Changelog
List of changes in-between DryMass releases.
version 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
version 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
version 0.10.6
docs: update how-to-cite sections
version 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
version 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
version 0.10.3
docs: update trouble-shooting section and cleanup design
version 0.10.2
enh: display progress in percent when using the CLI
version 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
version 0.10.0
ref: migrate to scikit-image 0.16.1
version 0.9.4
fix: correctly sort ignored ROIs in config (previously used float-representation, now use version-representation)
version 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)
version 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)
version 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
version 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
version 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
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 0.7.0
feat: support recursive analysis with the “–recursive” command-line argument (#15)
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