Release iMars3D v1.0.0

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 use parameterized function by @KedoKudo in #185
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #183
• [IMG312] Refactor denoise filter to use parameterizedFunction by @KedoKudo in #186
• [IMG314] Refactor tilt correction to use param.ParameterizedFunction by @KedoKudo in #187
• Gzi fluctuation filter by @gecage952 in #188
• [IMG343] Add docstring check via pydocstyle by @KedoKudo in #189
• Add documentation for the schema by @peterfpeterson in #191
• Add codecov configuration by @peterfpeterson in #193
• convert rotation.py to parameterizedfunction, add logging, updated tests by @walshmm in #190
• Convert reconstruction to parameterized function and adjust test by @gecage952 in #194
• migrate ring_removal.py to parameterizedfunction, updated unit tests by @walshmm in #195
• Add high-level design doc by @hetrickjm in #192
• refactor ring removal (ketcham) to be parameterizedfunction by @walshmm in #197
• Doc formatting by @peterfpeterson in #198
• [IMG292] Fix issue related to unsorted list from generator by @KedoKudo in #199
• Refactor the workflow engine for autoreduction by @jmborr in #200
• [IMG377] Base layout for iMars3D UI by @KedoKudo in #201
• Bump codecov action to v3 by @peterfpeterson in #203
• No longer allow the config schema to be customizable by @peterfpeterson in #202
• Move conda to only build on protected branches by @peterfpeterson in #204
• Logging config by @peterfpeterson in #206
• deprecated prefix "globals." by @jmborr in #207
• [IMG377] Implement visualization window for iMars3D ui by @KedoKudo in #205
• Test cades runner for integration tests by @rosswhitfield in #208
• Annotate build with integration test status by @peterfpeterson in #209
• implement assisted_window.py by @gecage952 in #210
• [IMG290] Add new crop widget for interactive cropping by @KedoKudo in #211
• Add test for invalid function name in workflow config by @gecage952 in #212
• Improve verification that functions in the config exist by @peterfpeterson in #215
• Function outputs need not be global parameters by @jmborr in #216
• Supress warnings from dxchange when importing by @peterfpeterson in #217
• Cli entrypoint by @peterfpeterson in #213
• Add codecov and CII badges by @rosswhitfield in #218
• Remove files for old CI technology by @peterfpeterson in #220
• Turn on flake8 in backend and fix issues by @peterfpeterson in #219
• Enable and fix flake8 in front end by @peterfpeterson in #222
• Remove ability for user to change schema by @peterfpeterson in #223
• add default=None for parameters with no default by @jmborr in #226
• Add CLI integration tests by @ckendrick in #224
• Slim down to a single environment file by @peterfpeterson in #225
• Add CodeQL by @rosswhitfield in #228
• Img376 add integration tests by @walshmm in #214
• Test data repository markers by @peterfpeterson in #229
• Create skeleton autoreduction script and test by @peterfpeterson in #227
• [IMGx] add PR stale bot config by @KedoKudo in #231
• Progress bar widget by @peterfpeterson in #230
• Integration tests with invalid parameters by @jmborr in #232
• Fix backend system tests by @peterfpeterson in #235
• Enable pydocstring by @peterfpeterson in #233
• Reuse JSON_DIR fixture from conftest.py by @peterfpeterson in #236
• added save/load bookend, refactored, incomplete workflow test by @walshmm in #234
• Extract json from system test by @peterfpeterson in #237
• [IMG391] add top level function calls for auto reduce by @KedoKudo in #238
• Integration test: tiff file doesn't exist by @jmborr in #240
• Add nbstripout pre-commit configuration by @peterfpeterson in #239
• Implement load_template_config for autoredux by @gecage952 in #241
• Add schema.json to the packaging by @peterfpeterson in #245
• Img391 extract data from path by @walshmm in #243
• document pre-commit by @jmborr in #242
• move file cleanup to conftest fixture by @walshmm in #244
• moved io to dataio by @jmborr in #246
• Add user documentation for entrypoints by @peterfpeterson in #249
• Stop ignoring F401 and F403 flake8 warnings by @rosswhitfield in #250
• Integration tests for missing configuration by @jmborr in #248
• integration test for auto_reduction_ready by @jmborr in #247
• json configuration input is corrupt by @jmborr in #251
• Switch to new cades runners by @rosswhitfield in #254
• Refactor code to use central save functions by @peterfpeterson in #253
• Engine error codes by @peterfpeterson in #255
• Change to np.testing for better difference messages by @peterfpeterson in #258
• Add docs for autoredux and clean up other places by @peterfpeterson in #256
• fix integration backend test_run by @jmborr in #257
• Log Autoreduction Messages to File by @jmborr in #259
• remove tomopy and replace with pure numpy solution by @walshmm in #260
• skip tests so we can push a build, to be fixed in branch happy_path by @walshmm in #261
• Change to use boa for building conda package by @peterfpeterson in #262
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #263
• integration test for a valid dataset by @jmborr in #252
• Move where boa is installed by @peterfpeterson in #264
• minus_log parameterized function by @jmborr in #265
• Set default number of pairs in rotation center by @peterfpeterson in #267
• [IMG448] Add thin wrapper around new ring removal method based on BM3D by @KedoKudo in #266
• Expose tompy normalize_roi method by @gecage952 in #268
• Fail the test if there is insufficient memory by @peterfpeterson in #269
• Update Expected Results for Integration Tests by @jmborr in #270
• [IMG444] atol can be inferred during 180 deg pair finding for sorted array by @KedoKudo in #271
• crop returns a copy for 3D arrays by @jmborr in #272
• allow for list of open beam and dark field directories by @jmborr in #274
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #273
• include olefile in the conda recipe by @jmborr in #275
• extend load_data's ob_dir and df_dir to handle a list of folders by @jmborr in #276
• Improve documentation on the num_pairs parameter by @peterfpeterson in #277
• Remove old facade in favor of standard class by @peterfpeterson in #278
• update docs on setup integration test data by @KedoKudo in #280
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #279
• Trouble shoot CI failure related to Github mamba solution by @KedoKudo in #281
• remove conflicting opts by @KedoKudo in #282
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #283

New Contributors

• @ilumsden made their first contribution in #63
• @wdzhou made their first contribution in #119
• @jrmcgaha-dev made their first contribution in #122
• @jmborr made their first contribution in #125
• @ckendrick made their first contribution in #128
• @JeanBilheux made their first contribution in #132
• @KedoKudo made their first contribution in #136
• @gecage952 made their first contribution in #158
• @walshmm made their first contribution in #159
• @peterfpeterson made their first contribution in #168
• @hetrickjm made their first contribution in #192
• @rosswhitfield made their first contribution in #208

Full Changelog: https://github.com/ornlneutronimaging/iMars3D/commits/v1.0.0