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Use new function!
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@tsalo
tsalo committed Oct 18, 2023
1 parent 2dec6ff commit 81e5ef4
Showing 1 changed file with 35 additions and 77 deletions.
112 changes: 35 additions & 77 deletions xcp_d/tests/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,18 +6,13 @@
import pandas as pd
import pytest
from nipype import logging
from pkg_resources import resource_filename as pkgrf

from xcp_d.cli import combineqc
from xcp_d.cli.parser import parse_args
from xcp_d.cli.workflow import build_boilerplate, build_workflow
from xcp_d.interfaces.report_core import generate_reports
from xcp_d.tests.utils import (
check_affines,
check_generated_files,
download_test_data,
get_test_data_path,
run_command,
)

LOGGER = logging.getLogger("nipype.utils")
Expand All @@ -36,7 +31,6 @@ def test_ds001419_nifti(data_dir, output_dir, working_dir):
filter_file = os.path.join(test_data_dir, "ds001419_nifti_filter.json")

parameters = [
"xcp_d",
dataset_dir,
out_dir,
"participant",
Expand All @@ -59,7 +53,7 @@ def test_ds001419_nifti(data_dir, output_dir, working_dir):
"200",
"--random-seed=8675309",
]
_run_and_generate_2(
_run_xcpd(
test_name=test_name,
parameters=parameters,
data_dir=data_dir,
Expand Down Expand Up @@ -104,9 +98,8 @@ def test_ds001419_cifti(data_dir, output_dir, working_dir):
"--upper-bpf=0.0",
f"--fs-license-file={fs_license_file}",
]
_run_and_generate(
_run_xcpd(
test_name=test_name,
participant_label="01",
parameters=parameters,
data_dir=data_dir,
out_dir=out_dir,
Expand Down Expand Up @@ -149,9 +142,8 @@ def test_pnc_nifti(data_dir, output_dir, working_dir):
"200",
"--random-seed=8675309",
]
_run_and_generate(
_run_xcpd(
test_name=test_name,
participant_label="1648798153",
parameters=parameters,
data_dir=data_dir,
out_dir=out_dir,
Expand Down Expand Up @@ -206,9 +198,8 @@ def test_pnc_cifti(data_dir, output_dir, working_dir):
"--fd-thresh=0.3",
"--upper-bpf=0.0",
]
_run_and_generate(
_run_xcpd(
test_name=test_name,
participant_label="1648798153",
parameters=parameters,
data_dir=data_dir,
out_dir=out_dir,
Expand Down Expand Up @@ -274,9 +265,8 @@ def test_pnc_cifti_t2wonly(data_dir, output_dir, working_dir):
"--fd-thresh=0.3",
"--lower-bpf=0.0",
]
_run_and_generate(
_run_xcpd(
test_name=test_name,
participant_label="1648798153",
parameters=parameters,
data_dir=data_dir,
out_dir=out_dir,
Expand Down Expand Up @@ -324,9 +314,8 @@ def test_nibabies(data_dir, output_dir, working_dir):
"--dcan-qc",
f"--custom_confounds={custom_confounds_dir}",
]
_run_and_generate(
_run_xcpd(
test_name=test_name,
participant_label="01",
parameters=parameters,
data_dir=data_dir,
out_dir=out_dir,
Expand Down Expand Up @@ -360,73 +349,39 @@ def test_fmriprep_without_freesurfer(data_dir, output_dir, working_dir):
out_dir = os.path.join(output_dir, test_name)
work_dir = os.path.join(working_dir, test_name)

test_data_dir = get_test_data_path()

cmd = (
f"xcp_d {dataset_dir} {out_dir} participant "
f"-w {work_dir} "
"--nthreads 2 "
"--omp-nthreads 2 "
"--despike "
"--head_radius 40 "
"--smoothing 6 "
"-f 100 "
"--nuisance-regressors 27P "
"--disable-bandpass-filter "
"--min-time 20 "
"--dcan-qc "
"--dummy-scans 1"
parameters = [
dataset_dir,
out_dir,
"participant",
f"-w={work_dir}",
"--despike",
"--head_radius=40",
"--smoothing=6",
"--fd-thresh=100",
"--nuisance-regressors=27P",
"--disable-bandpass-filter",
"--min-time=20",
"--dcan-qc",
"--dummy-scans=1",
"--omp-nthreads=2",
"--nthreads=2",
]
_run_xcpd(
test_name=test_name,
parameters=parameters,
data_dir=data_dir,
out_dir=out_dir,
input_type="nifti",
)

run_command(cmd)

# Run combine-qc too
xcpd_dir = os.path.join(out_dir, "xcp_d")
combineqc.main([xcpd_dir, "summary"])
combineqc.main([xcpd_dir, os.path.join(xcpd_dir, "summary")])

output_list_file = os.path.join(test_data_dir, "test_fmriprep_without_freesurfer_outputs.txt")
check_generated_files(out_dir, output_list_file)
assert os.path.isfile(os.path.join(xcpd_dir, "summary_allsubjects_qc.csv"))

check_affines(dataset_dir, out_dir, input_type="nifti")


def _run_and_generate(
test_name,
participant_label,
parameters,
data_dir,
out_dir,
input_type,
):
from xcp_d import config

parameters.append("--stop-on-first-crash")
parse_args(parameters)
config_file = config.execution.log_dir / f"config-{config.execution.run_uuid}.toml"
config.loggers.cli.warning(f"Saving config file to {config_file}")
config.to_filename(config_file)

retval = build_workflow(config_file, retval={})
xcpd_wf = retval["workflow"]
xcpd_wf.run()
build_boilerplate(str(config_file), xcpd_wf)
generate_reports(
subject_list=[participant_label],
fmri_dir=config.execution.fmri_dir,
work_dir=config.execution.work_dir,
output_dir=out_dir,
run_uuid=config.execution.run_uuid,
config=pkgrf("xcp_d", "data/reports-spec.yml"),
packagename="xcp_d",
)

output_list_file = os.path.join(get_test_data_path(), f"{test_name}_outputs.txt")
check_generated_files(out_dir, output_list_file)

check_affines(data_dir, out_dir, input_type=input_type)


def _run_and_generate_2(
def _run_xcpd(
test_name,
parameters,
data_dir,
Expand All @@ -438,6 +393,9 @@ def _run_and_generate_2(

from xcp_d.cli.run import main

# Prepend command name (can really be any string, since we're calling main directly).
parameters = ["xcp_d"] + parameters

with patch.object(sys, "argv", parameters):
main()

Expand Down

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