Changelog

List of changes in-between Shape-Out releases.

version 0.9.9

  • fix: change the way measurements are recognized (.rtdc files were falsely grouped together when located in the same directory) (#262)

version 0.9.8

  • fix: regression in polygon filter creation (event images not shown on hover) (#260)

version 0.9.7

  • fix: batch statistical analysis used one measurement per folder (#252)
  • fix: redrawing-issues of control panels (#253)
  • docs: minor update
  • setup: bump dclab from 0.14.7 to 0.18.0

version 0.9.6

  • enh: improved support for tdms data (dclab 0.12.0 -> 0.14.7) (e.g. #249)
  • enh: write Shape-Out version to exported .fcs and .tsv files (#250)
  • fix: remove nan/inf values before performing (g)lmm analysis (#248)
  • docs: request citation of Herbig2018 when performing (g)lmm analysis

version 0.9.5

  • fix: Allow to open measurement files that do not contain the features “area_um” or “deform” (#245)
  • fix: Hide unused fluorescence trace line plots
  • fix: Draw median trace data on top of raw trace data
  • enh: Display session name in window title
  • enh: Allow to hide raw fluorescence trace data

version 0.9.4

  • fix: Wrong image/trace data shown for a selected event in the scatter plot when working on a log-scale (#244)
  • enh: minor speed-up when working with hierarchy children and exporting the ‘contour’ feature (dclab 0.11.0)

version 0.9.3

  • enh: Allow to select colormap (#239)
  • fix: dclab 0.10.4 workaround for defective feature in Shape-In versions 2.0.6 and 2.0.7 (#241)
  • setup: remove pinning of numpy (works again on Ubuntu 18.04)

version 0.9.2

  • Allow to set contour levels at quantiles instead of KDE fractions (#180)
  • Allow to manually select contour levels
  • Log-scale contour plots are now available (#231)
  • Pin numpy version to <=1.13.0 to prevent ValueError caused by chaco testing whether an array object is contained in another object
  • Bugfixes:
    • Log-scale scatter plots did not show log-scale KDE data (#231)
    • Contour lines were shifted by a small amount due to an uncommon interpretation of contour plots in chaco (contour lines are now computed by dclab using the marching squares algorithm implemented in skimage)
    • Bad indexing in exported .rtdc datasets made it impossible to browse the video data (dclab 0.10.2)

version 0.9.1

  • Add tooltips for box filter settings
  • Rename Statistical analysis to Statistical summary in batch menu
  • Add link to documentation in help menu
  • Major documentation update
  • Bugfixes:
    • Remove temporary session-save directory when autosaving fails due to nonexisting analysis
    • Several minor fixes in dclab 0.9.1

version 0.9.0

  • Introduce new online documentation at http://shapeout.readthedocs.io
  • Consistently use the term Shape-Out
  • Code cleanup and compatibility with dclab 0.8.0
  • Enhancements:
    • Order input fields in measurement browser according to measurement number (#229)
    • Support new features “temperature” and “ambient temperature” (dclab 0.9.0)
  • Bugfixes:
    • Displaying the contour of .rtdc files that do not contain the “mask” feature resulted in an error.
    • ValueError in settings.py when stored data does not contain a key-value pair or when the value is missing.
    • IndexError when clicking on an event that has no image data
    • When the titles of all measurements are identical, the measurement selection in the combobox does not have any effect on the displayed measurement when creating a new polygon filter.
    • Possible errors when loading sessions containing empty datasets

version 0.8.8

  • Bugfixes:
    • “Mean of empty slice” error when attempting to plot bad data
  • New ancillary features in expert mode:
    • Principal inertia ratio (dclab 0.6.3.dev1)
    • Absolute tilt of raw contour (dclab 0.6.3.dev2)
  • Add computation of Young’s modulus for water medium (dclab 0.6.3.dev14)
  • Show fluorescence metadata in Information tab
  • Display data paths as tool tip in title editor (Contour Plot tab) (#227)

