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pre_patch_scan_shuffle.py
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pre_patch_scan_shuffle.py
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import argparse
import sys
import mpi_utils
import numpy as np
import os
import shutil
# Command line arguments
parser = argparse.ArgumentParser(description='shuffling scans from all patients before using patch code')
parser.add_argument('--input-folder', type=str, required=True, help='directory name containing training images')
parser.add_argument('--output-folder', type=str, required=True, help='new directory name to containing randomized scans for all patients')
parser.add_argument('--input-gen-folder', type=str, default='quarter_3mm', help="folder name containing noisy (input) measurements")
parser.add_argument('--target-gen-folder', type=str, default='full_3mm', help="folder name containing clean (target) measurements")
parser.add_argument('--file-extension', type=str, default='.IMA', help="extension name of training images")
parser.add_argument('--nsplit', type=int, default=1, help="no of splits of the output folder")
parser.add_argument('--multi-patients', action='store_true', help='if there are multiple-subfolders related to different parents?')
args = parser.parse_args()
def rename_n_copy_file(shuff_paths, ind, final_dest, hold_fld, file_ext):
init_path = shuff_paths[ind]
init_path_split = init_path.split('/')
init_fn = init_path_split[-1]
# first move to place holder
shutil.move(init_path, hold_fld)
# rename the file inside place holder
new_fn = hold_fld + '/' + str(ind) + file_ext
os.rename(os.path.join(hold_fld, init_fn), new_fn)
# copy the rename input to its final destination
shutil.move(new_fn, final_dest)
# args.input_folder = 'raw_data_mixed'
# args.output_folder= 'raw_data_randomize'
args.random_N = None
input_folder_cp = args.input_folder + '_cp'
shutil.copytree(args.input_folder, input_folder_cp)
args.input_folder = input_folder_cp
all_input_paths, all_target_paths = mpi_utils.img_paths4rm_training_directory(args)
Nimgs = len(all_input_paths)
shuffled_Nimgs_arr = np.arange(Nimgs)
np.random.shuffle(shuffled_Nimgs_arr)
shuff_input_paths = all_input_paths[shuffled_Nimgs_arr]
shuff_target_paths = all_target_paths[shuffled_Nimgs_arr]
print(shuff_input_paths)
print('target paths:')
print(shuff_target_paths)
placeholder_fld = 'placeholder'
if not os.path.isdir(placeholder_fld): os.makedirs(placeholder_fld)
if args.nsplit ==1:
input_final_dest = os.path.join(args.output_folder, 'mx_data', args.input_gen_folder)
target_final_dest = os.path.join(args.output_folder,'mx_data', args.target_gen_folder)
if not os.path.isdir(input_final_dest): os.makedirs(input_final_dest)
if not os.path.isdir(target_final_dest): os.makedirs(target_final_dest)
for ip in range(len(all_input_paths)):
# input and target files rename and move
rename_n_copy_file(shuff_input_paths, ip, input_final_dest, placeholder_fld, args.file_extension)
rename_n_copy_file(shuff_target_paths, ip, target_final_dest, placeholder_fld, args.file_extension)
else:
split_shuff_input_path =np.array_split(shuff_input_paths, args.nsplit)
split_shuff_target_path =np.array_split(shuff_target_paths, args.nsplit)
for iSp in range(args.nsplit):
input_final_dest = os.path.join(args.output_folder, 'part_' + str(iSp), 'mx_data', args.input_gen_folder)
target_final_dest = os.path.join(args.output_folder, 'part_' + str(iSp), 'mx_data', args.target_gen_folder)
if not os.path.isdir(input_final_dest): os.makedirs(input_final_dest)
if not os.path.isdir(target_final_dest): os.makedirs(target_final_dest)
for ip in range(len(split_shuff_input_path[iSp])):
