from nimbus_bci import NimbusLDA
from nimbus_bci.mne_integration import from_mne_epochs, extract_csp_features
import mne

# 1. Preprocess with MNE-Python
raw = mne.io.read_raw_brainvision('motor_imagery.vhdr', preload=True)
raw.filter(8.0, 30.0)

# 2. Create epochs
events = mne.find_events(raw)
event_id = {'Left': 1, 'Right': 2, 'Feet': 3, 'Tongue': 4}
epochs = mne.Epochs(raw, events, event_id, tmin=0, tmax=4.0, baseline=None, preload=True)

# 3. Extract CSP features using nimbus-bci
X_csp, y = extract_csp_features(epochs, n_components=6)

# 4. Train directly (no data export needed!)
clf = NimbusLDA()
clf.fit(X_csp, y)

# 5. Predict
predictions = clf.predict(X_csp)
print(f"Accuracy: {np.mean(predictions == y):.1%}")

pip install mne scipy scikit-learn numpy matplotlib

import mne
import numpy as np
from scipy.io import savemat
from mne.decoding import CSP
from mne.preprocessing import ICA

# Load raw EEG data
raw = mne.io.read_raw_brainvision('motor_imagery.vhdr', preload=True)

# Step 1: Set channel locations (if available)
# raw.set_montage('standard_1020')

# Step 2: Bandpass filter (8-30 Hz for motor imagery)
raw.filter(8.0, 30.0, method='iir', picks='eeg')

# Step 3: Remove artifacts with ICA
ica = ICA(n_components=15, random_state=42, max_iter='auto')
ica.fit(raw)

# Identify and exclude bad components (eye blinks, muscle)
ica.exclude = []  # You'll identify these by inspecting ica.plot_components()
# Example: ica.exclude = [0, 1]  # First two components are eye blinks

raw_clean = ica.apply(raw)

# Step 4: Find events
events = mne.find_events(raw_clean, stim_channel='STI')

# Create event mapping (adjust based on your setup)
event_id = {
    'Left Hand': 1,
    'Right Hand': 2,
    'Feet': 3,
    'Tongue': 4
}

# Step 5: Epoch data (0-4 seconds post-cue)
epochs = mne.Epochs(
    raw_clean,
    events,
    event_id=event_id,
    tmin=0,
    tmax=4.0,
    baseline=None,
    preload=True
)

# Step 6: Extract CSP features
# Get data for CSP (epochs × channels × time)
X = epochs.get_data()  # (n_epochs, n_channels, n_times)
y = epochs.events[:, -1]

# Train CSP
csp = CSP(n_components=8, transform_into='csp_space', reg='shrinkage')
X_csp = csp.fit_transform(X, y)  # (n_epochs, n_components, n_times)

# Step 7: Format for NimbusSDK.jl
# NimbusSDK expects: (n_features × n_samples × n_trials)
# From MNE we have: (n_trials, n_components, n_times)
# Need to: transpose to (n_components, n_times, n_trials)
X_csp_julia = np.transpose(X_csp, (1, 2, 0))

# Step 8: Save to .mat for Julia
savemat('motor_imagery_features.mat', {
    'features': X_csp_julia,  # (16, 1000, 40) - 16 features, 1 second, 40 trials
    'labels': y,              # [1, 2, 3, 4, 1, 2, ...]
    'channels': epochs.ch_names,
    'sampling_rate': epochs.info['sfreq']
})

print("✓ Preprocessing complete!")
print(f"  Features: {X_csp_julia.shape[0]} features × {X_csp_julia.shape[1]} samples × {X_csp_julia.shape[2]} trials")
print(f"  Labels: {len(np.unique(y))} classes")

using NimbusSDK, MAT

# Load features
data = matread("motor_imagery_features.mat")
features = data["features"]  # Should be (16, 1000, 40)
labels = vec(Int.(data["labels"]))

println("Loaded: $(size(features))")
println("Classes: $(unique(labels))")

# Create BCIData
metadata = BCIMetadata(
    sampling_rate = data["sampling_rate"],
    paradigm = :motor_imagery,
    feature_type = :csp,
    n_features = 16,
    n_classes = 4,
    chunk_size = nothing
)

bci_data = BCIData(features, metadata, labels)

# Authenticate and run inference
NimbusSDK.install_core("your-api-key")
# Choose model type based on your needs: NimbusLDA, NimbusQDA, or NimbusProbit
model = load_model(NimbusLDA, "motor_imagery_4class_v1")
results = predict_batch(model, bci_data)

println("Predictions: ", results.predictions)
println("Mean confidence: ", mean(results.confidences))

import mne
import numpy as np
from scipy.io import savemat

# Load and filter for P300 (0.5-10 Hz)
raw = mne.io.read_raw_brainvision('p300_data.vhdr', preload=True)
raw.filter(0.5, 10.0, method='iir')

# ICA artifact removal
ica = ICA(n_components=15, random_state=42)
ica.fit(raw)
ica.exclude = [0, 1]  # Eye blinks
raw_clean = ica.apply(raw)

# Events
events = mne.find_events(raw_clean)
event_id = {'Target': 1, 'Non-target': 2}

# Epoch around stimulus (-0.2 to 0.8 seconds)
epochs = mne.Epochs(
    raw_clean,
    events,
    event_id=event_id,
    tmin=-0.2,
    tmax=0.8,
    baseline=(-0.2, 0),
    preload=True
)

# Extract ERP amplitudes
X = epochs.get_data()  # (n_epochs, n_channels, n_times)
y = epochs.events[:, -1]

# Average across time window for each channel
X_erp = np.mean(X, axis=2)  # (n_epochs, n_channels)

# Save for Julia (transform to expected shape)
X_erp_julia = X_erp.T  # (n_channels, n_epochs)

savemat('p300_features.mat', {
    'features': X_erp_julia,
    'labels': y
})

