def select_input(self, event):
# get the info about the number of images in the file
self.input_path = IJ.getFilePath("Choose a File")
# if default naming is not changed use file name
if self.textfield2.text == self.default_naming:
self.file_core_name = path.basename(self.input_path).split('.czi')[0]
else:
self.file_core_name = self.textfield2.text
# put that name in the text field
self.panel.getComponents()[1].setText(self.file_core_name)
reader = ImageReader()
reader.setId(self.input_path)
metadata_list = reader.getCoreMetadataList()
# slide scanner makes a piramid of X for every ROI you draw
# resolution is not updated in the metadata so it needs to be calculated manually
number_of_images, self.num_of_piramids_list = get_data_structure(metadata_list)
print("Number of images is " + str(number_of_images))
# get the indexes of the maximum resolution images
self.max_res_indexes = get_maxres_indexes(self.num_of_piramids_list)
print("Number of pyramids are " + str(self.num_of_piramids_list))
# set names of subimages in the list, waiting to compare to current outputs
self.possible_slices = [self.file_core_name + "_slice-" + str(n)
for n in range(number_of_images)]
self.binFactor_list, self.binStep_list = get_binning_factor(self.max_res_indexes,
self.num_of_piramids_list, metadata_list)
print("Binning factors are " + str(self.binFactor_list))
print("Binning steps are " + str(self.binStep_list))
# create output directory if it doesn't exist
# get the animal id
animal_id = self.file_core_name.split('_')[0]
self.output_path = path.join(path.dirname(path.dirname(self.input_path)),
"Processed_data", animal_id, "ROIs")
if path.isdir(self.output_path):
print("Output path was already created")
else:
makedirs(self.output_path)
print("Output path created")
# update_lists depending on whether something has been processed already
self.update_list()
sys.path.append(path.abspath(path.dirname(__file__)))
from functions.czi_structure import get_data_structure, get_binning_factor, open_czi_series, \
get_maxres_indexes
from functions.image_manipulation import extractChannel
piramid_to_open = 1
channel_to_save = 3
final_resolution = 5
# Main
if __name__ in ['__builtin__', '__main__']:
# get the file
input_path = IJ.getFilePath("Choose a .czi file")
reader = ImageReader()
reader.setId(input_path)
metadata_list = reader.getCoreMetadataList()
# slide scanner makes a piramid of X for every ROI you draw
# resolution is not updated in the metadata so it needs to be calculated manually
number_of_images, num_of_piramids_list = get_data_structure(metadata_list)
IJ.log("Number of images is " + str(number_of_images))
# set names of subimages in the list, waiting to compare to current outputs
file_core_name = path.basename(input_path).split('.czi')[0]
# get the indexes of the maximum resolution images
max_res_indexes = get_maxres_indexes(num_of_piramids_list)
IJ.log("Number of pyramids are " + str(num_of_piramids_list))
# set names of subimages in the list, waiting to compare to current outputs
possible_slices = [
file_core_name + "_slice-" + str(n) for n in range(number_of_images)
]
binFactor_list, binStep_list = get_binning_factor(max_res_indexes,
