MAINT: Various configuration touch-ups

nibabies/config.py

@@ -202,7 +202,10 @@ def load(cls, settings, init=True, ignore=None):
             if k in ignore or v is None:
                 continue
             if k in cls._paths:
-                setattr(cls, k, Path(v).absolute())
+                if isinstance(v, (list, tuple)):  # Multiple paths
+                    setattr(cls, k, [Path(p).absolute() for p in v])
+                else:
+                    setattr(cls, k, Path(v).absolute())
             elif hasattr(cls, k):
                 setattr(cls, k, v)
 
@@ -221,7 +224,10 @@ def get(cls):
             if callable(getattr(cls, k)):
                 continue
             if k in cls._paths:
-                v = str(v)
+                if isinstance(v, (list, tuple)):  # Multiple paths
+                    v = [str(p) for p in v]
+                else:
+                    v = str(v)
             if isinstance(v, SpatialReferences):
                 v = " ".join([str(s) for s in v.references]) or None
             if isinstance(v, Reference):
@@ -412,6 +418,7 @@ class execution(_Config):
         "anat_derivatives",
         "bids_dir",
         "bids_database_dir",
+        "derivatives",
         "fs_license_file",
         "fs_subjects_dir",
         "layout",
@@ -609,6 +616,8 @@ class seeds(_Config):
     """Master random seed to initialize the Pseudorandom Number Generator (PRNG)"""
     ants = None
     """Seed used for antsRegistration, antsAI, antsMotionCorr"""
+    numpy = None
+    """Seed used by NumPy"""
 
     @classmethod
     def init(cls):
@@ -619,6 +628,7 @@ def init(cls):
         random.seed(cls.master)  # initialize the PRNG
         # functions to set program specific seeds
         cls.ants = _set_ants_seed()
+        cls.numpy = _set_numpy_seed()
 
 
 def _set_ants_seed():
@@ -628,6 +638,15 @@ def _set_ants_seed():
     return val
 
 
+def _set_numpy_seed():
+    """NumPy's random seed is independant from Python's `random` module"""
+    import numpy as np
+
+    val = random.randint(1, 65536)
+    np.random.seed(val)
+    return val
+
+
 def from_dict(settings):
     """Read settings from a flat dictionary."""
     nipype.load(settings)
@@ -707,7 +726,7 @@ def init_spaces(checkpoint=True):
         from .utils.misc import cohort_by_months
 
         cohort = cohort_by_months("MNIInfant", workflow.age_months)
-        spaces.add(Reference, {"cohort": cohort})
+        spaces.add(Reference("MNIInfant", {"cohort": cohort}))
 
     # Ensure user-defined spatial references for outputs are correctly parsed.
     # Certain options require normalization to a space not explicitly defined by users.

nibabies/data/tests/config.toml

@@ -0,0 +1,80 @@
+[environment]
+cpu_count = 8
+exec_docker_version = "20.10.12"
+exec_env = "nibabies-docker"
+free_mem = 0.4
+overcommit_policy = "heuristic"
+overcommit_limit = "50%"
+nipype_version = "1.6.1"
+templateflow_version = "0.7.2"
+version = "21.1.0"
+
+[execution]
+bids_dir = "/data"
+bids_database_dir = "/tmp/bids_db"
+bids_description_hash = "c47e9ebb943ca662556808b2aeac3f6c8bb2a242696c32850c64ec47aba80d9e"
+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
+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"
+reports_only = false
+run_uuid = "20220323-202555_01a7d80d-7ff4-4b13-a99c-ec399045e9ff"
+segmentation_atlases_dir = "/opt/segmentations"
+participant_label = [ "01",]
+templateflow_home = "/home/nibabies/.cache/templateflow"
+work_dir = "/scratch"
+write_graph = false
+
+[workflow]
+anat_only = false
+aroma_err_on_warn = false
+aroma_melodic_dim = -200
+bold2t1w_dof = 6
+bold2t1w_init = "register"
+cifti_output = false
+fd_radius = 45
+fmap_bspline = false
+force_syn = false
+hires = true
+ignore = [ "slicetiming",]
+longitudinal = false
+medial_surface_nan = 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_aroma = false
+use_bbr = false
+use_syn_sdc = false
+
+[nipype]
+crashfile_format = "txt"
+get_linked_libs = false
+memory_gb = 8
+nprocs = 4
+omp_nthreads = 2
+plugin = "MultiProc"
+resource_monitor = false
+stop_on_first_crash = false
+
+[nipype.plugin_args]
+maxtasksperchild = 1
+raise_insufficient = false

