spymicmac.image

spymicmac.image is a collection of tools for working with images.

spymicmac.image.balance_image(img)

Apply contrast-limited adaptive histogram equalization (CLAHE) on an image, then apply a de-noising filter.

Parameters:

img (array-like) – the image to balance.

Returns:

img_filt (array-like) – the balanced, filtered image.

spymicmac.image.contrast_enhance(fn_img, mask_value=None, qmin=0.02, qmax=0.98, gamma=1.25, disksize=3, imgmin=0)

Enhance image contrast in a three-step process. First, the image is processed with a median filter to reduce noise. Next, a linear contrast stretch is applied, and finally, a gamma adjustment is applied.

Parameters:

• fn_img (str) – the image filename.

• mask_value (int|float) – a mask value to use when filtering the image.

• qmin (float) – the minimum quantile to use for the linear contrast stretch (default: 0.02)

• qmax (float) – the maximum quantile to use for the linear contrast stretch (default: 0.98)

• gamma (float) – the value to use for the gamma adjustment

• disksize (int) – the filter disk size (input to skimage.morphology.disk; default: 3)

• imgmin (int|float) – the minimum value in the output image (default: 0)

Returns:

enhanced (array-like) – the contrast-enhanced image.

spymicmac.image.get_parts_list(im_pattern)

Find all of the parts of a scanned image that match a given filename pattern

Parameters:

im_pattern (str) – the image pattern to match

Returns:

parts_list (list) – a list of all parts of the image that match the pattern.

spymicmac.image.get_rough_frame(img)

Find the rough location of an image frame/border.

Parameters:

img (array-like) – the image to find a border for

Returns:

xmin, xmax, ymin, ymax (float) – the left, right, top, and bottom indices for the rough border.

spymicmac.image.highpass_filter(img)

Subtract a low-pass from an image, to return a highpass filter.

Parameters:

img (array-like) – the image to filter.

Returns:

highpass (array-like) – the highpass-filtered image

spymicmac.image.join_halves(left, right, overlap, block_size=None, blend=True, trim=None)

Join two halves of a scanned image together.

Parameters:

• left (array-like) – the left half of the image

• right (array-like) – the right half of the image

• overlap (int) – the amount of overlap, in pixels, between the two halves.

• block_size (int) – the number of rows each sub-block should cover. Defaults to overlap.

• blend (bool) – apply a linear blend between the two scanned halves (default: True).

• trim (int) – the amount to trim the right side of the image by. (default: None).

spymicmac.image.join_hexagon(im_pattern, overlap=2000, block_size=None, blend=True, is_reversed=False)

Join multiple parts of a scanned image.

Parameters:

• im_pattern (str) – the base name of the image to use (e.g., DZB1216-500280L002001).

• overlap (int) – the overlap, in pixels, between the image parts.

• block_size (int) – the number of rows each sub-block should cover. Defaults to overlap.

• blend (bool) – apply a linear blend between the two scanned halves (default: True).

• is_reversed (bool) – parts are in reversed order (i.e., part b is the left part, part a is the right part)

spymicmac.image.make_binary_mask(img, mult_value=255, erode=0, mask_value=0)

Create a binary mask for an image based on a given mask value. Values equal to mask_value will be given a value of 0 in the mask, while all other values will be set equal to mult_value.

Parameters:

• img (array-like) – the image to create a mask for.

• mult_value (int|float) – the value indicating a non-masked value (default: 255).

• erode (int) – the size of the erosion operation to apply (default: 0).

• mask_value (int) – the value to mask in the image (default: 0).

Returns:

mask (array-like) the binary mask.

spymicmac.image.remove_scanner_stripes(img, dtype=<class 'numpy.uint8'>, scan_axis=1)

Remove horizontal (or vertical) stripes from an image.

Parameters:

• img (array-like) – the image to remove stripes from.

• dtype (numpy.dtype) – the original datatype of the image.

• scan_axis (int) – the axis corresponding to the direction of the stripes. A scan_axis of 1 corresponds to horizontal stripes (the default), while a scan_axis of 0 corresponds to vertical stripes.

Returns:

destriped: the original image with the stripes (mostly) removed.

spymicmac.image.splitter(img, nblocks, overlap=0)

Split an image into (m, n) blocks with a given overlap.

Parameters:

• img (array-like) – the image to split

• nblocks (tuple) – the number of blocks to create along each axis (m, n)

• overlap (int) – the number of pixels to overlap each block. (default: 0)

Returns:

• blocks (list) – a list of the image blocks created

• top_inds (list) – a list of the original row index of the top edge of each block

• left_inds (list) – a list of the original column index of the left edge of each block

spymicmac.image.stretch_image(img, scale=(0.0, 1.0), mult=255, imgmin=0, outtype=<class 'numpy.uint8'>, mask=None)

Apply a linear stretch to an image by clipping and stretching to quantiles.

Parameters:

• img (array-like) – the image to stretch.

• scale (tuple) – the minimum and maximum quantile to stretch to. (default: (0, 1) - the minimum/maximum values of the image)

• mult (int|float) – a multiplier to scale the result to. (default: 255)

• imgmin (int|float) – the minimum value in the output image (default: 0)

• outtype (numpy.dtype) – the numpy datatype to return the stretched image as. (default: np.uint8)

• mask (array-like) – a mask of pixels to ignore when calculating quantiles.

Returns:

stretched (array-like) – the stretched image.