| 146e3bd | Andrey Fedorov | 03 January 2024, 22:30:34 UTC | Merge pull request #857 from DanXieJY/SafeLoadRemove SafeLoadRemove Error in Slicer | 03 January 2024, 22:30:34 UTC |
| b19c0dc | Junyi Xie | 06 December 2023, 19:09:24 UTC | SafeLoadRemove Error in Slicer | 06 December 2023, 19:09:24 UTC |
| 6a761c4 | JoostJM | 17 May 2023, 11:10:30 UTC | v3.1.0 Release | 17 May 2023, 11:14:05 UTC |
| 8017bdb | Joost van Griethuysen | 17 May 2023, 10:58:05 UTC | Merge pull request #788 from JoostJM/circle-ci-mac-os Fix errors in continuous integration | 17 May 2023, 10:58:05 UTC |
| d2f8102 | JoostJM | 17 May 2023, 10:42:01 UTC | Merge remote-tracking branch 'upstream/master' into circle-ci-mac-os | 17 May 2023, 10:42:50 UTC |
| 06bea71 | Joost van Griethuysen | 17 May 2023, 09:36:55 UTC | Merge pull request #817 from Risheng1128/master Fix typo about GLCM | 17 May 2023, 09:36:55 UTC |
| 7c53bde | JoostJM | 17 May 2023, 09:16:06 UTC | DOC: Add long_description_content_type | 17 May 2023, 09:16:06 UTC |
| 038f8a8 | JoostJM | 17 May 2023, 06:57:13 UTC | DOC: Update ReadMe Update status badges in readme to reflect new CI integration. | 17 May 2023, 06:57:13 UTC |
| fbccb99 | JoostJM | 17 May 2023, 06:41:06 UTC | CI: Fix long description Fix new definition of long description to ensure it is rendered on PyPi | 17 May 2023, 06:45:23 UTC |
| 3144f52 | joostjm | 09 May 2023, 14:55:56 UTC | BUG: Fix build step | 09 May 2023, 14:57:47 UTC |
| 66e9c17 | joostjm | 09 May 2023, 14:19:44 UTC | Merge branch 'refactor-structure' into circle-ci-mac-os | 09 May 2023, 14:19:44 UTC |
| 51b64b1 | joostjm | 09 May 2023, 14:16:59 UTC | ENH: Update imports in scripts | 09 May 2023, 14:16:59 UTC |
| c341b31 | joostjm | 09 May 2023, 14:15:35 UTC | REFACTOR: Use pyproject.toml project definition | 09 May 2023, 14:15:35 UTC |
| e889f94 | joostjm | 09 May 2023, 13:35:09 UTC | TEST: Switch to pytest | 09 May 2023, 13:35:09 UTC |
| a52f282 | joostjm | 09 May 2023, 11:29:27 UTC | DOCS: Add note on label and label_channel Label_channel was added to support 3D slicer's Segmentation format. However, with newer versions, Segmentations created in 3D slicer may be stored as labelmaps (more space efficient). Add a note to point users to this in `getMask` function. | 09 May 2023, 11:29:27 UTC |
| efb9756 | joostjm | 09 May 2023, 11:27:43 UTC | BUG: Force label and label_channel to int Both label and label_channel are used in SimpleITK, which is more sensitive to datatypes (i.e. will fail when either parameter is int64_t). Therefore, force these values to int. | 09 May 2023, 11:27:43 UTC |
| 7f49638 | joostjm | 09 May 2023, 11:23:43 UTC | DEP: Remove dependency versions Allow for newer versions to be used. Consistency in results is covered by testing. | 09 May 2023, 11:23:43 UTC |
| 8bf0b05 | Risheng1128 | 09 March 2023, 07:40:48 UTC | Fix typo about GLCM | 09 March 2023, 07:43:46 UTC |
| 4f12d42 | Joost van Griethuysen | 13 December 2022, 15:27:06 UTC | CI: Fix deployment steps - Call twine using python -m twine in Linux - Correctly setup miniconda environment in Appveyor. See also https://github.com/conda/conda/issues/8836 - Add compiler requirement conda meta.yaml | 13 December 2022, 20:03:54 UTC |
| 2bbbb21 | Joost van Griethuysen | 13 December 2022, 10:27:36 UTC | CI: appveyor python version test | 13 December 2022, 11:39:41 UTC |
