def query_sub_class(pro_method, image_method, slide_group, is_positive,
slide_name):
'''
:param pro_method:
:param image_method:
:param slide_group:
:param is_positive:
:param slide_name:
:return:
'''
sub_class = None
sql = '''select sub_class from slide_sub_class
where
pro_method like '%s' and
image_method like '%s' and
slide_group like '%s' and
is_positive like '%s' and
slide_name like '%s'; ''' % \
(
pro_method,
image_method,
slide_group,
is_positive,
slide_name,
)
results = sql_proxy.execute_query(sql)
if len(results) > 0:
sub_class = results[0][0]
return sub_class
def query_all_annos():
'''
查询所有标注
:return: 返回特定条件下查询标注的id集合
'''
sql = 'select * from annotations'
sql_proxy.connect()
results = sql_proxy.execute_query(sql)
sql_proxy.close()
id_list = list()
for res in results:
uints = res[9].split(';')
if len(uints) <= 5:
id_list.append(res[0])
return id_list
def query_hard(sid):
'''
:param pro_method:
:param image_method:
:param slide_group:
:param is_positive:
:param slide_name:
:return:
'''
is_hard = 'No'
sql = '''select * from slide_hard
where sid = %d; ''' % \
(
sid
)
results = sql_proxy.execute_query(sql)
if len(results) > 0:
is_hard = 'Yes'
return is_hard
def query_annos(sid):
'''
查询切片id = sid 的所有标注
:param sid: 与该标注关联的sid
:return:
'''
sql = '''select * from annotations where sid = %s;''' % sid
annos = list()
sql_proxy.connect()
results = sql_proxy.execute_query(sql)
sql_proxy.close()
for res in results:
center_point = Point.str_to_Point(res[2])
cir_rect = Rect.str_to_Rect(res[3])
anno_class = res[4]
anno_code = res[5]
type = res[6]
color = res[7]
is_typical = res[8]
contours = list()
uints = res[9].split(';')
for uint in uints:
if uint == '':
continue
us = uint.split(',')
contours.append([float(us[0]), float(us[1])])
is_hard = res[10]
has_contours = res[11]
anno = Annotation(center_point, cir_rect, contours, anno_class,
anno_code, type, has_contours, color, is_typical)
anno.set_is_hard(is_hard)
anno.set_aid(res[0])
anno.set_sid(res[1])
annos.append(anno)
return annos
from mysql.sql_op import query_slide_info, query_annos, del_anno_by_aid
sql_proxy.connect()
anno_imgs_path = 'L:/GXB/anno_imgs'
# query different group
sql = 'select pro_method, image_method, slide_group, is_positive, zoom \
from \
slides \
group by \
pro_method, image_method, slide_group, is_positive \
order by \
pro_method, image_method, slide_group;'
slide_batches = sql_proxy.execute_query(sql)
log = open(os.path.join(anno_imgs_path, 'log.txt'), 'w')
for slide_batch in slide_batches[2:4]:
slides = query_slide_info(pro_method=slide_batch[0],
image_method=slide_batch[1],
slide_group=slide_batch[2],
is_positive=slide_batch[3],
zoom=slide_batch[4])
print(slide_batch, len(slides))
if len(slides) <= 0:
continue
slide_reader = srf.get_proxy(slides[0].slide_format())
item = '%s__%s__%s__%s__%s' % (slide_batch[0], slide_batch[1],
def query_slide_info(pro_method='%',
image_method='%',
slide_group='%',
is_positive='%',
slide_format='%',
slide_name='%',
zoom='%'):
'''
查询切片信息，以Slide_List方式返回
:param pro_method: 制片方式 e.g. BD
:param image_method: 成像方式 e.g. 3DHistech
:param slide_group: 切片批次 e.g. Shengfuyou_1th
:param is_positive: 是否阳性 e.g. Yes
:param slide_format: 切片格式 e.g. mrxs
:param slide_name: 切片名称 e.g. xxxxx.mrxs
:param zoom: 切片倍率 e.g. 20x
:return:
'''
slides_list = list()
sql_proxy.connect()
# generate sql
sql = '''select * from slides
where
pro_method like '%s' and
image_method like '%s' and
slide_group like '%s' and
is_positive like '%s' and
slide_format like '%s' and
slide_name like '%s' and
zoom like '%s'; ''' %\
(
pro_method,
image_method,
slide_group,
is_positive,
slide_format,
slide_name,
zoom
)
slides = sql_proxy.execute_query(sql)
# print(len(slides))
for slide in slides:
slide_path = slide[1]
slide_name = slide[2]
slide_group = slide[3]
pro_method = slide[4]
image_method = slide[5]
mpp = slide[6]
zoom = slide[7]
slide_format = slide[8]
format_trans = slide[14]
is_positive = slide[9]
is_hard = query_hard(slide[0])
width = slide[10]
height = slide[11]
sub_class = query_sub_class(pro_method, image_method, slide_group,
is_positive, slide_name)
bounds_x = slide[12]
bounds_y = slide[13]
modify_info = None
file_permission = None
md5_info = None
slide_info = SlideInfo(slide_path, slide_name, slide_group, pro_method,
image_method, mpp, zoom, slide_format,
format_trans, is_positive, is_hard, width,
height, sub_class, bounds_x, bounds_y,
modify_info, file_permission, md5_info)
slide_info.set_sid(slide[0])
# slide_info.show_info()
slides_list.append(slide_info)
sql_proxy.close()
return slides_list