diff --git a/.gitignore b/.gitignore
index 2af88e4f7f93d36d627c391f55ad9e4c64c4657c..e88c5011040c6ab8d8f07c85625b3c3829635e31 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,4 +3,5 @@
/dist/
__pycache__
*.egg-info
-*temp.*
\ No newline at end of file
+*temp.*
+/dir2025/
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index d4ea4cb81bb3f1b3c65099939c5f557d31e4dd45..386fff40be904d8cfa1f147d45e7afc033ae8ada 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[project]
name = "cyxtrax"
-version = "0.1.0"
+version = "0.1.1"
description = "Add your description here"
readme = "README.md"
authors = [
@@ -14,8 +14,7 @@ dependencies = [
"jax>=0.4.35 ; sys_platform == 'win32'",
"jax[cuda12]>=0.4.35 ; sys_platform == 'linux'",
"kiwisolver>=1.4.7",
- "matplotlib>=3.9.2",
- "numpy>=2.1.3",
+ "numpy>=2.0.2",
"ruff>=0.7.3",
"scipy>=1.14.1",
"xraylib>=4.1.5",
diff --git a/scripts/02_generate_atlas.py b/scripts/02_generate_atlas.py
index a3401d6aeac5c37fd0945a8664b12c33f8b54a82..cd1358199f05a86393615fd5d2f1e854c491cda4 100644
--- a/scripts/02_generate_atlas.py
+++ b/scripts/02_generate_atlas.py
@@ -1,7 +1,8 @@
from cyxtrax.io import record_atlas
from cyxtrax.simulation import CylindricalProjection, load_mesh
-from cyxtrax.data import olaf_mesh
+from cyxtrax.data import olaf_mesh, MeshObject
from pathlib import Path
+import numpy as np
# Just get the temp folder to store the atlas
@@ -13,16 +14,18 @@ def main():
# code_embedder:A start
# Create the cylindrical projection interface
cyl_proj = CylindricalProjection()
- load_mesh(cyl_proj, [olaf_mesh])
+ obj = MeshObject(Path(r'C:\Program Files\BAM\aRTist 2.12\Data\Library\ExampleParts\Fun\Smurf.stl'),
+ np.array([0., 0., 0.]), np.array([0., 0., 0., 1.]))
+ load_mesh(cyl_proj, [obj])
# make an atlas
save_path = record_atlas(
cyl_proj,
- [olaf_mesh],
+ [obj],
"test",
TEMP_FOLDER,
map_bounding_box=[-10, 20],
- number_of_maps=2,
+ number_of_maps=1,
)
# code_embedder:A end
print(f"Atlas saved to the path: {save_path}")
diff --git a/scripts/03_load_atlas.py b/scripts/03_load_atlas.py
index e0ed4ed656b35843f68abcfc8ed5c19ff9d583b0..ff0e6d23d80d75dad6c8ba90bddf819e9d8e1cf9 100644
--- a/scripts/03_load_atlas.py
+++ b/scripts/03_load_atlas.py
@@ -5,12 +5,12 @@ 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 / "dir2025"
def main():
# code_embedder:A start
- files = list(TEMP_FOLDER.glob("*.h5"))
+ files = list(TEMP_FOLDER.glob("*1_smurf.h5"))
if not files:
raise FileNotFoundError("No .h5 files in temp folder. Run Example 02!")
