Preprocessing #10

devyansh · 2021-05-12T06:04:22Z

No description provided.

minneker · 2021-05-12T06:08:21Z

Pre-processing/PlotAllChannels.py

+
+
+#Load Data
+load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'


local path needs to change, won't work on another computer.

minneker · 2021-05-12T06:09:03Z

Pre-processing/PlotOneChannel.py

+
+
+#Load Data
+load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'


same here, need to point to file not an absolute path.

minneker · 2021-05-12T06:09:51Z

Pre-processing/PlotOneChannel.py

+raw = read_raw_edf(load_path, preload=True)
+
+#Inspect the .edf file
+print(raw.info['ch_names'])


do we need to inspect the file when running? Or are these just for debugging? If the latter, I think we can remove all inspection print statements.

minneker · 2021-05-12T06:10:35Z

package.json

  },
  "scripts": {
    "build:css": "postcss src/styles/tailwind.css -o src/styles/app.css",
    "watch:css": "postcss src/styles/tailwind.css -o src/styles/app.css --watch",
-    "react-scripts:start": "sleep 5 && react-scripts start",
+    "react-scripts:start": "timeout 5 && react-scripts start",


windows specific changes should be handled dynamically and not hardcoded. We should think about this carefully before merging to master.

minneker · 2021-05-12T06:11:03Z

yarn.lock

@@ -146,7 +146,7 @@
  "resolved" "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.13.13.tgz"
  "version" "7.13.13"
  dependencies:
-    "@babel/compat-data" "^7.13.12"
+    "@babel/compat-data" "^7.13.15"


same with these changes. We should probably have an OS-specific switch that determines the correct versions here.

2 plots for each Channel: one for RAW Data and other is Spectral Power Density PlotAllChannels plots and saves the images as well

saketh-n · 2021-05-17T00:11:10Z

Pre-processing/PlotAllChannels.py



 #Load Data
-load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'
+filename = '00003010_s003_t000'


I guess it's fine for now, but when I integrate with front end I want to pull this filename from the api call instead of hardcoded

saketh-n · 2021-05-17T00:11:46Z

Pre-processing/PlotAllChannels.py



 #Load Data
-load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'
+filename = '00003010_s003_t000'
+fileformat = '.edf'


Idk if this would be necessary if filename passed through api call

saketh-n · 2021-05-17T00:12:56Z

Pre-processing/PlotAllChannels.py

-load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'
+filename = '00003010_s003_t000'
+fileformat = '.edf'
+load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/' + filename + fileformat


In general relative paths are preferred, but passing in filename should make this a non-issue. When web-hosting this will be a more interesting problem. We should try to have pre-processing code run on the front end

saketh-n · 2021-05-17T00:13:36Z

Pre-processing/PlotAllChannels.py

-load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'
+filename = '00003010_s003_t000'
+fileformat = '.edf'
+load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/' + filename + fileformat
 print(load_path)


We should remove debugging code when we integrate w master

saketh-n · 2021-05-17T00:14:13Z

Pre-processing/PlotAllChannels.py

 print(load_path)
 raw = read_raw_edf(load_path, preload=True)

 #Inspect the .edf file
 print(raw.info)

+#Make a directory
+directory = filename + '_allChannels'
+parent_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/GeneratedPlots/'


Nice! once again relative paths, maybe something like os.pwd()

saketh-n · 2021-05-17T00:15:29Z

Pre-processing/PlotAllChannels.py

 #Plotting begins!
 #Raw data
-raw.plot(duration=100, block=True)
-plt.show()
+#todo: instead of scrolly image, get a static image


If we get this running on the front end, we might not even need to save anything! Tricky problem though since browser only runs js/css/html

saketh-n · 2021-05-17T00:17:28Z

Pre-processing/PlotOneChannel.py



 #Load Data
-load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'
+filename = '00003010_s003_t000'


Same note as above, relative paths + filename either passed in, or raw data is

saketh-n · 2021-05-17T00:19:32Z

Pre-processing/PlotOneChannel.py

+
+#Make a directory
+directory = filename
+parent_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/GeneratedPlots/'


relative path

Plots RAW data of all channels in an interactive GUI

minneker · 2021-05-25T16:24:23Z

Pre-processing/epochs.py

@@ -0,0 +1,69 @@
+import os


This code is largely taken from: https://mne.tools/mne-realtime/_modules/mne/epochs.html.

Please make sure to cite any code you copy-paste.

minneker · 2021-05-25T16:25:18Z

.idea/misc.xml

@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>


All of these .idea files are not necessary. They help render the project in your local IDE. Please remove any .idea/ files. We should add this to .gitignore to avoid in future pushes.

minneker · 2021-05-25T16:30:13Z

Pre-processing/epochs.py

@@ -0,0 +1,69 @@
+import os
+import mne
+import numpy as np


Also this code seems to already exists in the MNE package. Why are we writing it locally instead of calling it from the package?

RAW of all channels TFR of all channels SPD of all channels

also changed the relative path of parent_path

devyansh added 3 commits April 26, 2021 21:33

working on windows now

2cae096

Merge branch 'master' of https://github.com/saketh-n/seizure-classifi…

4b20ac7

…cation

plots

d63c821

devyansh requested review from minneker and saketh-n May 12, 2021 06:04

Update PlotOneChannel.py

fe6af28

minneker reviewed May 12, 2021

View reviewed changes

generating plots for each channel individually

ffe62eb

2 plots for each Channel: one for RAW Data and other is Spectral Power Density PlotAllChannels plots and saves the images as well

saketh-n requested changes May 17, 2021

View reviewed changes

devyansh added 2 commits May 18, 2021 06:19

Create PlotAllChannelsScrolly.py

066e288

Plots RAW data of all channels in an interactive GUI

creating Epochs for TFRs

cb30512

minneker requested changes May 25, 2021

View reviewed changes

minneker reviewed May 25, 2021

View reviewed changes

devyansh added 4 commits June 1, 2021 03:31

All desired plots generated

3053240

RAW of all channels TFR of all channels SPD of all channels

shifted functions to different file

4cdf309

also changed the relative path of parent_path

parent_path update

6ee5d20

Update main.py

bd7124d

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Preprocessing #10

Preprocessing #10

devyansh commented May 12, 2021

minneker May 12, 2021

minneker May 12, 2021

minneker May 12, 2021

minneker May 12, 2021

saketh-n May 12, 2021

minneker May 12, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

saketh-n May 17, 2021

minneker May 25, 2021

minneker May 25, 2021

minneker May 25, 2021



		#Load Data
		load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/00003010_s003_t000.edf'

Preprocessing #10

Are you sure you want to change the base?

Preprocessing #10

Conversation

devyansh commented May 12, 2021

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment