@ python-loader : introducing branch v3.

Author: elmbeech

.github/workflows/apple.yml

@@ -7,9 +7,7 @@ run-name: ${{ github.actor }}::pytest pcdl library on mac os x; the latest pytho
 
 on:
   push:
-    branches: ["utest", "master"]  # ["v3", "v4"]
-  pull_request:
-    branches: ["development", "master"]
+    branches: ["v3"]  # only!
 
 jobs:
   build-macosx:
@@ -33,7 +31,7 @@ jobs:
       run: |
         brew install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata 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

.github/workflows/linux.yml

@@ -7,9 +7,7 @@ run-name: ${{ github.actor }}::pytest pcdl library on linux os; all python3 vers
 
 on:
   push:
-    branches: ["utest", "master"]  # ["v3","v4"]
-  pull_request:
-    branches: ["development", "master"]
+    branches: ["v3"]  # only!
 
 jobs:
   build-linux:
@@ -33,7 +31,7 @@ jobs:
       run: |
         sudo apt install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata 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

@@ -7,9 +7,7 @@ run-name: ${{ github.actor }}::pytest pcdl library on windows os; the latest pyt
 
 on:
   push:
-    branches: ["utest", "master"]  # ["v3", "v4"]
-  pull_request:
-    branches: ["development", "master"]
+    branches: ["v3"]  # only!
 
 jobs:
   build-windows:
@@ -33,7 +31,7 @@ jobs:
       run: |
         choco install ffmpeg imagemagick
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest anndata bioio matplotlib numpy pandas requests scipy vtk
+        python -m pip install flake8 pytest anndata 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

man/HOWTO.md

@@ -146,6 +146,5 @@ pyMCDS.py and the pyMCDS class is very lightweight.
 Besides the python3 core library, this code has only matplotlib, numpy, pandas, scipy, and vtk library dependencies.\
 The pyMCDS class evolved into the pcdl.TimeStep class, which has additionally anndata dependency, which makes the library slightly heavier but much more powerful for downstream data analysis.
 Apart from that, pcdl offers the pcdl.TimeSeries class to handle the mcds snapshots from an entire PhysiCell run, and a set of functions that can be run straight from the command line, without even having to fire up a python3 shell.
-Finally, branch version 4 broke with this ancient library structure because it is just out of time to run the code like this.\
-Stay assured, if you like pyMCDS.py, it is there to last.
-We will keep on maintaining pyMCDS.py from branch version 3.
+Future branch version 4 will abandon this ancient library structure to become more concise.
+Don't fear. pyMCDS.py is there to last. We will keep on maintaining pyMCDS.py from branch version 3.

man/REFERENCE.md

@@ -34,7 +34,7 @@ Familiarize yourself well with their parameters!
 Basically, there are four types of functions:
 + set_ : set a python3 variable.
 + get_ : recall a python3 variable.
-+ make_ : make functions generate file output (gml, ome.tiff, vtk).
++ make_ : make functions generate file output (gml, vtk).
 + plot_ : plot functions generate a matplotlib figure, or axis object, or file output (jpeg, png, tiff), depending on your parameter settings.
 
