Add weeks

schedule.md

@@ -6,8 +6,23 @@ description: The weekly event schedule.
 
 # Weekly Schedule
 
-Schedule TBA
+* [Week 1, session 1](week1_session1.md)
+* [Week 1, session 2](week1_session2.md)
+* [Week 2, session 1](week2_session1.md)
+* [Week 2, session 2](week2_session2.md)
+* [Week 3, session 1](week3_session1.md)
+* [Week 3, session 2](week3_session2.md)
+* [Week 4, session 1](week4_session1.md)
+* [Week 4, session 2](week4_session2.md)
+* [Week 5, session 1](week5_session1.md)
+* [Week 5, session 2](week5_session2.md)
+* [Week 6, session 1](week6_session1.md)
+* [Week 6, session 2](week6_session2.md)
+* [Week 7, session 1](week7_session1.md)
+* [Week 7, session 2](week7_session2.md)
+* [Week 8, session 1](week8_session1.md)
+* [Week 8, session 2](week8_session2.md)
 
-{% for schedule in site.schedules %}
-{{ schedule }}
-{% endfor %}
+## Other pages
+
+* [Advice on editors](advice_on_editors.md)

week1_session1.md

@@ -0,0 +1,112 @@
+The first session is the Monday session. The second session is the Thursday
+session.
+
+These are the notes for the Monday session.
+
+We will update them before and after the session, to please keep checking back
+for updates.  Just refresh the page in your browser to get updates.
+
+The Zoom link for all sessions is
+<https://numfocus-org.zoom.us/j/89458437731?pwd=eTF0V252bHlKOXBucnBUWlVBSm9uUT09>.
+
+## Recording
+
+[Recording of Monday Week 1 session
+1](https://numfocus-org.zoom.us/rec/share/nxcgD4PGsc-RI3QdTAiR2GBU1xkMrB5CPmf-sPSC52FSqTkXW7T55CPH1gS7lSSZ.PINmaKGVNAmPXOi-)
+
+## Schedule and plan
+
+- We will be referring often to the [textbook](https://textbook.nipraxis.org).
+- Hello and welcome.
+- Thanks to the [Chan Zuckerberg
+  Initiative](https://chanzuckerberg.com/eoss/proposals/strengthening-community-and-code-foundations-for-brain-imaging/).
+- [Surviving the
+  computer](https://textbook.nipraxis.org/surviving_computers.html).  See video link below.
+- Machinery:
+    - <https://textbook.nipraxis.org>
+    - <https://learn.nipraxis.org>
+    - <https://hub.nipraxis.org> and the Jupyter notebook.
+    - <https://github.com/nipraxis>
+- About the project.
+- We will gradually move away from notebooks.
+- [Using Jupyter notebooks](https://textbook.nipraxis.org/using_jupyter.html)
+  and [more on Jupyter
+  notebooks](https://textbook.nipraxis.org/more_on_jupyter.html)
+- For reference: [Very fast introduction to
+  Python](https://textbook.nipraxis.org/introducing_python.html)
+
+
+## For homework
+
+If you need to catch up on Python and Numpy, you have a double-dose of
+homework this week. In particular, you really will need to do the second
+section here, to get fluent in basic Python and Numpy.  If you are already fluent, you only need to do the first section.
+
+Any problems, email <matthew.brett@gmail.com>, I will point you to someone else
+who can help if I can't help you.
+
+### For everyone: surviving computer, installing on your own machine
+
+Make sure you have watched:
+
+<iframe title="Surviving the computer" src="https://player.vimeo.com/video/693542789?h=63ccfc6dfa" width="640" height="360" frameborder="0" allowfullscreen></iframe>
+
+Next:
+
+* Check your knowledge with the [fast introduction to
+  Python](https://textbook.nipraxis.org/brisk_python.html).
+* [Install Python and required libraries on your
+  computer](https://textbook.nipraxis.org/installation.html).  Make sure you
+  have run the install check at the end of that page.
+
+That's all for those of you who are comfortable with Python and Numpy. See below for those of you who need to catch up.
+
+### If you need practice with Python or Numpy
+
+If you don't know Python well, we strongly suggest you do these exercises to
+catch up, otherwise the rest of the course will be too fast.  Make sure, too, that you've read the fast introduction to Python above.
+
+#### Python
+
+If you are new to Python, do the [expressions and statements
+exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/uob-cfd/exprs_states&subPath=exprs_states.ipynb),
+to get into the swing of things.
+
+Next, do these exercises from the [Google Python
+class](https://developers.google.com/edu/python/).  There are links in the
+exercises to the sections to read to revise the ideas you need.
+
+- [string1
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_string1&subPath=string1.ipynb)
+- [list1
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_list1&subPath=list1.ipynb)
+
+We also suggest you try the slightly more advanced exercises:
+
+- [string2
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_string2&subPath=string2.ipynb)
+- [list2
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_list2&subPath=list2.ipynb)
+
+#### Numpy
+
+(Re-)Read the [introduction to
+Numpy](https://textbook.nipraxis.org/numpy_intro.html).
+
+For a fuller introduction to Numpy, please see [the Scientific Python Numpy tutorial](https://lectures.scientific-python.org/intro/numpy/index.html).
+
+Specifically, see:
+
+* The [numpy array
+  object](https://lectures.scientific-python.org/intro/numpy/array_object.html);
+* [Array
+  operations](https://lectures.scientific-python.org/intro/numpy/operations.html).
+* If you know Matlab, you might want to look over this page on [Numpy for
+  Matlab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html).
+
+Make sure you can do the [arrays
+exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/arrays&subPath=arrays.ipynb)
+
+## The end
+
+That's it for this session.

