Changelog¶
List of changes in-between Shape-Out releases.
version 1.0.2¶
- setup: bump dclab from 0.20.1 to 0.21.1
version 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
version 0.9.7¶
version 0.9.6¶
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¶
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:
- 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¶
version 0.8.0¶
- Remember directory for searching missing measurement data
- Bugfixes:
- 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¶
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:
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:
- Bugfixes:
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¶
version 0.6.9¶
- Disable kernel density estimation and contour plot by default (#116)
- Add avi export option
- Bugfixes:
- dclab:
- Add user defined data fields 0…9
- Add principal components 1 and 2
- Change Cell size to Area
version 0.6.7¶
version 0.6.6¶
version 0.6.5¶
version 0.6.4¶
- Bugfixes:
- New filter hierarchy allows to investigate subpopulations (#87, #63)
- dclab
- Add InertiaRatio and InertiaRatioRaw to tdms files (typo)
version 0.6.3¶
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¶
version 0.6.0¶
version 0.5.9¶
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:
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¶
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¶
version 0.5.2¶
- Bugfix: PDF export did not work (#33)
- Fix disappearance of scrollbars upon hitting apply in controls
version 0.5.1¶
version 0.5.0¶
version 0.4.9¶
- Bugfix: statistics panel head was in wrong order
- Allow to fix contour plot scaling (#9)
- Ordered parameters in control panels