import subprocess

import os

def excute_cmd(command):

    '''

    Execute a command and check for success.

    Args:

        command ('str'): Command to execute.

    Returns:

        result ('str'): Output of the command if successful.

    '''

    # excute the command

    result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, shell=True)

    # Check the return code to see if the command was successful

    if result.returncode == 0:

        # print("Command executed successfully.")

        # print("Output:")

        return result.stdout

    else:

        print(f"Command failed with an error: {command}")

        print(result.stderr)

        return result.stderr

# Perform registration and label propagation

def register_elastix(fixed_path, 

                    moving_path, 

                    reg_params, 

                    reg_params_key,

                    create_dir_callback, 

                    excute_cmd_callback,

                    fMask = None,

                    mMask = None):

    '''

    Perform image registration using elastix.

    Args:

        fixed_path ('str'): Path to the fixed image.

        moving_path ('str'): Path to the moving image.

        reg_params ('str'): Registration parameters for elastix.

        reg_params_key ('str'): Key to identify the registration parameters output folder.

        create_dir_callback ('function'): Callback function to create directories.

        excute_cmd_callback ('function'): Callback function to execute commands.

        fMask ('str'): Optional path to a mask file.

        mMask ('str'): Optional path to a mask file.

    Returns:

        None

    '''

    # Get the names of the fixed and moving images for the output directory, names without the file extensions

    reg_fixed_name  = fixed_path.replace("\\", "/").split("/")[-1].split(".")[0] # \\

    reg_moving_name = moving_path.replace("\\", "/").split("/")[-1].split(".")[0]

    # create output dir

    output_dir = f'output/{reg_params_key}/images/output_{reg_fixed_name}/{reg_moving_name}'

    create_dir_callback(output_dir)

    # create elastix command line

    if fMask and not mMask:

        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" -fMask {fMask} {reg_params} -out "{output_dir}"'

    elif mMask and not fMask:

        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" -mMask {mMask} {reg_params} -out "{output_dir}"'

    elif mMask and fMask:

        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" -fMask {fMask} -mMask {mMask} {reg_params} -out "{output_dir}"'

    else:

        command_line = f'elastix -f "{fixed_path}" -m "{moving_path}" {reg_params} -out "{output_dir}"'

    print("Excuting command: ", command_line)

    # call elastix command

    excute_cmd_callback(command_line)

def label_propagation_transformix(

    fixed_path, 

    moving_path, 

    input_label, 

    transform_path, 

    replace_text_in_file_callback, 

    create_dir_callback, 

    excute_cmd_callback):

    '''

    Apply label propagation using transformix.

    Args:

        fixed_path ('str'): Path to the fixed image.

        moving_path ('str'): Path to the moving image.

        input_label ('str'): Path to the input label image.

        transform_path ('str'): Path to the transformation parameters.

        replace_text_in_file_callback ('function'): Callback function to replace text in a file.

        create_dir_callback ('function'): Callback function to create directories.

        excute_cmd_callback ('function'): Callback function to execute commands.

    Returns:

        None

    '''

    replace_text_in_file_callback(

        transform_path, 

        search_text = '(FinalBSplineInterpolationOrder 3)', 

        replacement_text =  '(FinalBSplineInterpolationOrder 0)')

    # Get the names of the fixed and moving images for the output directory, names without the file extensions

    reg_fixed_name  = fixed_path.replace("\\", "/").split("/")[-1].split(".")[0] 

    reg_moving_name = os.path.join(moving_path.replace("\\", "/").split("/")[0], moving_path.replace("\\", "/").split("/")[-1].split(".")[0])

    # create an output directory for the labels

    output_dir = f'output/labels/output_{reg_fixed_name}/{reg_moving_name}' # rem _float64

    # creates the output directory

    create_dir_callback(output_dir)

    # create transformix command line

    command_line = f'transformix -in "{input_label}" -tp "{transform_path}"  -out "{output_dir}"'

    # run transformix on all combinations

    excute_cmd_callback(command_line)

def control_points_transformix(

    fixed_path, 

    moving_path, 

    reg_params_key,

    input_points,

    transform_path,

    replace_text_in_file_callback,

    create_dir_callback, 

    excute_cmd_callback

):

    replace_text_in_file_callback(

        transform_path, 

        search_text = '(FinalBSplineInterpolationOrder 3)', 

        replacement_text =  '(FinalBSplineInterpolationOrder 0)')

    replace_text_in_file_callback(

            transform_path, 

            search_text = '(ResultImagePixelType "short")', 

            replacement_text =  '(ResultImagePixelType "float")')

    # Get the names of the fixed and moving images for the output directory, names without the file extensions

    reg_fixed_name  = fixed_path.replace("\\", "/").split("/")[-1].split(".")[0] 

    reg_moving_name = moving_path.replace("\\", "/").split("/")[-1].split(".")[0]

    # create an output directory for the labels

    output_dir = f'output/{reg_params_key}/points/output_{reg_fixed_name}/{reg_moving_name}' # rem _float64

    # creates the output directory

    create_dir_callback(output_dir)

    # create transformix command line

    command_line = f'transformix -def "{input_points}" -tp "{transform_path}"  -out "{output_dir}"'

    # run transformix on all combinations

    excute_cmd_callback(command_line)

    return output_dir