Recent Releases of trackpy
trackpy - v0.6.2
trackpy v0.6.2 includes bug fixes, and compatibility fixes with newer dependency versions.
A special thanks to everyone who reported the issues fixed in this release!
Bug fixes
- Fixed an issue with feature-finding in 4D image sequences (@VeraMTitze, #739)
- Fixed a rare issue in which subtract_drift() with multiple particles resulted in a Pandas indexing error. (@kevin-duclos, #735)
Dependencies
- Adds official support for Python 3.12. (@caspervdw, #747)
- Adds support for latest Pandas, NumPy, and SciPy (@marcocaggioni, #740; @nkeim, #743, @vivarose and @rodrigo-j-goncalves, #742; @caspervdw, #747)
- Drops official support for Python 3.7 and earlier, NumPy 1.17 and earlier, Pandas 0.x, and SciPy 1.3 and earlier.
- Python
Published by nkeim about 2 years ago
trackpy - v0.6.1
trackpy v0.6.1 is functionally equivalent to v0.6.0. It is being released to fix an issue with Zenodo, so that this trackpy release has a citable DOI.
See the release notes for v0.6.0 for more information.
- Python
Published by nkeim about 3 years ago
trackpy - v0.6.1rc1
trackpy v0.6.1 is functionally equivalent to v0.6.0. It is being released to fix an issue with Zenodo, so that this trackpy release has a citable DOI.
See the release notes for v0.6.0 for more information.
- Python
Published by nkeim about 3 years ago
trackpy - v0.6.0
This release focuses on fixing bugs and some inconsistencies in the prediction capabilities. Some existing code that used prediction may now fail to run until a (minor) update is made.
This release includes contributions by @magnunor, @freemansw1, @crisp-snakey, @rbnvrw, @caspervdw, @tacaswell, and @nkeim.
Enhancements
- Linking can now use any
DistanceMetricclass from sklearn to compute distances (#692 by @freemansw1) - Several documentation fixes by @magnunor and @nkeim
API Changes
- When supplying an initial velocity guess to NearestVelocityPredict or DriftPredict, you must also supply the poscolumns argument to identify the names of the columns in your array. (For example, "poscolumns = ['y', 'x']".) Otherwise, creating the predictor will raise an exception that explains this change. If you provide poscolumns when creating the predictor, you do not have to supply it when subsequently using the linkdf() or linkdfiter() methods to link your features. (@nkeim, #710)
reconnect_traj_patch()is now available astrackpy.reconnect_traj_patchand is described in the API documentation. (@nkeim, #648)
Bug Fixes
- When linking with prediction, the predictor now correctly uses the same position columns as the linker, and correctly handles the pos_columns argument if specified. (@nkeim, #710)
- The link_df() method of predictor objects now works correctly. (@nkeim, #710)
Dependencies
- trackpy is now being tested in conda environments with Python 3.10.
- trackpy is no longer tested with Python 3.6.
- trackpy now requires the
looseversionpackage to work with newer scipy (@crisp-snakey, #706) - Much work on testing and packaging infrastructure by @tacaswell and @caspervdw
Note: This release is tagged v0.6.0.1 on GitHub to address an issue with Zenodo DOI generation. There are no other differences between the GitHub version and the v0.6.0 packages.
- Python
Published by nkeim about 3 years ago
trackpy - Trackpy v0.5.0
This is a major release focused on enhancements. Most notably, parallel processing is now turned on by default for “trackpy.batch” and “trackpy.locatebrightfieldring”, resulting in a large performance increase for many users. Another minor speedup changes the way in which particle numbers are generated, which may cause issues with reproducibility in some existing workflows (see “API Changes” below).
Note that Python 2 reached end-of-life in 2020, and it is no longer officially supported by trackpy. Also, trackpy dropped support for older NumPy, Scipy and Pandas. The current minimum requirements are: python>=3.6 numpy>=1.14 scipy>=1.1 pandas>=0.22.
See the "What's new in the package" page in the documentation for a full list of changes.
- Python
Published by caspervdw almost 5 years ago
trackpy - Trackpy v0.4.2
This is a minor release with two major new features: parallel processing to speed up feature-finding, and a new method for locating features in bright-field microscopy. There is also an overhaul of the walkthrough and other tutorials, and compatibility with the latest version of Pandas (0.25.1).
