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
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