% Load dataset
EEG = pop_loadset('motor_imagery_data.set');

% Step 1: Bandpass filter (8-30 Hz)
EEG = pop_eegfiltnew(EEG, 8, 30, [], [], 0, 0, 'fir', 'onepass-zerophase');

% Step 2: Run ICA
EEG = pop_runica(EEG, 'icatype', 'runica');

% Step 3: Inspect components and remove artifacts
% Use EEGLAB GUI: EEGLAB > Tools > Inspect components
% Mark bad components for rejection

EEG = pop_subcomp(EEG, bad_components, 0);  % Remove bad components

% Step 4: Create epochs
EEG = pop_epoch(EEG, {'1', '2', '3', '4'}, [0 4], 'newname', 'epoched');

% Step 5: Save for CSP extraction (use external tool or Python)
pop_saveset(EEG, 'filename', 'epoched_data.set');

% Export to Python for CSP
pop_exportbids(EEG, 'output', 'bids_export');  % Or use pop_eeglab2mne

% Use BCILAB for CSP feature extraction
% BCILAB is an EEGLAB extension for BCI analysis

% Install BCILAB
cd ~/eeglab/plugins
wget('http://www.bcilab.org/download/bcilab.zip')
unzip('bcilab.zip')

% Use BCILAB CSP
[sources, patterns, eigenvalues] = proc_multiclass_csp(EEG.data, ...
    EEG.epoch(:, :, labels), 'classes', [1, 2, 3, 4], 'ncomp', 8);

% Extract CSP features
csp_features = proc_spatialfilter(EEG.data, patterns);
features = reshape(csp_features, 16, size(csp_features, 2), size(csp_features, 3));

import pandas as pd
import numpy as np

# OpenVibe exports as CSV
df = pd.read_csv('openvibe_output.csv')

# Assuming format: Time, Channel1, Channel2, ..., Label
features_raw = df.iloc[:, 1:-1].values.T  # Transpose to (channels × samples)
labels = df['Label'].values

# Reshape for NimbusSDK (if you have trial boundaries)
# You'll need to segment based on labels
features_segmented = segment_by_labels(features_raw, labels)
# Result: (n_features, n_samples_per_trial, n_trials)

# Save for Julia
import scipy.io as sio
sio.savemat('openvibe_features.mat', {
    'features': features_segmented,
    'labels': labels
})

# MNE: (n_epochs, n_components, n_times)
features_mne  # (40, 8, 1000)

# Julia SDK expects: (n_features × n_samples × n_trials)
features_julia = np.transpose(features_mne, (1, 2, 0))  # (8, 1000, 40)

% MATLAB: (channels, samples, epochs)
features_matlab  % (16, 1000, 40)

% Already correct for Julia! No transformation needed

# CSV: Time series with labels
df = pd.read_csv('data.csv')

# Convert to trials (segment by label changes)
features_julia = segment_to_trials(df)  # (n_features, n_samples, n_trials)

def check_preprocessing_quality(features, labels):
    """Check data quality before saving for Julia"""
    
    # Check shape
    assert features.ndim == 3, "Features must be 3D: (features, samples, trials)"
    n_features, n_samples, n_trials = features.shape
    
    # Check for NaN/Inf
    assert not np.any(np.isnan(features)), "Features contain NaN values"
    assert not np.any(np.isinf(features)), "Features contain Inf values"
    
    # Check labels
    assert len(labels) == n_trials, "Labels must match number of trials"
    assert labels.min() >= 1, "Labels must be 1-indexed (start at 1)"
    assert labels.max() <= len(np.unique(labels)), "Labels must be consecutive"
    
    # Check value ranges (not too large)
    assert np.abs(features).max() < 1e6, "Features have suspiciously large values"
    
    print("✓ All quality checks passed!")
    print(f"  Shape: ({n_features}, {n_samples}, {n_trials})")
    print(f"  Classes: {np.unique(labels)}")
    print(f"  Range: [{features.min():.3f}, {features.max():.3f}]")
    
    return True

# Use it
check_preprocessing_quality(X_csp_julia, y)

using NimbusSDK

# Load and validate
data = matread("features.mat")
features = data["features"]
labels = Int.(vec(data["labels"]))

println("Loaded shape: ", size(features))
println("Labels: ", unique(labels))

# Check with SDK
metadata = BCIMetadata(
    sampling_rate = 250.0,
    paradigm = :motor_imagery,
    feature_type = :csp,
    n_features = size(features, 1),
    n_classes = length(unique(labels))
)

bci_data = BCIData(features, metadata, labels)

# Run diagnostics
report = diagnose_preprocessing(bci_data)
if !isempty(report.errors)
    @error "Issues found: $(report.errors)"
end

println("Quality score: ", round(report.quality_score * 100, digits=1), "%")

using NimbusSDK

# 1. Estimate normalization parameters from TRAINING data
train_features = csp_features_train  # (16 × 250 × 80)
norm_params = estimate_normalization_params(train_features; method=:zscore)

# 2. Apply to BOTH training and test data
train_norm = apply_normalization(train_features, norm_params)
test_norm = apply_normalization(test_features, norm_params)

# 3. Save parameters with your model
@save "model_with_norm.jld2" model norm_params

# 4. Later: Load and apply same parameters
@load "model_with_norm.jld2" model norm_params
new_data_norm = apply_normalization(new_data, norm_params)

# Transpose from MNE format to Julia format
features_julia = np.transpose(features_mne, (1, 2, 0))

# MNE labels start at 0, Julia expects 1-indexed
labels_julia = labels + 1

# In Julia, ensure proper types
features = Float64.(data["features"])
labels = Int.(vec(data["labels"]))