def freehand_annotation_record():
slide_id = request.args.get('slide_id', default=1, type=int)
annotator_id = request.args.get('annotator_id', default=1, type=int)
annotation_project = request.args.get('project',
default="None",
type=str)
slide_uuid = request.args.get('slide_uuid', default="", type=str)
annotation_root_folder = freehand_annotation_data_root + annotation_project + '/' + slide_uuid + '/'
if not os.path.exists(annotation_root_folder):
os.mkdir(annotation_root_folder)
annotaion_db = annotation_root_folder + 'a' + str(annotator_id) + '.db'
req_form = request.form
num_of_points = int(len(req_form) / 3)
pt_list_att = ('[x]', '[y]', '[grading]')
db = freehand_annotation_sqlite.SqliteConnector(annotaion_db)
# In one round, the grading and pslv could be updated only once.
data = []
branch_id = -1
branch_id_find = []
for i in range(num_of_points):
if int(req_form[str(i) + '[grading]']) > 0:
if i == 0:
continue
if (int(req_form[str(i - 1) + '[x]']) == int(req_form[str(i) + '[x]'])) \
and (int(req_form[str(i - 1) + '[y]']) == int(req_form[str(i) + '[y]'])):
continue
data.append(
tuple([
int(req_form[str(i - 1) + '[x]']),
int(req_form[str(i - 1) + '[y]']),
int(req_form[str(i) + '[x]']),
int(req_form[str(i) + '[y]']),
int(req_form[str(i) + '[grading]'])
]))
elif int(req_form[str(i) + '[grading]']) == 0:
db.delete_points(int(req_form[str(i) + '[x]']),
int(req_form[str(i) + '[y]']))
elif int(req_form[str(i) + '[grading]']) == -1:
db.delete_lines(int(req_form[str(i) + '[x]']),
int(req_form[str(i) + '[y]']))
elif int(req_form[str(i) + '[grading]']) == -2:
branch_id_find = db.find_lines(int(req_form[str(i) + '[x]']),
int(req_form[str(i) + '[y]']))
if len(data):
branch_id = db.incert_lines(data)
return jsonify(pt_false_x=[],
pt_false_y=[],
region_id=0,
branch_id=branch_id,
branch_id_find=branch_id_find)
def freehand_annotation_update_image():
slide_id = request.args.get('slide_id', default=1, type=int)
annotator_id = request.args.get('annotator_id', default=1, type=int)
annotation_project = request.args.get('project',
default="None",
type=str)
slide_uuid = request.args.get('slide_uuid', default="", type=str)
annotation_root_folder = freehand_annotation_data_root + annotation_project + '/' + slide_uuid + '/'
if not os.path.exists(annotation_root_folder):
os.mkdir(annotation_root_folder)
annotaion_db = annotation_root_folder + 'a' + str(annotator_id) + '.db'
error_message = 'N/A'
request_status = 0
v1 = request.args.get('var1', 0, type=int) # Top-left x coordinate
v2 = request.args.get('var2', 0, type=int) # Top-left y coordinate
v3 = request.args.get('var3', 0, type=int) # Bottom-right x
v4 = request.args.get('var4', 0, type=int) # Bottom-right y
v5 = request.args.get('var5', 0, type=int) # Viewer width (pixel)
v6 = request.args.get('var6', 0, type=int) # Viewer height (pixel)
loc_tl_coor = (v1, v2)
loc_viewing_size = (v3 - v1, v4 - v2)
loc_viewer_size = (v5, v6)
# Update URL configuration
slide_url = 'static/cache/' + str(uuid.uuid1())[:13] + '.png'
mask = numpy.zeros([v6, v5, 4])
db = freehand_annotation_sqlite.SqliteConnector(annotaion_db)
color = [[0, 0, 255, 255], [0, 255, 0, 255], [255, 0, 0, 255],
[0, 0, 0, 255]]
# print(db.get_lines())
for temp in db.get_lines_in_area(int(v1), int(v2), int(v3), int(v4)):
cv2.line(mask, (int(
(temp[1] - v1) /
(v3 - v1) * v5), int((temp[2] - v2) / (v4 - v2) * v6)), (int(
(temp[3] - v1) /
(v3 - v1) * v5), int((temp[4] - v2) / (v4 - v2) * v6)),
color[temp[5] - 1], 3)
write_url = slide_url
cv2.imwrite(write_url, mask)
return jsonify(slide_url=slide_url + '?a=' + str(uuid.uuid1()),
top_left_x=loc_tl_coor[0],
top_left_y=loc_tl_coor[1],
viewing_size_x=loc_viewing_size[0],
