def copy_over_jp2_files(stack, raw_jp2_input_fn_fp, raw_jp2_input_fp):
# Use name of jp2 image to find how the resolution is encoded
if 'raw' in raw_jp2_input_fn_fp:
resolution = '_raw'
elif 'lossless' in raw_jp2_input_fn_fp:
resolution = '_lossless'
else:
resolution = ''
# CONVERT *.jp2 to *.tif
json_fn = stack + '_raw_input_spec.json'
# Create the data file necessary to run the jp2_to_tiff script
json_data = [{
"version":
None,
"resolution":
"raw",
"data_dirs":
raw_jp2_input_fp,
"filepath_to_imageName_mapping":
raw_jp2_input_fp + "/(.*?)" + resolution + ".jp2",
"imageName_to_filepath_mapping":
raw_jp2_input_fp + "/%s" + resolution + ".jp2"
}]
with open(json_fn, 'w') as outfile:
json.dump(json_data, outfile)
command = ["python", "jp2_to_tiff.py", stack, json_fn]
completion_message = 'Completed converting and copying jp2 to tiff for all files in folder.'
call_and_time(command, completion_message=completion_message)
def update_prep1_images(self):
version = stain_to_metainfo[self.stain]['img_version_1']
create_input_spec_ini_all(name='input_spec.ini', \
stack=stack, prep_id='None', version=version, resol='thumbnail')
# Call "compose" to regenerate the csv file
command = [
'python', 'compose_v3.py', 'input_spec.ini', '--op',
'from_none_to_aligned'
]
completion_message = 'Finished creating transforms to anchor csv file.'
call_and_time(command, completion_message=completion_message)
# Apply transformations from csv and save as prep1 images
command = [
'python', 'warp_crop_v3.py', '--input_spec', 'input_spec.ini',
'--op_id', 'from_none_to_padded', '--njobs', '8', '--pad_color',
get_padding_color(stack)
]
completion_message = 'Finished transformation to padded (prep1).'
call_and_time(command, completion_message=completion_message)
)
print(
'_________________________________________________________________________________'
)
sys.exit()
if stain == 'NTB':
# Extract the BLUE channel, for NTB brains
create_input_spec_ini_all(name='input_spec.ini',
stack=stack,
prep_id='None',
version='None',
resol='raw')
command = ["python", "extract_channel.py", "input_spec.ini", "2", "Ntb"]
completion_message = 'Extracted BLUE channel.'
call_and_time(command, completion_message=completion_message)
# Create Thumbnails of each raw image
create_input_spec_ini_all(name='input_spec.ini',
stack=stack,
prep_id='None',
version='Ntb',
resol='raw')
command = [
"python", "rescale.py", "input_spec.ini", "thumbnail", "-f", "0.03125"
]
completion_message = 'Generated thumbnails.'
call_and_time(command, completion_message=completion_message)
# Normalize intensity using thumbnails
create_input_spec_ini_all(name='input_spec.ini',
def copy_over_sorted_filenames(stack, sfns_input_fp):
correct_sorted_fns_fp = DataManager.get_sorted_filenames_filename(stack)
command = ["cp", sfns_input_fp, correct_sorted_fns_fp]
completion_message = 'Successfully copied sorted_filenames.txt over.'
call_and_time(command, completion_message=completion_message)