Skip to content
Commits on Source (12)
Show whitespace changes
Inline Side-by-side
CHANGELOG 0 → 100644
View file @ 8bded9ce
1.1.1
- Fix plotting error with LaTeX (thanks @toubol) (#179)
- Update documentation
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
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
1.0.0
- New confocal fitting models T+T+2D and T+T+3D
- Fix regression: .sin files could not be opened (#167)
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)
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
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)
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
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)
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)
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)
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
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
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)
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
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
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)
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)
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
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
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
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
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)
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)
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 "[]{}^"
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
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
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
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
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.
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.
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
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
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.
0.6.9
- Initital GitHub commit
\ No newline at end of file
ChangeLog.txt
View file @ 8bded9ce
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
1.0.0
- New confocal fitting models T+T+2D and T+T+3D
- Fix regression: .sin files could not be opened (#167)
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)
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
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
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
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)
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)
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)
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
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
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)
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
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
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)
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)
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
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
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
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
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)
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)
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 "[]{}^"
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
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
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
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
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.
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.
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
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
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.).
- Loading files that do not contain data a pointed out to the
user and the program continues with the other files.
- 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.
0.6.9
- Initital GitHub commit
1.1.0
- The changelog has moved. This file will be removed eventually,
but is kept to allow older versions of PyCorrFit to be notified
that a new version has been released.
MANIFEST.in
View file @ 8bded9ce
include ChangeLog.txt
include CHANGELOG
include LICENSE
include README.rst
recursive-include examples *.txt
recursive-include doc *.tex *.bib *.pdf *.md *.png *.svg
recursive-include docs *.py *.md *.txt *.rst *.bib *.gif *.jpg *.png
recursive-include tests *.py *.md
recursive-include pycorrfit *.py LICENCE README *.pyx
recursive-include pycorrfit LICENCE README
prune docs/_build
exclude docs/_version_save.py
README.rst
View file @ 8bded9ce
......@@ -3,35 +3,11 @@
|PyPI Version| |Build Status Win| |Build Status Travis| |Coverage Status|
A graphical fitting tool for fluorescence correlation spectroscopy (FCS) that comes with support for several file formats, can be applied to a large variety of problems, and attempts to be as user-friendly as possible. Some of the features are
- Averaging of curves
- Background correction
- Batch processing
- Overlay tool to identify outliers
- Fast simulation of model parameter behavior
- Session management
- User-defined model functions
- High quality plot export using LaTeX (bitmap or vector graphics)
Getting started
===============
Installation
------------
Installers for PyCorrFit are available at the `release page <https://github.com/FCS-analysis/PyCorrFit/releases>`__.
Documentation
-------------
A detailed documentation including an explanation of the graphical user interface and available model
functions is available as a `PDF file <https://github.com/FCS-analysis/PyCorrFit/wiki/PyCorrFit_doc.pdf>`__.
The documentation of PyCorrFit is available at https://pycorrfit.readthedocs.org.
Wiki
----
If you are interested in a specific topic or wish to contribute with your own HowTo, have a look at the
`PyCorrFit wiki <https://github.com/FCS-analysis/PyCorrFit/wiki/>`__. There you will also find information
on `how to write your own model functions <https://github.com/FCS-analysis/PyCorrFit/wiki/Writing-model-functions>`__.
Problems
--------
......@@ -39,56 +15,6 @@ If you find a bug or need help with a specific topic, do not hesitate to ask a q
at the `issues page <https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-new-issue>`__.
Advanced usage
--------------
If you have Python installed you can install PyCorrFit, including its scripting functionalities, from the Python package index:
::
pip install pycorrfit[GUI]
More information is available in the `PyCorrFit wiki <https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source>`__.
Information for developers
==========================
Running from source
-------------------
The easiest way to run PyCorrFit from source is to use
`Anaconda <http://continuum.io/downloads>`__. PyCorrFit requires wxPython which is not
available at the Python package index. Make sure you install a unicode version of wxPython.
Detailed installation instructions are `here <https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source>`__.
Contributing
------------
The main branch for developing PyCorrFit is *develop*. Small changes that do not
break anything can be submitted to this branch.
If you want to do big changes, please (fork ShapeOut and) create a separate branch,
e.g. ``my_new_feature_dev``, and create a pull-request to *develop* once you are done making
your changes.
Please make sure to also update the
`changelog <https://github.com/FCS-analysis/PyCorrFit/blob/develop/ChangeLog.txt>`__.
Tests
-----
PyCorrFit is tested using pytest. If you have the time, please write test
methods for your code and put them in the ``tests`` directory. You may
run the tests manually by issuing:
::
python setup.py test
Windows test binaries
---------------------
After each commit to the PyCorrFit repository, a binary installer is created
by `Appveyor <https://ci.appveyor.com/project/paulmueller/PyCorrFit>`__. Click
on a build and navigate to ``ARTIFACTS`` (upper right corner right under
the running time of the build). From there you can download the Windows installer of the commit.
