„README.md“ ändern

README.md

@@ -1,21 +1,36 @@
-## Semesterproject of the lecture "Semesterproject Signal processing and Analysis
-of human brain potentials (eeg) WS 2020/21
+## Semesterproject of the lecture "Semesterproject Signal processing and Analysis of human brain potentials (eeg)" WS 2020/21
 
-This repository holds the code of the semesterproject as well as the report.
-The main files are 'preprocessing_and_cleaning.py', 'erp_analysis.py' and 'decoding_tf_analyis.py'.
-The files hold:
-- preprocessing_and_cleaning.py : Holds the pre-processing pipeline of the project. By executing the file all subjects are pre-processed. Subjects 001, 003, 014 are pre-processed with manually selected pre-processing information, all other subjects are pre-processed with the given pre-processing information. Pre-processed cleaned data is saved in the BIDS file structure as 'sub-XXX_task-N170_cleaned.fif' where XXX is the subject number.
-Details can be found in the comments of the code.
-- erp_analysis.py : Holds the code for the erp-analysis. Computes the peak-differences and t-tests for several experimental contrasts. Details can be found in the comments of the code.
-- decoding_tf_analysis.py : Holds the code for the decoding and time-frequency analysis. Details can be found in the comments of the code.
+This repository holds the code of the semesterproject as well as the report, created by Julius Voggesberger.
+As the dataset for the project, the N170-dataset was chosen.
+As the three subjects, to be manually pre-processed, the subjects 001, 003 and 014 were chosen.
+The rest of the subjects were pre-processed with provided pre-processing information.
 
-The folder 'utils' holds helper functions for some plots needed for the analysis and to load data, generate strings etc. and holds the code given in the lecture.
-The folder 'test' holds mostly unittests that test helper functions and one function which visually checks if N170 peaks are extracted correctly.
+### Structure
+```
+├── Dataset: The dataset of the project as well as the manually selected bad segments are stored here. 
+|   ├── n170: Store the dataset here. 
+|   └── preprocessed: Bad segments are stored here. 
+├── cached_data: Data that is generated in the analysis part is stored here. 
+|   ├── decoding_data: Results of the classifiers. 
+|   ├── erp_peaks: ERP peaks needed for the ERP analysis. 
+|   └── tf_data: Time-frequency data needed for the tf-analysis. 
+├── test: Contains unittests and one visual check. 
+├── utils: Contains helper methods 
+|   ├── ccs_eeg_semesterproject: Methods given in the lecture. 
+|   ├── ccs_eeg_utils_reduced: Method for reading in BIDS provided in the lecture. 
+|   ├── file_utils.py: Methods for reading in files and getting epochs. 
+|   └── plot_utils.py: Methods for manually created plots. 
+├── preprocessing_and_cleaning.py: The preprocessing pipeline. 
+├── erp_analysis.py: The ERP-Analysis and computation of ERP peaks.
+├── decoding_tf_analysis.py: Decoding and time-frequency analysis.
+└── semesterproject_report_voggesberger: The report of the project.
+```
 
-For the code to work properly, the N170 dataset needs to be provided.
-When first running the analysis, it may take a while. After running it one time the data is cached, so that it can be reused if the analysis should be executed again. Be careful though, as a parameter has to be explicitly set in the code, so that the already computed data is used. This parameter is a boolean given to each analysis function which caches data.
-
-This code was created using Python 3.7 and the following libraries:
+### Running the project
+To run the project python 3.7 is required and anaconda recommended.\
+To ensure reproducability, randomstates were used for methods which are non-deterministic.
+The randomstates used are either '123' or '1234'.\
+The following libraries are needed:
 - Matplotlib 3.3.3
 - MNE 0.22.0
 - MNE-Bids 0.6
@@ -23,3 +38,18 @@ This code was created using Python 3.7 and the following libraries:
 - Scikit-Learn 0.23.2
 - Pandas 1.2.0
 - Scipy 1.5.4
+
+For the code to work, the N170 dataset needs to be provided and put into the folder 'Dataset/n170/', so that the file structure 'Dataset/n170/sub-001', etc. exists.
+The pre-processed raw objects are saved in their respective subject folder, in 'Dataset/n170/'.
+When first running the analysis, it may take a while. 
+After running it one time the data is cached, so that it can be reused if the analysis should be executed again at a later time.
+For the cached data to be used, a boolean parameter has to be set in the respective analysis method.
+
+It may be necessary to set the parent directory 'semesterproject_lecture_eeg' as 'Sources Root' for the project, if pycharm is used as an IDE.
+
+### Parameters
+Parameters have to be changed manually in the code, if different settings want to be tried.
+
+### Visualisation
+The visualisation methods that were used to generate the visualisations in the report, are contained in the code, if they were created manually.
+If a visualisation method from mne was used to create the visualisation, it may exist in the code or not.

