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pytest on 2193729161ef1b90d76eb2c4554eea4414532a34
Raw
Pytest
[5/11/20 10:31:11] (base) alex@NeuroPoly-MacBook-Pro shimming-toolbox % git rev-parse origin/master
2193729161ef1b90d76eb2c4554eea4414532a34
[5/11/20 10:29:24] (base) alex@NeuroPoly-MacBook-Pro shimming-toolbox % pytest
INFO:root:/Users/alex/code/shimming-toolbox/testing_data, testing_data
INFO:shimmingtoolbox.download:Trying URL: https://github.com/shimming-toolbox/data-testing/archive/r20201021.zip
INFO:shimmingtoolbox.download:Downloading: data-testing-r20201021.zip
Status: 11.4MB [00:02, 4.85MB/s]
INFO:shimmingtoolbox.download:Unzip data to: /var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/st_download_a37h4cm7
INFO:shimmingtoolbox.download:Removing temporary folders...
========================================================================================================================= test session starts =========================================================================================================================
platform darwin -- Python 3.8.3, pytest-4.6.11, py-1.9.0, pluggy-0.13.1
rootdir: /Users/alex/code/shimming-toolbox, inifile: pytest.ini
plugins: cov-2.5.1
collected 62 items
test/test_biot_savart.py ... [ 4%]
test/test_dicom_to_nifti.py ... [ 9%]
test/test_example_scripts.py F [ 11%]
test/test_init.py . [ 12%]
test/test_load_nifti.py .....F.... [ 29%]
test/test_masking.py ...... [ 38%]
test/test_pmu.py ... [ 43%]
test/test_prelude.py EEEEEEEE [ 56%]
test/test_sequential_zslice.py . [ 58%]
test/test_siemens_basis.py .. [ 61%]
test/test_spherical_harmonics.py ... [ 66%]
test/cli/test_cli_dicom_to_nifti.py . [ 67%]
test/simulate/test_numerical_model.py .................... [100%]
=============================================================================================================================== ERRORS ================================================================================================================================
__________________________________________________________________________________________________________ ERROR at setup of TestCore.test_default_works[0] ___________________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
_________________________________________________________________________________________________________ ERROR at setup of TestCore.test_non_default_mask[0] _________________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
_________________________________________________________________________________________________________ ERROR at setup of TestCore.test_wrong_size_mask[0] __________________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
______________________________________________________________________________________________________ ERROR at setup of TestCore.test_wrong_phase_dimensions[0] ______________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
_______________________________________________________________________________________________________ ERROR at setup of TestCore.test_wrong_mag_dimensions[0] _______________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
__________________________________________________________________________________________________ ERROR at setup of TestCore.test_wrong_mag_and_phase_dimensions[0] __________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
_____________________________________________________________________________________________________________ ERROR at setup of TestCore.test_phase_2d[0] _____________________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
____________________________________________________________________________________________________________ ERROR at setup of TestCore.test_threshold[0] _____________________________________________________________________________________________________________
@pytest.fixture(params=[pytest.param(0, marks=pytest.mark.prelude)])
def test_prelude_installation():
# note that subprocess.check_call() returns 0 on success, so it must be
# negated for the assertion.
> assert not subprocess.check_call(['which', 'prelude'])
conftest.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
popenargs = (['which', 'prelude'],), kwargs = {}, retcode = 1, cmd = ['which', 'prelude']
def check_call(*popenargs, **kwargs):
"""Run command with arguments. Wait for command to complete. If
the exit code was zero then return, otherwise raise
CalledProcessError. The CalledProcessError object will have the
return code in the returncode attribute.
The arguments are the same as for the call function. Example:
check_call(["ls", "-l"])
"""
retcode = call(*popenargs, **kwargs)
if retcode:
cmd = kwargs.get("args")
if cmd is None:
cmd = popenargs[0]
> raise CalledProcessError(retcode, cmd)
E subprocess.CalledProcessError: Command '['which', 'prelude']' returned non-zero exit status 1.