version 0.8.7

  • Bugfixes:
    • Search for missing datasets was falsely extended to directories not chosen by the user
    • Add recording date/time tooltip in the analysis tab to avoid ambiguities (#223)
    • Allow arbitrary number of repetitions for mixed model analysis with a spin control (#222)
    • Setting the treatment to “None” for (g)lmm analysis did not exclude it from the analysis, but introduced it as a different treatment (#224)
    • Channel width not correctly identified for old tdms files (dclab 0.6.2.dev7)
    • Do not draw isoelastics in contour plot if measurements have different channel widths
  • Automatically identify treatment and repetition for mixed model analysis (#222)
  • Automated release to PyPI with appveyor
  • Begin migration of docs to sphinx/readthedocs.org

version 0.8.6

  • Refactoring:
    • Use pathlib instead of os.path for
      • All session handling/conversion tasks
      • Configuration file management
      • Measurement/Analysis management
    • Support all changes to dclab.definitions (dclab 0.4.0)
    • Support all changes to dclab.features (dclab 0.5.0)
  • Bugfixes:
    • Opening sessions containing paths to data with a hash “#” failed
    • AttributeError during autosave when no measurement data is available
    • Exporting to .fcs files failed due to NaN-valued events; Events containing NaN values are now ignored (fcswrite 0.1.3.dev22) (#215)
    • Improve displayed float values for selected configuration keys (#216)
    • Unicode error when searching for data sets on disk (#218)
    • Unicode error when performing LMM analysis on some setups (#217)
    • IndexError when obtaining meta data from previous, broken analysis
    • KeyError when starting a new analysis with unavailable plotting axes
    • Ignore broken .rtdc data files

version 0.8.5

  • Update plotting range when switching to log scale (#198)
  • Allow to fix plotting range to retain previous behavior (#198)
  • Initial plotting range is determined from min/max values of all plots (#213)
  • Improved standard contour and kde accuracies using Doane’s formula (#147)
  • Bugfixes:
    • Support opening tdms files with capitalized “userDef” column names (dclab dclab 0.3.2.dev5) (#212)
    • Wx colors and chaco not compatible anymore (Windows appveyor build)
  • Refactoring:
    • Use pathlib when saving and opening sessions and do not use os.chdir

version 0.8.4

  • Add pixelation-corrected numerical and analytical isoelastics (#203)
  • Update emodulus look-up table (dclab 0.3.1.dev3) (#202)
  • Improved handling of polygon filters (partly #95)
  • Updated R version to 3.2.5 due to build errors
  • Bugfixes:
    • Young’s modulus computation is wrong due to faulty FEM simulations (dclab 0.3.1.dev20) (#207)
    • Image/trace panel shows wrong event when the mouse pointer hovers from one scatter plot to another
    • Hierarchy children: image, contour, and trace data were not displayed in the image/trace panel (dclab 0.3.1.dev1) (#100)
    • Hierarchy children did not support manual filters (dclab 0.3.1.dev2)
    • Regression: Setting plotting range manually not possible (#201)
    • Pixel size not read from tdms-based data (dclab 0.3.1.dev13) (#205)
    • “limit events” filtering must be integer not boolean (dclab 0.3.2.dev3) (#210)

version 0.8.3

  • Prefer sample name from para.ini over data folder name (dclab 0.3.0.dev15)
  • Support new .rtdc file format (dclab 0.3.0.dev20) (#151)
  • Bugfixes:
    • Automatically fix inverted plotting range
    • Enable scrolling in data export dialogs
    • Ignore missing features during data export
    • Plotting circularity with isoelastics failed (dclab 0.3.0.dev21) (#197)
    • Plotting errors with log-scale axes (#194, #195)
    • SHIFT+ENTER shortcut did not update filters
    • Fixed memory leak (#187)

