def export_region_annotation_list(manifest_name):
manifest_txt = open(export_annotation_root + manifest_name +
'_slide_table.txt').readlines()
result = []
for wsi in manifest_txt:
info = wsi.split('\t')
nuclei_annotation_root = "Data/nuclei_annotation_data/"
annotation_project_root = nuclei_annotation_root + manifest_name + '/'
if not os.path.exists(annotation_project_root + info[1] + '/'):
continue
tba_list_db = annotation_project_root + info[1] + '/' + 'tba_list.db'
if not os.path.exists(tba_list_db):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
if len(tba_result) == 0:
continue
wsi += "\t" + str(len(tba_result)) + "\t" + time.strftime(
'%Y-%m-%d %H:%M:%S', time.localtime(
os.stat(tba_list_db).st_mtime)) + "\t\t\t\t\t"
temp = {
"Slide ID": wsi.split("\t")[0],
"UUID": wsi.split("\t")[1],
"svs file": wsi.split("\t")[2],
"a1": wsi.split("\t")[3],
"a2": wsi.split("\t")[4],
"a3": wsi.split("\t")[5],
"a4": wsi.split("\t")[6],
"a5": wsi.split("\t")[7],
"a6": wsi.split("\t")[8],
}
result.append(temp)
return result
def nuclei_annotation_add_sw():
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)
allowed_annotator = range(7)
if annotator_id in allowed_annotator:
x = request.args.get('x', 0, type=int)
y = request.args.get('y', 0, type=int)
annotation_root_folder = nuclei_annotation_data_root + annotation_project + '/' + slide_uuid + '/'
if not os.path.exists(annotation_root_folder):
os.mkdir(annotation_root_folder)
tba_list_db = annotation_root_folder + 'tba_list.db'
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
db.incert_RegionCentre(-1, x, y)
message = 'Successfully added diagnostic region'
else:
message = 'Only annotator ' + str(
allowed_annotator) + ' is allowed to add diagnostic region'
return jsonify(status=message, num_status=1)
def export_nuclei_annotation_list(manifest_name):
manifest_txt = open(export_annotation_root + manifest_name +
'_slide_table.txt').readlines()
annotation_project_root = freehand_annotation_root + manifest_name + '/'
annotator_no = 6
result = []
for wsi in manifest_txt:
info = wsi.split('\t')
flag = 0
nuclei_annotation_root = "Data/nuclei_annotation_data/"
annotation_project_root = nuclei_annotation_root + manifest_name + '/'
if not os.path.exists(annotation_project_root + info[1] + '/'):
continue
tba_list_db = annotation_project_root + info[1] + '/' + 'tba_list.db'
if not os.path.exists(tba_list_db):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
if len(tba_result) == 0:
continue
for annotator_id in range(annotator_no):
annotated = 0
st_time_list = []
for item in tba_result:
if os.path.exists(annotation_project_root + info[1] + '/' +
'a' + str(annotator_id) + '_r' + str(item[0]) + "_annotation.txt") and \
sum(numpy.loadtxt(annotation_project_root + info[1] + '/' + 'a' + str(annotator_id) +
'_r' + str(item[0]) + "_annotation.txt")) > 0:
annotated += 1
st_time_list.append(
os.stat(annotation_project_root + info[1] + '/' + 'a' +
str(annotator_id) + '_r' + str(item[0]) +
"_annotation.txt").st_mtime)
if len(st_time_list) > 0:
wsi += time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(max(st_time_list))) \
+ ' (' + str(annotated) + '/' + str(len(tba_result)) + ') ' + '\t'
flag = 1
else:
wsi += "No Annotation" + '\t'
if flag:
temp = {
"Slide ID": wsi.split("\t")[0],
"UUID": wsi.split("\t")[1],
"svs file": wsi.split("\t")[2],
"a1": wsi.split("\t")[3],
"a2": wsi.split("\t")[4],
"a3": wsi.split("\t")[5],
"a4": wsi.split("\t")[6],
"a5": wsi.split("\t")[7],
"a6": wsi.split("\t")[8],
"Download Link": "<a target='_blank' href='/export_nuclei_annotation_single?" \
"manifest_file=Data/annotation_project_manifest/" + manifest_name + \
".txt&slide_id=" + wsi.split("\t")[1] + "'> Export </a>",
}
result.append(temp)
return result
def nuclei_annotation_v2_rm_sw():
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)
allowed_annotator = range(7)
if annotator_id in allowed_annotator:
sw_id = request.args.get('sw_id', 0, type=int)
annotation_root_folder = nuclei_annotation_data_root + annotation_project + '/' + slide_uuid + '/'
tba_list_db = annotation_root_folder + 'tba_list.db'
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
db.delete_RegionCentre(sw_id)
original_pic_url = annotation_root_folder + 'r' + str(
sw_id) + '.png'
if os.path.exists(original_pic_url):
os.remove(original_pic_url)
region_image_url = annotation_root_folder + 'r' + str(
sw_id) + '.txt'
if os.path.exists(region_image_url):
os.remove(region_image_url)
for annotator_id in range(7):
annotator_data_url = annotation_root_folder + 'a' + str(
annotator_id) + '_r' + str(sw_id) + '.txt'
if os.path.exists(annotator_data_url):
os.remove(annotator_data_url)
result_pic_url = annotation_root_folder + 'a' + str(
annotator_id) + '_r' + str(sw_id) + '.png'
if os.path.exists(result_pic_url):
os.remove(result_pic_url)
points_file_name = annotation_root_folder + 'a' + str(annotator_id) + '_r' + \
str(sw_id) + '_points' + '.txt'
if os.path.exists(points_file_name):
os.remove(points_file_name)
grades_file_name = annotation_root_folder + 'a' + str(annotator_id) + '_r' + \
str(sw_id) + '_grades' + '.txt'
if os.path.exists(grades_file_name):
os.remove(grades_file_name)
message = 'Successfully removed diagnostic region'
else:
message = message = 'Only annotator ' + str(
allowed_annotator) + ' is allowed to remove diagnostic region'
return jsonify(status=message, num_status=1)
def refresh_nuclei_annotation_progress():
global annotation_project_table
filename = manifest_root + 'table.npy'
if not os.path.exists(filename):
refresh_npy()
else:
result = annotation_project_table.copy() # numpy.load(filename)
for i in range(len(result)):
manifest_txt = open(manifest_root + result[i][0] +
'.txt').readlines()
annotation_project_root = nuclei_annotation_root + result[i][
0] + '/'
annotator_no = 6
region_no = 0
finish_region_no = numpy.zeros(annotator_no)
for wsi in manifest_txt:
info = wsi.split('\t')
if not os.path.exists(annotation_project_root + info[0] + '/'):
continue
tba_list_db = annotation_project_root + info[
0] + '/' + 'tba_list.db'
if not os.path.exists(tba_list_db):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
region_no = region_no + len(tba_result)
for item in tba_result:
for annotator_id in range(annotator_no):
if os.path.exists(annotation_project_root + info[0] + '/' +
'a' + str(annotator_id + 1) + '_r' + str(item[0]) + "_annotation.txt") and \
sum(numpy.loadtxt(annotation_project_root + info[0] + '/' +
'a' + str(annotator_id + 1) + '_r' + str(
item[0]) + "_annotation.txt")) > 0:
finish_region_no[annotator_id] += 1
result_str = "" # 'Total: ' + str(region_no) + ', <br/>'
for annotator_id in range(annotator_no):
result_str += str(annotator_id + 1) + ': ' + \
str(int(finish_region_no[annotator_id])) + ' /' + str(region_no) + ', '
if annotator_id % 2:
result_str += '<br/>'
result[i][4] = result_str
filename = manifest_root + 'table.npy'
result = numpy.array(result)
annotation_project_table = result.copy()
numpy.save(filename, result) # 保存为.npy格式
return
def nuclei_annotation_update_tb_list():
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 = nuclei_annotation_data_root + annotation_project + '/' + slide_uuid + '/'
if not os.path.exists(annotation_root_folder):
os.mkdir(annotation_root_folder)
tba_list_db = annotation_root_folder + 'tba_list.db'
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
return jsonify(max_region=len(tba_result), reg_list=tba_result)
def make_region_back(manifest_name, region_size, slide_ids=None):
original_data_root = 'static/data/Original_data/'
nuclei_annotation_data_root = "static/data/nuclei_annotation_data/"
export_folder = "region/" + manifest_name + "_" + str(region_size) + "/"
if os.path.exists(export_folder):
shutil.rmtree(export_folder)
os.mkdir(export_folder)
manifest_file = open(export_folder + "manifest.txt", "w")
if slide_ids == None:
slide_ids = os.listdir(nuclei_annotation_data_root + manifest_name +
'/')
for slide_ID in slide_ids:
try:
print(slide_ID)
wsi = manifest_controller.get_info_by_uuid(slide_ID)
svs_file_path = original_data_root + wsi[1] + '/' + wsi[2]
tba_list_db = nuclei_annotation_data_root + manifest_name + '/' + wsi[
