fix doc

docs/advanced_guide/writing_config_file.md

@@ -4,11 +4,3 @@
 
 ```
 
-<!-- #raw -->
-```{include} ../../../src/snkf/conf/simulation/sl_basic.yaml
-```
-<!-- #endraw -->
-
-<!-- #raw -->
-
-<!-- #endraw -->

docs/examples/example_big.py

@@ -1,12 +1,11 @@
 # %% [markdown]
-"""
-# Custom Phantom and ROI
+# # Custom Phantom and ROI
 
-In this example we are going to show the different way to generate phantom data, using
-the BIG phantom.
-This phantom is more realistic than the Shepp-Logan Phantom, but is a 2D phantom.
-"""
+# In this example we are going to show the different way to generate phantom data, using
+# the BIG phantom.
+# This phantom is more realistic than the Shepp-Logan Phantom, but is a 2D phantom.
 
+# %%
 import matplotlib.pyplot as plt
 from snkf.handlers.phantom._big import generate_phantom, raster_phantom
 

docs/examples/example_shepp_logan.py

@@ -1,10 +1,9 @@
 # %% [markdown]
-"""
-# Generate a 3d+t Simple Phantom
-
-In this example we simulate a 3D phantom and add a simple activation pattern.
-"""
+# # Generate a 3d+t Simple Phantom
+#
+# In this example we simulate a 3D phantom and add a simple activation pattern.
 
+# %%
 import matplotlib.pyplot as plt
 
 from snkf.simulation import SimData

docs/examples/example_simulation_with_factory.py

@@ -1,11 +1,9 @@
 # %% [markdown]
-"""
-# Using a simulation configuration file
+# # Using a simulation configuration file
 
-This example present how to use a simulation config file.
-"""
+# This example present how to use a simulation config file.
+# %%
 
-import io  # to simulate a file access.
 
 from snkf import load_from_yaml
 
@@ -18,6 +16,7 @@
 #
 # For instance to create a 2D+T
 
+# %%
 sim_config = """
 ### Simulation for a Shepp Logan phantom with activation.
 
@@ -47,17 +46,22 @@
 
 # %% [markdown]
 # ```{note}
-#     In the handlers section, the name of each handler matter!
-#     it is the key for finding the related handler object.
-#     They will be processed in order.
+# In the handlers section, the name of each handler matter!
+# it is the key for finding the related handler object.
+# They will be processed in order.
 # ```
 #
 # ## Launching the simulation
 #
 # Thanks to the detailled configuration it is as simple as:
 
-# equivalent to
+# %%
+
+# The two following lines are equivalent to
 # with open("your_config.yaml") as config_file:
+
+import io  # to simulate a file access.
+
 with io.StringIO(sim_config) as config_file:
 
     simulator, sim = load_from_yaml(config_file)

docs/examples/example_vds_simrec.py

@@ -1,9 +1,6 @@
 # %% [markdown]
-"""
-# Simulation and Reconstruction
-
-This example shows how to simulate and reconstruct a simple 2D vds simulation.
-"""
+# # Simulation and Reconstruction
+# This example shows how to simulate and reconstruct a simple 2D vds simulation.
 
 # %%
 
@@ -40,7 +37,7 @@
 #
 # We initialize the simulator from the availables handlers
 
-# %%
+# %% execution={"timeout": "1000"}
 print(list_handlers())
 
 simulator = (
@@ -80,7 +77,7 @@
 #
 # Simple adjoint fourier transform.
 
-# %%
+# %% execution={"timeout": "1000"}
 
 adj_data = ZeroFilledReconstructor().reconstruct(sim)
 
@@ -89,7 +86,8 @@
 # %% [markdown]
 # ### Sequential Reconstruction
 
-# %%
+# %% execution={"timeout": "1000"}
+
 seq_data = SequentialReconstructor(
     max_iter_per_frame=20, threshold="sure", compute_backend="numpy"
 ).reconstruct(sim)
@@ -98,6 +96,7 @@
 # %% [markdown]
 # ### LowRank + Sparse Reconstruction
 
+# %% execution={"timeout": "1000"}
 lr_s = LowRankPlusSparseReconstructor(
     lambda_l=0.1, lambda_s="sure", algorithm="otazo_raw", max_iter=20
 ).reconstruct(sim)

src/snkf/handlers/acquisition/base.py

@@ -284,10 +284,14 @@ class NonCartesianAcquisitionHandler(BaseAcquisitionHandler):
 
     The MRI acquisition is modelled as follows:
     .. math::
+
         s(t) = \int_{\Omega} \rho(x,t) \exp(-2i\pi k(t) \cdot x) dx
+
     where :math:`\rho` is the object, :math:`k(t)` is the k-space trajectory.
+
     In practice:
     .. math::
+
         s(t) = \sum_{x \in \Omega} \rho(x,t) \exp(-2i\pi k(t) \cdot x) \Delta x
     """
 

src/snkf/handlers/motion/__init__.py

@@ -1,3 +1,6 @@
 """Motion Module."""
 
 from .image import RandomMotionImageHandler
+from .kspace import RandomMotionKspaceHandler
+
+__all__ = ["RandomMotionImageHandler", "RandomMotionKspaceHandler"]

src/snkf/handlers/motion/image.py

@@ -3,8 +3,6 @@
 import numpy as np
 from numpy.typing import NDArray
 
-from snkf.base import validate_rng
-
 from ...simulation import SimData
 from ..base import AbstractHandler, requires_field
 from .utils import apply_shift, apply_rotation_at_center, motion_generator

src/snkf/handlers/motion/kspace.py

@@ -6,11 +6,11 @@
 """
 
 import numpy as np
-from np.typing import NDArray
+from numpy.typing import NDArray
 
 from ...simulation import SimData
 from ..base import AbstractHandler, requires_field
-from .utils import motion_generator, rotation3D
+from .utils import motion_generator, rotation3d
 
 
 @requires_field(["kspace_data", "kspace_mask"])
@@ -36,7 +36,7 @@ class RandomMotionKspaceHandler(AbstractHandler):
     time resolution for the simulation.
     """
 
-    __handler_name__ = "motion-image"
+    __handler_name__ = "motion-kspace"
 
     ts_std_mm: tuple[float, float, float]
     rs_std_mm: tuple[float, float, float]
@@ -104,7 +104,7 @@ def rotate(kspace_loc_to_corrupt: NDArray, rotation: NDArray) -> NDArray:
     """
     new_loc = np.zeros_like(kspace_loc_to_corrupt)
     for t in range(kspace_loc_to_corrupt.shape[0]):
-        R = rotation3D(rotation[:, t])
+        R = rotation3d(rotation[:, t])
         new_loc[t, :, :] = np.matmul(kspace_loc_to_corrupt[t, :, :], R)
 
     return new_loc