viewing_size_y=loc_viewing_size[1],
exit_code=request_status,
error_message=error_message)
def check_freehand_annotation(annotation_file):
global freehand_annotation_flag
if not annotation_file in freehand_annotation_flag.keys() or \
freehand_annotation_flag[annotation_file][1] != os.stat(annotation_file).st_mtime:
freehand_annotation_flag[annotation_file] = [
len(
freehand_annotation_sqlite.SqliteConnector(
annotation_file).get_lines()),
os.stat(annotation_file).st_mtime
]
return freehand_annotation_flag[annotation_file][0]
def freehand_annotation_clear_lines():
slide_id = request.args.get('slide_id', default=1, type=int)
annotator_id = request.args.get('annotator_id', default=1, type=int)
annotation_project = request.args.get('project',
default="None",
type=str)
slide_uuid = request.args.get('slide_uuid', default="", type=str)
annotation_root_folder = freehand_annotation_data_root + annotation_project + '/' + slide_uuid + '/'
if not os.path.exists(annotation_root_folder):
os.mkdir(annotation_root_folder)
annotaion_db = annotation_root_folder + 'a' + str(annotator_id) + '.db'
db = freehand_annotation_sqlite.SqliteConnector(annotaion_db)
db.delete_all_lines()
return jsonify(exit_code=True, )
def export_freehand_annotation_data(manifest_file_url,
manifest_txt=None,
export_file=None):
annotation_project_root = freehand_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '/'
if manifest_txt != None:
export_annotation_root_temp = "static/cache/" + str(uuid.uuid4()) + "/"
if export_file == None:
export_file = export_annotation_root_temp.replace("/cache",
"")[:-1] + '.zip'
print(export_file)
if os.path.exists(export_file):
os.remove(export_file)
export_path = export_annotation_root_temp
if os.path.exists(export_path):
shutil.rmtree(export_path)
os.mkdir(export_path)
else:
manifest_txt = open(manifest_file_url).readlines()
if not (not (manifest_file_url.rsplit("/", 1)[1][:-4] == "")
and not (manifest_file_url.rsplit("/", 1)[1][:-4] is None)):
print(manifest_file_url.rsplit("/", 1)[1][:-4])
return
export_file = export_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '_freehand_annotation.zip'
if os.path.exists(export_file):
os.remove(export_file)
export_path = export_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '/freehand_annotation/'
if os.path.exists(export_path):
shutil.rmtree(export_path)
elif not os.path.exists(export_annotation_root +
manifest_file_url.rsplit("/", 1)[1][:-4]):
os.mkdir(export_annotation_root +
manifest_file_url.rsplit("/", 1)[1][:-4])
os.mkdir(export_path)
annotator_no = 6
for annotator_id in range(annotator_no):
os.mkdir(export_path + 'a' + str(annotator_id + 1) + '/')
down = 4
down_save = 32
wsi_count = 1
# print(manifest_txt)
for wsi in manifest_txt:
print(wsi)
print(
time.asctime(time.localtime(time.time())),
"start export freehand annotation:" + str(wsi_count) + '/' +
str(len(manifest_txt)))
wsi_count += 1
info = wsi.split('\t')
if not os.path.exists(annotation_project_root + info[0] + '/'):
continue
dimensions = None
for annotator_id in range(annotator_no):
if os.path.exists(annotation_project_root + info[0] + '/' +
'a' + str(annotator_id + 1) + '.db') and \
len(freehand_annotation_sqlite.SqliteConnector(annotation_project_root + info[0] + '/' +
'a' + str(annotator_id + 1) + '.db').get_lines()) > 0:
if not dimensions:
try:
dimensions = openslide.open_slide(original_data_root +
info[0] + '/' +
info[1]).dimensions
except Exception as e:
print('Error:', e)
continue
img_height = dimensions[1]
img_width = dimensions[0]
if not os.path.exists(export_path + 'a' +
str(annotator_id + 1) + '/' +
'Background'):
os.mkdir(export_path + 'a' + str(annotator_id + 1) + '/' +
'Background')
oslide = openslide.OpenSlide(original_data_root + info[0] +
'/' + info[1])
level = oslide.get_best_level_for_downsample(16)
reading_size = [
int(img_width / oslide.level_downsamples[level]),
int(img_height / oslide.level_downsamples[level])
]
try:
mask = oslide.read_region((0, 0), level, reading_size)
except Exception as e:
print('Error:', e)
continue
mask = numpy.array(mask)
mask = cv2.resize(mask,
(int(img_width / 16), int(img_height / 16)))
r, g, b, a = cv2.split(mask)
mask = cv2.merge([r, g, b])
mask = cv2.cvtColor(mask, cv2.COLOR_RGB2GRAY)
mask = cv2.GaussianBlur(mask, (61, 61), 0)
ret, mask = cv2.threshold(mask, 0, 255,
cv2.THRESH_BINARY + cv2.THRESH_OTSU)
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + 'Background' + '/' \
+ info[0] + '.png'
mask = cv2.resize(
mask,
(int(img_width / down_save), int(img_height / down_save)))
cv2.imwrite(write_url, mask)
oslide.close()
db = freehand_annotation_sqlite.SqliteConnector(
annotation_project_root + info[0] + '/' + 'a' +
str(annotator_id + 1) + '.db')
for grade in range(1, 5):
mask = numpy.zeros(
[int(img_height / down),
int(img_width / down), 1], numpy.uint8)
if not os.path.exists(export_path + 'a' +
str(annotator_id + 1) + '/' +
'Grade' + str(grade)):
os.mkdir(export_path + 'a' + str(annotator_id + 1) +
'/' + 'Grade' + str(grade))
for temp in db.get_lines():
if temp[5] != grade:
continue
if temp[1] < down_save:
temp1 = down_save
elif temp[1] >= img_width - down_save:
temp1 = img_width - down_save
else:
temp1 = temp[1]
if temp[2] < down_save:
temp2 = down_save
elif temp[2] >= img_height - down_save:
temp2 = img_height - down_save
else:
temp2 = temp[2]
if temp[3] < down_save:
temp3 = down_save
elif temp[3] >= img_width - down_save:
temp3 = img_width - down_save
else:
temp3 = temp[3]
if temp[4] < down_save:
temp4 = down_save
elif temp[4] >= img_height - down_save:
temp4 = img_height - down_save
else:
temp4 = temp[4]
cv2.line(mask, (int(temp1 / down), int(temp2 / down)),
(int(temp3 / down), int(temp4 / down)), 255,
4)
# kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3, 3))
# mask = cv2.morphologyEx(mask, cv2.MORPH_CLOSE, kernel)
# contours, hierarchy = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
# cv2.drawContours(mask, contours, -1, 255, -1)
#
# mask_new = mask.copy()
# contours_new, hierarchy_new = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
# cv2.drawContours(mask_new, contours_new, -1, 255, -1)
#
# while not (mask_new == mask).all():
# mask = mask_new.copy()
# contours_new, hierarchy_new = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
# cv2.drawContours(mask_new, contours_new, -1, 255, -1)
#
# mask = mask_new.copy()
contours, hierarchy = cv2.findContours(
mask, cv2.RETR_TREE, cv2.CHAIN_APPROX_NONE)
mask = numpy.zeros(
[int(img_height / down),
int(img_width / down), 1], numpy.uint8)
# print(hierarchy)
for index in range(len(contours)):
if hierarchy[0][index][3] != -1:
cv2.drawContours(mask, contours, index, 255, -1)
# kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (3, 3))
# mask = cv2.morphologyEx(mask, cv2.MORPH_OPEN, kernel)
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + 'Grade' + str(grade) + '/' \
+ info[0] + '.png'
mask = cv2.resize(mask, (int(
img_width / down_save), int(img_height / down_save)))
cv2.imwrite(write_url, mask)
contours_list = []
for grade in range(1, 5):
temp = cv2.imread(export_path + 'a' + str(annotator_id + 1) + '/' + 'Grade' + str(grade) + '/' \
+ info[0] + '.png', 0)
contours, hierarchy = cv2.findContours(
temp, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
contours_list.append(contours)
mask = numpy.zeros([
int(img_height / down_save),
int(img_width / down_save), 3
], numpy.uint8)
