Merge pull request #20 from elmbeech/master

pcdl release v3.3.3

Author: elmbeech

README.md

@@ -56,9 +56,7 @@ Extras tutorials python3 language:
 Extras tutorials for other languages than python3:
 
 + [pcdl and julia](https://github.com/elmbeech/physicelldataloader/tree/master/man/TUTORIAL_julia.md)
-<!--
-+ [pcdl and matlab or octave](https://github.com/elmbeech/physicelldataloader/tree/master/man/TUTORIAL_matlab_octave.md)
--->
++ [pcdl and matlab](https://github.com/elmbeech/physicelldataloader/tree/master/man/TUTORIAL_matlab_octave.md)
 + [pcdl and R](https://github.com/elmbeech/physicelldataloader/tree/master/man/TUTORIAL_r.md)
 
 Extras tutorials for GUI software:
@@ -104,6 +102,8 @@ Within the pcdl library, we tried to stick to the documentation policy laid out
   Nick Oldfather (unit test model),
   Thierry-Pascal Fleurant (plot\_timeseries)
 
+Developers, please make pull requests to the https://github.com/elmbeech/physicelldataloader/tree/development branch. Thanks!
+
 
 ## Cite:
 
@@ -121,12 +121,21 @@ Within the pcdl library, we tried to stick to the documentation policy laid out
 
 ## Road Map:
 
-+ add make\_conc\_vtk visualization parameter.
-+ new next generation unit test dataset.
-+ rewrite make\_ome\_tiff to use less RAM.
++ 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).
+
 
 ## Release Notes:
++ 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!
+    + add pyMCDS **make_conc_vtk** on the fly visualization. special thanks to Randy Heiland and Nick Oldfather!
+    + pyMCDS and pyMCDSts **make_graph_gml** and pyAnnData **get_anndata** handles now spring\_attached\_cells graph too.
+
++ version 3.3.2 (2024-11-24): elmbeech/physicelldataloader
+    + **Warnings** will no longer be piped to standard output if verbose is set to False.
+    + pyMCDS **make_ome_tiff** function rewriten to be less RAM hungry and more versatile.
 
 + version 3.3.1 (2024-09-22): elmbeech/physicelldataloader
     + bugfix pyMCDS custom vectors loading.
@@ -170,11 +179,11 @@ Within the pcdl library, we tried to stick to the documentation policy laid out
     + new pyMCDS **set_verbosity_false** function, to complete pcdl.TimeStep(verbosity=True/False) experience.
     + new pyMCDSts **get_cell_df** function, to extract one big dataframe or a list of dataframes from the whole time series.
     + new pyMCDSts **get_conc_df** function, to extract one big dataframe or a list of dataframes from the whole time series.
-    + new pyMCDSts **make_cell_vtk** function, to save substrate data as rectilinear grid vtk files.
-    + new pyMCDSts **make_conc_vtk** function, to save cell data as glyph vtk files.
-    + new pyMCDSts **make_graph_gml** function, to save graphs in a networkx and igraph compatible files format.
+    + new pyMCDSts **make_cell_vtk** function, to save substrate data as rectilinear grid vtk files. special thanks to Furkan Kurtoglu!
+    + new pyMCDSts **make_conc_vtk** function, to save cell data as glyph vtk files. special thanks to Furkan Kurtoglu!
+    + new pyMCDSts **make_graph_gml** function, to save graphs in a networkx and igraph compatible files format. special thanks to Benjamin Jacobs!
     + new pyMCDSts **make_ome_tiff** function, to save the output data in ome tiff file format.
-    + new pyMCDSts **plot_timeseries** function, to plot time series.
+    + new pyMCDSts **plot_timeseries** function, to plot time series. special thanks to Thierry-Pascal Fleurant!
     + new pyMCDSts **set_verbosity_true** function, to complete the pcdl.TimeSeries(verbosity=True/False) experience.
     + new pyMCDSts **set_verbosity_false** function to complete the pcdl.TimeSeries(verbosity=True/False) experience.
 
@@ -247,7 +256,7 @@ Within the pcdl library, we tried to stick to the documentation policy laid out
       given the computer is connected to the internet, test data can easily be installed and removed with the **pcdl.install_data()** and **pcdl.uninstall_data()** functions now.
 
