def create_roi(image, shapes):
updateService = image._conn.getUpdateService()
roi = RoiI()
roi.setImage(image._obj)
for shape in shapes:
roi.addShape(shape)
return updateService.saveAndReturnObject(roi)
def image_rois(self, user1, shapes):
"""Return Image with ROIs."""
image = ImageI()
image.name = rstring('Image for ROIs')
image = get_update_service(user1).saveAndReturnObject(image)
# ROI with all but one shapes
rois = []
roi = RoiI()
for shape in shapes[:-1]:
roi.addShape(shape)
roi.setImage(image)
rois.append(roi)
# roi without shapes
roi = RoiI()
roi.setImage(image)
rois.append(roi)
# roi without image
roi = RoiI()
roi.addShape(shapes[-1])
rois.append(roi)
rois = get_update_service(user1).saveAndReturnArray(rois)
rois.sort(key=lambda x: x.id.val)
return image, rois
def create_roi(conn, img, shapes):
updateService = conn.getUpdateService()
roi = RoiI()
roi.setImage(img._obj)
for shape in shapes:
roi.addShape(shape)
group_id = img.getDetails().getGroup().getId()
print(group_id)
ctx = {'omero.group': str(group_id)}
return updateService.saveAndReturnObject(roi, ctx)
def addRoi(self, request, imageid):
img = self.getImage0(imageid)
if img is None:
return None
data = json.loads(request.body)
shapes = data['shapes']
x = y = l = z = t = -1
for s in shapes:
for k in s:
val = s[k]
if k == "x":
x = int(val)
elif k == "y":
y = int(val)
elif k == "width":
l = int(val)
elif k == "theZ":
z = int(val)
elif k == "theT":
t = int(val)
elif k == "fillColorAsInt":
fill = int(val)
elif k == "strokeColorAsInt":
stroke = int(val)
elif k == "strokeWidth":
strokeWidth = int(val)
if (x < 0 or y < 0 or z < 0 or t < 0 or l <= 0):
return None
updateService = self._connection.getUpdateService()
roi = RoiI()
roi.setImage(img._obj)
rect = RectangleI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(l)
rect.height = rdouble(l)
rect.theZ = rint(z)
rect.theT = rint(t)
rect.setFillColor(rint(fill))
strokeLen = LengthI()
strokeLen.setValue(strokeWidth)
strokeLen.setUnit(UnitsLength.PIXEL)
rect.setStrokeWidth(strokeLen)
rect.setStrokeColor(rint(stroke))
roi.addShape(rect)
if (updateService.saveAndReturnObject(roi) is None):
return None
return self.get_rois(imageid)
def addRoi(self, request, imageid):
img = self.getImage0(imageid)
if img is None:
return None
data = json.loads(request.body)
shapes = data['shapes']
x = y = l = z = t = -1
for s in shapes:
for k in s:
val = s[k]
if k == "x":
x = int(val)
elif k == "y":
y = int(val)
elif k == "width":
l = int(val)
elif k == "theZ":
z = int(val)
elif k == "theT":
t = int(val)
elif k == "fillColorAsInt":
fill = int(val)
elif k == "strokeColorAsInt":
stroke = int(val)
elif k == "strokeWidth":
strokeWidth = int(val)
if (x < 0 or y < 0 or z < 0 or t < 0 or l <= 0):
return None
updateService = self._connection.getUpdateService()
roi = RoiI()
roi.setImage(img._obj)
rect = RectangleI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(l)
rect.height = rdouble(l)
rect.theZ = rint(z)
rect.theT = rint(t)
rect.setFillColor(rint(fill))
strokeLen = LengthI()
strokeLen.setValue(strokeWidth)
strokeLen.setUnit(UnitsLength.PIXEL)
rect.setStrokeWidth(strokeLen)
rect.setStrokeColor(rint(stroke))
roi.addShape(rect)
if (updateService.saveAndReturnObject(roi) is None):
return None
return self.get_rois(imageid)
def process_file(inputfile, image, svc, offset):
"""
Read each line of the file
"""
parents = dict()
line_count = 0
roi = None
parent_shape_id = -1
parent_id = -1
cell_id = 0
x = image.getSizeX() / 2
y = 0
if offset is not None:
y = image.getSizeY() - int(offset[1])
last_frame = 0
with open(inputfile) as fp:
csv_reader = csv.reader(fp, delimiter="\t", quotechar='"')
for row in csv_reader:
if line_count > 1:
# Check the first element to parse
name = row[0]
if name.find(">CELL") >= 0:
# extract cell info
if roi is not None:
# we save the roi before starting a new shape
roi = svc.saveAndReturnObject(roi)
parents[cell_id] = get_last_shape(roi, last_frame)
last_frame = -1
