Lecture 2 - HW1,numpy arrays, matplotlib, and git 2020.4.14 Review - - PowerPoint PPT Presentation

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Lecture 2 - HW1,numpy arrays, matplotlib, and git 2020.4.14 Review - - PowerPoint PPT Presentation

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Lecture 2 - HW1,numpy arrays, matplotlib, and git 2020.4.14 Review of Python Basics from Lecture 1 Topics from Lecture 1 Lists Strings, ints, floats Dicts Objects, attributes, methods (Tuples,) Functions {sets} Importing .py

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Lecture 2 - HW1,numpy arrays, matplotlib, and git

2020.4.14

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Review of Python Basics from Lecture 1

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Topics from Lecture 1

Lists Dicts (Tuples,) {sets} Strings, ints, floats Objects, attributes, methods Functions Importing .py files/libraries

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slides, hws, solutions are posted here: neuropython.com/calendar

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Recorded zoom lectures will be accessible via courseworks (more fun in real time though)

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HW1 Solutions

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Numpy Arrays (see slides)

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Plotting with Matplotlib (see slides)

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%matplotlib inline

  • sends png to browser
  • no panning or zooming
  • new figure for each cell
  • no changes to previous figures

%matplotlib notebook

  • interactivity in old notebook
  • doesn't work in jupyter lab
  • need to create separate figures
  • ability to update figures

%matplotlib widget

  • interactive widget
  • all figure features
  • need to create separate figures explicitly
  • ability to update figures
  • installation instructions: https://github.com/matplotlib/jupyter-matplotlib
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https://matplotlib.org/3.2.1/gallery/color/colormap_reference.html

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Matplotlib Resources

  • Matplotlib Tutorials: https://matplotlib.org/tutorials/
  • Matplotlib Gallery: http://matplotlib.org/gallery.html
  • Plotting commands summary:

http://matplotlib.org/api/pyplot_summary.html

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Fun Resource: https://serialmentor.com/dataviz/

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Use perceptually uniform colormaps 😲

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Don’t cut the vertical axis 😲

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https://seaborn.pydata.org/tutorial.html

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Break (5 mins)

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Version Control with git

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Why version control?

Nothing that is committed to version control is ever lost We have this record of who made what changes when Version control is the lab notebook of the digital world: it’s what professionals use to keep track of what they’ve done and to collaborate with other people. Every large software development project relies on it, and most programmers use it for their small jobs as well. And it isn’t just for software: books, papers, small data sets, and anything that changes over time or needs to be shared can and should be stored in a version control system

https://zuckermanbrain.github.io/git-novice/

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Why git specifically?

It is fast Work offline - decentralized, everything is on your local machine Can undo mistakes - almost every action in Git only adds data The cool kids are doing it

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https://xkcd.com/1597/

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Do not copy same code into every data folder 😲

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We seem to share a simultaneously naive but nonetheless tenable belief that we can “understand” or at least “interpret” how each cell-type processes information in the fruit fmy optic lobe.

paper_v0

... Experimental and theoretical methods and frameworks that have been discarded by vertebrate researchers are still treated with obeisance;

paper_v1 paper_v1_aggressive

... We are slaves to the myopic methods of the previous generation.

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... moving bars do a poor job of revealing the mysteries of V1, but they might just work for fmies; separation of RGCs into binary ON and OFF cells is equivocal at best, but the the fmy eye might just be that simple.

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We seem to share a simultaneously naive but nonetheless tenable belief that we can “understand” or at least “interpret” how each cell-type processes information in the fruit fmy optic lobe. Experimental and theoretical methods and frameworks that have been discarded by vertebrate researchers are still treated with obeisance; moving bars do a poor job of revealing the mysteries

  • f V1, but they might just work for fmies;

separation of RGCs into binary ON and OFF cells is equivocal at best, but the the fmy eye might just be that simple. The allure of an easily interpretable framework is too great to resist.

paper_v1_better2

... After all, how complicated can a fmy eye be?

paper_v1_better2_advisor

We seem to share a simultaneously naive but nonetheless tenable belief that we can “understand”

  • r at least “interpret” how each cell-type processes

information in the fruit fmy optic lobe. Experimental and theoretical methods and frameworks that have been discarded by vertebrate researchers are still treated with obeisance; moving bars do a poor job of revealing the mysteries of V1, but they might just work for fmies; separation of RGCs into binary ON and OFF cells is equivocal at best, but the the fmy eye might just be that simple. The allure of an easily interpretable framework is too great to resist. After all, how complicated can a fmy eye be?

paper_v1_better2_advisor_1

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git add git commit

HEAD master

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git add git commit

HEAD master

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HEAD master

git branch br1 git checkout br1

br1

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master br1 HEAD

git add git commit

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master

git checkout master

br1 HEAD

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master br1 HEAD

git branch br2

br2

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master br1 HEAD

git commit git add

br2

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br1

git checkout br2

br2 master HEAD

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br1

git add

br2 master HEAD

git commit

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br1

git add

master

git commit

br2 HEAD

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br1

git add

master

git commit

br2 HEAD

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br1 br2 master HEAD

git merge br2

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br1 br2 master HEAD

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git add adds changes in the working directory to the staging area git commit records aka “gives id” to changes git branch br1 creates new branch git checkout br1 switches current workspace to branch “br1”

“Local” version control - keeping it solo

git merge br1 merges br1 into current branch (e.g. master)

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git push git pull

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When you create a repository, it exists as a remote repository. You can clone your repository to create a local copy on your computer and sync between the two locations.

Cloning a Repository

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Create a free, private github account

https://github.com/join

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Git Resources

https://zuckermanbrain.github.io/git-novice/

  • Thorough git tutorial (~30 min)

http://rogerdudler.github.io/git-guide/

  • Very rough overview (~10 min)
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Aside: Extensions to Jupyter Notebook/Lab

  • Hinterland - autocompletion while typing 😏

○ https://jupyter-contrib-nbextensions.readthedocs.io/en/lat est/nbextensions/hinterland/README.html

  • Variable inspector - you can see your vars!! 😃

○ https://jupyter-contrib-nbextensions.readthedocs.io/en/lat est/nbextensions/varInspector/README.html

  • Autopep8 - formatting for publishing code documentation

🤔 ○ https://jupyter-contrib-nbextensions.readthedocs.io/en/lat est/nbextensions/code_prettify/README_autopep8.html

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HW2

  • Plotting Coronavirus Data

○ JHU data https://data.humdata.org/dataset/novel-coronavirus-2019-ncov-ca ses ○ NYT github repo https://github.com/nytimes/covid-19-data

  • Setting up your own github account
  • Bonus: create a personal website with github pages

https://guides.github.com/features/pages/ ○ https://jekyllthemes.io/theme/online-cv website templates

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https://github.com/sharu725/online-cv