xmcdpy.shifts

xmcdpy.shifts.apply_shift(img, shift)

Apply the shift to the img

xmcdpy.shifts.apply_stack_shifts(images, shifts)

Applies the list of shifts to the images. Images need to be a numpy array with last axis listing images.

Parameters

  • images ((n,m, k) array) – Stack of images

  • shifts (list of (2,) arrays) – Shifts per image

Returns

shifted images

Return type

(n,m,k) array

xmcdpy.shifts.get_stack_shifts(images, ref_image=None, rect_coord=None, upsample_factor=10, gaussian_sigma=5)

Returns the list of shifts for the images in the stack. Rect parameter specifies the coordinates of the region of interest

Parameters

  • images ((n,m,k) array) – stack of images

  • ref_image ((n,m) array, optional) – Image to align to. If None, use the first image in the stack. Defaults to None.

  • rect_coord ((4,) array, optional) – ROI coordinates. Defaults to None.

  • upsample_factor (int, optional) – Defaults to 10.

  • gaussian_sigma (int, optional) – Blur to apply to get rid of high frequency noise. Defaults to 5.

xmcdpy.shifts.stack_shifts(images_stack, rect_coord, alignment_threshold=0.25, start_upsample=1, max_iter=7, gaussian_sigma=5)

Finds the shifts based on the alignment stack and applies them to the image stack

Parameters

  • images_stack ((n,m, k) array) – Stack of images

  • rect_coord ((4,) array, optional) – ROI coordinates.

  • alignment_threshold (float, optional) – See align_stack. Defaults to 0.25.

  • start_upsample (int, optional) – initial upsample. It will increase until it reaches 3/alignment_threshold. Defaults to 1.

  • max_iter (int, optional) – Maximum number of alignment iterations. Defaults to 7.

  • gaussian_sigma (int, optional) – Blur to apply for the alignment. See get_stack_shifts. Defaults to 5.

Returns

Shifted images

Return type

(n,m, k) array