diff --git a/scripts/01_aRTist_bridge.py b/scripts/01_aRTist_bridge.py
index 2d93de9ed2a942eca9d6c6b1a6d6d00e61f118b4..0c992223e735ce532768b5bee1e00ac4707d2a1d 100644
--- a/scripts/01_aRTist_bridge.py
+++ b/scripts/01_aRTist_bridge.py
@@ -8,7 +8,7 @@ from pathlib import Path
FOLDER = Path(__file__)
-TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+TEMP_FOLDER = FOLDER.parent.parent / "temp"
def main():
@@ -16,16 +16,14 @@ def main():
# Create the cylindrical projection interface
cyl_proj = CylindricalProjection()
-
# Load the test object 'olaf'. It is automatically installed to your site-packages
- print(f'STL Path: {scones_mesh.object_path}')
+ print(f"STL Path: {scones_mesh.object_path}")
# Obect are loaded in a dataclass: MeshObject.
- print(f'Mesh is a MeshObject: {isinstance(scones_mesh, MeshObject)}')
+ print(f"Mesh is a MeshObject: {isinstance(scones_mesh, MeshObject)}")
scones_mesh.position_mm = np.array([0, 0, 0])
- scones_mesh.orientation_quat = np.array([0., -0., 0., 0.1])
-
-
+ scones_mesh.orientation_quat = np.array([0.0, -0.0, 0.0, 0.1])
+
# The `load_mesh` function load a list of MeshObject
load_mesh(cyl_proj, [scones_mesh])
@@ -33,8 +31,12 @@ def main():
map_position = np.array([0, 0, 0])
# Generate local cylindrical projection
- half_rays = cyl_proj.compute_projection(map_position, output_full_ray_projection=False)
- full_rays = cyl_proj.compute_projection(map_position, output_full_ray_projection=True)
+ half_rays = cyl_proj.compute_projection(
+ map_position, output_full_ray_projection=False
+ )
+ full_rays = cyl_proj.compute_projection(
+ map_position, output_full_ray_projection=True
+ )
# code_embedder:A end
# Make some nice plots!
@@ -42,26 +44,26 @@ def main():
ax1 = fig.add_subplot(121)
ax1.imshow(half_rays)
- ax1.set_xlabel(r'$Z$ / mm')
- ax1.set_ylabel(r'$\alpha$ / rad')
- ax1.set_title('Half Rays')
- ax1.set_xticks([0, 1000, 2000])
- ax1.set_xticklabels([r'$-3141.5$', r'$0.$', r'$3141.5$'])
- ax1.set_yticks([0, 1000, 2000])
- ax1.set_yticklabels([r'$-\pi$', r'$0.$', r'$\pi$'])
+ ax1.set_xlabel(r"$Z$ / mm")
+ ax1.set_ylabel(r"$\alpha$ / rad")
+ ax1.set_title("Half Rays")
+ ax1.set_xticks([0, 1000, 2000])
+ ax1.set_xticklabels([r"$-3141.5$", r"$0.$", r"$3141.5$"])
+ ax1.set_yticks([0, 1000, 2000])
+ ax1.set_yticklabels([r"$-\pi$", r"$0.$", r"$\pi$"])
ax2 = fig.add_subplot(122)
ax2.imshow(full_rays)
- ax2.set_xlabel(r'$Z$ / mm')
- ax2.set_ylabel(r'$\alpha$ / rad')
- ax2.set_title('Full Rays')
- ax2.set_xticks([0, 1000, 2000])
- ax2.set_xticklabels([r'$-3141.5$', r'$0.$', r'$3141.5$'])
- ax2.set_yticks([0, 1000, 2000])
- ax2.set_yticklabels([r'$-\pi$', r'$0.$', r'$\pi$'])
+ ax2.set_xlabel(r"$Z$ / mm")
+ ax2.set_ylabel(r"$\alpha$ / rad")
+ ax2.set_title("Full Rays")
+ ax2.set_xticks([0, 1000, 2000])
+ ax2.set_xticklabels([r"$-3141.5$", r"$0.$", r"$3141.5$"])
+ ax2.set_yticks([0, 1000, 2000])
