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| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| from mne.io import concatenate_raws, read_raw_edf | ||
| import os | ||
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| #Load Data | ||
| filename = '00003010_s003_t000' | ||
| fileformat = '.edf' | ||
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There was a problem hiding this comment. Idk if this would be necessary if filename passed through api call |
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| load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/' + filename + fileformat | ||
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There was a problem hiding this comment. 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 |
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| print(load_path) | ||
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There was a problem hiding this comment. We should remove debugging code when we integrate w master |
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| raw = read_raw_edf(load_path, preload=True) | ||
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| #Inspect the .edf file | ||
| print(raw.info) | ||
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| #Make a directory | ||
| directory = filename + '_allChannels' | ||
| parent_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/GeneratedPlots/' | ||
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There was a problem hiding this comment. Nice! once again relative paths, maybe something like os.pwd() |
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| path = os.path.join(parent_path, directory) | ||
| os.mkdir(path) | ||
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| #Plotting begins! | ||
| #Raw data | ||
| #todo: instead of scrolly image, get a static image | ||
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There was a problem hiding this comment. 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 |
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| bigPlot = raw.plot(duration=1200, block=True, show_scrollbars = False) | ||
| bigPlotName = path + '/' + filename + '_all' + '_RAW' | ||
| bigPlot.savefig(bigPlotName) | ||
| #plt.show() | ||
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| #Power spectrum | ||
| #raw.plot_psd(tmax=np.inf) | ||
| #plt.show() | ||
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| #Power spectrum | ||
| psd_fig = raw.plot_psd(show=False) | ||
| saveNamePower = path + '/' + filename + '_all' + '_psd' | ||
| psd_fig.savefig(saveNamePower, dpi = 300) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,51 @@ | ||
| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| from mne.io import concatenate_raws, read_raw_edf | ||
| import os | ||
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| #Load Data | ||
| filename = '00003010_s003_t000' | ||
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There was a problem hiding this comment. Same note as above, relative paths + filename either passed in, or raw data is |
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| fileformat = '.edf' | ||
| load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUH/' + filename + fileformat | ||
| print(load_path) | ||
| raw = read_raw_edf(load_path, preload=True) | ||
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| #Inspect the .edf file | ||
| channel_names = raw.info['ch_names'] | ||
| len_channels = len(channel_names) | ||
| print(channel_names) | ||
| print("Total Channels: ", len_channels) | ||
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| #Make a directory | ||
| directory = filename | ||
| parent_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/GeneratedPlots/' | ||
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| path = os.path.join(parent_path, directory) | ||
| os.mkdir(path) | ||
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| def makePlots(i): | ||
| #Select the required Channel | ||
| requiredChannel = channel_names[i] | ||
| copy = raw.copy() | ||
| copy.pick(requiredChannel) | ||
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| #Plotting begins! | ||
| data, times = copy[:, :] | ||
| fig = plt.figure() | ||
| plt.plot(times, data.T); | ||
| plt.xlabel('Seconds') | ||
| plt.ylabel('$\mu V$') | ||
| plt.title('Channel: ' + str(requiredChannel)); | ||
| saveNameRAW = path + '/' + filename + '_' + requiredChannel + '_RAW' | ||
| plt.savefig(saveNameRAW, dpi = 300) | ||
| plt.close(fig) | ||
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| #Power spectrum | ||
| psd_fig = copy.plot_psd(show=False) | ||
| saveNamePower = path + '/' + filename + '_' + requiredChannel + '_psd' | ||
| psd_fig.savefig(saveNamePower, dpi = 300) | ||
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| ran = range(1, len_channels) | ||
| for i in ran: | ||
| makePlots(i) | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -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" "^7.13.15" | ||
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There was a problem hiding this comment. same with these changes. We should probably have an OS-specific switch that determines the correct versions here. |
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| "@babel/helper-validator-option" "^7.12.17" | ||
| "browserslist" "^4.14.5" | ||
| "semver" "^6.3.0" | ||
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@@ -237,8 +237,8 @@ | |
| "resolved" "https://registry.npmjs.org/@babel/helper-hoist-variables/-/helper-hoist-variables-7.13.0.tgz" | ||
| "version" "7.13.0" | ||
| dependencies: | ||
| "@babel/traverse" "^7.13.15" | ||
| "@babel/types" "^7.13.16" | ||
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| "@babel/helper-member-expression-to-functions@^7.13.0", "@babel/helper-member-expression-to-functions@^7.13.12": | ||
| "integrity" "sha512-48ql1CLL59aKbU94Y88Xgb2VFy7a95ykGRbJJaaVv+LX5U8wFpLfiGXJJGUozsmA1oEh/o5Bp60Voq7ACyA/Sw==" | ||
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@@ -836,7 +836,7 @@ | |
| "resolved" "https://registry.npmjs.org/@babel/plugin-transform-block-scoping/-/plugin-transform-block-scoping-7.12.13.tgz" | ||
| "version" "7.12.13" | ||
| dependencies: | ||
| "@babel/helper-plugin-utils" "^7.13.0" | ||
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| "@babel/plugin-transform-classes@^7.12.1", "@babel/plugin-transform-classes@^7.13.0": | ||
| "integrity" "sha512-9BtHCPUARyVH1oXGcSJD3YpsqRLROJx5ZNP6tN5vnk17N0SVf9WCtf8Nuh1CFmgByKKAIMstitKduoCmsaDK5g==" | ||
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@@ -1443,7 +1443,7 @@ | |
| "version" "7.13.15" | ||
| dependencies: | ||
| "@babel/code-frame" "^7.12.13" | ||
| "@babel/generator" "^7.13.16" | ||
| "@babel/helper-function-name" "^7.12.13" | ||
| "@babel/helper-split-export-declaration" "^7.12.13" | ||
| "@babel/parser" "^7.13.15" | ||
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@@ -2092,7 +2092,6 @@ | |
| "resolved" "https://registry.npmjs.org/@types/glob/-/glob-7.1.1.tgz" | ||
| "version" "7.1.1" | ||
| dependencies: | ||
| "@types/minimatch" "*" | ||
| "@types/node" "*" | ||
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@@ -2306,8 +2305,8 @@ | |
| "resolved" "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-4.21.0.tgz" | ||
| "version" "4.21.0" | ||
| dependencies: | ||
| "@typescript-eslint/types" "4.22.0" | ||
| "@typescript-eslint/visitor-keys" "4.22.0" | ||
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| "@typescript-eslint/[email protected]": | ||
| "integrity" "sha512-+3+FCUJIahE9q0lDi1WleYzjCwJs5hIsbugIgnbB+dSCYUxl8L6PwmsyOPFZde2hc1DlTo/xnkOgiTLSyAbHiQ==" | ||
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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