Add waveform stream and use ismrmrd ndarray (#1263)

* stream out kspace as ismrmrd ND array; add stream for waveform * update test for data stream * fix the BucketToBufferGadget for sampling.sampling_limits * update ismrmrd=1.14.1 * update onnxruntime to 1.18.1 * siemens_to_ismrmrd to use 1.2.12 * make bucket to buffer can be derived * udpate cases/ismrmrd_dump_gadget_test.cfg ref data * fix cases/ismrmrd_dump_gadget_test.cfg * fix the ismrmrd dump test * update image base in azure-pipeline.yml * update build-images.sh * further fix ismrmrd dump test --------- Co-authored-by: Hui Xue <[email protected]>
gadgetron · Aug 12, 2024 · 24fe05d · 24fe05d
1 parent 9f88dcd
commit 24fe05d
Show file tree

Hide file tree

Showing 13 changed files with 335 additions and 177 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -1,6 +1,6 @@
 variables:
   AzureConnection: 'BiomedicalImaging-NonProd(87d8acb3-5176-4651-b457-6ab9cefd8e3d)'
-  imageBaseName: 'ghcr.io/gadgetron/gadgetron/gadgetron_ubuntu'
+  imageBaseName: 'ghcr.io/gadgetron/gadgetron/ubuntu22.04'
   DOCKER_BUILDKIT: 1
   isPR: $[eq(variables['Build.Reason'], 'PullRequest')]
   isCI: $[or(eq(variables['Build.Reason'], 'IndividualCI'), eq(variables['Build.Reason'], 'BatchedCI'))]

diff --git a/build-images.sh b/build-images.sh
@@ -29,7 +29,7 @@ flavors=()
 flavors_default=("cuda" "nocuda")
 
 image_tag="latest"
-base_name="ghcr.io/gadgetron/gadgetron/gadgetron_ubuntu"
+base_name="ghcr.io/gadgetron/gadgetron/ubuntu22.04"
 
 while [[ $# -gt 0 ]]; do
   key="$1"

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -28,7 +28,7 @@ requirements:
     - h5py=3.7.0
     - hdf5=1.10.6
     - howardhinnant_date=3.0.1
-    - ismrmrd=1.13.7
+    - ismrmrd=1.14.1
     - ismrmrd-python=1.14.0
     - libblas=*=*mkl
     - libcurl=7.86.0
@@ -56,7 +56,7 @@ requirements:
     - gadgetron-python>=1.4.1
     - h5py=3.7.0
     - hdf5=1.10.6
-    - ismrmrd=1.13.7
+    - ismrmrd=1.14.1
     - ismrmrd-python=1.14.0
     - jq=1.7.1
     - libblas=*=*mkl
@@ -65,7 +65,7 @@ requirements:
     - mkl>=2024.1.0
     - mrd-storage-server=0.0.12
     - numpy=1.26.4
-    - onnxruntime=1.18.0
+    - onnxruntime=1.18.1
     - pugixml=1.12.1
     - pyfftw=0.13.1
     - python=3.10
@@ -74,7 +74,7 @@ requirements:
 
 test:
   requires:
-    - siemens_to_ismrmrd=1.2.11
+    - siemens_to_ismrmrd=1.2.12
 
 about:
   home: https://github.com/gadgetron/gadgetron

diff --git a/environment.yml b/environment.yml
@@ -38,7 +38,7 @@ dependencies:
   - h5py=3.7.0
   - hdf5=1.10.6
   - howardhinnant_date=3.0.1                # dev
-  - ismrmrd=1.13.7
+  - ismrmrd=1.14.1
   - ismrmrd-python=1.14.0
   - junitparser=3.1.2
   - jupyter=1.0.0                           # dev
@@ -54,7 +54,7 @@ dependencies:
   - ninja=1.12.1                            # dev
   - nlohmann_json=3.11.3                    # dev
   - numpy=1.26.4
-  - onnxruntime=1.18.0
+  - onnxruntime=1.18.1
   - pyyaml=6.0.1                            # dev
   - pip=24.0                                # dev
   - packaging=24.0
@@ -66,7 +66,7 @@ dependencies:
   - recommonmark=0.7.1                      # dev
   - scipy=1.13.1
   - shellcheck=0.10.0                       # dev
-  - siemens_to_ismrmrd=1.2.11
+  - siemens_to_ismrmrd=1.2.12
   - sphinx=7.3.7                            # dev
   - sphinx_rtd_theme=2.0.0                  # dev
   - sysroot_linux-64=2.12

