deepliif 1.2.1__py3-none-any.whl → 1.2.3__py3-none-any.whl

deepliif/postprocessing__OLD__DELETE.py

@@ -1,440 +0,0 @@
-import math
-import cv2
-from PIL import Image
-import skimage.measure
-from skimage import feature
-from skimage.morphology import remove_small_objects
-import numpy as np
-import scipy.ndimage as ndi
-from numba import jit
-
-
-def remove_small_objects_from_image(img, min_size=100):
-    image_copy = img.copy()
-    image_copy[img > 0] = 1
-    image_copy = image_copy.astype(bool)
-    removed_red_channel = remove_small_objects(image_copy, min_size=min_size).astype(np.uint8)
-    img[removed_red_channel == 0] = 0
-
-    return img
-
-
-def remove_background_noise(mask, mask_boundary):
-    labeled = skimage.measure.label(mask, background=0)
-    padding = 5
-    for i in range(1, len(np.unique(labeled))):
-        component = np.zeros_like(mask)
-        component[labeled == i] = mask[labeled == i]
-        component_bound = np.zeros_like(mask_boundary)
-        component_bound[max(0, min(np.nonzero(component)[0]) - padding): min(mask_boundary.shape[1],
-                                                                             max(np.nonzero(component)[0]) + padding),
-        max(0, min(np.nonzero(component)[1]) - padding): min(mask_boundary.shape[1],
-                                                             max(np.nonzero(component)[1]) + padding)] \
-            = mask_boundary[max(0, min(np.nonzero(component)[0]) - padding): min(mask_boundary.shape[1], max(
-            np.nonzero(component)[0]) + padding),
-              max(0, min(np.nonzero(component)[1]) - padding): min(mask_boundary.shape[1],
-                                                                   max(np.nonzero(component)[1]) + padding)]
-        if len(np.nonzero(component_bound)[0]) < len(np.nonzero(component)[0]) / 3:
-            mask[labeled == i] = 0
-    return mask
-
-
-def remove_cell_noise(mask1, mask2):
-    labeled = skimage.measure.label(mask1, background=0)
-    padding = 2
-    for i in range(1, len(np.unique(labeled))):
-        component = np.zeros_like(mask1)
-        component[labeled == i] = mask1[labeled == i]
-        component_bound = np.zeros_like(mask2)
-        component_bound[
-        max(0, min(np.nonzero(component)[0]) - padding): min(mask2.shape[1], max(np.nonzero(component)[0]) + padding),
-        max(0, min(np.nonzero(component)[1]) - padding): min(mask2.shape[1], max(np.nonzero(component)[1]) + padding)] \
-            = mask2[max(0, min(np.nonzero(component)[0]) - padding): min(mask2.shape[1],
-                                                                         max(np.nonzero(component)[0]) + padding),
-              max(0, min(np.nonzero(component)[1]) - padding): min(mask2.shape[1],
-                                                                   max(np.nonzero(component)[1]) + padding)]
-        if len(np.nonzero(component_bound)[0]) > len(np.nonzero(component)[0]) / 3:
-            mask1[labeled == i] = 0
-            mask2[labeled == i] = 255
-    return mask1, mask2
-
-
-def create_basic_segmentation_mask(img, seg_img, thresh=80, noise_objects_size=20, small_object_size=50):
-    positive_mask, negative_mask = positive_negative_masks_basic(img, seg_img, thresh, noise_objects_size, small_object_size)
-
-    mask = np.zeros_like(img)
-
-    mask[positive_mask > 0] = (255, 0, 0)
-    mask[negative_mask > 0] = (0, 0, 255)
