diff --git a/CyXTraX/io/generate_atlas.py b/CyXTraX/io/generate_atlas.py
index 239f985a92950e45d3dd87807b0c57fa96015e59..1df4b4fa98a68112e744c51af86a08ab2dae6808 100644
--- a/CyXTraX/io/generate_atlas.py
+++ b/CyXTraX/io/generate_atlas.py
@@ -21,14 +21,14 @@ def record_atlas(cylindrical_projection: CylindricalProjection, mesh_list: list[
file = h5py.File(save_path, 'a')
projection = file.require_dataset(
'maps',
- shape=(cylindrical_projection.x_px, cylindrical_projection.y_px, 0), # Initial shape with third dimension as 0
- maxshape=(cylindrical_projection.x_px, cylindrical_projection.y_px, None),
+ shape=(cylindrical_projection.x_px, cylindrical_projection.y_px, number_of_maps**3), # Initial shape with third dimension as 0
+ maxshape=(cylindrical_projection.x_px, cylindrical_projection.y_px, number_of_maps**3),
dtype=np.float32)
projection_points = file.require_dataset(
'positions',
- shape=(3, 0), # Initial shape with third dimension as 0
- maxshape=(3, None),
+ shape=(3, number_of_maps**3), # Initial shape with third dimension as 0
+ maxshape=(3, number_of_maps**3),
dtype=np.float32)
@@ -38,7 +38,7 @@ def record_atlas(cylindrical_projection: CylindricalProjection, mesh_list: list[
file.attrs['mesh_list'] = json.dumps(mesh_list_dict)
-
+ counter = 0
for x in grid:
for y in grid:
for z in grid:
@@ -49,10 +49,10 @@ def record_atlas(cylindrical_projection: CylindricalProjection, mesh_list: list[
image = cylindrical_projection.compute_projection(position, output_full_ray_projection=True)
current_size = projection.shape[2]
new_size = current_size + 1
- projection.resize((cylindrical_projection.x_px, cylindrical_projection.y_px, new_size))
- projection[:, :, current_size:new_size] = image[:, :, np.newaxis].astype(np.float32)
-
- projection_points.resize((3, new_size))
- projection_points[:, current_size:new_size] = position.reshape((3, 1))
+ #projection.resize((cylindrical_projection.x_px, cylindrical_projection.y_px, new_size))
+ projection[:, :, counter:counter+1] = image[:, :, np.newaxis].astype(np.float32)
+ #projection_points.resize((3, new_size))
+ projection_points[:, counter:counter+1] = position.reshape((3, 1))
+ counter += 1
return save_path
diff --git a/CyXTraX/mapping/mapping.py b/CyXTraX/mapping/mapping.py
index f697a51bae3125517b9c8627adb535e0b7eda9e2..8a153a69e65c86030a7c36520d408e8940f761d6 100644
--- a/CyXTraX/mapping/mapping.py
+++ b/CyXTraX/mapping/mapping.py
@@ -71,6 +71,10 @@ def map_geometry_2_projection(source: jnp.ndarray, detector: jnp.ndarray, detect
projection_value: m
"""
+ source = source.reshape((1, 3))
+ detector = detector.reshape((1, 3))
+ detector_orientation = detector_orientation.reshape((1, 4))
+
projection_geometry = projection_matrix(source, detector, detector_orientation) # 3 x 4
map_positions_homogen = jnp.ones((1, map_positions.shape[1])) # 1 x m
diff --git a/CyXTraX/util/visualisation/__init__.py b/CyXTraX/util/visualisation/__init__.py
index a6378045a5ae883231d1160735f4ccc5afe9f293..589931f1beaaf10328afcd4cafd2efc5dbbd40c0 100644
--- a/CyXTraX/util/visualisation/__init__.py
+++ b/CyXTraX/util/visualisation/__init__.py
@@ -1 +1,2 @@
-from .plt import save_map_plot_with_index
\ No newline at end of file
+from .plt import save_map_plot_with_index, voxel_cone_maps
+from .gif import make_gif
\ No newline at end of file
diff --git a/CyXTraX/util/visualisation/gif.py b/CyXTraX/util/visualisation/gif.py