diff --git a/gadgets/mri_core/BucketToBufferGadget.cpp b/gadgets/mri_core/BucketToBufferGadget.cpp
@@ -227,6 +227,7 @@ namespace Gadgetron {
         }
         return NLOC;
     }
+
     uint16_t BucketToBufferGadget::getNE2(
         const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, bool forref) const {
         uint16_t NE2;
@@ -259,6 +260,7 @@ namespace Gadgetron {
         }
         return NE2;
     }
+
     uint16_t BucketToBufferGadget::getNE1(
         const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, bool forref) const {
         uint16_t NE1;
@@ -290,6 +292,7 @@ namespace Gadgetron {
         }
         return NE1;
     }
+
     uint16_t BucketToBufferGadget::getNE0(
         const ISMRMRD::AcquisitionHeader& acqhdr, const ISMRMRD::Encoding& encoding) const {
         uint16_t NE0;
@@ -321,6 +324,35 @@ namespace Gadgetron {
         sampling.recon_FOV_      = xyz_to_vector(encoding.reconSpace.fieldOfView_mm);
         sampling.recon_matrix_   = xyz_to_vector(encoding.reconSpace.matrixSize);
 
+        sampling.sampling_limits_[0].min_ = 0;
+        sampling.sampling_limits_[0].max_ = acqhdr.number_of_samples-1;
+        sampling.sampling_limits_[0].center_ = acqhdr.number_of_samples/2;
+
+        sampling.sampling_limits_[1].min_ = encoding.encodingLimits.kspace_encoding_step_1->minimum;
+        sampling.sampling_limits_[1].max_ = encoding.encodingLimits.kspace_encoding_step_1->maximum;
+        sampling.sampling_limits_[1].center_ = encoding.encodingLimits.kspace_encoding_step_1->center;
+
+        sampling.sampling_limits_[2].min_ = encoding.encodingLimits.kspace_encoding_step_2->minimum;
+        sampling.sampling_limits_[2].max_ = encoding.encodingLimits.kspace_encoding_step_2->maximum;
+        sampling.sampling_limits_[2].center_ = encoding.encodingLimits.kspace_encoding_step_2->center;
+
+        if (verbose) {
+            GDEBUG_STREAM("Encoding space : " << acqhdr.encoding_space_ref << " - "
+                          << int(encoding.trajectory) << " - FOV : [ " << encoding.encodedSpace.fieldOfView_mm.x << " "
+                          << encoding.encodedSpace.fieldOfView_mm.y << " " << encoding.encodedSpace.fieldOfView_mm.z
+                          << " ] "
+                          << " - Matris size : [ " << encoding.encodedSpace.matrixSize.x << " "
+                          << encoding.encodedSpace.matrixSize.y << " " << encoding.encodedSpace.matrixSize.z << " ] ");
+
+            GDEBUG_STREAM("Sampling limits : "
+                          << "- RO : [ " << sampling.sampling_limits_[0].min_ << " "
+                          << sampling.sampling_limits_[0].center_ << " " << sampling.sampling_limits_[0].max_
+                          << " ] - E1 : [ " << sampling.sampling_limits_[1].min_ << " "
+                          << sampling.sampling_limits_[1].center_ << " " << sampling.sampling_limits_[1].max_
+                          << " ] - E2 : [ " << sampling.sampling_limits_[2].min_ << " "
+                          << sampling.sampling_limits_[2].center_ << " " << sampling.sampling_limits_[2].max_ << " ]");
+        }
+
         // For cartesian trajectories, assume that any oversampling has been removed.
         if (encoding.trajectory == ISMRMRD::TrajectoryType::CARTESIAN) {
             sampling.encoded_FOV_[0]    = encoding.reconSpace.fieldOfView_mm.x;
@@ -391,22 +423,6 @@ namespace Gadgetron {
             sampling.sampling_limits_[2].center_ = encoding.encodingLimits.kspace_encoding_step_2->center;
         }
 
