fixes

examples/example_vds_simrec.py

@@ -77,9 +77,9 @@
 # Sequential Reconstruction
 # ~~~~~~~~~~~~~~~~~~~~~~~~~
 
-seq_data = SequentialReconstructor(max_iter_per_frame=20, threshold="sure").reconstruct(
-    sim
-)
+seq_data = SequentialReconstructor(
+    max_iter_per_frame=20, threshold="sure", compute_backend="numpy"
+).reconstruct(sim)
 fig4 = tile_view(abs(seq_data), samples=0.1, axis=0)
 
 # %%

src/conf/scenario1.yaml

@@ -1,5 +1,14 @@
 # This files contains the configuration to reproduce the scenario 1 of the Snkf paper.
 
+defaults:
+  - handlers:
+    - phantom-brainweb
+    - activation-block
+    - noise-gaussian
+    - acquisition-vds
+  - reconstructors: adjoint
+  - _self_
+
 force_sim: false
 cache_dir: ${oc.env:PWD}/cache
 result_dir: results
@@ -16,9 +25,10 @@ sim_params:
   n_coils: 1
   rng: 19980408
   lazy: True
+
 handlers:
   phantom-brainweb:
-    subject_id: 5
+    sub_id: 5
     bbox: [0.225,-0.07, 0.06, -0.055, null, null]
     brainweb_folder: ${cache_dir}/brainweb
     res: [3.0, 3.0,2.81 ]
@@ -29,14 +39,14 @@ handlers:
     duration: 300
     bold_strength: 0.05
   noise-gaussian:
-    snr: 100
+    snr: 30
   acquisition-vds:
     shot_time_ms: 50
     acs: 1
     accel: 1
     accel_axis: 0
     constant: true
-    direction: top-down
+    order: TOP_DOWN
     smaps: false
     n_jobs: 5
 

src/conf/scenario2.yaml

@@ -37,7 +37,7 @@ handlers:
     duration: 300
     bold_strength: 0.02
   noise-gaussian:
-    snr: 100
+    snr: 30
   acquisition-sos:
     shot_time_ms: 50
     acsz: 0.125

src/conf/scenario3.yaml

@@ -36,11 +36,11 @@ handlers:
     duration: 300
     bold_strength: 0.02
   noise-gaussian:
-    snr: 100
+    snr: 30
   acquisition-generic-noncartesian:
     shot_time_ms: 50
     n_jobs: 4
-    traj_files: ${oc.env:PWD}/cache/trajectory/sparkling3d-48-2688x5.bin
+    traj_files: ${cache_dir}/trajectory/sparkling3d-48-2688x5.bin
     traj_osf: 5
     smaps: true
     backend: "cufinufft"

src/snkf/handlers/acquisition/workers.py

@@ -132,7 +132,7 @@ def acq_cartesian(
             if sim.n_coils == 1:
                 kdata[kk, 0, mask] = kdata_t[i][ii]
             else:
-                kdata[kk, 0, mask] = kdata_t[i][ii]
+                kdata[kk, :, mask] = kdata_t[i][ii].T
             kmask[kk] += mask
     return kdata, kmask
 

src/snkf/reconstructors/base.py

@@ -1,6 +1,7 @@
 """Base Interfaces for the reconstructors."""
 
 import logging
+from dataclasses import field
 import numpy as np
 from typing import Protocol, Any, ClassVar
 from snkf.simulation import SimData
@@ -38,7 +39,10 @@ class BaseReconstructor(metaclass=MetaReconstructor):
     __registry__: ClassVar[dict]
     __reconstructor_name__: ClassVar[str]
 
-    nufft_kwargs: dict[str, Any]
+    nufft_kwargs: dict[str, Any] = field(default_factory=dict)
+
+    def __post_init__(self):
+        pass
 
     def setup(self, sim: SimData) -> None:
         """Set up the reconstructor."""

src/snkf/reconstructors/pysap.py

@@ -6,12 +6,11 @@
 
 from __future__ import annotations
 from dataclasses import field
-from typing import Literal, Any
+from typing import Any
 import logging
 import numpy as np
 
-from modopt.opt.linear import LinearParent, Identity
-from modopt.opt.proximity import ProximityParent
+from modopt.opt.linear import Identity
 
 from .base import BaseReconstructor, SpaceFourierProto
 from snkf.simulation import SimData
@@ -55,7 +54,8 @@ def get_fourier_operator(
     if backend_name in ["cufinufft", "stacked-cufinufft"]:
         import cupy as cp
 
-        smaps = cp.array(smaps)
+        if smaps is not None:
+            smaps = cp.array(smaps)
         kwargs["smaps_cached"] = True
     if sim.extra_infos["traj_params"]["constant"] is True and backend_name != "":
         logger.debug("using a duplicated operator.")
@@ -106,10 +106,9 @@ class ZeroFilledReconstructor(BaseReconstructor):
 
     __reconstructor_name__ = "adjoint"
 
-    def __init__(self, nufft_kwargs: dict = None):
-        if nufft_kwargs is None:
-            nufft_kwargs = {}
-        self.nufft_kwargs = nufft_kwargs
+    def __post_init__(self):
+        super().__post_init__()
+        self.fourier_op = None
 
     def setup(self, sim: SimData) -> None:
         """Set up the reconstructor."""
@@ -223,28 +222,18 @@ class LowRankPlusSparseReconstructor(BaseReconstructor):
 
     __reconstructor_name__ = "lr_f"
 
-    def __init__(
-        self,
-        lambda_l: float = 0.1,
-        lambda_s: float | Literal["sure"] = 1,
-        algorithm: str = "otazo",
-        max_iter: int = 20,
-        time_linear_op: LinearParent = None,
-        time_prox_op: ProximityParent = None,
-        space_prox_op: ProximityParent = None,
-        fourier_op: SpaceFourierProto | None = None,
-        nufft_kwargs: dict[str, Any] | None = None,
-    ):
-        super().__init__(nufft_kwargs)
-        self.lambda_l = lambda_l
-        self.lambda_s = lambda_s
-        self.max_iter = max_iter
-        self.algorithm = algorithm
-
-        self.time_linear_op = time_linear_op
-        self.time_prox_op = time_prox_op
-        self.space_prox_op = space_prox_op
-        self.fourier_op = fourier_op
+    nufft_kwargs: dict[str, Any] = field(default_factory=dict)
+    lambda_l: float = 0.1
+    lambda_s: float | str = 0.1
+    algorithm: str = "otazo"
+    max_iter: int = 20
+
+    def __post_init__(self):
+        super().__post_init__()
+        self.time_linear_op = None
+        self.time_prox_op = None
+        self.space_prox_op = None
+        self.fourier_op = None
 
     def __str__(self):
         if isinstance(self.lambda_s, float):
@@ -262,7 +251,6 @@ def setup(self, sim: SimData) -> None:
         if self.fourier_op is None:
             self.fourier_op = get_fourier_operator(
                 sim,
-                cartesian_repeat=False,
                 **self.nufft_kwargs,
             )
 

tests/test_cli.py

@@ -7,4 +7,4 @@
 
 def test_scenario1():
     cmd = ["src/snkf/cli/main.py", "--config-name=scenario1.yaml"]
-    result, _err = run_python_script(cmd)
+    result, _err = run_python_script(cmd, allow_warnings=True)