Fix mrd_phantom named pipe bug (#18)

ismrmrd · Oct 23, 2024 · 134b338 · 134b338
1 parent 466bd9a
commit 134b338
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Showing 14 changed files with 46 additions and 49 deletions.
diff --git a/.github/actions/configure-mrd-build-environment/action.yml b/.github/actions/configure-mrd-build-environment/action.yml
@@ -2,8 +2,8 @@ name: Configure MRD Build Environment
 description: Configures the conda development environment
 
 # The following inputs are currently expected environment variables:
-# YARDL_VERSION, e.g. 0.5.0
-# CONDA_CACHE_NUMBER, e.g. 0
+# YARDL_VERSION
+# CONDA_CACHE_NUMBER
 
 runs:
   using: composite
@@ -20,7 +20,6 @@ runs:
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v3
       with:
-        miniforge-variant: Miniforge3
         miniforge-version: latest
         # Do not specify environment file - see Cache step below
         activate-environment: mrd

diff --git a/.github/workflows/mrd_conda.yml b/.github/workflows/mrd_conda.yml
@@ -23,20 +23,11 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Download MacOSX SDK
-        if: startsWith(matrix.os, 'macos')
-        run: |
-          curl -o MacOSX10.13.sdk.tar.xz -L https://github.com/phracker/MacOSX-SDKs/releases/download/11.3/MacOSX10.13.sdk.tar.xz && \
-          tar xf MacOSX10.13.sdk.tar.xz && \
-          sudo mv -v MacOSX10.13.sdk /opt/ && \
-          ls /opt/
-
       - name: Set up Miniconda
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-activate-base: true
           activate-environment: ""
-          miniforge-variant: Miniforge3
           miniforge-version: latest
 
       - name: Set up just command runner

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.0.0
+2.0.1
diff --git a/cpp/conda/build.sh b/cpp/conda/build.sh
@@ -5,15 +5,13 @@ set -euo pipefail
 mkdir -p build-conda
 cd build-conda
 
-if [[ $(uname) == Darwin ]]; then
-    export CFLAGS="${CFLAGS:-} -isysroot ${CONDA_BUILD_SYSROOT} -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}"
-    export CXXFLAGS="${CXXFLAGS:-} -isysroot ${CONDA_BUILD_SYSROOT} -mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}"
-#     export SDKROOT="${CONDA_BUILD_SYSROOT}"
-fi
-
 echo 'Building mrd conda package using CMake...'
 
-cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-      ../
+cmake -GNinja \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_CXX_STANDARD=17 \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT} \
+    ../
 
 ninja install
diff --git a/cpp/conda/conda_build_config.yaml b/cpp/conda/conda_build_config.yaml
@@ -1,11 +1,9 @@
 c_compiler_version:
   - 11.2.0                      # [linux]
-  - 14                          # [osx]
+  - 14.0.6                      # [osx]
 cxx_compiler_version:
   - 11.2.0                      # [linux]
-  - 14                          # [osx]
+  - 14.0.6                      # [osx]
 
 MACOSX_DEPLOYMENT_TARGET:       # [osx]
   - 10.13                       # [osx]
-CONDA_BUILD_SYSROOT:            # [osx]
-  - /opt/MacOSX10.13.sdk        # [osx]
diff --git a/cpp/conda/meta.yaml b/cpp/conda/meta.yaml
@@ -13,7 +13,6 @@ build:
 
 requirements:
   build:
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - cmake
     - ninja

diff --git a/cpp/mrd-tools/ismrmrd_to_mrd.cc b/cpp/mrd-tools/ismrmrd_to_mrd.cc
@@ -991,8 +991,8 @@ mrd::Image<T> convert(ISMRMRD::Image<T>& im) {
 
 void print_usage(std::string program_name) {
   std::cerr << "Usage: " << program_name << std::endl;
-  std::cerr << "  -i|--input-file   <input ISMRMRD stream> (default: stdin)" << std::endl;
-  std::cerr << "  -o|--output-file  <output MRD stream> (default: stdout)" << std::endl;
+  std::cerr << "  -i|--input   <input ISMRMRD stream> (default: stdin)" << std::endl;
+  std::cerr << "  -o|--output  <output MRD stream> (default: stdout)" << std::endl;
   std::cerr << "  -h|--help" << std::endl;
 }
 
