Changelog

List of changes in-between PyCorrFit releases.

version 1.1.8

  • docs: fix typo in legacy PDF (#195)

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 1.1.5

  • docs: fix build with recent version of latex (#191)

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 1.1.1

  • Fix plotting error with LaTeX (thanks @toubol) (#179)
  • Update documentation

version 1.1.0

  • BREAKING CHANGE: Move to Python3 (thanks @toubol) (#173)
  • GUI:
    • Add option in Preferences to automatically close tools after usage
    • Add keyboard shortcuts (thanks @toubol)
  • Fix entry point for GUI (#172)
  • Refactor several asserts into raises

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

  • Remove admin-requirement during install (Windows)
  • Support newer correlator.com .sin file format (experimental, #135)
  • Add smart progress dialog for fitting (#155)
  • Statistics: check “filename/title” by default (#151)
  • Documentation: fix bad LaTeX commands (#163)

version 0.9.8

  • Bugfixes:
    • Indexing error when saving sessions (#154)
    • Page number truncated in csv export (#159)
    • Export of csv files used incorrect normalization (#153)
    • Normalization parameter was not displayed in the ‘Info’ tool

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

  • Bugfixes
    • Closing the batch control window causes segfault bug (#142)
    • Closing page causes error when batch control is active (#143)
    • Plot normalization causes “Save Session” to fail (#144)
    • Plot normalization not loaded from session (#145)

version 0.9.4

  • Batch control allows to select individual parameters (#108)
  • Allow to exclude pages from batch fitting (#107)
  • Bugfixes:
    • Fix ‘ValueError’ in parameter display
    • Possibly fixed error with ‘yaml.safe_dump’ on Mac OSx 10.8.5
    • Make sure background is lower than signal (#137)

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:
    • Sessions saved with 64bit Windows were not opened (#136)
    • Old sessions and “KeyError: ‘chi2’”
    • Old session file extension was not recognized (#106)

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

  • Tool ‘Overlay curves’: improve UI (#117)
  • Tool ‘Statistics view’: improve UI (#113)
  • Tool ‘Trace view’: display countrate (#121)
  • Bugfixes:
    • Unicode errors in statistics tool (#131)
    • Load session errors with empty pages

version 0.9.0

  • Improve parameter display (#52, #114)
  • Display Chi2 on each page (#115)
  • The displayed Chi2-value for non-weighted fits is now normalized to the expected values of the fit. The documentation has been updated accordingly.
  • Add “All files” option in save dialogs (#97)
  • Improved plot export dialog (#99)

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:
    • Weighted fits at borders of fit interval were computed incorrectly due to integer division
    • Fitting algorithms did not work (#94)
    • Creating averages did not work (#123)
    • ASCII errors in statistics tool (#112)
  • 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

  • Removed unused fitting parameter d_eva from model 6022 and secured backwards compatibility.
  • Improved support for ALV700X (#92)
  • Bugfix: Corrected false display of Unicode characters on Windows
  • Under the hood:
    • Code cleanup with pyflakes
    • Repo cleanup (#98)

version 0.8.6

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
    • User could accidently clear a session (#65)
    • wxPython plotting problem on MacOSx (#64)
    • Statistics view: some parameters were duplicated (#76)
    • Caught zero-division warnings (models with triplet component)
    • Corrected x-axis scaling of statistics view and trace view

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
    • Some ConfoCor files were not imported
    • The cpp was not calculated correctly in case of background correction (#45)
    • Enabled averaging of single pages (#58)
    • Background correction for cross-correlation data is now computed (#46)
  • 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

  • Filename/title of each tab now shows up in the notebook (#39)
  • Statistics tool can plot parameters and page selection with the Overlay tool is possible (#31)

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