Python morphology.watershed方法代码示例

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def generate_wsl(ws):
    """
    Generates watershed line that correspond to areas of
    touching objects.
    """
    se = square(3)
    ero = ws.copy()
    ero[ero == 0] = ero.max() + 1
    ero = erosion(ero, se)
    ero[ws == 0] = 0

    grad = dilation(ws, se) - ero
    grad[ws == 0] = 0
    grad[grad > 0] = 255
    grad = grad.astype(np.uint8)
    return grad 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def DynamicWatershedAlias(p_img, lamb, p_thresh = 0.5):
    """
    Applies our dynamic watershed to 2D prob/dist image.
    """
    b_img = (p_img > p_thresh) + 0
    Probs_inv = PrepareProb(p_img)


    Hrecons = HreconstructionErosion(Probs_inv, lamb)
    markers_Probs_inv = find_maxima(Hrecons, mask = b_img)
    markers_Probs_inv = label(markers_Probs_inv)
    ws_labels = watershed(Hrecons, markers_Probs_inv, mask=b_img)
    arrange_label = ArrangeLabel(ws_labels)
    wsl = generate_wsl(arrange_label)
    arrange_label[wsl > 0] = 0
    

    return arrange_label 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def overlay_cut_masks(images_dir, subdir_name, target_dir, cut_size=1):
    train_dir = os.path.join(images_dir, subdir_name)
    for mask_dirname in tqdm(glob.glob('{}/*/masks'.format(train_dir))):
        masks = []
        for ind, image_filepath in enumerate(glob.glob('{}/*'.format(mask_dirname))):
            image = np.asarray(Image.open(image_filepath))
            image = np.where(image > 0, ind + 1, 0)
            masks.append(image)
        labeled_masks = np.sum(masks, axis=0)
        overlayed_masks = np.where(labeled_masks, 1, 0)

        watershed_mask = watershed(overlayed_masks.astype(np.bool), labeled_masks, watershed_line=True)
        if watershed_mask.max() == watershed_mask.min():
            cut_masks = overlayed_masks
        else:
            borders = (watershed_mask == 0) & overlayed_masks
            selem = rectangle(cut_size, cut_size)
            dilated_borders = dilation(borders, selem=selem)
            cut_masks = np.where(dilated_borders, 0, overlayed_masks)

        target_filepath = '/'.join(mask_dirname.replace(images_dir, target_dir).split('/')[:-1]) + '.png'
        os.makedirs(os.path.dirname(target_filepath), exist_ok=True)
        imwrite(target_filepath, cut_masks) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def label_mask(pred, main_threshold=0.3, seed_threshold=0.7, w_pixel_t=20, pixel_t=100):
    av_pred = pred / 255.
    av_pred = av_pred[..., 0] * (1 - av_pred[..., 2])
    av_pred = 1 * (av_pred > seed_threshold)
    av_pred = av_pred.astype(np.uint8)

    y_pred = measure.label(av_pred, neighbors=8, background=0)
    props = measure.regionprops(y_pred)
    for i in range(len(props)):
        if props[i].area < w_pixel_t:
            y_pred[y_pred == i + 1] = 0
    y_pred = measure.label(y_pred, neighbors=8, background=0)

    nucl_msk = (255 - pred[..., 0])
    nucl_msk = nucl_msk.astype('uint8')
    y_pred = watershed(nucl_msk, y_pred, mask=(pred[..., 0] > main_threshold * 255), watershed_line=True)

    props = measure.regionprops(y_pred)

    for i in range(len(props)):
        if props[i].area < pixel_t:
            y_pred[y_pred == i + 1] = 0
    y_pred = measure.label(y_pred, neighbors=8, background=0)
    return y_pred 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def postprocess_victor(pred):
    av_pred = pred / 255.
    av_pred = av_pred[..., 2] * (1 - av_pred[..., 1])
    av_pred = 1 * (av_pred > 0.5)
    av_pred = av_pred.astype(np.uint8)

    y_pred = measure.label(av_pred, neighbors=8, background=0)
    props = measure.regionprops(y_pred)
    for i in range(len(props)):
        if props[i].area < 12:
            y_pred[y_pred == i + 1] = 0
    y_pred = measure.label(y_pred, neighbors=8, background=0)

    nucl_msk = (255 - pred[..., 2])
    nucl_msk = nucl_msk.astype('uint8')
    y_pred = watershed(nucl_msk, y_pred, mask=((pred[..., 2] > 80)), watershed_line=True)
    return y_pred