+ ax2.set_yticklabels([r"$-\pi$", r"$0.$", r"$\pi$"])
- plt.savefig(TEMP_FOLDER / 'scones.png')
+ plt.savefig(TEMP_FOLDER / "scones.png")
-if __name__ == '__main__':
- main()
\ No newline at end of file
+if __name__ == "__main__":
+ main()
diff --git a/scripts/02_generate_atlas.py b/scripts/02_generate_atlas.py
index d3417c626bb60df82a64937dd7693b7311e549a9..a3401d6aeac5c37fd0945a8664b12c33f8b54a82 100644
--- a/scripts/02_generate_atlas.py
+++ b/scripts/02_generate_atlas.py
@@ -6,7 +6,7 @@ from pathlib import Path
# Just get the temp folder to store the atlas
FOLDER = Path(__file__)
-TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+TEMP_FOLDER = FOLDER.parent.parent / "temp"
def main():
@@ -15,13 +15,18 @@ def main():
cyl_proj = CylindricalProjection()
load_mesh(cyl_proj, [olaf_mesh])
# make an atlas
-
- save_path = record_atlas(cyl_proj, [olaf_mesh], 'test', TEMP_FOLDER,
- map_bounding_box=[-10, 20], number_of_maps=2)
+
+ save_path = record_atlas(
+ cyl_proj,
+ [olaf_mesh],
+ "test",
+ TEMP_FOLDER,
+ map_bounding_box=[-10, 20],
+ number_of_maps=2,
+ )
# code_embedder:A end
- print(f'Atlas saved to the path: {save_path}')
-
-
+ print(f"Atlas saved to the path: {save_path}")
+
-if __name__ == '__main__':
- main()
\ No newline at end of file
+if __name__ == "__main__":
+ main()
diff --git a/scripts/03_load_atlas.py b/scripts/03_load_atlas.py
index f20a8afcc7ce574865d2a7e765e171a003bdb044..e0ed4ed656b35843f68abcfc8ed5c19ff9d583b0 100644
--- a/scripts/03_load_atlas.py
+++ b/scripts/03_load_atlas.py
@@ -5,22 +5,23 @@ from pathlib import Path
# Just get the temp folder to store the atlas
FOLDER = Path(__file__)
-TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+TEMP_FOLDER = FOLDER.parent.parent / "temp"
def main():
# code_embedder:A start
- files = list(TEMP_FOLDER.glob('*.h5'))
+ files = list(TEMP_FOLDER.glob("*.h5"))
if not files:
- raise FileNotFoundError('No .h5 files in temp folder. Run Example 02!')
+ raise FileNotFoundError("No .h5 files in temp folder. Run Example 02!")
maps, points, mesh_object_list = load_atlas(files[-1])
# code_embedder:A end
- print(f'Loaded Map Shape: {maps.shape}')
- print(f'Loaded Map Centre Shape: {points.shape}')
- print(f'First Object: {mesh_object_list[0]}')
+ print(f"Loaded Map Shape: {maps.shape}")
+ print(f"Loaded Map Centre Shape: {points.shape}")
+ print(f"First Object: {mesh_object_list[0]}")
- voxel_maps(maps, TEMP_FOLDER / 'scones_maps.png', title='Scones Atlas')
+ voxel_maps(maps, TEMP_FOLDER / "scones_maps.png", title="Scones Atlas")
-if __name__ == '__main__':
- main()
\ No newline at end of file
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/09_data_aug_pipeline.py b/scripts/09_data_aug_pipeline.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/src/cyxtrax/common/__init__.py b/src/cyxtrax/common/__init__.py