nibabies/tests/test_config.py

@@ -0,0 +1,136 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
+#
+# 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/
+#
+"""Check the configuration module and file."""
+import os
+from pathlib import Path
+from pkg_resources import resource_filename as pkgrf
+from unittest.mock import patch
+
+import pytest
+from toml import loads
+from niworkflows.utils.spaces import format_reference
+
+from .. import config
+
+
+def _reset_config():
+    """
+    Forcibly reload the configuration module to restore defaults.
+    .. caution::
+      `importlib.reload` creates new sets of objects, but will not remove
+      previous references to those objects."""
+    import importlib
+
+    importlib.reload(config)
+
+
+def test_reset_config():
+    execution = config.execution
+    setattr(execution, 'bids_dir', 'TESTING')
+    assert config.execution.bids_dir == 'TESTING'
+    _reset_config()
+    assert config.execution.bids_dir is None
+    # Even though the config module was reset,
+    # previous references to config classes
+    # have not been touched.
+    assert execution.bids_dir == 'TESTING'
+
+
+def test_config_spaces():
+    """Check that all necessary spaces are recorded in the config."""
+    filename = Path(pkgrf('nibabies', 'data/tests/config.toml'))
+    settings = loads(filename.read_text())
+    for sectionname, configs in settings.items():
+        if sectionname != 'environment':
+            section = getattr(config, sectionname)
+            section.load(configs, init=False)
+    config.nipype.init()
+    config.loggers.init()
+    config.init_spaces()
+
+    spaces = config.workflow.spaces
+    assert "MNI152NLin6Asym:res-2" not in [str(s) for s in spaces.get_standard(full_spec=True)]
+
+    assert "MNI152NLin6Asym_res-2" not in [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references
+        if s.standard and s.dim == 3
+    ]
+
+    config.workflow.use_aroma = True
+    config.init_spaces()
+    spaces = config.workflow.spaces
+
+    assert "MNI152NLin6Asym:res-2" in [str(s) for s in spaces.get_standard(full_spec=True)]
+
+    assert "MNI152NLin6Asym_res-2" in [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references
+        if s.standard and s.dim == 3
+    ]
+
+    config.execution.output_spaces = None
+    config.workflow.use_aroma = False
+    config.workflow.age_months = None
+    config.init_spaces()
+    spaces = config.workflow.spaces
+
+    assert [str(s) for s in spaces.get_standard(full_spec=True)] == []
+    assert [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references
+        if s.standard and s.dim == 3
+    ] == []
+
+    # but adding age will populate output spaces with a default
+    config.execution.output_spaces = None
+    config.workflow.use_aroma = False
+    config.workflow.age_months = 1
+    config.init_spaces()
+    spaces = config.workflow.spaces
+
+    assert [str(s) for s in spaces.get_standard(full_spec=True)] == []
+    assert [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references
+        if s.standard and s.dim == 3
+    ] == ['MNIInfant_cohort-1']
+    _reset_config()
+
+
+@pytest.mark.parametrize(
+    "master_seed,ants_seed,numpy_seed", [(1, 17612, 8272), (100, 19094, 60232)]
+)
+def test_prng_seed(master_seed, ants_seed, numpy_seed):
+    """Ensure seeds are properly tracked"""
+    seeds = config.seeds
+    with patch.dict(os.environ, {}):
+        seeds.load({'_random_seed': master_seed}, init=True)
+        assert getattr(seeds, 'master') == master_seed
+        assert seeds.ants == ants_seed
+        assert seeds.numpy == numpy_seed
+        assert os.getenv("ANTS_RANDOM_SEED") == str(ants_seed)
+
+    _reset_config()
+    for seed in ('_random_seed', 'master', 'ants', 'numpy'):
+        assert getattr(config.seeds, seed) is None

wrapper/nibabies_wrapper.py

@@ -26,7 +26,7 @@
 MISSING = """
 Image '{}' is missing
 Would you like to download? [Y/n] """
-PKG_PATH = "/usr/local/miniconda/lib/python3.8/site-packages"
+PKG_PATH = "/opt/conda/lib/python3.8/site-packages"
 TF_TEMPLATES = (
     "MNI152Lin",
     "MNI152NLin2009cAsym",