diff --git a/pyproject.toml b/pyproject.toml
index 155c39529d5bfb7b9c6729094257052976e3ffab..91b03059a663904a9640f16aaa0063e2b555978e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,14 +1,18 @@
[project]
-name = "CyXTraX"
+name = "cyxtrax"
version = "0.1.0"
description = "Add your description here"
readme = "README.md"
+authors = [
+ { name = "swittl", email = "simon.wittl@th-deg.de" }
+]
requires-python = ">=3.10"
dependencies = [
"artistlib",
"dm-pix>=0.4.3",
"h5py>=3.12.1",
- "jax[cuda12]>=0.4.35",
+ "jax>=0.4.35 ; sys_platform == 'windows'",
+ "jax[cuda12]>=0.4.35 ; sys_platform == 'linux'",
"matplotlib>=3.9.2",
"numpy>=2.1.3",
"ruff>=0.7.3",
@@ -16,17 +20,16 @@ dependencies = [
"xraylib>=4.1.5",
]
-[tool.hatch.build]
-include = [
- "src/CyXTraX/data/olaf_6.stl",
- "src/CyXTraX/data/scones.stl",
- "src/CyXTraX/data/cone.aRTist",
- "src/CyXTraX/data/cylinder.aRTist"
-]
[tool.uv.sources]
artistlib = { git = "https://github.com/wittlsn/aRTist-PythonLib" }
+cyxtrax = { workspace = true }
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
+
+[tool.ruff]
+exclude = [
+ ".venv",
+]
diff --git a/scripts/01_aRTist_bridge.py b/scripts/01_aRTist_bridge.py
index e54f36f2fb667cced30d4f33a168a3fb20eaf72c..2d93de9ed2a942eca9d6c6b1a6d6d00e61f118b4 100644
--- a/scripts/01_aRTist_bridge.py
+++ b/scripts/01_aRTist_bridge.py
@@ -1,6 +1,6 @@
-from CyXTraX.simulation import CylindricalProjection, load_mesh
-from CyXTraX.data import scones_mesh
-from CyXTraX.common import 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
diff --git a/scripts/03_load_atlas.py b/scripts/03_load_atlas.py
index 3cbec12056fc5c578e7c77c55b879c5831b3aa04..f20a8afcc7ce574865d2a7e765e171a003bdb044 100644
--- a/scripts/03_load_atlas.py
+++ b/scripts/03_load_atlas.py
@@ -1,5 +1,5 @@
-from CyXTraX.io import load_atlas
-from CyXTraX.util.visualisation import voxel_maps
+from cyxtrax.io import load_atlas
+from cyxtrax.util.visualisation import voxel_maps
from pathlib import Path
diff --git a/src/CyXTraX/data/__init__.py b/src/CyXTraX/data/__init__.py
index 6860b28e821b71416e91b252bd1f6c8f2871dc34..8921d24d347c3d8351cd769c4ee42e5c2212550e 100644
--- a/src/CyXTraX/data/__init__.py
+++ b/src/CyXTraX/data/__init__.py
@@ -3,7 +3,7 @@ import numpy as np
from ..common import MeshObject
-with importlib.resources.path("CyXTraX.data", "olaf_6.stl") as file_path:
+with importlib.resources.path("cyxtrax.data", "olaf_6.stl") as file_path:
olaf_stl = file_path
olaf_mesh = MeshObject(
olaf_stl,
@@ -11,7 +11,7 @@ with importlib.resources.path("CyXTraX.data", "olaf_6.stl") as file_path:
orientation_quat=np.array([0.0, 0.0, 0.0, 1.0]),
)
-with importlib.resources.path("CyXTraX.data", "scones.stl") as file_path:
+with importlib.resources.path("cyxtrax.data", "scones.stl") as file_path:
scones_stl = file_path
scones_mesh = MeshObject(
scones_stl,
diff --git a/src/CyXTraX/simulation/artist_bridge.py b/src/CyXTraX/simulation/artist_bridge.py
index ba274d1e3e15f7e38ad7b455d0cc478c58a7ae46..93d32f2fc703c50a38eaa4e251554effb13c3856 100644
