List of changes in-between Shape-Out releases.

version 2.16.0

  • feat: enable storage strategy (basin control) in export dialog (#159)

  • fix: ask for .tsv output path before computing statistics

  • enh: color feature data in QuickView combobox according to availability

  • enh: hide basinmap features in scatter plot selections (#159)

  • docs: remove reference to Shape-Out 1 in introduction

  • docs: mention basins and link to dclab (#159)

  • docs: add quick guide for data export

  • ref: reduce usage of dclab.dfn.scalar_feature_names (#108)

  • setup: bump dclab to 0.58.2

version 2.15.5

  • fix: right-click menu not working for plot widgets (#160)

  • ref: introduce FeatureComboBox class for listing features

version 2.15.4

  • fix: very small numbers not parsed when showing metadata (#158)

  • fix: do not allow question mark “?” in exported file names (#156)

  • fix: do not override files when exporting data (#153)

  • fix: remove the “so2exp” prefix when exporting data (#157)

version 2.15.3

  • build: PyInstaller to rebuild its bootloader (avoid false positive malware detection)

version 2.15.2

  • fix: handle zero-valued contour spacing

  • setup: bump dclab to 0.57.4 (handle zero-valued spacing for KDE contour)

version 2.15.1

  • fix: statistics not updating when changing plot axes (#154)

  • setup: bump dclab from 0.57.0 to 0.57.1

version 2.15.0

  • enh: avoid creating hierarchy when no filters are applied (speed)

  • enh: cache computed statistics

  • ref: avoid division-by-zero warning

  • setup: bump dclab from 0.56.3 to 0.57.0 (speed)

version 2.14.3

  • fix: intermediate plotting of first event whenever a slot is added

  • fix: catch zero-division warning when plotting empty image

  • enh: remember selected events in QuickView

  • enh: avoid showing first dataset event when user clicks in QuickView

  • setup: bump dclab from 0.55.7 to 0.56.3 (enhanced basin support)

version 2.14.2

  • setup: bump dclab from 0.55.6 to 0.55.7

version 2.14.1

  • fix: perform sanity check for contour spacing before plotting

  • fix: use pyqtgraph.SpinBox to edit box filters (#149)

  • enh: minor optimization of min/max feature algorithm

  • enh: only preselect innate features when computing statistics (#150)

  • setup: bump dclab to 0.55.6 (new scalar features, dcor access)

  • setup: bump pyqtgraph from 0.12.4 to 0.13.3

version 2.14.0

  • ref: don’t set RTDCBase.identifier to slot identifier

  • setup: drop support for Python 3.8

  • setup: bump dclab from 0.54.2 to 0.55.4 (better DCOR support)

  • build: use Python 3.10 for building executables

version 2.13.7

  • ci: fix rtd build pipeline

  • setup: bump dclab from 0.52.0 to 0.54.2 (improved basin support)

version 2.13.6

  • ci: fix Windows build pipeline

version 2.13.5

  • setup: bump requests to 2.31.0 (CVE-2023-32681)

  • setup: bump scipy to 1.10.0 (CVE-2023-25399)

  • setup: bump dclab from 0.50.4 to 0.52.0

version 2.13.4

  • tests: fix fake dataset creation

version 2.13.3

  • fix: casting error when using integer feature for plot color

  • fix: also export logs and tables to .rtdc with prefix “so2exp_”

  • enh: minor minimization in waiting times

  • ref: unify json dumps when saving sessions

  • setup: bump dclab from 0.48.4 to 0.50.4

version 2.13.2

  • docs: don’t build PDF on rtd (failed)

  • setup: bump dclab from 0.48.2 to 0.48.4 (don’t load invalid inertia ratio data from existing HDF5 files)

version 2.13.1

  • setup: bump dclab from 0.48.1 to 0.48.2 (improved speed, fixed bug with inertia ratio in long channels)

version 2.13.0

  • feat: support new viscosity model buyukurganci-2022 (#136)

  • enh: increase speed of QuickView event visualization

  • enh: turn on auto-apply in QuickView by default

  • setup: bump dclab from 0.47.2 to 0.48.1

version 2.12.0

  • feat: allow to disable KDE or use feature data as marker hue in QuickView

  • fix: do not perform auto-apply when changing downsampling value and downsampling is disabled in QuickView

  • fix: catch IndexError when trying to view an event that is not there anymore in polygon-selection-mode in QuickView

  • enh: make auto-apply in QuickView plot settings optional

  • docs: update screenshot scripts

version 2.11.11

  • enh: strip http(s):// from DCOR server string in settings

  • enh: improve GUI of QuickView (#133, #43)