rename_n_copy_file(split_shuff_input_path[iSp], ip, input_final_dest, placeholder_fld, args.file_extension)
rename_n_copy_file(split_shuff_target_path[iSp], ip, target_final_dest, placeholder_fld, args.file_extension)
os.rmdir(placeholder_fld)
shutil.rmtree(input_folder_cp)
# input_folder_cp = args.input_folder + '_cp'
'''
all_patient_folder = os.listdir(args.input_folder)
if nsplit == 1:
for ii in range(len(all_patient_folder)):
new_input_folder = args.output_folder + '/' + all_patient_folder[ii] + '/' + args.input_gen_folder
new_target_folder = args.output_folder + '/' + all_patient_folder[ii] + '/' + args.target_gen_folder
if not os.path.isdir(new_input_folder): os.makedirs(new_input_folder)
if not os.path.isdir(new_target_folder): os.makedirs(new_target_folder)
for ip in range(len(all_input_paths)):
each_init_path_4r_input = shuff_input_paths[ip]
each_init_path_split_4r_input = each_init_path_4r_input.split('/')
each_final_path_4r_input = os.path.join(args.output_folder, each_init_path_split_4r_input[-3], each_init_path_split_4r_input[-2])
shutil.copy(each_init_path_4r_input, each_final_path_4r_input)
each_init_path_4r_target = shuff_target_paths[ip]
each_init_path_split_4r_target = each_init_path_4r_target.split('/')
each_final_path_4r_target = os.path.join(args.output_folder, each_init_path_split_4r_target[-3], each_init_path_split_4r_target[-2])
shutil.copy(each_init_path_4r_target, each_final_path_4r_target)
else:
split_dt=np.array_split(sub_input_of_all_inputs, nsplit, axis=0)
split_tgt=np.array_split(sub_label_of_all_labels, nsplit, axis=0)
for i in range(nsplit):
hf = h5py.File(args.output_fname[:-3] + '_' + str(i) + '.h5', mode='w')
hf.create_dataset('input', data=(split_dt[i]).astype(sdtype), dtype=sdtype)
hf.create_dataset('target', data=(split_tgt[i]).astype(sdtype), dtype=sdtype)
hf.close()
print(all_input_paths)
for ii in range(len(all_patient_folder)):
new_input_folder = args.output_folder + '/' + all_patient_folder[ii] + '/' + args.input_gen_folder
new_target_folder = args.output_folder + '/' + all_patient_folder[ii] + '/' + args.target_gen_folder
if not os.path.isdir(new_input_folder): os.makedirs(new_input_folder)
if not os.path.isdir(new_target_folder): os.makedirs(new_target_folder)
# ------------------------------------------------------
# input data
#--------------------------------------------------------
each_init_path_4r_input = shuff_input_paths[ip]
each_init_path_split_4r_input = each_init_path_4r_input.split('/')
each_init_intput_fn = each_init_path_split_4r_input[-1]
# first move to place holder
shutil.move(each_init_path_4r_input, placeholder_fld)
# rename the file inside place holder
new_input_fn = placeholder_fld + '/' + str(ip) + args.file_extension
os.rename(os.path.join(placeholder_fld, each_init_intput_fn), new_input_fn)
# copy the rename input to its final destination
shutil.move(new_input_fn, input_final_dest)
rename_n_copy_file(shuff_input_paths, ind, input_final_dest, placeholder_fld, args.file_extension)
# ------------------------------------------------------
# target data
#--------------------------------------------------------
each_init_path_4r_target = shuff_target_paths[ip]
each_init_path_split_4r_target = each_init_path_4r_target.split('/')
each_init_target_fn = each_init_path_split_4r_target[-1]
# first move to place holder
shutil.move(each_init_path_4r_target, placeholder_fld)
# rename the file inside place holder
new_target_fn = placeholder_fld + '/' + str(ip) + args.file_extension
os.rename(os.path.join(placeholder_fld, each_init_target_fn), new_target_fn)
# copy the rename input to its final destination
shutil.move(new_target_fn, target_final_dest)
'''