 ### TimeStep initialize
@@ -80,6 +80,8 @@ Basically, there are four types of functions:
 + [help(mcds.get_substrate_list)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_substrate_list.md)  #! workhorse function
 + [help(mcds.get_substrate_dict)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_substrate_dict.md)
 + [help(mcds.get_substrate_df)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_substrate_df.md)
++ [help(mcds.get_concentration)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_concentration.md)
++ [help(mcds.get_concentration_at)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_concentration_at.md)
 + [help(mcds.get_conc_df)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_conc_df.md)  #! workhorse function
 + [help(mcds.plot_contour)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.plot_contour.md)  #! workhorse function
 + [help(mcds.make_conc_vtk)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.make_conc_vtk.md)  #! workhorse function
@@ -88,6 +90,7 @@ Basically, there are four types of functions:
 + [help(mcds.get_celltype_list)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_celltype_list.md)  #! workhorse function
 + [help(mcds.get_celltype_dict)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_celltype_dict.md)
 + [help(mcds.get_cell_df)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_cell_df.md)  #! workhorse function
++ [help(mcds.get_cell_df_at)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_cell_df_at.md)
 + [help(mcds.plot_scatter)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.plot_scatter.md)  #! workhorse function
 + [help(mcds.make_cell_vtk)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.make_cell_vtk.md)  #! workhorse function
 + [help(mcds.get_anndata)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_anndata.md)  #! workhorse function
@@ -97,16 +100,12 @@ Basically, there are four types of functions:
 + [help(mcds.get_neighbor_graph_dict)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.get_neighbor_graph_dict.md)
 + [help(mcds.make_graph_gml)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.make_graph_gml.md)  #! workhose function
 
-### TimeStep microenvironment and cells
-+ [help(mcds.make_ome_tiff)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.make_ome_tiff.md)  #! workhose function
-+ [help(mcds.make_neuroglancer)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcds.make_neuroglancer.md)  #! workhose function
-
 ### TimeStep internal functions
 + [help(pcdl.scaler)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl.scaler.md)  # anndata
 + [help(pcdl.graphfile_parser)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl.graphfile_parser.md)  # mcds
 ```python3
-help(pcdl.TimeStep._read_xml)
-help(pcdl.TimeStep._anndextract)
+help(pcdl.pyMCDS._read_xml)
+help(pcdl.pyAnnData._anndextract)
 ```
 
 
@@ -115,7 +114,7 @@ help(pcdl.TimeStep._anndextract)
 Basically, there are four types of functions:
 + set_ : set a python3 variable.
 + get_ : recall a python3 variable.
-+ make_ : make functions generate file output (gif, gml, mp4, ome.tiff, vtk).
++ make_ : make functions generate file output (gif, gml, mp4, vtk).
 + plot_ : plot functions generate a matplotlib figure, or axis object, or file output (jpeg, png, tiff), depending on your parameter settings.
 
 ### TimeSeries initialization
@@ -143,10 +142,6 @@ Basically, there are four types of functions:
 ### TimeSeries cell graph
 + [help(mcdsts.get_graph_gml)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcdsts.make_graph_gml.md)  #! workhose function
 
-### TimeSteries microenvironment and cells
-+ [help(mcdsts.make_ome_tiff)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcdsts.make_ome_tiff.md)  #! workhose function
-+ [help(mcdsts.make_neuroglancer)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcdsts.make_neuroglancer.md)  #! workhose function
-
 ### Timeseries timeseries
 + [help(mcdsts.plot_timeseries)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/mcdsts.plot_timeseries.md)  #! workhorse function
 
@@ -159,8 +154,8 @@ Basically, there are four types of functions:
 ### TimeSeries internal functions
 + [help(pcdl.scaler)](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl.scaler.md)  # anndata
 ```python3
-help(pcdl.TimeSeries._handle_magick)
-help(pcdl.TimeSeries._anndextract)
+help(pcdl.pyMCDSts._handle_magick)
+help(pcdl.pyAnnData._anndextract)
 ```
 
 
@@ -193,10 +188,6 @@ The command line interface functions mimic the name and parameter arguments as c
 ### Command line cell graph
 + [pcdl_make_graph_gml --help](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl_make_graph_gml.md)  #! workhorse function
 
-### Command line cells and microenvironment
-+ [pcdl_make_ome_tiff --help](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl_make_ome_tiff.md)  #! workhorse function
-+ [pcdl_make_neuroglancer --help](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl_make_neuroglancer.md)  #! workhorse function
-
 ### Command line timeseries
 + [pcdl_plot_timeseries --help](https://github.com/elmbeech/physicelldataloader/tree/master/man/docstring/pcdl_plot_timeseries.md)  #! workhorse function
 

man/TUTORIAL_blender.md

@@ -3,7 +3,6 @@
 [Blender](https://www.blender.org/) is a modeling, rigging, animation, simulation, rendering, compositing,  motion tracking, video editing, and game creation software.
 Blender is free and open source.
 There exists a vtk nodes plugin, that lets us load <!-- vtk rectilinear grid data, -->vtk polynomial data files.
-And there exists a bioxel nodes plugin, that lets us load ome tiff files.
 
