import os import mne import numpy as np import pandas as pd import gradio as gr from transformers import AutoTokenizer, AutoModelForCausalLM import torch # Load LLM model_name = "tiiuae/falcon-7b-instruct" tokenizer = AutoTokenizer.from_pretrained(model_name) model = AutoModelForCausalLM.from_pretrained( model_name, trust_remote_code=True, torch_dtype=torch.float16, device_map="auto" ) def compute_band_power(psd, freqs, fmin, fmax): freq_mask = (freqs >= fmin) & (freqs <= fmax) band_psd = psd[:, freq_mask].mean() return float(band_psd) def inspect_file(file): """ Inspect the uploaded file to determine available columns. If FIF: Just inform that it's an MNE file and no time column is needed. If CSV: Return a list of columns (both numeric and non-numeric). """ if file is None: return "No file uploaded.", [], "No preview available." file_path = file.name _, file_ext = os.path.splitext(file_path) file_ext = file_ext.lower() if file_ext == ".fif": # FIF files: We know they're MNE compatible # No columns to choose from, just proceed with default analysis return ( "FIF file detected. No need for time column selection. Default sampling frequency will be read from file.", [], "FIF file doesn't require further inspection." ) elif file_ext == ".csv": # Read a small portion of the CSV to determine columns try: df = pd.read_csv(file_path, nrows=5) except Exception as e: return f"Error reading CSV: {e}", [], "Could not read CSV preview." cols = list(df.columns) preview = df.head().to_markdown() return ( "CSV file detected. Select a time column if available, or leave it blank and specify a default frequency.", cols, preview ) else: return "Unsupported file format.", [], "No preview available." def load_eeg_data(file_path, default_sfreq=256.0, time_col='time'): """ Load EEG data with flexibility. If FIF: Use MNE's read_raw_fif directly. If CSV: - If time_col is given and present in the file, use it. - Otherwise, assume default_sfreq. """ _, file_ext = os.path.splitext(file_path) file_ext = file_ext.lower() if file_ext == '.fif': raw = mne.io.read_raw_fif(file_path, preload=True) elif file_ext == '.csv': df = pd.read_csv(file_path) # If time_col is specified and in df, use it to compute sfreq if time_col and time_col in df.columns: time = df[time_col].values data_df = df.drop(columns=[time_col]) # Drop non-numeric columns for col in data_df.columns: if not pd.api.types.is_numeric_dtype(data_df[col]): data_df = data_df.drop(columns=[col]) if len(time) < 2: # Not enough time points, fallback to default_sfreq sfreq = default_sfreq else: # Compute sfreq from time sfreq = 1.0 / np.mean(np.diff(time)) else: # No time column used, assume default_sfreq # Drop non-numeric columns for col in df.columns: if not pd.api.types.is_numeric_dtype(df[col]): df = df.drop(columns=[col]) data_df = df sfreq = default_sfreq ch_names = list(data_df.columns) data = data_df.values.T # shape: (n_channels, n_samples) ch_types = ['eeg'] * len(ch_names) info = mne.create_info(ch_names=ch_names, sfreq=sfreq, ch_types=ch_types) raw = mne.io.RawArray(data, info) else: raise ValueError("Unsupported file format. Provide a FIF or CSV file.") return raw def analyze_eeg(file, default_sfreq, time_col): if file is None: return "No file uploaded." raw = load_eeg_data(file.name, default_sfreq=float(default_sfreq), time_col=time_col) psd, freqs = mne.time_frequency.psd_welch(raw, fmin=1, fmax=40) alpha_power = compute_band_power(psd, freqs, 8, 12) beta_power = compute_band_power(psd, freqs, 13, 30) data_summary = ( f"Alpha power: {alpha_power:.3f}, Beta power: {beta_power:.3f}. " f"The EEG shows stable alpha rhythms and slightly elevated beta activity." ) prompt = f"""You are a neuroscientist analyzing EEG features. Data Summary: {data_summary} Provide a concise, user-friendly interpretation of these findings in simple terms. """ inputs = tokenizer.encode(prompt, return_tensors="pt").to(model.device) outputs = model.generate( inputs, max_length=200, do_sample=True, top_k=50, top_p=0.95 ) summary = tokenizer.decode(outputs[0], skip_special_tokens=True) return summary ######################### # BUILD THE GRADIO INTERFACE ######################### # Step 1: Inspect file def preview_file(file): msg, cols, preview = inspect_file(file) # Instead of gr.Dropdown.update(...) return msg, {"choices": cols, "value": None}, preview with gr.Blocks() as demo: gr.Markdown("# NeuroNarrative-Lite: EEG Summary with Flexible Preprocessing") gr.Markdown( "Upload an EEG file (FIF or CSV). If it's CSV, we will inspect the file and let you choose a time column. " "If no suitable time column is found, leave it blank and provide a default sampling frequency." ) file_input = gr.File(label="Upload your EEG data (FIF or CSV)") preview_button = gr.Button("Inspect File") msg_output = gr.Markdown() cols_dropdown = gr.Dropdown(label="Select Time Column (optional)", interactive=True) preview_output = gr.Markdown() preview_button.click(preview_file, inputs=[file_input], outputs=[msg_output, cols_dropdown, preview_output]) default_sfreq_input = gr.Textbox(label="Default Sampling Frequency (Hz) if no time column", value="256") analyze_button = gr.Button("Run Analysis") result_output = gr.Textbox(label="Analysis Summary") analyze_button.click(analyze_eeg, inputs=[file_input, default_sfreq_input, cols_dropdown], outputs=[result_output]) if __name__ == "__main__": demo.launch()