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* #193 'bump pydicom' - bumped pydicom to 2.2.2, local tests green, changelog update, added PyCharm to gitignore * WIP 197 remove + keep combo should keep (#198) * #197 'remove and keep combo' - added tests that describe situation where remove overrules keep, and also explicitly show that except is using value as substring/regex match * #197 'remove and keep combo' - added quite straightforward "add fields marked with KEEP to skiplist", also fixed docstring on parser#perform_action and removed unused parameter, fixed typo in random place * #197 'remove and keep combo' - quotes changed as per code format convention * #197 'remove and keep combo' - changed keep list to be separate property, updated docs on action order, added two tests for ensuring blank action order * #197 'remove and keep combo' - changed keep fields collector to be more pythonic * #197 'remove and keep combo' - more safeguards in keep fields collector, clarified docs upon field that should not be None * #197 'remove and keep combo' - changelog update, typo fix, version bump * #197 'remove and replace/jitter combo' - added once-evaluated list of fields being jittered or replaced to prevent them from being removed, tests, extended description of @keep property, changelog update, typo fix, version bump * #197 'remove and replace/jitter combo' - run black * Update deid/version.py - agreed to bump to 0.3 * Bug with return of derive_ctp_coordinate Downstream code expects coordinate definitions to be a comma separated list of values, not a list of ints. * Update deid/dicom/parser.py Committing suggestion. * change derive_ctp_coordinates to private function Co-authored-by: Gleb <[email protected]> Co-authored-by: Vanessasaurus <[email protected]>
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| # CHANGELOG | ||
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| This is a manually generated log to track changes to the repository for each release. | ||
| Each section should include general headers such as **Implemented enhancements** | ||
| This is a manually generated log to track changes to the repository for each release. | ||
| Each section should include general headers such as **Implemented enhancements** | ||
| and **Merged pull requests**. Critical items to know are: | ||
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| - renamed commands | ||
| - deprecated / removed commands | ||
| - changed defaults | ||
| - backward incompatible changes (recipe file format? image file format?) | ||
| - migration guidance (how to convert images?) | ||
| - changed behaviour (recipe sections work differently) | ||
| - renamed commands | ||
| - deprecated / removed commands | ||
| - changed defaults | ||
| - backward incompatible changes (recipe file format? image file format?) | ||
| - migration guidance (how to convert images?) | ||
| - changed behaviour (recipe sections work differently) | ||
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| Referenced versions in headers are tagged on Github, in parentheses are for pypi. | ||
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| ## [vxx](https://github.com/pydicom/deid/tree/master) (master) | ||
| - Add `ctpcoordinates` and `ctpkeepcoordinates` to handle different formats (0.3.0) | ||
| - Minimum Python required is 3.7, numpy 1.20 | ||
| - Remove unecessary typing - adds bugs (0.2.37) | ||
| - Provide data as an external package (0.2.36) | ||
| - Restore expand_sequences to get_identifiers (0.2.35) | ||
| - Add function to clean datasets without `DicomCleaner` [#223](https://github.com/pydicom/deid/pull/223) (0.2.34) | ||
| - add select:vr:XX field expander to select elements by VR (0.2.33) | ||
| - rename group:XXXX field expander to select:group:XXXX | ||
| - add group:XXXX field expander to select all elements with a specified DICOM tag group (0.2.32) | ||
| - custom class example for using dicom.Dataset, not requiring on client init [#211](https://github.com/pydicom/deid/pull/211) (0.2.31) | ||
| - adding support for deid provided functions [#207](https://github.com/pydicom/deid/issues/207) (0.2.3) | ||
| - update CTP deid.dicom up until [this commit](https://github.com/johnperry/CTP/commit/345b05b157c046532e8791a63ababbf6d0dba59b) (0.2.29) | ||
