Merge pull request #32 from KrisThielemans/prd_to_petsird

renamed prd to petsird

.devcontainer/Dockerfile

@@ -29,7 +29,7 @@ ARG USERNAME="vscode"
 ARG USER_UID=1000
 ARG USER_GID=$USER_UID
 ARG CONDA_GID=900
-ARG CONDA_ENVIRONMENT_NAME=prd
+ARG CONDA_ENVIRONMENT_NAME=petsird
 ARG VSCODE_DEV_CONTAINERS_SCRIPT_LIBRARY_VERSION=v0.229.0
 
 RUN apt-get update && apt-get install -y \
@@ -87,7 +87,7 @@ ENV CMAKE_GENERATOR=Ninja
 
 # Create a kits file for the VSCode CMake Tools extension, so you are not prompted for which kit to select whenever you open VSCode
 RUN mkdir -p /home/vscode/.local/share/CMakeTools \
-    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/prd/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
+    && echo '[{"name":"GCC-10","compilers":{"C":"/opt/conda/envs/petsird/bin/x86_64-conda_cos6-linux-gnu-gcc","CXX":"/opt/conda/envs/petsird/bin/x86_64-conda_cos6-linux-gnu-g++"}}]' > /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json \
     && chown vscode:conda /home/vscode/.local/share/CMakeTools/cmake-tools-kits.json
 
 # Install the yardl tool

.devcontainer/devcontainer.bashrc

@@ -2,7 +2,7 @@
 # shellcheck source=/dev/null
 
 source /opt/conda/etc/profile.d/conda.sh
-conda activate prd
+conda activate petsird
 source <(yardl completion bash)
 
 if [[ "${BASH_ENV:-}" == "$(readlink -f "${BASH_SOURCE[0]:-}")" ]]; then

.devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
 // https://github.com/microsoft/vscode-dev-containerdevcotns/tree/v0.238.0/containers/go
 {
-  "name": "prd",
+  "name": "petsird",
   "build": {
     "dockerfile": "Dockerfile",
     "context": ".."
@@ -41,7 +41,7 @@
         "cmake.buildDirectory": "${workspaceFolder}/cpp/build",
         "cmake.configureOnOpen": false,
 
-        "python.defaultInterpreterPath": "/opt/conda/envs/prd/bin/python",
+        "python.defaultInterpreterPath": "/opt/conda/envs/petsird/bin/python",
         "python.analysis.typeCheckingMode": "strict",
         "python.analysis.diagnosticMode": "workspace",
         "python.analysis.diagnosticSeverityOverrides": {
@@ -81,7 +81,7 @@
           "gitlens.showWhatsNewAfterUpgrades": false
         },
 
-        "gcovViewer.gcovBinary": "/opt/conda/envs/prd/bin/x86_64-conda-linux-gnu-gcov",
+        "gcovViewer.gcovBinary": "/opt/conda/envs/petsird/bin/x86_64-conda-linux-gnu-gcov",
         "gcovViewer.buildDirectories": ["${workspaceFolder}/cpp/build"],
 
         "search.useIgnoreFiles": false,

.github/workflows/ci.yml

@@ -49,12 +49,12 @@ jobs:
       - name: Python
         run: |
           cd python
-          python prd_generator.py | python prd_analysis.py
+          python petsird_generator.py | python petsird_analysis.py
 
       - name: Cpp
         run: |
           cd cpp && mkdir -p build && cd build
           cmake -G Ninja -S .. -DHDF5_ROOT="$CONDA_PREFIX"
           ninja
-          ./prd_generator test.h5
-          ./prd_analysis test.h5
+          ./petsird_generator test.h5
+          ./petsird_analysis test.h5

.gitignore

@@ -3,7 +3,7 @@
 cpp/generated/
 cpp/build/
 
-python/prd/
+python/petsird/
 **/__pycache__/
 
 # Common editor backups

cpp/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12.0) # older would work, but could give warnings on policy CMP0074
-project(prd VERSION 0.1.1)
+project(petsird VERSION 0.2.0)
 
 set(CMAKE_CXX_STANDARD 17)
 
@@ -9,10 +9,10 @@ else()
   add_compile_options(-Wall -Wextra -pedantic)
 endif()
 