-
-    return mask
-
-
-def imadjust(x, gamma=0.7, c=0, d=1):
-    """
-    Adjusting the image contrast and brightness
-
-    :param x: Input array
-    :param gamma: Gamma value
-    :param c: Minimum value
-    :param d: Maximum value
-    :return: Adjusted image
-    """
-    a = x.min()
-    b = x.max()
-    y = (((x - a) / (b - a)) ** gamma) * (d - c) + c
-    return y
-
-
-def adjust_dapi(inferred_tile, orig_tile):
-    """Adjusts the intensity of mpIF DAPI image
-
-    Parameters:
-        inferred_tile (Image) -- inferred tile image
-        orig_tile (Image) -- original tile image
-
-    Returns:
-        processed_tile (Image) -- the adjusted mpIF DAPI image
-    """
-    inferred_tile_array = np.array(inferred_tile)
-    orig_tile_array = np.array(orig_tile)
-
-    multiplier = 8 / math.log(np.max(orig_tile_array))
-
-    if np.mean(orig_tile_array) < 200:
-        processed_tile = imadjust(inferred_tile_array,
-                                  gamma=multiplier * math.log(np.mean(inferred_tile_array)) / math.log(
-                                      np.mean(orig_tile_array)),
-                                  c=5, d=255).astype(np.uint8)
-
-    else:
-        processed_tile = imadjust(inferred_tile_array,
-                                  gamma=multiplier,
-                                  c=5, d=255).astype(np.uint8)
-    return Image.fromarray(processed_tile)
-
-
-def adjust_marker(inferred_tile, orig_tile):
-    """Adjusts the intensity of mpIF marker image
-
-    Parameters:
-        inferred_tile (Image) -- inferred tile image
-        orig_tile (Image) -- original tile image
-
-    Returns:
-        processed_tile (Image) -- the adjusted marker image
-    """
-    inferred_tile_array = np.array(inferred_tile)
-    orig_tile_array = np.array(orig_tile)
-
-    multiplier = 8 / math.log(np.max(orig_tile_array))
-
-    if np.mean(orig_tile_array) < 200:
-        processed_tile = imadjust(inferred_tile_array,
-                                  gamma=multiplier * math.log(np.std(inferred_tile_array)) / math.log(
-                                      np.std(orig_tile_array)),
-                                  c=5, d=255).astype(np.uint8)
-
-    else:
-        processed_tile = imadjust(inferred_tile_array,
-                                  gamma=multiplier,
-                                  c=5, d=255).astype(np.uint8)
-    return Image.fromarray(processed_tile)
-
-
-# Values for uint8 masks
-MASK_UNKNOWN = 50
-MASK_POSITIVE = 200
-MASK_NEGATIVE = 150
-MASK_BACKGROUND = 0
-MASK_CELL = 255
-MASK_CELL_POSITIVE = 201
-MASK_CELL_NEGATIVE = 151
-MASK_BOUNDARY_POSITIVE = 202
-MASK_BOUNDARY_NEGATIVE = 152
-
-
-@jit(nopython=True)
-def in_bounds(array, index):
-    return index[0] >= 0 and index[0] < array.shape[0] and index[1] >= 0 and index[1] < array.shape[1]
-
-
-def create_posneg_mask(seg, thresh):
-    """Create a mask of positive and negative pixels."""
-
-    cell = np.logical_and(np.add(seg[:,:,0], seg[:,:,2], dtype=np.uint16) > thresh, seg[:,:,1] <= 80)
-    pos = np.logical_and(cell, seg[:,:,0] >= seg[:,:,2])
-    neg = np.logical_xor(cell, pos)
-
-    mask = np.full(seg.shape[0:2], MASK_UNKNOWN, dtype=np.uint8)
-    mask[pos] = MASK_POSITIVE
-    mask[neg] = MASK_NEGATIVE
-
-    return mask
-
-
-@jit(nopython=True)
-def mark_background(mask):
-    """Mask all background pixels by 4-connected region growing unknown boundary pixels."""