../../miniconda3/lib/python3.8/subprocess.py:364: CalledProcessError
============================================================================================================================== FAILURES ===============================================================================================================================
______________________________________________________________________________________________________________ TestCore.test_demo_script_outputs_figure _______________________________________________________________________________________________________________
self = <test_example_scripts.TestCore object at 0x7f899d1a8700>
def test_demo_script_outputs_figure(self):
> fname_nifti = general_demo(self.tmp_path)
test/test_example_scripts.py:28:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
examples/general_demo.py:72: in general_demo
unwrapped_phase_e1 = prelude(phase_e1, nii_mag_e1.get_fdata(), nii_phase_e1.affine)
shimmingtoolbox/unwrap/prelude.py:79: in prelude
run_subprocess(unwrap_command)
shimmingtoolbox/utils.py:20: in run_subprocess
subprocess.run(cmd.split(' '), stdout=subprocess.PIPE, text=True, check=True)
../../miniconda3/lib/python3.8/subprocess.py:489: in run
with Popen(*popenargs, **kwargs) as process:
../../miniconda3/lib/python3.8/subprocess.py:854: in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <subprocess.Popen object at 0x7f899c7c9e20>, args = ['prelude', '-p', '/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/st_preludemr63v_hc/rawPhase', '-a', '/var/folders/11/q0s99tk17rj_7jtmj1psydbr0000gn/T/st_preludemr63v_hc/mag', '-o', ...]
executable = b'prelude', preexec_fn = None, close_fds = True, pass_fds = (), cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False, p2cread = -1, p2cwrite = -1, c2pread = 14, c2pwrite = 15, errread = -1, errwrite = -1
restore_signals = True, start_new_session = False
def _execute_child(self, args, executable, preexec_fn, close_fds,
pass_fds, cwd, env,
startupinfo, creationflags, shell,
p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite,
restore_signals, start_new_session):
"""Execute program (POSIX version)"""
if isinstance(args, (str, bytes)):
args = [args]
elif isinstance(args, os.PathLike):
if shell:
raise TypeError('path-like args is not allowed when '
'shell is true')
args = [args]
else:
args = list(args)
if shell:
# On Android the default shell is at '/system/bin/sh'.
unix_shell = ('/system/bin/sh' if
hasattr(sys, 'getandroidapilevel') else '/bin/sh')
args = [unix_shell, "-c"] + args
if executable:
args[0] = executable
if executable is None:
executable = args[0]
sys.audit("subprocess.Popen", executable, args, cwd, env)
if (_USE_POSIX_SPAWN
and os.path.dirname(executable)
and preexec_fn is None
and not close_fds
and not pass_fds
and cwd is None
and (p2cread == -1 or p2cread > 2)
and (c2pwrite == -1 or c2pwrite > 2)
and (errwrite == -1 or errwrite > 2)
and not start_new_session):
self._posix_spawn(args, executable, env, restore_signals,
p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite)
return
orig_executable = executable
# For transferring possible exec failure from child to parent.
# Data format: "exception name:hex errno:description"
# Pickle is not used; it is complex and involves memory allocation.
errpipe_read, errpipe_write = os.pipe()
# errpipe_write must not be in the standard io 0, 1, or 2 fd range.
low_fds_to_close = []
while errpipe_write < 3:
low_fds_to_close.append(errpipe_write)
errpipe_write = os.dup(errpipe_write)
for low_fd in low_fds_to_close:
os.close(low_fd)
try:
try:
# We must avoid complex work that could involve
# malloc or free in the child process to avoid
# potential deadlocks, thus we do all this here.
# and pass it to fork_exec()
if env is not None:
env_list = []
for k, v in env.items():
k = os.fsencode(k)
if b'=' in k:
raise ValueError("illegal environment variable name")
env_list.append(k + b'=' + os.fsencode(v))
else:
env_list = None # Use execv instead of execve.
