Changelog¶
List of changes in-between DryMass releases.
version 0.8.7¶
- setup: pin numpy<1.16.0 because of pinned scikit-image==0.14.0
version 0.8.6¶
- docs: minor improvements
- setup: pin scikit-image version again to 0.14.0 until the threshold_li issue is resolved once and for all
version 0.8.5¶
- docs: minor update
version 0.8.4¶
- enh: bump dependencies on qpformat, qpimage, and qpsphere
- improved file format support
- improved speed of in-memory operations
- several other minor fixes
- docs: minor cleanup
version 0.8.3¶
- enh: when using incomplete profile files, they are now merged with (instead of overriding) existing profiles (drymass.cfg) in the respective output directories (#27)
- docs: minor update
version 0.8.2¶
- fix: pin scikit-image version to 0.14.0 because threshold_li has changed (https://github.com/scikit-image/scikit-image/issues/3605)
- enh: implement “roi” configuration option “force” (#8)
- ref: replace default config values of nan with None (#13)
- ref: turn comments in definitions.py into real strings (#23)
- docs: add automation tutorial (usage of profiles and scripts)
version 0.8.1¶
- fix: replaced hack for plotting units with better solution due to incompatibility with tight_layout in matplotilb 3.0.2
version 0.8.0¶
- feat: implement profile management via dm_profile command and allow to select profiles via the “–profile” command-line argument in the command-line interface (#20)
- fix: if time is unknown, write “nan” instead of “0” to the output statistics file
- ref: explicitly use row-column coordinates in skimage’s regionprops (bump skimage version to 0.14.1)
version 0.7.3¶
- fix: do not create “_dm” results directory for root directory in recursive analysis mode (#19)
- docs:
- add DryMass logo
- update software description
version 0.7.2¶
- skipped
version 0.7.1¶
- maintenance release
version 0.6.2¶
- fix: regression in 0.6.0 ImageJ cannot open compressed hyperstack data; disabling compression for now (see #14)
version 0.6.1¶
- fix: MetaDataMissingError for some data types (qpformat 0.4.3)
version 0.6.0¶
- fix: error when removing ROIs that overlap with two ROIs in the background image
- feat: allow to exclude individual ROIs in drymass.cfg (#5)
- enh: improve error message verbosity
- enh: use compression for TIFF output
- enh: use new class for handling ROIs internally (#9)
- enh: start counting of ROIs and sensor images at 1 instead of 0 (#11)
- ref: handle ‘None’ values directly in config.ConfigFile
version 0.5.0¶
- feat: automatically extract meta data from QPImage/QPSeries data (qpformat 0.4.0)
- fix: setting “dist border px” to 0 still removed objects from border
- fix: scikit-image methods could not be used for “binary threshold”
- fix: set “image fix phase offset” to True by default, otherwise objects in the background cause a false offset
- improvement: optimize CLI plots
- docs:
- update tutorials with new CLI plots
- add tutorial for background correction (#3)
version 0.4.1:¶
- fix: extracted wrong phase image from SID4Bio data (qpformat 0.3.5)
version 0.4.0¶
- feat: ROI background correction supports masking of the imaged object via the “amplitude mask sphere” and “phase mask sphere” settings in the [bg] section.
- setup: support qpimage>=0.4.0
- tests: improve coverage
- docs: minor update (#7)
version 0.3.3¶
- ci: automate PyPI release with travis-ci
- setup: bump versions of dependent packages
version 0.3.2¶
- docs: update of introduction and minor changes
version 0.3.1¶
- bump version because of regression fixed in qpformat 0.2.1
- feat: flush statistics file during writing
version 0.3.0¶
- drop support for Python 3.5
- ref: background correction in convert.py uses background indices starting at 0 while the CLI keeps using indices starting at 1
- fix: hologram keyword arguments were not used for background correction
- fix: case where index-based background correction does not work
- feat: sphere analysis is picked up where left off in previous run
- command line interface:
- fix: allow white spaces for input data path argument
- fix: improve verbosity of status messages
- docs: add troubleshooting section
version 0.2.0¶
- feat: reuse computed ROI data from previous runs
- ref: update [roi] configuration key names to reflect pixel units: “dist border px”, “exclude overlap px”, “pad border px”
- fix: improve verbosity of error messages
- fix: config value “[roi] size variation” must be in interval [0,1]
- fix: handle ROIs with failed edge detection in “dm_analyze_sphere”
version 0.1.4¶
- feat: add local thresholding step before segmentation
- fix: check number of qpimages in sensor_data.h5 during dm_convert
- fix: “exclude overlap” only used for background image
- fix: not possible to analyze phasics data folder when raw data is present (qpformat 0.1.5)
version 0.1.3¶
- automatically fix inverted ranges when loading “roi_slices.txt”
- remove “holo” section from drymass.cfg if not relevant
- allow user-defined ROI selection via “[roi] enabled = False”
- added hologram analysis parameter tuning (qpimage 0.1.6)
- added 2D model fitting to sphere analysis (qpsphere 0.1.4)
- fixed cfg_funcs.int_or_str
version 0.1.2¶
- allow to disable sensor image tif export
- support input QPI data with different shapes
- fixed wrong assumption about definition of dry mass in cells (water vs. intracellular salt solution)
- allow to use separate file or series index for background correction with experimental data (#6)
- small visualization improvements
version 0.1.1¶
- add file name to image identifier and update plotting (#4)
- renamed “object” to “identifier” in statistics output
- binary-based background correction (manual or automated threshold)
- allow to disable background correction with “[bg] enabled = False”
- ask for missing meta data keys in CLI only when they are required
version 0.1.0¶
- initial release