diff --git a/scripts/04_mapping.py b/scripts/04_mapping.py
index 937ca25ecb73cfbabb80f6f516d312c53647ee00..4813e3eb73eaf2b5799949f9ec8e1a6b2d9c3d79 100644
--- a/scripts/04_mapping.py
+++ b/scripts/04_mapping.py
@@ -10,6 +10,7 @@ from matplotlib import pyplot as plt, figure
# Just get the temp folder to store the atlas
FOLDER = Path("/mnt/data/xray_studies_data/")
TEMP_FOLDER = FOLDER / "dataset_64"
+TEMP_FOLDER = Path('temp')
def main():
@@ -24,9 +25,9 @@ def main():
print(f"Cone Beam Mode set: {cyl_proj.cone_mode}")
rot = 30
- x, y = 2000 * jnp.cos(rot * jnp.pi / 180), 500 * jnp.sin(rot * jnp.pi / 180)
+ x, y = 500 * jnp.cos(rot * jnp.pi / 180), 500 * jnp.sin(rot * jnp.pi / 180)
source_position = jnp.array([x, y, 0.0]).reshape((1, 3))
- detector_position = jnp.array([-x, -y, -10.0]).reshape((1, 3))
+ detector_position = jnp.array([-x, -y, 0.0]).reshape((1, 3)) / 2.
detctor_orientation_scipy = Rotation.from_euler("xyz", [0, -90, rot], degrees=True)
temp_projection = Path("temp.tif")
@@ -39,7 +40,7 @@ def main():
"D", detector_position[0, 0], detector_position[0, 1], detector_position[0, 2]
)
cyl_proj.api.rotate_from_quat("D", detctor_orientation[0])
- cyl_proj.api.save_image(temp_projection, save_mode=SAVEMODES.FLOAT_TIFF)
+ cyl_proj.api.save_image(temp_projection, save_mode=SAVEMODES.FLOAT_TIFF, save_projection_geometry=1)
projection, geometry = utility.load_projection(temp_projection)
@@ -88,11 +89,12 @@ def main():
ax2 = subfig2.add_subplot(111)
ax2.set_title("Cylindrical Mapping")
ax2.axis(False)
- for _ in range(3):
- for _ in range(3):
+ nums_subplots = 1
+ for _ in range(nums_subplots):
+ for _ in range(nums_subplots):
if counter >= number_of_maps:
continue
- ax = subfig2.add_subplot(3, 3, counter + 1)
+ ax = subfig2.add_subplot(nums_subplots, nums_subplots, counter + 1)
ax.imshow(maps[:, :, counter], vmin=maps.min(), vmax=maps.max())
ax.scatter(
angles_calc[0, counter], angles_calc[1, counter], c=colors[counter]
diff --git a/scripts/07_presentation.py b/scripts/07_presentation.py
index cb39066804d82840bee2ea8b292d307507cceea8..9ce4831e0b63965879aad3ed8729267050d64c2f 100644
--- a/scripts/07_presentation.py
+++ b/scripts/07_presentation.py
@@ -22,11 +22,11 @@ MAP_FOLDER = Path(r"C:\data\XrayTransformLow")
def main():
- files = list(MAP_FOLDER.glob("*.h5"))
+ files = list(TEMP_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])
+ maps, points, mesh_object_list = load_atlas(files[-1])
cyl_proj = CylindricalProjection()
load_mesh(cyl_proj, mesh_object_list, False)
diff --git a/scripts/09_compute_smurf_map.py b/scripts/09_compute_smurf_map.py
new file mode 100644
index 0000000000000000000000000000000000000000..efa3fd5f8cc59a5313d5877b27538333a3da860a
--- /dev/null
+++ b/scripts/09_compute_smurf_map.py
@@ -0,0 +1,34 @@
+from cyxtrax.io import record_map
+from cyxtrax.simulation import CylindricalProjection, load_mesh
+from cyxtrax.data import olaf_mesh, MeshObject
+from pathlib import Path
+import numpy as np
+
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / "temp"
+
+
+def main():
+ # code_embedder:A start
+ # Create the cylindrical projection interface
+ cyl_proj = CylindricalProjection()
+ obj = MeshObject(Path(r'C:\Program Files\BAM\aRTist 2.12\Data\Library\ExampleParts\Fun\Smurf.stl'),
+ np.array([0., 0., 0.]), np.array([0., 0., 0., 1.]))
+ load_mesh(cyl_proj, [obj])
+ # make an atlas
+
+ save_path = record_map(
+ cyl_proj,
+ [obj],
+ "test",
+ TEMP_FOLDER,
+ position=np.array([56., 10.5, 2.])
