Changelog¶
List of changes in-between PyCorrFit releases.
version 1.1.7¶
- docs: add sponsor links to contribute section
- docs: add gallery with all images in docs/gallery
version 1.1.6¶
- fix: improve support for Confocor FCS file format (see discussion in #37)
- ref: make pathlib.Path a standard in readfiles
- code cleanup
- drop support for Python<3.6
version 1.1.4¶
- maintenance release
version 1.1.3¶
- maintenance release
version 1.1.2¶
- ci: Automated release to PyPI with appveyor and travis-ci
- fix: support lmfit >= 0.9.11
version 1.1.0¶
version 1.0.1¶
- Improved support for ALV “.ASC” file format (#169)
- NumPy 0.13 support for “.ptu” file reader
- Code cleanup:
- Fetch latest available version from GitHub releases
- New dependency for “simplejson” Python package
- Move appveyor recipe to separate folder
version 1.0.0¶
- New confocal fitting models T+T+2D and T+T+3D
- Fix regression: .sin files could not be opened (#167)
version 0.9.9¶
version 0.9.8¶
version 0.9.7¶
- Second triplet time is now larger than first triplet time by default
- Remove a hack that causes a run through all pages e.g. when an average is created
- Bugfixes:
- Opening sessions with user-defined models
- Saving sessions with comments containing non-ASCII characters
- Windows build: Graphical plot export was misconfigured (added matplotlibrc patch in .spec file)
version 0.9.6¶
- Bugfixes:
- Fixed minor wx sizer problems for the tools
- Fixed ‘AttributeError’ in page.py if no weights are present
- New confocal fitting models (#111):
- 3D+3D, 2D+2D, 3D+2D; no triplet
- T+T+2D+2D, T+T+3D+2D; double triplet
- T+3D+3D+3D, T+3D+3D+2D (#40, #59)
- Under the hood:
- Separation of core and GUI modules
- Include tests in distributions for PyPI
- Improve automated testing on Windows and Mac OS
- More constraint options for fitting
version 0.9.5¶
version 0.9.4¶
version 0.9.3¶
- Fitting: migrate to lmfit
- This introduces a new dependency for building PyCorrFit. (e.g. in Debian, the package “python-lmfit” is required)
- Improved fitting behavior at parameter boundaries
- Removed “Polak-Ribiere” fitting algorithm
- Added “Sequential Linear Squares Programming” algorithm
- Heuristic fit (#109):
- Detect parameters that are stuck during fitting
- Fit each curve five times or less and check whether the fit converges.
- If two diffusion time parameter exist in a model, always make sure that one parameter is the larger one. This feature can currently not be disabled (#110).
- Allow infinity (“inf” and “-inf”) parameters for models and boundaries.
- New model: confocal T+T+3D+3D
- Bugfixes:
version 0.9.2¶
- Bugfixes:
- “Slider Simulation”/”Parm Range” broken (#133)
- Computation of average intensity did not work correctly for unequally spaced traces
- Update .pt3 reader to version 8399ff7401
- Import traces of .pt3 files (experimental, #118) Warning: Absolute values for intensity might be wrong
version 0.9.1¶
version 0.9.0¶
version 0.8.9¶
- Improved support for “ALV-7004” files (#104)
- Increase resolution for image export
- Load weights from PyCorrFit csv files
- Tool ‘Overlay Curves’: show cropped correlation curves
- Tool ‘Trace view’: increase size of window (#93)
- Tool ‘Global fitting’: remove forced, joint weights
- Session comment dialog: more intuitive behavior (#116)
- Improve plot export (#95)
- Bugfixes:
- Under the hood:
- Introduce new classes: Correlation, Fit, Trace
- Code cleanup and rewrite to support planned features
- In some cases support older versions of NumPy
version 0.8.8¶
- Improved support for “ALV-7004” files
- If you install the GUI with pip, you now need to include the ‘GUI’ requirement: ‘pip install pycorrfit[GUI]’. The GUI depends on matplotlib and wxPython which is not required for scripting with the pycorrfit module.