index 7c315e4bdfc523b5f0b0ecc157a3dcc366044e11..3b30905a6749b89d564f2cb19c98ed62b7be642f 100644
--- a/src/cyxtrax/common/__init__.py
+++ b/src/cyxtrax/common/__init__.py
@@ -1,6 +1,4 @@
from .mesh_object import MeshObject
-__all__ = [
- 'MeshObject'
-]
\ No newline at end of file
+__all__ = ["MeshObject"]
diff --git a/src/cyxtrax/io/__init__.py b/src/cyxtrax/io/__init__.py
index 2fff89e6e43e6ba570c599b610827e48cf68a198..f73e11006a7178bea608543438dd320b976650be 100644
--- a/src/cyxtrax/io/__init__.py
+++ b/src/cyxtrax/io/__init__.py
@@ -1,8 +1,6 @@
from .generate_atlas import record_atlas
from .load_maps import load_atlas
+from .save_map import save_atlas
-__all__ = [
- 'record_atlas',
- 'load_atlas'
-]
\ No newline at end of file
+__all__ = ["record_atlas", "load_atlas", "save_atlas"]
diff --git a/src/cyxtrax/io/save_map.py b/src/cyxtrax/io/save_map.py
new file mode 100644
index 0000000000000000000000000000000000000000..429070770cf312eb02ded5406348e7e3d97b0f27
--- /dev/null
+++ b/src/cyxtrax/io/save_map.py
@@ -0,0 +1,52 @@
+from cyxtrax.common.mesh_object import MeshObject
+from pathlib import Path
+import numpy as np
+import h5py
+import json
+
+
+def to_dict(mesh_object=MeshObject) -> dict:
+ return mesh_object.as_dict()
+
+
+def save_atlas(
+ mesh_list: list[MeshObject],
+ maps: np.ndarray,
+ map_position: np.ndarray,
+ atlas_name: str,
+ save_folder: Path,
+):
+ save_path = save_folder / f"{atlas_name}.h5"
+ file = h5py.File(save_path, "a")
+
+ x_px = maps.shape[0]
+ y_px = maps.shape[1]
+ number_of_maps = maps.shape[2]
+
+ projection = file.require_dataset(
+ "maps",
+ shape=(
+ x_px,
+ y_px,
+ number_of_maps,
+ ), # Initial shape with third dimension as 0
+ maxshape=(
+ x_px,
+ y_px,
+ number_of_maps,
+ ),
+ dtype=np.float32,
+ )
+
+ projection_points = file.require_dataset(
+ "positions",
+ shape=(3, number_of_maps**3), # Initial shape with third dimension as 0
+ maxshape=(3, number_of_maps**3),
+ dtype=np.float32,
+ )
+
+ mesh_list_dict = list(map(to_dict, mesh_list))
+ file.attrs["mesh_list"] = json.dumps(mesh_list_dict)
+
+ projection[:] = maps
+ projection_points[:] = map_position
diff --git a/src/cyxtrax/mapping/__init__.py b/src/cyxtrax/mapping/__init__.py
index 122cf03b2fe8d11b76711526d46360f17f553186..30956ad80a26f94a42a7f94c9dd2321cbc40eae9 100644
--- a/src/cyxtrax/mapping/__init__.py
+++ b/src/cyxtrax/mapping/__init__.py
@@ -1,6 +1,3 @@
from .mapping import map_geometry_2_projection, map_source_2_cylinder
-__all__ = [
- 'map_geometry_2_projection',
- 'map_source_2_cylinder'
-]
+__all__ = ["map_geometry_2_projection", "map_source_2_cylinder"]
diff --git a/src/cyxtrax/simulation/__init__.py b/src/cyxtrax/simulation/__init__.py
index ceddce2bc31b45b48999c027cb574f4fba0a2b2c..3b5fe4ee7274a17030859c9147303a56f39d650d 100644
--- a/src/cyxtrax/simulation/__init__.py
+++ b/src/cyxtrax/simulation/__init__.py
@@ -1,8 +1,3 @@
