def _parse_mnu_roi(self, columns):
"""Parses out ROI from OmeroTables columns for 'MNU' datasets."""
log.debug("Parsing %s MNU ROIs..." % (len(columns[0].values)))
image_ids = columns[self.IMAGE_COL].values
rois = list()
# Save our file annotation to the database so we can use an unloaded
# annotation for the saveAndReturnIds that will be triggered below.
self.file_annotation = self.update_service.saveAndReturnObject(self.file_annotation)
unloaded_file_annotation = FileAnnotationI(self.file_annotation.id.val, False)
batch_no = 1
batches = dict()
for i, image_id in enumerate(image_ids):
unloaded_image = ImageI(image_id, False)
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
values = columns[3].values
shape.cx = rdouble(float(values[i]))
values = columns[2].values
shape.cy = rdouble(float(values[i]))
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
if len(rois) == self.ROI_UPDATE_LIMIT:
self.thread_pool.add_task(self.update_rois, rois, batches, batch_no)
rois = list()
batch_no += 1
self.thread_pool.add_task(self.update_rois, rois, batches, batch_no)
self.thread_pool.wait_completion()
batch_keys = batches.keys()
batch_keys.sort()
for k in batch_keys:
columns[self.ROI_COL].values += batches[k]
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 to_rois(cx_column, cy_column, pixels):
unloaded_image = ImageI(pixels.image.id, False)
rois = list()
for index in range(len(cx_column.values)):
cx = rdouble(cx_column.values[index])
cy = rdouble(cy_column.values[index])
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
shape.cx = cx
shape.cy = cy
roi.addShape(shape)
roi.image = unloaded_image
rois.append(roi)
return rois
def main(conn, argv):
parser = argparse.ArgumentParser()
parser.add_argument("image", help="Image ID")
args = parser.parse_args(argv)
image_id = args.image
data = swc.read(
"20200628-ftp/RL_35_guassian_4_4_80.tif_x94_y327_z241_app2_(GSBT).swc"
).data_block
# img_name = 'FADU_tumour_Lectin_substack_deconvolved_RL_35iters_guassian_psf_4_4_80.tif'
image = conn.getObject("Image", image_id)
# delete existing ROIs
roi_service = conn.getRoiService()
result = roi_service.findByImage(image.id, None)
roi_ids = [roi.id.val for roi in result.rois]
if roi_ids:
print("Deleting ROIs...")
conn.deleteObjects("Roi", roi_ids, wait=True)
size_y = image.getSizeY()
paths = parse_swc(data, size_y)
red_int = int.from_bytes([255, 0, 0, 255], byteorder="big", signed=True)
for count, path in enumerate(paths):
points = []
for zyx in path:
z, y, x = zyx
point = PointI()
point.x = rdouble(x)
point.y = rdouble(y)
point.theZ = rint(round(z))
point.strokeColor = rint(red_int)
points.append(point)
print(f"{count}/{len(paths)} Creating ROI with {len(points)} points")
create_roi(image, points)
def _parse_mnu_roi(self, columns):
"""Parses out ROI from OmeroTables columns for 'MNU' datasets."""
log.debug("Parsing %s MNU ROIs..." % (len(columns[0].values)))
image_ids = columns[self.IMAGE_COL].values
rois = list()
# Save our file annotation to the database so we can use an unloaded
# annotation for the saveAndReturnIds that will be triggered below.
self.file_annotation = \
self.update_service.saveAndReturnObject(self.file_annotation)
unloaded_file_annotation = \
FileAnnotationI(self.file_annotation.id.val, False)
batch_no = 1
batches = dict()
for i, image_id in enumerate(image_ids):
unloaded_image = ImageI(image_id, False)
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
values = columns[3].values
shape.cx = rdouble(float(values[i]))
values = columns[2].values
shape.cy = rdouble(float(values[i]))
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
if len(rois) == self.ROI_UPDATE_LIMIT:
self.thread_pool.add_task(
self.update_rois, rois, batches, batch_no)
rois = list()
batch_no += 1
self.thread_pool.add_task(self.update_rois, rois, batches, batch_no)
self.thread_pool.wait_completion()
batch_keys = batches.keys()
batch_keys.sort()
for k in batch_keys:
columns[self.ROI_COL].values += batches[k]
def parse_and_populate_roi(self, columns_as_list):
# First sanity check our provided columns
names = [column.name for column in columns_as_list]
log.debug('Parsing columns: %r' % names)
cells_expected = [name in names for name in self.CELLS_CG_EXPECTED]
nuclei_expected = [name in names for name in self.NUCLEI_CG_EXPECTED]
if (False in cells_expected) and (False in nuclei_expected):
log.warn("Missing CGs for InCell dataset: %r" % names)
log.warn('Removing resultant empty ROI column.')