| - various LGTM alert fixes [#186](https://github.com/pydicom/deid/pull/186) (0.0.28) | ||
| - bug fix for exception when attempting to jitter DA/DT which cannot be jittered (space) [#189] (https://github.com/pydicom/deid/issues/189) (0.2.27) | ||
| - adding support to manipulate file meta [#183](https://github.com/pydicom/deid/issues/183) (0.2.26) | ||
| - updated pydicom dependency from 1.3.0 to 2.1.1 [#171](https://github.com/pydicom/deid/issues/171) (0.2.25) | ||
| - bug fix for multivalued fields in %values lists [#174](https://github.com/pydicom/deid/issues/174) | ||
| - allowing other VR types for jitter [#175](https://github.com/pydicom/deid/issues/175) | ||
| - ensuring that an add/replace of an existing value is also updated in fields [#173](https://github.com/pydicom/deid/issues/173) | ||
| - change to correct issue with deidentifying RGB images [#165](https://github.com/pydicom/deid/issues/165) (0.2.24) | ||
| - removing verbosity of debug logger (0.2.23) | ||
| - changing iteration technique through fields to properly add nested uids [#153](https://github.com/pydicom/deid/issues/153) (0.2.22) | ||
| - change to return results from detect when recipe does not contain filters [#155](https://github.com/pydicom/deid/issues/155) | ||
| - fix to correct bug in detect [#142](https://github.com/pydicom/deid/issues/142) (0.2.21) | ||
| - fixes to detect and clean to better represent keep/coordinates (0.2.20) | ||
| - modify default VR for added tags [#146](https://github.com/pydicom/deid/issues/146), bug with private tags in %fields section [#147](https://github.com/pydicom/deid/issues/147) (0.2.19) | ||
| - adding keepcoordinates to allow for reverse specified coordinates (0.2.18) | ||
| - bug with empty values within %values sections [#144](https://github.com/pydicom/deid/issues/144) (0.2.17) | ||
| - ability to save 4d dicom series as animation (0.2.16) | ||
| - bug with multiple actions on the same header field [#140](https://github.com/pydicom/deid/issues/140) (0.2.15) | ||
| - nested sequence in replace_identifiers/strip_sequences bug [#137](https://github.com/pydicom/deid/issues/137) (0.2.14) | ||
| - adding custom cleaner to specify region fields (0.2.13) | ||
| - bug with replace for tested fields (0.2.12) | ||
| - fixing func args to be kwargs (0.2.11) | ||
| - DicomCleaner empty method does not handle list (0.2.1) | ||
| - refactor to use iterall for all fields (0.2.0) | ||
| - including private tags in parsing (0.1.42) | ||
| - adding filters (contains through missing) for REMOVE (0.1.41) | ||
| - adding support for tag groups (values, fields) (0.1.4) | ||
| - Adding option to provide function to remove (must return boolean) (0.1.38) | ||
| - removing matplotlib version requirement (0.1.37) | ||
| - Matplotlib dependency >= 2.1.2 (0.1.36) | ||
| - Adding black formatting, tests run in GitHub actions (0.1.35) | ||
| - Adding option to recursively replace sequences (0.1.34) | ||
| - adding pylint to clean up code (0.1.33) | ||
| - removing dependency that isn't used (simplejson) (0.1.31) | ||
| - updating cleaner to use pixel array (0.1.30) | ||
| - validation function should use debug verbository, bumping license year [#92](https://github.com/pydicom/deid/issues/92) (0.1.29) | ||
| - bumping pydicom to 1.2.0 [#91](https://github.com/pydicom/deid/issues/91) (0.1.28) | ||
| - header expansions starts with and ends with should support regular expression OR (|) [#89](https://github.com/pydicom/deid/issues/89) (0.1.27) | ||
| - added all, allexcept, contains to field filters [#87](https://github.com/pydicom/deid/pull/87) (0.1.26) | ||
| - fixing bug in jitter timestamp function [#85](https://github.com/pydicom/deid/pull/85) (0.1.25) | ||
| - installation order of pydicom / matplotlib changes default python [#81](https://www.github.com/pydicom/deid/issues/81) (0.1.23) | ||
| - updating deid.dicom with contribution from @fimafurman [#63](https://github.com/pydicom/deid/issues/63) (0.1.22) | ||
| - adding "func" option for recipe to pass function (0.1.21) | ||
| - fixing client bug, redoing docs to be better organized (0.1.20) | ||
| - Removing MediaStorageSOPInstanceUID from file_meta, issue #72 (0.1.19) | ||
