Update all example notebooks #44
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Updating the following: - image pixel values are now normalized - adjusting mass values (now scaled by 255) - more documentation links for functions that point to source code
Updating performance notebook: - trackpy version - mass numbers (from [0-255] to [0-1]) - profiling numbers
There have been no significant changes around how to use iPython parallel between iPython v 4.0 (summer 2015) and iPython v 6.2.1 (November 2017). The date and version mentioned in the instructions have been updated to reflect this fact. No other changes made - iPython parlallel code still works fine.
Adding a link to the ipython-parallel project. changes in timeit output just reflect changes in timeit module's output. Updating date and version numbers for ipython and ipython-parallel. No significant changes between iPython v 4.0 (summer 2015), in prior nb, and iPython v 6.2.1 (November 2017), in current nb. ipython-parallel code was tested out and still works fine.
…ples * 'master' of https://github.com/charlesreid1/trackpy-examples: Add ipython-parallel link and update date.
Adding links to HDF5 group's website (portal for "official" resources) and to trackpy source code (linking to where classes are defined when they are mentioned).
There were several outdated references to the pims API and classes that have since been renamed. These were not used in any notebook code, which is probably why they have not been updated.
As with other notebooks, the "mass" parameter here is unscaled, and changes to trackpy have made it a scaled quantity, so this fixes those values. The values were chosen to give results very close to the previous notebook version's results.
The scikit-image function threshold_adaptive() is deprecated and is accordingly replaced with threshold_local(). See [scikit-image 0.13.0 release notes](https://github.com/scikit-image/scikit-image/blob/28c3b436c84d1db640bd939c5628f5373172d05a/doc/release/release_0.13.rst), which mention that threshold_adaptive() is now deprecated.
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This pull request will be updated as follows:
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…diagnostics notebook.
…paper, remake images.
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Uncovered another issue while updating these notebooks - installing trackpy from pip implements a legacy |
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Wow, thanks for taking the time for do this @charlesreid1. I appreciate the granular commits.
The HTML will be automatically generated and push into the docs repo when this PR is merged, so no separate PR into the docs repo is needed. Thanks for the offer to present a more reviewable form. I'm content to build it locally and take a look. Will give this a detailed review today or tomorrow. |
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So sorry for letting this languish so long, @charlesreid1. Merging! |
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No problem. Thanks for the pull! |
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This pull request contains a substantial number of changes, but the substance of the notebooks has been preserved in each case. The main changes in this pull request are:
threshold_adaptive()function in scikit-image) and updated mentions of old versions of software (e.g., ipython-parallel)There are also cosmetic changes caused by changes to modules/libraries since the last time these notebooks were updated (e.g., output of
timeitcommands or ipython notebooks lacking a "collapsed" state).Please comment on anything that you have doubts about or wish to discuss. When you're okay with these updates and they've been merged, I would also be happy to export them to HTML, add them to the soft-matter.github.io trackpy page, and send a pull request for that repo as well.