poi_manager_logic.py 文件源码

def autofind_pois(self, neighborhood_size=1, min_threshold=10000, max_threshold=1e6):
        """Automatically search the xy scan image for POIs.

        @param neighborhood_size: size in microns.  Only the brightest POI per neighborhood will be found.

        @param min_threshold: POIs must have c/s above this threshold.

        @param max_threshold: POIs must have c/s below this threshold.
        """

        # Calculate the neighborhood size in pixels from the image range and resolution
        x_range_microns = np.max(self.roi_map_data[:, :, 0]) - np.min(self.roi_map_data[:, :, 0])
        y_range_microns = np.max(self.roi_map_data[:, :, 1]) - np.min(self.roi_map_data[:, :, 1])
        y_pixels = len(self.roi_map_data)
        x_pixels = len(self.roi_map_data[1, :])

        pixels_per_micron = np.max([x_pixels, y_pixels]) / np.max([x_range_microns, y_range_microns])
        # The neighborhood in pixels is nbhd_size * pixels_per_um, but it must be 1 or greater
        neighborhood_pix = int(np.max([math.ceil(pixels_per_micron * neighborhood_size), 1]))

        data = self.roi_map_data[:, :, 3]

        data_max = filters.maximum_filter(data, neighborhood_pix)
        maxima = (data == data_max)
        data_min = filters.minimum_filter(data, 3 * neighborhood_pix)
        diff = ((data_max - data_min) > min_threshold)
        maxima[diff is False] = 0

        labeled, num_objects = ndimage.label(maxima)
        xy = np.array(ndimage.center_of_mass(data, labeled, range(1, num_objects + 1)))

        for count, pix_pos in enumerate(xy):
            poi_pos = self.roi_map_data[pix_pos[0], pix_pos[1], :][0:3]
            this_poi_key = self.add_poi(position=poi_pos, emit_change=False)
            self.rename_poi(poikey=this_poi_key, name='spot' + str(count), emit_change=False)

        # Now that all the POIs are created, emit the signal for other things (ie gui) to update
        self.signal_poi_updated.emit()