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.. py:module:: sdt

Change log

Generally, if the major version number was increased, there was an API break, so watch out for those!

18.2

18.1

18.0

17.5

17.4

17.3

17.2

17.1

  • Prevent performing flatfield correction multiple times in :py:class:`fret.SmFRETAnalyzer`
  • Localization algorithms now use frame numbers provided by :py:class:`io.ImageSequence`.
  • Fix edge handling and improve subpixel shift in py:mod:loc.cg. In particular, peaks close to image edges are ignored instead of (badly) guessing the missing data.

17.0

Older versions

16.1

16.0.2

  • Include Breeze icon theme's index.theme in build

16.0.1

  • Include QML files in build

16.0

15.2

15.1

  • Slightly increase tolerance on one test for CI

15.0

14.4

  • motion.MsdDist: Ensure proper assignment of MSDs/weights to components
  • fret.SmFretAnalyzer.bleach_step: Suport donor-only and acceptor-only samples

14.3.1 – 14.3.2

  • Fix tests for OSX and Windows
  • Use exclusively bundled slicerator

14.3

  • Include license files via setup.cfg

14.2

  • Publicly release under BSD 3-Clause license
  • Cleanups

14.1

  • Fix bug in :py:class:`fret.FrameSelector` which was triggered when the highest occuring frame number was divisible by the length of the excitation sequence.

14.0

13.4

  • Add a function to simulate Brownian motion to :py:mod:`sim`
  • Fix frame numbers (off by 1) and column names when loading ThunderSTORM single molecule data from CSV files
  • Add the :py:mod:`funcs` module, which implement step functions and eCDFs
  • Make the lmfit package an optional dependency
  • :py:func:`gaussian_fit.gaussian_2d`: Rotate mathematically positive
  • :py:class:`roi.PathROI`: Make sure that relative origin is not negative. Otherwise localization data will not fit the image data anymore, since for the latter the origin can never be negative. Fixes e.g. an issue with shifted localizations if the ROI in gui.locator is close to the image boundaries.

13.3

13.2

13.1

Bugfix release

  • Fix loading io.yaml on Windows, where there is no numpy.float128
  • Support ImageJ metadata in io.SdtTiffStack

13.0

12.0

11.1

  • Implement transforming PathROIs using chromatic.Corrector
  • Bug fixes
    • PathROI construction with no_noimage=True
    • Empty DataFrames in fret.SmFretData.track
    • Empty arrays in multicolor.find_colocalizations

11.0

  • Ability to tag features with near neighbors in localization data
  • For smFRET tracking, (optionally) use above feature to select only localizations that don't have any near neighbors, otherwise the brightness determination will yield bogus results.
  • Stop using :py:class:`pandas.Panel`. It has been deprecated in version 0.20. Use :py:class:`pandas.Panel` s with multi-indices for columns instead. This affects much of the :py:mod:`multicolor` and :py:mod:`fret` modules. This was used as an opportunity for more drastic redesigns of the data structures. (API break)
  • Move SDT-control specific stuff from :py:mod:`image_tools` as well as :py:mod:`pims` to the external micro_helpers package. Since locator depends on this, the whole sdt package depends on micro_helpers now. (API break)
  • Support .stk files in locator
  • Add ability to only return indices in :py:func:`multicolor.merge_channels`.
  • Allow for not dropping non-colocalized data in :py:func:`multicolor.find_colocalizations`.

10.3

  • Add the plot module. It contains
    • the density_scatter function. It produces scatter plots (supporting both matplotlib and bokeh) where data points are colored according to their density.
    • The NbColumnDataSource, which is a subclass of bokeh's ColumnDataSource, but its selected["1d"] attribute is updated even in jupyter notebooks. Starting with bokeh 0.12.5, this is obsolete however since bokeh now supports embedding bokeh apps in notebooks (via the function handler).
  • Remove unused and incomplete plots_viewer and sm_fret_viewer

10.2

  • Add classes for elliptical and rectangular path-based ROIs
  • Add an invert option to path-based ROIs
  • Implement YAML loaders and dumpers for various structures
  • Add fret module for analyzing single molecule FRET data
  • Make it possible to choose how to estimate the background in brightness.from_raw_image
  • Bug fixes