--- a/src/CyXTraX/simulation/artist_bridge.py
+++ b/src/CyXTraX/simulation/artist_bridge.py
@@ -15,7 +15,7 @@ import numpy as np
import os
import importlib.resources
from time import sleep
-from CyXTraX.common.mesh_object import MeshObject
+from cyxtrax.common.mesh_object import MeshObject
# !!!!!!!!!!!!!!!!!!!
# Read carefully
@@ -114,7 +114,7 @@ class CylindricalProjection:
return image
def set_cylindrical_mode(self):
- with importlib.resources.path("CyXTraX.data", "cylinder.aRTist") as file_path:
+ 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 = 2000.0
@@ -128,7 +128,7 @@ class CylindricalProjection:
)
def set_cone_mode(self):
- with importlib.resources.path("CyXTraX.data", "cone.aRTist") as file_path:
+ with importlib.resources.path("cyxtrax.data", "cone.aRTist") as file_path:
print(f"Load: {file_path}")
self.api.load_project(file_path)
self.pixel_pitch_mm = 0.139
diff --git a/temp/scones.png b/temp/scones.png
index ef0c50d277432a5fc7ea522fb971d35eb4468ced..b00343ab54e02835bcefa53b8471d7b909fa38ef 100644
Binary files a/temp/scones.png and b/temp/scones.png differ
diff --git a/uv.lock b/uv.lock
index 2483fcb6207c2df3aedd76018bbb1c9888cd4c49..7c477bf8a8b814d9274d5ed12f26652a6292caf6 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,10 +1,18 @@
version = 1
requires-python = ">=3.10"
resolution-markers = [
- "python_full_version < '3.11'",
- "python_full_version == '3.11.*'",
- "python_full_version == '3.12.*'",
- "python_full_version >= '3.13'",
+ "python_full_version < '3.11' and sys_platform == 'linux'",
+ "python_full_version < '3.11' and sys_platform == 'windows'",
+ "python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'windows'",
+ "python_full_version == '3.11.*' and sys_platform == 'linux'",
+ "python_full_version == '3.11.*' and sys_platform == 'windows'",
+ "python_full_version == '3.11.*' and sys_platform != 'linux' and sys_platform != 'windows'",
+ "python_full_version == '3.12.*' and sys_platform == 'linux'",
+ "python_full_version == '3.12.*' and sys_platform == 'windows'",
+ "python_full_version == '3.12.*' and sys_platform != 'linux' and sys_platform != 'windows'",
+ "python_full_version >= '3.13' and sys_platform == 'linux'",
+ "python_full_version >= '3.13' and sys_platform == 'windows'",
+ "python_full_version >= '3.13' and sys_platform != 'linux' and sys_platform != 'windows'",
]
[[package]]
@@ -118,7 +126,8 @@ dependencies = [
{ name = "artistlib" },
{ name = "dm-pix" },
{ name = "h5py" },
- { name = "jax", extra = ["cuda12"] },
+ { name = "jax", marker = "sys_platform == 'linux' or sys_platform == 'windows'" },
+ { name = "jax", extra = ["cuda12"], marker = "sys_platform == 'linux'" },
{ name = "matplotlib" },
{ name = "numpy" },
{ name = "ruff" },
@@ -131,7 +140,8 @@ requires-dist = [
{ name = "artistlib", git = "https://github.com/wittlsn/aRTist-PythonLib" },
{ name = "dm-pix", specifier = ">=0.4.3" },
{ name = "h5py", specifier = ">=3.12.1" },
- { name = "jax", extras = ["cuda12"], specifier = ">=0.4.35" },
+ { name = "jax", marker = "sys_platform == 'windows'", specifier = ">=0.4.35" },
+ { name = "jax", extras = ["cuda12"], marker = "sys_platform == 'linux'", specifier = ">=0.4.35" },
{ name = "matplotlib", specifier = ">=3.9.2" },
{ name = "numpy", specifier = ">=2.1.3" },
{ name = "ruff", specifier = ">=0.7.3" },
@@ -239,8 +249,8 @@ wheels = [