+ )
+ # code_embedder:A end
+ print(f"Atlas saved to the path: {save_path}")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/10_dir2025.py b/scripts/10_dir2025.py
new file mode 100644
index 0000000000000000000000000000000000000000..cbe4de8275ac5596b8a29ec94fc7fd2c6b3d1357
--- /dev/null
+++ b/scripts/10_dir2025.py
@@ -0,0 +1,35 @@
+from cyxtrax.io import record_atlas
+from cyxtrax.simulation import CylindricalProjection, load_mesh
+from cyxtrax.data import olaf_mesh, MeshObject
+from pathlib import Path
+import numpy as np
+
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / "dir2025"
+
+
+def main():
+ # code_embedder:A start
+ # Create the cylindrical projection interface
+ cyl_proj = CylindricalProjection()
+ obj = MeshObject(Path(r'C:\Program Files\BAM\aRTist 2.12\Data\Library\ExampleParts\Fun\Smurf.stl'),
+ np.array([0., 0., 0.]), np.array([0., 0., 0., 1.]))
+ load_mesh(cyl_proj, [obj])
+ # make an atlas
+
+ save_path = record_atlas(
+ cyl_proj,
+ [obj],
+ "smurf",
+ TEMP_FOLDER,
+ map_bounding_box=[-50, 50],
+ number_of_maps=4,
+ )
+ # code_embedder:A end
+ print(f"Atlas saved to the path: {save_path}")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/scripts/10_dir2025_2.py b/scripts/10_dir2025_2.py
new file mode 100644
index 0000000000000000000000000000000000000000..d89203dc9c4528528d8b7b485caad6392bc55ced
--- /dev/null
+++ b/scripts/10_dir2025_2.py
@@ -0,0 +1,35 @@
+from cyxtrax.io import record_atlas
+from cyxtrax.simulation import CylindricalProjection, load_mesh
+from cyxtrax.data import olaf_mesh, MeshObject
+from pathlib import Path
+import numpy as np
+
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / "dir2025"
+
+
+def main():
+ # code_embedder:A start
+ # Create the cylindrical projection interface
+ cyl_proj = CylindricalProjection()
+ obj = MeshObject(Path(r'C:\Program Files\BAM\aRTist 2.12\Data\Library\ExampleParts\Fun\Smurf.stl'),
+ position_mm=-np.array([56., 10.5, 2.]), orientation_quat=np.array([0., 0., 0., 1.]))
+ load_mesh(cyl_proj, [obj])
+ # make an atlas
+
+ save_path = record_atlas(
+ cyl_proj,
+ [obj],
+ "smurf",
+ TEMP_FOLDER,
+ map_bounding_box=[-2, 2],
+ number_of_maps=3,
+ )
+ # code_embedder:A end
+ print(f"Atlas saved to the path: {save_path}")
+
+
+if __name__ == "__main__":
+ main()
diff --git a/src/cyxtrax/io/__init__.py b/src/cyxtrax/io/__init__.py
index f73e11006a7178bea608543438dd320b976650be..d458468466006088e07c369da909d20362706ad2 100644
--- a/src/cyxtrax/io/__init__.py
+++ b/src/cyxtrax/io/__init__.py
@@ -1,6 +1,7 @@
from .generate_atlas import record_atlas
from .load_maps import load_atlas
from .save_map import save_atlas
+from .generate_single_map import record_map
-__all__ = ["record_atlas", "load_atlas", "save_atlas"]
+__all__ = ["record_atlas", "load_atlas", "save_atlas", "record_map"]
diff --git a/src/cyxtrax/io/generate_single_map.py b/src/cyxtrax/io/generate_single_map.py
new file mode 100644
index 0000000000000000000000000000000000000000..e2df32a3dff8f60632a8af093b1a92f8c7c6184a
--- /dev/null
+++ b/src/cyxtrax/io/generate_single_map.py
@@ -0,0 +1,65 @@