-add_executable(prd_generator prd_generator.cpp)
-target_link_libraries(prd_generator prd_generated)
+add_executable(petsird_generator petsird_generator.cpp)
+target_link_libraries(petsird_generator petsird_generated)
 
-add_executable(prd_analysis prd_analysis.cpp)
-target_link_libraries(prd_analysis prd_generated)
+add_executable(petsird_analysis petsird_analysis.cpp)
+target_link_libraries(petsird_analysis petsird_generated)
 
 add_subdirectory(generated)

cpp/README.md

@@ -13,7 +13,7 @@ The C++ code shows writing to and reading from an HDF5 file
    ```
    If you did not use `conda` to install HDF5, do not add the `-DHDF5_ROOT=$CONDA_PREFIX` part of the `cmake` line.
 
-2. Run the generator: `./prd_generator test.h5`
-3. Run the analyzer: `./prd_analysis test.h5`
+2. Run the generator: `./petsird_generator test.h5`
+3. Run the analyzer: `./petsird_analysis test.h5`
 4. You can inspect the HDF5 file by running `h5dump test.h5`
 

cpp/prd_analysis.cpp → cpp/petsird_analysis.cpp

@@ -10,10 +10,10 @@
 
 #ifdef USE_HDF5
 #  include "generated/hdf5/protocols.h"
-using prd::hdf5::PrdExperimentReader;
+using petsird::hdf5::PETSIRDReader;
 #else
 #  include "generated/binary/protocols.h"
-using prd::binary::PrdExperimentReader;
+using petsird::binary::PETSIRDReader;
 #endif
 #include <xtensor/xview.hpp>
 #include <xtensor/xio.hpp>
@@ -30,8 +30,8 @@ main(int argc, char* argv[])
     }
 
   // Open the file
-  PrdExperimentReader reader(argv[1]);
-  prd::Header header;
+  PETSIRDReader reader(argv[1]);
+  petsird::Header header;
   reader.ReadHeader(header);
 
   std::cout << "Processing file: " << argv[1] << std::endl;
@@ -56,7 +56,7 @@ main(int argc, char* argv[])
                                  / 2;
   std::cout << "Energy mid points: " << energy_mid_points << std::endl;
 
-  prd::TimeBlock time_block;
+  petsird::TimeBlock time_block;
 
   // Process events in batches of up to 100
   float energy_1 = 0, energy_2 = 0;

cpp/prd_generator.cpp → cpp/petsird_generator.cpp

@@ -14,10 +14,10 @@
 
 #ifdef USE_HDF5
 #  include "generated/hdf5/protocols.h"
-using prd::hdf5::PrdExperimentWriter;
+using petsird::hdf5::PETSIRDWriter;
 #else
 #  include "generated/binary/protocols.h"
-using prd::binary::PrdExperimentWriter;
+using petsird::binary::PETSIRDWriter;
 #endif
 
 // these are constants for now
@@ -30,28 +30,28 @@ constexpr uint32_t NUMBER_OF_TIME_BLOCKS = 6;
 constexpr float COUNT_RATE = 500.F;
 
 //! return a cuboid volume
-prd::BoxSolidVolume
+petsird::BoxSolidVolume
 get_crystal()
 {
-  using prd::Coordinate;
-  prd::BoxShape crystal_shape{ Coordinate{ { 0, 0, 0 } },
-                               Coordinate{ { 0, 0, CRYSTAL_LENGTH[2] } },
-                               Coordinate{ { 0, CRYSTAL_LENGTH[1], CRYSTAL_LENGTH[2] } },
-                               Coordinate{ { 0, CRYSTAL_LENGTH[1], 0 } },
-                               Coordinate{ { CRYSTAL_LENGTH[0], 0, 0 } },
-                               Coordinate{ { CRYSTAL_LENGTH[0], 0, CRYSTAL_LENGTH[2] } },
-                               Coordinate{ { CRYSTAL_LENGTH[0], CRYSTAL_LENGTH[1], CRYSTAL_LENGTH[2] } },
-                               Coordinate{ { CRYSTAL_LENGTH[0], CRYSTAL_LENGTH[1], 0 } } };
-
-  prd::BoxSolidVolume crystal{ crystal_shape, /* material_id */ 1 };
+  using petsird::Coordinate;
+  petsird::BoxShape crystal_shape{ Coordinate{ { 0, 0, 0 } },
+                                   Coordinate{ { 0, 0, CRYSTAL_LENGTH[2] } },
+                                   Coordinate{ { 0, CRYSTAL_LENGTH[1], CRYSTAL_LENGTH[2] } },
+                                   Coordinate{ { 0, CRYSTAL_LENGTH[1], 0 } },
+                                   Coordinate{ { CRYSTAL_LENGTH[0], 0, 0 } },
+                                   Coordinate{ { CRYSTAL_LENGTH[0], 0, CRYSTAL_LENGTH[2] } },
+                                   Coordinate{ { CRYSTAL_LENGTH[0], CRYSTAL_LENGTH[1], CRYSTAL_LENGTH[2] } },
+                                   Coordinate{ { CRYSTAL_LENGTH[0], CRYSTAL_LENGTH[1], 0 } } };
+
+  petsird::BoxSolidVolume crystal{ crystal_shape, /* material_id */ 1 };
   return crystal;
 }
 
