Merge pull request #3 from ismrmrd/master

Merge from master
ismrmrd · Nov 23, 2022 · c83c2b9 · c83c2b9
2 parents 33686d2 + 60aefa5
commit c83c2b9
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Showing 14 changed files with 262 additions and 9 deletions.
diff --git a/.github/workflows/siemens_to_ismrmrd_conda.yml b/.github/workflows/siemens_to_ismrmrd_conda.yml
@@ -0,0 +1,36 @@
+on:
+  pull_request:
+    branches:    
+      - master
+  release:
+    types:
+      - created
+
+jobs:
+  build-conda-packages:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b
+      - uses: conda-incubator/setup-miniconda@e81abac10ce2c37423b54eae5af93aa3b4d3475c
+        with:
+          activate-environment: siemens-to-ismrmrd-build
+          environment-file: conda/environment.yml
+          python-version: 3.9
+          auto-activate-base: false
+      - name: Build conda package
+        shell: bash -l {0}
+        working-directory: conda
+        run: |
+          ./package.sh
+          echo "Packages built: $(find build_pkg -name siemens_to_ismrmrd*.tar.bz2)"
+      - name: Push conda package
+        shell: bash -l {0}
+        if: ${{ github.event_name == 'release' }}
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        working-directory: conda
+        run: |
+          ./publish_package.sh -u ismrmrd -t "$ANACONDA_TOKEN" -p `find build_pkg -name siemens_to_ismrmrd*.tar.bz2`
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -18,7 +18,7 @@ message(STATUS "Looking for packages in : ${CMAKE_PREFIX_PATH}")
 #VERSIONING
 set(SIEMENS_TO_ISMRMRD_VERSION_MAJOR 1)
 set(SIEMENS_TO_ISMRMRD_VERSION_MINOR 2)
-set(SIEMENS_TO_ISMRMRD_VERSION_PATCH 2)
+set(SIEMENS_TO_ISMRMRD_VERSION_PATCH 6)
 set(SIEMENS_TO_ISMRMRD_VERSION_STRING ${SIEMENS_TO_ISMRMRD_VERSION_MAJOR}.${SIEMENS_TO_ISMRMRD_VERSION_MINOR}.${SIEMENS_TO_ISMRMRD_VERSION_PATCH})
 
 # Generate the converter_version.h header file
@@ -67,7 +67,7 @@ set(Boost_USE_STATIC_RUNTIME OFF)
 
 
 find_package(Boost COMPONENTS system thread program_options filesystem timer REQUIRED)
-find_package(ISMRMRD 1.7.0 REQUIRED)
+find_package(ISMRMRD 1.8.0 REQUIRED)
 find_package(HDF5  REQUIRED COMPONENTS C)
 
 include_directories( ${ISMRMRD_INCLUDE_DIR} ${HDF5_C_INCLUDE_DIR} )