+import numpy as np
+import h5py
+from cyxtrax.simulation.artist_bridge import CylindricalProjection
+from cyxtrax.common.mesh_object import MeshObject
+from pathlib import Path
+import json
+
+
+def to_dict(mesh_object=MeshObject) -> dict:
+ return mesh_object.as_dict()
+
+
+def record_map(
+ cylindrical_projection: CylindricalProjection,
+ mesh_list: list[MeshObject],
+ atlas_name: str,
+ save_folder: Path,
+ position: np.ndarray = np.zeros((3, 1))
+) -> Path:
+ file_index = len(list(save_folder.glob("*.h5"))) + 1
+ save_path = save_folder / f"{file_index:05}_{atlas_name}.h5"
+ file = h5py.File(save_path, "a")
+ projection = file.require_dataset(
+ "maps",
+ shape=(
+ cylindrical_projection.x_px,
+ cylindrical_projection.y_px,
+ 1,
+ ), # Initial shape with third dimension as 0
+ maxshape=(
+ cylindrical_projection.x_px,
+ cylindrical_projection.y_px,
+ 1,
+ ),
+ dtype=np.float32,
+ )
+
+ projection_points = file.require_dataset(
+ "positions",
+ shape=(3, 1), # Initial shape with third dimension as 0
+ maxshape=(3, 1),
+ dtype=np.float32,
+ )
+
+ mesh_list_dict = list(map(to_dict, mesh_list))
+ print(mesh_list_dict)
+
+ file.attrs["mesh_list"] = json.dumps(mesh_list_dict)
+
+ counter = 0
+
+ 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[:, :, 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/src/cyxtrax/io/save_map.py b/src/cyxtrax/io/save_map.py
index 086b667d2664e75fd234bd6c08d1513ee18b8146..7fbbce13cefd61873b5ddb4ae01ef22a85e3474e 100644
--- a/src/cyxtrax/io/save_map.py
+++ b/src/cyxtrax/io/save_map.py
@@ -52,3 +52,22 @@ def save_atlas(
projection[:] = maps
projection_points[:] = map_position
+
+
+def add_rays_to_atlas(save_path: Path, ray_start: np.ndarray, ray_end: np.ndarray):
+ file = h5py.File(save_path, "a")
+ ray_endpoint = file.require_dataset(
+ "ray_endpoint",
+ shape=ray_end.shape,
+ dtype=np.float32,
+ )
+ ray_endpoint[:] = ray_end
+
+ ray_startpoint = file.require_dataset(
+ "ray_startpoint",
+ shape=ray_end.shape,
+ dtype=np.float32,
+ )
+ ray_startpoint[:] = ray_start
+
+
diff --git a/src/cyxtrax/simulation/artist/artist_bridge.py b/src/cyxtrax/simulation/artist/artist_bridge.py
new file mode 100644
index 0000000000000000000000000000000000000000..4cb62ceef36881dc3ce10df6e344fe8ae8c918ba
--- /dev/null
+++ b/src/cyxtrax/simulation/artist/artist_bridge.py
@@ -0,0 +1,178 @@
+try:
+ from artist_pythonlib import API, utility, SAVEMODES # type: ignore
+except ModuleNotFoundError:
+ from warnings import warn
+
+ 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
+import numpy as np
+import os
+import importlib.resources
+from time import sleep
+from cyxtrax.common.mesh_object import MeshObject
+
+# !!!!!!!!!!!!!!!!!!!
+# Read carefully
+#!!!!!!!!!!!!!!!!?!!!
+
+
+# This Script assumes that the detector has a size of 6283.19 mm / 2 pi
+# and the curvature is set to the y axis with center on the source.
+
+# The source Position has to be on [0, 0, 0]
+# The detector has to be on Position [1000,0, 0] and orientation [0, 90, 0] / curvature y
+
+# The Script assumes this geometry and only moves all the objects!