-
-    seeds = []
-    for i in range(mask.shape[0]):
-        if mask[i, 0] == MASK_UNKNOWN:
-            seeds.append((i, 0))
-        if mask[i, mask.shape[1]-1] == MASK_UNKNOWN:
-            seeds.append((i, mask.shape[1]-1))
-    for j in range(mask.shape[1]):
-        if mask[0, j] == MASK_UNKNOWN:
-            seeds.append((0, j))
-        if mask[mask.shape[0]-1, j] == MASK_UNKNOWN:
-            seeds.append((mask.shape[0]-1, j))
-
-    neighbors = [(-1, 0), (1, 0), (0, -1), (0, 1)]
-
-    while len(seeds) > 0:
-        seed = seeds.pop()
-        if mask[seed] == MASK_UNKNOWN:
-            mask[seed] = MASK_BACKGROUND
-            for n in neighbors:
-                idx = (seed[0] + n[0], seed[1] + n[1])
-                if in_bounds(mask, idx) and mask[idx] == MASK_UNKNOWN:
-                    seeds.append(idx)
-
-
-@jit(nopython=True)
-def compute_cell_classification(mask, marker, size_thresh, marker_thresh, size_thresh_upper = None):
-    """
-    Compute the mapping of the mask to positive and negative cell classification.
-
-    Parameters
-    ==========
-    mask: 2D uint8 numpy array with pixels labeled as positive, negative, background, or unknown.
-          After the function executes, the pixels will be labeled as background or cell/boundary pos/neg.
-    marker: 2D uint8 numpy array with the restained marker values
-    size_thresh: Lower size threshold in pixels. Only include cells larger than this count.
-    size_thresh_upper: Upper size threshold in pixels, or None. Only include cells smaller than this count.
-    marker_thresh: Classify cell as positive if any marker value within the cell is above this threshold.
-
-    Returns
-    =======
-    Dictionary with the following values:
-        num_total (integer) -- total number of cells in the image
-        num_pos (integer) -- number of positive cells in the image
-        num_neg (integer) -- number of negative calles in the image
-        percent_pos (floating point) -- percentage of positive cells to all cells (IHC score)
-    """
-
-    neighbors = [(-1, -1), (0, -1), (1, -1), (-1, 0), (1, 0), (-1, 1), (0, 1), (1, 1)]
-    border_neighbors = [(0, -1), (-1, 0), (1, 0), (0, 1)]
-    positive_cell_count, negative_cell_count = 0, 0
-
-    for y in range(mask.shape[0]):
-        for x in range(mask.shape[1]):
-            if mask[y, x] == MASK_POSITIVE or mask[y, x] == MASK_NEGATIVE:
-                seeds = [(y, x)]
-                cell_coords = []
-                count = 1
-                count_posneg = 1 if mask[y, x] != MASK_UNKNOWN else 0
-                count_positive = 1 if mask[y, x] == MASK_POSITIVE else 0
-                max_marker = marker[y, x] if marker is not None else 0
-                mask[y, x] = MASK_CELL
-                cell_coords.append((y, x))
-
-                while len(seeds) > 0:
-                    seed = seeds.pop()
-                    for n in neighbors:
-                        idx = (seed[0] + n[0], seed[1] + n[1])
-                        if in_bounds(mask, idx) and (mask[idx] == MASK_POSITIVE or mask[idx] == MASK_NEGATIVE or mask[idx] == MASK_UNKNOWN):
-                            seeds.append(idx)
-                            if mask[idx] == MASK_POSITIVE:
-                                count_positive += 1
-                            if mask[idx] != MASK_UNKNOWN:
-                                count_posneg += 1
-                            if marker is not None and marker[idx] > max_marker:
-                                max_marker = marker[idx]
-                            mask[idx] = MASK_CELL
-                            cell_coords.append(idx)
