spam 0.6.3

Version 0.6.3

2023-07-06

Fixes masking in register(), move to pyproject.toml, and 2D imShowProgress and applyPhiPython

Version 0.6.2.1

2023-03-21

Imports in graphical tools fixed

Version 0.6.2

2023-03-17

Fixes to registration, pep8 and black the whole code, dev on global and projection

Version 0.6.1.3

2022-10-25

Fix for histogramTools, a number of library calls updated for deprecation warnings

Version 0.6.1.2

2022-09-22

Parallelised tetLabel, safety in spam-pixelSearch, -skp in spam-ldic

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