index 146a4fc5a9ad5ad8c3e393a59ca1193b269f586d..68e0a043a05348a4c736100c3904db02462cdb2b 100644
--- a/CyXTraX/util/visualisation/gif.py
+++ b/CyXTraX/util/visualisation/gif.py
@@ -1,7 +1,23 @@
from CyXTraX.io import load_atlas
from pathlib import Path
+from PIL import Image
def atlas_gif(load_path: Path):
maps, map_position, meshes = load_atlas(load_path)
-
\ No newline at end of file
+
+
+def load_pil(path: Path) -> Image.Image:
+ return Image.open(path)
+
+
+def make_gif(load_path: Path, pattern: str, name: str, duration_ms: float = 100):
+ frames = sorted(list(load_path.glob(pattern)))
+ frames = list(map(load_pil, frames))
+ frames[0].save(
+ load_path / name,
+ save_all=True,
+ append_images=frames[1:],
+ duration=duration_ms,
+ loop=0)
+
diff --git a/CyXTraX/util/visualisation/plt.py b/CyXTraX/util/visualisation/plt.py
index c992c37c316f3e9b75cc4e8882d4d4f43c63c1fa..799e528e3702ca60e4d17e5ff24417f698c4b6b2 100644
--- a/CyXTraX/util/visualisation/plt.py
+++ b/CyXTraX/util/visualisation/plt.py
@@ -1,10 +1,10 @@
-from matplotlib import pyplot as plt
+from matplotlib import pyplot as plt, figure
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])
@@ -22,4 +22,118 @@ def save_map_plot_with_index(maps: jnp.ndarray, index: int, save_path: Path, fig
plt.savefig(save_path)
plt.close(fig)
-
\ No newline at end of file
+
+
+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')
+ 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')
+ 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')
+
+
+ ax2 = subfig2.add_subplot(111)
+ ax2.set_title('Cylindrical Mapping')
+ ax2.axis(False)
+
+ side_length = int(jnp.round(number_of_maps ** (1. / 3.)))
+
+ 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
+ if counter >= number_of_maps:
+ continue
+ 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'$\pi$'])
+
+ counter += 1
+
+ if title is not None:
+ plt.title(title)
+
+ plt.tight_layout()
+ 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):
+ 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')
+ 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')
+ 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')
+
+
+ ax2 = subfig2.add_subplot(111)
+ ax2.set_title('Cylindrical Mapping')
+ ax2.axis(False)
+
+ side_length = int(jnp.round(number_of_maps ** (1. / 3.)))
+
+ 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
+ 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'$\pi$'])
+
+
+ counter += 1
+
+ if title is not None:
+ plt.title(title)
+
+ plt.tight_layout()
+ plt.savefig(save_path)
\ No newline at end of file
diff --git a/scripts/04_mapping.py b/scripts/04_mapping.py
index 657fe50f8c8895113acfadcfe5272adfa35cd997..45f729becf805b33ba531a58e094c20bab3e620b 100644
--- a/scripts/04_mapping.py
+++ b/scripts/04_mapping.py
@@ -82,8 +82,8 @@ def main():
ax2 = subfig2.add_subplot(111)
ax2.set_title('Cylindrical Mapping')
ax2.axis(False)
- for i in range(3):
- for j in range(3):
+ for _ in range(3):
+ for _ in range(3):
if counter >= number_of_maps:
continue
ax = subfig2.add_subplot(3, 3, counter+1)
diff --git a/scripts/06_generate_dataset.py b/scripts/06_generate_dataset.py
index 516e803405fa2903715f011c93fead392dc42426..d3fb72fe9f009a739d7ac385f8b1914b55f294d3 100644
--- a/scripts/06_generate_dataset.py
+++ b/scripts/06_generate_dataset.py
@@ -11,7 +11,7 @@ and needs 100gb of space.
