from SlideRunner.dataAccess.database import Database
delete_slides = [
"13,8,4,7,17,22,28,26,23,24,36,29,15,14,19,32,25,12", # 3 WSI
"13,8,4,7,17,22,28,26,23,24,36,29,15,14,19", #6 WSI
"13,8,4,7,17,22,28,26,23"
] #12 WSI
import os
DB = Database()
WSI_lists = ['3', '6', '12']
for i, k in enumerate(WSI_lists):
os.system(
'cp databases/MITOS_WSI_CMCT_ODAEL.sqlite databases/MITOS_WSI_CMCT_ODAEL_%sWSI.sqlite'
% k)
DB.open('databases/MITOS_WSI_CMCT_ODAEL_%sWSI.sqlite' % k)
cnt = DB.execute(
'DELETE FROM Annotations_label where annoid in (SELECT uid from Annotations where slide in (%s))'
% delete_slides[i])
cnt = DB.execute(
'DELETE FROM Annotations_coordinates where slide in (%s)' %
delete_slides[i])
cnt = DB.execute('DELETE FROM Annotations where slide in (%s)' %
delete_slides[i])
cnt = DB.execute('DELETE FROM Slides where uid in (%s)' % delete_slides[i])
DB.commit()
print('Center is: ', center, pos, size, W_hpf, H_hpf)
img = slide.read_region(location=pos, level=0, size=(W_hpf, H_hpf))
x2 = pos[0] + W_hpf
y2 = pos[1] + H_hpf
x1 = pos[0]
y1 = pos[1]
print('Img:', np.array(img).shape)
newfilename = filename[:-4] + '.tiff'
img.save('%dHPF/%s' % (hpf, newfilename))
DBnew.execute('UPDATE Slides set filename="%s" where uid==%d' %
(newfilename, uid))
DBnew.loadIntoMemory(uid)
annolist = list(DBnew.annotations.keys())
for annoId in annolist:
anno = DBnew.annotations[annoId]
if (anno.x1 < x1) or (anno.x1 > x2) or (anno.y1 < y1) or (anno.y1 >
y2):
DBnew.removeAnnotation(anno.uid)
else:
DBnew.execute(
'UPDATE Annotations_coordinates SET coordinateX=%d, coordinateY=%d where annoId==%d'
% (anno.x1 - x1, anno.y1 - y1, anno.uid))
DBnew.commit()