| 8911ea1 | Joost van Griethuysen | 13 December 2022, 08:15:58 UTC | CI: Fix Appveyor build Force scikit-ci to also use the configured python by first correcting the path. Removes support of python 3.6 build, also remove this from the linux build. | 13 December 2022, 09:45:42 UTC |
| 0c573bc | Joost van Griethuysen | 13 December 2022, 08:03:57 UTC | CI: Start auditwheel via python -m | 13 December 2022, 08:03:57 UTC |
| 9e9b3eb | Joost van Griethuysen | 11 October 2022, 16:36:26 UTC | BUG: Fix label_channel selection bug When Label_channel column is present in the CSV input, it needs to be parsed as an int. However, due to a bug, the value for label was used instead. Related to 54a37822, but now for voxel-based extraction | 11 October 2022, 16:36:26 UTC |
| be9f2b2 | Joost van Griethuysen | 20 September 2022, 15:45:58 UTC | STYL: Fix Flake8 error | 20 September 2022, 15:45:58 UTC |
| 9f20151 | Joost van Griethuysen | 20 September 2022, 15:40:33 UTC | Merge remote-tracking branch 'upstream/master' into circle-ci-mac-os | 20 September 2022, 15:40:33 UTC |
| 110aa14 | Joost van Griethuysen | 13 June 2022, 14:39:14 UTC | BUG: Fix error in passing PyPi credentials Twin upload is handled in powershell, requiring a different reference to environment variables. | 13 June 2022, 14:39:14 UTC |
| 9290e17 | Joost van Griethuysen | 13 June 2022, 13:53:19 UTC | CI: Fix deployment bugs Ensure patchelf can be installed in linux Fix tag check in AppVeyor | 13 June 2022, 14:16:32 UTC |
| 62c5577 | Joost van Griethuysen | 13 June 2022, 10:35:22 UTC | CI: Update Repo check Repo organization name has changed to AIM-Harvard, update the check to reflect this. | 13 June 2022, 10:35:22 UTC |
| 98cdd0f | Joost van Griethuysen | 13 June 2022, 10:29:48 UTC | ENH: Remove Python 3.5 support No longer supported since September 13th, 2020 | 13 June 2022, 10:29:48 UTC |
| e719901 | Joost van Griethuysen | 13 June 2022, 10:01:13 UTC | ENH: implement distribution to test pypi When tag version specifies alfa, beta or rc release, push to test pypi server. | 13 June 2022, 10:13:58 UTC |
| aa6a1a3 | Joost van Griethuysen | 03 April 2022, 15:23:07 UTC | CI: Remove Mac OS support for python 3.5 and 3.6 These python distributions fail to build on CircleCI (failing during setup of python environment). | 03 April 2022, 15:24:10 UTC |
| 2791e23 | Joost van Griethuysen | 03 April 2022, 14:58:40 UTC | Merge pull request #756 from ysuter/fix-label-batchprocessingparallel fix: label assignment for feature extraction | 03 April 2022, 14:58:40 UTC |
| 6bd59fa | Joost van Griethuysen | 03 April 2022, 14:41:05 UTC | CI: Update MacOs Python versions | 03 April 2022, 14:41:05 UTC |
| ae3fba5 | Joost van Griethuysen | 03 April 2022, 14:08:04 UTC | CI: Manually install python version for mac | 03 April 2022, 14:08:04 UTC |
| 4a2e26b | Joost van Griethuysen | 03 April 2022, 14:01:22 UTC | CI: Update MacOS config in Circle CI | 03 April 2022, 14:01:22 UTC |
| d53d40a | Joost van Griethuysen | 03 April 2022, 12:35:45 UTC | BUG: Dynamically set PATH | 03 April 2022, 13:22:52 UTC |
| c57f28d | Joost van Griethuysen | 03 April 2022, 12:19:32 UTC | BUG: Add HOME bin folder to PATH | 03 April 2022, 12:19:32 UTC |
| 4754fae | Joost van Griethuysen | 31 March 2022, 21:23:06 UTC | BUG: Add -p on mkdir command ensures it does not fail if the directory already exists | 31 March 2022, 21:23:06 UTC |
