pcDataLoader provides a platform independent, python3 based, pip installable interface to load output, generated with the PhysiCell agent based modeling framework, into python3.
pcDataLoader was forked from the original PhysiCell-Tools python-loader implementation.
The pcDataLoader python3 library will maintain two main branches:
- Branch version 2 will be strictly compatible with the original PhysiCell-Tools/python-loader code, although pip installable.
- Branch version 3 might break with old habits, although tries to be as much downward compatible as possible. The aim of the v3 branch is to get a very lean and agile python3 physicell output interface, for the ones coming from the python world.
Note: there can only be one version of pcDataLoader installed in each python3 environment. In the HowTo guide is in detail explained, how to install and uninstall pcDataLoader branches.
- Language: python >= 3.6
- Library dependencies: anndata, matplotlib, numpy, pandas
- Programmer: Patrick Wall, Elmar Bucher, Randy Heiland, Paul Macklin
- Date of origin original PhysiCell-Tools python-loader: 2019-09-02
- Date of origin pcDataLoader fork: 2022-08-30
- License: BSD-3-Clause
- User manual: this README.md file
- Source code: https://github.com/elmbeech/pcDataLoader
- Check out: man/HOWTO.md!
- Check out: man/TUTORIAL.md!
- Check out: man/REFERENCE.md!
To be developed.
Within the pcDataLoader library, we tried to stick to the documentation policy lined out by Daniele Procida in his "what nobody tells you about documentation" talk at PyCon 2017 in Portland, Oregon.
- original PhysiCell-Tools python-loader implementation: Patrick Wall, Randy Heiland, Paul Macklin
- fork pcDataLoader implementation: Elmar Bucher
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version 3.0.5 (2023-02-26): elmbeech/pcDataLoader mcds.get_contour plots span now the whole domain and not only to the border voxel centers.
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version 3.0.4 (2023-02-21): elmbeech/pcDataLoader
- pyMCDS mcds.get_contour function, to easily generate for substrates matplotlib contourf and contour plots because they do not exist as pandas plots.
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version 3.0.3 (2023-02-19): elmbeech/pcDataLoader branch 3 has no longer anndata and as such hdf5 dependency.
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version 3.0.2 (2023-01-06): elmbeech/pcDataLoader bugfix installing package data.
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version 3.0.0 (2023-01-06): elmbeech/pcDataLoader
- pyMCDS parameter xml_file can now handle path/file.xml (unix) or path\file.xml (dos) input, as long output_path is the default.
- pyMCDS has a new additional boolean microenv parameter, to specify if the microenvironment (substrates) should be read (for completeness) or not (for speed increase and less memory usage).
- pyMCDS has a new additional boolean graph parameter, to specify if the attached and neighbor graph should be read.
- pyMCDS has a new additional boolean verbose parameter, to specify if there should be text output while processing.
- pyMCDS mcds.get_2D_mesh was renamed to mcds.get_mesh_2D for consistency.
- pyMCDS mcds.get_linear_voxels was renamed to mcds.get_mesh_coordinate for consistency.
- pyMCDS mcds.get_containing_voxel_ijk was renamed to mcds.get_voxel_ijk for briefness.
- pyMCDS mcds.get_voxel_spacing returns now 3 specific values, one for x, y, and z, instead of 1 general value.
- pyMCDS mcds.get_concentrations was renamed to mcds.get_concentration for consistency
- pyMCDS mcds.get_concentrations_at was renamed to mcds.get_concentration_at for consistency
- pyMCDS mcds.get_concentration_at if z_slice is not a mesh center value, the function will by default adjust to nearest and no longer break.
- pyMCDS mcds.get_cell_variables and mcds.get_substrate_names return now a strictly alphabetically ordered list.
- pyMCDS mcds.get_cell_df returns now a pandas dataframe with the cell IDs as the index and not as a column. additionally, this dataframe contains now voxel, mesh_center, substrate parameter, substrate concentration, and cell density information too.
- new pyMCDS mcds.get_concentration_df function.
- new pyMCDS mcds.get_substrate_df function.
- new pyMCDS mcds.get_unit_df function.
- new pyMCDS mcds.get_multicellds_version function.
- new pyMCDS mcds.get_physicell_version function.
- new pyMCDS mcds.get_runtime function.
- new pyMCDS mcds.get_timestamp function.
- new pyMCDS mcds.get_voxel_ijk_range function.
- new pyMCDS mcds.get_voxel_ijk_axis function.
- new pyMCDS mcds.get_voxel_spacing function.
- new pyMCDS mcds.get_voxel_volume function.
- new pyMCDS mcds.get_mesh_mnp_range function.
- new pyMCDS mcds.get_mesh_mnp_axis function.
- new pyMCDS mcds.get_xyz_range function.
- new pyMCDS mcds.is_in_mesh function.
- new pyMCDS mcds.get_attached_graph_dict function.
- new pyMCDS mcds.get_neigbor_graph_dict function.
- class pyMCDS_timeseries was renamed to pyMCDSts and completely rewritten.
- new pyMCDSts get_xmlfile_list function.
- new pyMCDSts read_mcds function.
- new pyMCDSts make_jpeg function.
- new pyMCDSts make_png function.
- new pyMCDSts make_tiff function.
- new pyMCDSts make_gif function.
- new pyMCDSts make_movie function.
- all plotting functions were removed because pcDataLoader only focus on making the raw data in python easy accessible for in-depth analysis.
- cell position coordinates are now constantly labeled as x,y,z, mesh center coordinates as m,n,p, and voxel coordinates as i,j,k.
- the underling mcds object data dictionary structure has changed.
- pytest unit tests exist now for all pyMCDS and pyMCDSts functions.
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version 2.0.2 (2023-01-06): elmbeech/pcDataLoader reset patch voxel spacing bugfix, so that branch2 is full compatible with branch1 again. use branch3 for a bugfixed version!
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version 2.0.1 (2022-11-08): elmbeech/pcDataLoader beta release patch voxel spacing bugfix.
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version 2.0.0 (2022-08-30): elmbeech/pcDataLoader pip installable release, derived from and compatible with PhysiCell-Tools/python-loader release 1.1.0 (2022-07-20).
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version 1.1.0 (2022-05-09): Physicell-Tools/python-loader release compatible with pre-v1.10.x of PhysiCell
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version 1.0.1 (2020-01-25): Physicell-Tools/python-loader time-series related bug fix
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version 1.0.0 (2019-09-28): Physicell-Tools/python-loader first public release!