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Commit 129e6898 authored by Simon Wittl's avatar Simon Wittl
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changed for win style

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pyproject.toml
+ 12
− 9
View file @ 129e6898
[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",
]
scripts/01_aRTist_bridge.py
+ 3
− 3
View file @ 129e6898
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
......
scripts/03_load_atlas.py
+ 2
− 2
View file @ 129e6898
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
......
src/CyXTraX/data/__init__.py
+ 2
− 2
View file @ 129e6898
......@@ -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,
......
src/CyXTraX/simulation/artist_bridge.py
+ 3
− 3
View file @ 129e6898
......@@ -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
......
temp/scones.png
+ 0
− 0
View replaced file @ 13542c0f View file @ 129e6898
temp/scones.png

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temp/scones.png

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temp/scones.png
temp/scones.png
temp/scones.png
temp/scones.png
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uv.lock
+ 35
− 34
View file @ 129e6898
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'" },
]
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......@@ -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'" },
]
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......@@ -576,12 +582,11 @@ name = "nvidia-cudnn-cu12"
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......@@ -589,12 +594,11 @@ name = "nvidia-cufft-cu12"
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source = { registry = "https://pypi.org/simple" }
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......@@ -602,14 +606,13 @@ name = "nvidia-cusolver-cu12"
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......
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