Add config in MRD-header

.gitignore

@@ -17,7 +17,8 @@ docs_build
 .mypy_cache/
 .ipynb_checkpoints/
 .ropeproject/
-
+__pycache__/
+*.egg-info/
 _version.py
 
 *.mrd

examples/example_gpu_anat_spirals_slice.py

@@ -13,7 +13,6 @@
 # %%
 
 # Imports
-import numpy as np
 import matplotlib.pyplot as plt
 
 from snake.core.simulation import SimConfig, default_hardware, GreConfig

src/cli-conf/scenario2-2d.yaml

@@ -0,0 +1,92 @@
+# This files contains the configuration to produce the scenario 2  of the Snkf paper but with a 2D slice acquisition and reconstruction.
+
+defaults:
+  - base_config
+  - handlers:
+    - activation-block
+  - sampler:
+    - stack-of-spiral
+  - reconstructors:
+      - adjoint
+      #- sequential
+  - _self_
+
+cache_dir: ${oc.env:PWD}/cache
+result_dir: results/scenario2
+filename:  ${cache_dir}/scenario2_2d_${engine.model}_${engine.snr}_${sampler.stack-of-spiral.constant}_${sampler.stack-of-spiral.accelz}.mrd
+
+sim_conf:
+  max_sim_time: 360
+  seq: {TR: 50, TE: 25,  FA: 12}
+  hardware:
+    n_coils: 1
+    dwell_time_ms: 0.001
+  shape: [60, 72, 60]
+  fov_mm: [181.0, 217.0, 181.0]
+
+phantom:
+  name: brainweb
+  sub_id: 4
+  tissue_file: "tissue_7T"
+
+handlers:
+  activation-block:
+    event_name: block_on
+    block_on: 20 # seconds
+    block_off: 20 #seconds
+    duration: 360 # seconds
+
+sampler:
+  stack-of-spiral:
+    acsz: 1
+    accelz: 1
+    nb_revolutions: 10
+    constant: true
+    spiral_name: "galilean"
+
+engine:
+  n_jobs: 1
+  chunk_size: 10
+  model: "simple"
+  snr: 10000
+  nufft_backend: "gpuNUFFT"
+  slice_2d: true
+
+reconstructors:
+  adjoint:
+    nufft_backend: "gpuNUFFT"
+    density_compensation: "pipe"
+  # sequential:
+  #   nufft_backend: "gpuNUFFT"
+  #   density_compensation: false
+  #   restart_strategy: WARM
+  #   max_iter_per_frame: 50
+  #   wavelet: "sym4"
+
+
+
+
+
+hydra:
+  job:
+    chdir: true
+
+  run:
+    dir: ${result_dir}/outputs/${hydra.job.name}/${now:%Y-%m-%d_%H-%M-%S}
+  sweep:
+    dir: ${result_dir}/multirun/${hydra.job.name}/${now:%Y-%m-%d_%H-%M-%S}
+    subdir: ${hydra.job.num}
+
+  callbacks:
+    # gather_files:
+    #   _target_: hydra_callbacks.MultiRunGatherer
+    #   aggregator:
+    #     _partial_: true
+    #     _target_: snkf.cli.utils.aggregate_results
+
+    log_job:
+      _target_: hydra.experimental.callbacks.LogJobReturnCallback
+    latest_run:
+      _target_: hydra_callbacks.LatestRunLink
+      run_base_dir:  ${result_dir}/outputs
+      multirun_base_dir:  ${result_dir}/multirun

src/cli-conf/scenario2.yaml

@@ -87,4 +87,4 @@ hydra:
     latest_run:
       _target_: hydra_callbacks.LatestRunLink
       run_base_dir:  ${result_dir}/outputs
-      multirun_base_dir:  ${result_dir}/multirun
+      multirun_base_dir:  ${result_dir}/multirun

src/snake/core/engine/base.py

@@ -209,7 +209,17 @@ def __call__(
         `_job_model_simple` methods.
         """
         # Create the base dataset
-        make_base_mrd(filename, sampler, phantom, sim_conf, handlers, smaps, coil_cov)
+        make_base_mrd(
+            filename,
+            sampler,
+            phantom,
+            sim_conf,
+            handlers,
+            smaps,
+            coil_cov,
+            self.model,
+            self.slice_2d,
+        )
 
         # Guesstimate the workload
         if worker_chunk_size <= 0:

src/snake/core/engine/cartesian.py

@@ -1,6 +1,5 @@
 """Acquisition engine for Cartesian trajectories."""
 
-from typing import Any
 from collections.abc import Sequence
 from copy import deepcopy
 

src/snake/core/sampling/samplers.py

@@ -1,7 +1,6 @@
 """Samplers generate kspace trajectories."""
 
 from __future__ import annotations
-from typing import Literal
 import ismrmrd as mrd
 import numpy as np
 from numpy.typing import NDArray
@@ -32,7 +31,8 @@ class NonCartesianAcquisitionSampler(BaseSampler):
     obs_time_ms: int
         Time spent to acquire a single shot
     in_out: bool
-        If true, the trajectory is acquired with a double join pattern from/to the periphery
+        If true, the trajectory is acquired with a double join pattern
+        from/to the periphery
     ndim: int
         Number of dimensions of the trajectory (2 or 3)
     """
@@ -198,7 +198,8 @@ class LoadTrajectorySampler(NonCartesianAcquisitionSampler):
     obs_time_ms: int
         Time spent to acquire a single shot
     in_out: bool
-        If true, the trajectory is acquired with a double join pattern from/to the periphery
+        If true, the trajectory is acquired with a double join pattern
+        from/to the periphery
     """
 