  • setup: bump dclab from 0.47.0 to 0.47.2

version 2.11.10

  • fix: detect chaged files on disk when reloading metadata

  • setup: bump dclab from 0.46.4 to 0.47.0 (new bg_med feature and other convenience methods)

version 2.11.9

  • fix: include logs when exporting data (#126)

  • setup: bump dclab from 0.46.2 to 0.46.4 (new features)

version 2.11.8

  • setup: bump dclab from 0.45.0 to 0.46.2 (#132)

  • build: pin pyinstaller version to 5.3

  • ref: use hashobj from upstream dclab (#132)

version 2.11.7

  • build: fix build pipelines

version 2.11.6

  • setup: bump dclab from 0.43.0 to 0.45.0 (scalar feature support)

version 2.11.5

  • build: use InnoSetup “autopf” feature for installation directory

version 2.11.4

  • enh: preselect only innate features in data export to reduce computation time

  • docs: minor improvements

  • setup: bump dclab from 0.42.2 to 0.43.0 (improved compression)

  • setup: include zstandard library in distribution installer

version 2.11.3

  • setup: bump dclab from 0.42.1 to 0.42.2 (lazy-load .rtdc data which increases initial opening times)

  • setup: bump pyqtgraph from 0.12.3 to 0.12.4

version 2.11.2

  • setup: bump dclab from 0.42.0 to 0.42.1 (support background image access from DCOR)

version 2.11.1

  • fix: allow to specify 0.5 increments when filtering integer features (#123)

  • setup: bump dclab from 0.41.0 to 0.42.0

version 2.11.0

  • feat: allow to load encrypted dcor access tokens (#122)

  • setup: bump dclab from 0.39.17 to 0.41.0

  • setup: bump scipy to 1.8.0

  • build: bump Python version to 3.9

version 2.10.0

  • feat: export filter ray for each dataset via shortcut (#119)

  • setup: bump dclab from 0.39.15 to 0.39.17 (#118)

version 2.9.6

  • fix: extensions not loaded during startup on Windows (#117)

version 2.9.5

  • fix: polygon translation via drag-n-drop in polygon edit mode was not taken into account (#115)

  • enh: add (de-)select all button for lists in ComputeStatistics (#116)

  • enh: convert all selectable lists in dialogs to new BulkList class

  • setup: bump dclab from 0.39.13 to 0.39.15

version 2.9.4

  • enh: display session file name in window title

  • setup: drop support for older numpy versions

  • setup: bump dclab from 0.39.9 to 0.39.13 (fix visualization of the “ml_class” score when the ml_score features contain nans)

version 2.9.3

  • fix: implement closeEvent in main and ask user before exiting

  • fix: fix possible failure during update check

  • fix: show a message box when the R version is incompatible (#114)

  • ref: only reload R/lme4 information in preferences when the corresponding tab is selected to avoid preferences lock-up (#114)

  • tests: use hidden settings variable to skip asking the user to clear the session

  • setup: bump dclab from 0.39.5 to 0.39.9

version 2.9.2

  • setup: bump dclab from 0.39.3 to 0.39.5 (fix opening files with some online filter settings)

version 2.9.1

  • enh: add button “Find best spacing” in Plot tab in Analysis View that iteratively finds sane spacing values (#110)

  • enh: notify user in plot if contour spacing is too large (#110)

  • enh: add action to remove all datasets from a session (#97)

  • fix: mysterious behavior of subclassed pg.ColorBarItem (#109)

  • setup: bump dclab from 0.39.1 to 0.39.3 (increased verbosity, renamed feature labels, refactored DCOR access)

version 2.9.0

  • feat: add support for extensions in the form of loading dclab plugin and machine-learning features (#85)

  • setup: drop support for Python 3.7

  • setup: bump dclab from 0.37.2 to 0.39.1

version 2.8.1

  • fix: wrong scale for viscosity in bulk emodulus computation (#104)

  • fix: save unused polygon filters in sessions (#101)

  • fix: allow to delete polygon filters (#100)

  • setup: bump dclab from 0.37.0 to 0.37.2 (enhanced speed for operations involving contour computation)

version 2.8.0

  • BREAKING CHANGE: The volume feature in all previous versions was overestimated by about 2µm³. Please re-run your analysis pipeline.