| b0ea347 | Joost van Griethuysen | 31 March 2022, 21:07:41 UTC | CI: Setup MacOS environment prior to code checkout | 31 March 2022, 21:07:41 UTC |
| ed67b14 | ysuter | 29 March 2022, 14:38:03 UTC | fix: label assignment for feature extraction | 29 March 2022, 14:38:03 UTC |
| a749566 | Joost van Griethuysen | 23 March 2022, 10:50:27 UTC | BUG: Fix errors in MacOS image | 23 March 2022, 10:50:27 UTC |
| 2140f0c | Joost van Griethuysen | 23 March 2022, 10:24:34 UTC | BUG: Install git on MacOS image | 23 March 2022, 10:24:34 UTC |
| 9b4f71a | Joost van Griethuysen | 23 March 2022, 10:15:35 UTC | BUG: Update config Periods are not allowed in job name. | 23 March 2022, 10:22:29 UTC |
| a8b63c8 | Joost van Griethuysen | 23 March 2022, 10:11:14 UTC | BUG: Build in home dir on Mac | 23 March 2022, 10:11:14 UTC |
| f663a2e | Joost van Griethuysen | 23 March 2022, 10:04:06 UTC | ENH: Build and test Mac OS on CircleCI | 23 March 2022, 10:06:41 UTC |
| 5751a1f | Joost van Griethuysen | 08 March 2022, 17:08:43 UTC | BUG: Fix error in CircleCI config.yml Use quotes to ensure correct installation of version-constrained pip installs. | 08 March 2022, 17:08:43 UTC |
| f769e3e | Joost van Griethuysen | 08 March 2022, 14:43:42 UTC | ENH: Fix Appveyor config | 08 March 2022, 16:47:25 UTC |
| c4553fd | Joost van Griethuysen | 08 March 2022, 11:22:05 UTC | ENH: Add Python 3.8 and 3.9 support | 08 March 2022, 14:30:58 UTC |
| ee1879b | Joost van Griethuysen | 08 March 2022, 14:21:57 UTC | STYL: Fix flake8 errors | 08 March 2022, 14:21:57 UTC |
| 2e0b76e | Joost van Griethuysen | 10 January 2022, 13:21:45 UTC | Merge pull request #740 from lyhyl/master fix typos | 10 January 2022, 13:21:45 UTC |
| 33f5649 | wingkou | 06 January 2022, 09:38:16 UTC | fix typos | 06 January 2022, 09:38:16 UTC |
| 03d23f7 | Joost van Griethuysen | 14 December 2021, 11:31:52 UTC | Merge pull request #734 from anthonyjatoba/usage-docs DOCS: Update notebooks directory in usage docs | 14 December 2021, 11:31:52 UTC |
| 5eb407a | Anthony Jatobá | 21 November 2021, 20:06:59 UTC | DOCS: Update notebooks directory in usage docs | 21 November 2021, 20:06:59 UTC |
| dfe2c14 | Andrey Fedorov | 01 October 2021, 02:01:40 UTC | Merge pull request #724 from piiq/feature/dcm-mask-correction Expose mask correction and geometry tolerance to the pyradiomics-dcm CLI | 01 October 2021, 02:01:40 UTC |
| c434ff7 | Theodore Aptekarev | 30 September 2021, 21:10:02 UTC | DOCS: Fix metavars in argparse help messages | 30 September 2021, 21:10:02 UTC |
| 7fcae4c | Theodore Aptekarev | 30 September 2021, 21:04:57 UTC | DOCS: Update changelog for the next release | 30 September 2021, 21:04:57 UTC |
| b1a7613 | Theodore Aptekarev | 30 September 2021, 20:41:54 UTC | DOCS: Update pyradiomics-dcm documentation | 30 September 2021, 21:01:53 UTC |
| d02d899 | Theodore Aptekarev | 30 September 2021, 20:39:05 UTC | ENH: Expose pyradiomics-dcm mask correction settings in the CLI | 30 September 2021, 20:39:05 UTC |
| ad5b2de | hugoaerts | 14 April 2021, 13:21:48 UTC | Update README.md | 14 April 2021, 13:21:48 UTC |
| 0c53d1d | Andrey Fedorov | 15 December 2020, 14:48:12 UTC | update the community link | 15 December 2020, 14:48:12 UTC |
| 9ccbec1 | Joost van Griethuysen | 17 November 2020, 17:23:11 UTC | Merge pull request #660 from Radiomics/issue-658 BUG: Allow specification of full mask. | 17 November 2020, 17:23:11 UTC |
