Merge pull request #409 from mgxd/tst/workflow-construction

TST: Build workflow across different conditions

nibabies/data/tests/config.toml

@@ -1,78 +1,67 @@
 [environment]
 cpu_count = 8
-exec_docker_version = "20.10.12"
-exec_env = "nibabies-docker"
-free_mem = 0.4
+exec_env = "posix"
+free_mem = 2.2
 overcommit_policy = "heuristic"
 overcommit_limit = "50%"
-nipype_version = "1.6.1"
-templateflow_version = "0.7.2"
-version = "21.1.0"
+nipype_version = "1.5.0"
+templateflow_version = "24.2.2"
+version = "24.1.0"
 
 [execution]
-bids_dir = "/data"
-bids_database_dir = "/tmp/bids_db"
-bids_description_hash = "c47e9ebb943ca662556808b2aeac3f6c8bb2a242696c32850c64ec47aba80d9e"
+bids_dir = "ds000005/"
+bids_description_hash = "5d42e27751bbc884eca87cb4e62b9a0cca0cd86f8e578747fe89b77e6c5b21e5"
 boilerplate_only = false
-sloppy = true
-debug = []
-derivatives = [ "/opt/derivatives/precomputed",]
 fs_license_file = "/opt/freesurfer/license.txt"
-fs_subjects_dir = "/opt/subjects"
-layout = "BIDS Layout: .../data | Subjects: 1 | Sessions: 1 | Runs: 1"
-log_dir = "/tmp/logs"
-log_level = 20
+fs_subjects_dir = "/opt/freesurfer/subjects"
+log_dir = "/tmp/fmriprep/logs"
+log_level = 40
 low_mem = false
 md_only_boilerplate = false
-nibabies_dir = "/out"
-notrack = false
-output_dir = "/out"
-me_output_echos = false
-output_layout = "bids"
-output_spaces = "MNIInfant:cohort-1:res-native"
+notrack = true
+output_dir = "/tmp"
+output_spaces = "MNIInfant:cohort-1"
 reports_only = false
-run_uuid = "20220323-202555_01a7d80d-7ff4-4b13-a99c-ec399045e9ff"
-segmentation_atlases_dir = "/opt/segmentations"
+run_uuid = "20200306-105302_d365772b-fd60-4741-a722-372c2f558b50"
 participant_label = [ "01",]
-templateflow_home = "/home/nibabies/.cache/templateflow"
-work_dir = "/scratch"
+templateflow_home = "~/.cache/templateflow"
+work_dir = "work/"
 write_graph = false
 
 [workflow]
 anat_only = false
-bold2t1w_dof = 6
-bold2t1w_init = "register"
-cifti_output = false
+bold2anat_dof = 6
 fd_radius = 45
 fmap_bspline = false
 force_syn = false
 hires = true
-ignore = [ "slicetiming",]
+ignore = []
 longitudinal = false
 medial_surface_nan = false
 project_goodvoxels = false
 regressors_all_comps = false
 regressors_dvars_th = 1.5
 regressors_fd_th = 0.5
-run_reconall = true
 skull_strip_fixed_seed = false
 skull_strip_template = "UNCInfant:cohort-1"
-skull_strip_t1w = "force"
-slice_time_ref = 0.5
-spaces = "MNIInfant:cohort-1:res-native MNIInfant:cohort-1"
-use_bbr = false
-use_syn_sdc = false
+surface_recon_method = "auto"
 
 [nipype]
 crashfile_format = "txt"
 get_linked_libs = false
-memory_gb = 8
-nprocs = 4
-omp_nthreads = 2
+memory_gb = 32
+nprocs = 8
+omp_nthreads = 8
 plugin = "MultiProc"
 resource_monitor = false
 stop_on_first_crash = false
 
