Clean CPU examples

docs/conf.py

@@ -78,6 +78,7 @@
     "reference_url": {"mrinufft": None},
     "examples_dirs": ["../examples/"],
     "gallery_dirs": ["generated/autoexamples"],
+    "within_subsection_order": "ExampleTitleSortKey",
     "filename_pattern": "/example_",
     "ignore_pattern": r"(__init__|conftest|utils).py",
     "nested_sections": True,

examples/example_cg.py → examples/GPU/example_cg.py

@@ -1,24 +1,27 @@
-# %%
 """
-Example of using the Conjugate Gradient method.
+======================================
+Reconstruction with conjugate gradient
+======================================
+
+An example to show how to reconstruct volumes using conjugate gradient method.
 
-This script demonstrates the use of the Conjugate Gradient (CG) method 
-for solving systems of linear equations of the form Ax = b, where A is a symmetric 
-positive-definite matrix. The CG method is an iterative algorithm that is particularly 
+This script demonstrates the use of the Conjugate Gradient (CG) method
+for solving systems of linear equations of the form Ax = b, where A is a symmetric
+positive-definite matrix. The CG method is an iterative algorithm that is particularly
 useful for large, sparse systems where direct methods are computationally expensive.
 
-The Conjugate Gradient method is widely used in various scientific and engineering 
-applications, including solving partial differential equations, optimization problems, 
+The Conjugate Gradient method is widely used in various scientific and engineering
+applications, including solving partial differential equations, optimization problems,
 and machine learning tasks.
 
 References
 ----------
-- Inpirations: 
+- Inpirations:
         - https://sigpy.readthedocs.io/en/latest/_modules/sigpy/alg.html#ConjugateGradient
         - https://aquaulb.github.io/book_solving_pde_mooc/solving_pde_mooc/notebooks/05_IterativeMethods/05_02_Conjugate_Gradient.html
-- Wikipedia: 
-        - https://en.wikipedia.org/wiki/Conjugate_gradient_method 
-        - https://en.wikipedia.org/wiki/Momentum 
+- Wikipedia:
+        - https://en.wikipedia.org/wiki/Conjugate_gradient_method
+        - https://en.wikipedia.org/wiki/Momentum
 """
 
 # %%
@@ -42,7 +45,10 @@
 density = voronoi(samples_loc)  # get the density
 
 nufft = NufftOperator(
-    samples_loc, shape=image.shape, density=density, n_coils=1
+    samples_loc,
+    shape=image.shape,
+    density=density,
+    n_coils=1,
 )  # create the NUFFT operator
 
 # %%
@@ -52,17 +58,17 @@
 
 # %%
 # Display the results
-plt.figure(figsize=(10, 5))
+plt.figure(figsize=(9, 3))
 plt.subplot(1, 3, 1)
-plt.title("Original Image")
+plt.title("Original image")
 plt.imshow(abs(image), cmap="gray")
 
 plt.subplot(1, 3, 2)
-plt.title("Reconstructed Image with CG")
+plt.title("Conjugate gradient")
 plt.imshow(abs(reconstructed_image), cmap="gray")
 
 plt.subplot(1, 3, 3)
-plt.title("Reconstructed Image with adjoint")
+plt.title("Adjoint NUFFT")
 plt.imshow(abs(nufft.adj_op(kspace_data)), cmap="gray")
 
 plt.show()

examples/README.rst

@@ -3,4 +3,4 @@
 Examples
 ========
 
-This is a collection of examples showing how to use mri-nufft to perform MR image reconstruction.
+This is a collection of examples showing how to use MRI-nufft to perform MR image reconstruction.

examples/conftest.py

@@ -12,8 +12,8 @@
 
 """
 
-import sys
 import runpy
+import sys
 from pathlib import Path
 
 import matplotlib as mpl

examples/example_2D_trajectories.py

@@ -13,20 +13,16 @@
 # are redundant across the different patterns, some of the documentation
 # will refer to previous patterns for explanation.
 #
-# Note that most sources have not been added yet, but will be in the near
-# future.
-#
 