executable = os.fsencode(executable)
if os.path.dirname(executable):
executable_list = (executable,)
else:
# This matches the behavior of os._execvpe().
executable_list = tuple(
os.path.join(os.fsencode(dir), executable)
for dir in os.get_exec_path(env))
fds_to_keep = set(pass_fds)
fds_to_keep.add(errpipe_write)
self.pid = _posixsubprocess.fork_exec(
args, executable_list,
close_fds, tuple(sorted(map(int, fds_to_keep))),
cwd, env_list,
p2cread, p2cwrite, c2pread, c2pwrite,
errread, errwrite,
errpipe_read, errpipe_write,
restore_signals, start_new_session, preexec_fn)
self._child_created = True
finally:
# be sure the FD is closed no matter what
os.close(errpipe_write)
self._close_pipe_fds(p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite)
# Wait for exec to fail or succeed; possibly raising an
# exception (limited in size)
errpipe_data = bytearray()
while True:
part = os.read(errpipe_read, 50000)
errpipe_data += part
if not part or len(errpipe_data) > 50000:
break
finally:
# be sure the FD is closed no matter what
os.close(errpipe_read)
if errpipe_data:
try:
pid, sts = os.waitpid(self.pid, 0)
if pid == self.pid:
self._handle_exitstatus(sts)
else:
self.returncode = sys.maxsize
except ChildProcessError:
pass
try:
exception_name, hex_errno, err_msg = (
errpipe_data.split(b':', 2))
# The encoding here should match the encoding
# written in by the subprocess implementations
# like _posixsubprocess
err_msg = err_msg.decode()
except ValueError:
exception_name = b'SubprocessError'
hex_errno = b'0'
err_msg = 'Bad exception data from child: {!r}'.format(
bytes(errpipe_data))
child_exception_type = getattr(
builtins, exception_name.decode('ascii'),
SubprocessError)
if issubclass(child_exception_type, OSError) and hex_errno:
errno_num = int(hex_errno, 16)
child_exec_never_called = (err_msg == "noexec")
if child_exec_never_called:
err_msg = ""
# The error must be from chdir(cwd).
err_filename = cwd
else:
err_filename = orig_executable
if errno_num != 0:
err_msg = os.strerror(errno_num)
> raise child_exception_type(errno_num, err_msg, err_filename)
E FileNotFoundError: [Errno 2] No such file or directory: 'prelude'
../../miniconda3/lib/python3.8/subprocess.py:1702: FileNotFoundError
------------------------------------------------------------------------------------------------------------------------ Captured stdout call -------------------------------------------------------------------------------------------------------------------------
Example in:
/Users/alex/code/shimming-toolbox/test/__tmp__/niftis/tmp_dcm2bids/helper
------------------------------------------------------------------------------------------------------------------------ Captured stderr call -------------------------------------------------------------------------------------------------------------------------
Status: 11.4MB [00:01, 7.51MB/s]
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: macOS-10.15.7-x86_64-i386-64bit
INFO:dcm2bids.dcm2bids:python:version: 3.8.3 (default, May 19 2020, 13:54:14) [Clang 10.0.0 ]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20201102
INFO:dcm2bids.dcm2bids:participant: sub-01
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: /Users/alex/code/shimming-toolbox/config/dcm2bids.json
INFO:dcm2bids.dcm2bids:BIDS directory: /Users/alex/code/shimming-toolbox/test/__tmp__/niftis
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o /Users/alex/code/shimming-toolbox/test/__tmp__/niftis/tmp_dcm2bids/sub-01 /Users/alex/code/shimming-toolbox/test/__tmp__/testing_data/dicom_unsorted
INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
INFO:dcm2bids.sidecar:Sidecars pairing:
INFO:dcm2bids.sidecar:_magnitude1 <- 006_dicom_unsorted_a_gre_DYNshim_20191101153345_e1
INFO:dcm2bids.sidecar:_phase1 <- 007_dicom_unsorted_a_gre_DYNshim_20191101153345_e1_ph
INFO:dcm2bids.sidecar:_magnitude2 <- 006_dicom_unsorted_a_gre_DYNshim_20191101153345_e2