     __sampler_name__ = "load-trajectory"

src/snake/core/simulation.py

@@ -28,7 +28,6 @@ def _repr_html_(obj: Any, vertical: bool = True) -> str:
         '<caption style="border:1px solid lightgray;">'
         f"<strong>{class_name}</strong></caption>"
     ]
-    from typing import get_type_hints
     from dataclasses import fields
 
     resolved_hints = obj.__annotations__

src/snake/mrd_utils/loader.py

@@ -211,6 +211,16 @@ def n_shots(self) -> int:
         """
         return self.header.encoding[0].encodingLimits.kspace_encoding_step_1.maximum
 
+    @property
+    def engine_model(self) -> str:
+        """Get the engine model."""
+        return self.header.userParameters.userParameterString[0].value
+
+    @property
+    def slice_2d(self) -> bool:
+        """Is the acquisition run on 2D slices."""
+        return bool(self.header.userParameters.userParameterString[1].value)
+
     #############
     # Get data  #
     #############

src/snake/mrd_utils/writer.py

@@ -22,7 +22,9 @@
 log = logging.getLogger(__name__)
 
 
-def get_mrd_header(sim_conf: SimConfig, engine: str) -> mrd.xsd.ismrmrdHeader:
+def get_mrd_header(
+    sim_conf: SimConfig, engine: str, model: str, slice_2d: bool
+) -> mrd.xsd.ismrmrdHeader:
     """Create a MRD Header for snake-fmri data."""
     H = mrd.xsd.ismrmrdHeader()
     # Experimental conditions
@@ -78,7 +80,14 @@ def get_mrd_header(sim_conf: SimConfig, engine: str) -> mrd.xsd.ismrmrdHeader:
                 ("rng_seed", sim_conf.rng_seed),
                 ("max_sim_time", sim_conf.max_sim_time),
             ]
-        ]
+        ],
+        userParameterString=[
+            mrd.xsd.userParameterStringType(name=name, value=value)
+            for name, value in [
+                ("engine_model", model),
+                ("slice_2d", str(slice_2d)),
+            ]
+        ],
     )
 
     return H
@@ -204,6 +213,8 @@ def make_base_mrd(
     handlers: list[AbstractHandler] | HandlerList | None = None,
     smaps: NDArray | None = None,
     coil_cov: NDArray | None = None,
+    model: str = "simple",
+    slice_2d: bool = False,
 ) -> mrd.Dataset:
     """
     Create a base `.mrd` file from the simulation configurations.
@@ -233,7 +244,7 @@ def make_base_mrd(
         pass
     dataset = mrd.Dataset(filename, "dataset", create_if_needed=True)
     dataset.write_xml_header(
-        mrd.xsd.ToXML(get_mrd_header(sim_conf, sampler.__engine__))
+        mrd.xsd.ToXML(get_mrd_header(sim_conf, sampler.__engine__, model, slice_2d))
     )
     with PerfLogger(logger=log, name="acq"):
         sampler.add_all_acq_mrd(dataset, sim_conf)

src/snake/toolkit/cli/__init__.py

@@ -1 +1 @@
-""""Command Line Interface for SNAKE."""
+"""Command Line Interface for SNAKE."""

src/snake/toolkit/cli/acquisition.py

@@ -51,7 +51,9 @@ def acquisition(cfg: ConfigSNAKE) -> None:
     kwargs = {}
     if engine_klass.__engine_name__ == "NUFFT":
         kwargs["nufft_backend"] = cfg.engine.nufft_backend
-    engine = engine_klass(model=cfg.engine.model, snr=cfg.engine.snr, slice_2d=cfg.engine.slice_2d)  # type: ignore
+    engine = engine_klass(
+        model=cfg.engine.model, snr=cfg.engine.snr, slice_2d=cfg.engine.slice_2d
+    )  # type: ignore
 
     engine(
         cfg.filename,

src/snake/toolkit/reconstructors/pysap.py

@@ -114,7 +114,6 @@ def _reconstruct_cartesian(
                 ): idx
                 for idx in range(data_loader.n_frames)
             }
-
             for future in as_completed(futures):
                 future.result()
                 pbar.update(1)
@@ -132,10 +131,15 @@ def _reconstruct_nufft(
         from mrinufft import get_operator
 
         smaps = data_loader.get_smaps()
-
+        shape = data_loader.shape
         traj, kspace_data = data_loader.get_kspace_frame(0)
+
+        if data_loader.slice_2d:
+            shape = data_loader.shape[:2]
+            traj = traj.reshape(data_loader.n_shots, -1, traj.shape[-1])[0, :, :2]
+
         kwargs = dict(
-            shape=data_loader.shape,
+            shape=shape,
             n_coils=data_loader.n_coils,
             smaps=smaps,
         )
@@ -146,6 +150,7 @@ def _reconstruct_nufft(
             kwargs["density"] = self.density_compensation
         if "stacked" in self.nufft_backend:
             kwargs["z_index"] = "auto"
+
         nufft_operator = get_operator(
             self.nufft_backend,
             samples=traj,
@@ -158,8 +163,16 @@ def _reconstruct_nufft(
 
         for i in tqdm(range(data_loader.n_frames)):
             traj, data = data_loader.get_kspace_frame(i)
-            nufft_operator.samples = traj
-            final_images[i] = abs(nufft_operator.adj_op(data))
+            if data_loader.slice_2d:
+                nufft_operator.samples = traj.reshape(
+                    data_loader.n_shots, -1, traj.shape[-1]
+                )[0, :, :2]
+                data = np.reshape(data, (data.shape[0], data_loader.n_shots, -1))
+                for j in range(data.shape[1]):
+                    final_images[i, :, :, j] = abs(nufft_operator.adj_op(data[:, j]))
+            else:
+                nufft_operator.samples = traj
+                final_images[i] = abs(nufft_operator.adj_op(data))
         return final_images