| 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 |
| 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 |
| 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 |
| 33b974c | Andrey Fedorov | 09 February 2020, 03:58:46 UTC | Merge pull request #558 from rcuocolo/master 2D MRI extraction parameter file example | 09 February 2020, 03:58:46 UTC |
| 3b4fdd6 | Andrey Fedorov | 06 February 2020, 16:22:05 UTC | Merge pull request #559 from zivy/updateDocumentation Remove duplicate word. | 06 February 2020, 16:22:05 UTC |
| 47f8598 | Ziv Yaniv | 06 February 2020, 15:57:19 UTC | Remove duplicate word. | 06 February 2020, 15:57:19 UTC |
| bafd7e2 | Renato Cuocolo | 04 February 2020, 13:29:41 UTC | Update customization.rst Fixed another typo and minor language edit. | 04 February 2020, 13:29:41 UTC |
| e24a67e | Renato Cuocolo | 04 February 2020, 13:26:49 UTC | Update customization.rst Edited a typo. | 04 February 2020, 13:26:49 UTC |
| 0ded0f5 | Renato Cuocolo | 04 February 2020, 11:18:16 UTC | Merge branch 'master' into master | 04 February 2020, 11:18:16 UTC |
| c3de30b | Renato Cuocolo | 04 February 2020, 11:15:02 UTC | Update customization.rst Edited for clarity the explanation of resampling and force2DDimension settings. | 04 February 2020, 11:15:02 UTC |
| 2005bd2 | Joost van Griethuysen | 04 February 2020, 10:00:59 UTC | TEST: Fix bug in loading image/mask during testing In commit 43578f7, use of class instance scope settings was changed to local scope settings allow correct parallel extraction using a shared instance of the extractor. However, this also meant that the settings had to be passed to the function that loads the image and mask. While this was done so for the call to this function from inside RadiomicsFeatureExtractor, this was not done so for the call to this function in TestUtils, which is the workflow for loading the image/mask during testing. This resulted in ignoring settings during loading, which meant no normalization or resampling was applied. This only affected the testing, and not the regular flow of PyRadiomics. | 04 February 2020, 10:00:59 UTC |
| 1f8c778 | Renato Cuocolo | 03 February 2020, 10:01:51 UTC | Update MR_2D_extraction.yaml | 03 February 2020, 10:01:51 UTC |
| 02cd38e | Renato Cuocolo | 03 February 2020, 09:59:28 UTC | Merge pull request #1 from rcuocolo/rcuocolo-2D-example Example of 2D extraction from MRI images. | 03 February 2020, 09:59:28 UTC |
| 91e7d3e | Renato Cuocolo | 03 February 2020, 09:57:57 UTC | Example of 2D extraction from MRI images. Commented settings regarding 2D extraction. | 03 February 2020, 09:57:57 UTC |
| f719e5e | Joost van Griethuysen | 07 January 2020, 17:01:57 UTC | Merge pull request #545 from KathrynSch/fix-2d-resampling Fix resampling operation for 2d images | 07 January 2020, 17:01:57 UTC |
| 3c17192 | KathrynS | 30 December 2019, 13:24:47 UTC | fixes resampling operation for 2d images | 30 December 2019, 13:24:47 UTC |
| c46ed88 | Andrey Fedorov | 11 December 2019, 21:58:03 UTC | BUG: fix typo Resolves #538 | 11 December 2019, 21:58:03 UTC |
| 6644f12 | Joost van Griethuysen | 27 November 2019, 17:03:04 UTC | Merge pull request #536 from JoostJM/refactor-docs Refactor docs | 27 November 2019, 17:03:04 UTC |
| fb67525 | Joost van Griethuysen | 27 November 2019, 16:19:13 UTC | DOCS: Change community Switch to Slicer Discourse community instead of google groups. | 27 November 2019, 16:19:13 UTC |
| 89cc953 | Andrey Fedorov | 27 November 2019, 16:13:38 UTC | Update pointer to the forum | 27 November 2019, 16:13:38 UTC |
| 078835c | Joost van Griethuysen | 01 November 2019, 09:55:37 UTC | DOCS: Update command line usage section - Fix incorrectly encoded links - Add documentation on multiprocessing - Use sub headers instead of bullet points to improve readability | 01 November 2019, 09:55:37 UTC |
| 8da1db7 | Andrey Fedorov | 14 October 2019, 18:06:36 UTC | STYLE: add link to the publication | 14 October 2019, 18:06:36 UTC |
| 43578f7 | Joost van Griethuysen | 26 September 2019, 08:47:08 UTC | BUG: Use local scope copy of settings When extracting features in parallel, the extractor instance is shared across workers. To prevent customized updates of `label` and `label_channel` from affecting different cases, use a local copy of `self.settings`. Then, perform per-case custom updates of settings on this local copy, and pass it to the required functions. | 26 September 2019, 08:49:03 UTC |
| 54a3782 | Joost van Griethuysen | 26 September 2019, 08:17:14 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. | 26 September 2019, 08:17:14 UTC |
| 7bab402 | Joost van Griethuysen | 25 September 2019, 07:56:55 UTC | Merge pull request #527 from JoostJM/docker Add Docker for PyRadiomics-dcm Labs | 25 September 2019, 07:56:55 UTC |
| 1559ade | Joost van Griethuysen | 04 September 2019, 14:24:20 UTC | BUG: Include all pyradiomics-dcm lab files in the docker Include the resources folder and example parameters as well. | 04 September 2019, 14:24:20 UTC |
| 6683061 | Joost van Griethuysen | 02 September 2019, 13:21:23 UTC | ENH: Update CLI Dockerfile Setup PyRadiomics from the build context instead of cloning & installing it. | 02 September 2019, 13:21:23 UTC |
| c5bc148 | Joost van Griethuysen | 02 September 2019, 12:50:03 UTC | BUG: Fix path to the pyradiomics-dcm.py script | 02 September 2019, 12:50:03 UTC |
| 9e6d486 | Joost van Griethuysen | 29 August 2019, 15:34:20 UTC | Update issue templates | 29 August 2019, 15:34:20 UTC |
| 4478b0c | Joost van Griethuysen | 29 August 2019, 15:19:16 UTC | DOCS: Refactor documentation - Update FAQ section - Move information on using the feature classes directly to the developers section, as it is not intended for standard usage. Additionally, fix typo in _cmatrices | 29 August 2019, 15:19:16 UTC |
| 7fb9423 | Joost van Griethuysen | 21 August 2019, 14:27:39 UTC | ENH: Add docker for pyradiomics-dcm labs script - Based on Docker file for PyRadiomics CLI, and copy required applications from the qiicr/dcmqi docker (segimage2itkimage and tid1500writer) - Update PyRadiomics CLI dockerfile to include bzip2-devel, which is needed to run pandas - Fix bug in pyradiomics-dcm.py: when using dcm2niix as converter, the expected filename should be included in the commandline arguments | 21 August 2019, 14:27:39 UTC |