[package.optional-dependencies]
cuda12 = [
- { name = "jax-cuda12-plugin", extra = ["with-cuda"] },
- { name = "jaxlib" },
+ { name = "jax-cuda12-plugin", extra = ["with-cuda"], marker = "sys_platform == 'linux'" },
+ { name = "jaxlib", marker = "sys_platform == 'linux'" },
]
[[package]]
@@ -257,7 +267,7 @@ name = "jax-cuda12-plugin"
version = "0.4.35"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "jax-cuda12-pjrt" },
+ { name = "jax-cuda12-pjrt", marker = "sys_platform == 'linux'" },
]
wheels = [
{ url = "https://files.pythonhosted.org/packages/d7/eb/f317f426b8ea56a9e634d6eb06230d9d2d01cc34066defeb7d3fd6ab5708/jax_cuda12_plugin-0.4.35-cp310-cp310-manylinux2014_aarch64.whl", hash = "sha256:30290570a8a0547e59c1fd927aefb693d4a4fe15aae23c0a1e5c34eed82bef49", size = 15545891 },
@@ -272,16 +282,16 @@ wheels = [
[package.optional-dependencies]
with-cuda = [
- { name = "nvidia-cublas-cu12" },
- { name = "nvidia-cuda-cupti-cu12" },
- { name = "nvidia-cuda-nvcc-cu12" },
- { name = "nvidia-cuda-runtime-cu12" },
- { name = "nvidia-cudnn-cu12" },
- { name = "nvidia-cufft-cu12" },
- { name = "nvidia-cusolver-cu12" },
- { name = "nvidia-cusparse-cu12" },
- { name = "nvidia-nccl-cu12" },
- { name = "nvidia-nvjitlink-cu12" },
+ { name = "nvidia-cublas-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cuda-cupti-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cuda-nvcc-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cuda-runtime-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cudnn-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cufft-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cusolver-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cusparse-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-nccl-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-nvjitlink-cu12", marker = "sys_platform == 'linux'" },
]
[[package]]
@@ -538,7 +548,6 @@ source = { registry = "https://pypi.org/simple" }
wheels = [
{ url = "https://files.pythonhosted.org/packages/78/02/9fe3ca905d4838d716669de65006e0fb34fef7b849868f403416526f0e05/nvidia_cublas_cu12-12.6.3.3-py3-none-manylinux2014_aarch64.whl", hash = "sha256:e531199ca4f1f764fb45bc1dde49a006f6765033f9c89c737e4553b9502ca1f5", size = 390792508 },
{ url = "https://files.pythonhosted.org/packages/f3/e7/c186a31c234fce776436753bfef4807df7f9b4cb3eeff358fcfcbf64b547/nvidia_cublas_cu12-12.6.3.3-py3-none-manylinux2014_x86_64.whl", hash = "sha256:f33fb68e101d99470c82d17f92a0dd9f74de2a21685c217f4716cdd63b1316eb", size = 393135292 },
- { url = "https://files.pythonhosted.org/packages/93/7a/2e502382b268277c4c36d26fb1c3aab13efa37a3d058fc993bd024ced8fe/nvidia_cublas_cu12-12.6.3.3-py3-none-win_amd64.whl", hash = "sha256:e1f70bee38b964eac1907293b336bceb24498a4243e61eaf91a52977c59aebc4", size = 434535005 },
]
[[package]]
@@ -548,7 +557,6 @@ source = { registry = "https://pypi.org/simple" }
wheels = [
{ url = "https://files.pythonhosted.org/packages/25/0f/acb326ac8fd26e13c799e0b4f3b2751543e1834f04d62e729485872198d4/nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_aarch64.whl", hash = "sha256:358b4a1d35370353d52e12f0a7d1769fc01ff74a191689d3870b2123156184c4", size = 8236756 },
{ url = "https://files.pythonhosted.org/packages/a5/24/120ee57b218d9952c379d1e026c4479c9ece9997a4fb46303611ee48f038/nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.whl", hash = "sha256:a3eff6cdfcc6a4c35db968a06fcadb061cbc7d6dde548609a941ff8701b98b73", size = 8917972 },