def main():
# Dataset save folder
- save_folder = Path(r'C:\data\XrayTransform')
+ save_folder = Path(r'C:\data\XrayTransformLow')
# Dataset of multiple random stl files from: https://ten-thousand-models.appspot.com/
load_folder = Path(r'C:\Users\swittl\Downloads\Thingi10K\Thingi10K\raw_meshes')
@@ -22,7 +22,7 @@ def main():
print(i)
key = random.PRNGKey(i)
generate_atlas_from_folder(
- load_folder, key, save_folder)
+ load_folder, key, save_folder, map_bounding_box=(-10, 10), number_of_maps=2)
if __name__ == '__main__':
diff --git a/scripts/07_presentation.py b/scripts/07_presentation.py
new file mode 100644
index 0000000000000000000000000000000000000000..8540a44f317729c9f73b17f65db0551ab28eb8cc
--- /dev/null
+++ b/scripts/07_presentation.py
@@ -0,0 +1,71 @@
+from CyXTraX.simulation import CylindricalProjection, load_mesh, SAVEMODES, utility
+from CyXTraX.io import load_atlas
+from CyXTraX.mapping import map_geometry_2_projection, map_source_2_cylinder
+from CyXTraX.util.visualisation import voxel_cone_maps
+
+from pathlib import Path
+from jax import numpy as jnp
+from jax.scipy.spatial.transform import Rotation
+
+from cyxtrax_object import set_geometry_at_index, circular_trajectory, add_world_orign, zero_quat, x_90_quat, z_90_quat, add_offset
+
+
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+MAP_FOLDER = Path(r'C:\data\XrayTransformLow')
+
+
+def main():
+ files = list(MAP_FOLDER.glob('*.h5'))
+ if not files:
+ raise FileNotFoundError('No .h5 files in temp folder. Run Example 02!')
+
+ maps, points, mesh_object_list = load_atlas(files[3])
+ cyl_proj = CylindricalProjection()
+
+ load_mesh(cyl_proj, mesh_object_list, False)
+ print(f'Cone Beam Mode set: {cyl_proj.cone_mode}')
+
+
+ number_of_projections = 30
+
+ fod_mm = jnp.array([1000,])
+ fdd_mm = jnp.array([2000,])
+ alpha_rad = jnp.linspace(0, jnp.pi, number_of_projections).reshape((-1, 1))
+
+ source, orientation_source, detector, orientation_detector = circular_trajectory(fod_mm, fdd_mm, alpha_rad)
+ source, orientation_source, detector, orientation_detector = add_world_orign(
+ source, orientation_source, detector, orientation_detector, jnp.array([1, 2., -1.]), jnp.array([0.8, 0.1, -0.1, 0.9]))
+ detector, orientation_detector = add_offset(detector, orientation_detector, jnp.array([1, 20., -1.]), zero_quat)
+
+ temp_projection = Path('temp.tif')
+
+
+
+ for i in range(number_of_projections):
+ set_geometry_at_index(source, orientation_source, detector, orientation_detector, i, temp_projection)
+
+ projection, geometry = utility.load_projection(temp_projection)
+ mapped_values, uv_px = map_geometry_2_projection(
+ source[i],
+ detector[i],
+ orientation_detector[i],
+ points,
+ projection,
+ cyl_proj.pixel_pitch_mm)
+
+ values_calc, angles_calc = map_source_2_cylinder(
+ source[i],
+ maps,
+ points,
+ cyl_proj.detector_radius_mm,
+ cyl_proj.x_px,
+ cyl_proj.x_resolution_mm)
+
+ voxel_cone_maps(maps, projection, uv_px, angles_calc, TEMP_FOLDER / f'{i:03}_presentation.png')
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/scripts/08_make_gif.py b/scripts/08_make_gif.py
new file mode 100644
index 0000000000000000000000000000000000000000..2498d0c90a3219b37f04f22ad18a0286babbc283
--- /dev/null
+++ b/scripts/08_make_gif.py
@@ -0,0 +1,13 @@
+from CyXTraX.util.visualisation import make_gif
+from pathlib import Path
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+
+def main():
+ make_gif(TEMP_FOLDER, '*_presentation.png', 'cyxtrax.gif', 333)
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file