.. |PyCorrFit| image:: https://raw.github.com/FCS-analysis/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png
.. |PyPI Version| image:: http://img.shields.io/pypi/v/PyCorrFit.svg
......
debian/changelog
View file @ 8bded9ce
pycorrfit (1.1.1+dfsg-1) UNRELEASED; urgency=medium
[ Steffen Moeller ]
* upstream/metadata RRID->SciCrunch
[ Andreas Tille ]
* Remove invalid fields
[ Alexandre Mestiashvili ]
* Add .readthedocs.yml to Files-Excluded list
* d/control:
- bump policy to 4.1.4
- bump debhelper to 11
- update VCS headers to point to salsa
- switch to python3
- add python3-dev, python3-wxgtk4.0 and python3-matplotlib to build-depends
* Update d/rules, use --with python3
* New upstream version 1.1.1+dfsg
* Update d/source/options to ignore pycorrfit/_version_save.py
* Drop obsoleted patch fix_entry_point_for_gui.patch
* TODO:
- Upstream requires scipy > 1.0.1
- Consider installing python modules to private_dir
-- Alexandre Mestiashvili <mestia@debian.org> Thu, 14 Jun 2018 11:41:50 +0200
pycorrfit (1.0.1+dfsg-2) unstable; urgency=medium
[ Steffen Moeller ]
......
debian/control
View file @ 8bded9ce
......@@ -4,47 +4,48 @@ Uploaders: Alexandre Mestiashvili <alex@biotec.tu-dresden.de>,
Andreas Tille <tille@debian.org>
Section: python
Priority: optional
Build-Depends: cython,
debhelper (>= 10),
Build-Depends: cython3,
debhelper (>= 11),
dh-python,
faketime,
imagemagick,
libpython2.7-dev,
librsvg2-bin,
python-all,
python-lmfit (>= 0.9.2),
python-numpy,
python-pytest,
python-pytest-runner,
python-setuptools,
python-simplejson,
python-urllib3,
python-yaml,
python3-all,
python3-dev,
python3-lmfit (>= 0.9.2),
python3-numpy,
python3-pytest,
python3-pytest-runner,
python3-setuptools,
python3-simplejson,
python3-urllib3,
python3-wxgtk4.0,
python3-yaml,
python3-matplotlib,
texlive-bibtex-extra,
texlive-extra-utils,
texlive-fonts-recommended,
texlive-latex-recommended,
texlive-latex-extra,
texlive-latex-recommended,
texlive-science
Standards-Version: 4.1.1
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pycorrfit.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/pycorrfit.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/pycorrfit
Vcs-Git: https://salsa.debian.org/med-team/pycorrfit.git
Homepage: http://fcs-analysis.github.io/PyCorrFit/
Package: pycorrfit
Architecture: any
Depends: python-matplotlib,
python-numpy,
python-scipy,
python-wxgtk3.0,
python-yaml,
Depends: python3-matplotlib,
python3-numpy,
python3-scipy,
python3-sympy,
python3-wxgtk4.0,
python3-yaml,
${misc:Depends},
${python:Depends},
${shlibs:Depends}
Recommends: dvipng,
python-sympy,
texlive-latex-base,
texlive-science
Recommends: dvipng, texlive-latex-base, texlive-science
Description: tool for fitting correlation curves on a logarithmic plot
PyCorrFit is a general-purpose FCS evaluation software that,
amongst other formats, supports the established Zeiss ConfoCor3 ~.fcs
......
debian/copyright
View file @ 8bded9ce
......@@ -6,6 +6,7 @@ Files-Excluded:
.appveyor/*
appveyor.yml
.gitignore
.readthedocs.yml
Files: *
Copyright: 2015 Paul Mueller <paul.mueller@biotec.tu-dresden.de>
......
debian/patches/fix_entry_point_for_gui.patch deleted 100644 → 0
View file @ 43a291fb
From: Alex Mestiashvili <mailatgoogl@gmail.com>
Origin: https://github.com/FCS-analysis/PyCorrFit/commit/6eb76e09b9418c57d14bd71e62ad7b64272c452b
Description: Fix pycorfit GUI start
--- pycorrfit.orig/setup.py
+++ pycorrfit/setup.py
@@ -122,7 +122,7 @@
tests_require=["pytest", "urllib3", "simplejson"],
# scripts
entry_points={
- "gui_scripts": ["{name:s}={name:s}:Main".format(
- **{"name":name})]
+ "gui_scripts": ["{name:s}={name:s}.gui.main:Main".format(
+ **{"name":name})]
}
)
debian/patches/series deleted 100644 → 0
View file @ 43a291fb
fix_entry_point_for_gui.patch
debian/rules
View file @ 8bded9ce
......@@ -17,7 +17,7 @@ PDFLATEX = pdflatex -synctex=1 -interaction=nonstopmode $(TEXDOC)
FAKETIME = faketime -f "$(DEB_DATE_RFC_3339)"
%:
dh $@ --with python2 --buildsystem=pybuild
dh $@ --with python3 --buildsystem=pybuild
override_dh_auto_clean:
touch doc/PyCorrFit_doc.pdf
......
debian/source/options
View file @ 8bded9ce
extend-diff-ignore="^doc/PyCorrFit_doc.pdf|^[^/]*[.]egg-info/|_version_save.py"
extend-diff-ignore="^doc/PyCorrFit_doc.pdf|^[^/]*[.]egg-info/|pycorrfit/_version_save.py"
docs/README.md 0 → 100644
View file @ 8bded9ce
PyCorrFit documentation
=======================
This is the new sphinx-based documentation of PyCorrFit which will replace
the LaTeX-based documentation eventually.