- { url = "https://files.pythonhosted.org/packages/1c/81/7796f096afaf726796b1b648f3bc80cafc61fe7f77f44a483c89e6c5ef34/nvidia_cuda_cupti_cu12-12.6.80-py3-none-win_amd64.whl", hash = "sha256:bbe6ae76e83ce5251b56e8c8e61a964f757175682bbad058b170b136266ab00a", size = 5724175 },
]
[[package]]
@@ -558,7 +566,6 @@ source = { registry = "https://pypi.org/simple" }
wheels = [
{ url = "https://files.pythonhosted.org/packages/01/4a/d153d4ec0bfb42889584de351dd168ebb06d293fd43b96f0d0c763b8b029/nvidia_cuda_nvcc_cu12-12.6.77-py3-none-manylinux2014_aarch64.whl", hash = "sha256:9a2aad43b8f4e4be9c237ece04f64450df77871eeebffad5a5a872714a97ca77", size = 19261369 },
{ url = "https://files.pythonhosted.org/packages/62/8f/cd3032281ba7bb531fe3159337af00c5c805fd6a31dc700f0715c8748c8c/nvidia_cuda_nvcc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl", hash = "sha256:b66bb5dd6b8ae62262586691977d3b4a425e91db61b4b9bc2f6b42bcd4154b96", size = 21169073 },
- { url = "https://files.pythonhosted.org/packages/45/a6/90b049466959c0f8c4a9c55f67f65b71f6ca4e1283e073a8522ccc9eee79/nvidia_cuda_nvcc_cu12-12.6.77-py3-none-win_amd64.whl", hash = "sha256:26e118b4dae4ebd316ab6f5ee3f3c4cb929f8265f717a8e016ba57e254c0b4f1", size = 16812720 },
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[[package]]
@@ -568,7 +575,6 @@ source = { registry = "https://pypi.org/simple" }
wheels = [
{ url = "https://files.pythonhosted.org/packages/b7/3d/159023799677126e20c8fd580cca09eeb28d5c5a624adc7f793b9aa8bbfa/nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_aarch64.whl", hash = "sha256:d461264ecb429c84c8879a7153499ddc7b19b5f8d84c204307491989a365588e", size = 908040 },
{ url = "https://files.pythonhosted.org/packages/f0/62/65c05e161eeddbafeca24dc461f47de550d9fa8a7e04eb213e32b55cfd99/nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl", hash = "sha256:a84d15d5e1da416dd4774cb42edf5e954a3e60cc945698dc1d5be02321c44dc8", size = 897678 },
- { url = "https://files.pythonhosted.org/packages/fa/76/4c80fa138333cc975743fd0687a745fccb30d167f906f13c1c7f9a85e5ea/nvidia_cuda_runtime_cu12-12.6.77-py3-none-win_amd64.whl", hash = "sha256:86c58044c824bf3c173c49a2dbc7a6c8b53cb4e4dca50068be0bf64e9dab3f7f", size = 891773 },
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[[package]]
@@ -576,12 +582,11 @@ name = "nvidia-cudnn-cu12"
version = "9.5.1.17"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "nvidia-cublas-cu12" },
+ { name = "nvidia-cublas-cu12", marker = "sys_platform == 'linux'" },
]
wheels = [
{ url = "https://files.pythonhosted.org/packages/99/93/a201a12d3ec1caa8c6ac34c1c2f9eeb696b886f0c36ff23c638b46603bd0/nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_aarch64.whl", hash = "sha256:9fd4584468533c61873e5fda8ca41bac3a38bcb2d12350830c69b0a96a7e4def", size = 570523509 },
{ url = "https://files.pythonhosted.org/packages/2a/78/4535c9c7f859a64781e43c969a3a7e84c54634e319a996d43ef32ce46f83/nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl", hash = "sha256:30ac3869f6db17d170e0e556dd6cc5eee02647abc31ca856634d5a40f82c15b2", size = 570988386 },
- { url = "https://files.pythonhosted.org/packages/b6/b2/3f60d15f037fa5419d9d7f788b100ef33ea913ae5315c87ca6d6fa606c35/nvidia_cudnn_cu12-9.5.1.17-py3-none-win_amd64.whl", hash = "sha256:d7af0f8a4f3b4b9dbb3122f2ef553b45694ed9c384d5a75bab197b8eefb79ab8", size = 565440743 },
