Merge pull request #29 from PhysiCell-Tools/master

pcdl release v3.3.4

Author: elmbeech

.github/workflows/apple.yml

@@ -8,17 +8,17 @@ run-name: ${{ github.actor }}::pytest pcdl library on mac os x; the latest pytho
 on:
   push:
     branches: ["master", "v3", "v4"]
-  pull_request:
-    branches: ["master", "v3", "v4"]
+  #pull_request:
+  #  branches: ["master", "v3", "v4"]
 
 jobs:
   build-macosx:
     runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.12"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.13"]
+        #python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     env:
       PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader
@@ -33,7 +33,7 @@ jobs:
       run: |
         brew install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest aicsimageio anndata matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
         python -m pip install /Users/runner/work/physicelldataloader/physicelldataloader -v
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: lint with flake8
@@ -45,4 +45,3 @@ jobs:
     - name: test with pytest
       run: |
         pytest
-

.github/workflows/linux.yml

@@ -8,17 +8,17 @@ run-name: ${{ github.actor }}::pytest pcdl library on linux os; all python3 vers
 on:
   push:
     branches: ["master", "v3", "v4"]
-  pull_request:
-    branches: ["master", "v3", "v4"]
+  #pull_request:
+  #  branches: ["master", "v3", "v4"]
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.12"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.13"]
+        #python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     env:
       PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader
@@ -33,7 +33,7 @@ jobs:
       run: |
         sudo apt install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest aicsimageio anndata matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
         python -m pip install /home/runner/work/physicelldataloader/physicelldataloader -v
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: lint with flake8

.github/workflows/windows.yml

@@ -8,17 +8,17 @@ run-name: ${{ github.actor }}::pytest pcdl library on windows os; the latest pyt
 on:
   push:
     branches: ["master", "v3", "v4"]
-  pull_request:
-    branches: ["master", "v3", "v4"]
+  #pull_request:
+  #  branches: ["master", "v3", "v4"]
 
 jobs:
   build-windows:
     runs-on: windows-latest
     strategy:
       fail-fast: false
       matrix:
-        #python-version: ["3.12"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.13"]
+        #python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     env:
       PYTHONPATH: D:\a\physicelldataloader\physicelldataloader
@@ -33,7 +33,7 @@ jobs:
       run: |
         choco install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest aicsimageio anndata matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
         python -m pip install D:\a\physicelldataloader\physicelldataloader -v
         #echo 'set PYTHONPATH=D:\a\physicelldataloader\physicelldataloader' >> $GITHUB_ENV
         #if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

README.md

@@ -1,6 +1,5 @@
 ![physicellcdataloader logo & title](man/img/physicelldataloader_title_v3.0.0.png)
 
-
 ## Abstract:
 
 physicelldataloader (pcdl) provides a platform independent, python3 based, [pip](https://en.wikipedia.org/wiki/Pip_(package_manager)) installable interface
@@ -20,7 +19,7 @@ The pcdl python3 library maintains three branches:
 ## Header:
 
 + Language: python [>= 3.9](https://devguide.python.org/versions/)
-+ Library dependencies: aicsimageio, anndata, matplotlib, numpy, pandas, (requests), scipy, vtk
++ Library dependencies: anndata, bioio, matplotlib, numpy, pandas, (requests), scipy, vtk
 + Date of origin original PhysiCell-Tools python-loader: 2019-09-02
 + Date of origin pcdl fork: 2022-08-30
 + Doi: https://doi.org/10.5281/ZENODO.8176399
@@ -123,10 +122,14 @@ Developers, please make pull requests to the https://github.com/elmbeech/physice
 
 + evt generate lineage tree graph output files.
 + evt add neuroglancer ome.tiff support.
-+ switch from aicsimageio to bioio library, when the library is ripe (napari has switched to bioio).
-
++ evt add DataDiVR support.
 
 ## Release Notes:
++ version 3.3.4 (2025-03-07): elmbeech/physicelldataloader
+    + replace the **aicsimageio** library dependency with its successor **bioio**. special thanks to Joel Eliason!
+    + **make_ome_tiff** can handle automatically generated file names with > 255 characters. special thank to Genevieve Stein-O'Brien and DanielBergman!
+    + **get_mesh_spacing** handels now an edge case correctly that would have resulted in a division by zero. special thanks to Randy Heiland!
+
 + version 3.3.3 (2025-01-10): elmbeech/physicelldataloader
     + bug fix **plot_contour** plot orientation. special thanks to Marco Ruscone!
     + add test data for new improved **unittest physicell model**. special thanks to Nick Oldfather!

man/TUTORIAL_blender.md

@@ -66,25 +66,21 @@ To learn more about Blender and BVTK Node plugin, please study the official docu
 
 ## ✨ Handle ome tiff files
 
-The blender bioxel nodes plugin allows us load ome tiff files into blender.
+The blender bioxel nodes plugin allows us load single time step ome tiff files into blender.
 
-### Generate vtk files from the command line
+### Generate ome tiff files from the command line
 
 ```bash
-pcdl_make_conc_vtk output
-```
-```bash
-pcdl_make_cell_vtk output
+pcdl_make_ome_tiff output --collapse false
 ```
 
-### Generate vtk files from within python
+### Generate ome tiff files from within python
 
 ```python
 import pcdl
 
 mcdsts = pcdl.TimeSeries('output/')
-mcdsts.make_conc_vtk()
-mcdsts.make_cell_vtk()
+mcdsts.make_ome_tiff(collapse=False)
 ```
 
 ### The blender bioxel nodes plugin

man/TUTORIAL_python3_napari.md

@@ -8,13 +8,8 @@ https://github.com/AllenCellModeling/napari-aicsimageio
 
 ## Install napari
 
-And install the [aicsimageio](https://github.com/AllenCellModeling/aicsimageio) library,
-which installs the "ome-types" napari plugin,
-that napari can read ome.tiff images inclusive ome metadata.
-
 ```bash
 pip3 install napari[all]
-pip3 install aicsimageio
 ```
 
 

man/TUTORIAL_python3_ometiff.md

@@ -14,7 +14,7 @@ and [TUTORIAL_fiji_imagej.md](https://github.com/elmbeech/physicelldataloader/bl
 
 Additionally ome.tiff, tiff, png, and jpeg files can as well be loaded back in to python as [numpy](https://numpy.org/) array, for example with the [sci-kit image](https://scikit-image.org/) library (image data only).
 
-Besides that, ome.tiff files can be loaded with Allen Institute for Cell Science's [aicsimageio](https://github.com/AllenCellModeling/aicsimageio) library and possibly with its successor library [bioio](https://github.com/bioio-devs/bioio) (image and metadata).
+Besides that, ome.tiff files can be loaded with the [bioio](https://github.com/bioio-devs/bioio) library (image and metadata).
 
 
 ### Save pcdl data constructs from the command line into tiff and ome.tiff files
@@ -64,12 +64,12 @@ a_ome.shape  # (25, 2, 200, 300)
 ```
 
 
-### Load ome.tiff files as AICSImage object into python
+### Load ome.tiff files as BioImage object into python
 
 ```python
-from aicsimageio import AICSImage
+from bioio import BioImage
 
-img = AICSImage('output/timeseries_ID.ome.tiff')
+img = BioImage('output/timeseries_ID.ome.tiff')
 img.shape  # (25, 2, 1, 200, 300)
 ```
 ```python

pcdl/VERSION.py

@@ -1 +1 @@
-__version__ = '3.3.3'
+__version__ = '3.3.4'