@@ -1006,7 +1006,7 @@ int main(int argc, char** argv) {
     if (*current_arg == "--help" || *current_arg == "-h") {
       print_usage(args[0]);
       return 0;
-    } else if (*current_arg == "--input-file" || *current_arg == "-i") {
+    } else if (*current_arg == "--input" || *current_arg == "-i") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing input file" << std::endl;
@@ -1015,7 +1015,7 @@ int main(int argc, char** argv) {
       }
       input_path = *current_arg;
       current_arg++;
-    } else if (*current_arg == "--output-file" || *current_arg == "-o") {
+    } else if (*current_arg == "--output" || *current_arg == "-o") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing output file" << std::endl;

diff --git a/cpp/mrd-tools/mrd_image_stream_to_png.cc b/cpp/mrd-tools/mrd_image_stream_to_png.cc
@@ -5,7 +5,7 @@
 
 void print_usage(std::string program_name) {
   std::cerr << "Usage: " << program_name << std::endl;
-  std::cerr << "  -i|--input-file     <input MRD stream> (default: stdin)" << std::endl;
+  std::cerr << "  -i|--input          <input MRD stream> (default: stdin)" << std::endl;
   std::cerr << "  -o|--output-prefix  <output file prefix>   (default: image_)" << std::endl;
   std::cerr << "  -h|--help" << std::endl;
 }
@@ -21,7 +21,7 @@ int main(int argc, char** argv) {
     if (*current_arg == "--help" || *current_arg == "-h") {
       print_usage(args[0]);
       return 0;
-    } else if (*current_arg == "--input-file" || *current_arg == "-i") {
+    } else if (*current_arg == "--input" || *current_arg == "-i") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing input file" << std::endl;

diff --git a/cpp/mrd-tools/mrd_phantom.cc b/cpp/mrd-tools/mrd_phantom.cc
@@ -46,10 +46,10 @@ mrd::ImageData<std::complex<float>> generate_coil_kspace(size_t matrix, size_t n
 
 void print_usage(std::string program_name) {
   std::cerr << "Usage: " << program_name << std::endl;
-  std::cerr << "  -o|--output-file <output MRD stream> (default: stdout)" << std::endl;
-  std::cerr << "  -c|--coils       <number of coils>" << std::endl;
-  std::cerr << "  -m|--matrix      <matrix size>" << std::endl;
-  std::cerr << "  -r|--repetitions <number of repetitions>" << std::endl;
+  std::cerr << "  -o|--output       <output MRD stream> (default: stdout)" << std::endl;
+  std::cerr << "  -c|--coils        <number of coils>" << std::endl;
+  std::cerr << "  -m|--matrix       <matrix size>" << std::endl;
+  std::cerr << "  -r|--repetitions  <number of repetitions>" << std::endl;
   std::cerr << "  -s|--oversampling <oversampling>" << std::endl;
   std::cerr << "  -h|--help" << std::endl;
 }
@@ -68,7 +68,7 @@ int main(int argc, char** argv) {
     if (*current_arg == "--help" || *current_arg == "-h") {
       print_usage(args[0]);
       return 0;
-    } else if (*current_arg == "--output-file" || *current_arg == "-o") {
+    } else if (*current_arg == "--output" || *current_arg == "-o") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing output file" << std::endl;
@@ -134,7 +134,6 @@ int main(int argc, char** argv) {
   if (filename.empty()) {
     w = std::make_unique<mrd::binary::MrdWriter>(std::cout);
   } else {
-    std::remove(filename.c_str());
     w = std::make_unique<mrd::binary::MrdWriter>(filename);
   }
 

diff --git a/cpp/mrd-tools/mrd_stream_recon.cc b/cpp/mrd-tools/mrd_stream_recon.cc
@@ -33,8 +33,8 @@ void remove_oversampling(mrd::Acquisition& acq, const mrd::EncodingType& enc) {
 
 void print_usage(std::string program_name) {
   std::cerr << "Usage: " << program_name << std::endl;
-  std::cerr << "  -i|--input-file   <input MRD stream> (default: stdin)" << std::endl;
-  std::cerr << "  -o|--output-file  <output MRD stream> (default: stdout)" << std::endl;
+  std::cerr << "  -i|--input   <input MRD stream> (default: stdin)" << std::endl;
+  std::cerr << "  -o|--output  <output MRD stream> (default: stdout)" << std::endl;
   std::cerr << "  -h|--help" << std::endl;
 }
 
