First commit intro files

Author: markschatza

.ipynb_checkpoints/Main-checkpoint.ipynb

@@ -1 +1,48 @@
-# learning-python
+# TNEL Python Tutorial
+
+Using python for ephys data
+
+## Step 1 (by yourself)
+### Setting up Python
+Only for windows. Mac and Linux are good to go already.
+
+Option 1) Install anaconda (has a bunch of very useful modules and programs built-in) (https://www.anaconda.com/distribution/)
+
+Option 2) Install basic python (https://www.python.org/)
+
+### Learn basic python
+This may take a bit depending on your experience programming. learnpython.org looks like a very good starting point. Lots of other options too. Youtube, w3schools (only up to file handling), etc.
+
+## Step 2 (With us)
+### Setting up GitHub
+- Create a github account. (DON'T USE UMN EMAIL!)
+
+- Download git (https://gitforwindows.org/).
+
+- Open Git Bash
+
+- Use commands "cd" (change directory) and "ls" (list) to change to where you want to save your files. i.e. "cd Documents"
+
+- Create a new folder for GitHub "mkdir GitHub" (make directory), and go into it "cd GitHub".
+
+- Now back to your browser and go to our github repository (https://github.com/tne-lab/learning-python). Click fork in the upper right corner. Then click on your account. This will make a private version for yourself.
+
+- Now go to your private repo (https://github.com/CHANGETOYOURUSERNAME/learning-python) and copy the link from the green clone button.
+
+- Back to git bash and type "git clone https://github.com/CHANGETOYOURUSERNAME/learning-python". This creates a local copy for yourself.
+
+
+### Open Main in juypter
+Start a juypter notdebook and open up the main.ipynb file which is located in the folder that you cloned from github.
+
+Complete it.
+
+## Step 3
+### Push your new changes to github so they will be backed up.
+- Return to git bash and "cd" into your learning-python folder.
+
+- Use the command "git add -A" to add all files to be staged to be commited.
+
+- Use the command "git commit -m "My first commit"" to commit the changes. This means that these files are the most up to date changes.
+
+- Use the command "git push" to push the files up your github repository so they will be saved both locally and in the cloud. Go to your github repo (https://github.com/CHANGETOYOURUSERNAME/learning-python) and make sure your new changes are there.

Main.ipynb

@@ -0,0 +1,28 @@
+from scipy.signal import butter, lfilter
+
+'''
+Option 1
+
+How Mark S did this.
+'''
+def butter_bandpass(lowcut, highcut, fs, order=5):
+    nyq = 0.5 * fs
+    low = lowcut / nyq
+    high = highcut / nyq
+    b, a = butter(order, [low, high], btype='band')
+    return b, a
+
+
+def butter_bandpass_filter(data, lowcut, highcut, fs, order=5):
+    b, a = butter_bandpass(lowcut, highcut, fs, order=order)
+    filteredData = lfilter(b, a, data)
+    return filteredData
+
+
+'''
+Option 2
+
+Example from scipy.
+'''
+sos = signal.butter(10, 15, 'hp', fs=1000, output='sos')
+filtered = signal.sosfilt(sos, sig)

OpenEphys.py

@@ -0,0 +1,50 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<EXPERIMENT version="0.40000000000000002" number="1" separatefiles="0">
+  <RECORDING number="0" samplerate="30000">
+    <PROCESSOR id="100">
+      <CHANNEL name="CH1" bitVolts="0.19499999284744263" filename="100_CH1.continuous"
+               position="1024"/>
+      <CHANNEL name="CH2" bitVolts="0.19499999284744263" filename="100_CH2.continuous"
+               position="1024"/>
+      <CHANNEL name="CH3" bitVolts="0.19499999284744263" filename="100_CH3.continuous"
+               position="1024"/>
+      <CHANNEL name="CH4" bitVolts="0.19499999284744263" filename="100_CH4.continuous"
+               position="1024"/>
+      <CHANNEL name="CH5" bitVolts="0.19499999284744263" filename="100_CH5.continuous"
+               position="1024"/>
+      <CHANNEL name="CH6" bitVolts="0.19499999284744263" filename="100_CH6.continuous"
+               position="1024"/>
+      <CHANNEL name="CH7" bitVolts="0.19499999284744263" filename="100_CH7.continuous"
+               position="1024"/>
+      <CHANNEL name="CH8" bitVolts="0.19499999284744263" filename="100_CH8.continuous"
+               position="1024"/>
+      <CHANNEL name="CH17" bitVolts="0.19499999284744263" filename="100_CH17.continuous"
+               position="1024"/>
+      <CHANNEL name="CH18" bitVolts="0.19499999284744263" filename="100_CH18.continuous"
+               position="1024"/>
+      <CHANNEL name="CH19" bitVolts="0.19499999284744263" filename="100_CH19.continuous"
+               position="1024"/>
+      <CHANNEL name="CH20" bitVolts="0.19499999284744263" filename="100_CH20.continuous"
+               position="1024"/>
+      <CHANNEL name="CH21" bitVolts="0.19499999284744263" filename="100_CH21.continuous"
+               position="1024"/>
+      <CHANNEL name="CH22" bitVolts="0.19499999284744263" filename="100_CH22.continuous"
+               position="1024"/>
+      <CHANNEL name="CH23" bitVolts="0.19499999284744263" filename="100_CH23.continuous"
+               position="1024"/>
+      <CHANNEL name="CH24" bitVolts="0.19499999284744263" filename="100_CH24.continuous"
+               position="1024"/>
+      <CHANNEL name="AUX1" bitVolts="3.7400001019705087e-005" filename="100_AUX1.continuous"
+               position="1024"/>
+      <CHANNEL name="AUX2" bitVolts="3.7400001019705087e-005" filename="100_AUX2.continuous"
+               position="1024"/>
+      <CHANNEL name="AUX3" bitVolts="3.7400001019705087e-005" filename="100_AUX3.continuous"
+               position="1024"/>
+    </PROCESSOR>
+    <PROCESSOR id="104">
+      <CHANNEL name="CH1" bitVolts="0.19499999284744263" filename="104_CH1.continuous"
+               position="1024"/>
+    </PROCESSOR>
+  </RECORDING>
+</EXPERIMENT>

README.md

@@ -0,0 +1,2 @@
+Crossing target = 130
+(Stim target = 180)

__pycache__/OpenEphys.cpython-36.pyc

@@ -0,0 +1,2 @@
+41176507 Software time: 41176507@3328261Hz
+41176500 Processor: Rhythm FPGA Id: 100 subProcessor: 0 start time: 41176500@30000Hz