color = [(0, 0, 255), (0, 255, 0), (255, 0, 0), (0, 0, 0)]
for loop_times in range(5):
for grade in range(4):
contours_temp = contours_list[grade].copy()
for index in range(len(contours_temp)):
mask_new = mask.copy()
cv2.drawContours(mask_new, contours_temp, index,
color[grade], 1)
if not (mask_new == mask).all():
cv2.drawContours(mask_new, contours_temp,
index, color[grade], -1)
mask = mask_new.copy()
else:
for i in range(len(contours_list[grade])):
try:
if ((contours_list[grade][i]) == (
contours_temp[index])).all():
contours_list[grade].pop(i)
break
except:
if (contours_list[grade][i]) == (
contours_temp[index]):
contours_list[grade].pop(i)
break
if not os.path.exists(export_path + 'a' +
str(annotator_id + 1) + '/' + 'summary'):
os.mkdir(export_path + 'a' + str(annotator_id + 1) + '/' +
'summary')
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + 'summary' + '/' \
+ info[0] + '.png'
cv2.imwrite(write_url, mask)
annotator_no = 6
for annotator_id in range(annotator_no):
if not os.listdir(export_path + 'a' + str(annotator_id + 1)):
shutil.rmtree(export_path + 'a' + str(annotator_id + 1))
if os.listdir(export_path):
make_archive_threadsafe(export_file, export_path)
return export_file
def print_logs(project=""):
# project = request.args.get('project', default="", type=str)
if project == "":
abort(404)
else:
data = []
count = 0
if os.path.exists('export/' + project + '_slide_table.txt'):
for wsi in open('export/' + project +
'_slide_table.txt').readlines():
slide_id = int(wsi.split('\t')[0])
temp = {
"id": slide_id,
"text": wsi.replace('\t', ' ').replace('\n', '')
}
data.append(temp)
def takeSecond(elem):
return elem["id"]
for index in range(len(data)):
nuclei_annotation_root = "Data/nuclei_annotation_data/"
annotation_project_root = nuclei_annotation_root + project + '/'
# if not os.path.exists(annotation_project_root + data[index]["text"].split(" ")[1] + '/'):
# continue
tba_list_db = annotation_project_root + data[index]["text"].split(
" ")[1] + '/' + 'tba_list.db'
if not os.path.exists(tba_list_db):
data[index]["text"] += " 0 0 0 0 0 0 0"
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
data[index]["text"] += " " + str(len(tba_result))
for annotator_id in range(1, 7):
annotated = 0
for item in tba_result:
if os.path.exists(annotation_project_root + data[index]["text"].split(" ")[1] + '/' +
'a' + str(annotator_id) + '_r' + str(item[0]) + "_annotation.txt") and \
sum(numpy.loadtxt(annotation_project_root + data[index]["text"].split(" ")[1] + '/' +
'a' + str(annotator_id) + '_r' + str(item[0]) + "_annotation.txt")) > 0:
annotated += 1
data[index]["text"] += " " + str(annotated)
for index in range(len(data)):
for annotator_id in range(1, 7):
nuclei_annotation_root = "Data/freehand_annotation_data/"
annotation_project_root = nuclei_annotation_root + project + '/'
if not os.path.exists(annotation_project_root +
data[index]["text"].split(" ")[1] + '/'):
data[index]["text"] += " 0"
continue
if os.path.exists(annotation_project_root + data[index]["text"].split(" ")[1] + '/' +
'a' + str(annotator_id) + '.db') and \
len(freehand_annotation_sqlite.SqliteConnector(annotation_project_root +
data[index]["text"].split(" ")[1] + '/' +
'a' + str(annotator_id) + '.db').get_lines()) > 0:
data[index]["text"] += " 1"
else:
data[index]["text"] += " 0"
data.sort(key=takeSecond)
for index in range(len(data)):
count += 1
data[index]["text"] = str(count) + " " + data[index]["text"]
output = "ID SlideID UUID SVS_File " \
"NucleiTotal Nuclei1 Nuclei2 Nuclei3 Nuclei4 Nuclei5 Nuclei6 " \
"Freehand1 Freehand2 Freehand3 Freehand4 Freehand5 Freehand6\n"
for index in range(len(data)):
output += data[index]["text"] + '\n'
return Response(output, mimetype='text/plain')