diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..a6b232ae238214a64d2a431d84f258e751d37e5d
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+/build/
+/temp/
+__pycache__
+*.egg-info
\ No newline at end of file
diff --git a/CyXTraX/__init__.py b/CyXTraX/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..d45a1322301b4c1dfe92aa53f58f27f6d39587be
--- /dev/null
+++ b/CyXTraX/__init__.py
@@ -0,0 +1,15 @@
+from .artist_bridge import CylindricalProjection, load_mesh
+from .mesh_object import MeshObject
+from .generate_atlas import record_atlas
+from .load_maps import load_atlas
+
+import importlib.resources
+
+
+with importlib.resources.path('CyXTraX.data', 'olaf_6.stl') as file_path:
+ olaf_stl = file_path
+ import numpy as np
+
+ olaf_mesh = MeshObject(olaf_stl,
+ position_mm=np.array([1, 2, 3]),
+ orientation_quat=np.array([0., 0., 0., 1.]))
\ No newline at end of file
diff --git a/CyXTraX/artist_bridge.py b/CyXTraX/artist_bridge.py
new file mode 100644
index 0000000000000000000000000000000000000000..a8a91235363127283803eb210c19361aa04548c0
--- /dev/null
+++ b/CyXTraX/artist_bridge.py
@@ -0,0 +1,92 @@
+from artistlib import API, utility, SAVEMODES
+from pathlib import Path
+import numpy as np
+import os
+from scipy.spatial.transform import Rotation
+import importlib.resources
+
+from .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!!!
+
+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.x_px = 2000
+ self.y_px = 2000
+ self.detector_radius_mm = 1000.
+ self.objects = list()
+
+ 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(f'::XDetector::SetDownCurvedView;')
+
+
+ def compute_projection(self, position: np.ndarray, temp_file_path: Path = Path('temp.tiff'), output_full_ray_projection: bool = True) -> np.ndarray:
+ self.translate(position)
+ self.api.save_image(temp_file_path, save_projection_geometry=False, save_mode=SAVEMODES.FLOAT_TIFF)
+ image = utility.load_projection(temp_file_path, load_projection_geometry=False)[0]
+ os.remove(temp_file_path)
+
+ 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):
+ with importlib.resources.path('CyXTraX.data', 'cylinder.aRTist') as file_path:
+ print(f'Load: {file_path}')
+ self.api.load_project(file_path)
+ self.x_px = 2000.
+ self.y_px = 2000.
+ self.x_resolution_mm = np.pi
+ self.y_resolution_mm = np.pi
+ self.detector_radius_mm = 1000.
+
+ def set_cone_mode(self):
+ with importlib.resources.path('CyXTraX.data', 'cone.aRTist') as file_path:
+ print(f'Load: {file_path}')
+ self.api.load_project(file_path)
+
+
+
+
+def load_mesh(cylindrical_projection: CylindricalProjection, object_list: list[MeshObject]) -> bool:
+ cylindrical_projection.set_cylindrical_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/CyXTraX/data/cone.aRTist b/CyXTraX/data/cone.aRTist
new file mode 100644
index 0000000000000000000000000000000000000000..7c92c2eaf561c53c85465f8c73db5686732c2ff8
Binary files /dev/null and b/CyXTraX/data/cone.aRTist differ
diff --git a/CyXTraX/data/cylinder.aRTist b/CyXTraX/data/cylinder.aRTist
new file mode 100644
index 0000000000000000000000000000000000000000..d7ccf000d51c5376729ecdacfa9ee3d1a420b7e7
Binary files /dev/null and b/CyXTraX/data/cylinder.aRTist differ
diff --git a/CyXTraX/data/olaf_6.stl b/CyXTraX/data/olaf_6.stl
new file mode 100644
index 0000000000000000000000000000000000000000..908979f538d74e1d0809e0c0c5bdbc77ba3246a1
Binary files /dev/null and b/CyXTraX/data/olaf_6.stl differ
diff --git a/CyXTraX/generate_atlas.py b/CyXTraX/generate_atlas.py
new file mode 100644
index 0000000000000000000000000000000000000000..7506562c7f9406d7002f2dd2b6dc531bdbc3eb71
--- /dev/null
+++ b/CyXTraX/generate_atlas.py
@@ -0,0 +1,58 @@
+import numpy as np
+import h5py
+from .artist_bridge import CylindricalProjection
+from .mesh_object import MeshObject