decoding_tf_analysis.py

@@ -46,6 +46,7 @@ def events_to_labels(evts, events_dict, mask=None):  # TODO Test schreiben
 def permutation_test(baseline, score, n_iter):
     """
     An implementation of a permutation test for classification scores.
+
     :param baseline: The classification scores of the baseline, i.e. selection by chance
     :param score: The classification scores which are tested for significance
     :param n_iter: number of permutations
@@ -120,6 +121,8 @@ def decoding(dataset, filename, compute_metric=True, mask=None):
     # Compute index of time point 0
     index = math.floor((len(metric[0]) / time_scale) * 100)
     baseline = np.array(metric[:index]).flatten()
+
+    # Plot the result
     plt.plot(np.linspace(-200, 1000, 1127), np.mean(metric, axis=0))
     plt.ylabel('Accuracy (%)')
     plt.xlabel('Time (ms)')
@@ -129,11 +132,12 @@ def decoding(dataset, filename, compute_metric=True, mask=None):
     # Compute the permutation tests
     for t in range(len(metric[0][index:])):
         score_t = np.asarray(metric[:, t + index])
-        p = permutation_test(baseline, score_t, 100)
+        p = permutation_test(baseline, score_t, 1000)
         p_values.append(p)
         if t % 50 == 0:
             print(str(t) + " Out of " + str(len(metric[0][index:])))
 
+    # Plot the result
     plt.plot(times[index:], p_values)
     plt.ylabel('P-Value')
     plt.xlabel('Time (ms)')
@@ -143,14 +147,17 @@ def decoding(dataset, filename, compute_metric=True, mask=None):
 
 def create_tfr(raw, condition, freqs, n_cycles, response='induced', baseline=None, plot=False):
     """
-    Compute the time frequency representation (TFR) of data for a given condition via morlet wavelets
+    Compute the time frequency representation (TFR) of data for a given condition via Morlet wavelets
+
     :param raw: the data
-    :param condition: the condition for which to compute the TFR. Given as a list of tuples of the form (stimulus, condition) # TODO ambiguous use of condition
+    :param condition: the condition for which to compute the TFR. Given as a list of tuples of the form (stimulus, texture)
     :param freqs: the frequencies for which to compute the TFR
-    :param n_cycles: the number of cycles used by the morlet wavelets
-    :param response: type of expected TFR. Can be total, induced or evoked. Default is induced
+    :param n_cycles: the number of cycles used by the Morlet wavelets
+    :param response: type of expected TFR. Can be total, induced or evoked. Default is induced,
+                    the others were not used for the report, only for exploration
     :param baseline: baseline used to correct the power. A tuple of the form (start, end).
-        Default is None and no baseline correction will be applid
+        Default is None and no baseline correction will be applied
+    :param plot: True if results should be plotted, else false.
     :return: The TFR or the given data for a given condition. Has type AverageTFR
     """
     epochs, _ = get_epochs(raw, condition, tmin=-0.2, tmax=1)
@@ -168,6 +175,7 @@ def create_tfr(raw, condition, freqs, n_cycles, response='induced', baseline=Non
         power_induced = tfr_morlet(epochs.subtract_evoked(), freqs=freqs, n_cycles=n_cycles, return_itc=False, n_jobs=4)
         power = mne.combine_evoked([power_total, power_induced], weights=[1, -1])
     if plot: power.plot(picks='P7')
+    # Apply a baseline correction to the power data
     power.apply_baseline(mode='ratio', baseline=baseline)
     if plot:
         plot_oscillation_bands(power)
@@ -175,7 +183,7 @@ def create_tfr(raw, condition, freqs, n_cycles, response='induced', baseline=Non
     return power
 
 
-def time_frequency(dataset, filename, compute_tfr=True):
+def time_frequency(dataset, filename, scaling='lin', compute_tfr=True):
     """
     Runs time frequency analysis
 
@@ -183,15 +191,14 @@ def time_frequency(dataset, filename, compute_tfr=True):
     :param filename: Filename of either the file from which the TFRs will be loaded
         or to which they will be saved
     :param compute_tfr: If True the TFRs will be created, else the TFRs will be loaded from a precomputed file
+    :param scaling: default 'lin' for linear scaling, else can be 'log' for logarithmic scaling
     """
     # Parameters
-    # Frequency space (from, to, steps) -> Control frequency resolution : Between num=50-80 good for 1-50Hz
-    # freqs = np.linspace(0.1, 50, num=50) # Use this for linear space scaling
-    freqs = np.logspace(*np.log10([0.1, 50]), num=50)
-    # Number of cycles -> Controls time resolution ? At ~freqs/2 good for high frequency resolution
-    n_cycles = freqs / 2  # 1 for high time resolution & freq smoothing, freqs/2 for high freq resolution & time smooth
-    # Baseline -> Should not go post-stimulus, i.e. > 0 -> Best ist pre-stimulus (e.g. -400 to -200ms)
-    baseline = [-0.5, 0]
+    if scaling == 'lin':
+        freqs = np.linspace(0.1, 50, num=50)  # Use this for linear space scaling
+    else:
+        freqs = np.logspace(*np.log10([0.1, 50]), num=50)
+    n_cycles = freqs / 2
     cond1 = []
     cond2 = []
     times = None
@@ -209,6 +216,8 @@ def time_frequency(dataset, filename, compute_tfr=True):
             raw.set_montage('standard_1020', match_case=False)
 