week1_session2.md

@@ -0,0 +1,39 @@
+The *second session* is the Thursday session.
+
+These are the notes for the second session, for week 1.
+
+We will update them before and after the session, to please keep checking back for updates.  Just refresh the page in your browser to get updates.
+
+The Zoom link for all sessions is
+<https://numfocus-org.zoom.us/j/89458437731?pwd=eTF0V252bHlKOXBucnBUWlVBSm9uUT09>.
+
+## Recording
+
+[Week 1 session
+2 recording](https://numfocus-org.zoom.us/rec/share/KzZxz_u4kOloz-bjfa9xFwEkxmoR_NknZo9un-wjlpuLnGwLnAqApLgRkyx5-jVk.P-Zk3Vcl31LMqkhq)
+
+## Schedule and plan
+
+- Please log on to <https://hub.nipraxis.org>.
+- About homework:
+  - It will appear at the bottom of the session 1 page for each week.
+  - We will depend on you having done the homework for the _following week_.
+- Reminder about the project
+- [Surviving the
+  computer](https://textbook.nipraxis.org/surviving_computers.html).  See
+  [video](https://player.vimeo.com/video/693542789?h=63ccfc6dfa) (also linked from Session 1 page.
+- [Pathlib](https://textbook.nipraxis.org/pathlib.html)
+- Skip through the [introduction to
+  Numpy](https://textbook.nipraxis.org/numpy_intro.html)
+- The OKpy testing system and a [practice with arrays
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/array_practice&subPath=array_practice.ipynb)
+
+## For homework
+
+See the [Week 1 session 1 page](https://apps.learn.nipraxis.org/learning/course/course-v1:Nipraxis+NI1+2023_NI1/block-v1:Nipraxis+NI1+2023_NI1+type@sequential+block@a292732b08514bbaa13ca5f862182dcd/block-v1:Nipraxis+NI1+2023_NI1+type@vertical+block@73fc602fe7034cd1913edd805920cf7e)
+
+In general, look for the homework in the session 1 page for each week.
+
+## The end
+
+That's it for this session.