+from pathlib import Path
+import json
+
+
+
+
+def to_dict(mesh_object = MeshObject) -> dict:
+ return mesh_object.as_dict()
+
+def record_atlas(cylindrical_projection: CylindricalProjection, mesh_list: list[MeshObject],
+ atlas_name: str, save_folder: Path,
+ map_bounding_box: tuple[float]=(-50., 50.), number_of_maps: int = 4) -> Path:
+
+ grid = np.linspace(map_bounding_box[0], map_bounding_box[1], number_of_maps)
+ file_index = len(list(save_folder.glob('*.h5')))
+ 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, 0), # Initial shape with third dimension as 0
+ maxshape=(cylindrical_projection.x_px, cylindrical_projection.y_px, None),
+ dtype=np.float32)
+
+ projection_points = file.require_dataset(
+ 'positions',
+ shape=(3, 0), # Initial shape with third dimension as 0
+ maxshape=(3, None),
+ 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)
+
+
+
+ for x in grid:
+ for y in grid:
+ for z in grid:
+ # x, y, z = 0, y, 0
+ print(x, y, z)
+ position = np.array([x, y, z])
+
+ 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))
+
+ return save_path
diff --git a/CyXTraX/load_maps.py b/CyXTraX/load_maps.py
new file mode 100644
index 0000000000000000000000000000000000000000..8d5105cd9bcc92ad2825756fb3aa53a3b0573e9c
--- /dev/null
+++ b/CyXTraX/load_maps.py
@@ -0,0 +1,23 @@
+import h5py
+from jax import numpy as jnp
+from .mesh_object import MeshObject
+import json
+from pathlib import Path
+
+
+def from_dict(mesh_dict) -> MeshObject:
+ return MeshObject.from_dict(mesh_dict)
+
+
+def load_atlas(load_path: Path
+ ) -> tuple[jnp.ndarray, jnp.ndarray, list[MeshObject]]:
+
+ with h5py.File(load_path, 'r') as f:
+ maps = f['/maps'][:]
+ points = f['/positions'][:]
+
+ mesh_object_str = f.attrs['mesh_list']
+ mesh_object_dict = json.loads(mesh_object_str)
+ mesh_object_list = list(map(from_dict, mesh_object_dict))
+ return maps, points, mesh_object_list
+
diff --git a/CyXTraX/mapping.py b/CyXTraX/mapping.py
new file mode 100644
index 0000000000000000000000000000000000000000..cacc2f13b898f7bdd184a6f9d9e7ab4cc94bb6e5
--- /dev/null
+++ b/CyXTraX/mapping.py
@@ -0,0 +1,115 @@
+from jax import numpy as jnp
+import dm_pix as pix
+from jax import jit, vmap
+from jax.scipy.spatial.transform import Rotation
+
+
+@jit
+def map_source_2_cylinder(source: jnp.ndarray, maps: jnp.ndarray, map_positions: jnp.ndarray, radius: float = 1000.,
+ angle_discretisation: int = 2000, pitch: float = jnp.pi) -> tuple[jnp.ndarray, jnp.ndarray]:
+ """
+ source: 1 x 3
+ maps: u x v x m
+ map_positions: 3 x m
+
+ ---
+
+ cylinder_value: m x 1
+ """
+
+ #map_positions = map_positions.T # m x 3
+
+ angles = cylindrical_angles(source, map_positions, radius, angle_discretisation, pitch)
+
+ u = jnp.expand_dims(angles[0], 0) # 1 x m
+ v = jnp.expand_dims(angles[1], 0) # 1 x m
+ w = jnp.arange(0, maps.shape[2])[jnp.newaxis, ...] #+0.0001 # 1 x m
+
+ uvw = jnp.concatenate([v, u, w], 0) # 3 x m
+ values = pix.flat_nd_linear_interpolate(maps, uvw)
+
+
+ return values, uvw # m,
+
+@jit
+def cylindrical_angles(source: jnp.ndarray, map_positions: jnp.ndarray, radius: float = 1000.,
+ angle_discretisation: int = 2000, pitch: float = jnp.pi) -> tuple[jnp.ndarray, jnp.ndarray]:
+ source = source.reshape((-1, 1)) # 1 x 3
+ directions = map_positions - source # m x 3
+ direction_norm_factor = jnp.linalg.norm(directions[:2], axis=0, keepdims=True)
+ directions = directions / direction_norm_factor # m x 3
+ intersection = directions * radius
+ sign = jnp.where(intersection[2]>=0, 1, -1)
+ intersection = intersection * sign
+
+
+ z_value = intersection[2] / pitch
+ z = z_value + (angle_discretisation) / 2.
+ beta_value = (jnp.arctan2(intersection[0], intersection[1]) / jnp.pi) * angle_discretisation / 2
+ beta = beta_value - ((angle_discretisation - 1.) / 4.)
