Recent python

.github/workflows/test_and_deploy.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, '3.10']
+        python-version: [3.9, '3.10',  '3.11', '3.12', '3.13']
         platform: [ubuntu-latest] #, macos-latest]  # windows-latest broken for now
     steps:
       - uses: actions/checkout@v2
@@ -37,8 +37,8 @@ jobs:
           python --version
           conda install -y pyopencl
           python -m pip install --upgrade pip
-          pip install setuptools wheel pytest pytest-cov pytest-benchmark dask networkx igraph pandas scikit-image==0.19.3
-          pip install -e .
+          pip install setuptools wheel pytest pytest-cov pytest-benchmark dask networkx igraph pandas scikit-image
+
       - name: Test
         shell: bash -l {0}
         run: pytest -v --cov=./ --cov-report=xml
@@ -65,5 +65,5 @@ jobs:
   #         TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
   #       run: |
   #         git tag
-  #         python setup.py sdist bdist_wheel
+  #         python -m build
   #         twine upload dist/*

pyclesperanto_prototype/__init__.py

@@ -10,5 +10,5 @@
 from ._tier10 import *
 from ._tier11 import *
 
-__version__ = "0.24.5"
+__version__ = "0.24.6"
 __common_alias__ = "cle"

pyclesperanto_prototype/_tier8/_AffineTransform3D.py

@@ -1,7 +1,6 @@
 from warnings import warn
 
 import numpy as np
-import transforms3d
 import math
 from ._utilities import shear_angle_to_shear_factor
 
@@ -16,9 +15,55 @@ class AffineTransform3D:
 
     """
 
+    @staticmethod
+    def _identity_matrix():
+        return np.eye(4, dtype=float)
+
+    @staticmethod
+    def _scale_matrix(sx=1.0, sy=1.0, sz=1.0):
+        return np.asarray([
+            [sx, 0, 0, 0],
+            [0, sy, 0, 0],
+            [0, 0, sz, 0],
+            [0, 0, 0, 1],
+        ], dtype=float)
+
+    @staticmethod
+    def _rotation_matrix_x(angle_in_rad):
+        c = np.cos(angle_in_rad)
+        s = np.sin(angle_in_rad)
+        return np.asarray([
+            [1, 0, 0, 0],
+            [0, c, -s, 0],
+            [0, s, c, 0],
+            [0, 0, 0, 1],
+        ], dtype=float)
+
+    @staticmethod
+    def _rotation_matrix_y(angle_in_rad):
+        c = np.cos(angle_in_rad)
+        s = np.sin(angle_in_rad)
+        return np.asarray([
+            [c, 0, s, 0],
+            [0, 1, 0, 0],
+            [-s, 0, c, 0],
+            [0, 0, 0, 1],
+        ], dtype=float)
+
+    @staticmethod
+    def _rotation_matrix_z(angle_in_rad):
+        c = np.cos(angle_in_rad)
+        s = np.sin(angle_in_rad)
+        return np.asarray([
+            [c, -s, 0, 0],
+            [s, c, 0, 0],
+            [0, 0, 1, 0],
+            [0, 0, 0, 1],
+        ], dtype=float)
+
     def __init__(self, transform = None, image=None):
         if transform is None:
-            self._matrix = transforms3d.zooms.zfdir2aff(1)
+            self._matrix = self._identity_matrix()
         if isinstance(transform, AffineTransform3D):
             self._matrix = np.copy(transform._matrix)
         if isinstance(transform, str):
@@ -56,11 +101,11 @@ def scale(self, scale_x: float = None, scale_y: float = None, scale_z: float = N
             warn('scale_z must not be 0')
             scale_z = 1
         if scale_x is not None:
-            self._concatenate(transforms3d.zooms.zfdir2aff(scale_x, direction=(1, 0, 0), origin=(0, 0, 0)))
+            self._concatenate(self._scale_matrix(sx=scale_x))
         if scale_y is not None:
-            self._concatenate(transforms3d.zooms.zfdir2aff(scale_y, direction=(0, 1, 0), origin=(0, 0, 0)))
+            self._concatenate(self._scale_matrix(sy=scale_y))
         if scale_z is not None:
-            self._concatenate(transforms3d.zooms.zfdir2aff(scale_z, direction=(0, 0, 1), origin=(0, 0, 0)))
+            self._concatenate(self._scale_matrix(sz=scale_z))
 
         return self
 
@@ -83,11 +128,11 @@ def rotate(self, axis : int = 2, angle_in_degrees : float = 0):
         angle_in_rad = angle_in_degrees * np.pi / 180.0
 
         if axis == 0:
-            self._concatenate(self._3x3_to_4x4(transforms3d.euler.euler2mat(angle_in_rad, 0, 0)))
+            self._concatenate(self._rotation_matrix_x(angle_in_rad))
         if axis == 1:
-            self._concatenate(self._3x3_to_4x4(transforms3d.euler.euler2mat(0, angle_in_rad, 0)))
+            self._concatenate(self._rotation_matrix_y(angle_in_rad))
         if axis == 2:
-            self._concatenate(self._3x3_to_4x4(transforms3d.euler.euler2mat(0, 0, angle_in_rad)))
+            self._concatenate(self._rotation_matrix_z(angle_in_rad))
 
         return self
 

pyproject.toml

@@ -0,0 +1,52 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyclesperanto_prototype"
+version = "0.24.6"
+description = "GPU-accelerated image processing in python using OpenCL"
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.9"
+license = { text = "BSD-3-Clause" }
+authors = [
+    { name = "Robert Haase", email = "robert.haase@uni-leipzig.de" }
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: BSD License"
+]
+dependencies = [
+    "numpy>=2.0.0",
+    "pyopencl",
+    "toolz",
+    "scikit-image>0.20.0",
+    "matplotlib"
+]
+
+[project.urls]
+"Bug Tracker" = "https://github.com/clEsperanto/pyclesperanto_prototype/issues"
+Documentation = "https://github.com/clEsperanto/pyclesperanto_prototype#README.md"
+"Source Code" = "https://github.com/clEsperanto/pyclesperanto_prototype"
+"User Support" = "https://github.com/clEsperanto/pyclesperanto_prototype/issues"
+
+[project.entry-points."bia_bob_plugins"]
+plugin1 = "pyclesperanto_prototype._bia_bob_plugins:list_bia_bob_plugins"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+include = ["pyclesperanto_prototype*"]

tests/test_skimage_imsave.py

@@ -3,4 +3,4 @@ def test_skimage_imsave():
     image = cle.push([1, 2, 3])
 
     from skimage.io import imsave
-    imsave('test.tif', image)
+    imsave('test.tif', image, photometric='minisblack')