INFO:dcm2bids.sidecar:_magnitude3 <- 006_dicom_unsorted_a_gre_DYNshim_20191101153345_e3
INFO:dcm2bids.sidecar:_magnitude5 <- 006_dicom_unsorted_a_gre_DYNshim_20191101153345_e5
INFO:dcm2bids.sidecar:_phase2 <- 007_dicom_unsorted_a_gre_DYNshim_20191101153345_e2_ph
INFO:dcm2bids.sidecar:_phase3 <- 007_dicom_unsorted_a_gre_DYNshim_20191101153345_e3_ph
INFO:dcm2bids.sidecar:_magnitude4 <- 006_dicom_unsorted_a_gre_DYNshim_20191101153345_e4
INFO:dcm2bids.sidecar:_magnitude6 <- 006_dicom_unsorted_a_gre_DYNshim_20191101153345_e6
INFO:dcm2bids.sidecar:_phase4 <- 007_dicom_unsorted_a_gre_DYNshim_20191101153345_e4_ph
INFO:dcm2bids.sidecar:_phase5 <- 007_dicom_unsorted_a_gre_DYNshim_20191101153345_e5_ph
INFO:dcm2bids.sidecar:_phase6 <- 007_dicom_unsorted_a_gre_DYNshim_20191101153345_e6_ph
INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder
INFO:root:Unwrap with prelude
-------------------------------------------------------------------------------------------------------------------------- Captured log call --------------------------------------------------------------------------------------------------------------------------
INFO root:prelude.py:78 Unwrap with prelude
______________________________________________________________________________________________________________ TestCore.test_load_nifti_multiple_echoes _______________________________________________________________________________________________________________
self = <test_load_nifti.TestCore object at 0x7f899d04b8e0>, monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7f899d075250>
def test_load_nifti_multiple_echoes(self, monkeypatch):
"""
Assert passes with correct data for multiple echoes
:return:
"""
if self.tmp_path.exists():
shutil.rmtree(self.data_path_volume)
monkeypatch.setattr('sys.stdin', StringIO('0\n'))
niftis, info, json_info = load_nifti(self.tmp_path)
assert (len(info) == 2), "Wrong number od info data 1"
assert (len(json_info) == 2), "Wrong number of JSON data 1"
self._json_phase['EchoNumber'] = 2
> assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)), \
"JSON file is not correctly loaded for first JSON1"
E AssertionError: JSON file is not correctly loaded for first JSON1
E assert '{"Acquisitio...mp": 222.944}' == '{"Acquisition...mp": 222.944}'
E Skipping 357 identical leading characters in diff, use -v to show
E Skipping 1213 identical trailing characters in diff, use -v to show
E - oNumber": 1, "EchoTi
E ? ^
E + oNumber": 2, "EchoTi
E ? ^
test/test_load_nifti.py:267: AssertionError
------------------------------------------------------------------------------------------------------------------------ Captured stdout call -------------------------------------------------------------------------------------------------------------------------
0:test_data
1:test_data_2
Enter the number for the appropriate acquisition folder, (type 'q' to quit) :
------------------------------------------------------------------------------------------------------------------------ Captured stderr call -------------------------------------------------------------------------------------------------------------------------
INFO:root:Multiple acquisition directories in path. Choosing only one.
INFO:root:Reading acquisitions for run 1
-------------------------------------------------------------------------------------------------------------------------- Captured log call --------------------------------------------------------------------------------------------------------------------------
INFO root:load_nifti.py:66 Multiple acquisition directories in path. Choosing only one.
INFO root:load_nifti.py:128 Reading acquisitions for run 1
============================================================================================================ 2 failed, 52 passed, 8 error in 15.40 seconds ============================================================================================================
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