| - need to clean up temporary directory (mkdtemp), issue #68 (0.1.18) | ||
| - fixing issue #65, save for compressed data (0.1.17) | ||
| - matplotlib must be less than or equal to 2.1.2 for install (0.1.16) | ||
| - fixing bug with clean coordinate flipping rectangle | ||
| - Fixing bug with saving self.cleaned (0.1.15) | ||
| - Allowing for datasets to be passed in functions (not necessary for files) (0.1.14) | ||
| - index should be full path in header.py (0.1.13) | ||
| - pydicom bumped to install latest (1.0.2) (0.1.12) | ||
| - ensuring that ids for images are full paths (0.1.11) | ||
| - addition of the DeidRecipe class to better interact with and combine deid recipe files. | ||
| - the get_files function now returns a generator instead of a list. | ||
|
|
||
| - Add `ctpcoordinates` and `ctpkeepcoordinates` to handle different formats (0.3.0) | ||
| - Minimum Python required is 3.7, numpy 1.20 | ||
| - Remove unecessary typing - adds bugs (0.2.37) | ||
| - Provide data as an external package (0.2.36) | ||
| - Restore expand_sequences to get_identifiers (0.2.35) | ||
| - Add function to clean datasets without `DicomCleaner` [#223](https://github.com/pydicom/deid/pull/223) (0.2.34) | ||
| - add select:vr:XX field expander to select elements by VR (0.2.33) | ||
| - rename group:XXXX field expander to select:group:XXXX | ||
| - add group:XXXX field expander to select all elements with a specified DICOM tag group (0.2.32) | ||
| - custom class example for using dicom.Dataset, not requiring on client init [#211](https://github.com/pydicom/deid/pull/211) (0.2.31) | ||
| - adding support for deid provided functions [#207](https://github.com/pydicom/deid/issues/207) (0.2.3) | ||
| - update CTP deid.dicom up until [this commit](https://github.com/johnperry/CTP/commit/345b05b157c046532e8791a63ababbf6d0dba59b) (0.2.29) | ||
| - various LGTM alert fixes [#186](https://github.com/pydicom/deid/pull/186) (0.0.28) | ||
| - `REPLACE/JITTER` actions have now higher priority than `REMOVE`, allowing to whitelist fields from `REMOVE ALL/Field` [#197](https://github.com/pydicom/deid/issues/197) | ||
| - `ADD/KEEP` actions have now higher priority than `REMOVE`, allowing to whitelist fields from `REMOVE ALL/Field` [#197](https://github.com/pydicom/deid/issues/197) | ||
| - updated pydicom dependency from 2.1.1 to 2.2.2 [#194](https://github.com/pydicom/deid/issues/194) | ||
| - bug fix for exception when attempting to jitter DA/DT which cannot be jittered (space) [#189] (<https://github.com/pydicom/deid/issues/189>) (0.2.27) | ||
| - adding support to manipulate file meta [#183](https://github.com/pydicom/deid/issues/183) (0.2.26) | ||
| - updated pydicom dependency from 1.3.0 to 2.1.1 [#171](https://github.com/pydicom/deid/issues/171) (0.2.25) | ||
| - bug fix for multivalued fields in %values lists [#174](https://github.com/pydicom/deid/issues/174) | ||
| - allowing other VR types for jitter [#175](https://github.com/pydicom/deid/issues/175) | ||
| - ensuring that an add/replace of an existing value is also updated in fields [#173](https://github.com/pydicom/deid/issues/173) | ||
| - change to correct issue with deidentifying RGB images [#165](https://github.com/pydicom/deid/issues/165) (0.2.24) | ||
| - removing verbosity of debug logger (0.2.23) | ||
| - changing iteration technique through fields to properly add nested uids [#153](https://github.com/pydicom/deid/issues/153) (0.2.22) | ||
| - change to return results from detect when recipe does not contain filters [#155](https://github.com/pydicom/deid/issues/155) | ||
| - fix to correct bug in detect [#142](https://github.com/pydicom/deid/issues/142) (0.2.21) | ||
| - fixes to detect and clean to better represent keep/coordinates (0.2.20) | ||
| - modify default VR for added tags [#146](https://github.com/pydicom/deid/issues/146), bug with private tags in %fields section [#147](https://github.com/pydicom/deid/issues/147) (0.2.19) | ||
| - adding keepcoordinates to allow for reverse specified coordinates (0.2.18) | ||
| - bug with empty values within %values sections [#144](https://github.com/pydicom/deid/issues/144) (0.2.17) | ||
| - ability to save 4d dicom series as animation (0.2.16) | ||