             # Create the two conditions we want to compare
+            # IMPORTANT: If different conditions should be compared you have to change them here, by altering the second
+            # argument passed to create_tfr
             power_cond1 = create_tfr(raw, [('face', 'intact')], freqs, n_cycles, 'induced', (-0.2, 0))
             print('    CONDITION 1 LOADED')
             cond1.append(power_cond1)
@@ -219,25 +228,32 @@ def time_frequency(dataset, filename, compute_tfr=True):
             cond2.append(power_cond2)
             print('    DONE')
 
+        # Save the data so we can access the results more easily
         np.save('cached_data/tf_data/' + filename + '_cond1', cond1)
         np.save('cached_data/tf_data/' + filename + '_cond2', cond2)
     else:
+        # If the data should not be recomputed, load the given filename
         cond1 = np.load('cached_data/tf_data/' + filename + '_cond1.npy', allow_pickle=True).tolist()
         cond2 = np.load('cached_data/tf_data/' + filename + '_cond2.npy', allow_pickle=True).tolist()
     if times is None:
         times = cond1[0].times
+
+    # Some plots
     mne.grand_average(cond1).plot(picks=['P7'], vmin=-3, vmax=3, title='Grand Average P7')
     mne.grand_average(cond2).plot(picks=['P7'], vmin=-3, vmax=3, title='Grand Average P7')
     plot_oscillation_bands(mne.grand_average(cond1))
     plot_oscillation_bands(mne.grand_average(cond2))
+
+    # Compute the cluster permutation
     F, clusters, cluster_p_values, h0 = mne.stats.permutation_cluster_test(
         [mne.grand_average(cond1).data, mne.grand_average(cond2).data], n_jobs=4, verbose='INFO',
         seed=123)
-    plot_tf_cluster(F, clusters, cluster_p_values, freqs, times)
+    plot_tf_cluster(F, clusters, cluster_p_values, freqs, times, scaling)
 
 
 if __name__ == '__main__':
     mne.set_log_level(verbose=VERBOSE_LEVEL)
     ds = 'N170'
     decoding(ds, 'faces_vs_cars', True)
-    time_frequency(ds, 'face_intact_vs_all_0.1_50hz_ncf2', True)
+    time_frequency(ds, 'face_intact_vs_all_0.1_50hz_ncf2', 'log', True)
+

erp_analysis.py

@@ -93,16 +93,18 @@ def create_peak_difference_feature(df, max_subj=40):
 
 def analyze_erp(channels, precompute=True):
     """
-    Execute several statistical tests for different hypothesis, to analyze ERPs
+    Execute several statistical tests for different hypothesis, to analyse ERPs
     :param channels: The channels for which the tests are executed
     :param precompute: If true, the peak-difference data will be computed. Else it will be loaded from a precomputed file,
                         if it exists. This should only be set 'False' if the method was already executed once!
     """
     if precompute:
+        # Precompute the erp peaks
         precompute_erp_df('N170')
 
     for c in channels:
         print("CHANNEL: " + c)
+        # Load the erp peak data and create the features for the t-tests
         erp_df = pd.read_csv('cached_data/erp_peaks/erp_peaks_' + c + '.csv', index_col=0)
         feature_df = create_peak_difference_feature(erp_df)
         # 1. H_a : There is a difference between the N170 peak of recognizing faces and cars

preprocessing_and_cleaning.py

@@ -52,7 +52,7 @@ def filter_data(raw):
     """
     Filter the data of a single subject with a bandpass filter.
     The lower bound ist 0.5Hz to compensate the slow drifts.
-    The upper bound is 50Hz to compensate the high frequencies, including the power line spike at 60Hz
+    The upper bound is 48Hz to compensate the high frequencies, including the power line spike at 60Hz
     :param raw: The data to be filtered
     :return: The filtered data
     """

utils/file_utils.py

@@ -18,7 +18,7 @@ def load_bad_annotations(filepath, fileending="badSegments.csv"):
 
 def load_preprocessed_data(subject, dataset):
     """
-    Load the raw object as well as the annotations of the preprocessed file
+    Load the raw object of the preprocessed file
     :param subject: The subject, for which we want to load the raw object
     :param dataset: The currently viewed dataset
     :param selected_subjects: The manually preprocessed subjects

utils/plot_utils.py

@@ -56,15 +56,17 @@ def plot_grand_average(dataset):
                                      linestyles=['solid', 'solid', 'dotted', 'dotted'])
 
