CHANGELOG

1.0.10
 - ci: Windows build not working since version 1.0.7, because of
   incompatible numpy versions during dclab build
1.0.9
 - fix: do not trust the "index" feature of a dataset to contain a
   correctly enumerated index (dclab<0.25.0 might have generated false
   values when joining datasets)
 - setup: bump dclab from 0.24.8 to 0.25.0
1.0.8
 - setup: bump dclab from 0.24.0 to 0.24.8 (faster polygon filtering)
1.0.7
 - setup: bump dclab from 0.22.5 to 0.24.0 (equidistant isoelasticity
   lines, slightly larger emodulus LUT)
 - setup: bump nptdms to 0.23.0
 - docs: build failed (#269)
1.0.6
 - fix: case-sensitivity issue when getting the chip region from
   an .rtdc file (#268)
1.0.5
 - fix: use UTF-8 encoding by default when dealing with text files (#267)
1.0.4
 - fix: minor issue with converting pos_y feature in sessions from
   before 0.7.6
 - setup: bump dclab from 0.21.1 to 0.22.5 (improve contour retrieval
   for mask images with artefacts, disable computation of Young's
   modulus for reservoir measurements)
1.0.3
 - fix: contour plot not possible (regression introduced in 1.0.1) (#265)
1.0.2
 - setup: bump dclab from 0.20.1 to 0.21.1
1.0.1
 - fix: MemoryError when plotting log-log data (#264)
1.0.0
 - fix: change the way measurements are recognized (.rtdc files were
   falsely grouped together when located in the same directory) (#262)
 - fix: automatic update did not include link to executable 
 - docs: rewrite section for LMM analysis
0.9.8
 - fix: regression in polygon filter creation (event images not shown
   on hover) (#260)
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
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
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
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)
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)
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)
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
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
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)
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
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
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
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)
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)
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)
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)
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
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)
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
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
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 
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)
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
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
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)
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
0.7.0
 - Allow to rename polygon filters (#119)
 - dclab:
   - Traces are loaded lazily (on demand)
   - Add "Event index" column (#124)
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
0.6.8
 - Speed-ups:
   - search for measurements (#113)
   - dclab 0.1.9.dev10: contour handling
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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
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)
0.5.5
 - Bugfixes:
   - String formatter did not work (#40)
   - Regression in dclab<0.1.5 (#43)
0.5.4
 - Changes in dclab:
   - Support for 3-channel fluorescence data (add corrections 21:42)
   - Fix behaviour with empty columns (#1 dclab)
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
0.5.2
 - Bugfix: PDF export did not work (#33)
 - Fix disappearance of scrollbars upon hitting apply in controls
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
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)
0.4.9
 - Bugfix: statistics panel head was in wrong order
 - Allow to fix contour plot scaling (#9)
 - Ordered parameters in control panels 
0.4.8
 - New statistics tab (#6)
 - Minor improvements of GUI
 - Update from dclab: errors when using MV KDE (#20)
0.4.7
 - Fix loading of sessions (#17)
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)