2024_Ruthe_SND/code/GetQuantitativeValues.py

import os
import glob
import pandas as pd
import nibabel as nib
import numpy as np
from tqdm import tqdm
from concurrent.futures import ProcessPoolExecutor
from scipy.ndimage import binary_dilation

def create_output_dir(output_dir):
    """Create the output directory if it does not exist."""
    if not os.path.exists(output_dir):
        os.makedirs(output_dir)

def save_mask_as_nifti(mask_data, output_file):
    """Save mask data as NIfTI file."""
    mask_data_int = mask_data.astype(np.uint8)
    mask_img = nib.Nifti1Image(mask_data_int, affine=None)
    nib.save(mask_img, output_file)

def process_single_file(file_info):
    """Process a single file path."""
    file_path, session_mapping, output_path, save_nifti_mask = file_info
    
    csvdata = []  # Local CSV data collector
    
    # Extract information from the file path
    subject_id = file_path.split(os.sep)[-5]
    time_point = file_path.split(os.sep)[-4]

    # Map the extracted time_point directly using session_mapping
    merged_time_point = session_mapping.get(time_point, None)

    if merged_time_point is None:
        print(f"Warning: No mapping found for {time_point}. Skipping file: {file_path}")
        return []

    # Extract the q_type from the filename
    q_type = os.path.basename(file_path).split("_flipped")[0]

    # Attempt to find the stroke mask path
    try:
        search_stroke = os.path.join(os.path.dirname(file_path), "*StrokeMask_scaled.nii")
        stroke_path = glob.glob(search_stroke)[0]
    except IndexError:
        stroke_path = None

    # Create the temp path to search for dwi_masks
    temp_path = os.path.join(os.path.dirname(file_path), "RegisteredTractMasks_adjusted")
    dwi_masks = glob.glob(os.path.join(temp_path, "*dwi_flipped.nii.gz"))
    white_matter_index = next((i for i, path in enumerate(dwi_masks) if "White_matter" in path), None)
    white_matter_path = dwi_masks.pop(white_matter_index)
    
    # Load white matter mask
    white_matter_img = nib.load(white_matter_path)
    white_matter_data = white_matter_img.get_fdata()

    # Load DWI data using nibabel
    dwi_img = nib.load(file_path)
    dwi_data = dwi_img.get_fdata()

    # Loop through masks and calculate average values
    pix_dialation = [0, 1, 2, 3, 4]
    for mask_path in dwi_masks:
        mask_name = os.path.basename(mask_path).replace("registered", "").replace("flipped", "").replace(".nii.gz", "").replace("__dwi_", "").replace("_dwi_", "")
        mask_img = nib.load(mask_path)
        mask_data_pre_dilation = mask_img.get_fdata()

        # Determine if it's an AMBA mask
        AMBA_flag = "AMBA" in mask_name

        # Calculate the average value within the mask region for each dilation
        for pp in pix_dialation:
            if pp != 0:
                mask_data0 = binary_dilation(mask_data_pre_dilation, iterations=pp)
            else:
                mask_data0 = mask_data_pre_dilation > 0

            mask_data = mask_data0 #& (white_matter_data > 0)
            if stroke_path:
                stroke_image = nib.load(stroke_path)
                stroke_data = stroke_image.get_fdata()
                # Subtracting stroke region from mask except in baseline
                if merged_time_point != 0:
                    mask_data = mask_data & (stroke_data < 1)
                strokeFlag = "Stroke"
            else:
                strokeFlag = "Sham"

            # Calculate average DWI value within the mask
            masked_data = dwi_data[mask_data > 0]
            non_zero_masked_data = masked_data[masked_data != 0]  # Exclude zero values
            average_value = np.nanmean(non_zero_masked_data)  # Calculate mean only on non-zero elements

            # Save the mask as NIfTI file if the flag is set
            if save_nifti_mask and pp > 0 and merged_time_point in [3] and q_type == "fa":
                output_nifti_file = os.path.join(output_path,
                                                  f"{subject_id}_tp_{merged_time_point}_{q_type}_{mask_name}_{pp}.nii.gz")
                save_mask_as_nifti(mask_data, output_nifti_file)

            # Append data to local CSV data
            csvdata.append([file_path, subject_id, time_point, merged_time_point, q_type, mask_name, pp, average_value, strokeFlag, AMBA_flag])

    return csvdata

def process_files(input_path, output_path, save_nifti_mask):
    """Process DWI files and generate data using parallel processing."""
    session_mapping = {
        "ses-Baseline": 0, "ses-Baseline1": 0, "ses-pre": 0,
        "ses-P1": 3, "ses-P2": 3, "ses-P3": 3, "ses-P4": 3, "ses-P5": 3,
        "ses-P6": 7, "ses-P7": 7, "ses-P8": 7, "ses-P9": 7, "ses-P10": 7,
        "ses-P11": 14, "ses-P12": 14, "ses-P13": 14, "ses-P14": 14, 
        "ses-P15": 14, "ses-P16": 14, "ses-P17": 14, "ses-P18": 14, 
        "ses-P19": 21, "ses-D21": 21, "ses-P20": 21, "ses-P21": 21,
        "ses-P22": 21, "ses-P23": 21, "ses-P24": 21, "ses-P25": 21,
        "ses-P26": 28, "ses-P27": 28, "ses-P28": 28, "ses-P29": 28, 
        "ses-P30": 28, "ses-P42": 42, "ses-P43": 42,
        "ses-P56": 56, "ses-P57": 56, "ses-P58": 56,
        "ses-P151": 28
    }

    # Get all relevant file paths
    file_paths = glob.glob(os.path.join(input_path, "**", "dwi", "DSI_studio", "*_flipped.nii.gz"), recursive=True)

    # Prepare arguments for parallel processing
    arguments = [(file_path, session_mapping, output_path, save_nifti_mask) for file_path in file_paths]

    # Initialize a list to store results
    csv_data = []

    # Use ProcessPoolExecutor to parallelize the file path processing
    with ProcessPoolExecutor(max_workers=6) as executor:
        # Process files in parallel
        results = list(tqdm(executor.map(process_single_file, arguments), total=len(file_paths), desc="Processing files"))

    # Aggregate the results
    for result in results:
        csv_data.extend(result)

    # Create a DataFrame
    df = pd.DataFrame(csv_data,
                      columns=["fullpath", "subjectID", "timePoint", "merged_timepoint", "Qtype", "mask_name",
                               "dialation_amount", "Value", "Group", "is_it_AMBA"])

    return df

def main():
    # Use argparse to get command-line inputs
    import argparse
    parser = argparse.ArgumentParser(description="Process DWI files and generate data.")
    parser.add_argument("-i", "--input", type=str, required=True, help="Input directory containing DWI files.")
    parser.add_argument("-o", "--output", type=str, required=True, help="Output directory to save results.")
    parser.add_argument("-n", "--nifti-mask", action="store_true", default=False, help="Set to save masks as NIfTI files.")
    args = parser.parse_args()

    # Create the output directory if it does not exist
    create_output_dir(args.output)

    # Process files
    df = process_files(args.input, args.output, args.nifti_mask)

    # Save the DataFrame as CSV
    csv_file = os.path.join(args.output, "Quantitative_results_from_dwi_processing.csv")
    df.to_csv(csv_file, index=False)
    print("CSV file created at:", csv_file)

if __name__ == "__main__":
    main()