-        if (verbose) {
-            GDEBUG_STREAM("Encoding space : "
-                          << int(encoding.trajectory) << " - FOV : [ " << encoding.encodedSpace.fieldOfView_mm.x << " "
-                          << encoding.encodedSpace.fieldOfView_mm.y << " " << encoding.encodedSpace.fieldOfView_mm.z
-                          << " ] "
-                          << " - Matris size : [ " << encoding.encodedSpace.matrixSize.x << " "
-                          << encoding.encodedSpace.matrixSize.y << " " << encoding.encodedSpace.matrixSize.z << " ] ");
-
-            GDEBUG_STREAM("Sampling limits : "
-                          << "- RO : [ " << sampling.sampling_limits_[0].min_ << " "
-                          << sampling.sampling_limits_[0].center_ << " " << sampling.sampling_limits_[0].max_
-                          << " ] - E1 : [ " << sampling.sampling_limits_[1].min_ << " "
-                          << sampling.sampling_limits_[1].center_ << " " << sampling.sampling_limits_[1].max_
-                          << " ] - E2 : [ " << sampling.sampling_limits_[2].min_ << " "
-                          << sampling.sampling_limits_[2].center_ << " " << sampling.sampling_limits_[2].max_ << " ]");
-        }
         return sampling;
     }
 

diff --git a/gadgets/mri_core/BucketToBufferGadget.h b/gadgets/mri_core/BucketToBufferGadget.h
@@ -30,10 +30,9 @@ namespace Gadgetron {
     struct BufferKey {
         uint16_t average,slice,contrast,phase,repetition,set,segment;
         BufferKey(const BufferKey&) = default;
-        BufferKey(const ISMRMRD::EncodingCounters& idx) : average{idx.average}, slice{idx.slice},contrast{idx.contrast}, phase{idx.phase},repetition{idx.repetition},set{idx.set},segment{idx.segment}{
-
-        }
+        BufferKey(const ISMRMRD::EncodingCounters& idx) : average{idx.average}, slice{idx.slice},contrast{idx.contrast}, phase{idx.phase},repetition{idx.repetition},set{idx.set},segment{idx.segment} {}
     };
+
     protected:
         NODE_PROPERTY(N_dimension, Dimension, "N-Dimensions", Dimension::none);
         NODE_PROPERTY(S_dimension, Dimension, "S-Dimensions", Dimension::none);
@@ -47,17 +46,16 @@ namespace Gadgetron {
         void process(Core::InputChannel<AcquisitionBucket>& in, Core::OutputChannel& out) override;
         BufferKey getKey(const ISMRMRD::EncodingCounters& idx) const;
 
+        IsmrmrdDataBuffered makeDataBuffer(const ISMRMRD::AcquisitionHeader& acqhdr, ISMRMRD::Encoding encoding, const AcquisitionBucketStats& stats, bool forref) const;
+
+        virtual SamplingDescription createSamplingDescription(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, const ISMRMRD::AcquisitionHeader& acqhdr, bool forref) const ;
+
+        void add_acquisition(IsmrmrdDataBuffered& dataBuffer, const Core::Acquisition& acq, ISMRMRD::Encoding encoding, const AcquisitionBucketStats& stats, bool forref);
 
