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Software for the Practical Analysis of Materials

Project description

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Spam is a piece of Python software built upon NumPy and SciPy for the analysis and manipulation of 3D and 2D data sets in material science, be they from x-ray tomography, random fields or any other source.

A number of common functions are provided that are either lacking or slow in Numpy and Scipy, which are expected to be used by users within new python scripts. These functions are in the tools/ directory, and include tools to work with random fields, morphological operations, digital image correlation, and labelled images. Some of spam’s functions transparently call C/C++ functions for speed.

Some user-callable scipts are also provided – they are more complex pieces of code that combine a number of functions and which have a command-line interface. For the moment the scripts are 3 different image correlation techniques.

Please have a look at our online documentation for:

If you find bugs, need help, or want to talk to the developers, we use a element.io/matrix.org chat room for organisation, please join it here and come and talk to us – it is easy, there is a chat client that can run in your web broswer. All you need to do is choose a user name!

Changelog

Version Date Notes
Version 0.6.1.1 2022-01-20 Registration subtraction option for spam-passPhiField (-regs)
Version 0.6.1 2021-10-29 New package spam.orientations and segmentations functions
Version 0.6.0.3 2021-07-08 Fixed -applyF check. Now registration guess is correctly applied to a set of points
Version 0.6.0.2 2021-06-23 Fixed spam-mmr-graphical and PyQt5 dependencies. New spam.plotting.plotSphericalHistogram renders a 3D orientation distribution!
Version 0.6.0.1 2021-05-20 Small fixes to spam-filterPhifield and spam-regularStrain
Version 0.6.0 2021-05-04 Massive rewrite of image correlation scripts, introduction of spam-pixelSearchPropagate, spam-filterPhiField, spam-passPhiField. The spam-pixelSearch is now separate from spam-ldic and spam-ddic, and works both in grid and labelled mode. Please check out new script documentation for a flowchart of how these should be used in series. Loads of scripts and quite a few functions are now multiprocess, and MPI parallelisation is completely dropped along with mpi4py. pygmsh dependency is also now dropped
Version 0.5.3.4 2021-03-19 Last version to support python 3.5. Update gradient option in spam-ldic, new function to generate pixelated spheroids: spam.kalisphera.makeBlurryNoisySpheroid()
Version 0.5.3.3 2020-11-27 spam-reg script, spam-ereg-discrete writing fix, spam-ldic update gradient option, implementation of Geers in 2D
Version 0.5.3.2 2020-10-27 spam-ereg-discrete mask option reinstated, many fixes for spam-ldic and registerMultiscale() for 2D images
Version 0.5.3.1 2020-10-23 spam-ereg-discrete make safer with slicePadded and moveGrains now renamed to moveLabels and proposed as function with erodeLabels
Version 0.5.3 2020-10-07 Improvements in edge cases in spam-ldic and spam-ddic, thanks to a helper function called spam.helpers.slicePadded(). New debug mode for spam-ddic as well as a graphical tool to manually align labels called spam-ereg-discrete
Version 0.5.2.1 2020-07-20 This is the version in the JOSS paper. Making python 3.8 package for PyPI, along with classifiers. Python 2.7 dropped
Version 0.5.2 2020-06-03 Big improvements in spam-mmr and spam-mmr-graphical, all TSVs im1->im2 and gradients always computed in im2
Version 0.5.1.5 2020-05-28 Don’t recompute Jacobian in register if not needed. Safety in pixel search
Version 0.5.1.4 2020-05-16 Fix spam-deformImageFromField, C++14
Version 0.5.1.3 2020-04-20 Fix spam-mmr and improvements to pixel search in spam-ddic
Version 0.5.1.2 2020-04-20 Fix and test for large initial guesses in register(), spam-mmr-graphical revived
Version 0.5.1.1 2020-04-08 Fix for running spam-ldic for pixel search
Version 0.5.1 2020-04-07 Fix for running spam-ddic with mpi, implementation of S. Brisard’s Directional Erosion
Version 0.5.0 2020-03-27

Big rename of scripts, functions, variables, parameters, with some backwards compatibility in TSV file reading. Some examples:

  • spam.correlate.lucasKanade -> spam.correlate.register
  • spam.helpers.readTSV -> spam.helpers.readCorrelationTSV

New framework for the calculation of strains, where the computation of F is separated from its decomposition. Output fields from correlation with prefixes “SubPix” and “SubPixel” become prefixless In TSV outputs from correlation the components like “F12” are now called “Fzy”

Version 0.4.3 2020-01-16 Various fixes to graphical clients (able to save TSV from spam-mmr-graphical and do a last, precise run with spam-mmr). Improvement to triangulation (now with CGAL alpha shapes) and discrete strain calculator (tested results)
Version 0.4.2 2019-09-25 spam-mmr-graphical now working, improvements in spam-mmr.
Version 0.4.1 2019-09-13 spam-mmr-graphical now working (c-python type error). Various bugfixes in clients. spam-ITKwatershed now accepts markers
Version 0.4.0 2019-07-18 c++ now bound with pybind11. New graphical script spam-mmr-graphical for multi-modal registration. New graphical script spam-ereg for eye (manual) registration. Python3 upgrade recommended for all users
Version 0.3.3.1 2019-05-27 Binning 2^31 fix, remove lines for immediate prints that are not py3 compatible First version with CGAL triangulation
Version 0.3.2.1 2019-05-14 Update pip documentation and changelog
Version 0.3.2 2019-04-30 Fix segfault with images larger than 2^31 voxels, and output both subtracted and original fields in spam-ldic
Version 0.3.1 2019-04-08 Fix a number of forgotten spam.DIC.transformationOperator functions
Version 0.3.0 2019-03-28 Consistent naming in DIC: Phi is 4x4 homogeneous deformation function and F is its internal 3x3 displacement gradient
Version 0.2.2.2 2019-03-21 First version on pip with complete dependencies. This version of spam runs fully in a venv with pip install spam
Version 0.2.2.1 2019-03-20 Pull in requirements.txt into setup.py automatically. This aligns the build from git with the build from pip.
Version 0.2.2 2019-02-21 Approximate python3 compatibility
Version 0.2.1 2019-02-18 Add PyPI documentation to pip in RST
Version 0.2.0 2019-02-18 Add PyPI documentation to README.rst to appear on pip. Note that the build status and coverage badges won’t appear until access to gitlab is opened

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