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)