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)