- Bugfix: missing version string on SuSe linux (#101)
- Under the hood:
- Python entry point script replaces “bin/” script
- Windows build system hosted by appveyor.com
- MacOS X build system hosted by travis-ci.org
- New builds use wxPython3 (#85)
- Unicode support without ‘reload(sys)’
- Error messages are more verbose
version 0.8.7¶
version 0.8.6¶
- Bugfix: Opening .fcs files with only one AC curve works now
- Zip files with measurements may now contain subfolders
- Improved pt3-file support from https://github.com/dwaithe/FCS_point_correlator (#89)
version 0.8.5¶
- Fixed bug that made it impossible to load data (#88)
- Exceptions are now handled by wxPython
- Under the hood:
- Pythonic repository structure
- Relative imports
- Windows build machine is now Windows 7
- Removed strict dependency on matplotlib
version 0.8.4¶
- Support for PicoQuant data file format Many thanks to Dominic Waithe (@dwaithe)
- Improved compatibility with Zeiss .fcs file format
- PyCorrFit is now dependent on Cython
- The module ‘openfile’ is now available from within Python
- Installer for Windows
version 0.8.3¶
- New .pcfs (PyCorrFit Session) file format (#60)
- Additional fitting algorithms: Nelder-Mead, BFGS, Powell, Polak-Ribiere (#71)
- Improvements
- Massive speed-up when working with large data sets (#77)
- Plot export: legend position and displayed parameters (#54)
- Average tool: traces may now start at time points != 0
- Statistics tool: display on smaller screens
- ALV data files: updated parser to identify curve types and segment traces
- Zeiss ConfoCor3 data files: some files could not be opened due to dummy AC curves
- Models: default parameters were changed to prevent unstable fits
- Software: notification dialogs for missing modules or other software
- Bugfixes
version 0.8.2¶
- The documentation has been thoroughly reworked
- The user is now warned if he does not have a TeX distribution installed
- Improvements:
- Complete support for installing PyCorrFit with virtualenv and pip (This is documented in the wiki)
- Statistics tool now displays average and SD (#43)
- Bugfix: TeX did not work on Ubuntu due to missing imports
version 0.8.1¶
- Thanks to Alex Mestiashvili for providing initial setup.py files and for debianizing PyCorrFit (@mestia)
- Thanks to Thomas Weidemann for his contributions to the documentation (@weidemann)
- Bugfixes
- Improvements of the user interface
- The menus have been reordered (#47, #50)
- The fitting panel has been optimized (#49)
- the slider simulation got a reset button (#51)
- The Help menu contains documentation and wiki (#56)
- Model functions that are somehow redundant have been removed from the menu, but are still supported
- The model doc strings were fully converted to Unicode
- Several text messages were modified for better coherence
- The background correction tool is more intuitive
- Statistics panel improvements (#43)
- Run information is included in the Data set title
- The page counter starts at “1” instead of “0” (#44)
- New handling of background correction (#46, #53)
version 0.8.0¶
version 0.7.9¶
- Support for Mac OSx
- Enhancements:
- Export file format (.csv) layout improved
- Model function info text in UTF-8
- Improved waring message when opening sessions from future versions
- New feature lets user set the range for the fitting parameters
- Bugfixes:
- Cleaned minor tracebacks and exceptions created by the frontend
- Mac version now works as expected, but .app bundling failed
- Latex plotting features now support more characters such as “[]{}^”
version 0.7.8¶
- Enhancements:
- Averages can now be calculated from user-selected pages
- Pages selected in the Overlay tool are now automatically set for computation of average and for global fitting
- Source pages are now displayed in average title
- Graph normalization with particle numbers is now possible
- Bugfixes:
- Errors during fitting with weights equal to zero
- Overlay tool displayed last curve after all pages have been removed
- Global fit did not work with weights
- Session saving now uses 20 digits accuracy
- CSV export is now using tab-delimited data for easier Excel-import
- Added version checking for session management
version 0.7.7¶