from .artist_bridge import CylindricalProjection, load_mesh, SAVEMODES, utility
-__all__ = [
- 'CylindricalProjection',
- 'load_mesh',
- 'SAVEMODES',
- 'utility'
-]
\ No newline at end of file
+__all__ = ["CylindricalProjection", "load_mesh", "SAVEMODES", "utility"]
diff --git a/src/cyxtrax/simulation/artist_bridge.py b/src/cyxtrax/simulation/artist_bridge.py
index 2a472cff07340b599498569643aaba862269c335..9d35f2300415c243d9e8be4ee535bc9c3d4ca7b7 100644
--- a/src/cyxtrax/simulation/artist_bridge.py
+++ b/src/cyxtrax/simulation/artist_bridge.py
@@ -6,8 +6,10 @@ except ModuleNotFoundError:
warn(
"The module `artistlib`is not installed. The simulation module is not 100\% usable! \nInstall: https://github.com/wittlsn/aRTist-PythonLib"
)
+
def API():
return None
+
utility = None
SAVEMODES = None
from pathlib import Path
@@ -44,7 +46,6 @@ def set_cone_mode(api: API):
with importlib.resources.path("cyxtrax.data", "cone.aRTist") as file_path:
print(f"Load: {file_path}")
api.load_project(file_path)
-
class CylindricalProjection:
diff --git a/src/cyxtrax/simulation/model/__init__.py b/src/cyxtrax/simulation/model/__init__.py
index ddd257a4ea7a8a6ad86558ce53971d1a321947ee..187de9f0bbf17f07c8294967c4693fb5539be783 100644
--- a/src/cyxtrax/simulation/model/__init__.py
+++ b/src/cyxtrax/simulation/model/__init__.py
@@ -3,8 +3,8 @@ from .noise import add_white_noise, add_gaussian_blur
from .xray import add_material
__all__ = [
- 'AugemntationParameter',
- 'add_white_noise',
- 'add_gaussian_blur',
- 'add_material'
-]
\ No newline at end of file
+ "AugemntationParameter",
+ "add_white_noise",
+ "add_gaussian_blur",
+ "add_material",
+]
diff --git a/src/cyxtrax/util/datasets/__init__.py b/src/cyxtrax/util/datasets/__init__.py
index 8388c33666b5dd9fd516da6dab5af5ce7b9f3d64..35509910e32257a2813cd6ab5bec1cb1a44bd91b 100644
--- a/src/cyxtrax/util/datasets/__init__.py
+++ b/src/cyxtrax/util/datasets/__init__.py
@@ -2,8 +2,8 @@ from .merge import merge_atlas_and_dict, merge_atlases, merge_lists
from .pipeline import generate_atlas_from_folder
__all__ = [
- 'merge_atlas_and_dict',
- 'merge_atlases',
- 'merge_lists',
- 'generate_atlas_from_folder'
-]
\ No newline at end of file
+ "merge_atlas_and_dict",
+ "merge_atlases",
+ "merge_lists",
+ "generate_atlas_from_folder",
+]
diff --git a/src/cyxtrax/util/visualisation/__init__.py b/src/cyxtrax/util/visualisation/__init__.py
index 995194029d4ad90bb3a622024fdb845cc1096783..ce653dfb43782a1c2720b84d004df0d7f779ac7f 100644
--- a/src/cyxtrax/util/visualisation/__init__.py
+++ b/src/cyxtrax/util/visualisation/__init__.py
@@ -1,9 +1,4 @@
from .plt import save_map_plot_with_index, voxel_cone_maps, voxel_maps
from .gif import make_gif
-__all__ = [
- 'save_map_plot_with_index',
- 'voxel_cone_maps',
- 'make_gif',
- 'voxel_maps'
-]
\ No newline at end of file
+__all__ = ["save_map_plot_with_index", "voxel_cone_maps", "make_gif", "voxel_maps"]