-        IsmrmrdDataBuffered makeDataBuffer(const ISMRMRD::AcquisitionHeader& acqhdr, ISMRMRD::Encoding encoding,
-            const AcquisitionBucketStats& stats, bool forref) const;
-        SamplingDescription createSamplingDescription(const ISMRMRD::Encoding& encoding,
-            const AcquisitionBucketStats& stats, const ISMRMRD::AcquisitionHeader& acqhdr, bool forref) const ;
-        void add_acquisition(IsmrmrdDataBuffered& dataBuffer, const Core::Acquisition& acq, ISMRMRD::Encoding encoding,
-            const AcquisitionBucketStats& stats, bool forref);
-        uint16_t getNE0(const ISMRMRD::AcquisitionHeader& acqhdr, const ISMRMRD::Encoding& encoding) const;
-        uint16_t getNE1(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, bool forref) const;
-        uint16_t getNE2(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, bool forref) const;
-        uint16_t getNLOC(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats) const;
+        virtual uint16_t getNE0(const ISMRMRD::AcquisitionHeader& acqhdr, const ISMRMRD::Encoding& encoding) const;
+        virtual uint16_t getNE1(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, bool forref) const;
+        virtual uint16_t getNE2(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats, bool forref) const;
+        virtual uint16_t getNLOC(const ISMRMRD::Encoding& encoding, const AcquisitionBucketStats& stats) const;
     };
 
     void from_string(const std::string&, BucketToBufferGadget::Dimension&);

diff --git a/gadgets/mri_core/generic_recon_gadgets/GenericReconCartesianGrappaGadget.cpp b/gadgets/mri_core/generic_recon_gadgets/GenericReconCartesianGrappaGadget.cpp
@@ -213,7 +213,11 @@ namespace Gadgetron {
 
                 // ---------------------------------------------------------------
                 // pass down waveform
-                if (wav) this->set_wave_form_to_image_array(*wav->getObjectPtr(), recon_obj_[e].recon_res_);
+                if (wav)
+                {
+                    this->set_wave_form_to_image_array(*wav->getObjectPtr(), recon_obj_[e].recon_res_);
+                    this->gt_streamer_.stream_ismrmrd_waveform(*recon_obj_[e].recon_res_.waveform_);
+                }
                 recon_obj_[e].recon_res_.acq_headers_ = recon_bit_->rbit_[e].data_.headers_;
 
                 // ---------------------------------------------------------------

diff --git a/test/integration/cases/ismrmrd_dump_gadget_test.cfg b/test/integration/cases/ismrmrd_dump_gadget_test.cfg
@@ -6,11 +6,11 @@ template=ismrmrd_dump_gadget_test.template.xml
 
 [reconstruction.equals]
 dataset_prefix=ismrmrd_dump_output
-reference_file=simple_gre/simple_gre_in_20220831.mrd
+reference_file=simple_gre/ismrmrd_dump_output_20240811.h5
 
 [reconstruction.test]
-reference_file=simple_gre/simple_gre_out_20210909_klk.mrd
-reference_images=simple/image_0
+reference_file=simple_gre/ref_20240810.mrd
+reference_images=reconstruction.client/image_0
 output_images=reconstruction.client/image_0
 value_comparison_threshold=0.002
 scale_comparison_threshold=0.001

diff --git a/test/integration/data.json b/test/integration/data.json
@@ -354,5 +354,13 @@
   {
     "file": "cmr/RTCine/CH4/ref_20220124_173736.mrd",
     "md5": "b5e9c37bbd3eb4be076d89fd7dd7db6d"
-  }
+  },
+  {
+    "file": "simple_gre/ismrmrd_dump_output_20240811.h5",
+    "md5": "d4dbdd40f7becc4cf5aae3e21eef26b4"
+  },
+  {
+    "file": "simple_gre/ref_20240810.mrd",
+    "md5": "152dd0ee1b259756107c9fd36965fadb"
+  } 
 ]