print(strTmp)
os.remove((strDirRes + '/' + strTmp))
# -------------------------------------------------------------------------
# *** Clean up intermediate results (hdf5 files)
# Path of directory with time courses converted to hdf5:
strDirRes = strDir + '/'
# Get list of files in results directory:
lstFls = [f for f in os.listdir(strDirRes) if isfile(join(strDirRes, f))]
# Delete results of test:
for strTmp in lstFls:
if '.hdf5' in strTmp:
# print(strTmp)
os.remove((strDirRes + '/' + strTmp))