+# Preview must be reseted!!!
+
+GLOBAL_COUNTER = 0
+
+
+def set_cylindrical_mode(api: API):
+ with importlib.resources.path("cyxtrax.data", "cylinder.aRTist") as file_path:
+ print(f"Load: {file_path}")
+ api.load_project(file_path)
+
+
+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)
+
+def set_cone_poly_mode(api: API):
+ with importlib.resources.path("cyxtrax.data", "cone_poly.aRTist") as file_path:
+ print(f"Load: {file_path}")
+ api.load_project(file_path)
+
+
+class CylindricalProjection:
+ def __init__(self, api: API = API()) -> None:
+ self.api = api
+ self.x_resolution_mm = np.pi
+ self.y_resolution_mm = np.pi
+ self.pixel_pitch_mm = 0.139
+ self.x_px = 2000
+ self.y_px = 2000
+ self.detector_radius_mm = 1000.0
+ self.objects = list()
+ self._cylindrical = True
+
+ @property
+ def cylindrical_mode(self) -> bool:
+ return self._cylindrical
+
+ @property
+ def cone_mode(self) -> bool:
+ return not self._cylindrical
+
+ def translate(self, position: np.ndarray):
+ # for obj in self.objects:
+ x_d, y_d, z_d = 1000, 0, 0
+ x_s, y_s, z_s = 0, 0, 0
+ x_p, y_p, z_p = position[0], position[1], position[2]
+
+ self.api.rc.send(
+ f'::PartList::Invoke {str("S")} SetPosition {str(x_s + x_p)} {str(y_s + y_p)} {str(z_s + z_p)};'
+ )
+ self.api.rc.send(
+ f'::PartList::Invoke {str("S")} SetRefPos {str(x_s + x_p)} {str(y_s + y_p)} {str(z_s + z_p)};'
+ )
+
+ self.api.rc.send(
+ f'::PartList::Invoke {str("D")} SetRefPos {str(x_s + x_p)} {str(y_s + y_p)} {str(z_s + z_p)};'
+ )
+ self.api.rc.send(
+ f'::PartList::Invoke {str("D")} SetPosition {str(x_d + x_p)} {str(y_d + y_p)} {str(z_d + z_p)};'
+ )
+ self.api.rc.send("::XDetector::SetDownCurvedView;")
+
+ def compute_projection(
+ self,
+ position: np.ndarray,
+ temp_file_path: Path = Path(r"C:\data"),
+ output_full_ray_projection: bool = True,
+ ) -> np.ndarray:
+ global GLOBAL_COUNTER
+ self.translate(position)
+ temp_file = temp_file_path / f"temp_{GLOBAL_COUNTER:01}.tiff"
+ GLOBAL_COUNTER += 1
+ GLOBAL_COUNTER = GLOBAL_COUNTER % 10
+
+ self.api.save_image(
+ temp_file, save_projection_geometry=False, save_mode=SAVEMODES.FLOAT_TIFF
+ )
+
+ while not temp_file.exists():
+ print("sleepy sleep sleep ...")
+ # The computation of the cylindrical xray tansforms takes time ... aRTist is not programmed for it.
+ # This catches problems with the computation and the remote control interfaces
+ # It is ugly ... but works ...
+ # Also if the mesh is not waterprof the triangle filter of artist seems to have problems.
+
+ sleep(2.0)
+
+ image = utility.load_projection(temp_file, load_projection_geometry=False)[0]
+ os.remove(temp_file)
+
+ if output_full_ray_projection:
+ return self.convert_rays(image)
+ else:
+ return image
+
+ def convert_rays(self, image):
+ inter_image = np.roll(image, 1000, 0)
+ image += np.flip(inter_image, 1)
+ return image
+
+ def set_cylindrical_mode(self):
+ set_cylindrical_mode(self.api)
+ self.x_px = 2000.0
+ self.y_px = 2000.0
+ self.x_resolution_mm = np.pi
+ self.y_resolution_mm = np.pi
+ self.detector_radius_mm = 1000.0
+ self._cylindrical = True
+ print(
+ "Care! The default pixel pitch etc is set. If changes are made change the state of this class ..."
