allensdk.mouse_connectivity.grid.subimage.base_subimage module

class allensdk.mouse_connectivity.grid.subimage.base_subimage.IntensitySubImage(reduce_level, in_dims, in_spacing, coarse_spacing, intensity_paths, *args, **kwargs)

Bases: allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage

get_intensity(self)

required_intensities = []

setup_images(self)

class allensdk.mouse_connectivity.grid.subimage.base_subimage.PolygonSubImage(reduce_level, in_dims, in_spacing, coarse_spacing, polygon_info, *args, **kwargs)

Bases: allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage

get_polygons(self)

optional_polys = []

required_polys = []

setup_images(self)

class allensdk.mouse_connectivity.grid.subimage.base_subimage.SegmentationSubImage(reduce_level, in_dims, in_spacing, coarse_spacing, segmentation_paths, *args, **kwargs)

Bases: allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage

extract_injection_from_segmentation(self, segmentation_name='segmentation', injection_name='injection')

Notes

Currently, the segmentation uses a series of codes to map 8-bit values onto meaningful classifications. The code for signal pixels is a 1 in at least one of of the 5 rightmost bits.

extract_signal_from_segmentation(self, segmentation_name='segmentation', signal_name='signal')

Notes

Currently, the segmentation uses a series of codes to map 8-bit values onto meaningful classifications. The code for signal pixels is a 1 in the leftmost bit.

In some cases, bit 5 indicates that the pixel was not removed in a posfiltering process. Optionally, this postfilter can be applied in gridding.

get_segmentation(self)

process_segmentation(self)

read_segmentation_image(self, segmentation_name='segmentation')

Notes

We downsample in memory rather than using the jp2 pyramid because the segmentation is a label image.

required_segmentations = []

setup_images(self)

class allensdk.mouse_connectivity.grid.subimage.base_subimage.SubImage(reduce_level, in_dims, in_spacing, coarse_spacing, *args, **kwargs)

Bases: object

apply_mask(self, image_name, mask_name, positive=True)

apply_pixel_counter(self, accumulator_name, image)

binarize(self, image_name)

compute_coarse_planes(self)

make_pixel_counter(self)

pixel_counter

setup_images(self)

allensdk.mouse_connectivity.grid.subimage.base_subimage.run_subimage(input_data)