| 3064793 | Joost van Griethuysen | 17 November 2020, 12:19:11 UTC | BUG: Allow specification of full mask. If a mask contains only a single label, a ValueError is raised stating no labels are found in the mask. However, this error should only be raised if the only label found is '0'. | 17 November 2020, 12:19:11 UTC |
| 08bea70 | Joost van Griethuysen | 11 October 2020, 09:37:00 UTC | v3.0.1 Release | 11 October 2020, 09:37:00 UTC |
| 943756a | Joost van Griethuysen | 01 October 2020, 07:58:28 UTC | Merge pull request #646 from Radiomics/travis-ci-bug Travis CI Integration | 01 October 2020, 07:58:28 UTC |
| 9532c33 | Joost van Griethuysen | 30 September 2020, 12:45:01 UTC | ENH: Update Brew before installing gettext | 30 September 2020, 13:34:14 UTC |
| cbb3cab | Joost van Griethuysen | 30 September 2020, 12:25:04 UTC | Merge pull request #645 from Radiomics/docker Update Docker files | 30 September 2020, 12:25:04 UTC |
| 8bfbe86 | Joost van Griethuysen | 30 September 2020, 11:29:18 UTC | Merge pull request #644 from Radiomics/mr-2d-example DOCS: Add force2D setting to example settings | 30 September 2020, 11:29:18 UTC |
| 6b6bbea | Joost van Griethuysen | 30 September 2020, 11:16:04 UTC | ENH: Remove Python 2 support from notebooks in Dockerfile | 30 September 2020, 11:16:04 UTC |
| 9542ff0 | Joost van Griethuysen | 30 September 2020, 10:09:20 UTC | BUG: Update CMAKE repository URL git://cmake.org/cmake.git is unreachable. Get the repository from https://gitlab.kitware.com/cmake/cmake.git. | 30 September 2020, 10:09:20 UTC |
| b79edbf | Joost van Griethuysen | 30 September 2020, 08:50:07 UTC | DOCS: Add force2D setting to example settings In the example showing settings for 2D MR extraction, the setting `force2D` was missing. Add this setting with a value of `true` to ensure this example forces a 2D extraction. | 30 September 2020, 08:50:07 UTC |
| 7639a16 | Joost van Griethuysen | 30 September 2020, 08:41:22 UTC | Merge pull request #613 from rcuocolo/patch-1 Update MR_2D_extraction.yaml | 30 September 2020, 08:41:22 UTC |
| e1424e3 | Joost van Griethuysen | 30 September 2020, 08:40:17 UTC | Merge pull request #643 from Radiomics/travis-ci-bug BUG: Fix Travis CI bug | 30 September 2020, 08:40:17 UTC |
| f41002b | Joost van Griethuysen | 29 September 2020, 16:53:29 UTC | SETUP: Remove upper limit from PyWavelet version Initially introduced due to a problem with building PyWavelet extension in slicer build (https://github.com/Radiomics/SlicerRadiomics/issues/50). This was introduced in PyRadiomics commit c828b99. Slicer now uses Python3, removing the need to build PyWavelet from source. Therefore, remove the upper limit to allow using latest release of PyWavelet. | 29 September 2020, 16:53:29 UTC |
| b8dc600 | Joost van Griethuysen | 29 September 2020, 15:42:58 UTC | Install brew gettext for all tested python versions. libintl error also occurs during testing of python 3.5.5 and 3.6.5 | 29 September 2020, 15:42:58 UTC |
| 8626efa | Joost van Griethuysen | 29 September 2020, 15:33:23 UTC | BUG: 2nd fix of TravisCI bug Follows a similar update made by @jcfr (https://github.com/scikit-build/ninja-python-distributions/commit/389db1359a1b3985c13320be603cf6b503e3f99a). | 29 September 2020, 15:33:23 UTC |