-                            count += 1
-
-                if count > size_thresh and (size_thresh_upper is None or count < size_thresh_upper):
-                    if (count_positive/count_posneg) >= 0.5 or max_marker > marker_thresh:
-                        fill_value = MASK_CELL_POSITIVE
-                        border_value = MASK_BOUNDARY_POSITIVE
-                        positive_cell_count += 1
-                    else:
-                        fill_value = MASK_CELL_NEGATIVE
-                        border_value = MASK_BOUNDARY_NEGATIVE
-                        negative_cell_count += 1
-                else:
-                    fill_value = MASK_BACKGROUND
-                    border_value = MASK_BACKGROUND
-
-                for coord in cell_coords:
-                    is_boundary = False
-                    for n in border_neighbors:
-                        idx = (coord[0] + n[0], coord[1] + n[1])
-                        if in_bounds(mask, idx) and mask[idx] == MASK_BACKGROUND:
-                            is_boundary = True
-                            break
-                    if is_boundary:
-                        mask[coord] = border_value
-                    else:
-                        mask[coord] = fill_value
-
-    counts = {
-        'num_total': positive_cell_count + negative_cell_count,
-        'num_pos': positive_cell_count,
-        'num_neg': negative_cell_count,
-    }
-    return counts
-
-
-@jit(nopython=True)
-def enlarge_cell_boundaries(mask):
-    neighbors = [(-1, -1), (0, -1), (1, -1), (-1, 0), (1, 0), (-1, 1), (0, 1), (1, 1)]
-    for y in range(mask.shape[0]):
-        for x in range(mask.shape[1]):
-            if mask[y, x] == MASK_BOUNDARY_POSITIVE or mask[y, x] == MASK_BOUNDARY_NEGATIVE:
-                value = MASK_POSITIVE if mask[y, x] == MASK_BOUNDARY_POSITIVE else MASK_NEGATIVE
-                for n in neighbors:
-                    idx = (y + n[0], x + n[1])
-                    if in_bounds(mask, idx) and mask[idx] != MASK_BOUNDARY_POSITIVE and mask[idx] != MASK_BOUNDARY_NEGATIVE:
-                        mask[idx] = value
-    for y in range(mask.shape[0]):
-        for x in range(mask.shape[1]):
-            if mask[y, x] == MASK_POSITIVE:
-                mask[y, x] = MASK_BOUNDARY_POSITIVE
-            elif mask[y, x] == MASK_NEGATIVE:
-                mask[y, x] = MASK_BOUNDARY_NEGATIVE
-
-
-@jit(nopython=True)
-def compute_cell_sizes(mask):
-    neighbors = [(-1, -1), (0, -1), (1, -1), (-1, 0), (1, 0), (-1, 1), (0, 1), (1, 1)]
-    sizes = []
-
-    for y in range(mask.shape[0]):
-        for x in range(mask.shape[1]):
-            if mask[y, x] == MASK_POSITIVE or mask[y, x] == MASK_NEGATIVE:
-                seeds = [(y, x)]
-                count = 1
-                mask[y, x] = MASK_CELL_POSITIVE if mask[y, x] == MASK_POSITIVE else MASK_CELL_NEGATIVE
-
-                while len(seeds) > 0:
-                    seed = seeds.pop()
-                    for n in neighbors:
-                        idx = (seed[0] + n[0], seed[1] + n[1])
-                        if in_bounds(mask, idx) and (mask[idx] == MASK_POSITIVE or mask[idx] == MASK_NEGATIVE or mask[idx] == MASK_UNKNOWN):
-                            seeds.append(idx)
-                            if mask[idx] == MASK_POSITIVE:
-                                mask[idx] = MASK_CELL_POSITIVE
-                            elif mask[idx] == MASK_NEGATIVE:
-                                mask[idx] = MASK_CELL_NEGATIVE
-                            else:
-                                mask[idx] = MASK_CELL
