def main():
args = get_args(sys.argv[1:])
in_dir = args['in_directory']
out_dir = args['out_directory']
onlyjpg = extract_target_files(in_dir, 'jpg')
for jpg in onlyjpg:
sample_path = in_dir + jpg
output_path = out_dir + 'filtered_' + jpg
pil_img = Image.open(sample_path)
np_img = np.asarray(pil_img)
filtered_np_img = apply_image_filters(np_img,
slide_num=None,
info=None,
save=False,
display=False)
filtered_pil_img = np_to_pil(filtered_np_img)
filtered_pil_img.save(output_path)
def save_filtered_image(np_img, slide_num, filter_num, filter_text):
"""
Save a filtered image to the file system.
Args:
np_img: Image as a NumPy array.
slide_num: The slide number.
filter_num: The filter number.
filter_text: Descriptive text to add to the image filename.
"""
t = Time()
filepath = slide.get_filter_image_path(slide_num, filter_num, filter_text)
pil_img = util.np_to_pil(np_img)
pil_img.save(filepath)
print("%-20s | Time: %-14s Name: %s" % ("Save Image", str(t.elapsed()), filepath))
t1 = Time()
thumbnail_filepath = slide.get_filter_thumbnail_path(slide_num, filter_num, filter_text)
slide.save_thumbnail(pil_img, slide.THUMBNAIL_SIZE, thumbnail_filepath)
print("%-20s | Time: %-14s Name: %s" % ("Save Thumbnail", str(t1.elapsed()), thumbnail_filepath))
def apply_filters_to_image(slide_num, save=True, display=False):
"""
Apply a set of filters to an image and optionally save and/or display filtered images.
Args:
slide_num: The slide number.
save: If True, save filtered images.
display: If True, display filtered images to screen.
Returns:
Tuple consisting of 1) the resulting filtered image as a NumPy array, and 2) dictionary of image information
(used for HTML page generation).
"""
t = Time()
print("Processing slide #%d" % slide_num)
info = dict()
if save and not os.path.exists(slide.FILTER_DIR):
os.makedirs(slide.FILTER_DIR)
img_path = slide.get_training_image_path(slide_num)
np_orig = slide.open_image_np(img_path)
filtered_np_img = apply_image_filters(np_orig, slide_num, info, save=save, display=display)
if save:
t1 = Time()
result_path = slide.get_filter_image_result(slide_num)
pil_img = util.np_to_pil(filtered_np_img)
pil_img.save(result_path)
print("%-20s | Time: %-14s Name: %s" % ("Save Image", str(t1.elapsed()), result_path))
t1 = Time()
thumbnail_path = slide.get_filter_thumbnail_result(slide_num)
slide.save_thumbnail(pil_img, slide.THUMBNAIL_SIZE, thumbnail_path)
print("%-20s | Time: %-14s Name: %s" % ("Save Thumbnail", str(t1.elapsed()), thumbnail_path))
print("Slide #%03d processing time: %s\n" % (slide_num, str(t.elapsed())))
return filtered_np_img, info
np_img.shape[1],
ROW_TILE_SIZE,
COL_TILE_SIZE, 0.5)
img_mask_path = get_mask_image_path(img_num)
np_img_mask = slide.open_image_np(img_mask_path)
for t in tile_indices:
r_s, r_e, c_s, c_e = t
np_tile = np_img[r_s:r_e, c_s:c_e]
np_tile_mask = np_img_mask[r_s:r_e, c_s:c_e]
score = tiles.unique_count_app(
np_tile_mask) #do not use unique this is not acceptable
if (score > 0):
count += 1
patch = util.np_to_pil(np_tile)
patch_path = get_patch_path("train", score, count)
dir = os.path.dirname(patch_path)
if not os.path.exists(dir):
os.makedirs(dir)
patch.save(patch_path)
#print(img_path)