1] + '/' + 'tba_list.db'
if not os.path.exists(tba_list_db):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
if len(tba_result) > 0:
if not os.path.exists(export_folder + wsi[2]):
os.mkdir(export_folder + wsi[2])
oslide = openslide.OpenSlide(svs_file_path)
manifest_file.writelines(wsi[1] + '\t' + wsi[2] + '\t' +
'None' + os.linesep)
for item in tba_result:
patch = oslide.read_region(
(item[1] - 256 - int(region_size / 2),
item[2] - 256 - int(region_size / 2)), 0,
(region_size, region_size))
patch.save(export_folder + wsi[2] + '/' + str(item[0]) +
'_' + str(item[1]) + '_' + str(item[2]) + '_' +
str(region_size) + '.png')
oslide.close()
except Exception as e:
print("ERROR: " + slide_ID)
print(e)
manifest_file.close()
make_archive_threadsafe(
"export/" + manifest_name + "_" + str(region_size) + 'zip',
export_folder)
def export_region_annotation_data(manifest_file_url,
region_size,
manifest_txt=None,
export_file=None):
annotation_project_root = nuclei_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)):
return
export_file = export_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '_region_annotation.zip'
if os.path.exists(export_file):
os.remove(export_file)
export_path = export_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '/region_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)
wsi_count = 0
for wsi in manifest_txt:
print(wsi)
wsi_count += 1
print(
time.asctime(time.localtime(time.time())),
"start export nuclei annotation:" + str(wsi_count) + '/' +
str(len(manifest_txt)))
info = wsi.split('\t')
try:
svs_file_path = original_data_root + info[0] + '/' + info[1]
tba_list_db = annotation_project_root + '/' + info[
0] + '/' + 'tba_list.db'
print(svs_file_path)
if not os.path.exists(tba_list_db):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
if len(tba_result) > 0:
if not os.path.exists(export_path + info[0]):
os.mkdir(export_path + info[0])
oslide = openslide.OpenSlide(svs_file_path)
for item in tba_result:
patch = oslide.read_region(
(item[1] - 256 - int(int(region_size) / 2),
item[2] - 256 - int(int(region_size) / 2)), 0,
(int(region_size), int(region_size)))
patch.save(export_path + info[0] + '/' + str(item[0]) +
'_' + str(item[1]) + '_' + str(item[2]) + '_' +
str(int(region_size)) + '.png')
oslide.close()
except Exception as e:
print("ERROR: ", wsi)
print(e)
if os.listdir(export_path):
make_archive_threadsafe(export_file, export_path)
return export_file
def export_nuclei_annotation_data(manifest_file_url,
manifest_txt=None,
export_file=None):
annotation_project_root = nuclei_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)):
return
export_file = export_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '_nuclei_annotation.zip'
if os.path.exists(export_file):
os.remove(export_file)
export_path = export_annotation_root + manifest_file_url.rsplit(
"/", 1)[1][:-4] + '/nuclei_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)
colour = [[255, 0, 209], [0, 255, 255], [0, 0, 255], [0, 0, 255],
[255, 191, 0], [0, 0, 0], [0, 0, 0]]
# colour = [tuple([124, 252, 0]), tuple([0, 255, 255]), tuple([137, 43, 224]),
# tuple([255 * 0.82, 255 * 0.41, 255 * 0.12]), tuple([255, 0, 0]), tuple([0, 128, 255])]
# color_scheme = [
# [0.49, 0.99, 0], [0, 1, 1], [0.54, 0.17, 0.88], [0.82, 0.41, 0.12],
# [1, 0, 0], [0, 0.5, 1]
# ]
annotator_no = 6
for annotator_id in range(annotator_no):
os.mkdir(export_path + 'a' + str(annotator_id + 1) + '/')
wsi_count = 0
for wsi in manifest_txt:
print(wsi)
wsi_count += 1
print(
time.asctime(time.localtime(time.time())),
"start export nuclei annotation:" + str(wsi_count) + '/' +
str(len(manifest_txt)))
info = wsi.split('\t')
if not os.path.exists(annotation_project_root + info[0] + '/'):
continue
tba_list_db = annotation_project_root + info[0] + '/' + 'tba_list.db'
if not os.path.exists(tba_list_db):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
for item in tba_result:
original_pic_url = annotation_project_root + info[
0] + '/' + 'r' + str(item[0]) + '.png'
original_pic = cv2.imread(original_pic_url)
for annotator_id in range(annotator_no):
