Move template fetching to a script. (#29)

Dockerfile

@@ -190,13 +190,10 @@ ENV HOME="/home/xcp_d"
 RUN python -c "from matplotlib import font_manager" && \
     sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
 
-# Precaching atlases: UPDATE TEMPLATEFLOW VERSION TO MATCH XCP_D
-RUN python -c "from templateflow import api as tfapi; \
-               tfapi.get('MNI152NLin2009cAsym', resolution=2, suffix='T1w', desc=None); \
-               tfapi.get(template='MNI152NLin6Asym', resolution=2, suffix='T1w'); \
-               tfapi.get('MNI152NLin2009cAsym', resolution=1, desc='carpet',suffix='dseg'); \
-               tfapi.get(template='MNI152NLin2009cAsym', mode='image', suffix='xfm', extension='.h5'); \
-               tfapi.get('fsLR', density='32k');" && \
+# Precaching templates
+COPY scripts/fetch_templates.py fetch_templates.py
+RUN python fetch_templates.py && \
+    rm fetch_templates.py && \
     find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \
     find $HOME/.cache/templateflow -type f -exec chmod go=u {} +
 

scripts/fetch_templates.py

@@ -0,0 +1,166 @@
+#!/usr/bin/env python
+#
+# STATEMENT OF CHANGES: This file is derived from sources licensed under the Apache-2.0 terms,
+# and uses the following portion of the original code:
+# https://github.com/nipreps/fmriprep/blob/fe7c9ff8731635d7f25749f2afd99eb77d26305d/scripts/
+# fetch_templates.py#L10-L136
+#
+# ORIGINAL WORK'S ATTRIBUTION NOTICE:
+#
+#     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/
+"""
+Standalone script to facilitate caching of required TemplateFlow templates.
+
+To download and view how to use this script, run the following commands inside a terminal:
+1. wget https://raw.githubusercontent.com/pennlinc/qsirecon_build/main/scripts/fetch_templates.py
+2. python fetch_templates.py -h
+"""
+
+import argparse
+import os
+
+
+def fetch_MNI2009():
+    """
+    Expected templates:
+
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_from-MNI152NLin6Asym_mode-image_xfm.h5
+    """
+    template = "MNI152NLin2009cAsym"
+
+    tf.get(template, resolution=1, desc=None, suffix="T1w")
+    tf.get(template, resolution=1, desc="carpet", suffix="dseg")
+    tf.get(template, resolution=2, desc="brain", suffix="mask")
+    tf.get(template, mode="image", suffix="xfm", extension=".h5", **{"from": "MNI152NLin6Asym"})
+
+
+def fetch_MNI6():
+    """
+    Expected templates:
+
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_T1w.nii.gz
+    tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_from-MNI152NLin2009cAsym_mode-image_xfm.h5
+    """
+    template = "MNI152NLin6Asym"
+
+    tf.get(template, resolution=1, desc=None, suffix="T1w")
+    tf.get(template, mode="image", suffix="xfm", extension=".h5", **{"from": "MNI152NLin2009cAsym"})
+
+
+def fetch_MNIInfant():
+    """
+    Expected templates:
+
+    tpl-MNIInfant/tpl-MNIInfant_cohort-1_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-2_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-3_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-4_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-5_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-6_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-7_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-8_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-9_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-10_res-01_T1w.nii.gz
+    tpl-MNIInfant/tpl-MNIInfant_cohort-11_res-01_T1w.nii.gz
+    """
+    template = "MNIInfant"
+
+    tf.get(template, resolution=1, desc=None, suffix="T1w")
+
+
+def fetch_fsaverage():
+    """
+    Expected templates:
+
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_sphere.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-L_den-41k_sphere.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_sphere.surf.gii
+    tpl-fsaverage/tpl-fsaverage_hemi-R_den-41k_sphere.surf.gii
+    """
+    template = "fsaverage"
+
+    tf.get(template, density="164k", desc=None, suffix="sphere")
+    tf.get(template, density="41k", desc=None, suffix="sphere")
+
+
+def fetch_fsLR():
+    """
+    Expected templates:
+
+    tpl-fsLR/tpl-fsLR_hemi-L_den-32k_desc-vaavg_midthickness.shape.gii
+    tpl-fsLR/tpl-fsLR_hemi-L_den-32k_midthickness.shape.gii
+    tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii
+    tpl-fsLR/tpl-fsLR_hemi-R_den-32k_desc-vaavg_midthickness.shape.gii
+    tpl-fsLR/tpl-fsLR_hemi-R_den-32k_midthickness.shape.gii
+    tpl-fsLR/tpl-fsLR_hemi-R_den-32k_sphere.surf.gii
+    """
+    tf.get("fsLR", density="32k", desc=None, suffix="midthickness")
+    tf.get("fsLR", density="32k", desc="vaavg", suffix="midthickness")
+    tf.get("fsLR", space=None, density="32k", suffix="sphere")
+
+
+def fetch_dhcpAsym():
+    """
+    Expected templates:
+
+    tpl-dhcpAsym/tpl-dhcpAsym_cohort-42_hemi-L_den-32k_sphere.surf.gii
+    tpl-dhcpAsym/tpl-dhcpAsym_cohort-42_hemi-R_den-32k_sphere.surf.gii
+    tpl-dhcpAsym/tpl-dhcpAsym_cohort-42_space-fsaverage_hemi-L_den-41k_desc-reg_sphere.surf.gii
+    tpl-dhcpAsym/tpl-dhcpAsym_cohort-42_space-fsaverage_hemi-R_den-41k_desc-reg_sphere.surf.gii
+    """
+    template = "dhcpAsym"
+
+    tf.get(template, cohort="42", space="fsaverage", density="41k", desc="reg", suffix="sphere")
+    tf.get(template, cohort="42", space=None, density="32k", desc=None, suffix="sphere")
+
+
+def fetch_all():
+    fetch_MNI2009()
+    fetch_MNI6()
+    fetch_MNIInfant()
+    fetch_fsaverage()
+    fetch_fsLR()
+    fetch_dhcpAsym()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Helper script for pre-caching required templates to run fMRIPrep",
+    )
+    parser.add_argument(
+        "--tf-dir",
+        type=os.path.abspath,
+        help=(
+            "Directory to save templates in. "
+            "If not provided, templates will be saved to `${HOME}/.cache/templateflow`."
+        ),
+    )
+    opts = parser.parse_args()
+
+    # set envvar (if necessary) prior to templateflow import
+    if opts.tf_dir is not None:
+        os.environ["TEMPLATEFLOW_HOME"] = opts.tf_dir
+
+    import templateflow.api as tf
+
+    fetch_all()