v2.4.2

🔧 Maintenance

• Changed skeletonize_3d to skeletonize to address skimage deprecation, along with related fixes.
• Updated requirements in pyproject.toml to enforce skimage==0.24, since watershed in 0.25 produces different results.

v2.4.1

v2.4.1

🔧 Maintenace

• Removed nanomesh from dependencies as it broke our conda-forge builds (because it's pip-only)

v2.4.0

v2.4.0

🚀 New features

• Added polydisperse_cylinders function to beta
• Added a rectangular_pillars micro-model generator to the beta module
• Add flux and tau_from_cmap to simulations module
• Added tortuosity_gdd method to compute tortuosity using domain decomposition
• Added ramp to beta module for inclusion in generators eventually
• Added local_diff filter to beta module for inclusion in filters eventually
• Added beta module for introducing new functions which may still need tweaking
• Added pc_to_seq function
• Added pc_map_to_pc_curve function for much faster generation of pc curves from images

🍰 Enhancements

• Added several micromodels functions to the generators module
• Improved speed of cylinders 5x by using _insert_disk_at_points_parallel method instead of dilating using edt
• Sped up sphere insertions using parallelization
• Readded tic and toc functions to tools module
• Enhanced satn_profile function to accept pre-thresholded image
• Enhanced satn_profile function to throw an exception if requested saturation cannot be obtained

🔧 Maintenace

• Migrated from bump2version to hatch for resolving version number
• Refactored and updated Actions
• Deprecated Python 3.8 and 3.9
• Added linter Action: ruff
• Unified project config (pytest.ini, setup.cfg) files in pyproject.toml
• Removed pyfastnoisesimd from dependencies as it no longer works on Python 3.9+
• Migrated from setup.py to pyproject.toml
• Migrated from flat layout to the PyPA recommended src layout
• Enhanced api with type annotations and defaults
• Updated the python version coverage to include 3.11
• Tidyied up after some recent PRs
• Enhanced satn_profile function to return a Results object with data as attributes

v2.3.0

🚀 New features

• Added function to compute diffusive size factor using dns #new
• Added zip_to_stack for converting 2D tiff files in a zip folder into a 3D tiff image #new
• Added folder_to_stack for converting 2D tiff files in a folder into a 3D tiff image #new
• Added random_spheres as a wrapper to rsa for more descriptive name (rsa to be deprecated eventually) #new
• Added show_panels function to visualizations module #new
• Added spheres_from_coords to generators #new
• Added find_bbox to tools #new
• Add better sierpinski foam generator that accepts shape #new

🍰 Enhancements

• Added mode='drainage/imbibition' argument to all seq/size/satn functions, to accomodate upcoming imbibition simulations #enh
• Make Results object more useful by including name of function that produced it, and time #enh
• Added seed argument to all random generators #enh
• Enhanced spheres_from_coords to work with negative coordinates #enh #bug
• Improved the speed of find_bbox #enh
• Added protrusion argument to rsa #enh

🔧 Maintenace

• adding release.yml to package to assist with automatic changelog generation #maint
• Fixed imageio deprecation warnings in 2 examples #doc, #maint
• using _all_ everywhere for imports #maint
• Removed optional dependencies from setup.py #maint

⚠️ API changes

• Changed radius to r in voronoi_edges #api
• Moved ibip percolation functions to simulations module

🐛 Bugfixes

• Included dtype in np.sum calls throughout to ensure it returns the correct value on large images #bug
• Fixed bug in find_trapped_regions when no solid present on outlet face #bug
• Fix parse bug in _parse_pad_width used by snow2 if boundary_width was a list of lists #bug
• Fix divs bug in blobs #bug
• Improved output of Results object when large dicts present #bug
• Enhanced spheres_from_coords to work with negative coordinates #enh #bug
• Fixed some bugs pertaining to numpy deprecations becoming reality #bug
• Fixed bugs in rsa when using clearance #bug
• Fixed dynamically changing loglevel #bug
• tortuosity_fd should raise Exception if all pores are floating pores #bug

📗 Documentation

• Fixed formatting of the Results table in tortuosity notebook #doc
• Fixed imageio deprecation warnings in 2 examples #doc, #maint
• Added tutorial notebook explaining the use of spheres_from_coords on various csv files #doc
• Fix link to installation guide in readme #docs
• Added examples on snow2, regions_to_network, and other network extraction related function #docs
• Added examples on often asked questions in the Discussions #doc

Installation

The txt files below contain the specific packages and their versions to install to get a functioning installation for archival purposes using conda. Instructions for installing are in the top of the file.