- Fixed: Tools windows could not be closed (or moved on MS Windows)
- Fixed: .csv export failed in some cases where no weights were used
- Enhancement: The user is now asked before a page is closed
- Enhancement: Tool “Page Info” and in exported .csv files, variables and values are now separated by a tab stop instead of a “=”
- Fixed: Opening a session with an empty page failed in some cases
- Fixed: Tool “Statistics” missed to output the column “filename/title” if that key value is empty - replaced empty strings with “NoName”
- Enhancement: Tool “Overlay” now asks the user to check kept curves instead of showing the curves to be removed
- Enhancement: Tool “Overlay” now has a “Cancel” button
version 0.7.6¶
- Improved handling
- Tools are now sorted according to a standard work-flow
- Renamed “Curve selection” to “Overlay tool” - this is more intuitive
- Tools will now stay open or may be opened when there are no open pages (#25)
- Filenames and runs are now displayed on each page (also added filename/title tag) (#23)
- Notebook: moved close button to each tab to prevent accidental closing of tabs
- Improved tool “Statistics” (#21)
- Fixed the case where “useless” data was produced - instead we write “NaN” data, removed warning message accordingly
- Row-wise ordering according to page numbers (#22)
- Column-wise ordering is now more intuitive (Fitted parameters with errors first)
- Some columns are now checked by default
- PyCorrFit remembers checked parameters for a page (not saved in session)
- Improved tool “Overlay” (#23)
- New feature: Overlay shows run number of each file (upon import), the run (or index) of an experimental file is unique to PyCorrFit
- Upon import, filenames and runs are displayed
- In a session, the filename/title is displayed
- Web address of PyCorrFit changed from “fcstools.dyndns.org/pycorrfit” to “pycorrfit.craban.de”
- Minor bugfixes: Batch control, Global fitting, import dialog
version 0.7.5¶
- Added model functions to documentation.
- Weights from fitting are now exported in .csv files.
- Rework of info panel for fitting
- Cleared unintuitive behavior of session saving: The fitting parameters were read from the frontend. This could have led to saving false fit meta data.
- During fitting, units are now displayed as “human readable” (#17).
- Slider simulation now also uses human readable units (#17).
- Secured support for Ubuntu 12.10 and 13.04
- Fixed: new line (n) characters for LaTeX plotting on Windows
version 0.7.4¶
- New tool: Colorful curve selection
- Import data: Curve selection possible
- Average: Crop average according to current page.
- Fixed: Page now displays Chi-squared of global fit.
- Fixed: Chi-squared and parameters of global fitting are now stored in sessions.
version 0.7.3¶
- Issue closed. External weights from averages saved in session (#11).
- Solved minor bugs
- Added estimation of errors of fit (Issue #12/#14)
- Fixed: Some .fcs files containing averages were not imported.
version 0.7.2¶
- Bugfix: Issue #10; we now have a goodness of the fit, if weighted fitting is performed
- Bugfix: Weights for fitting not properly calculated (sqrt(std)).
- Bugfix: Batch control IndexError with Info window opened
- Tool Statistics: Sort values according to page numbers
- Tool global: Added weighted fitting
- Residuals: According to weighted fitting, weighted residuals are plotted
- Average: Variances from averaging can be used for weighted fitting
version 0.7.1¶
- Feature: Added Python shell
- Bugfix: Saving image was not performed using WXAgg
- Bugfix: Notebook pages were drag’n’dropable
- Update function now works in its own thread
- Code cleanup: documentation of model functions
- Added program icon
version 0.7.0¶
- File import dialog was enhanced (#4, #5 - subsequently #7, #8):
- Now there is only one “load data” dialog in the file menu
- The model function is chosen for each type of data that is to be imported (AC, CC, etc.)
- Bugfix: Channel selection window causes crash on file import (#1).
- Bugfix: Hidden feature changes fixed parameters during fitting (#2).
- Feature: Convert TIR model function parameters lambda and NA to sigma (#3).
- Code cleanup: Opening data files is now handled internally differently.
version 0.6.9¶
- Initital GitHub commit