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CHANGELOG
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0.12.0
- feat: support new "raw-oah" and "raw-qlsi" file formats from qpformat
- enh: write FFTW wisdom to cache directory
- setup: bump qpformat from 0.13.1 to 0.14.0
- setup: bump qpimage from 0.8.5 to 0.9.1
- setup: bump qpretrieve from 0.2.2 to 0.2.8
0.11.0
- BREAKING CHANGE: handling folders in recursive mode changed slightly
- feat: improve metadata extraction from file formats where only
individual images contain metadata and global metadata per file
cannot be used (user is prompted in this case)
- enh: allow background correction with series data file by only
taking the first image (warning is still issued)
- enh: set the default method of sphere analysis to rytov-sc
- enh: reduce default verbosity for image fitting
- setup: bump qpformat from 0.10.6 to 0.13.0
- setup: bump qpimage from 0.6.2 to 0.8.4
- setup: bump qpsphere from 0.5.7 to 0.5.9
- setup: drop support for all Python versions below 3.9
- setup: add direct dependency on qpretrieve 0.2.2
- docs: update tutorials and documentation accordingly
0.10.6
- docs: update how-to-cite sections
0.10.5
- setup: migrate to GitHub actions
- setup: setup.py test is deprecated
- setup: pin tifffile to 2020.5.25 (moving target)
- tests: cleanup; fix tests on Windows
0.10.4
- setup: use tifffile directly to write images (scikit-image has no
externals module anymore)
- setup: bump qpformat from 0.10.4 to 0.10.6
- setup: bump qpimage from 0.6.1 to 0.6.2
0.10.3
- docs: update trouble-shooting section and cleanup design
0.10.2
- enh: display progress in percent when using the CLI
0.10.1
- setup: bump qpformat from 0.10.3 to 0.10.4
- setup: bump qpimage from 0.6.0 to 0.6.1
- setup: bump qpsphere frmo 0.5.5 to 0.5.7
0.10.0
- ref: migrate to scikit-image 0.16.1
0.9.4
- fix: correctly sort ignored ROIs in config
(previously used float-representation, now use version-representation)
0.9.3
- fix: correctly sort ignored ROIs in config
- enh: reuse fits from previous runs in "dm_analyze_sphere"
- enh: print number of reused fits in "dm_analyze_sphere"
- ref: changed convention for QPSeries and QPImage data identifiers
(QPSeries contains full trace of hashes, QPImage only contains
dataset hash, image index, and simulation type)
- docs: update tutorials (rerender figures and link to figshare data)
0.9.2
- fix: fitted phase images with the Rytov approximation sometimes
exhibited 2PI phase offsets (bump qpimage from 0.5.4 to 0.6.0)
0.9.1
- fix: skip sphere analysis when bad model parameters are detected
- fix: allow to force-regenerate the sphere analysis images file by
deleting it prior to running "dm_analyze_sphere"
- fix: do not plot profile in sphere analysis when the center position
not within the image data area
- setup: bump qpsphere from 0.5.3 to 0.5.4
- tests: fix failed test due to previous refactorization
0.9.0
- feat: allow to change the thresholding filter or use a manual threshold
- feat: new thresholding filter "dm-nuclei" designed for HL60 cell
nuclei segmentation
- fix: configuration file was "touched" even though it was only read
- setup: bump qpsphere from 0.5.2 to 0.5.3
- ref: increase verbosity of error messages when edge detection step
fails
- ref: new `threshold` submodule for all thresholding operations
0.8.8
- setup: bump qpformat from 0.10.2 to 0.10.3 (changes dataset identifiers)
- setup: bump qpsphere from 0.5.1 to 0.5.2
0.8.7
- setup: pin numpy<1.16.0 because of pinned scikit-image==0.14.0
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
0.8.5
- docs: minor update
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
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
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)
0.8.1
- fix: replaced hack for plotting units with better solution due
to incompatibility with tight_layout in matplotilb 3.0.2
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)
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
0.7.2
- skipped
0.7.1
- maintenance release
0.7.0
- feat: support recursive analysis with the "--recursive" command-line
argument (#15)
0.6.2
- fix: regression in 0.6.0 ImageJ cannot open compressed hyperstack data;
disabling compression for now (see #14)
0.6.1
- fix: MetaDataMissingError for some data types (qpformat 0.4.3)
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
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)
0.4.1:
- fix: extracted wrong phase image from SID4Bio data (qpformat 0.3.5)
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)
0.3.3
- ci: automate PyPI release with travis-ci
- setup: bump versions of dependent packages
0.3.2
- docs: update of introduction and minor changes
0.3.1
- bump version because of regression fixed in qpformat 0.2.1
- feat: flush statistics file during writing
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
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"
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)
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`
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
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
0.1.0
- initial release