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[[package]]
@@ -589,12 +594,11 @@ name = "nvidia-cufft-cu12"
version = "11.3.0.4"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "nvidia-nvjitlink-cu12" },
+ { name = "nvidia-nvjitlink-cu12", marker = "sys_platform == 'linux'" },
]
wheels = [
{ url = "https://files.pythonhosted.org/packages/ce/f5/188566814b7339e893f8d210d3a5332352b1409815908dad6a363dcceac1/nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_aarch64.whl", hash = "sha256:8510990de9f96c803a051822618d42bf6cb8f069ff3f48d93a8486efdacb48fb", size = 200164135 },
{ url = "https://files.pythonhosted.org/packages/60/de/99ec247a07ea40c969d904fc14f3a356b3e2a704121675b75c366b694ee1/nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_x86_64.whl", hash = "sha256:768160ac89f6f7b459bee747e8d175dbf53619cfe74b2a5636264163138013ca", size = 200221622 },
- { url = "https://files.pythonhosted.org/packages/b4/38/36fd800cec8f6e89b7c1576edaaf8076e69ec631644cdbc1b5f2e2b5a9df/nvidia_cufft_cu12-11.3.0.4-py3-none-win_amd64.whl", hash = "sha256:6048ebddfb90d09d2707efb1fd78d4e3a77cb3ae4dc60e19aab6be0ece2ae464", size = 199356881 },
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[[package]]
@@ -602,14 +606,13 @@ name = "nvidia-cusolver-cu12"
version = "11.7.1.2"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "nvidia-cublas-cu12" },
- { name = "nvidia-cusparse-cu12" },
- { name = "nvidia-nvjitlink-cu12" },
+ { name = "nvidia-cublas-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-cusparse-cu12", marker = "sys_platform == 'linux'" },
+ { name = "nvidia-nvjitlink-cu12", marker = "sys_platform == 'linux'" },
]
wheels = [
{ url = "https://files.pythonhosted.org/packages/93/17/dbe1aa865e4fdc7b6d4d0dd308fdd5aaab60f939abfc0ea1954eac4fb113/nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_aarch64.whl", hash = "sha256:0ce237ef60acde1efc457335a2ddadfd7610b892d94efee7b776c64bb1cac9e0", size = 157833628 },
{ url = "https://files.pythonhosted.org/packages/9f/81/baba53585da791d043c10084cf9553e074548408e04ae884cfe9193bd484/nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.whl", hash = "sha256:6cf28f17f64107a0c4d7802be5ff5537b2130bfc112f25d5a30df227058ca0e6", size = 158229780 },
- { url = "https://files.pythonhosted.org/packages/d4/53/fff50a0808df7113d77e3bbc7c2b7eaed6f57d5eb80fbe93ead2aea1e09a/nvidia_cusolver_cu12-11.7.1.2-py3-none-win_amd64.whl", hash = "sha256:6813f9d8073f555444a8705f3ab0296d3e1cb37a16d694c5fc8b862a0d8706d7", size = 149287877 },
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[[package]]
@@ -617,12 +620,11 @@ name = "nvidia-cusparse-cu12"
version = "12.5.4.2"
source = { registry = "https://pypi.org/simple" }
dependencies = [
- { name = "nvidia-nvjitlink-cu12" },
+ { name = "nvidia-nvjitlink-cu12", marker = "sys_platform == 'linux'" },
]
wheels = [
{ url = "https://files.pythonhosted.org/packages/d3/56/3af21e43014eb40134dea004e8d0f1ef19d9596a39e4d497d5a7de01669f/nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_aarch64.whl", hash = "sha256:7aa32fa5470cf754f72d1116c7cbc300b4e638d3ae5304cfa4a638a5b87161b1", size = 216451135 },
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@@ -641,7 +643,6 @@ source = { registry = "https://pypi.org/simple" }
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[[package]]