for column in columns_as_list:
if RoiColumn == column.__class__:
columns_as_list.remove(column)
return
# Reconstruct a column name to column map
columns = dict()
for column in columns_as_list:
columns[column.name] = column
image_ids = columns['Image'].values
rois = list()
# Save our file annotation to the database so we can use an unloaded
# annotation for the saveAndReturnIds that will be triggered below.
self.file_annotation = \
self.update_service.saveAndReturnObject(self.file_annotation)
unloaded_file_annotation = \
FileAnnotationI(self.file_annotation.id.val, False)
# Parse and append ROI
batch_no = 1
batches = dict()
for i, image_id in enumerate(image_ids):
unloaded_image = ImageI(image_id, False)
if False in nuclei_expected:
# Cell centre of gravity
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
shape.cx = rdouble(float(columns['Cell: cgX'].values[i]))
shape.cy = rdouble(float(columns['Cell: cgY'].values[i]))
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
elif False in cells_expected:
# Nucleus centre of gravity
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
shape.cx = rdouble(float(columns['Nucleus: cgX'].values[i]))
shape.cy = rdouble(float(columns['Nucleus: cgY'].values[i]))
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
else:
raise MeasurementError('Not a nucleus or cell ROI')
if len(rois) == self.ROI_UPDATE_LIMIT:
thread_pool.add_task(self.update_rois, rois, batches, batch_no)
rois = list()
batch_no += 1
thread_pool.add_task(self.update_rois, rois, batches, batch_no)
thread_pool.wait_completion()
batch_keys = batches.keys()
batch_keys.sort()
for k in batch_keys:
columns['ROI'].values += batches[k]
def parse_and_populate_roi(self, columns_as_list):
# First sanity check our provided columns
names = [column.name for column in columns_as_list]
log.debug('Parsing columns: %r' % names)
cells_expected = [name in names for name in self.CELLS_CG_EXPECTED]
nuclei_expected = [name in names for name in self.NUCLEI_CG_EXPECTED]
if (False in cells_expected) and (False in nuclei_expected):
log.warn("Missing CGs for InCell dataset: %r" % names)
log.warn('Removing resultant empty ROI column.')
for column in columns_as_list:
if RoiColumn == column.__class__:
columns_as_list.remove(column)
return
# Reconstruct a column name to column map
columns = dict()
for column in columns_as_list:
columns[column.name] = column
image_ids = columns['Image'].values
rois = list()
# Save our file annotation to the database so we can use an unloaded
# annotation for the saveAndReturnIds that will be triggered below.
self.file_annotation = \
self.update_service.saveAndReturnObject(self.file_annotation)
unloaded_file_annotation = \
FileAnnotationI(self.file_annotation.id.val, False)
# Parse and append ROI
batch_no = 1
batches = dict()
for i, image_id in enumerate(image_ids):
unloaded_image = ImageI(image_id, False)
if False in nuclei_expected:
# Cell centre of gravity
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
shape.cx = rdouble(float(columns['Cell: cgX'].values[i]))
shape.cy = rdouble(float(columns['Cell: cgY'].values[i]))
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
elif False in cells_expected:
# Nucleus centre of gravity
roi = RoiI()
shape = PointI()
shape.theZ = rint(0)
shape.theT = rint(0)
shape.cx = rdouble(float(columns['Nucleus: cgX'].values[i]))
shape.cy = rdouble(float(columns['Nucleus: cgY'].values[i]))
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
else:
raise MeasurementError('Not a nucleus or cell ROI')
if len(rois) == self.ROI_UPDATE_LIMIT:
self.thread_pool.add_task(
self.update_rois, rois, batches, batch_no)
rois = list()
batch_no += 1
self.thread_pool.add_task(self.update_rois, rois, batches, batch_no)
self.thread_pool.wait_completion()
batch_keys = batches.keys()
batch_keys.sort()
for k in batch_keys:
columns['ROI'].values += batches[k]