import warnings import itertools import numpy as np from skimage import img_as_float from .colorconv import rgb2gray, gray2rgb from . import rgb_colors import six from six.moves import zip __all__ = ['color_dict', 'label2rgb', 'DEFAULT_COLORS'] DEFAULT_COLORS = ('red', 'blue', 'yellow', 'magenta', 'green', 'indigo', 'darkorange', 'cyan', 'pink', 'yellowgreen') color_dict = dict((k, v) for k, v in six.iteritems(rgb_colors.__dict__) if isinstance(v, tuple)) def _rgb_vector(color): """Return RGB color as (1, 3) array. This RGB array gets multiplied by masked regions of an RGB image, which are partially flattened by masking (i.e. dimensions 2D + RGB -> 1D + RGB). Parameters ---------- color : str or array Color name in `color_dict` or RGB float values between [0, 1]. """ if isinstance(color, six.string_types): color = color_dict[color] # Slice to handle RGBA colors. return np.array(color[:3]) def _match_label_with_color(label, colors, bg_label, bg_color): """Return `unique_labels` and `color_cycle` for label array and color list. Colors are cycled for normal labels, but the background color should only be used for the background. """ # Temporarily set background color; it will be removed later. if bg_color is None: bg_color = (0, 0, 0) bg_color = _rgb_vector([bg_color]) unique_labels = list(set(label.flat)) # Ensure that the background label is in front to match call to `chain`. if bg_label in unique_labels: unique_labels.remove(bg_label) unique_labels.insert(0, bg_label) # Modify labels and color cycle so background color is used only once. color_cycle = itertools.cycle(colors) color_cycle = itertools.chain(bg_color, color_cycle) return unique_labels, color_cycle def label2rgb(label, image=None, colors=None, alpha=0.3, bg_label=-1, bg_color=None, image_alpha=1): """Return an RGB image where color-coded labels are painted over the image. Parameters ---------- label : array Integer array of labels with the same shape as `image`. image : array Image used as underlay for labels. If the input is an RGB image, it's converted to grayscale before coloring. colors : list List of colors. If the number of labels exceeds the number of colors, then the colors are cycled. alpha : float [0, 1] Opacity of colorized labels. Ignored if image is `None`. bg_label : int Label that's treated as the background. bg_color : str or array Background color. Must be a name in `color_dict` or RGB float values between [0, 1]. image_alpha : float [0, 1] Opacity of the image. """ if colors is None: colors = DEFAULT_COLORS colors = [_rgb_vector(c) for c in colors] if image is None: image = np.zeros(label.shape + (3,), dtype=np.float64) # Opacity doesn't make sense if no image exists. alpha = 1 else: if not image.shape[:2] == label.shape: raise ValueError("`image` and `label` must be the same shape") if image.min() < 0: warnings.warn("Negative intensities in `image` are not supported") image = img_as_float(rgb2gray(image)) image = gray2rgb(image) * image_alpha + (1 - image_alpha) # Ensure that all labels are non-negative so we can index into # `label_to_color` correctly. offset = min(label.min(), bg_label) if offset != 0: label = label - offset # Make sure you don't modify the input array. bg_label -= offset new_type = np.min_scalar_type(int(label.max())) if new_type == np.bool: new_type = np.uint8 label = label.astype(new_type) unique_labels, color_cycle = _match_label_with_color(label, colors, bg_label, bg_color) if len(unique_labels) == 0: return image dense_labels = range(max(unique_labels) + 1) label_to_color = np.array([c for i, c in zip(dense_labels, color_cycle)]) result = label_to_color[label] * alpha + image * (1 - alpha) # Remove background label if its color was not specified. remove_background = bg_label in unique_labels and bg_color is None if remove_background: result[label == bg_label] = image[label == bg_label] return result