analysis:nsb2017:week1
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analysis:nsb2017:week1 [2018/06/30 14:46] mvdm [Cloning the module codebase] |
analysis:nsb2017:week1 [2018/09/25 13:48] mvdm |
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| ~~DISCUSSION~~ | ~~DISCUSSION~~ | ||
| - | === Module 1: Setting up === | + | ==== Module 1: Setting up ==== |
| Goals: | Goals: | ||
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| === Installing MATLAB === | === Installing MATLAB === | ||
| - | At MBL, MATLAB should already be installed on lab computers. Verify it starts correctly; you should see its main window open up, including a panel called "Command Window" greeting you with a prompt (''>>''). | + | At MBL, MATLAB should already be installed on lab computers. Verify it starts correctly; you should see its main window open up, including a panel called "Command Window" greeting you with a prompt (''>>''). At Dartmouth, follow [[https://tech.dartmouth.edu/itc/services-support/help-yourself/knowledge-base/matlab|these instructions]] to install MATLAB. Release 2018a seems to work. |
| === Setting up GitHub === | === Setting up GitHub === | ||
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| === Configuring MATLAB to use the code from GitHub === | === Configuring MATLAB to use the code from GitHub === | ||
| - | Now, we need to tell MATLAB where to find all this code we have just obtained. Open MATLAB and [[http://www.mathworks.com/help/matlab/matlab_env/create-matlab-shortcuts-to-rerun-commands.html | create a shortcut]] titled something like "Neural Data Analysis". The code for the shortcut should be | + | Now, we need to tell MATLAB where to find all this code we have just obtained. Open MATLAB and [[http://www.mathworks.com/help/matlab/matlab_env/create-matlab-shortcuts-to-rerun-commands.html | create a shortcut]] (2017b and earlier) or a [[https://www.mathworks.com/help/matlab/matlab_env/create-matlab-favorites-to-rerun-commands.html?searchHighlight=Favorite%20Commands&s_tid=doc_srchtitle | Favorite]] (2018a+) titled something like "Neural Data Analysis". The code for the shortcut should be |
| <code matlab> | <code matlab> | ||
| restoredefaultpath; clear classes; % start with a clean slate | restoredefaultpath; clear classes; % start with a clean slate | ||
| - | cd('D:\My_Documents\GitHub\nsb2017\code-matlab\shared'); % or, wherever your code is located -- NOTE \shared subfolder! | + | cd('D:\My_Documents\GitHub\nsb2018\code-matlab\shared'); % or, wherever your code is located -- NOTE \shared subfolder! |
| p = genpath(pwd); % create list of all folders from here | p = genpath(pwd); % create list of all folders from here | ||
| addpath(p); | addpath(p); | ||
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| This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories. | This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories. | ||
| - | :!: When setting your path in MATLAB to add the ''shared'' folder only and //not// a parent folder such as ''nsb2017''. Adding the entire ''nsb2017'' folder will result in an error when you try to run the LoadCSC command later in the module! | + | :!: When setting your path in MATLAB to add the ''shared'' folder only and //not// a parent folder such as ''nsb2018''. Adding the entire ''nsb2018'' folder will result in an error when you try to run the LoadCSC command later in the module! |
| Optional: if you don't like the ''.git'' folders in your path, you can get clever with [[http://www.mathworks.com/help/matlab/matlab_prog/regular-expressions.html|regular expressions]] to remove these: | Optional: if you don't like the ''.git'' folders in your path, you can get clever with [[http://www.mathworks.com/help/matlab/matlab_prog/regular-expressions.html|regular expressions]] to remove these: | ||
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| === Grab an example data session === | === Grab an example data session === | ||
| - | Next, let's get some data! Go to the NS&B share and find the ''tutorial_data'' folder (within the MouseStriatum folder). | + | Next, let's get some data! At MBL, go the NS&B share and find the ''tutorial_data'' folder (within the MouseStriatum folder). At Dartmouth or elsewhere, you'll need to connect to the lab server. E-mail MvdM for instructions on how to do that. |
| For this module you will need the ''R016-2012-10-08'' folder (containing data from one recording session), which you can find in the ''\promoted\R016'' folder on the share. Copy this folder onto your own computer. A good place to put it is in something like ''D:\data\promoted\'' (Rxxx indicate different rats, followed by the date of each session). As mentioned, in general you want to keep your data separate from your code; for instance, multiple analysis projects may use the same data, so you don't want to duplicate it. | For this module you will need the ''R016-2012-10-08'' folder (containing data from one recording session), which you can find in the ''\promoted\R016'' folder on the share. Copy this folder onto your own computer. A good place to put it is in something like ''D:\data\promoted\'' (Rxxx indicate different rats, followed by the date of each session). As mentioned, in general you want to keep your data separate from your code; for instance, multiple analysis projects may use the same data, so you don't want to duplicate it. | ||
analysis/nsb2017/week1.txt ยท Last modified: 2023/04/13 12:21 (external edit)
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