Summary

This is the official release of iMars3D, v1.0.0.
The detailed changes can be found in section What's Changed, and the development team would like to extend our thanks to all the contributors listed in section New Contributors.

In this release, the core functionality for reconstructing neutron CT scans are implemented, along with a CLI engine that can perform reconstruction with given configuration file (see demo.json for example).

The next step would be maturing the GUI components (based on holoviz, partially implemented) that provides interactive reconstruction within Jupyter and as a standalone web app.

What's Changed

sniffing of CT/OB/DF data files by @yxqd in #45
PR: S3 for test data by @yxqd in #50
PR: Improve Intensity Fluctuation Correction by @yxqd in #56
PR: travis CI test of recon workflow by @yxqd in #57
Ian-fileselector-ui: Fileselector.py by @ilumsden in #63
switch to use ipywe widgets by @yxqd in #71
Tomorecon by @ilumsden in #74
Add TomoRecon-Wizard by @ilumsden in #77
notebook UI ver 1: make it work at local computers by @yxqd in #80
Skip CT filenames that are not recognized by @yxqd in #82
gamma filter bug by @yxqd in #86
allow user to customize preprocessors in CT by @yxqd in #89
allow DF to be optional by @yxqd in #90
travis cron test setup by @yxqd in #94
options of cleaning intermediate results by @yxqd in #95
reconstructed filenames: use 4 digits by @yxqd in #96
travis cache by @yxqd in #97
CT: mirror by @yxqd in #98
CT recon notebook UI: buttons to switch to select OB and DF files from arbitrary folders by @yxqd in #101
CT recon notebook UI: support skipping DF by @yxqd in #102
notebook UI version 2 by @yxqd in #103
automatic reconstruction by @yxqd in #106
improve autocrop by @yxqd in #108
improving auto reconstruction by @yxqd in #110
Put archiving in background by @yxqd in #113
Upgrade to python 3.6 by @wdzhou in #119
python36: fix mpi test by fixing popen by @jrmcgaha-dev in #122
Update tomoreconui.py by @jmborr in #125
Make encoding only for python version < 3 by @jmborr in #126
patch current version by @jmborr in #127
Remove deprecated tomopy option by @ckendrick in #128
Update tomopy version in readme by @ckendrick in #129
migrate to python 3.8 and tomopy 1.10 by @yxqd in #130
Removed flag. this refs #131 by @JeanBilheux in #132
added documentation. this refs #133 by @JeanBilheux in #134
[IMG123] Add developer documentations by @KedoKudo in #136
Create LICENSE by @KedoKudo in #137
[IMG124] update packaging by @KedoKudo in #138
[IMG131] restructure the test folder by @KedoKudo in #139
added Jiao's presentations by @jmborr in #140
[IMG152] rewrite gamma filter for new imars3d by @KedoKudo in #141
[IMG153] add normalization filter for imars3dv2 by @KedoKudo in #142
[IMG154] add crop and auto bounds detection for imars3dv2 by @KedoKudo in #143
[IMG155] denoiser for iMars3D_v2 by @KedoKudo in #144
[IMG156] add intensity fluctuation correction filter for imar3d_v2 by @KedoKudo in #145
[IMG178] update pre-commit to include more hooks by @KedoKudo in #147
[IMG176] add rotation axis tilt correction by @KedoKudo in #146
[IMG158] add rotation center finder imars3d v2 by @KedoKudo in #148
[IMG113] enable unit test with code coverage by @KedoKudo in #149
[IMG159] Modernize Ketcham ring removal method by @KedoKudo in #150
Wrapper for tomopy recon by @ckendrick in #151
[IMG201] Enable shared memory and progress bar for denoise filter by @KedoKudo in #153
[IMG221] developer documentation on multiprocessing and progress bar by @KedoKudo in #154
Add progress bar and shared memory for tilt correction by @ckendrick in #156
[IMG227] add progress bar and shared mem model for intensity fluctuation correction by @KedoKudo in #155
[IMG243] reconstruction wizard prototype with holoviz stack by @KedoKudo in #157
Gzi playwright prototype by @gecage952 in #158
Create Wheel for imars as part of github workflow by @walshmm in #159
only report fail if the coverage drops below 60 by @KedoKudo in #160
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #152
Readme rewrite by @walshmm in #161
[IMG265] Restructure project structure with new design guide by @KedoKudo in #163
[IMG303] Add gui development guid to dev_docs by @KedoKudo in #165
[IMG237] update docs for iMars3D_v2.0 by @KedoKudo in #166
Create CODE_OF_CONDUCT.md by @KedoKudo in #167
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #164
Re-enable building the wheel by @peterfpeterson in #168
add yamllint to pre-commit by @KedoKudo in #169
Update README.md by @KedoKudo in #170
[IMG233] update conda recipe to enable package building by @KedoKudo in #171
Update deploy triggers by @peterfpeterson in #172
Sequence diagram for Loading input data by @jmborr in #174
[IMG282] add data_load function via param.ParametrizedFunction by @KedoKudo in #175
update badge to match the github action yml change by @KedoKudo in #173
[IMG282] UI for load data by @KedoKudo in #176
[IMG282] new MetaData class to help identify files from same scan by @KedoKudo in #178
[IMG306] add developer documentation for parameterized function from param by @KedoKudo in #181
[IMG282] Auto find openbeam and darkcurrent based on metadata from ct by @KedoKudo in #180
IMG 306 Covert Normalization.py to be ParameterizedFunction with validation and Logger by @walshmm in #182
Validate json schema files by @peterfpeterson in #177
Convert crop to paramterized function and adjust its calls by @gecage952 in #184
Workflow engine by @jmborr in #179
[IMG311] Refactor gamma filter to us...