24 enh test and push docker container for petdeface to dockerhub

.gitignore

@@ -35,3 +35,4 @@ integration_testing.sh
 petdeface/Dockerfile
 petdeface/README.md
 petdeface/pyproject.toml
+freesurfer_binaries/*

Dockerfile

@@ -24,15 +24,32 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libglib2.0-0 \
     libxft2 \
     libxrender1 \
-    libxt6
+    libxt6 \
+    ffmpeg \
+    libsm6
 
 # Install Freesurfer
 ENV FREESURFER_HOME="/opt/freesurfer" \
     PATH="/opt/freesurfer/bin:$PATH" \
     FREESURFER_VERSION=7.4.1
 
-RUN curl -L --progress-bar https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}/freesurfer-linux-centos7_x86_64-${FREESURFER_VERSION}.tar.gz | tar xzC /opt && \
-    echo ". /opt/freesurfer/SetUpFreeSurfer.sh" >> ~/.bashrc
+# copy over local freesurfer binaries
+RUN mkdir /freesurfer_binaries
+COPY freesurfer_binaries/freesurfer-linux-centos7_x86_64-${FREESURFER_VERSION}.tar.gz /freesurfer_binaries/
+
+ARG USE_LOCAL_FREESURFER
+RUN echo USE_LOCAL_FREESURFER=${USE_LOCAL_FREESURFER}
+
+RUN if [ "$USE_LOCAL_FREESURFER" = "True" ]; then \
+      echo "Using local freesurfer binaries."; \
+      tar xzC /opt -f /freesurfer_binaries/freesurfer-linux-centos7_x86_64-${FREESURFER_VERSION}.tar.gz && \
+      echo ". /opt/freesurfer/SetUpFreeSurfer.sh" >> ~/.bashrc; \
+    fi && \
+    if [ "$USE_LOCAL_FREESURFER" = "False" ]; then \
+      echo "Using freesurfer binaries from surfer.nmr.mgh.harvard.edu."; \
+      curl -L --progress-bar https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}/freesurfer-linux-centos7_x86_64-${FREESURFER_VERSION}.tar.gz | tar xzC /opt && \
+      echo ". /opt/freesurfer/SetUpFreeSurfer.sh" >> ~/.bashrc; \
+    fi
 
 # set bash as default terminal
 SHELL ["/bin/bash", "-ce"]

Makefile

@@ -17,3 +17,15 @@ testall: testlayouts
 # install python dependencies
 pythondeps:
 	pip install --upgrade pip && pip install  -e .
+
+# create petdafec docker image with tag (petdeface:X.X.X) from toml file by using cat and grep to 
+# extract the project name from the pyproject.toml file
+
+
+USE_LOCAL_FREESURFER ?= False
+dockerbuild:
+	docker build --build-arg="USE_LOCAL_FREESURFER=$(USE_LOCAL_FREESURFER)" -t $(shell cat pyproject.toml | grep name | cut -d '"' -f 2):$(shell cat pyproject.toml | grep version | head -n 1 | cut -d '"' -f 2) .
+	docker build --build-arg="USE_LOCAL_FREESURFER=$(USE_LOCAL_FREESURFER)" -t $(shell cat pyproject.toml | grep name | cut -d '"' -f 2):latest .
+
+dockerbuildlatest:
+	docker build --build-arg="USE_LOCAL_FREESURFER=$(USE_LOCAL_FREESURFER)" -t $(shell cat pyproject.toml | grep name | cut -d '"' -f 2):latest .

freesurfer_binaries/freesurfer_binaries_readme.txt

@@ -0,0 +1,6 @@
+This folder exists as a place to keep copies of freesurfer binaries downloaded from:
+
+https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${Version}/freesurfer-linux-centos7_x86_64-${Version}.tar.gz
+
+This folder solely exists to speed up docker builds! All content in this folder barring this text file should
+be git ignored!!!

petdeface/petdeface.py

@@ -173,7 +173,7 @@ def deface(args: Union[dict, argparse.Namespace]) -> None:
         )
 
     # clean up and create derivatives directories
-    if args.output_dir is None:
+    if args.output_dir == "None" or args.output_dir is None:
         output_dir = os.path.join(args.bids_dir, "derivatives", "petdeface")
     else:
         output_dir = args.output_dir
@@ -276,8 +276,15 @@ def init_single_subject_wf(
         workflow_name = f"t1w_{anat_string}_wf"
 
         t1w_wf = Workflow(name=workflow_name)
+
+        # create preview pics
+        if determine_in_docker():
+            preview_pics = False
+        else:
+            preview_pics = True
+
         deface_t1w = Node(
-            Mideface(in_file=pathlib.Path(t1w_file), pics=True, odir=".", code=f"{anat_string}"),
+            Mideface(in_file=pathlib.Path(t1w_file), pics=preview_pics, odir=".", code=f"{anat_string}"),
             name=f"deface_t1w_{anat_string}",
         )
         t1w_wf.connect(
@@ -732,6 +739,10 @@ def main():  # noqa: max-complexity: 12
 
         input_mount_point = str(args.input_dir)
         output_mount_point = str(args.output_dir)
+
+        if output_mount_point == "None" or output_mount_point is None:
+            output_mount_point = str(args.input_dir / "derivatives" / "petdeface")
+
         args.input_dir = pathlib.Path("/input")
         args.output_dir = pathlib.Path("/output")
         print(

pyproject.toml

@@ -18,7 +18,7 @@ bids_version = "1.8.0"
 python = ">=3.10, <4.0"
 niworkflows = { git = "https://github.com/nipreps/niworkflows.git" }
 setuptools = "^68.1.2"
-petutils = "^0.0.0"
+petutils = "^0.0.1"
 
 [tool.poetry.group.dev.dependencies]
 black = "^23.7.0"