 + version 3.0.7 (2023-06-08): elmbeech/physicelldataloader
-    + pyMCDSts: replaces the svg dependent **mcdsts.make_jpeg**, **mcdsts.make_png**, and **mcdsts.make_tiff** with **mcdsts.make_imgcell** and **mcdsts.make_imgsubs** which generate images straight out of the loaded data. the **mcdsts.make_gif** and **mcdsts.make_movie** functions were adjusted accordingly.
+    + pyMCDSts: replaces the svg dependent **mcdsts.make_jpeg**, **mcdsts.make_png**, and **mcdsts.make_tiff** with **mcdsts.make_imgcell** and **mcdsts.make_imgsubs** which generate images straight out of the loaded data. the **mcdsts.make_gif** and **mcdsts.make_movie** functions were adjusted accordingly. special thanks to Marshal Gress!
     + pyMCDSts: **mcdsts.read_mcds** loads now automatically all mcds snapshots if no xmlfile\_list is provided (default).
 
 + version 3.0.6 (2023-04-29): elmbeech/physicelldataloader

data_timeseries_2d.tar.gz

@@ -29,7 +29,7 @@ cd path/to/PhysiCell
 ```
 ```bash
 make data-cleanup
-python3 -c"import pathlib, pcdl, shutil; pcdl.install_data(); s_ipath=str(pathlib.Path(pcdl.__file__).parent.resolve()/'data_timeseries_2d'); shutil.copytree(s_ipath, 'output', dirs_exist_ok=True)"
+python3 -c"import pathlib, pcdl, shutil; pcdl.install_data(); s_ipath=str(pathlib.Path(pcdl.__file__).parent.resolve()/'output_2d'); shutil.copytree(s_ipath, 'output', dirs_exist_ok=True)"
 ```
 
 

data_timeseries_3d.tar.gz

@@ -26,7 +26,7 @@ Package installation.
 
 ```julia
 using Pkg
-Pkg.add("CSV")
+Pkdg.add("CSV")
 Pkdg.add("DataFrames")
 ```
 

man/TUTORIAL_commandline.md

@@ -1,11 +1,11 @@
-# PhysiCell Data Loader Tutorial: pcdl and the Matlab and Octave programming language
+# PhysiCell Data Loader Tutorial: pcdl and the Matlab programming language  <!-- and Octave-->
 
-[Matlab](https://www.mathworks.com/products/matlab.html) / GNU [Octave](https://octave.org/)
+<!-- bue 20240903: could someone test and update who actuallty knows matlab or octave? -->
+
+[Matlab](https://www.mathworks.com/products/matlab.html)  <!-- / GNU [Octave](https://octave.org/) -->
 is a scientific programming language used by some engineers.
 The earliest predecessor of pcdl was actually a Matlab implementation.
-Coming full circle, this is how you can load some pcdl data constructs into Matlab and GNU Octave.
-
-<!-- bue 20240903: could someone test and update who actuallty knows matlab or octave? -->
+Coming full circle, this is how you can load some pcdl data constructs into Matlab.  <!-- and GNU Octave -->
 
 
 ## &#x2728; Handle csv files
@@ -22,7 +22,7 @@ pcdl_get_conc_df output
 pcdl_get_cell_df output
 ```
 
-### Load a csv file into Matlab or Octave as a tabel
+### Load a csv file into Matlab as a tabel  <!-- or Octave -->
 
 &#x26A0; **bue 2024-09-22:** the readtable function is not yet implemented in Octave.
 
@@ -51,7 +51,7 @@ pcdl_get_conc_attribute output 2
 pcdl_get_cell_attribute output 2
 ```
 
-### Load json files into Matlab or Octave
+### Load json files into Matlab  <!-- or Octave -->
 
 ```matlab
 struct_conc = jsondecode(fileread("output/timeseries_conc_attribute_minmax.json"))
@@ -72,10 +72,10 @@ cd path/to/PhysiCell
 pcdl_make_graph_gml output/output00000024.xml neighbor --node_attribute cell_type dead oxygen pressure
 ```
 
-### Load gml files into a Matlab or Octave data construct
+### Load gml files into a Matlab data construct  <!-- or Octave -->
 
-We will use the [matlab-igraph](https://www.mathworks.com/matlabcentral/fileexchange/159001-matlab-igraph) toolbox to load gml files into Matlab or Octave.
-+ https://github.com/DavidRConnell/matlab-igraph/releases/tag/v0.2.0
+We will use the [matlab-igraph](https://www.mathworks.com/matlabcentral/fileexchange/159001-matlab-igraph) toolbox to load gml files into Matlab.  <!-- or Octave -->
++ https://github.com/DavidRConnell/matlab-igraph
 + https://igraph.org/
 
 Install matlab-igaph toolbox.
@@ -101,14 +101,14 @@ pcdl_make_conc_vtk output/output00000024.xml
 pcdl_make_cell_vtk output/output00000024.xml
 ```
 
-### Load a vtr and vtp file into Matlab or Octave data construct
+### Load a vtr and vtp file into Matlab data construct  <!-- or Octave -->
 
 + https://www.mathworks.com/matlabcentral/fileexchange/94993-vtktoolbox
 + https://github.com/KIT-IBT/vtkToolbox
 
-Install matlab-igaph toolbox.
+Install vtk toolbox.
 