 # External
 import matplotlib.pyplot as plt
 import numpy as np
+from utils import show_argument, show_trajectory
 
 # Internal
 import mrinufft as mn
 import mrinufft.trajectories.maths as mntm
 from mrinufft import display_2D_trajectory
-from utils import show_argument, show_trajectory
-
 
 # %%
 # Script options

examples/example_3D_trajectories.py

@@ -13,10 +13,10 @@
 # are redundant across the different patterns, some of the documentation
 # will refer to previous patterns for explanation.
 #
-# Note that most sources have not been added yet, but will be in the near
-# future. Also the examples hereafter only cover natively 3D trajectories
+# Note that the examples hereafter only cover natively 3D trajectories
 # or famous 3D trajectories obtained from 2D. Examples on how to use
-# 2D-to-3D expansion methods will be presented over another page.
+# tools to make 3D trajectories out of 2D ones are presented in
+# :ref:`sphx_glr_generated_autoexamples_example_trajectory_tools.py`
 #
 # In this page in particular, we invite the user to manually run the script
 # to be able to manipulate the plot orientations with the matplotlib interface
@@ -26,12 +26,11 @@
 # External
 import matplotlib.pyplot as plt
 import numpy as np
+from utils import show_argument, show_trajectory
 
 # Internal
 import mrinufft as mn
 from mrinufft import display_2D_trajectory, display_3D_trajectory
-from utils import show_argument, show_trajectory
-
 
 # %%
 # Script options

examples/example_display_config.py

@@ -3,20 +3,24 @@
 Trajectory display configuration
 ================================
 
-The look of the display trajectories can be tweaked by using :py:class:`displayConfig`
+An example to show how to customize trajectory displays.
 
-You can tune these parameters to your own taste and needs.
+The parameters presented here can be tuned to your own taste and needs
+by using :py:class:`displayConfig`.
 """
 
 import matplotlib as mpl
 import matplotlib.pyplot as plt
-
-# %%
 import numpy as np
 
 from mrinufft import display_2D_trajectory, display_3D_trajectory, displayConfig
 from mrinufft.trajectories import conify, initialize_2D_spiral
 
+# %%
+# Script options
+# ==============
+# These options are used in the examples below to define trajectories and display options.
+
 # Trajectory parameters
 Nc = 120  # Number of shots
 Ns = 500  # Number of samples per shot
@@ -26,7 +30,6 @@
 subfigure_size = 6  # Figure size for subplots
 one_shot = -5  # Highlight one shot in particular
 
-
 # %%
 
 
@@ -47,28 +50,32 @@ def show_traj(traj, name, values, **kwargs):
 # %%
 #
 # Trajectory displays
-# ====================
-# To show case the display parameters of trajectories, we will use the following trajectory
-# The effect of trajectory parameter are explained in the :ref:`sphx_glr_generated_autoexamples_example_3D_trajectories.py` Example.
+# ===================
+#
+# The following trajectory will be used to showcase the display parameters.
+# The trajectory parameters are explained in the
+# :ref:`sphx_glr_generated_autoexamples_example_3D_trajectories.py` example.
 
 traj = conify(initialize_2D_spiral(Nc // 6, Ns), nb_cones=6)[::-1]
 
 # %%
 # ``linewidth``
 # -------------
-# The linewidth of the shot can be updated to have more or less empty space in the plot.
+# The ``linewidth`` corresponds to the curve thickness, and can be changed
+# to improve the shots visibility.
 show_traj(traj, "linewidth", [0.5, 2, 4])
 
 # %%
 # ``palette``
 # -----------
-# The ``palette`` parameter allows to change the color of the shots.
+# The ``palette`` parameter allows you to change the color of the shots.
 show_traj(traj, "palette", ["tab10", "magma", "jet"])
 