| 6c8dbd4 | Joost van Griethuysen | 06 September 2020, 08:48:42 UTC | BUG: Fix Travis CI bug Fixes the error thrown by travis CI about loading libintl, as suggested in https://github.com/scikit-build/cmake-python-distributions/pull/113. | 29 September 2020, 14:32:43 UTC |
| 46f651d | Joost van Griethuysen | 18 September 2020, 11:00:19 UTC | Merge pull request #639 from Radiomics/issue-632 DOCS: Fix typo in documentation of NGTDM | 18 September 2020, 11:00:19 UTC |
| 801df75 | Joost van Griethuysen | 18 September 2020, 09:44:51 UTC | DOCS: Fix typo in documentation of NGTDM Fixes issue #632 | 18 September 2020, 09:44:51 UTC |
| 7aab21d | Joost van Griethuysen | 18 September 2020, 08:44:48 UTC | Merge pull request #635 from Radiomics/issue-617 BUG: Fix out-of-range check in glszm C calculation | 18 September 2020, 08:44:48 UTC |
| b0ceb54 | Joost van Griethuysen | 18 September 2020, 08:44:31 UTC | Merge pull request #636 from Radiomics/voxel-progress ENH: Add optional progress reporting for voxel-based extraction | 18 September 2020, 08:44:31 UTC |
| c5820c2 | Joost van Griethuysen | 05 September 2020, 18:06:32 UTC | BUG: Fix out-of-range check in glszm C calculation When calculating the GLSZM matrix, processed voxel indices are temporarily stored in the `processedStack`, and the current position in stored in `processed_idx`. To ensure no overflow errors occur, the `processed_idx` value is compared to the maximum size of `processedStack` (=equal to `Ns`) prior to pushing an index. This index is used, and then increased, meaning that if it's value = Ns - 1, it is still valid (though the last index to be valid). However, the check compared value + 1 >= Ns, which would fail in this last case. Update the check to allow this value. | 05 September 2020, 18:06:32 UTC |
| a568ee0 | Joost van Griethuysen | 05 September 2020, 17:57:50 UTC | ENH: Add optional progress reporting for voxel-based extraction Update base.py to add progress reporting when computing voxel batches. Uses `radiomics.getProgressReporter`, which should be set to something like `tqdm.tqdm` to work. Only shows progress bar when logging level is at least INFO (so not when WARNING or higher). | 05 September 2020, 17:57:50 UTC |
| e17e3da | Joost van Griethuysen | 05 September 2020, 17:28:06 UTC | Merge pull request #602 from JoostJM/issue-579 BUG: Fail gracefully when grayvalue <= 0 | 05 September 2020, 17:28:06 UTC |
| 1e82192 | Renato Cuocolo | 24 July 2020, 20:16:22 UTC | Update MR_2D_extraction.yaml Added some details to bin width, fixed a typo, added ngtdm features for extraction. | 24 July 2020, 20:16:22 UTC |
| 9aa1b9d | Joost van Griethuysen | 02 July 2020, 05:03:26 UTC | BUG: Fail gracefully when grayvalue = 0 "0" is an invalid value for gray level and causes an index error in the calculation of texture matrices (e.g. for GLSZM, correct index in matrix is calculated as (i, j) = (grayvalue - 1, region size), which in case of gray value 0 results in index -1, which is invalid). In some case, this resulted in a graceful error where an IndexError is raised, but this is most likely because the datatype used for the index (`size_t`) does not allow for negative indices on some systems and therefore results in an overflow, which on the subsequent check is then indeed larger than the maximum allowed index (which is checked). In other cases, `size_t` datatype does allow for negative values and therefore passes the maximum index check and subsequently fails with a Process terminated. Add an additional check to ensure the gray level is > 0, otherwise, fail the C Extension gracefully. Non-gray level properties (i.e. run length, zone size, dependence counts) are calculated in the C extension and ensured to be >= 0. | 05 July 2020, 09:16:48 UTC |
