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: SubImage

get_intensity()

required_intensities = []

setup_images()

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

Bases: SubImage

get_polygons()

optional_polys = []

required_polys = []

setup_images()

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

Bases: SubImage

extract_injection_from_segmentation(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(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()

process_segmentation()

read_segmentation_image(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()

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

Bases: object

apply_mask(image_name, mask_name, positive=True)

apply_pixel_counter(accumulator_name, image)

binarize(image_name)

compute_coarse_planes()

make_pixel_counter()

property pixel_counter

setup_images()

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