def perform_max_z_creation(img_path_list, file_num, sub_save_location, split_training_test): os.chdir(sub_save_location) sub_folder = "sequences" sequence_path = os.path.join(sub_save_location, sub_folder) os.mkdir(sequence_path) os.chdir(sequence_path) t, z, y_dim,x_dim, img = load_img(img_path_list[file_num]) # txt_name_log = open(destination + "/name_log.txt", "a") # txt_name_log.write("{}, {}\n".format(new_folder_name, img_path_list[file_num]), ) # txt_name_log.close() for t_num in tqdm(range(0,t)): #create new directory-path file_folder = "%02d" % (t_num+1) t_folder = os.path.join(sequence_path, file_folder) os.mkdir(t_folder) os.chdir(t_folder) for z_num in range(0,z-2): slice_folder = "%04d" % (z_num+1) three_z_folder = os.path.join(t_folder, slice_folder) os.mkdir(three_z_folder) os.chdir(three_z_folder) #add new folder to txt-file decision_train_test = random.random() if decision_train_test < split_training_test: txt_file_train = open(sub_save_location + "/tri_trainlist.txt", "a") txt_file_train.write("{}/{}\n".format(file_folder,slice_folder)) txt_file_train.close() else: txt_file_test = open(sub_save_location + "/tri_testlist.txt", "a") txt_file_test.write("{}/{}\n".format(file_folder,slice_folder)) txt_file_test.close() #converting images in rgb and uint8 to save it like that img_save_1 = reshape_data(img, "TZXY","XY", T=t_num, Z=z_num) img_save_1 = create_3D_image(img_save_1, x_dim, y_dim) img_save_1 = convert(img_save_1, 0, 255, np.uint8) img_save_2 = reshape_data(img, "TZXY","XY", T=t_num, Z=z_num+1) img_save_2 = create_3D_image(img_save_2, x_dim, y_dim) img_save_2 = convert(img_save_2, 0, 255, np.uint8) img_save_3 = reshape_data(img, "TZXY","XY", T=t_num, Z=z_num+2) img_save_3 = create_3D_image(img_save_3, x_dim, y_dim) img_save_3 = convert(img_save_3, 0, 255, np.uint8) with png_writer.PngWriter("im1.png") as writer2: writer2.save(img_save_1) with png_writer.PngWriter("im2.png") as writer2: writer2.save(img_save_2) with png_writer.PngWriter("im3.png") as writer2: writer2.save(img_save_3) print("{}/{}\n".format(file_folder,slice_folder))
def perform_prep_predict_t_creation(img_path_list, file_num, sub_save_location): os.chdir(sub_save_location) t, z, y_dim,x_dim, img = load_img(img_path_list[file_num]) folder_gt = str(file_num) + "_gt" folder_gt = os.path.join(sub_save_location,folder_gt) os.mkdir(folder_gt) folder_steps = str(file_num) + "_steps" folder_steps = os.path.join(sub_save_location,folder_steps) os.mkdir(folder_steps) # txt_name_log = open(destination + "/name_log.txt", "a") # txt_name_log.write("{}, {}\n".format(new_folder_name, img_path_list[file_num]), ) # txt_name_log.close() images_jump =2 #create new directory-path for z_num in tqdm(range(0,z)): for t_num in range(math.ceil(t/images_jump)-1): #create new directory-path file_folder = ("f_%03d" %(file_num)+"-" +"z_%03d"%(z_num) + "-"+"t_%03d" %(t_num)) os.chdir(folder_gt) os.mkdir(file_folder) os.chdir(folder_steps) os.mkdir(file_folder) GT_path_folder = os.path.join(folder_gt, file_folder) steps_path_folder = os.path.join(folder_steps, file_folder) os.chdir(steps_path_folder) #here put the image pngs into the folder (instead of creating the folder) #convert image to unit8 otherwise warning first = t_num* images_jump second = t_num*images_jump+images_jump img_save_1 = reshape_data(img, "TZXY","XY", T=first, Z=z_num) img_save_1 = create_3D_image(img_save_1, x_dim, y_dim) img_save_1 = convert(img_save_1, 0, 255, np.uint8) img_save_3 = reshape_data(img, "TZXY","XY", T=second, Z=z_num) img_save_3 = create_3D_image(img_save_3, x_dim, y_dim) img_save_3 = convert(img_save_3, 0, 255, np.uint8) img_save_2 = reshape_data(img, "TZXY","XY", T=first+1, Z=z_num) img_save_2 = create_3D_image(img_save_2, x_dim, y_dim) img_save_2 = convert(img_save_2, 0, 255, np.uint8) # saving images as PNG with png_writer.PngWriter("im1.png") as writer1: writer1.save(img_save_1) with png_writer.PngWriter("im3.png") as writer2: writer2.save(img_save_3) os.chdir(GT_path_folder) with png_writer.PngWriter("im2.png") as writer2: writer2.save(img_save_2)
