List of changes in-between DryMass releases.

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 qpfromat 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 (
  • enh: implement “roi” configuration option “force” (#8)
  • ref: replace default config values of nan with None (#13)
  • ref: turn comments in 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 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