version 0.8.2

  • Add fluorescence crosstalk correction (#185)
  • Bugfixes:
    • Regression: Session autosaving broken (#191)
    • Young’s modulus not updated (dclab 0.2.9.dev9) (#190)
    • UnicodeDecodeError on fcs-export (fcswrite 0.1.3.dev15) (#189)
    • Mouse cursor stuck in wait when plotting hierarchy data (#188)
  • Code cleanup:
    • Use the term “feature” consistently (dclab 0.2.9.dev2)
    • Use file format agnostic fluorescence trace keys (dclab 0.2.9.dev4)

version 0.8.1

  • Update internal configuration parameter names (dclab 0.2.8)
  • Cache event counts of tdms-based data sets on disk (#179)
  • Bugfixes:
    • KeyError when isoelastics not defined for combination of axes (#177)
    • Wrong channel width when loading ShapeIn 2.0.1 tdms data (dclab 0.2.9)

version 0.8.0

  • Remember directory for searching missing measurement data
  • Bugfixes:
    • Cannot open old session files with hierarchies when the measurement data location has changed (#174)
    • Cannot open polygon filters exported versions < 0.7.6 (#174)
  • Code cleanup:
    • Move program-relevant data to “shapeout” directory
    • Move computation of isoelastics to dclab (dclab 0.2.6.dev23)
    • Create separate directory for appveyor recipe
    • Remove unused/incomplete support for internationalization

version 0.7.9

  • Add on-the-fly computation of contour inertia ratios
  • Add menu options to save current event image (#164)
  • Bugfixes:
    • Isoelastics are not shown (#145)

version 0.7.8

  • Introduce unique identifiers for measurements (dclab 0.2.5.dev4)
  • Include ffmpeg in the Windows installer (#165)
  • Bugfixes:
    • dclab 0.2.6.dev2: Correctly identify contour files (#166, #169)
    • dclab 0.2.5.dev11: Allow contour data indices larger than uint8 (#167)
  • Refactoring:
    • dclab 0.2.5.dev10: Event images are returned as 2D ndarray

version 0.7.7

  • Add “Preferences” menu:
    • Allow to (dis/en)able session autosaving
    • Allow to (dis/en)able checking for updates
    • Allow to (dis/en)able expert mode (#157)
  • Bugfixes:
    • Hidden axes (“area_cvx”, “area_msd”, “frame”) visible in analysis tab
    • Display of fluorescence traces broken (#159)
    • Display of contour plots broken (#160)
    • Error when loading sessions created with version 0.7.6 on Windows
    • dclab 0.2.5.dev1: Automatically fix ancillary column sizes
    • dclab 0.2.5.dev2: Correctly distinguish b/w hierarchy children of same parent

version 0.7.6

  • Add on-the-fly computation of average and SD for brightness
  • Bugfixes:
    • Save sessions with deep (>1) hierarchies correctly
    • Better backwards compatibility for old session files
  • Refactoring (dclab 0.2.5):
    • New standard column names
    • New class for handling filtering
    • Minor speed-up when dealing with hierarchies

version 0.7.5

  • Move from OpenCV to imageio (#129)
  • Allow to select region and flow rate in batch processing (#132)
  • Allow to create an inverted copy of a polygon filter (#127)
  • Define new configuration file path with appdirs
  • Add on-the-fly computation of volume (dclab 0.2.3.dev23)
  • Change: Disable “remove invalid events” in filtering to avoid computation of ancillary columns (performance)

version 0.7.4

  • Add de-/select all buttons to Batch | Statistical analysis
  • Add de-/select all buttons to export all events data (#148)
  • Bugfixes:
    • Young’s modulus not computed in batch analysis (#149)
    • dclab 0.2.3.dev4: Loading old session files with polygon filters (#152)
    • Sessions saved with Windows cannot be opened on Linux (#153)
    • Regression: save button did not work

version 0.7.3

  • Add interface to calculate elastic modulus
  • Bugfixes:
    • Regression analysis not working for some Windows regional settings (#142)
    • Filters not applied when loading a session
    • Regression: Not possible to manually set plotting range
    • Excluded events were plotted despite downsampling limit
    • Support columns containing NaN and infinite values
  • dclab 0.2.3:
    • Add filtering option “remove invalid events” to remove nan/inf
    • Add methods to compute elastic modulus
  • fcswrite 0.1.3.dev6
    • Range for fluorescence data is always 2**15
    • Range for Deformation/Circularity is 100 or 1.0