cell_id = int(row[1])
parent_id = int(row[2])
end_type = row[6]
roi = RoiI()
roi.setImage(image._obj)
value = "cellID:%s, parent_id: %s" % (cell_id, parent_id)
print(value)
if parent_id != -1:
parent_shape_id = parents[parent_id]
else:
parent_shape_id = -1
else:
last_frame = process_row(row, x, y, roi, end_type,
parent_shape_id)
parent_shape_id = -1
line_count += 1
def create_points(conn, df, image):
columns = [
"Sequence", "Tagged Protein", "Sequence is unique", "Location_X",
"Location_Y"
]
df2 = pandas.DataFrame(columns=(['Roi'] + columns))
index = df['Source Name'] == image.getName()
for (s, tp, u, x, y) in zip(*map(lambda x: df[index][x], columns)):
p = PointI()
p.x = rdouble(float(x))
p.y = rdouble(float(y))
p.setTextValue(rstring(tp))
roi = RoiI()
roi.addShape(p)
roi.setName(rstring(tp))
roi.setImage(ImageI(image.getId(), False))
roi = conn.getUpdateService().saveAndReturnObject(roi)
df2.loc[len(df2)] = (roi.getId().getValue(), s, tp, u, x, y)
return df2
def test_roi_thumbnail(self, theT, theZ):
update_service = self.sf.getUpdateService()
img = self.create_test_image(size_x=125,
size_y=125,
size_z=2,
size_t=2,
session=self.sf)
for s in self.shapes():
if theT is not None:
s.theT = rint(theT)
if theZ is not None:
s.theZ = rint(theZ)
roi = RoiI()
roi.addShape(s)
roi.setImage(img)
roi = update_service.saveAndReturnObject(roi)
shape = roi.copyShapes()[0]
# Test ROI thumbnail...
request_url = reverse('webgateway_render_roi_thumbnail',
kwargs={'roiId': roi.id.val})
rsp = get(self.django_client, request_url)
thumb_bytes = BytesIO(rsp.content)
try:
thumb = Image.open(thumb_bytes)
finally:
thumb_bytes.close()
assert thumb.size == (250, 166)
# and Shape thumbnail...
request_url = reverse('webgateway_render_shape_thumbnail',
kwargs={'shapeId': shape.id.val})
rsp = get(self.django_client, request_url)
thumb_bytes = BytesIO(rsp.content)
try:
thumb = Image.open(thumb_bytes)
finally:
thumb_bytes.close()
assert thumb.size == (250, 166)
def test_save_rois(self, conn, django_client):
"""Save new ROIs to an Image"""
image = self.make_image(client=conn.c)
roi = RoiI()
roi.name = rstring("roi_name")
roi.setImage(ImageI(image.id.val, False))
point = PointI()
point.x = rdouble(1)
point.y = rdouble(2)
encoder = get_encoder(point.__class__)
point_json = encoder.encode(point)
unsaved_id = "-1:-1"
point_json['oldId'] = unsaved_id
persist_url = reverse('omero_iviewer_persist_rois')
data = {
'imageId': image.id.val,
'rois': {
'count': 1,
'new': [point_json]
}
}
rsp = post_json(django_client, persist_url, data)
print('rsp', rsp)
# {"ids": {"-1:-1": "225504:416603"}}
assert "ids" in rsp
new_ids = rsp["ids"].values()
assert len(new_ids) == 1
new_id = rsp["ids"][unsaved_id]
roi_id = int(new_id.split(':')[0])
shape_id = int(new_id.split(':')[1])
# Add Tag to ROI and Shape
tag = TagAnnotationWrapper(conn)
tag.setValue("ROI/Shape Tag")
tag.save()
roi = conn.getObject("Roi", roi_id)
roi.linkAnnotation(tag)
shape = conn.getObject("Shape", shape_id)
shape.linkAnnotation(tag)
# check...
assert len(list(conn.getAnnotationLinks(
"Shape", parent_ids=[shape_id]))) == 1
# Load Shape
rois_url = reverse('api_rois', kwargs={'api_version': 0})
rois_url += '?image=%s' % image.id.val
rsp = get_json(django_client, rois_url)
assert len(rsp['data']) == 1
# Edit Shape
point_json = rsp['data'][0]['shapes'][0]
point_json["X"] = 100
point_json["Y"] = 200
# iviewer wants to know ROI:Shape ID
point_json["oldId"] = new_id
# Unload details
del point_json["omero:details"]
data = {
'imageId': image.id.val,
'rois': {
'count': 1,
'modified': [point_json]
}
}
rsp = post_json(django_client, persist_url, data)
# IDs shouldn't have changed, e.g.
# {"ids": {"225504:416603": "225504:416603"}}
print('post rsp', rsp)
assert rsp["ids"][new_id] == new_id
# Check annotations not lost
roi = conn.getObject("Roi", roi_id)
assert len(list(roi.listAnnotations())) == 1
assert len(list(conn.getAnnotationLinks(
"Shape", parent_ids=[shape_id]))) == 1