  • setup: bump pyqtgraph from 0.12.2 to 0.12.3

  • setup: bump dclab from 0.36.1 to 0.37.0 (faulty volume computation)

version 2.7.4

  • setup: bump dclab from 0.35.6 to 0.36.1 (improved export speed)

version 2.7.3

  • build: remove console window (#102)

version 2.7.2

  • setup: bump dclab from 0.35.4 to 0.35.6 (Young’s modulus could not be computed in some cases)

version 2.7.1

  • enh: display online polygon filters in metadata tab (#94)

  • enh: show user configuration section in metadata tab (#86)

  • setup: bump dclab from 0.34.3 to 0.35.4

  • tests: change test data to avoid warnings in dclab 0.35.0

version 2.7.0

  • feat: accept DCOR drag events from DCOR-Aid data browser

version 2.6.9

  • fix: don’t reset color and name of dataset during duplicate matrix action (#96)

version 2.6.8

  • fix: adapt color scheme to work in dark mode (#92)

version 2.6.7

  • fix: correctly handle missing features on data export (#80)

  • ref: cleanup (default arguments and PyQt5 object references)

  • setup: bump dclab from 0.34.2 to 0.34.3 (set R_HOME)

  • build: bump rpy2 from 3.4.2 to 3.4.5

  • build: bump pyqtgraph from 0.12.1 to 0.12.2 and remove colorbar export workarounds

version 2.6.6

  • fix: false alarms about wrong pyqtgraph version on startup (removed the responsible code, because there are now more regular releases of pyqtgraph)

  • enh: allow passing session files, datasets, and filters via the command line (#88)

  • enh: associate the .so2 file format with Shape-Out on Windows (#88)

  • build: migrate to Inno Setup 6

  • ref: avoid pyqtgraph DeprecationWarning due to translate

version 2.6.5

  • fix: migrate to pg.ColorBarItem (with some manual patches from upstream) to resolve issues with SVG export (#87)

  • fix: units of viscosity is mPa*s (#91)

  • setup: bump pyqtgraph from 0.12.0 to 0.12.1

  • setup: bump dclab from 0.33.3 to 0.34.2

  • ci: fix build issues for macOS

version 2.6.4

  • fix: HTML-escape plot titles and axis labels (#82)

version 2.6.3

  • build: pin rpy2 to 3.4.2 on Windows (#84)

version 2.6.2

  • setup: migrate to pyqtgraph 0.12.0

  • setup: bump dclab from 0.33.1 to 0.33.3

  • docs: fix rtd build

version 2.6.1

version 2.6.0

  • feat: add background correction in quickview (#54)

  • fix: workaround for different plot widths due to title label (#33)

version 2.5.2

  • build: add pyinstaller hook for pyqtgraph

version 2.5.1

  • fix: preferences dialog did not open in macOS App bundle (#76)

  • enh: disable R settings in preferences dialog if rpy2 is missing

  • build: bump dclab from 0.29.1 to 0.32.4 (this should have happened in the 2.5.0 release which introduced R-lme4 analysis)

  • build: bump pyqtgraph to commit c1900 (post 0.11.1) which mainly improves plot export (#59)

  • tests: introduce manual tests that require a human in “tests-manual”

  • ref: key [calculation]: “emodulus model” is deprecated in dclab

  • ref: use “lut_identifier” instead of deprecated “method” keyword when retrieving isoelasticity lines

version 2.5.0

  • feat: implement linear-mixed effects models with R/lme4 (#55)

  • ci: overhauled build process

version 2.4.15

  • ci: fix rtd build

  • fix: typo in infobox in analysis view (#69)

  • fix: macOS builds did not use our pyqtgraph fork (reported in #70)

version 2.4.14

  • maintenance release

version 2.4.13

  • maintenance release

version 2.4.12

  • maintenance release

version 2.4.11

  • maintenance release

version 2.4.10

  • maintenance release

version 2.4.9

  • maintenance release

version 2.4.8

  • maintenance release

version 2.4.7

  • maintenance release

version 2.4.6

  • maintenance release

version 2.4.5

  • maintenance release

version 2.4.4

  • fix: box filters selections bled to other filters (#67)

  • build: do not use development version of dclab

  • ci: move to GitHub Actions

version 2.4.3

  • enh: improve UI (tooltips, icons)

  • build: Windows build won’t start due to breaking change in Windows ucrtbase.dll (#64)

  • build: Migrate Windows build to PyInstaller 4.1

version 2.4.2

  • fix: a regression introduced during refactoring in 2.4.0 made it impossible to select the temperature for known media

  • fix: allow to reorder the dataset list (#46)

  • enh: iconify buttons at top of Analysis View

version 2.4.1

  • fix: strip white-space characters from line edits in the preferences to avoid line breaks introduced in the API key via copy-paste

  • fix: not possible to create plots for datasets without the bright_avg feature; added a check for feature availability before updating the interface (#62)

version 2.4.0

  • feat: allow to set Young’s modulus parameters for all open datasets via the “Bulk action” menu (#60)

  • fix: force temperature for Young’s modulus computation to the value stored in the dataset for the “config” scenario

  • enh: update menu keyboard shortcuts

version 2.3.0

  • enh: added preferences dialog

  • enh: improved user experience for searching DCOR data

  • ref: migrate settings to QSettings

  • setup: remove appdirs dependency, because we let QSettings determine where to store settings

version 2.2.6

  • fix: support user-defined media introduced in dclab 0.29.1 (#53)