# test_dir = r'C:\dev\dsbowl\results_test\bowl_remap3\merged'
# borders_dir = r'C:\dev\dsbowl\results_test\bowl_remap_border2\merged' 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def _watershed(self, inraster, th_tree=15.):
        """ Simple implementation of a watershed tree crown delineation

        Parameters
        ----------
        inraster :   ndarray
                     raster of height values (e.g., CHM)
        th_tree :    float
                     minimum height of tree crown

        Returns
        -------
        ndarray
            raster of individual tree crowns
        """
        inraster_mask = inraster.copy()
        inraster_mask[inraster <= th_tree] = 0
        raster = inraster.copy()
        raster[np.isnan(raster)] = 0.
        labels = watershed(-raster, self.tree_markers, mask=inraster_mask)
        return labels 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def skimage_watershed_segmentation(mask, kernel=k_3x3, k=1):
    # mask = cv.dilate(mask, kernel, iterations=k)

    distance = ndimage.distance_transform_edt(mask)
    local_maxi = peak_local_max(distance, indices=False, footprint=kernel, labels=mask)

    markers = measure.label(local_maxi)
    labels_ws = watershed(-distance, markers, mask=mask)

    if labels_ws.max() < 2:
        return [mask], labels_ws

    res_masks = []
    for idx in range(1,  labels_ws.max() + 1):
        m = labels_ws == idx
        if m.sum() > 20:
            res_masks.append(m.astype(np.uint8))
    return res_masks, labels_ws 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def watersplit(_probs, _points):
    points = _points.copy()

    points[points != 0] = np.arange(1, points.sum()+1)
    points = points.astype(float)

    probs = ndimage.black_tophat(_probs.copy(), 7)
    seg = watershed(probs, points)

    return find_boundaries(seg) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def proc_np_dist(pred):
    """
    Process Nuclei Prediction with Distance Map

    Args:
        pred: prediction output, assuming 
                channel 0 contain probability map of nuclei
                channel 1 containing the regressed distance map
    """
    blb_raw = pred[...,0]
    dst_raw = pred[...,1]

    blb = np.copy(blb_raw)
    blb[blb >  0.5] = 1
    blb[blb <= 0.5] = 0
    blb = measurements.label(blb)[0]
    blb = remove_small_objects(blb, min_size=10)
    blb[blb > 0] = 1   

    dst_raw[dst_raw < 0] = 0
    dst = np.copy(dst_raw)
    dst = dst * blb
    dst[dst  > 0.5] = 1
    dst[dst <= 0.5] = 0

    marker = dst.copy()
    marker = binary_fill_holes(marker) 
    marker = measurements.label(marker)[0]
    marker = remove_small_objects(marker, min_size=10)
    proced_pred = watershed(-dst_raw, marker, mask=blb)    
    return proced_pred

#### 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def watershed(masks, seeds, borders):
    seeds_detached = seeds * (1 - borders)
    markers = label(seeds_detached)
    labels = morph.watershed(masks, markers, mask=masks)
    return labels 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def overlay_masks_with_borders(images_dir, subdir_name, target_dir, borders_size=3, dilation_size=5):
    train_dir = os.path.join(images_dir, subdir_name)
    for mask_dirname in tqdm(glob.glob('{}/*/masks'.format(train_dir))):
        masks = []
        for ind, image_filepath in enumerate(glob.glob('{}/*'.format(mask_dirname))):
            image = np.asarray(Image.open(image_filepath))
            image = np.where(image > 0, ind + 1, 0)
            masks.append(image)
        labeled_masks = np.sum(masks, axis=0)
        overlayed_masks = np.where(labeled_masks, 1, 0)