 
 ## &#x2728; Handle vtk files
@@ -64,31 +63,4 @@ To learn more about Blender and BVTK Node plugin, please study the official docu
 + https://docs.blender.org/manual/en/latest/
 
 
-## &#x2728; Handle ome tiff files
-
-The blender bioxel nodes plugin allows us load single time step ome tiff files into blender.
-
-### Generate ome tiff files from the command line
-
-```bash
-pcdl_make_ome_tiff output --collapse false
-```
-
-### Generate ome tiff files from within python
-
-```python
-import pcdl
-
-mcdsts = pcdl.TimeSeries('output/')
-mcdsts.make_ome_tiff(collapse=False)
-```
-
-### The blender bioxel nodes plugin
-
-Please follow the official bioxel nodes instructions for installation
-and to learn how to use the plugin.
-
-+ https://omoolab.github.io/BioxelNodes/latest/
-
-
 That's it! The rest is analysis within blender!

man/TUTORIAL_commandline.md

@@ -1,5 +1,7 @@
 # PhysiCell Data Loader Tutorial: pcdl from the Commandline
 
+<!-- bue 2024-08-22: have to check if this works from dos and power shell. it will work somehow, because i can run the cli unit tests -->
+
 The most important commands for down stream data analysis,
 available in the pcdl TimeStep and TimeSeries class,
 can be run straight from a command line shell, like [bash](https://en.wikipedia.org/wiki/Bash_(Unix_shell)), [csh](https://en.wikipedia.org/wiki/C_shell), [dos](https://en.wikipedia.org/wiki/DOS), [fish](https://en.wikipedia.org/wiki/Fish_(Unix_shell)), [ksh](https://en.wikipedia.org/wiki/KornShell), [powershell](https://en.wikipedia.org/wiki/PowerShell), [sh](https://en.wikipedia.org/wiki/Bourne_shell), [tsh](https://en.wikipedia.org/wiki/Tcsh), or [zsh](https://en.wikipedia.org/wiki/Z_shell), to name a view.
@@ -9,7 +11,7 @@ The command parameter mimics the related python3 function arguments as closely a
 You can always call the [help](https://en.wikipedia.org/wiki/Help!) parameter ( pcdl\_command -h),
 to access the man page for a pcdl command!
 
-Please spend some time to learn about each of the about 20 commands, by studying its man page.
+Please spend some time to learn about each of the 18 commands, by studying its man page.
 This will truly make you a power user!
 
 
@@ -194,19 +196,6 @@ pcdl_get_celltype_list output/output00000000.xml
 pcdl_get_celltype_list -h
 ```
 
-### &#x2728; pcdl\_get\_cell\_attrribute\_list
-
-Output all recorded cell attributes.
-
-```bash
-pcdl_get_cell_attribute_list output
-```
-```bash
-pcdl_get_cell_attribute_list output/output00000000.xml
-```
-```bash
-pcdl_get_cell_attribute_list -h
-```
 
 ### &#x2728; pcdl\_get\_cell\_attribute
 
@@ -398,60 +387,21 @@ pcdl_plot_timeseries -h
 ```
 
