def main(self, mex_url=None, bisque_token=None, bq=None):
# Allow for testing by passing an alreay initialized session
if bq is None:
bq = BQSession().init_mex(mex_url, bisque_token)
pars = bq.parameters()
image_url = pars.get('dataset_url', None)
annotation_type = pars.get('annotation_type', None)
annotation_attribute = pars.get('annotation_attribute', None)
value_old = pars.get('value_old', None)
bq.update_mex('Starting')
mex_id = mex_url.split('/')[-1]
if image_url is None or len(image_url) < 2:
datasets = bq.fetchxml('/data_service/dataset')
datasets = [d.get('uri') for d in datasets.xpath('dataset')]
else:
datasets = [image_url]
total = 0
changes = []
# delete annotations for each element in the dataset
for ds_url in datasets:
dataset = bq.fetchxml(ds_url, view='deep')
dataset_name = dataset.get('name')
bq.update_mex('processing "%s"' % dataset_name)
refs = dataset.xpath('value[@type="object"]')
for r in refs:
url = r.text
image = bq.fetchxml(url, view='deep')
uuid = image.get('resource_uniq')
modified = delete(image,
value_old,
ann_type=annotation_type,
ann_attr=annotation_attribute)
if len(modified) > 0:
bq.postxml(url, image, method='PUT')
total = total + len(modified)
changes.append({
'name':
'%s (%s)' %
(image.get('name'), image.get('resource_uniq')),
'value':
'%s' % len(modified)
})
changes.insert(0, {'name': 'Total', 'value': '%s' % total})
bq.finish_mex(tags=[{
'name': 'outputs',
'tag': [{
'name': 'deleted',
'tag': changes,
}]
}])
def main(self, mex_url=None, bisque_token=None, image_url=None, bq=None):
# Allow for testing by passing an alreay initialized session
if bq is None:
bq = BQSession().init_mex(mex_url, bisque_token)
bq.update_mex('Classifying...')
pars = bq.parameters()
image_url = pars.get('data_url', None)
model_url = pars.get('model_url', None)
store_on_image = pars.get('store_on_image', False)
method = pars.get('method', 'points')
points = int(pars.get('number_of_points', 10))
confidence = int(pars.get('confidence', 95))
border = int(pars.get('border', 0))
_, image_uniq = image_url.rsplit('/', 1)
_, model_uniq = model_url.rsplit('/', 1)
url = '%s/connoisseur/%s/classify:%s/method:%s/points:%s/confidence:%s/border:%s' % (
bq.bisque_root, model_uniq, image_uniq, method, points, confidence,
border)
# dima: the moving of the image is not of the best taste, this should be changed later
if method != 'segmentation':
url += '/format:xml'
txt = bq.c.fetch(url,
headers={
'Content-Type': 'text/xml',
'Accept': 'text/xml'
})
gobs = etree.fromstring(txt)
else:
color_mode = 'colors'
url += '/colors:colors'
filename = '%s_%s_conf%.2f_n%s_b%s.png' % (
image_uniq, color_mode, confidence, points, border)
filename = bq.c.fetch(url, path=filename)
image_url = upload_file(bq, filename) or ''
gobs = None
bq.update_mex('Storing results...')
outputs = etree.Element('tag', name="outputs")
img = etree.SubElement(outputs,
'tag',
name="MyImage",
type="image",
value=image_url)
if gobs is not None:
img.append(gobs)
if store_on_image is True:
r = bq.postxml(image_url, xml=txt)
bq.finish_mex(tags=[outputs])
else:
etree.SubElement (mt, 'tag', name='pixel_resolution_x', type='number', value=str(res_x))
etree.SubElement (mt, 'tag', name='pixel_resolution_unit_x', value='m')
t = mt.xpath('tag[@name="pixel_resolution_y"]')
if len(t)>0:
t[0].set('value', str(res_y))
else:
etree.SubElement (mt, 'tag', name='pixel_resolution_y', type='number', value=str(res_y))
etree.SubElement (mt, 'tag', name='pixel_resolution_unit_y', value='m')
if len(imu.xpath('//tag'))<1:
print 'No updates needed for: %s'%image_name
continue
#post the image back
print 'Image updated, storing %s to %s'%(image_name, image_url)
print etree.tostring(imu)
r = session.postxml(image_url, imu, method='POST')
if r is None:
print 'Uploading update failed'
#print etree.tostring(r)
#remove image cache
cache_url = '%s?cleancache'%image_url.replace('/data_service/', '/image_service/')
url = session.c.prepare_url(cache_url)
r = session.c.webreq (method='GET', url=url)
pswd,
bisque_root=root,
create_mex=False)
start = datetime.now()
url = urlparse.urljoin(root, url_import)
members = []
for f in files:
resource = etree.Element('resource',
name=os.path.basename(f),
value=localpath2url(f))
print etree.tostring(resource)
r = save_blob(session, resource=resource)
#r = session.postblob(xml=resource)
if r is None or r.get('uri') is None:
print 'Upload failed for %s' % f
else:
members.append(r.get('uri'))
print "Inserted all in: %s" % (datetime.now() - start)
dataset = etree.Element('dataset',
name=os.path.basename(os.path.dirname(files[0])))
for m in members:
n = etree.SubElement(dataset, 'value')
n.text = m
#print etree.tostring(dataset)
url = urlparse.urljoin(root, url_data)
r = session.postxml(url, xml=etree.tostring(dataset))
print r
'tag',
name='false_negative',
type="number",