version 0.7.2

  • Set histogram-based kernel density estimator as default (#133)
  • Regression analysis:
    • Added generalized linear mixed effects model (#126)
    • Remember treatment and repetition for each measurement (#134)
  • Bugfixes:
    • Same default location for find/add measurements dialogs (#139)
    • Opening saved sessions with more than nine data sets failed (#141)

version 0.7.1

  • Improved speed by optimization of GUI functions
  • Hash checks: Replace exception with a user-friendly warning (#128)
  • Change: Renamed config key “kde multivariate” to “kde accuracy”
  • Bugfixes:
    • Contour plot displays unused contour accuracy parameters
    • Persistent busy cursor when trace or video data is missing
    • Directory selections not always remembered correctly
  • dclab:
    • Add histogram-based kernel density estimator
    • Refactoring to improve code quality

version 0.7.0

  • Allow to rename polygon filters (#119)
  • dclab:
    • Traces are loaded lazily (on demand)
    • Add “Event index” column (#124)

version 0.6.9

  • Disable kernel density estimation and contour plot by default (#116)
  • Add avi export option
  • Bugfixes:
    • Fluorescence traces not shown for some data sets (#118)
    • Prefer the R package that is shipped with the executable over a system installation (#120)
    • Image plot and fluorescence traces were not always updated correctly
    • Regression: Contour plot offset by one frame in some cases (#121)
  • dclab:
    • Add user defined data fields 0…9
    • Add principal components 1 and 2
    • Change Cell size to Area

version 0.6.8

  • Speed-ups:
    • search for measurements (#113)
    • dclab 0.1.9.dev10: contour handling

version 0.6.7

  • Minimize memory usage for batch processing (#108)
  • Allow export to flow cytometry standard file format (#54)
  • dclab 0.1.9.dev2: add support for “User Defined” column in tdms files
  • dclab 0.1.9.dev7: compute default parameters for contours (#55, #110)

version 0.6.6

  • Hide unimportant data in Info tab (#102)
  • Disable/Enable controls dependent on values of other controls (#103)
  • Bugfixes:
    • Regression: Error when batch analysis started (#105, #106)
    • Contour error when plot contains no events (#104)

version 0.6.5

  • Sessions are now autosaved every 60s (#97)
  • Bugfixes:
    • Loading of sessions with hierarchy children failed (#99)
    • Reduced a memory leak for new analyses that resulted in frequent memory errors (should be less frequent now)

version 0.6.4

  • Bugfixes:
    • Batch analysis: Individual measurement parameters not preserved (#96)
    • Legend plot: >9 measurements cannot be displayed in legend at the same time. Introduced new config key “Legend Autoscaled” (#91)
  • New filter hierarchy allows to investigate subpopulations (#87, #63)
  • dclab
    • Add InertiaRatio and InertiaRatioRaw to tdms files (typo)

version 0.6.3

  • Bugfixes:
    • Regression: Excluded events plotted on top of filtered events (#86)
    • PDF plot export: Scatter inspector event highlighted (#92)
  • Implement differential (w.r.t. reservoir) linear-mixed models analysis with bootstrapping (#88)

version 0.6.2

  • Add batch filter processing
  • Move statistics computation to dclab (0.1.7.dev12):
    • New columns: “Flow rate”, “%-gated”
  • Bugfixes:
    • Windows: Saving session on different drive than data causes ValueError
    • Memory leak: Re-plotting scatter plots (ControlPanel.OnChangeFilter)
    • Handle plots where all events are filtered correctly
    • Scatter plots: False filtered events shown in gray
    • dclab (0.1.7.dev9): Faulty hashing strategy in RTDC_DataSet.GetDownSampledScatter
    • dclab:
      • Corrections/additions in definitions (fRT-DC)