| 51639ec | Joost van Griethuysen | 29 June 2020, 04:44:35 UTC | Merge pull request #599 from mattwarkentin/master updated customization doc to clarify resampling | 29 June 2020, 04:44:35 UTC |
| 531de3c | Matthew T. Warkentin | 26 June 2020, 21:05:51 UTC | updated customization docs to clarify resampling | 26 June 2020, 21:05:51 UTC |
| 263d5b6 | Joost van Griethuysen | 23 June 2020, 18:50:27 UTC | Merge pull request #593 from Radiomics/issue-587 Fail if parameter file path is non-existent | 23 June 2020, 18:50:27 UTC |
| 2d9dda3 | Joost van Griethuysen | 23 June 2020, 10:14:54 UTC | BUG: Fail if parameter file path is non-existent When instantiating the feature extractor with a path pointing to a parameter file, it should fail if the path fails to resolve to an existing file. If that is the case, raise an IOError. Additionally, allow the path to be provided as a pathlib.PurePath (or subclass thereof). | 23 June 2020, 16:27:21 UTC |
| f06ac1d | Joost van Griethuysen | 23 June 2020, 16:26:33 UTC | Merge pull request #594 from Radiomics/issue-592 Force emptyGrayLevels datatype to int | 23 June 2020, 16:26:33 UTC |
| dc3068c | Joost van Griethuysen | 23 June 2020, 10:30:27 UTC | BUG: Force emptyGrayLevels datatype to int emptyGrayLevels is used as integer indices to remove the gray levels from the matrix. However, in linux python 3.6 and 3.7, the datatype defaults to int64, which is rejected by python when trying to use this as an index. Therefore, for the datatype of emptyGrayLevels to int, preventing the IndexError. | 23 June 2020, 10:44:35 UTC |
| e100f1d | Jean-Christophe Fillion-Robin | 28 May 2020, 18:36:43 UTC | README: Fix typo in author's name | 28 May 2020, 18:36:43 UTC |
| 896682d | Andrey Fedorov | 17 February 2020, 18:56:41 UTC | STYLE: fix typo | 17 February 2020, 18:56:41 UTC |
| 9d26a6b | Andrey Fedorov | 13 February 2020, 16:05:47 UTC | DOCS: fix parameter name | 13 February 2020, 16:05:47 UTC |
| ae1e14c | Joost van Griethuysen | 11 February 2020, 18:10:14 UTC | Merge pull request #561 from JoostJM/3.0-release 3.0 release | 11 February 2020, 18:10:14 UTC |
| a0c3875 | Joost van Griethuysen | 11 February 2020, 16:54:44 UTC | Update documentation and CHANGES Preparation for 3.0 release. | 11 February 2020, 16:54:44 UTC |
| 0101187 | Joost van Griethuysen | 11 February 2020, 16:16:04 UTC | DEPRECATE: Remove deprecated functions - Remove commandlinebatch.py - Remove CalculateFeatures() from radiomics.base.RadiomicsBase | 11 February 2020, 16:54:31 UTC |
| a5a7e61 | Joost van Griethuysen | 11 February 2020, 16:03:08 UTC | TESTING: Remove testing for Python 2.7 | 11 February 2020, 16:03:08 UTC |
| 9883f66 | Joost van Griethuysen | 11 February 2020, 14:42:29 UTC | Update Issue templates Refer to Slicer discourse instead of google groups. | 11 February 2020, 14:42:29 UTC |
| fbb6ac0 | Joost van Griethuysen | 11 February 2020, 13:59:51 UTC | TYPO: Fix typo in example settings for 2D extraction force2DDimension does not exist, it should be force2Ddimension. | 11 February 2020, 13:59:51 UTC |
