def ex1(image_filename, encoded_filename):
# image_filename = images.load(image_filename)
rettangoli = vertici(image_filename)
ordine = lista_ordine(rettangoli)
enc = encodedimage(rettangoli)
images.save(enc, encoded_filename)
return boundingbox(rettangoli)
def saveFinalOverlay(settings,image,edge,image_name):
'''
# Overlay unsmoothed edge on original image (grayscale) and save resulting image
'''
bg = cv2.cvtColor(image,cv2.COLOR_RGB2GRAY)
overlay = np.where(edge == 255,255,bg)
filename = os.path.join(settings['out_directory'],'outlines','_'.join([settings['sampleID'],image_name,'final.tif']))
images.save(overlay,filename)
# If save_intermediates is on, copy the final image into the intermediates
# folder for easier comparison of image filter results
if settings['save_intermediates']:
shutil.copy2(filename,os.path.join(settings['out_directory'],'intermediates'))
def fetch_by_size(target_size):
size, path = images.pick_by_size(target_size)
url = images.BASE_URL + path
octets = fetch(url)
name = images.save(url, octets)
return (size, name)
def final(orig_filename, box_list, run, plane_num, image=None):
if image is None:
image = images.load(orig_filename, run)
image_size = np.shape(image) # [width, height]
for box_num, box in enumerate(box_list):
# crop expects [x1, y1, x2, y2], box is [y1, x1, y2, x2]
crop_box = [box[1], box[0], box[3], box[2]]
width = crop_box[2] - crop_box[0]
height = crop_box[3] - crop_box[1]
image_subsample = images.crop(image, crop_box)
x_percent = float(crop_box[0]) / float(image_size[1]) * 100
y_percent = float(crop_box[1]) / float(image_size[0]) * 100
description = 'Object #%05d of %05d ( %d x %d pixels at slide position %05.2f x %05.2f )' \
% (box_num+1, len(box_list), width, height, x_percent, y_percent)
labeled_image_subsample, label = images.label_image(
image_subsample, orig_filename, description, run)
object_directory = '%s%s%s_obj%05d' % (run['full_output'], os.sep,
run['unique_id'], box_num + 1)
if not os.path.exists(object_directory):
os.makedirs(object_directory)
print object_directory
output_filename = '%s%s%s_obj%05d_plane%03d.%s' % (
object_directory, os.sep, run['unique_id'], box_num + 1, plane_num,
run['output_ext'])
tags = images.add_comment(output_filename, '. '.join(label))
print output_filename
images.save(labeled_image_subsample, output_filename, tags=tags)
def final(orig_filename, box_list, run, plane_num, image=None):
if image is None:
image = images.load(orig_filename, run)
image_size = np.shape(image) # [width, height]
for box_num, box in enumerate(box_list):
# crop expects [x1, y1, x2, y2], box is [y1, x1, y2, x2]
crop_box = [box[1], box[0], box[3], box[2]]
width = crop_box[2] - crop_box[0]
height = crop_box[3] - crop_box[1]
image_subsample = images.crop(image, crop_box)
x_percent = float(crop_box[0]) / float(image_size[1]) * 100
y_percent = float(crop_box[1]) / float(image_size[0]) * 100
description = 'Object #%05d of %05d ( %d x %d pixels at slide position %05.2f x %05.2f )' \
% (box_num+1, len(box_list), width, height, x_percent, y_percent)
labeled_image_subsample, label = images.label_image(image_subsample, orig_filename,
description, run)
object_directory = '%s%s%s_obj%05d' % (run['full_output'], os.sep, run['unique_id'], box_num+1)
if not os.path.exists(object_directory):
os.makedirs(object_directory)
print object_directory
output_filename = '%s%s%s_obj%05d_plane%03d.%s' % (object_directory, os.sep,
run['unique_id'], box_num+1, plane_num,
run['output_ext'])
tags = images.add_comment(output_filename, '. '.join(label))
print output_filename
images.save(labeled_image_subsample, output_filename, tags=tags)
def save(item, params, image, userId):
if Item.validParams(params, image):
item.name = params['name']
# item.categoryId = int(params['category'])
item.category = db.getOne(Category, "id", params['category'])
item.description = params['description'].strip()
# item.userId = userId
item.user = db.getOne(User, "email", userId)
db.session.add(item)
db.session.flush()
url = images.save(image, item)
if url:
item.image = url
db.session.commit()
flash("%s has been saved" % item.name)
return True
return False
def ex1(image_filename, encoded_filename): rettangoli = vertici(image_filename) enc = encodedimage(rettangoli) images.save(enc, encoded_filename) return boundingbox(rettangoli)
def saveIntermediates(settings,image,image_name,tag):
'''
Saves intermediate files (output of each individual image filter).
'''
images.save(image,os.path.join(settings['out_directory'],'intermediates','_'.join([settings['sampleID'],image_name,tag])))