+ )
+
+ def set_cone_mode(self):
+ set_cone_mode(self.api)
+ self.pixel_pitch_mm = 0.139
+ self._cylindrical = False
+ print(
+ "Care! The default pixel pitch etc is set. If changes are made change the state of this class ..."
+ )
+
+
+def load_mesh(
+ cylindrical_projection: CylindricalProjection,
+ object_list: list[MeshObject],
+ cylindrical_mode: bool = True,
+) -> bool:
+ if cylindrical_mode:
+ cylindrical_projection.set_cylindrical_mode()
+ else:
+ cylindrical_projection.set_cone_mode()
+
+ for mesh_object in object_list:
+ object_id = cylindrical_projection.api.load_part(mesh_object.object_path)
+ cylindrical_projection.api.translate(
+ object_id,
+ mesh_object.position_mm[0],
+ mesh_object.position_mm[1],
+ mesh_object.position_mm[2],
+ )
+ cylindrical_projection.api.rotate_from_quat(
+ object_id, mesh_object.orientation_quat
+ )
+
+ return True
diff --git a/src/cyxtrax/simulation/cylindrical_projection.py b/src/cyxtrax/simulation/cylindrical_projection.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/cyxtrax/simulation/cylindrical_projection_interface.py b/src/cyxtrax/simulation/cylindrical_projection_interface.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/cyxtrax/util/transform_to_rays.py b/src/cyxtrax/util/transform_to_rays.py
new file mode 100644
index 0000000000000000000000000000000000000000..8cff8122cc4c15265088293e4474f173277c6ff5
--- /dev/null
+++ b/src/cyxtrax/util/transform_to_rays.py
@@ -0,0 +1,63 @@
+from pathlib import Path
+
+from cyxtrax.io.load_maps import load_atlas
+from cyxtrax.io.save_map import add_rays_to_atlas
+import numpy as np
+
+
+def transform_to_rays(file: Path) -> np.ndarray:
+ maps, points, _ = load_atlas(file)
+ pixel_scale = (maps.shape[0] - 1.) / maps.shape[0]
+
+ def cylinder_coordinates(alpha: float, radius: float = 1000.) -> np.ndarray:
+ x = np.sin(alpha) * radius
+ y = np.cos(alpha) * radius
+ point = np.array([x, y, 0.])
+ return point
+
+ def map_z(point, radius: float = 1000.):
+ point = point.reshape((1, 3))
+ z = np.linspace(-radius, radius, maps.shape[1]) * np.pi * pixel_scale
+ z_array = np.zeros((maps.shape[1], 3))
+ z_array[..., 2] = z
+ return point + z_array
+
+
+ xyz = list(map(cylinder_coordinates, np.linspace(
+ -np.pi * pixel_scale, np.pi * pixel_scale, maps.shape[0], endpoint=False)))
+ xyz = np.array(list(map(map_z, xyz)))
+
+ start = points.swapaxes(0, 1)
+
+ ray_end = np.expand_dims(xyz, 2) + np.expand_dims(np.expand_dims(start, 0), 0)
+ ray_end = np.roll(ray_end, 500, 0)
+
+ ray_start = np.roll(ray_end, 1000, 0)
+ ray_start = np.flip(ray_start, 1)
+ return ray_start, ray_end
+
+
+if __name__ == '__main__':
+ save_path = Path(r'.\dir2025\00004_smurf.h5')
+ maps, points, mesh_object_list = load_atlas(save_path)
+
+
+ ray_start, ray_end = transform_to_rays(save_path)
+
+ from cyxtrax.io.save_map import add_rays_to_atlas
+ from cyxtrax.mapping import map_source_2_cylinder
+
+ add_rays_to_atlas(save_path, ray_start, ray_end)
+
+ index_0, index_1, map_index = 1432, 1111, 11
+
+ source = ray_start[index_0, index_1, map_index]
+
+ values, uvw = map_source_2_cylinder(source, maps, points)
+ print(values.shape)
+ print(uvw.shape)
+
+ value = values[map_index]
+ print(uvw[:2, map_index], values[map_index], maps[index_0, index_1, map_index])