diff --git a/conda/.gitignore b/conda/.gitignore
@@ -0,0 +1,3 @@
+build_pkg/
+.pytest_cache/
+__pycache__/
diff --git a/conda/build.sh b/conda/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+set -euo pipefail
+
+mkdir -p build
+cd build
+cmake -G Ninja -DBUILD_DYNAMIC=ON -DCMAKE_PREFIX_PATH=${PREFIX} -DCMAKE_INSTALL_PREFIX=${PREFIX} ../
+ninja
+ninja install
diff --git a/conda/environment.yml b/conda/environment.yml
@@ -0,0 +1,7 @@
+name: siemens-to-ismrmrd-build
+channels:
+  - conda-forge
+dependencies:
+  - conda-build
+  - anaconda-client
+
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -0,0 +1,39 @@
+{% set major = load_file_regex(load_file='CMakeLists.txt', regex_pattern='(?<=set\(SIEMENS_TO_ISMRMRD_VERSION_MAJOR )([^\)]+)') %}
+{% set minor = load_file_regex(load_file='CMakeLists.txt', regex_pattern='(?<=set\(SIEMENS_TO_ISMRMRD_VERSION_MINOR )([^\)]+)') %}
+{% set patch = load_file_regex(load_file='CMakeLists.txt', regex_pattern='(?<=set\(SIEMENS_TO_ISMRMRD_VERSION_PATCH )([^\)]+)') %}
+
+package:
+  name: siemens_to_ismrmrd
+  version: {{ major.group(1) }}.{{ minor.group(1) }}.{{ patch.group(1) }}
+
+source:
+  path: ../
+
+requirements:
+  build:
+    - boost=1.76.0
+    - clang>=13.0.1        # [osx]
+    - clangxx>=13.0.1      # [osx]
+    - cmake>=3.20.0
+    - gcc_linux-64>=9.0.0  # [linux64] 
+    - gxx_linux-64>=9.0.0  # [linux64]
+    - ismrmrd=1.12.0
+    - libxml2=2.9.12
+    - libxslt=1.1.33 
+    - ninja=1.10.*
+
+  run:
+    - ismrmrd=1.12.0
+    - boost=1.76.0
+    - libxml2=2.9.12
+    - libxslt=1.1.33 
+
+about:
+  home: https://github.com/ismrmrd/siemens_to_ismrmrd
+  license: MIT
+  summary: 'Siemens to ISMRM Raw Data (ISMRMRD) converter'
+  description: |
+    Command line tool for converting Siemens raw data (*.dat) files to ISMRMRD files.
+  dev_url: https://github.com/ismrmrd/siemens_to_ismrmrd
+  doc_url: https://github.com/ismrmrd/siemens_to_ismrmrd
+  doc_source_url: https://github.com/ismrmrd/siemens_to_ismrmrd/blob/master/README.md
diff --git a/conda/package.sh b/conda/package.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+set -euo pipefail
+
+usage()
+{
+  cat << EOF
+
+Builds the siemens_to_ismrmrd conda package.
+
+Usage: $0
+EOF
+}
+
+output_path="$(dirname "$0")/build_pkg"
+
+# Build up channel directives
+channels=(
+  ismrmrd
+  conda-forge
+)
+
+channel_directives=$(printf -- "-c %s " "${channels[@]}")
+
+mkdir -p "$output_path"
+bash -c "conda build --no-anaconda-upload --output-folder $output_path $channel_directives $(dirname "$0")"
diff --git a/conda/publish_package.sh b/conda/publish_package.sh
@@ -0,0 +1,77 @@
+#!/bin/bash
+set -euo pipefail
+
+usage()
+{
+  cat << EOF
+
+Publishes a conda package.
+
+Usage: $0 [options]
+
+Options:
+  -p|--package_path <path>               Path to the package (tar.gz) to push
+  -u|--user <user>                       Anaconda.org channeluser or organization
+  -t|--token <token>                     Token for uploading to anaconda.org
+  -f|--force                             Force push even if package exists
+  -h| --help  Brings up this menu
+EOF
+}
+
+while [[ $# -gt 0 ]]; do
+  key="$1"
+
+  case $key in
+    -p|--package_path)
+      package_path="$2"
+      shift
+      shift
+      ;;
+    -u|--user)
+      user="$2"
+      shift
+      shift
+      ;;
+    -t|--token)
+      token="$2"
+      shift
+      shift
+      ;;
+    --force)
+      force=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit
+      ;;
+    *)
+      echo "ERROR: unknown option \"$key\""
+      usage
+      exit 1
+      ;;
+  esac
+done
+
+if [[ -z "${package_path:-}" ]]; then
+  echo "You cannot push to anaconda without a package"
+  echo "Please supply a package path with the --package_path argument"
+  exit 1
+fi
+if [[ -z "${token:-}" ]]; then
+  echo "You cannot push to anaconda without a token"
+  echo "Please supply a token with the --token argument"
+  exit 1
+fi
+if [[ -z "${user:-}" ]]; then
+  echo "You cannot push to anaconda without a user"
+  echo "Please supply a user with the --user argument"
+  exit 1
+fi
+
+force_directive="--skip-existing"
+if [[ -n ${force:-} ]]; then
+  force_directive="--force"
+fi
+
+anaconda -t "$token" upload -u "$user" $force_directive "$package_path"
diff --git a/conda/run_test.sh b/conda/run_test.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -euo pipefail
+
+# We are just printing help text, which will fail if dependencies are missing
+siemens_to_ismrmrd -h
+siemens_to_ismrmrd -v
+
+
+
diff --git a/dependencies/ismrmrd b/dependencies/ismrmrd
@@ -1 +1 @@
-5672c474292f0b87e9c0aedcb5f1bc87ef0544f8
+f9e38ed8cda6428839005c060579d3dfdb043515
diff --git a/main.cpp b/main.cpp
@@ -515,15 +515,15 @@ int main(int argc, char* argv[]) {
 