if os.path.exists(annotation_project_root + info[0] + '/' +
'a' + str(annotator_id + 1) + '_r' + str(item[0]) + "_annotation.txt") and \
sum(numpy.loadtxt(annotation_project_root + info[0] + '/' +
'a' + str(annotator_id + 1) + '_r' + str(item[0]) + "_annotation.txt")) > 0:
region_image_url = annotation_project_root + info[0] + '/' + 'a' + str(annotator_id + 1) + \
'_r' + str(item[0]) + "_boundary.txt"
region_image = numpy.loadtxt(region_image_url,
delimiter=",",
dtype=int)
write_path = export_path + 'a' + str(
annotator_id + 1) + '/' + info[0] + '/'
if not os.path.exists(write_path):
os.mkdir(write_path)
annotator_data_url = annotation_project_root + info[0] + '/' + \
'a' + str(annotator_id + 1) + '_' + 'r' + str(item[0]) + "_annotation.txt"
annotator_data = numpy.loadtxt(annotator_data_url,
delimiter=",",
dtype=int)
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + info[0] + '/' \
+ '_' + 'r' + str(item[0]) + '_original.png'
cv2.imwrite(write_url, original_pic)
mask = numpy.zeros(original_pic.shape)
mask_original = numpy.zeros(original_pic.shape)
for i, val in enumerate(annotator_data):
if i != 1 and val != 0:
mask[region_image == i] = colour[int(val) - 1]
mask_original[region_image == i] = (
original_pic[region_image == i] * 2.7 +
colour[val - 1]) / 3.3
else:
mask_original[region_image == i] = original_pic[
region_image == i]
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + info[0] + '/' \
+ '_' + 'r' + str(item[0]) + '_mask.png'
cv2.imwrite(write_url, mask)
mask_original[region_image == -1] = tuple([0, 0, 0])
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + info[0] + '/' \
+ '_' + 'r' + str(item[0]) + '_mask_original.png'
cv2.imwrite(write_url, mask_original)
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + info[0] + '/' \
+ '_' + 'r' + str(item[0]) + '_annotator_data.txt'
numpy.savetxt(write_url,
annotator_data,
fmt="%d",
delimiter=",")
write_url = export_path + 'a' + str(annotator_id + 1) + '/' + info[0] + '/' \
+ '_' + 'r' + str(item[0]) + '_boundary.txt'
numpy.savetxt(write_url,
region_image,
fmt="%d",
delimiter=",")
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 available_slide():
annotator_id = current_user.get_id()
annotation_type = request.args.get('annotation_type', default="", type=str)
project = request.args.get('project', default="", type=str)
if project == "":
return jsonify(manifest_controller.get_available_slide_id())
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', ' ')}
data.append(temp)
def takeSecond(elem):
return elem["id"]
if annotation_type == "nuclei":
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):
continue
db = nuclei_annotation_sqlite.SqliteConnector(tba_list_db)
tba_result = db.get_RegionID_Centre()
annotated = 0
for item in tba_result:
if os.path.exists(annotation_project_root + data[index]["text"].split(" ")[1] + '/' +
'a' + annotator_id + '_r' + str(item[0]) + "_annotation.txt") and \
sum(numpy.loadtxt(annotation_project_root + data[index]["text"].split(" ")[1] + '/' +
'a' + annotator_id + '_r' + str(
item[0]) + "_annotation.txt")) > 0:
annotated += 1
if len(tba_result) > 0:
data[index]["text"] = "(" + str(annotated) + '/' + str(
len(tba_result)) + ") " + data[index]["text"]
elif annotation_type == "freehand" or annotation_type == "freehand_stomache":
for index in range(len(data)):
annotation_root = "Data/" + annotation_type + "_annotation_data/"
annotation_project_root = annotation_root + project + '/'
if not os.path.exists(annotation_project_root +
data[index]["text"].split(" ")[1] + '/'):
continue
if os.path.exists(annotation_project_root + data[index]["text"].split(" ")[1] + '/' +
'a' + annotator_id + '.db') and \
check_freehand_annotation(annotation_project_root +
data[index]["text"].split(" ")[1] + '/' +
'a' + annotator_id + '.db') > 0:
data[index]["text"] = "*" + data[index]["text"]
data.sort(key=takeSecond)
for index in range(len(data)):
count += 1
data[index]["text"] = "【" + str(count) + "】" + data[index]["text"]
return jsonify(data)
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')