version 0.6.1

  • Load session: Allow user to select missing data files (#80)
  • Sessions: Store relative paths in index file for user convenience (#80)
  • Bugfixes:
    • Setting order of plots not possible in Windows (#79)
    • Inability to search measurements due to broken data files (#81)

version 0.6.0

  • Compute mode in statistics tab using Freedman-Diaconis rule (#72)
  • Add channels: bounding box x- and y-size
  • Display number of events in measurement browser (#70)
  • Bugfixes:
    • “KeyError: ‘Plotting’” when filtering (#73)
    • “AttributeError” when plotting 2col 1row without legend (#76)

version 0.5.9

  • dclab add channel: distance between two first peaks
  • Allow logarithmic plot axes (#56)
  • Display fluorescence curve of events (#65)
  • Bugfixes:
    • OpenCV version 2 vs 3 variable name differences (CV_CAP…)
    • Gray dots in PDF export too large (#69)

version 0.5.8

  • dclab add fluorescence channels: peak area, peak position, number of peaks
  • dclab add position along channel axis from img
  • dclab (0.1.6.dev2): Allow to disable KDE computation
  • Allow to change order of plots (#51)
  • Implement indexing of events (#49)
  • Allow to exclude single events (#47)
  • Allow to show excluded events in scatter plot (#52)
  • Display cell images in the polygon selection window (#64)
  • Bugfixes:
    • Settings panel not redrawn in Ubuntu (#66)
    • Order of plots not reproduced from session (#51)
    • OpenCV version 2 vs 3 changes (#45)

version 0.5.7

  • Bugfixes:
    • Filtering: Plot selection resets to last item unexpectedly
    • User-defined titles were not saved in session
    • Remove ghost images of cells (#18)
    • dclab (0.1.5.dev13): Correct determination of video file
    • dclab (0.1.5.dev14): Multivariate KDE did not work
    • dclab (0.1.5.dev15): “Contour Fix Scale” did not work for Defo

version 0.5.6

  • Add menu option for data export (#22)
  • Add shortcut SHIFT+ENTER for “Apply” controls (#48)
  • Bugfixes:
    • Define “Video Frame Offset” parameter to correctly index frames (#46)

version 0.5.5

  • Bugfixes:
    • String formatter did not work (#40)
    • Regression in dclab<0.1.5 (#43)

version 0.5.4

  • Changes in dclab:
    • Support for 3-channel fluorescence data (add corrections 21:42)
    • Fix behaviour with empty columns (#1 dclab)

version 0.5.3

  • Fixes in dclab:
    • Use correct lateral position (from channel walls) (#37)
    • Compute aspect ratio according to elongation along flow (#38)
  • Allow to change thickness of contour lines (#34)
  • Display number of events in statistics tab (#35)
  • Improve visual representation in statistics tab

version 0.5.2

  • Bugfix: PDF export did not work (#33)
  • Fix disappearance of scrollbars upon hitting apply in controls

version 0.5.1

  • New logo (#25)
  • Bugfix: Analysis tab reset button (#30)
  • Display correct axis names in Plotting tab
  • Fix appveyor build script with pinning and downgrades

version 0.5.0

  • Include full R installation with lme4 package in Windows installer
  • Added Analysis tab for application of linear mixed-effects models (#15)
  • Allow individual polygon filters for each scatter plot
  • Bugfix: Changing filters did not update statistics tab (#24)

version 0.4.9

  • Bugfix: statistics panel head was in wrong order
  • Allow to fix contour plot scaling (#9)
  • Ordered parameters in control panels

version 0.4.8

  • New statistics tab (#6)
  • Minor improvements of GUI
  • Update from dclab: errors when using MV KDE (#20)

version 0.4.7

  • Fix loading of sessions (#17)

version 0.4.6

  • Limit number of events for data analysis (#11)
  • Automatically set number of events for multiple data sets (#11)
  • Display number of used events on plots (#10)