@@ -48,7 +48,7 @@ int main(int argc, char** argv) {
     if (*current_arg == "--help" || *current_arg == "-h") {
       print_usage(args[0]);
       return 0;
-    } else if (*current_arg == "--input-file" || *current_arg == "-i") {
+    } else if (*current_arg == "--input" || *current_arg == "-i") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing input file" << std::endl;
@@ -57,7 +57,7 @@ int main(int argc, char** argv) {
       }
       input_path = *current_arg;
       current_arg++;
-    } else if (*current_arg == "--output-file" || *current_arg == "-o") {
+    } else if (*current_arg == "--output" || *current_arg == "-o") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing output file" << std::endl;

diff --git a/cpp/mrd-tools/mrd_to_ismrmrd.cc b/cpp/mrd-tools/mrd_to_ismrmrd.cc
@@ -1048,8 +1048,8 @@ ISMRMRD::Image<T> convert(mrd::Image<T>& image) {
 
 void print_usage(std::string program_name) {
   std::cerr << "Usage: " << program_name << std::endl;
-  std::cerr << "  -i|--input-file   <input MRD stream> (default: stdin)" << std::endl;
-  std::cerr << "  -o|--output-file  <output ISMRMRD stream> (default: stdout)" << std::endl;
+  std::cerr << "  -i|--input   <input MRD stream> (default: stdin)" << std::endl;
+  std::cerr << "  -o|--output  <output ISMRMRD stream> (default: stdout)" << std::endl;
   std::cerr << "  -h|--help" << std::endl;
 }
 
@@ -1063,7 +1063,7 @@ int main(int argc, char** argv) {
     if (*current_arg == "--help" || *current_arg == "-h") {
       print_usage(args[0]);
       return 0;
-    } else if (*current_arg == "--input-file" || *current_arg == "-i") {
+    } else if (*current_arg == "--input" || *current_arg == "-i") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing input file" << std::endl;
@@ -1072,7 +1072,7 @@ int main(int argc, char** argv) {
       }
       input_path = *current_arg;
       current_arg++;
-    } else if (*current_arg == "--output-file" || *current_arg == "-o") {
+    } else if (*current_arg == "--output" || *current_arg == "-o") {
       current_arg++;
       if (current_arg == args.end()) {
         std::cerr << "Missing output file" << std::endl;

diff --git a/test/test.sh b/test/test.sh
@@ -43,5 +43,18 @@ cat py2py_images.bin    | python -m mrd.tools.export_png_images -o py2py
 ifmatlab && cat mat2mat_images.bin  | ./matlab_export_png_images.sh mat2mat
 
 
+echo Testing again using named pipes
+test -e recon_in.pipe || mkfifo recon_in.pipe
+test -e recon_out.pipe || mkfifo recon_out.pipe
+
+mrd_phantom --output recon_in.pipe &
+mrd_stream_recon --input recon_in.pipe --output recon_out.pipe &
+mrd_image_stream_to_png --input recon_out.pipe
+
+python -m mrd.tools.phantom --output recon_in.pipe &
+python -m mrd.tools.stream_recon --input recon_in.pipe --output recon_out.pipe &
+python -m mrd.tools.export_png_images --input recon_out.pipe
+
+
 echo Cleaning up
-rm -f ./*.bin ./*.png
+rm -f ./*.bin ./*.png ./*.pipe
diff --git a/utils/conda/package.sh b/utils/conda/package.sh
@@ -22,4 +22,4 @@ channels=(
 channel_directives=$(printf -- "-c %s " "${channels[@]}")
 
 mkdir -p "$output_path"
-bash -c "conda mambabuild --no-anaconda-upload --output-folder $output_path $channel_directives $(pwd)"
+bash -c "conda build --no-anaconda-upload --output-folder $output_path $channel_directives $(pwd)"
diff --git a/utils/conda/setup-conda-build.sh b/utils/conda/setup-conda-build.sh
@@ -3,5 +3,5 @@
 set -e
 
 # conda deactivate
-mamba install -y -n base conda-build conda-verify anaconda-client boa
+conda install -y -n base conda-build anaconda-client
 conda activate base