week2_session1.md

@@ -0,0 +1,43 @@
+## Recording
+
+[Week 2 session
+1](https://numfocus-org.zoom.us/rec/share/4DcuAFZduwAT9b-VllUxYlDnwdPq7air4JSb6y6uMo9wehVwJejysulxj12kQ69F.s8CFqaGB5bwagTsp)
+
+### Arrays, images and plotting
+
+* [What is an image?](https://textbook.nipraxis.org/what_is_an_image.html)
+* [Boolean arrays](https://textbook.nipraxis.org/boolean_arrays.html)
+* [Reshape and 2D](https://textbook.nipraxis.org/reshape_and_2d)
+* [Arrays and images](https://textbook.nipraxis.org/arrays_and_images)
+* [Camera
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/camera&subPath=camera.ipynb)
+
+## Homework
+
+Make sure you've done the exercises from the sessions:
+
+* Session 1:
+  * [Camera](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/camera&subPath=camera.ipynb)
+* Session 2:
+    * [Anatomical
+    exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/anatomical&subPath=anatomical.ipynb)
+    * Consider also: [Arteries
+    exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/arteries&subPath=arteries.ipynb)
+
+In the next session, we will be starting with Git, and to work on your own
+computer.
+
+Read, mark, learn and inwardly digest the [curious
+git](https://matthew-brett.github.io/curious-git/) tutorial.
+
+We think this will take you 90 minutes, at a careful read, and you will need
+to read it carefully, in order to benefit from it.
+
+If you do read it carefully, you will be investing in your own future
+productivity — Git version control is a powerful way to work more efficiently,
+especially in collaboration, and you need to understand the way that Git
+**thinks**, in order to use Git with fluency and efficiency.
+
+## That's it.
+
+That's it for this session.

week2_session2.md

@@ -0,0 +1,25 @@
+## Recording
+
+[Week 2 session
+2 recording](https://numfocus-org.zoom.us/rec/share/dG612zhE7qU4sE_Wo2oyOmFnkjxqY3sBcrF7kijixQ3zoVRST4__StpYv47bBQ.EsD2R2-D6ZCERmoj)
+
+## Schedule
+
+## Three-dimensional arrays
+
+* [Arrays in 3D](https://textbook.nipraxis.org/arrays_3d)
+* [Images in 3D](https://textbook.nipraxis.org/images_3d)
+* [Reshaping and three
+  dimensions](https://textbook.nipraxis.org/reshape_and_3d.html)
+* [Anatomical
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/anatomical&subPath=anatomical.ipynb)
+* If you have time: [Arteries
+  exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/arteries&subPath=arteries.ipynb)
+
+## For homework
+
+See the page for session 1.
+
+## That's it.
+
+That's it for this session.

