allensdk.internal.brain_observatory.annotated_region_metrics module¶
Module for calculating annotated region metrics from ISI data
- allensdk.internal.brain_observatory.annotated_region_metrics.create_region_mask(image_shape, x, y, width, height, mask)[source]¶
Create mask for region on retinotopic map
- Parameters:
- image_shapetuple
(height, width) of retinotopic map
- xint
x offset of region mask within retinotopic map
- yint
y offset of region mask within retinotopic map
- widthint
width of region mask
- heightint
height of region mask
- masklist
region mask as a list of lists
- Returns:
- numpy.ndarray
Region mask
- allensdk.internal.brain_observatory.annotated_region_metrics.eccentricity(az, alt, az_center, alt_center)[source]¶
Compute eccentricity
- Parameters:
- aznumpy.ndarray
Azimuth retinotopic map
- altnumpy.ndarray
Altitude retinotopic map
- az_centerfloat
Azimuth value to use as center of eccentricity map
- alt_centerfloat
Altitude value to use as center of eccentricity map
- Returns:
- numpy.ndarray
Eccentricity map
- allensdk.internal.brain_observatory.annotated_region_metrics.get_metrics(altitude_phase, azimuth_phase, x=None, y=None, width=None, height=None, mask=None, altitude_scale=0.322, azimuth_scale=0.383)[source]¶
Calculate annotated region metrics
- allensdk.internal.brain_observatory.annotated_region_metrics.retinotopy_metric(mask, isi_map)[source]¶
Compute retinotopic metrics for a responding area
- Parameters:
- masknumpy.ndarray
Mask representing the area over which to calculate metrics
- isi_mapnumpy.ndarray
Retinotopic map
- Returns:
- (float, float, float, float) tuple
min, max, range, bias of retinotopic map over masked region