def start(self):
self._gen_weights()
self.genCoords()
#metadata handling
self.mdh = MetaDataHandler.NestedClassMDHandler()
self.mdh.setEntry('StartTime', time.time())
self.mdh.setEntry('AcquisitionType', 'Tiled overview')
#loop over all providers of metadata
for mdgen in MetaDataHandler.provideStartMetadata:
mdgen(self.mdh)
self._x0 = self.xp[0]
self._y0 = self.yp[0]
self._pixel_size = self.mdh.getEntry('voxelsize.x')
self.background = self.mdh.getOrDefault('Camera.ADOffset',
self.background)
# make our x0, y0 independent of the camera ROI setting
x0_cam, y0_cam = MetaDataHandler.get_camera_physical_roi_origin(
self.mdh)
x0 = self._x0 + self._pixel_size * x0_cam
y0 = self._y0 + self._pixel_size * y0_cam
self.P = tile_pyramid.ImagePyramid(self._tiledir,
self._base_tile_size,
x0=x0,
y0=y0,
pixel_size=self._pixel_size)
pointScanner.PointScanner.start(self)
def start(self):
#self._weights =tile_pyramid.ImagePyramid.frame_weights(self.scope.frameWrangler.currentFrame.shape[:2]).squeeze()
self.genCoords()
#metadata handling
self.mdh = MetaDataHandler.NestedClassMDHandler()
self.mdh.setEntry('StartTime', time.time())
self.mdh.setEntry('AcquisitionType', 'Tiled overview')
#loop over all providers of metadata
for mdgen in MetaDataHandler.provideStartMetadata:
mdgen(self.mdh)
self._x0 = np.min(
self.xp
) # get the upper left corner of the scan, regardless of shape/fill/start
self._y0 = np.min(self.yp)
self._pixel_size = self.mdh.getEntry('voxelsize.x')
self.background = self.mdh.getOrDefault('Camera.ADOffset',
self.background)
# calculate origin independent of the camera ROI setting to store in
# metadata for use in e.g. SupertileDatasource.DataSource.tile_coords_um
x0_cam, y0_cam = MetaDataHandler.get_camera_physical_roi_origin(
self.mdh)
x0 = self._x0 + self._pixel_size * x0_cam # offset in [um]
y0 = self._y0 + self._pixel_size * y0_cam
if self._backend == 'cluster':
from PYME.Analysis import distributed_pyramid
self.P = distributed_pyramid.DistributedImagePyramid(
self._tiledir,
self._base_tile_size,
x0=x0,
y0=y0,
pixel_size=self._pixel_size)
else:
self.P = tile_pyramid.ImagePyramid(self._tiledir,
self._base_tile_size,
x0=x0,
y0=y0,
pixel_size=self._pixel_size)
pointScanner.PointScanner.start(self)
def _set_tile_source(self, tile_dir):
self.tile_dir = tile_dir
self.mdh = MetaDataHandler.load_json(
os.path.join(tile_dir, 'metadata.json'))
self._pyramid = tile_pyramid.ImagePyramid(
tile_dir, pyramid_tile_size=self.mdh['Pyramid.TileSize'])