week3_session1.md

@@ -0,0 +1,102 @@
+## Recording
+
+[Week 3 session 1
+recording](https://numfocus-org.zoom.us/rec/share/1DWWt27ub3hc7RX4rj4dy6yn8iFDPKHQxYr8rvInUvl_zwycUIwqvKWMTE0CSdXc.Xvs5ZTX5xE0D3TgK?startTime=1692022041000)
+
+## Schedule
+
+* Again, towards the project.
+* Bracketing Git, Github and working on your own computer.
+
+### Some background
+
+You will need to have followed the [installation
+instructions](https://textbook.nipraxis.org/installation.html).
+
+In particular, you are about to use your terminal application:
+
+* [Powershell on
+  Windows](https://textbook.nipraxis.org/installation_on_windows.html#powershell)
+* [Powshell on
+  Mac](https://textbook.nipraxis.org/installation_on_mac.html#terminal-app)
+
+### Modules and functions
+
+We start with the laptop way.
+
+* [on_modules](https://textbook.nipraxis.org/on_modules).
+
+### FMRI artifacts
+
+* [Principles of FMRI video](https://www.youtube.com/watch?v=7Kk_RsGycHs)
+* [Radiopedia article in MRI
+  artifacts](https://radiopaedia.org/articles/mri-artifacts-1)
+* [Common MRI artifacts and how to fix
+  them](https://gate.nmr.mgh.harvard.edu/wiki/whynhow/images/3/39/Artifacts_why_n_how_dec_14_2017_V7.pdf)
+
+The above don't focus much on fMRI (some coverage of susceptibility
+distortion), but here are some MRI quality control runs that show some
+interesting effects:
+
+* [Spin history artifact, motion spike, AP
+  ghosting](https://mriqc.s3.amazonaws.com/artifacts/sub-ds045s409874_task-machinegame_run-04_bold.html)
+* [Ringing, bands in
+  carpetplot](https://mriqc.s3.amazonaws.com/abide/sub-50039_task-rest_bold.html)
+* [Ghosting, possible hardware
+  failure](https://mriqc.s3.amazonaws.com/abide/sub-51489_task-rest_bold.html)
+* [LR ghosting evident in background
+  noise](https://mriqc.s3.amazonaws.com/abide/sub-51146_task-rest_bold.html)
+* [Hardware
+  failures](https://mriqc.s3.amazonaws.com/artifacts/sub-arielle02_task-uknown_bold.html)
+* [Electromagnetic
+  spikes](https://mriqc.s3.amazonaws.com/artifacts/sub-ben01_task-unknown_bold.html)
+
+## For homework
+
+### Using Git
+
+Watch the following two videos introducing Git in use, but relating what you
+see to the terms in the [curious
+git](https://matthew-brett.github.io/curious-git/) tutorial from last week.
+
+I'm referring to the "Git parable" in the videos, which is a similar
+introduction to the [Curious Git
+tutorial](https://matthew-brett.github.io/curious-git) from last week's
+homework — but the two tutorials take a very similar track, so you can
+consider them interchangeable.
+
+<iframe src="https://player.vimeo.com/video/121579300?h=ed8db39d7e" width="640" height="438" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen></iframe>
+<p><a href="https://vimeo.com/121579300">Introduction to the git working tree, repository and staging area</a> from <a href="https://vimeo.com/matthewbrett">Matthew Brett</a> on <a href="https://vimeo.com">Vimeo</a>.</p>
+
+The next video is a little out of date, in that the default branch name in Git
+has changed from "master" to "main".  You will likely find your copy of Git
+calls the default branch "main".  For "master" read "main" throughout.
+
+<iframe src="https://player.vimeo.com/video/121579601?h=5b937ff9ff" width="640" height="436" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen></iframe>
+<p><a href="https://vimeo.com/121579601">The links between git commits, and git branches.</a> from <a href="https://vimeo.com/matthewbrett">Matthew Brett</a> on <a href="https://vimeo.com">Vimeo</a>.</p>
+
+### Choosing a text editor
+
+Your second job for this week is to assess and [choose a text
+editor](https://textbook.nipraxis.org/choosing_editor.html).
+
+Here we a list of videos on choosing text editors:
+
+* Edited version of [Stéfan van der Walt on
+  Emacs](https://vimeo.com/740066780) (16 minutes).  You might prefer the [full
+  24 minute version of the conversation here](https://vimeo.com/702404210).
+* [Pamphile Roy on PyCharm](https://vimeo.com/702001724) (16 minutes).
+* Edited version of [Ilhan Polat on Spyder](https://vimeo.com/702215618) (14
+  minutes).  You can also watch the [54 minute full conversation with Ilhan](https://vimeo.com/706101324).
+* [Bhuvak Kalra on VSCode](https://vimeo.com/702402879) (16 minutes).
+* Edited version of [Paul Ivanov on
+  Vim](https://vimeo.com/740121174) (15 minutes).  You can watch the [full 43
+  minute conversation with Paul Ivanov here](https://vimeo.com/704733982). You
+  might watch the full version if you interested in more on how you know when
+  you have the right editor, how long it takes to get going with Vim.
+
+Please take time for this task, and investigate your options.
+
+## That's it.
+
+That's it for this session.

week3_session2.md

@@ -0,0 +1,20 @@
+## Recording
+
+[Week 3 session 2 recording](https://numfocus-org.zoom.us/rec/share/YIQUaJjjBQg2HCLm1VbXJ4hPE2T3EeGuMjSMYBw--VajunFmm_PWXKuZwAEiUuVj.8GMzoJ6lXQZHsrMj)
+
+## Schedule and plan
+
+* More towards the first project.
+* Bracketing Git, Github and working on your own computer.
+
+### Modules and functions
+
+More on the laptop way.
+
+* [on_modules](https://textbook.nipraxis.org/on_modules).
+
+We will come to the practice later (week 4).
+
+## That's it.
+
+That's it for this session.