From 1a6e5ee6a6c95fc3b4d4c1b6efc27493e8a77824 Mon Sep 17 00:00:00 2001
From: swittl <simon.wittl@th-deg.de>
Date: Tue, 29 Oct 2024 06:56:41 +0100
Subject: [PATCH] folder restructure
---
CyXTraX/__init__.py | 20 --------------------
CyXTraX/common/__init__.py | 1 +
CyXTraX/{ => common}/mesh_object.py | 0
CyXTraX/data/__init__.py | 16 ++++++++++++++++
CyXTraX/io/__init__.py | 2 ++
CyXTraX/{ => io}/generate_atlas.py | 4 ++--
CyXTraX/{ => io}/load_maps.py | 2 +-
CyXTraX/simulation/__init__.py | 1 +
CyXTraX/{ => simulation}/artist_bridge.py | 2 +-
scripts/01_aRTist_bridge.py | 7 +++++--
scripts/02_generate_atlas.py | 4 +++-
scripts/03_load_atlas.py | 2 +-
scripts/04_mapping.py | 4 ++--
13 files changed, 35 insertions(+), 30 deletions(-)
create mode 100644 CyXTraX/common/__init__.py
rename CyXTraX/{ => common}/mesh_object.py (100%)
create mode 100644 CyXTraX/data/__init__.py
create mode 100644 CyXTraX/io/__init__.py
rename CyXTraX/{ => io}/generate_atlas.py (94%)
rename CyXTraX/{ => io}/load_maps.py (93%)
create mode 100644 CyXTraX/simulation/__init__.py
rename CyXTraX/{ => simulation}/artist_bridge.py (98%)
diff --git a/CyXTraX/__init__.py b/CyXTraX/__init__.py
index 604e872..e69de29 100644
--- a/CyXTraX/__init__.py
+++ b/CyXTraX/__init__.py
@@ -1,20 +0,0 @@
-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
diff --git a/CyXTraX/common/__init__.py b/CyXTraX/common/__init__.py
new file mode 100644
index 0000000..0bcec68
--- /dev/null
+++ b/CyXTraX/common/__init__.py
@@ -0,0 +1 @@
+from .mesh_object import MeshObject
\ No newline at end of file
diff --git a/CyXTraX/mesh_object.py b/CyXTraX/common/mesh_object.py
similarity index 100%
rename from CyXTraX/mesh_object.py
rename to CyXTraX/common/mesh_object.py
diff --git a/CyXTraX/data/__init__.py b/CyXTraX/data/__init__.py
new file mode 100644
index 0000000..b1d7765
--- /dev/null
+++ b/CyXTraX/data/__init__.py
@@ -0,0 +1,16 @@
+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
diff --git a/CyXTraX/io/__init__.py b/CyXTraX/io/__init__.py
new file mode 100644
index 0000000..7ba211c
--- /dev/null
+++ b/CyXTraX/io/__init__.py
@@ -0,0 +1,2 @@
+from .generate_atlas import record_atlas
+from .load_maps import load_atlas
\ No newline at end of file
diff --git a/CyXTraX/generate_atlas.py b/CyXTraX/io/generate_atlas.py
similarity index 94%
rename from CyXTraX/generate_atlas.py
rename to CyXTraX/io/generate_atlas.py
index 5c08155..239f985 100644
--- a/CyXTraX/generate_atlas.py
+++ b/CyXTraX/io/generate_atlas.py
@@ -1,7 +1,7 @@
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
diff --git a/CyXTraX/load_maps.py b/CyXTraX/io/load_maps.py
similarity index 93%
rename from CyXTraX/load_maps.py
rename to CyXTraX/io/load_maps.py
index 8d5105c..b2cddbd 100644
--- a/CyXTraX/load_maps.py
+++ b/CyXTraX/io/load_maps.py
@@ -1,6 +1,6 @@
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
diff --git a/CyXTraX/simulation/__init__.py b/CyXTraX/simulation/__init__.py
new file mode 100644
index 0000000..c36a20e
--- /dev/null
+++ b/CyXTraX/simulation/__init__.py
@@ -0,0 +1 @@
+from .artist_bridge import CylindricalProjection, load_mesh
\ No newline at end of file
diff --git a/CyXTraX/artist_bridge.py b/CyXTraX/simulation/artist_bridge.py
similarity index 98%
rename from CyXTraX/artist_bridge.py
rename to CyXTraX/simulation/artist_bridge.py
index 5bf5ff3..e9243b6 100644
--- a/CyXTraX/artist_bridge.py
+++ b/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
diff --git a/scripts/01_aRTist_bridge.py b/scripts/01_aRTist_bridge.py
index db602c5..2263754 100644
--- a/scripts/01_aRTist_bridge.py
+++ b/scripts/01_aRTist_bridge.py
@@ -1,4 +1,7 @@
-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])
diff --git a/scripts/02_generate_atlas.py b/scripts/02_generate_atlas.py
index f7bd52f..39eff9d 100644
--- a/scripts/02_generate_atlas.py
+++ b/scripts/02_generate_atlas.py
@@ -1,4 +1,6 @@
-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
diff --git a/scripts/03_load_atlas.py b/scripts/03_load_atlas.py
index 2a0b349..b574781 100644
--- a/scripts/03_load_atlas.py
+++ b/scripts/03_load_atlas.py
@@ -1,4 +1,4 @@
-from CyXTraX import CylindricalProjection, load_atlas
+from CyXTraX.io import load_atlas
from pathlib import Path
diff --git a/scripts/04_mapping.py b/scripts/04_mapping.py
index 9c512c4..f63d84e 100644
--- a/scripts/04_mapping.py
+++ b/scripts/04_mapping.py
@@ -1,4 +1,5 @@
-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)
--
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