def create_omero_point(data, image):
point = PointI()
point.x = rdouble(get_x(data))
point.y = rdouble(get_y(data))
point.theZ = rint(get_z(data, image))
point.theT = rint(get_t(data, image))
point.textValue = rstring("point-from-napari")
return point
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
# Only save theT, not theZ
rect.theT = rint(0)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
# ellipse without saving theZ & theT
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(200)
line.x2 = rdouble(300)
line.y1 = rdouble(400)
line.y2 = rdouble(500)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(1)
point.y = rdouble(1)
point.theZ = rint(1)
point.theT = rint(1)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.theZ = rint(5)
polygon.theT = rint(5)
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 200,200, 250,75"
polygon.points = rstring(points)
mask = MaskI()
mask.setTheC(rint(0))
mask.setTheZ(rint(0))
mask.setTheT(rint(0))
mask.setX(rdouble(100))
mask.setY(rdouble(100))
mask.setWidth(rdouble(500))
mask.setHeight(rdouble(500))
mask.setTextValue(rstring("test-Mask"))
mask.setBytes(None)
return [rect, ellipse, line, point, polygon, mask]
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(20)
line.x2 = rdouble(30)
line.y1 = rdouble(40)
line.y2 = rdouble(50)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(50)
point.y = rdouble(50)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 100,100, 150,75"
polygon.points = rstring(points)
polyline = PolylineI()
polyline.points = rstring(points)
return [rect, ellipse, line, point, polygon, polyline]
def parse(self):
provider = self.original_file_provider
data = provider.get_original_file_data(self.original_file)
try:
rows = list(csv.reader(data, delimiter=","))
finally:
data.close()
columns = [
ImageColumn("Image", "", list()),
RoiColumn("ROI", "", list()),
StringColumn("Type", "", 12, list()),
]
for row in rows[1:]:
wellnumber = self.well_name_to_number(row[0])
image = self.analysis_ctx.\
image_from_wellnumber(wellnumber)
# TODO: what to do with the field?!
# field = int(row[1])
# image = images[field]
roi = RoiI()
shape = PointI()
shape.cx = rdouble(float(row[2]))
shape.cy = rdouble(float(row[3]))
shape.textValue = rstring(row[4])
roi.addShape(shape)
roi.image = image.proxy()
rid = self.update_service\
.saveAndReturnIds([roi])[0]
columns[0].values.append(image.id.val)
columns[1].values.append(rid)
columns[2].values.append(row[4])
return MeasurementParsingResult([columns])
def parse(self):
provider = self.original_file_provider
data = provider.get_original_file_data(self.original_file)
try:
rows = list(csv.reader(data, delimiter=","))
finally:
data.close()
columns = [
ImageColumn("Image", "", list()),
RoiColumn("ROI", "", list()),
StringColumn("Type", "", 12, list()),
]
for row in rows[1:]:
wellnumber = self.well_name_to_number(row[0])
image = self.analysis_ctx.\
image_from_wellnumber(wellnumber)
# TODO: what to do with the field?!
# field = int(row[1])
# image = images[field]
roi = RoiI()
shape = PointI()
shape.cx = rdouble(float(row[2]))
shape.cy = rdouble(float(row[3]))
shape.textValue = rstring(row[4])
roi.addShape(shape)
roi.image = image.proxy()
rid = self.update_service\
.saveAndReturnIds([roi])[0]
columns[0].values.append(image.id.val)
columns[1].values.append(rid)
columns[2].values.append(row[4])
return MeasurementParsingResult([columns])