         if (vm.count("help")) {
             std::cout << display_options << "\n";
-            return 1;
+            return 0;
         }
 
         if (vm.count("version")) {
             std::cout << "Converter version is: " << SIEMENS_TO_ISMRMRD_VERSION_MAJOR << "."
                 << SIEMENS_TO_ISMRMRD_VERSION_MINOR << "." << SIEMENS_TO_ISMRMRD_VERSION_PATCH << "\n";
             std::cout << "Built against ISMRMRD version: " << ISMRMRD_VERSION_MAJOR << "." << ISMRMRD_VERSION_MINOR
                 << "." << ISMRMRD_VERSION_PATCH << "\n";
-            return 1;
+            return 0;
         }
     }
 
@@ -1105,9 +1105,9 @@ getAcquisition(bool flash_pat_ref_scan, const Trajectory &trajectory, long dwell
     }
     // std::cout << "ismrmrd_acq.sample_time_us(): " << ismrmrd_acq.sample_time_us() << std::endl;
 
-    ismrmrd_acq.position()[0] = scanhead.sSliceData.sSlicePosVec.flSag + (float) (global_table_pos[0]);
-    ismrmrd_acq.position()[1] = scanhead.sSliceData.sSlicePosVec.flCor + (float) (global_table_pos[1]);
-    ismrmrd_acq.position()[2] = scanhead.sSliceData.sSlicePosVec.flTra + (float) (global_table_pos[2]);
+    ismrmrd_acq.position()[0] = scanhead.sSliceData.sSlicePosVec.flSag;// + (float) (global_table_pos[0]);
+    ismrmrd_acq.position()[1] = scanhead.sSliceData.sSlicePosVec.flCor;// + (float) (global_table_pos[1]);
+    ismrmrd_acq.position()[2] = scanhead.sSliceData.sSlicePosVec.flTra;// + (float) (global_table_pos[2]);
 
     // Convert Siemens quaternions to direction cosines.
     // In the Siemens convention the quaternion corresponds to a rotation matrix with columns P R S

diff --git a/parameter_maps/IsmrmrdParameterMap_Siemens.xml b/parameter_maps/IsmrmrdParameterMap_Siemens.xml
@@ -31,6 +31,7 @@
         <p><s>MEAS.sSliceArray.asSlice.0.dReadoutFOV</s>                        <d>siemens.MEAS.sSliceArray.asSlice.s0.dReadoutFOV</d></p>
         <p><s>MEAS.sSliceArray.asSlice.0.dPhaseFOV</s>                          <d>siemens.MEAS.sSliceArray.asSlice.s0.dPhaseFOV</d></p>
         <p><s>MEAS.sSliceArray.asSlice.0.dThickness</s>                         <d>siemens.MEAS.sSliceArray.asSlice.s0.dThickness</d></p>
+        <p><s>MEAS.sSliceArray.asSlice.0.dInPlaneRot</s>                        <d>siemens.MEAS.sSliceArray.asSlice.s0.dInPlaneRot</d></p>
         <p><s>MEAS.sAngio.sFlowArray.lSize</s>                                  <d>siemens.MEAS.sAngio.sFlowArray.lSize</d></p>
         <p><s>MEAS.sAngio.sFlowArray.asElm.0.nVelocity</s>                      <d>siemens.MEAS.sAngio.sFlowArray.asElm.s0.nVelocity</d></p>
         <p><s>YAPS.aflMaxwellCoefficients</s>                                   <d>siemens.YAPS.aflMaxwellCoefficients</d></p>
@@ -84,6 +85,9 @@
         <!-- measurementInformationType --> 
         <p><s>HEADER.MeasUID</s>                                                <d>siemens.HEADER.MeasUID</d></p>
         <p><s>YAPS.tPatientPosition</s>                                         <d>siemens.YAPS.tPatientPosition</d></p>
+        <p><s>DICOM.lGlobalTablePosSag</s>                                      <d>siemens.DICOM.lGlobalTablePosSag</d></p>
+        <p><s>DICOM.lGlobalTablePosCor</s>                                      <d>siemens.DICOM.lGlobalTablePosCor</d></p>
+        <p><s>DICOM.lGlobalTablePosTra</s>                                      <d>siemens.DICOM.lGlobalTablePosTra</d></p>
         <p><s>MEAS.tProtocolName</s>                                            <d>siemens.MEAS.tProtocolName</d></p>
         <p><s>YAPS.ReconMeasDependencies.0</s>                                  <d>siemens.YAPS.ReconMeasDependencies.RFMap</d></p>
         <p><s>YAPS.ReconMeasDependencies.1</s>                                  <d>siemens.YAPS.ReconMeasDependencies.SenMap</d></p>