-Load vtkfile into Matlab or Octave.
+Load vtkfile into Matlab.  <!-- or Octave -->
 
 ```matlab
 output/output00000024_conc.vtr

man/TUTORIAL_julia.md

@@ -1,5 +1,11 @@
 # PhysiCell Data Loader Tutorial: pcdl and Paraview
 
+<!--
+bue 2024-09-02: vtk and paraview can handle up to 32 bit ometiff images.
+fluorescent microscopy ome tiff standard is 16 bit.
++ https://discourse.vtk.org/t/failed-to-read-tiff-64-bit-samples/12118
+-->
+
 [Paraview](https://www.paraview.org/) is a free and open source scientific visualization software,
 that lets us load and analyze vtk rectilinear grid data and vtk polynomial data<!--, and even ome.tiff data files-->.
 

man/TUTORIAL_matlab_octave.md

@@ -3,7 +3,7 @@
 [Gml](https://github.com/elmbeech/physicelldataloader/blob/master/man/publication/himsolt1996gml_a_portable_graph_file_format.pdf) (graph modeling language) is a portable plain text file format for graphs,
 that can be read by the popular graph libraries [networkx](https://networkx.org/) (python), [igraph](https://igraph.org/) (C, C++, mathematica, python, R) <!--, [JuliaGraphs](ttps://github.com/JuliaGraphs/GraphIO.jl)-->, and possible other graph analysis software too.
 
-Pcdl can export neighborhood <!- and lineage tree --> graphs in gml format for downstream analysis.
+Pcdl can export neighborhood <!-- and lineage tree --> graphs in gml format for downstream analysis.
 
 If you are new to graph theory, then I recommend reading [A Simple Introduction to Graph Theory](https://www.brianheinold.net/graph_theory/A_Simple_Introduction_to_Graph_Theory_Heinold.pdf)
 from Prof. Brian Heinold from Mount Saint Mary's University in Emmitsburg, Maryland, USA.
@@ -48,7 +48,7 @@ print(sorted(g.edges.keys())[0:4])
 g.nodes['node_0']   # {'cell_type': 'cancer_cell', 'dead': 0, 'oxygen': 25.304510426523084, 'pressure': 10.519314516003435}
 ```
 ```python
-g.edgea[('node_0', 'node_1')]   # {'label': 'edge_0_1', 'distance_microns': 15}
+g.edges[('node_0', 'node_1')]   # {'label': 'edge_0_1', 'distance_microns': 15}
 ```
 
 
@@ -60,7 +60,7 @@ import igraph as ig
 g = ig.Graph.Read_GML('output/output00000024_neighbor.gml')
 print(g)
 ```
-``python
+```python
 ig.summary(g)
 ```
 

man/TUTORIAL_paraview.md

@@ -9,7 +9,7 @@ The [json library](https://docs.python.org/3/library/json.html) is a part of cor
 Json is the ideal data format for unstructured data constructs that not can be stored in csv file format, like a dictionary of lists.
 Please note, python objecta are not per se json comaptible.
 For example:
-Complex numbers are a standard data type in python, but complex numbers can not be stored in json.
+Complex numbers are a standard data type in python, but complex numbers cannot be stored in json.
 Python dictionary keys can be of almost any data type, but json object keys have to be strings.
 
 

man/TUTORIAL_python3_graph.md

@@ -1,14 +1,14 @@
 # PhysiCell Data Loader Tutorial: pcdl and Python and Napari
 
-[Napari](https://napari.org/stable/) is both, a python library and a GUI software.
+[Napari](https://napari.org/stable/) is both a python library and a GUI software.
 Napari is used by wetlab scientists and bioinformatician to analyze fluorescent microscopy data.
 Napari can read [ome.tiff](https://www.openmicroscopy.org/ome-files/) files.
 https://github.com/AllenCellModeling/napari-aicsimageio
 
 
 ## Install napari
 
-And install the [aicsimageio](https://allencellmodeling.github.io/aicsimageio/) library,
+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.