 //! return a module of NUM_CRYSTALS_PER_MODULE cuboids
-prd::DetectorModule
+petsird::DetectorModule
 get_detector_module()
 {
-  prd::ReplicatedBoxSolidVolume rep_volume;
+  petsird::ReplicatedBoxSolidVolume rep_volume;
   {
     rep_volume.object = get_crystal();
     constexpr auto N0 = NUM_CRYSTALS_PER_MODULE[0];
@@ -61,26 +61,26 @@ get_detector_module()
       for (int rep1 = 0; rep1 < N1; ++rep1)
         for (int rep2 = 0; rep2 < N2; ++rep2)
           {
-            prd::RigidTransformation transform{ { { 1.0, 0.0, 0.0, RADIUS + rep0 * CRYSTAL_LENGTH[0] },
-                                                  { 0.0, 1.0, 0.0, rep1 * CRYSTAL_LENGTH[1] },
-                                                  { 0.0, 0.0, 1.0, rep2 * CRYSTAL_LENGTH[2] } } };
+            petsird::RigidTransformation transform{ { { 1.0, 0.0, 0.0, RADIUS + rep0 * CRYSTAL_LENGTH[0] },
+                                                      { 0.0, 1.0, 0.0, rep1 * CRYSTAL_LENGTH[1] },
+                                                      { 0.0, 0.0, 1.0, rep2 * CRYSTAL_LENGTH[2] } } };
             rep_volume.transforms.push_back(transform);
             rep_volume.ids.push_back(rep0 + N0 * (rep1 + N1 * rep2));
           }
   }
 
-  prd::DetectorModule detector_module;
+  petsird::DetectorModule detector_module;
   detector_module.detecting_elements.push_back(rep_volume);
   detector_module.detecting_element_ids.push_back(0);
 
   return detector_module;
 }
 
 //! return scanner build by rotating a module around the (0,0,1) axis
-prd::ScannerGeometry
+petsird::ScannerGeometry
 get_scanner_geometry()
 {
-  prd::ReplicatedDetectorModule rep_module;
+  petsird::ReplicatedDetectorModule rep_module;
   {
     rep_module.object = get_detector_module();
     int module_id = 0;
@@ -91,23 +91,23 @@ get_scanner_geometry()
       }
     for (auto angle : angles)
       {
-        prd::RigidTransformation transform{ { { std::cos(angle), std::sin(angle), 0.F, 0.F },
-                                              { -std::sin(angle), std::cos(angle), 0.F, 0.F },
-                                              { 0.F, 0.F, 1.F, 0.F } } };
+        petsird::RigidTransformation transform{ { { std::cos(angle), std::sin(angle), 0.F, 0.F },
+                                                  { -std::sin(angle), std::cos(angle), 0.F, 0.F },
+                                                  { 0.F, 0.F, 1.F, 0.F } } };
         rep_module.ids.push_back(module_id++);
         rep_module.transforms.push_back(transform);
       }
   }
-  prd::ScannerGeometry scanner_geometry;
+  petsird::ScannerGeometry scanner_geometry;
   scanner_geometry.replicated_modules.push_back(rep_module);
   scanner_geometry.ids.push_back(0);
   return scanner_geometry;
 }
 