diff --git a/src/cyxtrax/util/visualisation/plt.py b/src/cyxtrax/util/visualisation/plt.py
index 29704f68e05e151f2855e1ab6c9be46b4f02e1f8..1fd3e55c3765a78cfa3b9a4d930a2323ce453a9e 100644
--- a/src/cyxtrax/util/visualisation/plt.py
+++ b/src/cyxtrax/util/visualisation/plt.py
@@ -3,17 +3,18 @@ from jax import numpy as jnp
from pathlib import Path
-def save_map_plot_with_index(maps: jnp.ndarray, index: int,
- save_path: Path, figsize=(8, 8), title: str = None):
+def save_map_plot_with_index(
+ maps: jnp.ndarray, index: int, save_path: Path, figsize=(8, 8), title: str = None
+):
fig = plt.figure(figsize=figsize)
ax = fig.add_subplot(111)
ax.imshow(maps[:, :, index])
- ax.set_xlabel(r'$z$ / mm')
- ax.set_ylabel(r'$\alpha$ / rad')
- ax.set_xticks([0, int(maps.shape[0] // 2), int(maps.shape[0])])
- ax.set_xticklabels([r'$-3141.5$', r'$0.$', r'$3141.5$'])
- ax.set_yticks([0, int(maps.shape[1] // 2), int(maps.shape[1])])
- ax.set_yticklabels([r'$-\pi$', r'$0.$', r'$\pi$'])
+ ax.set_xlabel(r"$z$ / mm")
+ ax.set_ylabel(r"$\alpha$ / rad")
+ ax.set_xticks([0, int(maps.shape[0] // 2), int(maps.shape[0])])
+ ax.set_xticklabels([r"$-3141.5$", r"$0.$", r"$3141.5$"])
+ ax.set_yticks([0, int(maps.shape[1] // 2), int(maps.shape[1])])
+ ax.set_yticklabels([r"$-\pi$", r"$0.$", r"$\pi$"])
if title is not None:
ax.set_title(title)
@@ -22,56 +23,70 @@ def save_map_plot_with_index(maps: jnp.ndarray, index: int,
plt.savefig(save_path)
plt.close(fig)
-
-def voxel_cone_maps(maps: jnp.ndarray, projection: jnp.ndarray,
- cone_coordinates: jnp.ndarray, cylindrical_coordinates: jnp.ndarray,
- save_path: Path, figsize=(24, 10), title: str = None, vmin: bool = False):
+
+def voxel_cone_maps(
+ maps: jnp.ndarray,
+ projection: jnp.ndarray,
+ cone_coordinates: jnp.ndarray,
+ cylindrical_coordinates: jnp.ndarray,
+ save_path: Path,
+ figsize=(24, 10),
+ title: str = None,
+ vmin: bool = False,
+):
fig = plt.figure(figsize=figsize)
subfig1: figure.Figure
subfig2: figure.Figure
subfig1, subfig2 = fig.subfigures(1, 2)
ax1 = subfig1.add_subplot(111)
- ax1.set_title('Projection Mapping')
+ ax1.set_title("Projection Mapping")
im = ax1.imshow(projection, vmin=maps.min(), vmax=maps.max())
counter = 0
number_of_maps = maps.shape[2]
color = jnp.linspace(0, 1, 9)[:number_of_maps]
- cmap = plt.get_cmap('hsv')
+ cmap = plt.get_cmap("hsv")
colors = cmap(color)
-
- ax1.set_xlabel(r'$u$ / px')
- ax1.set_ylabel(r'$v$ / px')
- subfig1.colorbar(im, ax=ax1, orientation='vertical', label='Ray Length / mm')
-
+ ax1.set_xlabel(r"$u$ / px")
+ ax1.set_ylabel(r"$v$ / px")
+ subfig1.colorbar(im, ax=ax1, orientation="vertical", label="Ray Length / mm")
+
ax2 = subfig2.add_subplot(111)
- ax2.set_title('Cylindrical Mapping')
+ ax2.set_title("Cylindrical Mapping")
ax2.axis(False)
- side_length = int(jnp.round(number_of_maps ** (1. / 3.)))