-                            count += 1
-
-                sizes.append(count)
-
-    return sizes
-
-
-@jit(nopython=True)
-def create_kde(values, count, bandwidth = 1.0):
-    gaussian_denom_inv = 1 / math.sqrt(2 * math.pi);
-    max_value = max(values) + 1;
-    step = max_value / count;
-    n = values.shape[0];
-    h = bandwidth;
-    h_inv = 1 / h;
-    kde = np.zeros(count, dtype=np.float32)
-
-    for i in range(count):
-        x = i * step
-        total = 0
-        for j in range(n):
-            val = (x - values[j]) * h_inv;
-            total += math.exp(-(val*val/2)) * gaussian_denom_inv; # Gaussian
-        kde[i] = total / (n*h);
-
-    return kde, step
-
-
-def calc_default_size_thresh(mask, resolution):
-    sizes = compute_cell_sizes(mask)
-    mask[mask == MASK_CELL_POSITIVE] = MASK_POSITIVE
-    mask[mask == MASK_CELL_NEGATIVE] = MASK_NEGATIVE
-    mask[mask == MASK_CELL] = MASK_UNKNOWN
-
-    if len(sizes) > 0:
-        kde, step = create_kde(np.sqrt(sizes), 500)
-        idx = 1
-        for i in range(1, kde.shape[0]-1):
-            if kde[i] < kde[i-1] and kde[i] < kde[i+1]:
-                idx = i
-                break
-        thresh_sqrt = (idx - 1) * step
-
-        allowed_range_sqrt = (4, 7, 10) # [min, default, max] for default sqrt size thresh at 40x
-        if resolution == '20x':
-            allowed_range_sqrt = (3, 4, 6)
-        elif resolution == '10x':
-            allowed_range_sqrt = (2, 2, 3)
-
-        if thresh_sqrt < allowed_range_sqrt[0]:
-            thresh_sqrt = allowed_range_sqrt[0]
-        elif thresh_sqrt > allowed_range_sqrt[2]:
-            thresh_sqrt = allowed_range_sqrt[1]
-
-        return round(thresh_sqrt * thresh_sqrt)
-
-    else:
-        return 0
-
-
-def calc_default_marker_thresh(marker):
-    if marker is not None:
-        nonzero = marker[marker != 0]
-        marker_range = (round(np.percentile(nonzero, 0.1)), round(np.percentile(nonzero, 99.9))) if nonzero.shape[0] > 0 else (0, 0)
-        return round((marker_range[1] - marker_range[0]) * 0.9) + marker_range[0]
-    else:
-        return 0
-
-
-def compute_results(orig, seg, marker, resolution=None, seg_thresh=150, size_thresh='auto', marker_thresh='auto', size_thresh_upper=None):
-    mask = create_posneg_mask(seg, seg_thresh)
-    mark_background(mask)
-
-    if size_thresh == 'auto':
-        size_thresh = calc_default_size_thresh(mask, resolution)
-    if marker_thresh is None:
-        marker_thresh = 0
-        marker = None
-    elif marker_thresh == 'auto':
-        marker_thresh = calc_default_marker_thresh(marker)
-
-    counts = compute_cell_classification(mask, marker, size_thresh, marker_thresh, size_thresh_upper)
-    enlarge_cell_boundaries(mask)
-
-    scoring = {
-        'num_total': counts['num_total'],
-        'num_pos': counts['num_pos'],
-        'num_neg': counts['num_neg'],
-        'percent_pos': round(counts['num_pos'] / counts['num_total'] * 100, 1) if counts['num_pos'] > 0 else 0,
-        'prob_thresh': seg_thresh,
-        'size_thresh': size_thresh,
-        'size_thresh_upper': size_thresh_upper,
-        'marker_thresh': marker_thresh if marker is not None else None,
-    }
-
-    overlay = np.copy(orig)
-    overlay[mask == MASK_BOUNDARY_POSITIVE] = (255, 0, 0)
-    overlay[mask == MASK_BOUNDARY_NEGATIVE] = (0, 0, 255)
-
-    refined = np.zeros_like(seg)
-    refined[mask == MASK_CELL_POSITIVE, 0] = 255
-    refined[mask == MASK_CELL_NEGATIVE, 2] = 255
-    refined[mask == MASK_BOUNDARY_POSITIVE, 1] = 255
-    refined[mask == MASK_BOUNDARY_NEGATIVE, 1] = 255
-
-    return overlay, refined, scoring