MAINT: Address various pain points (#159)

* MAINT: Preload some MNIInfant templates

* MAINT: Update git-annex version

* MAINT: Ensure required data is packaged

* MAINT: Prefetch MNIInfant brain masks

* FIX: Avoid requiring service when checking wrapper version

Author: mgxd

Dockerfile

@@ -38,7 +38,7 @@ RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
                     connectome-workbench=1.5.0-1~nd20.04+1 \
-                    git-annex-standalone=8.20210903-1~ndall+1 && \
+                    git-annex-standalone=8.20211123+git12-g02e3756bd-1~ndall+1 && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Installing ANTs 2.3.4 (NeuroDocker build)

nibabies/data/flirtsch/bbr.sch

@@ -0,0 +1,43 @@
+# 1mm scale
+setscale 1 force
+setoption costfunction bbr
+setoption optimisationtype brent
+setoption tolerance 0.0005 0.0005 0.0005 0.02 0.02 0.02 0.002 0.002 0.002 0.001 0.001 0.001
+#setoption tolerance 0.005 0.005 0.005 0.2 0.2 0.2 0.02 0.02 0.02 0.01 0.01 0.01
+setoption boundguess 1
+setoption bbrstep 200
+clear UA
+clear UU
+clear UV
+clear U
+setrowqsform UU
+setrow UU 1 0 0 0  0 1 0 0  0 0 1 0  0 0 0 1
+measurecost 6 UU:1-2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+gridmeasurecost 6 UU:1-2  -0.07 0.07 0.07  -0.07 0.07 0.07  -0.07 0.07 0.07  -4.0 4.0 4.0  -4.0 4.0 4.0  -4.0 4.0 4.0  0.0 0.0 0.0  abs 8
+sort U
+copy U UA
+clear U
+optimise 6 UA:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype powell
+optimise 6 U:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype brent
+optimise 6 U:2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4
+sort U
+setoption tolerance 0.0002 0.0002 0.0002 0.02 0.02 0.02 0.002 0.002 0.002 0.001 0.001 0.001
+setoption bbrstep 2
+clear UU
+copy U UU
+clear U
+gridmeasurecost 6 UU:1  -0.0017 0.0017 0.0017  -0.0017 0.0017 0.0017  -0.0017 0.0017 0.0017  -0.1 0.1 0.1  -0.1 0.1 0.1  -0.1 0.1 0.1  0.0 0.0 0.0  abs 8
+sort U
+clear UB
+copy U UB
+clear U
+setoption optimisationtype brent
+optimise 6 UB:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype powell
+optimise 12 U:1  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 8
+setoption optimisationtype brent
+optimise 12 U:2  0.0   0.0   0.0   0.0   0.0   0.0   0.0  rel 4
+sort U
+print U:1

nibabies/data/itkIdentityTransform.txt

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: 1 0 0 0 1 0 0 0 1 0 0 0
+FixedParameters: 0 0 0

scripts/fetch_templates.py

@@ -70,11 +70,27 @@ def fetch_fsLR():
     tf.get('fsLR', density='32k')
 
 
+def fetch_MNIInfant(cohort=1):
+    """
+    Expected templates:
+
+    tpl-MNIInfant/cohort-1/tpl-MNIInfant_cohort-1_res-1_T1w.nii.gz
+    tpl-MNIInfant/cohort-1/tpl-MNIInfant_cohort-1_res-2_T1w.nii.gz
+    tpl-MNIInfant/cohort-1/tpl-MNIInfant_cohort-1_res-1_desc-brain_mask.nii.gz
+    tpl-MNIInfant/cohort-1/tpl-MNIInfant_cohort-1_res-2_desc-brain_mask.nii.gz
+    """
+    template = 'MNIInfant'
+
+    tf.get(template, cohort=cohort, suffix="T1w")
+    tf.get(template, cohort=cohort, suffix="mask")
+
+
 def main():
     fetch_MNI6()
     fetch_UNCInfant()
     fetch_fsaverage()
     fetch_fsLR()
+    fetch_MNIInfant()
 
 
 if __name__ == "__main__":

setup.cfg

@@ -44,6 +44,15 @@ console_scripts =
 [options.package_data]
 nibabies =
     data/*.json
+    data/*.nii.gz
+    data/*.mat
+    data/*.txt
+    data/boilerplate.bib
+    data/itkIdentityTransform.txt
+    data/flirtsch/bbr.sch
+    data/reports-spec.yml
+    data/tests/config.toml
+    VERSION
 
 [options.packages.find]
 exclude =

wrapper/nibabies_wrapper.py

@@ -360,7 +360,7 @@ def _is_file(path, parser):
     IsFile = partial(_is_file, parser=parser)
 
     # require users to specify container service
-    parser.add_argument("service", choices=("docker", "singularity"))
+    parser.add_argument("service", nargs="?", choices=("docker", "singularity"))
     # Standard NiBabies arguments
     parser.add_argument("bids_dir", nargs="?", type=os.path.abspath, default="")
     parser.add_argument("output_dir", nargs="?", type=os.path.abspath, default="")
@@ -525,9 +525,14 @@ def main():
     # Capture additional arguments to pass inside container
     opts, unknown_args = parser.parse_known_args()
 
+    if opts.version:
+        print("nibabies wrapper {!s}".format(__version__))
+        return
+
     # Set help if no directories set
-    if (opts.bids_dir, opts.output_dir, opts.version) == ("", "", False):
-        opts.help = True
+    if not all((opts.service, opts.bids_dir, opts.output_dir)):
+        parser.print_help()
+        return 1
 
     container = ContainerManager(opts.service, image=opts.image)
     check = container.check_install()