Densities, random walks & travelling salesman (#206)

* Split trajectory.maths.py into a submodule * Add densities, random walk and travelling salesman trajectories * fixup! Add densities, random walk and travelling salesman trajectories * Add docstrings for random walk and TSP solver * fixup! Add densities, random walk and travelling salesman trajectories * Add docstrings to TSP & sampling densities * Add samplings to random walk initializations and fix boundaries * Add utils to examples to show densities * Add sampling density example skeleton * Add descriptions to sampling density examples * Add dependency to pywavelet * Improve cutoff/decay density, fix dependencies * Gather extra dependencies, homogeneize extra imports * Fix imports to pywavelets * Fix black format in smaps * Remove except duplicate in io/siemens * Update CI with new [extra] dependencies * [docs] Trigger documentation build --------- Co-authored-by: Chaithya G R <[email protected]>
mind-inria · Dec 16, 2024 · 9c41feb · 9c41feb
1 parent 0b641a6
commit 9c41feb
Show file tree

Hide file tree

Showing 25 changed files with 2,076 additions and 507 deletions.
diff --git a/.github/workflows/test-ci.yml b/.github/workflows/test-ci.yml
@@ -206,7 +206,7 @@ jobs:
         shell: bash
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -e .[test,dev]
+          python -m pip install -e .[extra,test,dev]
           python -m pip install finufft pooch brainweb-dl torch fastmri
         
       - name: Install GPU related interfaces

diff --git a/examples/example_2D_trajectories.py b/examples/example_2D_trajectories.py
@@ -17,7 +17,7 @@
 # External
 import matplotlib.pyplot as plt
 import numpy as np
-from utils import show_argument, show_trajectory
+from utils import show_trajectories, show_trajectory
 
 # Internal
 import mrinufft as mn
@@ -75,7 +75,7 @@
 
 arguments = [8, 16, 32, 64]
 function = lambda x: mn.initialize_2D_radial(x, Ns, tilt=tilt, in_out=in_out)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -89,7 +89,7 @@
 
 arguments = [8, 16, 32, 64]
 function = lambda x: mn.initialize_2D_radial(Nc, x, tilt=tilt, in_out=in_out)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -105,7 +105,7 @@
 
 arguments = ["uniform", "golden", "mri-golden", np.pi / 17]
 function = lambda x: mn.initialize_2D_radial(Nc, Ns, tilt=x, in_out=in_out)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -128,7 +128,7 @@
 
 arguments = [True, False]
 function = lambda x: mn.initialize_2D_radial(Nc, Ns, tilt=tilt, in_out=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -170,7 +170,7 @@
 function = lambda x: mn.initialize_2D_spiral(
     Nc, Ns, tilt=tilt, nb_revolutions=x, in_out=in_out
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -194,7 +194,7 @@
 
 arguments = ["galilean", "archimedes", "fermat", 1 / 4]
 function = lambda x: mn.initialize_2D_spiral(Nc, Ns, tilt=tilt, spiral=x, in_out=in_out)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -221,7 +221,7 @@
     Ns,
     patch_center=x,
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -267,7 +267,7 @@
     Ns,
     spiral_reduction=x,
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -293,7 +293,7 @@
     Ns,
     patch_center=x,
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -333,7 +333,7 @@
 function = lambda x: mn.initialize_2D_cones(
     Nc, Ns, tilt=tilt, in_out=in_out, nb_zigzags=x
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -348,7 +348,7 @@
 
 arguments = [0.2, 1, 2, 3]
 function = lambda x: mn.initialize_2D_cones(Nc, Ns, tilt=tilt, in_out=in_out, width=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -413,7 +413,7 @@
 
 arguments = [2, 3, 4, 6]
 function = lambda x: mn.initialize_2D_propeller(Nc, Ns, nb_strips=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -450,7 +450,7 @@
 
 arguments = [Nc, int(2 * Nc / 3), int(Nc / 3)]
 function = lambda x: mn.initialize_2D_rings(Nc=x, Ns=Ns, nb_rings=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 # %%
 #
@@ -461,7 +461,7 @@
 
 arguments = [Nc, int(4 * Nc / 3), 2 * Nc]
 function = lambda x: mn.initialize_2D_rings(Nc=x, Ns=Ns, nb_rings=Nc)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -501,7 +501,7 @@
 
 arguments = [0, 1, 5, 10]
 function = lambda x: mn.initialize_2D_rosette(Nc, Ns, in_out=in_out, coprime_index=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -541,7 +541,7 @@
 function = lambda x: mn.initialize_2D_polar_lissajous(
     Nc, Ns, in_out=in_out, coprime_index=x
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -564,7 +564,7 @@
 function = lambda x: mn.initialize_2D_polar_lissajous(
     Nc, Ns, in_out=in_out, nb_segments=x
 )
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -588,7 +588,7 @@
         function = lambda x: mn.initialize_2D_polar_lissajous(
             Nc, Ns, in_out=io, coprime_index=cpi, nb_segments=x
         )
-        show_argument(
+        show_trajectories(
             function, arguments, one_shot=one_shot, subfig_size=subfigure_size
         )
 
@@ -625,7 +625,7 @@
 
 arguments = [1, 2.5, 5, 10]
 function = lambda x: mn.initialize_2D_waves(Nc, Ns, nb_zigzags=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -644,7 +644,7 @@
 
 arguments = [0, 1, 1.5, 3]
 function = lambda x: mn.initialize_2D_waves(Nc, Ns, width=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%
@@ -679,7 +679,7 @@
 
 arguments = [1, 1.5, 2, 3]
 function = lambda x: mn.initialize_2D_lissajous(Nc, Ns, density=x)
-show_argument(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
+show_trajectories(function, arguments, one_shot=one_shot, subfig_size=subfigure_size)
 
 
 # %%