  • fix: porosity box filter precision at lower limit (#58)

  • docs: update bibliography

  • bump dclab from 0.29.0 to 0.29.1

version 2.2.5

  • setup: correct installation directory on Windows

  • setup: bump dclab from 0.27.11 to 0.29.0

  • fix: main window not focused after startup (#52)

version 2.2.4

  • fix: UI slot issues (probably a racing condition) in the analysis view; editing the viscosity for “other” medium not possible on frozen Windows and macOS application (#49)

version 2.2.3

  • fix: update Quick View plot when values for the Young’s modulus computation are changed (#44)

  • fix: use fixed point size in Block Matrix

  • enh: improve plot matrix column/row visualization and show flow rate (#45)

  • docs: update visualization of Young’s modulus look-up tables using new figure script from dclab

  • build: bump Python to 3.8 for Windows builds

  • setup: bump dclab from 0.27.5 to 0.27.11 (improvement of hierarchy child handling)

version 2.2.2

  • fix: correct box filter ranges when feature contains inf values

  • enh: add pretty tool icons from KDE breeze theme

version 2.2.1

  • fix: zero-division error when setting “one plot per dataset” for an empty plot (#41)

  • build: pin PyQt5 to 5.14.2 on Linux/macOS

version 2.2.0

  • setup: bump dclab from 0.26.2 to 0.27.5 (support for machine learning features)

  • fix: modify the GUI to enable box filtering for ml_score_??? features

  • ref: pipeline.get_features now only returns features that are available (previously all features were returned when no datasets were in the pipeline)

version 2.1.6

  • fix: export file names were allowed to have invalid characters

  • fix: Quick View showed filtered events that were not plotted (statistics were computed correctly though)

  • fix: Quick View was not very informative when all events were filtered away - a message is now shown

  • setup: bump dclab from 0.26.1 to 0.26.2 (fix bin num computation using Doane’s formula)

version 2.1.5

  • fix: marker hue feature data min/max was always computed even if not selected; for datasets without bright_avg (standard hue) this resulted in long waiting times

  • fix: avoid pyqtgraph error messages in pipeline plots by disabling hovering events (not used anyway)

  • fix: plot export did not work for single plots

  • fix: exported event images sometimes had wrong contrast

version 2.1.4

  • enh: add busy cursors wherever it seems fitting

  • setup: bump dclab from 0.24.7 to 0.26.1 (volume-deformation isoelasticity lines, improved DCOR caching)

version 2.1.3

  • fix: opening sessions did not work due to missing slot decorator

  • fix: in some cases the temperature/viscosity setting was not correctly written to the UI for individual slots when switching between slots with fundamentally different settings (e.g. channel and reservoir)

  • fix: KeyError when switching between slots with different temperature options

  • setup: bump dclab from 0.23.0 to 0.24.7 (equidistant isoelastics, faster polygon filtering, crosstalk correction failed due to improper configuration update since Shape-Out 2.1.1)

version 2.1.2

  • fix: ValueError when trying to compute contour spacing, because no datasets are selected for a plot

  • fix: coloring scatter plot by feature did not work when the feature contains nan values

  • fix: search path in session should not be filename but its directory

  • setup: bump dclab from 0.22.5 to 0.23.0 (possible HDF5 export issue)

version 2.1.1

  • fix: include private datasets when searching with DCOR API Key

  • fix: remove UI option to compute Young’s modulus for reservoir data (new “emodulus enabled” key in pipeline slot)

  • fix: Pipeline object not returned by session.open_session

  • setup: bump dclab from 0.22.1 to 0.22.5 (improve contour retrieval for mask images with artefacts, disable computation of Young’s modulus for reservoir measurements)

version 2.1.0

  • feat: basic DCOR support

  • fix: improved session support (older pre-release sessions)

  • docs: add DCOR guick guide

  • enh: export event image via context menu in Quick View (#35)

  • setup: bump dclab from 0.21.1 to 0.22.1 (DCOR support)

version 2.0.3

  • setup: bump dclab from 0.20.3 to 0.21.1

  • docs: add terminology section (#12)

version 2.0.2

  • fix: IndexError when removing a plot (#36)

  • fix: ValueError when filtering all events in Quick View (#37)

  • fix: TypeError when removing datasets and opening Quick View (#38)

  • fix: RuntimeError when removing datasets and opening Quick View (#38)

  • fix: ValueError when removing activated datasets and opening Quick View

version 2.0.1

  • fix: correctly distinguish prereleases when checking for new versions

  • enh: allow loading data via drag&drop

version 2.0.0

  • initial release