def file_export_id(self, include_otolith=False):
folder = tk.filedialog.askdirectory(title="Select export location")
if folder:
sulcus = self.otolith.get_sulcus() * 255
if include_otolith:
sulcus = self.otolith.slices + sulcus
general.arr_to_folder(sulcus,
"%s/%s_sulcus" % (folder, self.otolith.name),
verbose=True)
def run(input_folder, output_folder, visualize=False):
imgdata = vtk_functions.folder_to_imgdata(input_folder)
np_data, omega = prepare_slices(imgdata, visualize)
if is_upside_down(np_data[:, :, int(np_data.shape[2] / 2)]):
np_data = np.rot90(np_data, k=2, axes=(0, 1))
print("Finished flipping...")
basename = os.path.basename(input_folder)
if omega < 1:
general.arr_to_folder(np_data, "%s/%s_prepared_%s" % (output_folder,
basename, omega))
else:
general.arr_to_folder(np_data, "%s/%s_prepared" % (output_folder,
basename))
sys.path.insert(1, '../functions')
import vtk_functions
import general
import os
if __name__ == "__main__":
args = sys.argv[1:]
input_folder = str(args[0])
output_folder = args[1]
max_z = 2000
imgdata = vtk_functions.folder_to_imgdata(input_folder, verbose=True)
print("Loaded files...")
dims = imgdata.GetDimensions()
omega = 1
if dims[2] > max_z:
omega = general.trunc(max_z / dims[2], 1)
print("Omega: %s" % omega)
resized_imgdata = vtk_functions.resize_imgdata(imgdata, omega)
arr = vtk_functions.imgdata_to_arr(resized_imgdata)
basename = os.path.basename(input_folder)
general.arr_to_folder(arr, "%s/%s_%s" % (output_folder, basename, omega))
import sys
sys.path.insert(1, '../functions')
import vtk_functions
import general
import numpy as np
if __name__ == "__main__":
args = sys.argv[1:]
input_folder = str(args[0])
output_folder = args[1]
np_data = general.folder_to_arr(input_folder, file_format="tif",
verbose=False)
np_data = np.rot90(np_data, k=2, axes=(1, 2))
general.arr_to_folder(np_data, output_folder)