+ side_length = int(jnp.round(number_of_maps ** (1.0 / 3.0)))
for z in [0, side_length - 1]:
for y in [0, side_length - 1]:
for x in [0, side_length - 1]:
- position = x + y * side_length + z * side_length ** 2
+ position = x + y * side_length + z * side_length**2
if counter >= number_of_maps:
continue
- ax = subfig2.add_subplot(3, 3, counter+1)
+ ax = subfig2.add_subplot(3, 3, counter + 1)
if vmin:
ax.imshow(maps[:, :, position].T, vmin=maps.min(), vmax=maps.max())
else:
ax.imshow(maps[:, :, position].T, vmin=maps.min())
- ax.scatter(cylindrical_coordinates[0, position], cylindrical_coordinates[1, position], c=colors[counter])
- ax1.scatter(cone_coordinates[0, position], cone_coordinates[1, position], c=colors[counter])
- ax.set_ylabel(r'$z$ / mm')
- ax.set_xlabel(r'$\alpha$ / rad')
- ax.set_yticks([0, 1000, 2000])
- ax.set_yticklabels([r'$-3141.5$', r'$0.$', r'$3141.5$'])
- ax.set_xticks([0, 1000, 2000])
- ax.set_xticklabels([r'$-\pi$', r'$0.$', r'$\pi$'])
+ ax.scatter(
+ cylindrical_coordinates[0, position],
+ cylindrical_coordinates[1, position],
+ c=colors[counter],
+ )
+ ax1.scatter(
+ cone_coordinates[0, position],
+ cone_coordinates[1, position],
+ c=colors[counter],
+ )
+ ax.set_ylabel(r"$z$ / mm")
+ ax.set_xlabel(r"$\alpha$ / rad")
+ ax.set_yticks([0, 1000, 2000])
+ ax.set_yticklabels([r"$-3141.5$", r"$0.$", r"$3141.5$"])
+ ax.set_xticks([0, 1000, 2000])
+ ax.set_xticklabels([r"$-\pi$", r"$0.$", r"$\pi$"])
counter += 1
@@ -82,53 +97,68 @@ def voxel_cone_maps(maps: jnp.ndarray, projection: jnp.ndarray,
plt.savefig(save_path)
-def voxel_cone_maps_values(maps: jnp.ndarray, projection: jnp.ndarray,
- cone_coordinates: jnp.ndarray, cylindrical_coordinates: jnp.ndarray,
- cylindrical_values: jnp.ndarray,
- save_path: Path, figsize=(24, 10), title: str = None):
+def voxel_cone_maps_values(
+ maps: jnp.ndarray,
+ projection: jnp.ndarray,
+ cone_coordinates: jnp.ndarray,
+ cylindrical_coordinates: jnp.ndarray,
+ cylindrical_values: jnp.ndarray,
+ save_path: Path,
+ figsize=(24, 10),
+ title: str = None,
+):
fig = plt.figure(figsize=figsize)
subfig1: figure.Figure
subfig2: figure.Figure
subfig1, subfig2 = fig.subfigures(1, 2)
ax1 = subfig1.add_subplot(111)
- ax1.set_title('Projection Mapping')
+ ax1.set_title("Projection Mapping")
im = ax1.imshow(projection, vmin=maps.min(), vmax=maps.max())
counter = 0
number_of_maps = maps.shape[2]
color = jnp.linspace(0, 1, 9)[:number_of_maps]
- cmap = plt.get_cmap('hsv')
+ cmap = plt.get_cmap("hsv")
colors = cmap(color)
-
- ax1.set_xlabel(r'$u$ / px')
- ax1.set_ylabel(r'$v$ / px')
- subfig1.colorbar(im, ax=ax1, orientation='vertical', label='Ray Length / mm')
-
+ ax1.set_xlabel(r"$u$ / px")
+ ax1.set_ylabel(r"$v$ / px")
+ subfig1.colorbar(im, ax=ax1, orientation="vertical", label="Ray Length / mm")
+
ax2 = subfig2.add_subplot(111)
- ax2.set_title('Cylindrical Mapping')
+ ax2.set_title("Cylindrical Mapping")
ax2.axis(False)
- side_length = int(jnp.round(number_of_maps ** (1. / 3.)))