10.1

  • loc.daostorm_3d: Introduce size_range and min_distance parameters
  • loc.daostorm_3d: Allow for applying filters to the raw image data to increase the SNR for the feature finding process. Fitting is still done on the unmodified data.
  • locator: Rework the options UI to allow easy addition of new parameters.
  • Minor bug fixes

10.0

  • motion: Implement new find_immobilizations algorithm
  • locator: Use same default directory for all file dialogs
  • Port to qtpy 1.1
  • Add image.masks
  • Rename image_filter -> image.filters (API break)
  • brightness: Improve from_raw_image performance

9.0

  • Fix infinite loop in motion.find_immobilizations
  • Minor fixes in motion.find_immobilizations
  • Rename background -> image_filter since the module may at some point contain filters other than for background estimation. Also rename the individual filter functions (API break).
  • Add many tests (and/or make sure they are run).

8.0

  • Create background module for estimation and subtraction of background in fluorescence microscopy images. Unfortunately, there is no sphinx documentation yet since slicerator.pipeline does not work (yet) with sphinx autodoc.
  • Add motion.find_immobilizations to find immobilized sections of particle trajectories.
  • Fix an issue where NaNs where present in multicolor.find_codiffusion where they should not be.
  • Improve brightness.Distribution.__init__. It now accepts also lists of DataFrames (but no more lists of floats) and a new cam_eff parameter to account for camera photoconversion efficiency (API break).
  • Add unit tests for image_tools. In the course of this, some bugs were fixed, but also handling of ROI metadata in the sdt.pims classes changed; ROIs are now a list of dicts instead of a structured array (API break).

7.1

  • Introduce the multicolor module. This is a better version (faster, with tests) of the sm_fret module, which is now deprecated.
  • Minor fixes and improvements.

7.0

  • Fix chromatic.Corrector.__call__ when applied to Slicerator.
  • chromatic: Allow for using multiple files and files with multiple frames for calculation of the correction parameters in Corrector (slight API break: The feat1 and feat2 attributes are now lists of DataFrames, not plain DataFrames anymore.)
  • helper.singleton: Add a singleton type class decorator. Based on https://github.com/reyoung/singleton
  • Minor GUI and plotting tweaks
  • data, motion: Be more consistent with naming of things (e. g. use "lagt" everywhere and not also sometimes "tlag", make all variable names lower case, ...) (API break)
  • Fix crash in loc.daostorm_3d in images without localizations

6.1

  • Fix start-up of sdt.gui.locator on Windows

6.0

  • Add data.Filter class for filtering of single molecule microscopy data
  • Implement the "z" model in daostorm_3d for z position fitting (slight API break)
  • Create loc.z_fit with a class for z fit parameters and a fitter class for z positions from astigmatism
  • Better background handling in peak finding in daostorm_3d
  • sim: Allow for simultion of elliptical Gaussians (API break)

5.5

  • gui.locator: Add support for load options from file
  • brightness: Save information on how many data points were used

5.4

  • Improvements for gui.locator

5.3

  • Command line options for gui.locator
  • Add the sim module for Gaussian PSF simulation
  • Bug fixes

5.2

  • brightness: Add Distribution class

5.1

  • gui.locator: Fix saving settings on Qt4

5.0

  • Huge documentation update
  • Remove t_column, mass_column, etc. attributes (API break)
  • Change default method for motion.emsd_cdf to "lsq" (API break)
  • gaussian_fit: Rename guess_paramaters -> guess_parameters (API break)
  • beam_shape: Also correct the "signal" column (API break)

4.2

  • Add support for writing trc files

4.1

  • remove python-dateutil dependency

4.0

  • Support ROIs in loc.* locate/batch functions
  • Save additional metadata as YAML (previously it was JSON) with image_tools.save_as_tiff (API break)
  • Cosmetic overhaul of pims
  • Make pims load YAML metadata from TIFF files (API break)
  • Minor bug fixes

3.0

  • Use full affine transformation in chromatic. This also leads to a different save file format etc. (API break, file format break)
  • fix gui.chromatic accordingly

2.1

  • Fix race condition in gui.locator preview worker

2.0

  • Add PathROI in image_tools
  • Smaller improvements to gui.locator

1.0a1

First alpha release