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| name: mne | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
| - python>=3.8 | ||
| - pip | ||
| - numpy | ||
| - scipy | ||
| - matplotlib | ||
| - numba | ||
| - pandas | ||
| - xlrd | ||
| - scikit-learn | ||
| - h5py | ||
| - pillow | ||
| - statsmodels | ||
| - jupyter | ||
| - joblib | ||
| - psutil | ||
| - numexpr | ||
| - imageio | ||
| - tqdm | ||
| - spyder-kernels>=1.10.0 | ||
| - imageio-ffmpeg>=0.4.1 | ||
| - vtk>=9.0.1 | ||
| - pyvista>=0.30 | ||
| - pyvistaqt>=0.4 | ||
| - qdarkstyle | ||
| - darkdetect | ||
| - mayavi | ||
| - PySurfer | ||
| - dipy | ||
| - nibabel | ||
| - nilearn | ||
| - python-picard | ||
| - pyqt!=5.15.3 | ||
| - mne | ||
| - mffpy>=0.5.7 | ||
| - ipywidgets | ||
| - pip: | ||
| - ipyvtklink |
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| from mne.io import concatenate_raws, read_raw_edf | ||
| from tfr_raw_psd import spectral_power, plot_tfr_and_raw_bin_width_all_channel, load | ||
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| # ------------------------------------------------------ | ||
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| if __name__ == '__main__': | ||
| load_path, filename = load() | ||
| raw = read_raw_edf(load_path, preload=True) | ||
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| #Bandpass filter 0.1Hz - 50Hz | ||
| raw = raw.filter(0.1, 50) | ||
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| # Resample to 100 Hz | ||
| raw = raw.resample(100, npad='auto') | ||
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| print(raw.info) | ||
| binNumber = 10 | ||
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| #Plot TFR and RAW data for the corresponding time for all channels | ||
| plot_tfr_and_raw_bin_width_all_channel(raw = raw, start=100, stop=350, filename=filename, binNumber=binNumber) | ||
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| #Plot Spectral Power Density Plot of all channels | ||
| spectral_power(raw=raw, filename=filename) | ||
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| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| import mne | ||
| import os | ||
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| # ----------------------------------------------------- | ||
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| def spectral_power(raw, filename): | ||
| channel_names = raw.info['ch_names'] | ||
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| # Make a directory path | ||
| directory = filename + '_tfr_raw_spd' | ||
| # parent_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/GeneratedPlots/' | ||
| parent_path = os.getcwd() + '/saved_plots/' | ||
| path = os.path.join(parent_path, directory) | ||
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| # If directory does not exist then make it | ||
| if (os.path.exists(path) == False): | ||
| os.mkdir(path) | ||
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| for i in range(len(channel_names)): | ||
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| # Select the required channel | ||
| requiredChannel = channel_names[i] | ||
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| # Power spectrum | ||
| copy = raw.copy() | ||
| copy.pick(requiredChannel) | ||
| psd_fig = copy.plot_psd(show=False) | ||
| saveNamePower = path + '/' + filename + '_' + str(requiredChannel) + '_psd' | ||
| psd_fig.savefig(saveNamePower, dpi=300) | ||
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| # ----------------------------------------------------- | ||
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| def plot_tfr_and_raw_bin_width_all_channel(raw, start, stop, filename, binNumber): | ||
| # Channel Info | ||
| channel_names = raw.info['ch_names'] | ||
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| # Setting reference | ||
| raw.set_eeg_reference(ref_channels=['EEG CZ-LE']) | ||
| rawLength = int(len(raw) / raw.info['sfreq']) | ||
| print(rawLength) | ||
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| # Construct events | ||
| events = mne.make_fixed_length_events(raw, duration=rawLength - 1) | ||
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| # Construct Epochs | ||
| epochs = mne.Epochs(raw, events, preload=True, tmin=0, tmax=rawLength - 1, baseline=None) | ||
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| # Plotting TFRs | ||
| frequencies = np.arange(1, 50, 1) | ||
| power = mne.time_frequency.tfr_morlet(epochs, n_cycles=2, return_itc=False, freqs=frequencies, decim=3) # Run this only once | ||
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| #debug | ||
| print(filename) | ||
| print(binNumber) | ||
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| # Make a directory path | ||
| directory = filename + '_tfr_raw_spd' | ||
| # parent_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/GeneratedPlots/' | ||
| parent_path = os.getcwd() + '/saved_plots/' | ||
| path = os.path.join(parent_path, directory) | ||
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| #If directory does not exist then make it | ||
| if(os.path.exists(path) == False): | ||
| os.mkdir(path) | ||
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| for i in range(len(channel_names)): | ||
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| # Select the required channel | ||
| requiredChannel = channel_names[i] | ||
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| #Plot RAW | ||
| copy = raw.copy() | ||
| copy.pick(requiredChannel) | ||
| copy.crop(tmin=start, tmax=stop, include_tmax=True) | ||
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| # Plotting begins! | ||
| data, times = copy[:, :] | ||
| fig = plt.figure() | ||
| ax = fig.add_subplot(111) | ||
| ax.plot(times, data.T, linewidth=0.5); | ||
| ax.set_xticklabels([]) | ||
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| plt.xlabel('Seconds') | ||
| plt.ylabel('$\mu V$') | ||
| plt.title('Channel: ' + str(requiredChannel)); | ||
| positions = np.arange(0, start-stop, 1) | ||
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| saveNameRAW = path + '/' + filename + '_' + 'bn' + str(binNumber) + '_' + str(requiredChannel) + '_raw' | ||
| plt.savefig(saveNameRAW, dpi=300) | ||
| plt.close(fig) | ||
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| # Plot TFR | ||
| tfr_fig = power.plot(requiredChannel, tmin=start, tmax=stop, vmin=-0.000000005, vmax=0.000000005, show=False) | ||
| saveNamePower = path + '/' + filename + '_' + 'bn' + str(binNumber) + '_' + str(requiredChannel) + '_tfr' | ||
| tfr_fig.savefig(saveNamePower, dpi=300) | ||
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| # ----------------------------------------------------- | ||
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| def load(): | ||
| # Load Data | ||
| filename = '00000258_s001_t000' | ||
| fileformat = '.edf' | ||
| load_path = 'C:/Users/User/Desktop/CSE 481C - Neruo Capstone/Project Repo/Data/TUSZ/v1.5.2/edf/dev/02_tcp_le/002/00000258/s001_2003_07_16/' \ | ||
| + filename + fileformat | ||
| return load_path, filename | ||
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| # ----------------------------------------------------- |
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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" | ||
|
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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windows specific changes should be handled dynamically and not hardcoded. We should think about this carefully before merging to master.
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agreed.