def archive_human_masks(human_directory, new_directory, work_directory):
'''
For a directory of hand-drawn masks, mask out everything in the accompanying bright-field file except for the worm itself and a 100-pixel surrounding area to save disk space. Also, re-compress all images to maximize compression and space efficiency.
'''
for a_subdir in os.listdir(human_directory):
if os.path.isdir(human_directory + os.path.sep + a_subdir):
folderStuff.ensure_folder(new_directory + os.path.sep + a_subdir)
for a_file in os.listdir(human_directory + os.path.sep + a_subdir):
if a_file.split(' ')[-1] == 'hmask.png':
if not os.path.isfile(new_directory + os.path.sep + a_subdir + os.path.sep + a_file):
print('Up to ' + a_subdir + ' ' + a_file + '.')
my_stem = a_file.split(' ')[0]
my_mask = freeimage.read(human_directory + os.path.sep + a_subdir + os.path.sep + my_stem + ' ' + 'hmask.png')
bf_path = human_directory + os.path.sep + a_subdir + os.path.sep + my_stem + ' ' + 'bf.png'
if os.path.isfile(bf_path):
my_image = freeimage.read(bf_path)
else:
my_image = freeimage.read(bf_path.replace(human_directory, work_directory))
area_mask = my_mask.copy().astype('bool')
distance_from_mask = scipy.ndimage.morphology.distance_transform_edt(np.invert(area_mask)).astype('uint16')
area_mask[distance_from_mask > 0] = True
area_mask[distance_from_mask > 100] = False
my_image[np.invert(area_mask)] = False
freeimage.write(my_image, new_directory + os.path.sep + a_subdir + os.path.sep + my_stem + ' ' + 'bf.png', flags = freeimage.IO_FLAGS.PNG_Z_BEST_COMPRESSION)
freeimage.write(my_mask, new_directory + os.path.sep + a_subdir + os.path.sep + my_stem + ' ' + 'hmask.png', flags = freeimage.IO_FLAGS.PNG_Z_BEST_COMPRESSION)
elif a_file.split('.')[-1] == 'json':
shutil.copyfile(human_directory + os.path.sep + a_subdir + os.path.sep + a_file, new_directory + os.path.sep + a_subdir + os.path.sep + a_file)
return
def pick_full_masks(working_dir, human_dir, temporary_dir): ''' Copy the bright-field images to trace (giving up on automated wormFinding) from working_dir to temporary_dir. ''' my_masks = select_daily(working_dir) my_masks = remove_already_have(my_masks, human_dir) for a_mask in my_masks: base_folder = temporary_dir subdirectory_folder = os.path.sep.join(a_mask.split(os.path.sep)[:-1]).replace(working_dir, temporary_dir) folderStuff.ensure_folder(base_folder) folderStuff.ensure_folder(subdirectory_folder) shutil.copyfile(a_mask, a_mask.replace(working_dir, temporary_dir)) return
def pick_masks_to_trace(working_dir, human_dir, temporary_dir): ''' Copy the bright-field images to trace from working_dir to temporary_dir. ''' my_masks = random_select_egg_ages(working_dir) my_masks = remove_already_have(my_masks, human_dir) for a_mask in my_masks: base_folder = temporary_dir subdirectory_folder = os.path.sep.join(a_mask.split(os.path.sep)[:-1]).replace(working_dir, temporary_dir) folderStuff.ensure_folder(base_folder) folderStuff.ensure_folder(subdirectory_folder) if os.path.isfile(a_mask): shutil.copy(a_mask, a_mask.replace(working_dir, temporary_dir)) return
def totally_random(working_dir, human_dir, temporary_dir, image_number = 200): ''' Select image_number masks from working_dir without regard for age bins. ''' my_masks = random_select(working_dir, image_number) my_masks = remove_already_have(my_masks, human_dir) for a_mask in my_masks: base_folder = temporary_dir subdirectory_folder = os.path.sep.join(a_mask.split(os.path.sep)[:-1]).replace(working_dir, temporary_dir) folderStuff.ensure_folder(base_folder) folderStuff.ensure_folder(subdirectory_folder) if os.path.isfile(a_mask): shutil.copy(a_mask, a_mask.replace(working_dir, temporary_dir)) return
def select_final_outlines(color_directory, final_directory, working_directory, egg_mode = False):
'''
Select the properly filled outlines from color_directory and move them into final_directory along with the appropriate metadata and bright field files from working_directory.
'''
mask_ending = 'hmask'
if egg_mode:
mask_ending = 'emask'
for a_subdir in os.listdir(color_directory):
folderStuff.ensure_folder(final_directory + os.path.sep + a_subdir)
for an_image in os.listdir(color_directory + os.path.sep + a_subdir):
if an_image.split(' ')[-1] == 'outline.png':
destination_mask = final_directory + os.path.sep + a_subdir + os.path.sep + an_image.replace('outline', mask_ending)
outline_image = freeimage.read(color_directory + os.path.sep + a_subdir + os.path.sep + an_image)
my_dimensions = len(outline_image.shape)
if my_dimensions == 2:
shutil.copyfile(color_directory + os.path.sep + a_subdir + os.path.sep + an_image.replace('outline', mask_ending), destination_mask)
elif my_dimensions == 3:
fixed_outline = outline_image[:, :, 0].astype('uint8')
fixed_outline[fixed_outline > 0] = -1
freeimage.write(fixed_outline, destination_mask)
shutil.copyfile(working_directory + os.path.sep + a_subdir + os.path.sep + an_image.replace('outline', 'bf'), destination_mask.replace(mask_ending, 'bf'))
shutil.copyfile(working_directory + os.path.sep + a_subdir + os.path.sep + 'position_metadata_extended.json', final_directory + os.path.sep + a_subdir + os.path.sep + 'position_metadata_extended.json')
return