See the "What's new in the package" page in the documentation for a full list of changes.
- Python
Published by nkeim over 6 years ago
trackpy - Trackpy v0.4.1
This is a minor release with some important fixes. Additionally, PIMS is no longer a required dependency, which makes installation easier.
- Python
Published by caspervdw almost 8 years ago
trackpy - Trackpy v0.4
This is a major release that includes new choices for linking and feature-finding algorithms, as well as many performance increases and clean-ups. It is recommended for all trackpy users, but may require minor changes to existing code, as detailed below.
See http://soft-matter.github.io/trackpy/v0.4/whatsnew.html for a full overview of the changes.
- Python
Published by caspervdw almost 8 years ago
trackpy - Trackpy v0.3.3
This is the first trackpy release to support Python 3.6. It is identical to v0.3.2 except for a minor fix for Python 3.6 compatibility that does not change any scientific functionality.
- Python
Published by danielballan almost 9 years ago
trackpy - Trackpy v0.3.1
This release contains a number of bugfixes and enhancements: pair correlation functions, faster mean squared displacement calculations, and an increase of feature finding precision. See http://soft-matter.github.io/trackpy/v0.3.1/whatsnew.html for a full overview of the changes.
- Python
Published by caspervdw over 9 years ago
trackpy - Trackpy v0.3.0
This release is strongly recommended for all users, as it brings major improvements in speed and 3D feature-finding, and many other functionality and accuracy improvements.
Please be sure to read the "What's New" page in the documentation before upgrading, especially the item under "Enhancements" about calculating masses. You may have to make minor edits to your scripts and notebooks to use them with v0.3.
If you are an Anaconda user, upgrading is as simple as "conda update -c soft-matter trackpy". Other methods are shown on the Installation page in the documentation.
- Python
Published by nkeim over 10 years ago
trackpy - Trackpy v0.2.4
This is a simple maintenance release, introducing no functionality changes. The packaging and installation are simplified.
Henceforth, to install trackpy on any platform, we recommend conda install -c soft-matter trackpy, but pip install trackpy is also supported.
- Python
Published by danielballan over 11 years ago
trackpy - Trackpy v0.2.3
This release contains some important improvements, cleanup, and bug fixes:
- Compatibility with Python 3, official support for Python 2.7 and 3.4
- More efficient storage of frame-wise data in HDF format (~40X smaller files)
- Better-looking and more flexible annotate function for inspecting feature locations
- Cleaner installation and version-number handling (thanks, @leouieda )
- Various minor bug fixes
- Python
Published by danielballan over 11 years ago
trackpy - Trackpy v0.2.2
This is primarily a bugfix release. Changes include:
- Fixed bug in annotate when specifying a single threshold value.
- Added preliminary (passing) tests of 3D feature-identification capabilities.
- Fixed error in building API reference documentation.
- Removed ephemeral MANIFEST file from the distribution.
- Python
Published by nkeim over 11 years ago
trackpy - Trackpy v0.2.1
This release includes some enhancements, bug fixes, and cleanup:
- Enhancements and bug fixes to the new prediction framework
- Ability to use locate float-type image data (crucial for compatibility with the new PIMS release, v0.2)
- Faster access to on-disk framewise storage for streaming analysis
- Enhanced multi-color annotate
- Python
Published by danielballan over 11 years ago
trackpy - Trackpy v0.2
Version 0.2
The version contains significant enhancements, including:
- Much-improved feature-finding, merged from Daniel Allan's mr project (feature.py, replacing identification.py) with uncertainty estimation, along with tools for filtering, analyzing, and plotting trajectories
- Prediction framework for tracking particles whose motion is correlated between frames (Nathan Keim)
- KDTree-based linking, merged from Nathan Keim's branch of trackpy, which is 2X faster on typical data
- Numba-accelerated linking and feature-finding, falling back on pure Python if numba is not available
- Features for processing large data sets "out of core" (on disk)
- Access to different linking strategies through keyword arguments (Type help(link) or help(link_df) for details.)
- Simple, fast way to read and write data in files; easily extensible to formats used by individual research groups
- A set of examples and guides, provided separately
- Python
Published by danielballan almost 12 years ago