Notebook Entry

AIO for October 14, 2014

Last week's accomplishments

Objectives from last week:

Walking System ID

  • [1 hr, Done 0.7 hr] Read Manoj's recent paper.
    • The paper was ok, nothing revolutionary. They basically found linear correlatiosn between the current state of the hip and the next placement of the foot to try to suppor the theory that we balance by placing our foot based on feedback.

Inverted Pendulum Paper

  • [1 hr, Done 1.2 hr] Discuss paper direction with Ton.
    • Going to move the paper premise to a direct approach comparison to the indirect approach using direct collocation.
  • [1 hr, Done 0.8 hr] Implement the first example in the Betts et.al 2003 paper.
    • I had to do a little "hack" to deal with the explicit time and it doesn't handle the difference in nodes vs measurement samples as elegantly as Betts et. al but it works fine with the backwards Euler integration. See: betts2003.py.
  • [2 hr, Done 5 hr] Implement the Kuo standing model for the paper.
    • See park2004.py. Park et. al don't explain their model in detail enough to reproduce it exactly, so I made it similar. It is basically a two link version of the PyDy tutorial with base acceleration as an input.
  • [0.5 hr, Done 1.3 hr] Get the numerical values of the human model to match Kuo.
    • Park et. al don't seem to provide the numerical values of the body segment parameters in their paper, so I am making use of the output from my yeadon software with measurements from my body.
  • [3 hr, Done-ish 3.3] Get two relevant sympy prs into sympy.

Walking Data Paper

  • [0.5 hr, Done 0.1 hr] Decide what will and will not be published data.
    • I'm only going to share the "raw" data and the GATK software but include plots of processed data in the paper. See this Issue #2.

Bicycle Steer Torque Paper

  • [4 hr, Done 7.4 hr] Update BicycleParameters to work with the latest Yeadon and uncertainties 2+.
    • BicycleParameters 0.2.0 was released and now works with pinned dependencies and supports the newer versions of Yeadon and uncertainties.
    • A sample raw data set that can be used with BicycleParameters was prepared and released to Figshare.
  • [2 hr, Done 2.6 hr] Go through Mont's review, fix minor stuff, and prioritize larger changes.
    • Mont revised the paper and raised some issues. I spoke with him,took notes, and merged in his changes. See the steer torque manuscript repository for details.

Bicycle Data Paper

  • [3 hr, Done 3 hr] Update BicycleDataProcessor to work with latest DTK, BicycleParameters, and PyTables.
    • I made the first release (0.1.0) of the BicycleDataProcessor along with instructions to use it with the datasets shared on Figshare. See below.
  • [0.5 hr, Done 6 hr] Create a raw data H5 file for upload to Zenodo.
    • This ended up taking longer than expected, but I packaged all of the necessary raw data from the bicycle system id experiements and it is now available on Figshare. [Dataset 1], [Dataset 2], [Dataset 3], and [Dataset 4].
  • [1 hr, 1.4 hr] Create a raw and processed data H5 file (no filtering) for upload to Zenodo.
    • I prepared this file which ended up being 550 mb (compressed with bzip2) and it is too large to upload to Figshare (limit is 500 mb). Zenodo will accept it but they have a bug in their upload system and are looking into it.

Other stuff I did:

  • [1.5 hr] Watched an excellent talk by Gentry Lee at the Clinic.
  • [2.7 hr] Attende both of Jeff Speck's talks at CSU, which were also excellent.
  • [0.5 hr] Delt with trying to get the data from our old biosport website.
  • [0.5 hr] Wrote a SymPy wiki page for new contributors.

Last week's issues

I spent too much time on getting the bicycle data and software finalized and neglected some of my other objectives. The following objectices were not completed due to poor time management.

Inverted Pendulum Paper

  • [5 hr] Finish implementing the Ackermann 2010 example.
  • [4 hr] Implement process noise, measurement noise (both on states and torques), and perturbation accelerations.
  • [0.25 hr] Email Samin to inquire about co-authorship.
  • [1 hr] Rework the outline to reflect Ton and my discussion.
  • [0.5 hr] Obtain examples of process noise levels that will produce nominal wiggly human motion.
  • I'm having an issue with class attributes that are mutable with super and subclasses in my SymPy PR for dealing with reserved words in the C language.
  • The symbolic derivatives for the walking model are currently given real and imaginary parts. I need to investigate that more, it may be as simple as setting some variables to be real and/or positive.

Walking Data Paper

  • [1 hr] Describe the GaitAnalysisToolkit DFlow data and it's output.
  • [1 hr] Write a closing paragraph.
  • [1 hr] Decide on what plots to show that display the nature of the data and add to the outline.

Bicycle Steer Torque Paper

  • [2 hr] Use seaborn to improve the matplotlib plots.

Bicycle Data Paper

  • Zenodo has a bug and it will not let you upload large files. Their limit for file size is supposedly 2 GB per file. Their developers are looking in to it. I may be able to upload all of the walking data to Zenodo in one file if their limit is actually 2 GB, otherwise I've written a script to package the data into multiple files.

Other

  • [2 hr] Send ENG 4 teaching materials to Yuri.

This week's objectives

Inverted Pendulum Paper

  • [1 hr] Finish SymPy reserved words PR.
  • [5 hr] Implement simulation with process noise, measurement noise (both on states and torques), and perturbation accelerations.
  • [1 hr] Rework the outline to reflect Ton and my discussion.
  • [5 hr] Finish implementing the Ackermann 2010 example.
  • [0.25 hr] Email Samin to inquire about co-authorship.
  • [1 hr] Decide on specific figures to include.

Walking Data Paper

  • [1 hr] Describe the GaitAnalysisToolkit DFlow data and it's output.
  • [1 hr] Write a closing paragraph.
  • [1 hr] Decide on what plots to show that display the nature of the data and add to the outline.
  • [4 hr] Create the plots for the paper.

Bicycle Steer Torque Paper

  • [5 hr] Go over Mont's commments and fix them.
  • [2 hr] Use seaborn to improve the matplotlib histogram plots.

Bicycle Data Paper

  • [2 hr] Write section describing the instrumentation.
  • [2 hr] Write section describing the experiments.
  • [1 hr] Decide on figures in the paper.

Other

  • [2 hr] Send ENG 4 teaching materials to Yuri.
  • [2 hr] Setup my old website so the pedal desk students can access the information.
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