v2.2.2

🍰 Enhancements

• Replaced loguru with rich for logging
• tortuosity_fd now uses PyAMG instead of PyPardiso, which makes it way faster
• tortuosity_fd now optionally accepts an OpenPNM solver object for more fine-grained control

v2.2.1

🔧 Maintenace

• Add example notebook on how to create multiscale images
• PoreSpy is now compatible with OpenPNM v3 API

v2.2.0

🚀 New features

• Added AI_diffusive_size_factor to networks module for predicting diffusive conductance from watershed segmentation using tensorflow

🍰 Enhancements

• Enhanced parallelized operations (such as filters) to not oversubscribe the CPU, hence should run faster
• Enhanced two point correlation function for speed, flexibility and compatibility
• regions_to_network is now more flexible and can handle noncontiguous phase labels
• Added a jitted get_radial_sum to tpcf, updated parse histogram to incorporate tpcf outputs

🔧 Maintenace

• Added Python 3.10 to CI workflows
• Unified requirements.txt with install_requires in setup.py
• Fixed version regex in setup.cfg that incorrectly incremented the 4th digit

🐛 Bugfixes

• Fixed bundle_of_tubes to work with scipy 1.9+

📗 Documentation

• Fixed "diffusive conductance using AI" example notebooks
• Large batch of updates to the examples

v2.1.0

🚀 New features

• Added pc_to_satn function to filters #new
• Added satn_to_seq function to filters #new
• Added satn_profile to metrics #new
• Added find_h to metrics #new
• Added pc_curve to metrics which accepts either sizes or pressures #new
• Added satn_to_panels to visualization folder to create a montage of invasion steps #new
• Added prep_for_imshow to visualization folder to adjust image for passing to plt.imshow #new
• Created simulations module to replace dns #new #api
• Moved tortuosity function to simulations and renamed it tortuosity_fd for finite difference #new #api
• Added drainage function to the new simulations module, which incorporates the effect of gravity #new

🍰 Enhancements

• Added ability to pass custom peaks to snow algorithms #enh
• Phase labels no longer need to be contiguous in snow functions or snow2 extraction #enh
• Phase labels of 0 can now be passed to snow2, if phase_alias argument is provided #enh
• Added ability to specify residual invading phase in drainage #enh
• Added surface option to trim/fill functions to optionally remove artifacts on the surfaces #enh
• Added optional strel arg to trim_nonpercolating_paths #enh

🔧 Maintenance

• Removed joss folder from top level of repo #maint
• Decreased size of examples to accelerate testing and building #maint
• Added many quantitative unit tests for snow functions #maint
• Using much small images in snow tests to improve testing speed #maint
• Minor adjustments/improvements to various trim peaks functions #maint
• Consolidated jit sphere insertion funcs into a single file under tools #maint
• Streamlined and simplified CI workflows #maint
• Renamed how-tos to reference and other maintenance of docs #docs #maint
• Added citations file to repo #maint
• Dropped support for Python 3.6 and 3.7 per NEP29 #maint
• Fixed examples CI to use the official pytest-split #maint
• Temporarily excluded imagej module from coverage due to CI/dependency issues #maint
• Removed transforms3d from requirements as it's no longer needed #maint
• Added 4th digit to semantic version to indicate number of merges into dev branch

⚠️ API changes

• Deprecated pc_curve_from_mio in favor of just pc_curve(sizes=sizes) #api
• Created simulations module to replace dns #new #api
• Moved tortuosity function to simulations and renamed it tortuosity_fd for finite difference #new #api
• Deprecated dns.tortuosity though provided a wrapper to the moved and renamed version tortuosity_fd #api

🐛 Bugfixes

• Fixed bug in region_volumes method #bug
• Fixed cylindrical_plug generator to work in 2D #bug
• Fixed bugs in snow2 when accuracy was 'high': missing throat_perimeters and incorrect voxel scaling #bug
• Fixed a memory leak in tortuosity_fd

📗 Documentation

• Removed excess badges from readme #doc
• Major updates to all example notebooks #docs
• Renamed how-tos to reference and other maintenance of docs #docs #maint
• Added 2 new examples on the basic use of drainage and explaining its inner workings #docs
• Updated some notebooks to work with new version of openpnm (2.8+) #doc

Installation

Normally porespy can be installed using conda install -c conda-forge porespy=2.1; however, to reproduce the exact environment which this release was built upon (i.e. at some point in the future), download one of the requirements files below (i.e. requirements_ps21_py310_win64.txt), then run the following at the conda prompt:

conda create --name <env> --file requirements_ps21_py310_win64.txt
conda activate <env>

where <env> is your chosen environment name.

v2.0.2

🐛 Bugfixes

• Fixed snow2 which called missing function in accuracy='high' mode

📌 Pinned Dependencies

The following file can be used to produce a working installation of PoreSpy v2.0.2: conda_pinned_requirements_v2.0.2.txt

v2.0.1

🔧 Maintenace

• Make pyfastnoisesimd optional for conda-forge builds to work #maint