 [nipype.plugin_args]
 maxtasksperchild = 1
 raise_insufficient = false
+
+[execution.bids_filters.t1w]
+reconstruction = "<Query.NONE: 1>"
+
+[execution.bids_filters.t2w]
+reconstruction = "<Query.NONE: 1>"

nibabies/utils/bids.py

@@ -236,8 +236,8 @@ def parse_bids_for_age_months(
 
     # Play nice with sessions
     subject = f'sub-{subject_id}'
-    session = f'ses-{session_id}' or ''
-    prefix = f'{subject}' + f'_{session}' if session else ''
+    session = f'ses-{session_id}' if session_id else ''
+    prefix = f'{subject}' + (f'_{session}' if session else '')
 
     subject_level = session_level = Path(bids_root) / subject
     if session_id:

nibabies/workflows/anatomical/fit.py

@@ -940,7 +940,7 @@ def init_infant_anat_fit_wf(
 
     workflow.__desc__ = desc
 
-    if not recon_method:
+    if recon_method is None:
         LOGGER.info('ANAT Skipping Stages 6+')
         return workflow
 
@@ -1765,6 +1765,10 @@ def init_infant_single_anat_fit_wf(
 
     workflow.__desc__ = desc
 
+    if recon_method is None:
+        LOGGER.info('ANAT Skipping Stages 5+')
+        return workflow
+
     # Stage 5: Surface reconstruction
     if recon_method == 'mcribs':
         if reference_anat == 'T1w':

nibabies/workflows/base.py

@@ -70,11 +70,13 @@
     from bids.layout import BIDSLayout
     from niworkflows.utils.spaces import SpatialReferences
 
+    SubjectSession = tuple[str, str | None]
+
 
 AUTO_T2W_MAX_AGE = 8
 
 
-def init_nibabies_wf(subworkflows_list):
+def init_nibabies_wf(subworkflows_list: list[SubjectSession]):
     """
     Build *NiBabies*'s pipeline.
 
@@ -92,7 +94,7 @@ def init_nibabies_wf(subworkflows_list):
             from nibabies.workflows.tests import mock_config
             from nibabies.workflows.base import init_nibabies_wf
             with mock_config():
-                wf = init_nibabies_wf()
+                wf = init_nibabies_wf(['01', None])
 
     Parameters
     ----------

nibabies/workflows/bold/registration.py

@@ -603,7 +603,7 @@ def init_fsl_bbr_wf(
         flt_bbr.inputs.schedule = data.load('flirtsch/bbr.sch')
     # fmt:off
     workflow.connect([
-        (inputnode, wm_mask, [('t1w_dseg', 'in_seg')]),
+        (inputnode, wm_mask, [('anat_dseg', 'in_seg')]),
         (inputnode, flt_bbr, [('in_file', 'in_file')]),
         (lta_to_fsl, flt_bbr, [('out_fsl', 'in_matrix_file')]),
     ])

nibabies/workflows/tests/__init__.py

@@ -0,0 +1,71 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Utilities and mocks for testing and documentation building."""
+
+import os
+import shutil
+from contextlib import contextmanager
+from pathlib import Path
+from tempfile import mkdtemp
+
+from toml import loads
+
+from nibabies import data
+from nibabies.workflows.base import init_execution_spaces
+
+
+@contextmanager
+def mock_config(bids_dir=None):
+    """Create a mock config for documentation and testing purposes."""
+    from ... import config
+
+    _old_fs = os.getenv('FREESURFER_HOME')
+    if not _old_fs:
+        os.environ['FREESURFER_HOME'] = mkdtemp()
+
+    settings = loads(data.load.readable('tests/config.toml').read_text())
+    for sectionname, configs in settings.items():
+        if sectionname != 'environment':
+            section = getattr(config, sectionname)
+            section.load(configs, init=False)
+    config.nipype.omp_nthreads = 1
+    config.nipype.init()
+    config.loggers.init()
+    init_execution_spaces()
+
+    bids_dir = bids_dir or data.load('tests/ds000005').absolute()
+
+    config.execution.work_dir = Path(mkdtemp())
+    config.execution.bids_dir = bids_dir
+    config.execution.nibabies_dir = Path(mkdtemp())
+    config.execution.bids_database_dir = None
+    config.execution._layout = None
+    config.execution.init()
+
+    yield
+
+    shutil.rmtree(config.execution.work_dir)
+    shutil.rmtree(config.execution.nibabies_dir)
+
+    if not _old_fs:
+        del os.environ['FREESURFER_HOME']