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CHANGELOG.md

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CHANGELOG

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:

  • 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)

Referenced versions in headers are tagged on Github, in parentheses are for pypi.

vxx (master)

  • Support pydicom.Dataset objects created from BytesIO #265 (0.3.24)
  • Exception with missing filters for non-string VR #256 (0.3.23)
  • Allow filter tag names to be 0x-prefix hex numbers so private tags can be referenced in recipes #253 (0.3.22)
  • Fix incorrect coordinate definition for GE CT #249
  • Circular import error #247 (0.3.21)
  • Expand BLANK Action to additional VRs #241 (0.3.2)
    • Correct issues with REPLACE action on numeric VRs #244
    • Correct issue with actions on fields within sequences #243
  • pre-commit for linting and formatting (0.3.1)
  • 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 (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 (0.2.31)
  • adding support for deid provided functions #207 (0.2.3)
  • update CTP deid.dicom up until this commit (0.2.29)
  • various LGTM alert fixes #186 (0.0.28)
    • REPLACE/JITTER actions have now higher priority than REMOVE, allowing to whitelist fields from REMOVE ALL/Field #197
    • ADD/KEEP actions have now higher priority than REMOVE, allowing to whitelist fields from REMOVE ALL/Field #197
    • updated pydicom dependency from 2.1.1 to 2.2.2 #194
  • bug fix for exception when attempting to jitter DA/DT which cannot be jittered (space) [#189] (#189) (0.2.27)
  • adding support to manipulate file meta #183 (0.2.26)
  • updated pydicom dependency from 1.3.0 to 2.1.1 #171 (0.2.25)
    • bug fix for multivalued fields in %values lists #174
    • allowing other VR types for jitter #175
    • ensuring that an add/replace of an existing value is also updated in fields #173
  • change to correct issue with deidentifying RGB images #165 (0.2.24)
  • removing verbosity of debug logger (0.2.23)
  • changing iteration technique through fields to properly add nested uids #153 (0.2.22)
    • change to return results from detect when recipe does not contain filters #155
  • fix to correct bug in detect #142 (0.2.21)
  • fixes to detect and clean to better represent keep/coordinates (0.2.20)
  • modify default VR for added tags #146, bug with private tags in %fields section #147 (0.2.19)
  • adding keepcoordinates to allow for reverse specified coordinates (0.2.18)
  • bug with empty values within %values sections #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 (0.2.15)
  • nested sequence in replace_identifiers/strip_sequences bug #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 (0.1.29)
  • bumping pydicom to 1.2.0 #91 (0.1.28)
  • header expansions starts with and ends with should support regular expression OR (|) #89 (0.1.27)
  • added all, allexcept, contains to field filters #87 (0.1.26)
  • fixing bug in jitter timestamp function #85 (0.1.25)
  • installation order of pydicom / matplotlib changes default python #81 (0.1.23)
  • updating deid.dicom with contribution from @fimafurman #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 (0.1.1)

additions

  • 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. creation
  • this is the initial creation of deid, including recipes for cleaning of image headers and flagging of potential phi in pixels.