 
-def plot_tf_cluster(F, clusters, cluster_p_values, freqs, times):
+def plot_tf_cluster(F, clusters, cluster_p_values, freqs, times, scaling='lin'):
     """
-    Plot teh F-Statistic values of permutation clusters with p-values <= 0.05 in color and > 0.05 in grey.
+    Plot the F-Statistic values of permutation clusters with p-values <= 0.05 in color and > 0.05 in grey.
+    Currently only works well for the linear scaling. For the logarithmic scaling a different x-axis has to be chosen
 
     :param F: F-Statistics of the permutation clusters
     :param clusters: all permutation clusters
     :param cluster_p_values: p-values of the clusters
     :param freqs: frequency domain
     :param times: time domain
+    :param scaling: default 'lin' for linear scaling, else can be 'log' for logarithmic scaling
     """
     good_c = np.nan * np.ones_like(F)
     for clu, p_val in zip(clusters, cluster_p_values):
@@ -74,16 +76,33 @@ def plot_tf_cluster(F, clusters, cluster_p_values, freqs, times):
     bbox = [times[0], times[-1], freqs[0], freqs[-1]]
     plt.imshow(F, aspect='auto', origin='lower', cmap=cm.gray, extent=bbox, interpolation='None')
     a = plt.imshow(good_c, cmap=cm.RdBu_r, aspect='auto', origin='lower', extent=bbox, interpolation='None')
+
+    if scaling == 'log':
+        ticks = [1, 4, 8, 12, 14, 18, 22, 26, 30, 34, 38, 42, 46, 50]
+        labels = [round(freqs[i], 2) for i in range(len(freqs)) if i + 1 in ticks]
+        plt.yticks(ticks, labels)
+
     plt.colorbar(a)
     plt.xlabel('Time (s)')
     plt.ylabel('Frequency (Hz)')
     plt.show()
 
 
+
 def plot_oscillation_bands(condition):
+    """
+        Plot the oscillation bands for a given condition in the time from 130ms to 200ms
+        :param condition: the condition to plot the oscillation bands for
+        """
     fig, axis = plt.subplots(1, 5, figsize=(25, 5))
-    condition.plot_topomap(baseline=(-0.2, 0), fmin=0, fmax=4, title='Delta', axes=axis[0], show=False, vmin=0, vmax=1.5, tmin=0, tmax=1)
-    condition.plot_topomap(baseline=(-0.2, 0), fmin=4, fmax=8, title='Theta', axes=axis[1], show=False, vmin=0, vmax=0.7, tmin=0, tmax=1)
-    condition.plot_topomap(baseline=(-0.2, 0), fmin=8, fmax=12, title='Alpha', axes=axis[2], show=False, vmin=-0.15, vmax=0.2, tmin=0, tmax=1)
-    condition.plot_topomap(baseline=(-0.2, 0), fmin=13, fmax=30, title='Beta', axes=axis[3], show=False, vmin=-0.18, vmax=0.2, tmin=0, tmax=1)
-    condition.plot_topomap(baseline=(-0.2, 0), fmin=30, fmax=45, title='Gamma', axes=axis[4], vmin=0, vmax=0.2, tmin=0, tmax=1)
+    condition.plot_topomap(baseline=(-0.2, 0), fmin=0, fmax=4, title='Delta', axes=axis[0], show=False, vmin=0,
+                           vmax=1.5, tmin=0.13, tmax=0.2)
+    condition.plot_topomap(baseline=(-0.2, 0), fmin=4, fmax=8, title='Theta', axes=axis[1], show=False, vmin=0,
+                           vmax=0.7, tmin=0.13, tmax=0.2)
+    condition.plot_topomap(baseline=(-0.2, 0), fmin=8, fmax=12, title='Alpha', axes=axis[2], show=False, vmin=-0.25,
+                           vmax=0.2, tmin=0.13, tmax=0.2)
+    condition.plot_topomap(baseline=(-0.2, 0), fmin=13, fmax=30, title='Beta', axes=axis[3], show=False, vmin=-0.21,
+                           vmax=0.2, tmin=0.13, tmax=0.2)
+    condition.plot_topomap(baseline=(-0.2, 0), fmin=30, fmax=45, title='Gamma', axes=axis[4], vmin=-0.05, vmax=0.2,
+                           tmin=0.13,
+                           tmax=0.2)