def addContainer(self, nwbfile): nwbfile.add_imaging_plane(self.imaging_plane) img_seg = ImageSegmentation('plane segmentation round trip') img_seg.add_plane_segmentation(self.container) mod = nwbfile.create_processing_module( 'plane_seg_test_module', 'plane segmentation round trip', 'a plain module for testing') mod.add_data_interface(img_seg)
def addContainer(self, nwbfile): nwbfile.add_device(self.device) nwbfile.add_imaging_plane(self.imaging_plane) img_seg = ImageSegmentation() img_seg.add_plane_segmentation(self.container) mod = nwbfile.create_processing_module('plane_seg_test_module', 'a plain module for testing') mod.add(img_seg)
def addContainer(self, nwbfile): nwbfile.add_device(self.device) nwbfile.add_imaging_plane(self.imaging_plane) img_seg = ImageSegmentation() img_seg.add_plane_segmentation(self.plane_segmentation) mod = nwbfile.create_processing_module('plane_seg_test_module', 'a plain module for testing') mod.add(img_seg) super(TestRoiResponseSeriesIO, self).addContainer(nwbfile)
def addContainer(self, nwbfile): """ Add an ImageSegmentation in processing with a PlaneSegmentation and add Device and ImagingPlane to the given NWBFile """ nwbfile.add_device(self.device) nwbfile.add_imaging_plane(self.imaging_plane) img_seg = ImageSegmentation() img_seg.add_plane_segmentation(self.container) self.mod = nwbfile.create_processing_module( 'plane_seg_test_module', 'a plain module for testing') self.mod.add(img_seg)
def addContainer(self, nwbfile): """ Add the test RoiResponseSeries as an acquisition and add Device, ImagingPlane, ImageSegmentation, and PlaneSegmentation to the given NWBFile """ nwbfile.add_device(self.device) nwbfile.add_imaging_plane(self.imaging_plane) img_seg = ImageSegmentation() img_seg.add_plane_segmentation(self.plane_segmentation) mod = nwbfile.create_processing_module('plane_seg_test_module', 'a plain module for testing') mod.add(img_seg) super().addContainer(nwbfile)
img_seg = ImageSegmentation() mod.add(img_seg) ps = img_seg.create_plane_segmentation( 'output from segmenting my favorite imaging plane', imaging_plane, 'my_planeseg', image_series) w, h = 3, 3 pix_mask1 = [(0, 0, 1.1), (1, 1, 1.2), (2, 2, 1.3)] img_mask1 = [[0.0 for x in range(w)] for y in range(h)] img_mask1[0][0] = 1.1 img_mask1[1][1] = 1.2 img_mask1[2][2] = 1.3 ps.add_roi(pixel_mask=pix_mask1, image_mask=img_mask1) bob = pynwb.ophys.PlaneSegmentation('description', imaging_plane, name="bob") #Alas, I can't just tack stuff onto the plane segmentation #ps.add_container(cortical_surface) img_seg.add_plane_segmentation(bob) bob.add_roi(pixel_mask=pix_mask1, image_mask=img_mask1) duck = BlenderPlaneSegmentation('description', imaging_plane, name="blender seg", blender_surface=soma_surface) duck.add_roi(pixel_mask=pix_mask1, image_mask=img_mask1) img_seg.add_plane_segmentation(duck) with NWBHDF5IO('bubtest2.nwb', 'w') as io: io.write(nwbfile)