+ angles = jnp.concatenate(
+ (jnp.expand_dims(z, 0) % 2000,
+ jnp.expand_dims(beta, 0) % 2000),
+ axis=0)
+ return angles
+
+
+@jit
+def map_geometry_2_projection(source: jnp.ndarray, detector: jnp.ndarray, detector_orientation: jnp.ndarray,
+ map_positions: jnp.ndarray,
+ projections: jnp.ndarray, pixel_pitch_mm: float = 0.139):
+ """
+ source: 1 x 3
+ detector: 1 x 3
+ detector_orientation: 1 x 4
+ map_positions: 3 x m
+ projections: u x v
+ pixel_pitch_mm: 1,
+
+ ---
+
+ projection_value: m
+ """
+
+ projection_geometry = projection_matrix(source, detector, detector_orientation) # 3 x 4
+ map_positions_homogen = jnp.ones((1, map_positions.shape[1])) # 1 x m
+ map_positions_homogen = jnp.concatenate((map_positions, map_positions_homogen), 0) # 4 x m
+ uv_px = projection_geometry @ map_positions_homogen # 3 x m
+ uv_px = uv_px / uv_px[2]
+ uv_px = uv_px / pixel_pitch_mm
+ uv_px = uv_px.at[0,:].multiply(-1)
+ uv_px = uv_px.at[0,:].add((projections.shape[-2])/ 2.)
+ # uv_px = uv_px.at[0,:].multiply(-1)
+ uv_px = uv_px.at[1,:].add((projections.shape[-2])/ 2.)
+ uv_px = uv_px[:2]
+
+ uv_px_flip = jnp.flip(uv_px, 0)
+ # uv_px_flip = uv_px
+
+ return pix.flat_nd_linear_interpolate(projections, uv_px_flip), uv_px
+
+
+@jit
+def projection_matrix(source: jnp.ndarray, detector: jnp.ndarray, detector_orientation: jnp.ndarray
+ ) -> jnp.ndarray:
+ """
+ source: 1 x 3
+ detector: 1 x 3
+ detector_orientation: 1 x 4
+
+ ---
+
+ projection_matrix = 3 x 4
+ """
+ detector_orientation = detector_orientation / detector_orientation[1, 3]
+ rotation_matrix = Rotation.from_quat(detector_orientation).as_matrix()
+ detector_horizontal_vector = -rotation_matrix[0, :, 0]
+ detector_vertical_vector = -rotation_matrix[0, :, 1]
+ print(detector_horizontal_vector)
+ p3x3 = jnp.vstack([detector_horizontal_vector,
+ detector_vertical_vector,
+ (detector - source).reshape((-1, 3))]).T
+ p3x3_inv = jnp.linalg.inv(p3x3)
+ p4 = p3x3_inv @ (-source).reshape((3, 1))
+ matrix = jnp.concatenate([p3x3_inv, p4], 1) # 3 x 4
+ return matrix
\ No newline at end of file
diff --git a/CyXTraX/mesh_object.py b/CyXTraX/mesh_object.py
new file mode 100644
index 0000000000000000000000000000000000000000..df02eeb99f59da1facbb0c7e62702a88c93c9ac7
--- /dev/null
+++ b/CyXTraX/mesh_object.py
@@ -0,0 +1,23 @@
+from dataclasses import dataclass
+from pathlib import Path
+import numpy as np
+
+
+@dataclass
+class MeshObject:
+ object_path: Path
+ position_mm: np.ndarray
+ orientation_quat: np.ndarray
+
+ def as_dict(self):
+ return dict(object_path=str(self.object_path),
+ object_position=self.position_mm.astype(np.float64).tolist(),
+ object_orientation=self.orientation_quat.astype(np.float64).tolist())
+
+ @classmethod
+ def from_dict(cls: 'MeshObject', data_dict):
+ item = cls(
+ Path(data_dict['object_path']),
+ np.array(data_dict['object_position']),
+ np.array(data_dict['object_orientation']))
+ return item
\ No newline at end of file
diff --git a/README.md b/README.md
index 89d45e027100a78569533305a07dd944624b9025..f8710b368308854c05ffad2c072c9dec08a1edaa 100644
--- a/README.md
+++ b/README.md
@@ -1,93 +1,11 @@
-# CylindricalXrayTransform
+# Cy(lindrical)X(ray)Tra(nsform with Ja)X
+This repo uses aRTist to generate local cylindrical xray transform maps / atlases of meshes.
+It also defines the used `.h5` dataformata for the other projects, and I/O util function for the use with the autograd [JAX](https://github.com/jax-ml/jax).
+As simulation backend [aRTist](https://artist.bam.de/) is used with the [THD API](https://github.com/wittlsn/aRTist-PythonLib).
-## Getting started
+## Dataformat
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+The local cylindrical xray transform maps are stored as `.h5` file.
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://mygit.th-deg.de/roboct/xraytrafo/cylindricalxraytransform.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://mygit.th-deg.de/roboct/xraytrafo/cylindricalxraytransform/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
-
-## License
-For open source projects, say how it is licensed.