 # %%
 # ``one_shot_color``
 # ------------------
-# The ``one_shot_color`` parameter allows to highlight one shot in particular.
+# The ``one_shot_color`` parameter is used to highlight one shot in particular
+# with a specified color.
 with displayConfig(palette="viridis"):
     show_traj(
         traj, "one_shot_color", ["tab:blue", "tab:orange", "tab:green"], one_shot=-5
@@ -77,49 +84,37 @@ def show_traj(traj, name, values, **kwargs):
 # %%
 # ``nb_colors``
 # -------------
-# The ``nb_colors`` parameter allows to change the number of colors used to display the shots.
-
+# The ``nb_colors`` parameter allows you to change the number of colors used from the
+# specified color palette to display the shots.
 show_traj(traj, "nb_colors", [1, 4, 10])
 
+
 # %%
 # Labels, titles and legends
 # ==========================
 
 # %%
 # ``fontsize``
 # ------------
-# The ``fontsize`` parameter allows to change the fontsize of the labels /title
-
+# The ``fontsize`` parameter changes the fontsize of the labels/titles.
 show_traj(traj, "fontsize", [12, 18, 24])
 
 # %%
 # ``pointsize``
 # -------------
-# To show the gradient constraint violation we can use the ``pointsize`` parameter
+# The ``pointsize`` parameter is used when showing the gradient constraint violations
+# to change the violation point sizes.
 show_traj(traj, "pointsize", [0.5, 2, 4], show_constraints=True)
 
 # %%
 # ``gradient_point_color`` and ``slewrate_point_color``
 # -----------------------------------------------------
-# The ``gradient_point_color`` and ``slewrate_point_color`` parameters allows to change the color of the points
-# that are violating the gradient or slewrate constraints.
-
+# The ``gradient_point_color`` and ``slewrate_point_color`` parameters allows you
+# to change the color of the points where gradient or slew rate constraint violations
+# are observed.
 show_traj(
     traj,
     "slewrate_point_color",
     ["tab:blue", "tab:orange", "tab:red"],
     show_constraints=True,
 )
-
-
-# %%
-# Gradients profiles
-# ==================
-
-# %%
-
-# %%
-
-# %%
-
-# %%

examples/example_gif_2D.py

@@ -1,22 +1,27 @@
 """
-=======================
-2D Trajectories display
-=======================
+========================
+Animated 2D trajectories
+========================
 
-A collection of 2D trajectories are generated and saved as a gif.
+An animation to show 2D trajectory customization.
 
 """
 
+import time
+
 import joblib
 import matplotlib.pyplot as plt
 import numpy as np
+import tempfile as tmp
 from PIL import Image, ImageSequence
-import time
+
 import mrinufft.trajectories.display as mtd
 import mrinufft.trajectories.trajectory2D as mtt
 from mrinufft.trajectories.display import displayConfig
 
-# Options
+# %%
+# Script options
+# ==============
 
 Nc = 16
 Ns = 200
@@ -29,7 +34,9 @@
 duration = 150  # seconds
 
 
-# Generation
+# %%
+# Trajectory generation
+# =====================
 
 # Initialize trajectory function
 functions = [
@@ -125,14 +132,18 @@
 ]
 
 
+# %%
+# Animation rendering
+# ===================
+
 frame_setup = [
     (f, i, name, arg)
     for (name, f), args in list(zip(functions, arguments))
     for i, arg in enumerate(args)
 ]
 
 
-def draw_frame(func, index, name, arg, save_dir="/tmp/"):
+def draw_frame(func, index, name, arg):
     """Draw a single frame of the gif and save it to a tmp file."""
     trajectory = func(arg)
     # General configuration
@@ -158,8 +169,7 @@ def draw_frame(func, index, name, arg, save_dir="/tmp/"):
     )
 
     # Save figure
-    hashed = joblib.hash((index, name, arg, time.time()))
-    filename = save_dir + f"{hashed}.png"
+    filename = f"{tmp.NamedTemporaryFile().name}.png"
     plt.savefig(filename, bbox_inches="tight")
     plt.close()
     return filename