Get_Example_Images.py

import h5py
import os
import numpy as np
import Preprocessing_Utils

def get_example_images(base_directory, output_directory, default_position=10000):
    print("Getting Example Image For Session", base_directory)

    # Load Motion Corrected Data
    motion_corrected_filename = "Motion_Corrected_Downsampled_Data.hdf5"
    motion_corrected_file = os.path.join(base_directory, motion_corrected_filename)
    motion_corrected_data_container = h5py.File(motion_corrected_file, 'r')
    blue_matrix = motion_corrected_data_container["Blue_Data"]
    violet_matrix = motion_corrected_data_container["Violet_Data"]

    # Get Blue and Violet Example Images
    blue_image = blue_matrix[:, default_position]
    violet_image = violet_matrix[:, default_position]

    # Load Mask
    indicies, image_height, image_width = Preprocessing_Utils.load_downsampled_mask(base_directory)

    # Reconstruct Images
    blue_image = Preprocessing_Utils.create_image_from_data(blue_image, indicies, image_height, image_width)
    violet_image = Preprocessing_Utils.create_image_from_data(violet_image, indicies, image_height, image_width)

    # Save Images
    np.save(os.path.join(output_directory, "Blue_Example_Image.npy"), blue_image)
    np.save(os.path.join(output_directory, "Violet_Example_Image.npy"), violet_image)

    # Close File
    motion_corrected_data_container.close()


"""
base_directory = r"/media/matthew/External_Harddrive_2/Widefield_Data_New_Pipeline/Mutant_Data/NXAK16.1B"
session_list = os.listdir(base_directory)

for session in session_list:
    session_directory = os.path.join(base_directory, session)
    get_example_images(session_directory, session_directory)
"""