def run_code_sample(filepath_list, destination, i, t): # create virtual number of files images_jump = 1 print(filepath_list[i]) txt_name_log = open(destination + "/name_log.txt", "a") txt_name_log.write("{}, {}\n".format(("%03d" % (t) + "-" + "%03d" % (i)), filepath_list[i])) txt_name_log.close() img = AICSImage(filepath_list[i]) z_dim = img.shape[2] #dim for later for generating the image_3d files x_dim = img.shape[-2] y_dim = img.shape[-1] for j in range(z_dim - 1): #create new directory-path file_folder = ("%03d" % (t) + "-" + "%03d" % (i) + "-" + "%03d" % (j)) os.chdir(destination) os.mkdir(file_folder) new_folder_path_2 = os.path.join(destination, file_folder) os.chdir(new_folder_path_2) #here put the image pngs into the folder (instead of creating the folder) #convert image to unit8 otherwise warning first = j * images_jump second = j * images_jump + images_jump if second <= z_dim - 1: #*images_jump-images_jump: img_1 = img.get_image_data("YX", S=0, T=0, Z=0, C=first) img_1 = create_3D_image(img_1, x_dim, y_dim) img_1 = convert(img_1, 0, 255, np.uint8) img_2 = img.get_image_data("YX", S=0, T=0, Z=0, C=second) img_2 = create_3D_image(img_2, x_dim, y_dim) img_2 = convert(img_2, 0, 255, np.uint8) # saving images as PNG with png_writer.PngWriter("im1.png") as writer1: writer1.save(img_1) with png_writer.PngWriter("im3.png") as writer2: writer2.save(img_2) os.chdir(destination)
def upsample_z_creation(img_path_list, file_num, sub_save_location): os.chdir(sub_save_location) t, z, y_dim,x_dim, img = load_img(img_path_list[file_num]) folder_steps = str(file_num) + "_steps" folder_steps = os.path.join(sub_save_location,folder_steps) os.mkdir(folder_steps) # txt_name_log = open(destination + "/name_log.txt", "a") # txt_name_log.write("{}, {}\n".format(new_folder_name, img_path_list[file_num]), ) # txt_name_log.close() #create new directory-path for t_num in tqdm(range(0,t)): for z_num in range(z-1): #create new directory-path file_folder = ("f_%03d" %(file_num) + "-"+"t_%03d" %(t_num) +"-" +"z_%03d"%(z_num)) os.chdir(folder_steps) os.mkdir(file_folder) steps_path_folder = os.path.join(folder_steps, file_folder) os.chdir(steps_path_folder) # #here put the image pngs into the folder (instead of creating the folder) # #convert image to unit8 otherwise warning img_save_1 = reshape_data(img, "TZXY","XY", T=t_num, Z=z_num) img_save_1 = create_3D_image(img_save_1, x_dim, y_dim) img_save_1 = convert(img_save_1, 0, 255, np.uint8) img_save_2 = reshape_data(img, "TZXY","XY", T=t_num, Z=z_num+1) img_save_2 = create_3D_image(img_save_2, x_dim, y_dim) img_save_2 = convert(img_save_2, 0, 255, np.uint8) # # saving images as PNG with png_writer.PngWriter("im1.png") as writer1: writer1.save(img_save_1) with png_writer.PngWriter("im3.png") as writer2: writer2.save(img_save_2)
def run_create_training_T(filepath, destination, k, sequence_path, split_training_test): # get file-path-list filepath_list = get_file_list_T(filepath) # create virtual number of files for i in range(0, len(filepath_list)): print(filepath_list[i - 1]) # list_number_of_files.append(i) new_folder_name = ("%02d" % (k) + "-" + "%05d" % (i + 1)) os.mkdir(new_folder_name) txt_name_log = open(destination + "/name_log.txt", "a") txt_name_log.write( "{}, {}\n".format(new_folder_name, filepath_list[i - 1]), ) txt_name_log.close() img = AICSImage(filepath_list[i]) z_dim = img.shape[2] #dim for later for generating the image_3d files x_dim = img.shape[-2] y_dim = img.shape[-1] #because the naming of the folders in the original also starts with 1 and -1 because i take always 3 so need to stop 2 before the end for j in range(0, z_dim - 1): #create new directory-path new_folder_path_1 = os.path.join(sequence_path, new_folder_name) os.chdir(new_folder_path_1) file_folder = "%04d" % (j + 1) os.mkdir(file_folder) #add new folder to txt-file decision_train_test = random.random() if decision_train_test < split_training_test: txt_file_train = open(destination + "/tri_trainlist.txt", "a") txt_file_train.write("{}/{}\n".format(new_folder_name, file_folder)) txt_file_train.close() else: txt_file_test = open(destination + "/tri_testlist.txt", "a") txt_file_test.write("{}/{}\n".format(new_folder_name, file_folder)) txt_file_test.close() new_folder_path_2 = os.path.join(new_folder_path_1, file_folder) os.chdir(new_folder_path_2) #here put the image pngs into the folder (instead of creating the folder) #convert image to unit8 otherwise warning img_1 = img.get_image_data("YX", S=0, T=0, C=j - 1, Z=0) img_1 = create_3D_image(img_1, x_dim, y_dim) img_1 = convert(img_1, 0, 255, np.uint8) img_2 = img.get_image_data("YX", S=0, T=0, C=j, Z=0) img_2 = create_3D_image(img_2, x_dim, y_dim) img_2 = convert(img_2, 0, 255, np.uint8) img_3 = img.get_image_data("YX", S=0, T=0, C=j + 1, Z=0) img_3 = create_3D_image(img_3, x_dim, y_dim) img_3 = convert(img_3, 0, 255, np.uint8) # saving images as PNG with png_writer.PngWriter("im1.png") as writer2: writer2.save(img_1) with png_writer.PngWriter("im2.png") as writer2: writer2.save(img_2) with png_writer.PngWriter("im3.png") as writer2: writer2.save(img_3) os.chdir(sequence_path)