Pre-cache MNI2009 and MNIInfant templates (#5)

* Add fetch_templates script.

* Use the new script.

* Remove unused template script.

* Don't install TemplateFlow twice.

Author: tsalo

Dockerfile

@@ -204,23 +204,26 @@ ENV \
 
 WORKDIR /root/
 
-# Precaching atlases + AtlasPack
+# Precaching templates
+COPY scripts/fetch_templates.py fetch_templates.py
+RUN ${CONDA_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 {} +
+
+# Precaching AtlasPack atlases
 RUN mkdir /AtlasPack
 COPY --from=atlaspack /AtlasPack/tpl-fsLR_*.dlabel.nii /AtlasPack/
 COPY --from=atlaspack /AtlasPack/tpl-MNI152NLin6Asym_*.nii.gz /AtlasPack/
 COPY --from=atlaspack /AtlasPack/tpl-MNI152NLin2009cAsym_*.nii.gz /AtlasPack/
 COPY --from=atlaspack /AtlasPack/atlas-4S*.tsv /AtlasPack/
 COPY --from=atlaspack /AtlasPack/*.json /AtlasPack/
-ADD docker/scripts/get_templates.sh get_templates.sh
-RUN mkdir $CRN_SHARED_DATA && \
-    /root/get_templates.sh && \
-    chmod -R a+rX $CRN_SHARED_DATA
 
 # Make it ok for singularity on CentOS
 RUN strip --remove-section=.note.ABI-tag /opt/qt512/lib/libQt5Core.so.5.12.8 \
     && ldconfig
 
-# Download the atlases
+# Download the built-in atlases
 ENV QSIRECON_ATLAS /atlas/qsirecon_atlases
 RUN bash -c \
     'mkdir /atlas \

docker/scripts/get_templates.sh

@@ -0,0 +1,100 @@
+#!/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-02_T1w.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz
+    """
+    template = "MNI152NLin2009cAsym"
+
+    tf.get(template, resolution=(1, 2), desc=None, suffix="T1w")
+    tf.get(template, resolution=(1, 2), desc="brain", suffix="mask")
+    tf.get(template, resolution=1, atlas=None, desc="carpet", suffix="dseg")
+    tf.get(template, resolution=1, label="brain", suffix="probseg")
+
+
+def fetch_MNIInfant(cohort=2):
+    """
+    Expected templates:
+
+    tpl-MNIInfant/cohort-2/tpl-MNIInfant_cohort-2_res-1_T1w.nii.gz
+    tpl-MNIInfant/cohort-2/tpl-MNIInfant_cohort-2_res-1_T2w.nii.gz
+    tpl-MNIInfant/cohort-2/tpl-MNIInfant_cohort-2_res-1_desc-brain_mask.nii.gz
+    tpl-MNIInfant/cohort-2/tpl-MNIInfant_cohort-2_res-2_T1w.nii.gz
+    tpl-MNIInfant/cohort-2/tpl-MNIInfant_cohort-2_res-2_T1w.nii.gz
+    tpl-MNIInfant/cohort-2/tpl-MNIInfant_cohort-2_res-2_desc-brain_mask.nii.gz
+    """
+    template = "MNIInfant"
+
+    tf.get(template, cohort=cohort, suffix="T1w")
+    tf.get(template, cohort=cohort, suffix="T2w")
+    tf.get(template, cohort=cohort, desc="brain", suffix="mask")
+
+
+def fetch_all():
+    fetch_MNI2009()
+    fetch_MNIInfant()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Helper script for pre-caching required templates to run QSIRecon",
+    )
+    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()