+ side_length = int(jnp.round(number_of_maps ** (1.0 / 3.0)))
for z in [0, side_length - 1]:
for y in [0, side_length - 1]:
for x in [0, side_length - 1]:
- position = x + y * side_length + z * side_length ** 2
+ position = x + y * side_length + z * side_length**2
if counter >= number_of_maps:
continue
- ax = subfig2.add_subplot(3, 3, counter+1)
- ax.scatter(cylindrical_values[0], cylindrical_values[1], )
- ax.scatter(cylindrical_coordinates[0, position], cylindrical_coordinates[1, position], c=colors[counter])
- ax1.scatter(cone_coordinates[0, position], cone_coordinates[1, position], c=colors[counter])
- ax.set_ylabel(r'$z$ / mm')
- ax.set_xlabel(r'$\alpha$ / rad')
- ax.set_yticks([0, 1000, 2000])
- ax.set_yticklabels([r'$-3141.5$', r'$0.$', r'$3141.5$'])
- ax.set_xticks([0, 1000, 2000])
- ax.set_xticklabels([r'$-\pi$', r'$0.$', r'$\pi$'])
-
+ ax = subfig2.add_subplot(3, 3, counter + 1)
+ ax.scatter(
+ cylindrical_values[0],
+ cylindrical_values[1],
+ )
+ ax.scatter(
+ cylindrical_coordinates[0, position],
+ cylindrical_coordinates[1, position],
+ c=colors[counter],
+ )
+ ax1.scatter(
+ cone_coordinates[0, position],
+ cone_coordinates[1, position],
+ c=colors[counter],
+ )
+ ax.set_ylabel(r"$z$ / mm")
+ ax.set_xlabel(r"$\alpha$ / rad")
+ ax.set_yticks([0, 1000, 2000])
+ ax.set_yticklabels([r"$-3141.5$", r"$0.$", r"$3141.5$"])
+ ax.set_xticks([0, 1000, 2000])
+ ax.set_xticklabels([r"$-\pi$", r"$0.$", r"$\pi$"])
counter += 1
@@ -139,38 +169,44 @@ def voxel_cone_maps_values(maps: jnp.ndarray, projection: jnp.ndarray,
plt.savefig(save_path)
-def voxel_maps(maps: jnp.ndarray, save_path: Path, figsize=(24, 10), title: str = None, vmin: bool = False):
+def voxel_maps(
+ maps: jnp.ndarray,
+ save_path: Path,
+ figsize=(24, 10),
+ title: str = None,
+ vmin: bool = False,
+):
fig = plt.figure(figsize=figsize)
ax2 = fig.add_subplot(111)
- ax2.set_title('Cylindrical Mapping')
+ ax2.set_title("Cylindrical Mapping")
ax2.axis(False)
number_of_maps = maps.shape[2]
- side_length = int(jnp.round(number_of_maps ** (1. / 3.)))
+ side_length = int(jnp.round(number_of_maps ** (1.0 / 3.0)))
counter = 0
for z in [0, side_length - 1]:
for y in [0, side_length - 1]:
for x in [0, side_length - 1]:
- position = x + y * side_length + z * side_length ** 2
+ position = x + y * side_length + z * side_length**2
if counter >= number_of_maps:
continue
- ax = fig.add_subplot(3, 3, counter+1)
+ ax = fig.add_subplot(3, 3, counter + 1)
if vmin:
ax.imshow(maps[:, :, position].T, vmin=maps.min(), vmax=maps.max())
else:
ax.imshow(maps[:, :, position].T, vmin=maps.min())
- ax.set_ylabel(r'$z$ / mm')
- ax.set_xlabel(r'$\alpha$ / rad')
- ax.set_yticks([0, 1000, 2000])
- ax.set_yticklabels([r'$-3141.5$', r'$0.$', r'$3141.5$'])
- ax.set_xticks([0, 1000, 2000])
- ax.set_xticklabels([r'$-\pi$', r'$0.$', r'$\pi$'])
+ ax.set_ylabel(r"$z$ / mm")
+ ax.set_xlabel(r"$\alpha$ / rad")
+ ax.set_yticks([0, 1000, 2000])
+ ax.set_yticklabels([r"$-3141.5$", r"$0.$", r"$3141.5$"])
+ ax.set_xticks([0, 1000, 2000])
+ ax.set_xticklabels([r"$-\pi$", r"$0.$", r"$\pi$"])
counter += 1
-
+
if title is not None:
plt.title(title)
plt.tight_layout()
- plt.savefig(save_path)
\ No newline at end of file
+ plt.savefig(save_path)