 
-### &#x2728; pcdl\_make\_ome\_tiff
-
-Generate an [ome.tiff](https://ome-model.readthedocs.io/en/stable/index.html) file,
-to analyze a single time step or the whole time series,
-the same way as usually fluorescent microscopy data is analyzed.
-
-By default, the cell\_attribute outputted is the cell ID + 1.
-However, any numerical (bool, int, float) cell\_attribute can be outputted.
-For example: dead, cells\_per\_voxel, or pressure.
-
-These ome.tiff files can be further analyzed,
-for example with the [Napari](https://napari.org/stable/) or [Fiji Imagej](https://fiji.sc/) or [Neuroglancer](https://research.google/blog/an-interactive-automated-3d-reconstruction-of-a-fly-brain/) or [Blender](https://www.blender.org/) or similar software,
-as described in the extra tutorials.
-
-```bash
-pcdl_make_ome_tiff output/output00000000.xml pressure
-```
-```bash
-pcdl_make_ome_tiff output
-```
-```bash
-pcdl_make_ome_tiff -h
-```
-
-Further readings:
-+ [TUTORIAL_python3_napari.md](https://github.com/elmbeech/physicelldataloader/blob/master/man/TUTORIAL_python3_napari.md)
-+ [TUTORIAL_fiji_imagej.md](https://github.com/elmbeech/physicelldataloader/blob/master/man/TUTORIAL_fijiimagej.md)
-+ [TUTORIAL_neuroglancer.md](https://github.com/elmbeech/physicelldataloader/blob/master/man/TUTORIAL_neuroglancer.md)
-+ [TUTORIAL_blender.md](https://github.com/elmbeech/physicelldataloader/blob/master/man/TUTORIAL_blender.md)
+## [Making movies](https://en.wikipedia.org/wiki/Making_Movies)
 
 
-### &#x2728; pcdl\_render\_neuroglancer
+### &#x2728; pcdl\_make\_movie
 
-With this command, you can render a time step ome.tiff file or a time step from a whole time series ome.tiff file straight into [Neuroglancer](https://research.google/blog/an-interactive-automated-3d-reconstruction-of-a-fly-brain/), which is a [WebGL](https://en.wikipedia.org/wiki/WebGL)-based viewer that will render the ome.tiff straight in your browser.
+Make a [mp4](https://en.wikipedia.org/wiki/MP4_file_format) movie from the jpeg plots from a time series.
 
-Below, we render a time step into Neuroglancer, first utilizing the time step ome.tiff, then using the whole time series ome.tiff.
-You can only render one time step at a time and not a entire time series, like, for example, in napari.
 ```bash
-pcdl_make_ome_tiff output/output00000000.xml
-pcdl_render_neuroglancer output_2d/output00000000_oxygen_water_default_blood_cells_ID.ome.tiff
-```
-```bash
-pcdl_make_ome_tiff output
-pcdl_render_neuroglancer output_2d/timeseries_oxygen_water_default_blood_cells_ID.ome.tiff 3  # render time step 3 from the time series
+pcdl_plot_scatter output
+pcdl_make_movie output/cell_cell_type_z0.0/
 ```
 ```bash
-pcdl_make_ome_tiff -h
+pcdl_make_movie -h
 ```
 
-Further readings:
-+ [TUTORIAL_neuroglancer.md](https://github.com/elmbeech/physicelldataloader/blob/master/man/TUTORIAL_neuroglancer.md)
-
-
-## [Making movies](https://en.wikipedia.org/wiki/Making_Movies)
 
 ### &#x2728; pcdl\_make\_gif
 
@@ -465,17 +415,7 @@ pcdl_make_gif output/cell_cell_type_z0.0/
 pcdl_make_gif -h
 ```
 
-### &#x2728; pcdl\_make\_movie
-
-Make a [mp4](https://en.wikipedia.org/wiki/MP4_file_format) movie from the jpeg plots from a time series.
 
-```bash
-pcdl_plot_scatter output
-pcdl_make_movie output/cell_cell_type_z0.0/
-```
-```bash
-pcdl_make_movie -h
-```
 
 ## Data Clean Up