-prd::ScannerInformation
+petsird::ScannerInformation
 get_scanner_info()
 {
-  prd::ScannerInformation scanner_info;
+  petsird::ScannerInformation scanner_info;
   scanner_info.model_name = "PETSIRD_TEST";
 
   scanner_info.scanner_geometry = get_scanner_geometry();
@@ -136,18 +136,18 @@ get_scanner_info()
   return scanner_info;
 }
 
-prd::Header
+petsird::Header
 get_header()
 {
-  prd::Subject subject;
+  petsird::Subject subject;
   subject.id = "123456";
-  prd::Institution institution;
+  petsird::Institution institution;
   institution.name = "Diamond Light Source";
   institution.address = "Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK";
-  prd::ExamInformation exam_info;
+  petsird::ExamInformation exam_info;
   exam_info.subject = subject;
   exam_info.institution = institution;
-  prd::Header header;
+  petsird::Header header;
   header.exam = exam_info;
   header.scanner = get_scanner_info();
   return header;
@@ -174,15 +174,15 @@ get_random_tof_value()
   return rand() % NUMBER_OF_TOF_BINS;
 }
 
-std::vector<prd::CoincidenceEvent>
-get_events(const prd::Header&, std::size_t num_events)
+std::vector<petsird::CoincidenceEvent>
+get_events(const petsird::Header&, std::size_t num_events)
 {
-  std::vector<prd::CoincidenceEvent> events;
+  std::vector<petsird::CoincidenceEvent> events;
   events.reserve(num_events);
   for (std::size_t i = 0; i < num_events; ++i)
     {
       const auto detectors = get_random_pair(1); // TODO header.scanner.NumberOfDetectors());
-      prd::CoincidenceEvent e;
+      petsird::CoincidenceEvent e;
       e.detector_ids[0] = detectors.first;
       e.detector_ids[1] = detectors.second;
       e.energy_indices[0] = get_random_energy_value();
@@ -205,7 +205,7 @@ main(int argc, char* argv[])
 
   std::string outfile = argv[1];
   std::remove(outfile.c_str());
-  PrdExperimentWriter writer(outfile);
+  PETSIRDWriter writer(outfile);
 
   const auto header = get_header();
   writer.WriteHeader(header);
@@ -217,7 +217,7 @@ main(int argc, char* argv[])
       std::poisson_distribution<> poisson(COUNT_RATE);
       const auto num_prompts_this_block = poisson(gen);
       const auto prompts_this_block = get_events(header, num_prompts_this_block);
-      prd::TimeBlock time_block;
+      petsird::TimeBlock time_block;
       time_block.id = t;
       time_block.prompt_events = prompts_this_block;
       writer.WriteTimeBlocks(time_block);

environment.yml

@@ -1,4 +1,4 @@
-name: prd
+name: petsird
 channels:
   - conda-forge
   - defaults

model/Protocol.yml

@@ -1,5 +1,5 @@
 # Definition of the stream of data
-PrdExperiment: !protocol
+PETSIRD: !protocol
   sequence:
     header: Header
     timeBlocks: !stream

model/_package.yml

@@ -1,4 +1,4 @@
-namespace: Prd
+namespace: PETSIRD
 
 cpp:
   sourcesOutputDir: ../cpp/generated

python/README.md

@@ -6,10 +6,10 @@ The Python code shows piping the compact binary format to standard out and
 reading it from standard in. This can be used as follows:
 
 1. From the repo root `cd python`
-1. `python prd_generator.py | python prd_analysis.py`
+1. `python petsird_generator.py | python petsird_analysis.py`
 
 There is also a very basic utility to plot the scanner geometry. For instance
 ```
-python prd_generator.py > test.bin
-python prd_plot_scanner.py < test.bin`
+python petsird_generator.py > test.bin
+python petsird_plot_scanner.py < test.bin`
 

python/prd_analysis.py → python/petsird_analysis.py

@@ -5,11 +5,11 @@
 
 import sys
 import numpy
-import prd
+import petsird
 
 
 if __name__ == "__main__":
-    with prd.BinaryPrdExperimentReader(sys.stdin.buffer) as reader:
+    with petsird.BinaryPETSIRDReader(sys.stdin.buffer) as reader:
         header = reader.read_header()
         print(f"Subject ID: {header.exam.subject.id}")
         print(f"Scanner name: { header.scanner.model_name}")