Merge pull request #36 from KrisThielemans/minor_fixes

Minor fixes

.devcontainer/Dockerfile

@@ -48,7 +48,7 @@ RUN script=$(curl -fsSL "https://raw.githubusercontent.com/microsoft/vscode-dev-
 ENTRYPOINT [ "/usr/local/share/docker-init.sh" ]
 CMD [ "sleep", "infinity" ]
 
-ARG MAMBAFORGE_VERSION=22.9.0-2
+ARG MAMBAFORGE_VERSION=24.9.0-0
 
 # Based on https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile
 RUN wget --no-hsts --quiet https://github.com/conda-forge/miniforge/releases/download/${MAMBAFORGE_VERSION}/Mambaforge-${MAMBAFORGE_VERSION}-Linux-$(uname -m).sh -O /tmp/miniforge.sh \
@@ -91,7 +91,7 @@ RUN mkdir -p /home/vscode/.local/share/CMakeTools \
     && chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json
 
 # Install the yardl tool
-ARG YARDL_VERSION=0.3.2
+ARG YARDL_VERSION=0.6.2
 RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_VERSION}/yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
     && tar -xzf "yardl_${YARDL_VERSION}_linux_x86_64.tar.gz" \
     && mv yardl "/opt/conda/envs/${CONDA_ENVIRONMENT_NAME}/bin/" \

environment.yml

@@ -15,6 +15,7 @@ dependencies:
   - nlohmann_json>=3.11.2
   - numpy>=1.24.3
   - python>=3.11.3
+  - matplotlib
   - shellcheck>=0.8.0
   - xtensor-fftw>=0.2.5
   - xtensor>=0.24.2

model/ScannerInformation.yml

@@ -42,7 +42,8 @@ ScannerInformation: !record
     tofBinEdges: !array
       items: float
       dimensions: 1
-    # TOF resolution in mm
+    # TOF resolution (as FWHM) in mm
+    # Scanner coincidence timing resolution (CTR) without tof-binning
     tofResolution: float
 
     # Edge information for energy windows in keV (given as from first to last edge, so there is one more edge than the number of bins)

python/petsird_analysis.py

@@ -11,7 +11,8 @@
 if __name__ == "__main__":
     with petsird.BinaryPETSIRDReader(sys.stdin.buffer) as reader:
         header = reader.read_header()
-        print(f"Subject ID: {header.exam.subject.id}")
+        if header.exam is not None:
+            print(f"Subject ID: {header.exam.subject.id}")
         print(f"Scanner name: { header.scanner.model_name}")
         print(
             f"Types of modules: {len(header.scanner.scanner_geometry.replicated_modules)}"