-
-## Project status
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
diff --git a/scripts/01_aRTist_bridge.py b/scripts/01_aRTist_bridge.py
new file mode 100644
index 0000000000000000000000000000000000000000..918f6623ee2b6eed5f1f33f13308a3caa5dc6a2b
--- /dev/null
+++ b/scripts/01_aRTist_bridge.py
@@ -0,0 +1,50 @@
+from CyXTraX import CylindricalProjection, load_mesh, olaf_mesh, MeshObject
+import numpy as np
+from matplotlib import pyplot as plt
+
+
+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: {olaf_mesh.object_path}')
+
+ # Obect are loaded in a dataclass: MeshObject.
+ print(f'Olaf is a MeshObject: {isinstance(olaf_mesh, MeshObject)}')
+ olaf_mesh.position_mm = np.array([42, 69, 0])
+ olaf_mesh.orientation_quat = np.array([0.1, -0.1, 0.11, 0.99])
+
+
+ # The `load_mesh` function load a list of MeshObject
+ load_mesh(cyl_proj, [olaf_mesh])
+
+ # Set local position of cylindrical projection
+ map_position = np.array([1, 2, 4])
+
+ # Generate local cylindrical projection
+ half_rays = cyl_proj.compute_projection(map_position, output_full_ray_projection=False)
+ # output_full_ray_projection=True is the same As
+ # half_rays = cyl_proj.compute_projection(position, output_full_ray_projection=False)
+ # full_rays = cyl_proj.convert_rays(half_rays)
+ full_rays = cyl_proj.compute_projection(map_position, output_full_ray_projection=True)
+
+
+ # Make some nice plots!
+ fig = plt.figure(figsize=(12, 6))
+
+ ax1 = fig.add_subplot(121)
+ ax1.imshow(half_rays)
+ ax1.set_xlabel(r'$Z$ / mm')
+ ax1.set_ylabel(r'$\alpha$ / rad')
+
+ ax2 = fig.add_subplot(122)
+ ax2.imshow(full_rays)
+ ax2.set_xlabel(r'$Z$ / mm')
+ ax2.set_ylabel(r'$\alpha$ / rad')
+
+ plt.show()
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/scripts/02_generate_atlas.py b/scripts/02_generate_atlas.py
new file mode 100644
index 0000000000000000000000000000000000000000..9c1cfd3d98d2920b8daef3b7a2883814d20824ec
--- /dev/null
+++ b/scripts/02_generate_atlas.py
@@ -0,0 +1,22 @@
+from CyXTraX import CylindricalProjection, olaf_mesh, record_atlas
+from pathlib import Path
+
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+
+
+def main():
+ # Create the cylindrical projection interface
+ cyl_proj = CylindricalProjection()
+
+ # make an atlas
+ save_path = record_atlas(cyl_proj, [olaf_mesh], 'test', TEMP_FOLDER,
+ map_bounding_box=[-20, 20], number_of_maps=2)
+ print(f'Atlas saved to the path: {save_path}')
+
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/scripts/03_load_atlas.py b/scripts/03_load_atlas.py
new file mode 100644
index 0000000000000000000000000000000000000000..2a0b349407a86600295c8f4849b76bdbd79ace9b
--- /dev/null
+++ b/scripts/03_load_atlas.py
@@ -0,0 +1,23 @@
+from CyXTraX import CylindricalProjection, load_atlas
+from pathlib import Path
+
+
+# Just get the temp folder to store the atlas
+FOLDER = Path(__file__)
+TEMP_FOLDER = FOLDER.parent.parent / 'temp'
+
+
+def main():
+ 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[-1])
+
+ print(f'Loaded Map Shape: {maps.shape}')
+ print(f'Loaded Map Centre Shape: {points.shape}')
+ print(f'First Object: {mesh_object_list[0]}')
+
+
+if __name__ == '__main__':
+ main()
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000000000000000000000000000000000000..d616638ff63e84bda8432900669f7338e7438a01
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,18 @@
+[metadata]
+name = CyXTraX
+version = 0.1.0
+description = A Python module to play with local cylindrical xray transform maps or atlases.
+author = Simon Wittl
+author_email = simon.wittl@th-deg.de / simonwittl@gmail.com
+url = https://mygit.th-deg.de/roboct/xraytrafo
+
+[options]
+packages = find:
+include_package_data = True # Ensures data files are included
+zip_safe = False
+
+[options.package_data]
+CyXTraX =
+ data/cone.aRTist
+ data/cylinder.aRTist
+ data/olaf_6.stl
\ No newline at end of file
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..fc1f76c84d17b458f7090667d495592c9abda034
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,3 @@
+from setuptools import setup
+
+setup()
\ No newline at end of file