+
+
\ No newline at end of file
diff --git a/temp/mapping.png b/temp/mapping.png
deleted file mode 100644
index 4af6c15f22fe97cc7cea7579c2e417b86164ee86..0000000000000000000000000000000000000000
Binary files a/temp/mapping.png and /dev/null differ
diff --git a/temp/scones.png b/temp/scones.png
deleted file mode 100644
index b00343ab54e02835bcefa53b8471d7b909fa38ef..0000000000000000000000000000000000000000
Binary files a/temp/scones.png and /dev/null differ
diff --git a/temp/scones_maps.png b/temp/scones_maps.png
deleted file mode 100644
index 402700766767ee7fc2aaffb36bb0fab823dcb89d..0000000000000000000000000000000000000000
Binary files a/temp/scones_maps.png and /dev/null differ
diff --git a/uv.lock b/uv.lock
index 02e176040a12d373816790c934f742684620af40..e222b8176545ac77af758c730e7d8efb235f1a4f 100644
--- a/uv.lock
+++ b/uv.lock
@@ -27,13 +27,15 @@ wheels = [
[[package]]
name = "artist-pythonlib"
version = "0.1.0"
-source = { git = "https://mygit.th-deg.de/roboct-public/artist-api#26ae2c7e3f6a9151d0fa339ff9d7d2f885c018e4" }
+source = { git = "https://mygit.th-deg.de/roboct-public/artist-api#f4d9dd7a4823ec0f7f28df4d455fb95e1700d43b" }
dependencies = [
+ { name = "h5schemas", marker = "sys_platform == 'win32'" },
{ name = "matplotlib", marker = "sys_platform == 'win32'" },
- { name = "numpy", marker = "sys_platform == 'win32'" },
+ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" },
{ name = "pillow", marker = "sys_platform == 'win32'" },
{ name = "scipy", marker = "sys_platform == 'win32'" },
{ name = "thd-json", marker = "sys_platform == 'win32'" },
+ { name = "tqdm", marker = "sys_platform == 'win32'" },
{ name = "xraydb", marker = "sys_platform == 'win32'" },
]
@@ -46,6 +48,27 @@ wheels = [
{ url = "https://files.pythonhosted.org/packages/6a/21/5b6702a7f963e95456c0de2d495f67bf5fd62840ac655dc451586d23d39a/attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2", size = 63001 },
]
+[[package]]
+name = "blosc2"
+version = "2.7.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+ { name = "msgpack", marker = "sys_platform == 'win32'" },
+ { name = "ndindex", marker = "sys_platform == 'win32'" },
+ { name = "numexpr", marker = "sys_platform == 'win32'" },
+ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" },
+ { name = "py-cpuinfo", marker = "sys_platform == 'win32'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ef/bb/19a5d672f86dd26be0fc4f3a4c04264c088f3309b7b9d4e3e853a1f3cfda/blosc2-2.7.1.tar.gz", hash = "sha256:34db4d41543b16e894d507d6c7d10a9a67c9dd420ff40b072f7c39185cbb8fe8", size = 5149754 }
+wheels = [
+ { url = "https://files.pythonhosted.org/packages/db/64/6e11754d7498aa9e7fa13436e9eef00aaf1c74a9c67f74b36e134bd2c81a/blosc2-2.7.1-cp310-cp310-win32.whl", hash = "sha256:d5e03ec783841c82ba6704638f5847a80cac8625186932a8f3b47bc5fbda4f7e", size = 1982839 },
+ { url = "https://files.pythonhosted.org/packages/9b/a5/0bf10f282853aaf77f8f7b919ca79813b56b2d7955625400d527eb268449/blosc2-2.7.1-cp310-cp310-win_amd64.whl", hash = "sha256:150030e81bd5037f802ce7844281a37ff67e0998aa1735c48b02f3c6401bf0a1", size = 2374796 },
+ { url = "https://files.pythonhosted.org/packages/d8/f6/aeb8cd6c0184870ad2be3cf3664a23e45595024b47cc036e83f20b2d039f/blosc2-2.7.1-cp311-cp311-win32.whl", hash = "sha256:bf55816beaf34eaba021904ee7d6c428ca338d0f3ec7a5be04dda552258d0a8b", size = 1982521 },
