folder restructure

CyXTraX/__init__.py

-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
-import numpy as np
-
-
-with importlib.resources.path('CyXTraX.data', 'olaf_6.stl') as file_path:
-    olaf_stl = file_path
-    olaf_mesh = MeshObject(olaf_stl, 
-                           position_mm=np.array([1, 2, 3]),
-                           orientation_quat=np.array([0., 0., 0., 1.]))
-    
-with importlib.resources.path('CyXTraX.data', 'scones.stl') as file_path:
-    scones_stl = file_path
-    scones_mesh = MeshObject(scones_stl, 
-                             position_mm=np.array([0, 0, 0]),
-                             orientation_quat=np.array([0., 0., 0., 1.]))
\ No newline at end of file

CyXTraX/common/__init__.py

+from .mesh_object import MeshObject
\ No newline at end of file

CyXTraX/data/__init__.py

+import importlib.resources
+import numpy as np
+from ..common import MeshObject
+
+
+with importlib.resources.path('CyXTraX.data', 'olaf_6.stl') as file_path:
+    olaf_stl = file_path
+    olaf_mesh = MeshObject(olaf_stl, 
+                           position_mm=np.array([1, 2, 3]),
+                           orientation_quat=np.array([0., 0., 0., 1.]))
+    
+with importlib.resources.path('CyXTraX.data', 'scones.stl') as file_path:
+    scones_stl = file_path
+    scones_mesh = MeshObject(scones_stl, 
+                             position_mm=np.array([0, 0, 0]),
+                             orientation_quat=np.array([0., 0., 0., 1.]))
\ No newline at end of file

CyXTraX/io/__init__.py

+from .generate_atlas import record_atlas
+from .load_maps import load_atlas
\ No newline at end of file

CyXTraX/generate_atlas.py → CyXTraX/io/generate_atlas.py

 import numpy as np
 import h5py
-from .artist_bridge import CylindricalProjection
-from .mesh_object import MeshObject
+from CyXTraX.simulation.artist_bridge import CylindricalProjection
+from CyXTraX.common.mesh_object import MeshObject
 from pathlib import Path
 import json
 

CyXTraX/load_maps.py → CyXTraX/io/load_maps.py

 import h5py
 from jax import numpy as jnp
-from .mesh_object import MeshObject
+from ..common.mesh_object import MeshObject
 import json
 from pathlib import Path
 

CyXTraX/simulation/__init__.py

+from .artist_bridge import CylindricalProjection, load_mesh
\ No newline at end of file

CyXTraX/artist_bridge.py → CyXTraX/simulation/artist_bridge.py

@@ -5,7 +5,7 @@ import os
 from scipy.spatial.transform import Rotation
 import importlib.resources
 
-from .mesh_object import MeshObject
+from CyXTraX.common.mesh_object import MeshObject
 
 # !!!!!!!!!!!!!!!!!!!
 # Read carefully

scripts/01_aRTist_bridge.py

-from CyXTraX import CylindricalProjection, load_mesh, scones_mesh, MeshObject
+from CyXTraX.simulation import CylindricalProjection, load_mesh
+from CyXTraX.data import scones_mesh
+from CyXTraX.common import MeshObject
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -12,7 +15,7 @@ def main():
     print(f'STL Path: {scones_mesh.object_path}')
 
     # Obect are loaded in a dataclass: MeshObject.
-    print(f'Olaf 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])
     

scripts/02_generate_atlas.py

-from CyXTraX import CylindricalProjection, olaf_mesh, record_atlas, load_mesh
+from CyXTraX.io import record_atlas
+from CyXTraX.simulation import CylindricalProjection, load_mesh
+from CyXTraX.data import olaf_mesh
 from pathlib import Path
 
 

scripts/03_load_atlas.py

-from CyXTraX import CylindricalProjection, load_atlas
+from CyXTraX.io import load_atlas
 from pathlib import Path
 
 

scripts/04_mapping.py

-from CyXTraX import CylindricalProjection, load_atlas, load_mesh
+from CyXTraX.simulation import CylindricalProjection, load_mesh
+from CyXTraX.io import load_atlas
 from CyXTraX.mapping import map_geometry_2_projection, map_source_2_cylinder
 from pathlib import Path
 from jax import numpy as jnp
@@ -59,7 +60,6 @@ def main():
         print(values_calc[i], mapped_values[i])
         map_ = maps[:, :, i]
         value = map_[int(angles_calc[0, i]), int(angles_calc[1, i])]
-        print(value)
 
     fig = plt.figure()
     ax1 = fig.add_subplot(111)