Пример #1
0
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
Пример #2
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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
Пример #3
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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
Пример #4
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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
Пример #5
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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],
Пример #6
0
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