+ { url = "https://files.pythonhosted.org/packages/df/e1/36db3625759c8e620ed992450e9579a02f023538292883e04189845d98d0/blosc2-2.7.1-cp311-cp311-win_amd64.whl", hash = "sha256:9b00bcaeaf125491cc6dec5508389f95152de69cc678a63a0310a756511f3d21", size = 2375006 },
+ { url = "https://files.pythonhosted.org/packages/9b/f6/3864933ef0d51845a78f260dce9eba4e3938ff136d1dcd7a4b9d91d25191/blosc2-2.7.1-cp312-cp312-win32.whl", hash = "sha256:6c894ef42fabc49c6bd1c41d2e45ac24e911b3b711c1e26f9be93dbcbf5fd4e2", size = 1977960 },
+ { url = "https://files.pythonhosted.org/packages/77/81/44def26a468e14309a4cb7d5f6f0534e3e9eec292c0453a9624a4d9c0ebd/blosc2-2.7.1-cp312-cp312-win_amd64.whl", hash = "sha256:a1a884f181a2a9612470bcd589794c7adda3eebdaed918e1a8b6e69683524b70", size = 2370429 },
+]
+
[[package]]
name = "chex"
version = "0.1.87"
@@ -53,8 +76,10 @@ source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "absl-py" },
{ name = "jax" },
- { name = "jaxlib" },
- { name = "numpy" },
+ { name = "jaxlib", version = "0.4.34", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'linux'" },
+ { name = "jaxlib", version = "0.4.35", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'linux'" },
+ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" },
+ { name = "numpy", version = "2.1.3", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'win32'" },
{ name = "setuptools", marker = "python_full_version >= '3.12'" },
{ name = "toolz" },
{ name = "typing-extensions" },
@@ -64,67 +89,34 @@ wheels = [
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]
+[[package]]
+name = "colorama"
+version = "0.4.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/d8/53/6f443c9a4a8358a93a6792e2acffb9d9d5cb0a5cfd8802644b7b1c9a02e4/colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44", size = 27697 }
+wheels = [
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+
[[package]]
name = "contourpy"
version = "1.3.1"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "numpy" },
+ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" },
]
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+ { url = "https://files.pythonhosted.org/packages/5c/23/c7abc0ca0a1526a0774eca151daeb8de62ec457e77262b66b359c3c7679e/tzdata-2025.2-py2.py3-none-any.whl", hash = "sha256:1a403fada01ff9221ca8044d701868fa132215d84beb92242d9acd2147f667a8", size = 347839 },
+]
+
[[package]]
name = "xraydb"
version = "4.5.4"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "numpy", marker = "sys_platform == 'win32'" },
+ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" },
{ name = "packaging", marker = "sys_platform == 'win32'" },
{ name = "platformdirs", marker = "sys_platform == 'win32'" },
{ name = "scipy", marker = "sys_platform == 'win32'" },
@@ -1134,7 +1304,8 @@ name = "xraylib"
version = "4.1.5"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "numpy" },
+ { name = "numpy", version = "2.0.2", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform == 'win32'" },
+ { name = "numpy", version = "2.1.3", source = { registry = "https://pypi.org/simple" }, marker = "sys_platform != 'win32'" },
]
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wheels = [