        selem = rectangle(dilation_size, dilation_size)
        dilated_mask = dilation(overlayed_masks, selem=selem)
        watershed_mask = watershed((dilated_mask >= 0).astype(np.bool), labeled_masks, watershed_line=True)

        if watershed_mask.max() == watershed_mask.min():
            masks_with_borders = overlayed_masks
        else:
            borders = (watershed_mask == 0) & (dilated_mask > 0)
            selem = rectangle(borders_size, borders_size)
            dilated_borders = dilation(borders, selem=selem)
            masks_with_borders = np.where(dilated_borders, 2, overlayed_masks)

        target_filepath = '/'.join(mask_dirname.replace(images_dir, target_dir).split('/')[:-1]) + '.png'
        os.makedirs(os.path.dirname(target_filepath), exist_ok=True)
        imwrite(target_filepath, masks_with_borders) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def overlay_masks_with_borders_json(images_dir, subdir_name, target_dir, borders_size=3, dilation_size=5):
    train_dir = os.path.join(images_dir, subdir_name)
    for mask_dirname in tqdm(glob.glob('{}/*/masks'.format(train_dir))):
        masks = []
        for ind, image_filepath in enumerate(glob.glob('{}/*'.format(mask_dirname))):
            image = np.asarray(Image.open(image_filepath))
            image = np.where(image > 0, ind + 1, 0)
            masks.append(image)
        labeled_masks = np.sum(masks, axis=0)
        overlayed_masks = np.where(labeled_masks, 1, 0)

        selem = rectangle(dilation_size, dilation_size)
        dilated_mask = dilation(overlayed_masks, selem=selem)
        watershed_mask = watershed((dilated_mask >= 0).astype(np.bool), labeled_masks, watershed_line=True)

        if watershed_mask.max() == watershed_mask.min():
            dilated_borders = np.zeros_like(overlayed_masks)
        else:
            borders = (watershed_mask == 0) & (dilated_mask > 0)
            selem = rectangle(borders_size, borders_size)
            dilated_borders = dilation(borders, selem=selem)

        nuclei = prepare_class_encoding(overlayed_masks)
        borders = prepare_class_encoding(dilated_borders)

        target_filepath = '/'.join(mask_dirname.replace(images_dir, target_dir).split('/')[:-1]) + '.json'
        os.makedirs(os.path.dirname(target_filepath), exist_ok=True)
        save_target_masks(target_filepath, nuclei, borders) 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def create_separation(labels):
    tmp = dilation(labels > 0, square(12))
    tmp2 = watershed(tmp, labels, mask=tmp, watershed_line=True) > 0
    tmp = tmp ^ tmp2
    tmp = dilation(tmp, square(3))

    props = measure.regionprops(labels)

    msk1 = np.zeros_like(labels, dtype='bool')

    for y0 in range(labels.shape[0]):
        for x0 in range(labels.shape[1]):
            if not tmp[y0, x0]:
                continue
            if labels[y0, x0] == 0:
                sz = 5
            else:
                sz = 7
                if props[labels[y0, x0] - 1].area < 300:
                    sz = 5
                elif props[labels[y0, x0] - 1].area < 2000:
                    sz = 6
            uniq = np.unique(labels[max(0, y0 - sz):min(labels.shape[0], y0 + sz + 1),
                             max(0, x0 - sz):min(labels.shape[1], x0 + sz + 1)])
            if len(uniq[uniq > 0]) > 1:
                msk1[y0, x0] = True
    return msk1 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def my_watershed(what, mask1, mask2):
    markers = ndi.label(mask2, output=np.uint32)[0]
    labels = watershed(what, markers, mask=mask1, watershed_line=True)
    return labels 

# 需要导入模块: from skimage import morphology [as 别名]
# 或者: from skimage.morphology import watershed [as 别名]
def segmentation_3D(features,field,dxy,threshold=3e-3,target='maximum',level=None,method='watershed',max_distance=None):
    return segmentation(features,field,dxy,threshold=threshold,target=target,level=level,method=method,max_distance=max_distance)