diff --git a/parameter_maps/IsmrmrdParameterMap_Siemens.xsl b/parameter_maps/IsmrmrdParameterMap_Siemens.xsl
@@ -99,9 +99,38 @@
                     <xsl:value-of
                             select="concat(string(siemens/DICOM/DeviceSerialNumber), $strSeperator, $patientID, $strSeperator, $studyID, $strSeperator, string(siemens/HEADER/MeasUID))"/>
                 </measurementID>
+
                 <patientPosition>
                     <xsl:value-of select="siemens/YAPS/tPatientPosition"/>
                 </patientPosition>
+
+                <relativeTablePosition>
+                    <x>
+                    <xsl:choose>
+                        <xsl:when test="siemens/DICOM/lGlobalTablePosSag">
+                            <xsl:value-of select="siemens/DICOM/lGlobalTablePosSag"/>
+                        </xsl:when>
+                        <xsl:otherwise>0.0</xsl:otherwise>
+                    </xsl:choose>
+                    </x>
+                    <y>
+                    <xsl:choose>
+                        <xsl:when test="siemens/DICOM/lGlobalTablePosCor">
+                            <xsl:value-of select="siemens/DICOM/lGlobalTablePosCor"/>
+                        </xsl:when>
+                        <xsl:otherwise>0.0</xsl:otherwise>
+                    </xsl:choose>
+                    </y>
+                    <z>
+                    <xsl:choose>
+                        <xsl:when test="siemens/DICOM/lGlobalTablePosTra">
+                            <xsl:value-of select="siemens/DICOM/lGlobalTablePosTra"/>
+                        </xsl:when>
+                        <xsl:otherwise>0.0</xsl:otherwise>
+                    </xsl:choose>
+                    </z>
+                </relativeTablePosition>
+
                 <protocolName>
                     <xsl:value-of select="siemens/MEAS/tProtocolName"/>
                 </protocolName>
@@ -1016,6 +1045,15 @@
                     </userParameterDouble>
                 </xsl:if>
 
+                <xsl:if test="siemens/MEAS/sSliceArray/asSlice/s0/dInPlaneRot">
+                    <userParameterDouble>
+                        <name>InPlaneRot</name>
+                        <value>
+                            <xsl:value-of select="siemens/MEAS/sSliceArray/asSlice/s0/dInPlaneRot" />
+                        </value>
+                    </userParameterDouble>
+                </xsl:if>
+
                 <xsl:if test="siemens/YAPS/flContrastBolusVolume">
                     <userParameterDouble>
                         <name>ContrastBolusVolume</name>

diff --git a/parameter_maps/IsmrmrdParameterMap_Siemens_EPI_FLASHREF.xsl b/parameter_maps/IsmrmrdParameterMap_Siemens_EPI_FLASHREF.xsl
@@ -559,7 +559,12 @@ xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
                             <xsl:value-of select="siemens/MEAS/sKSpace/lPhaseEncodingLines"/>
                         </y>
                         <z>
-                            <xsl:value-of select="siemens/MEAS/sPAT/lRefLines3D"/>
+                            <xsl:choose>
+                                <xsl:when test="not(siemens/MEAS/sPAT/lRefLines3D)">1</xsl:when>
+                                <xsl:otherwise>
+                                    <xsl:value-of select="(siemens/MEAS/sPAT/lRefLines3D)"/>
+                                </xsl:otherwise>
+                            </xsl:choose>
                         </z>
                     </matrixSize>
                     <fieldOfView_mm>
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		5672c474292f0b87e9c0aedcb5f1bc87ef0544f8
		f9e38ed8cda6428839005c060579d3dfdb043515