value=str(v['false_negative']))
etree.SubElement(cc,
'tag',
name='true_positive',
type="number",
value=str(v['true_positive']))
print 'Number of classes in model: ', len(classes_test)
##################################################################
# Upload
##################################################################
config = ConfigParser.ConfigParser()
config.read(config_file)
root = config.get('Host', 'root') or 'localhost:8080'
user = config.get('Host', 'user') or 'test'
pswd = config.get('Host', 'password') or 'test'
session = BQSession().init_local(user,
pswd,
bisque_root=root,
create_mex=False)
url = urlparse.urljoin(root, url_data)
r = session.postxml(url, xml=etree.tostring(resource))
print r.get('uri')
etree.SubElement(poly,
'tag',
name='color',
value='#%s%s%s' % (int2hex(r), int2hex(g), int2hex(b)))
zz = random.randint(0, z)
tt = random.randint(0, t)
vrtx = []
for i in range(10):
x = dx + random.randint(-gobs_sz, gobs_sz)
y = dy + random.randint(-gobs_sz, gobs_sz)
vrtx.append((x, y))
vrtx = sorted(vrtx, key=lambda x: x[0])
for v in vrtx:
etree.SubElement(poly,
'vertex',
x='%s' % v[0],
y='%s' % v[1],
z='%s' % zz,
t='%s' % tt)
#print etree.tostring(mex)
url = session.service_url('data_service', 'mex')
r = session.postxml(url, mex, method='POST')
if r is None:
print 'Upload failed'
print 'id: %s' % r.get('resource_uniq')
print 'url: %s' % r.get('uri')
polygon = '<polygon name="%s"><vertex x="%s" y="%s" /><tag name="color" value="%s" /></polygon>'
polygons = []
for i in range(10):
x = random.randint(0, 900)
y = random.randint(0, 900)
r = random.randint(0, 255)
g = random.randint(0, 255)
b = random.randint(0, 255)
d1 = random.randint(10, 150)
d2 = random.randint(10, 150)
d3 = random.randint(10, 150)
color = '#%s%s%s'%(int2hex(r), int2hex(g), int2hex(b))
polygon = '<polygon name="%s"><vertex x="%s" y="%s" /><vertex x="%s" y="%s" /><vertex x="%s" y="%s" /><tag name="color" value="%s" type="color" /></polygon>'%(i, x, y, x+d1, y, x+d2, y+d3, color)
polygons.append(polygon)
request = '<request>%s</request>'%''.join(polygons)
print request
url = session.service_url('data_service', 'image')
url = '%s/175501/gobject'%url
print url
r = session.postxml(url, etree.fromstring(request), method='POST')
if r is None:
print 'Upload failed'
print 'id: %s'%r.get('resource_uniq')
print 'url: %s'%r.get('uri')
# use import service to /import/transfer activating import service
r = etree.XML(session.postblob(filepath, xml=resource)).find('./')
if r is None or r.get('uri') is None:
print 'Upload failed'
else:
print 'Uploaded ID: %s, URL: %s' % (r.get('resource_uniq'),
r.get('uri'))
f['url'] = r.get('uri')
# upload dataset
dataset = etree.Element('dataset', name=dataset_name)
for f in files:
if 'url' not in f:
continue
v = etree.SubElement(dataset, 'value', type="object")
v.text = f['url']
print etree.tostring(dataset)
url = session.service_url('data_service')
r = session.postxml(url, dataset)
if r is None or r.get('uri') is None:
print 'Dataset failed'
else:
print 'Dataset ID: %s, URL: %s' % (r.get('resource_uniq'), r.get('uri'))
f['url'] = r.get('uri')
session.close()
create_mex=False)
path_on_bisque = 'demo/nuclei_%s/img_name' % (
datetime.now().strftime('%Y%m%dT%H%M%S'))
resource = etree.Element('image', name=path_on_bisque)
print etree.tostring(resource)
# use import service to /import/transfer activating import service
r = etree.XML(session.postblob(img_path, xml=resource)).find('./')
if r is None or r.get('uri') is None:
print 'Upload failed'
else:
print 'Uploaded ID: %s, URL: %s\n' % (r.get('resource_uniq'), r.get('uri'))
print etree.tostring(r)
g = etree.SubElement(r, 'gobject', type='My nuclei')
for a in annos:
p = etree.SubElement(g, 'point')
etree.SubElement(p, 'tag', name='fish', value=a)
print etree.tostring(r)
url = session.service_url('data_service')
r = session.postxml(url, r)
if r is None or r.get('uri') is None:
print 'Adding annotations failed'
else:
print 'Image ID: %s, URL: %s' % (r.get('resource_uniq'), r.get('uri'))
##################################################################
config = ConfigParser.ConfigParser()
config.read('config.cfg')
root = config.get('Host', 'root') or 'localhost:8080'
user = config.get('Host', 'user') or 'test'
pswd = config.get('Host', 'password') or 'test'
session = BQSession().init_local(user, pswd, bisque_root=root, create_mex=False)
url = session.service_url('data_service', 'image')
path = sys.argv[1]
r = R[1]
c = C[0]
field = FIELD[0]
resource = create_resource(path, name, r, c, field)
print etree.tostring(resource)
r = session.postxml(url, resource, method='POST')
print r.get('uri')
#r = save_blob(session, resource=request)
#if r is None or r.get('uri') is None:
# print 'Upload failed'
#else:
# print 'id: %s'%r.get('resource_uniq')
# print 'url: %s'%r.get('uri')