| - bug with multiple actions on the same header field [#140](https://github.com/pydicom/deid/issues/140) (0.2.15) | ||
| - nested sequence in replace_identifiers/strip_sequences bug [#137](https://github.com/pydicom/deid/issues/137) (0.2.14) | ||
| - adding custom cleaner to specify region fields (0.2.13) | ||
| - bug with replace for tested fields (0.2.12) | ||
| - fixing func args to be kwargs (0.2.11) | ||
| - DicomCleaner empty method does not handle list (0.2.1) | ||
| - refactor to use iterall for all fields (0.2.0) | ||
| - including private tags in parsing (0.1.42) | ||
| - adding filters (contains through missing) for REMOVE (0.1.41) | ||
| - adding support for tag groups (values, fields) (0.1.4) | ||
| - Adding option to provide function to remove (must return boolean) (0.1.38) | ||
| - removing matplotlib version requirement (0.1.37) | ||
| - Matplotlib dependency >= 2.1.2 (0.1.36) | ||
| - Adding black formatting, tests run in GitHub actions (0.1.35) | ||
| - Adding option to recursively replace sequences (0.1.34) | ||
| - adding pylint to clean up code (0.1.33) | ||
| - removing dependency that isn't used (simplejson) (0.1.31) | ||
| - updating cleaner to use pixel array (0.1.30) | ||
| - validation function should use debug verbository, bumping license year [#92](https://github.com/pydicom/deid/issues/92) (0.1.29) | ||
| - bumping pydicom to 1.2.0 [#91](https://github.com/pydicom/deid/issues/91) (0.1.28) | ||
| - header expansions starts with and ends with should support regular expression OR (|) [#89](https://github.com/pydicom/deid/issues/89) (0.1.27) | ||
| - added all, allexcept, contains to field filters [#87](https://github.com/pydicom/deid/pull/87) (0.1.26) | ||
| - fixing bug in jitter timestamp function [#85](https://github.com/pydicom/deid/pull/85) (0.1.25) | ||
| - installation order of pydicom / matplotlib changes default python [#81](https://www.github.com/pydicom/deid/issues/81) (0.1.23) | ||
| - updating deid.dicom with contribution from @fimafurman [#63](https://github.com/pydicom/deid/issues/63) (0.1.22) | ||
| - adding "func" option for recipe to pass function (0.1.21) | ||
| - fixing client bug, redoing docs to be better organized (0.1.20) | ||
| - Removing MediaStorageSOPInstanceUID from file_meta, issue #72 (0.1.19) | ||
| - need to clean up temporary directory (mkdtemp), issue #68 (0.1.18) | ||
| - fixing issue #65, save for compressed data (0.1.17) | ||
| - matplotlib must be less than or equal to 2.1.2 for install (0.1.16) | ||
| - fixing bug with clean coordinate flipping rectangle | ||
| - Fixing bug with saving self.cleaned (0.1.15) | ||
| - Allowing for datasets to be passed in functions (not necessary for files) (0.1.14) | ||
| - index should be full path in header.py (0.1.13) | ||
| - pydicom bumped to install latest (1.0.2) (0.1.12) | ||
| - ensuring that ids for images are full paths (0.1.11) | ||
| - addition of the DeidRecipe class to better interact with and combine deid recipe files. | ||
| - the get_files function now returns a generator instead of a list. | ||
|
|
||
| ## [0.1.1](https://pypi.python.org/packages/28/26/ee80e7f1c3f65fae1c901497bb2388701158f0c96e0d633ab301abeaa478/deid-0.1.1.tar.gz#md5=39df7efb03e5d3b63308016742062a43) (0.1.1) | ||
|
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| **additions** | ||
| - addition of this CHANGELOG and an AUTHORS and CONTRIBUTING file to properly open source the project. | ||
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| - addition of this CHANGELOG and an AUTHORS and CONTRIBUTING file to properly open source the project. | ||
| **bug fix** | ||
| - when the user specifies a deid recipe, instead of adding it to a base template we honor the choice and don't append a base. | ||
| - when the user specifies a deid recipe, instead of adding it to a base template we honor the choice and don't append a base. | ||
| **creation** | ||
| - this is the initial creation of deid, including recipes for cleaning of image headers and flagging of potential phi in pixels. | ||
| - this is the initial creation of deid, including recipes for cleaning of image headers and flagging of potential phi in pixels. |
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