To install the requirements for building the documentation, run
pip install -r requirements.txt
To compile the documentation, run
sphinx-build . _build
Notes
=====
To view the sphinx inventory of PyCorrFit, run
python -m sphinx.ext.intersphinx 'http://pycorrfit.readthedocs.io/en/latest/objects.inv'
docs/conf.py 0 → 100644
View file @ 8bded9ce
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# PyCorrFit documentation build configuration file, created by
# sphinx-quickstart on Tue Sep 26 17:55:31 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# Get version number from PyCorrFit._version file
import mock
import os
import os.path as op
import sys
# include parent directory
pdir = op.dirname(op.dirname(op.abspath(__file__)))
sys.path.insert(0, pdir)
# include extenstions
sys.path.append(op.abspath('extensions'))
# Mock all dependencies
install_requires = ["lmfit", "numpy", "matplotlib", "pyyaml", "scipy",
"sympy", "simplejson", "wxPython"]
for mod_name in install_requires:
sys.modules[mod_name] = mock.Mock()
# http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order
# Order class attributes and functions in separate blocks
autodoc_member_order = 'bysource'
autodoc_mock_imports = install_requires
# Display link to GitHub repo instead of doc on rtfd
rst_prolog = """
:github_url: https://github.com/FCS-analysis/PyCorrFit
"""
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.intersphinx',
'sphinx.ext.mathjax',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'github_changelog',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = 'PyCorrFit'
copyright = '2014, Paul Müller'
author = 'Paul Müller'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
#
# The full version, including alpha/beta/rc tags.
# This gets 'version'
exec(open(op.join(pdir, "pycorrfit/_version.py")).read())
release = version #@UndefinedVariable
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'default'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
#html_static_path = ['_static']
# -- Options for HTMLHelp output ------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'PyCorrFitdoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'PyCorrFit.tex', 'PyCorrFit Documentation',
'Paul Müller', 'manual'),
]
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'PyCorrFit', 'PyCorrFit Documentation',
[author], 1)
]
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, project, project + ' Documentation',
author, project, 'Phase imaging analysis software.',
'Scientific'),
]
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {"python": ('https://docs.python.org/', None),
"numpy": ('http://docs.scipy.org/doc/numpy', None),
"scipy": ('https://docs.scipy.org/doc/scipy/reference/', None),
"lmfit": ('http://lmfit.github.io/lmfit-py/', None),
}
docs/extensions/github_changelog.py 0 → 100644
View file @ 8bded9ce
"""Display changelog with links to GitHub issues
Usage
-----
The directive
.. include_changelog:: ../CHANGELOG
adds the content of the changelog file into the current document.
References to GitHub issues are identified as "(#XY)" (with parentheses
and hash) and a link is inserted
https://github.com/RI-imaging/{PROJECT}/issues/{XY}
where PROJECT ist the `project` variable defined in conf.py.
"""
import io
import re
from docutils.statemachine import ViewList
from docutils.parsers.rst import Directive
from sphinx.util.nodes import nested_parse_with_titles
from docutils import nodes
class IncludeDirective(Directive):
required_arguments = 1
optional_arguments = 0
def run(self):
full_path = self.arguments[0]
project = self.state.document.settings.env.config.project
def insert_github_link(reobj):
line = reobj.string
instr = line[reobj.start():reobj.end()]
issue = instr.strip("#()")
link = "https://github.com/RI-imaging/{}/issues/".format(project)
rstlink = "(`#{issue} <{link}{issue}>`_)".format(issue=issue,
link=link)
return rstlink
with io.open(full_path, "r") as myfile:
text = myfile.readlines()
rst = []
for line in text:
line = line.strip("\n")
if line.startswith(" ") and line.strip().startswith("-"):
# list in list:
rst.append("")
if not line.startswith(" "):
rst.append("")
line = "version " + line
rst.append(line)
rst.append("-"*len(line))
elif not line.strip():
rst.append(line)
else:
line = re.sub(r"\(#[0-9]*\)", insert_github_link, line)
rst.append(line)
vl = ViewList(rst, "fakefile.rst")
# Create a node.
node = nodes.section()
node.document = self.state.document
# Parse the rst.
nested_parse_with_titles(self.state, vl, node)
return node.children
def setup(app):
app.add_directive('include_changelog', IncludeDirective)
return {'version': '0.1'} # identifies the version of our extension