Python segmentation.mark_boundaries函数代码示例

def fun_compare_colorsegmentation_and_display(image_data, number_segments=250, compactness_factor=10):
    """
    The function is a copy of what does this link http://scikit-image.org/docs/dev/auto_examples/plot_segmentations.html
    """
    segments_fz = felzenszwalb(image_data, scale=100, sigma=0.5, min_size=50)
    segments_slic = slic(image_data, n_segments=number_segments, compactness=compactness_factor, sigma=1)
    segments_quick = quickshift(image_data, kernel_size=3, max_dist=6, ratio=0.5)

    print ("Felzenszwalb's number of segments: %d" % len(np.unique(segments_fz)))
    print ("Slic number of segments: %d" % len(np.unique(segments_slic)))
    print ("Quickshift number of segments: %d" % len(np.unique(segments_quick)))

    fig, ax = plt.subplots(1, 3, sharex=True, sharey=True, subplot_kw={"adjustable": "box-forced"})
    fig.set_size_inches(8, 3, forward=True)
    fig.subplots_adjust(0.05, 0.05, 0.95, 0.95, 0.05, 0.05)

    ax[0].imshow(mark_boundaries(image_data, segments_fz, color=(1, 0, 0)))
    ax[0].set_title("Felzenszwalbs's method")
    ax[1].imshow(mark_boundaries(image_data, segments_slic, color=(1, 0, 0)))
    ax[1].set_title("SLIC")
    ax[2].imshow(mark_boundaries(image_data, segments_quick, color=(1, 0, 0)))
    ax[2].set_title("Quickshift")
    for a in ax:
        a.set_xticks(())
        a.set_yticks(())
    plt.show()

def human_afterloop(output_directory, pre_time, fle_name, buffer_directory):
    start2 = time()

    d_c = import_edited(buffer_directory)
    rebw = load(open(buffer_directory+'-'+'DO_NOT_TOUCH_ME.dmp','rb'))
    seg_dc = (label(d_c,neighbors=4)+1)*d_c
    if np.max(seg_dc)<4:
        return 'FAILED: mask for %s looks unsegmented' % fle_name

    colormap = repaint_culsters(int(np.max(seg_dc)))

    segs = len(set(seg_dc.flatten().tolist()))-1

    # shows the result before saving the clustering and printing to the user the number of the images
    plt.subplot(1,2,1)
    plt.title(fle_name)
    plt.imshow(rebw, cmap='gray', interpolation='nearest')

    plt.subplot(1,2,2)
    plt.title('Segmentation - clusters: %s'%str(segs))
    plt.imshow(mark_boundaries(rebw, d_c))
    plt.imshow(seg_dc, cmap=colormap, interpolation='nearest', alpha=0.3)

    plt.show()

    plt.imshow(mark_boundaries(rebw, d_c))
    plt.imshow(seg_dc, cmap=colormap, interpolation='nearest', alpha=0.3)

    plt.savefig(path.join(output_directory, fle_name+'_%s_clusters.png'%str(segs)), dpi=500, bbox_inches='tight', pad_inches=0.0)

    return fle_name+'\t clusters: %s,\t total time : %s'%(segs, "{0:.2f}".format(time()-start2+pre_time))

def test_mark_boundaries():
    image = np.zeros((10, 10))
    label_image = np.zeros((10, 10))
    label_image[2:7, 2:7] = 1

    ref = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
                    [0, 0, 1, 0, 0, 0, 0, 1, 0, 0],
                    [0, 0, 1, 0, 0, 0, 0, 1, 0, 0],
                    [0, 0, 1, 0, 0, 0, 0, 1, 0, 0],
                    [0, 0, 1, 0, 0, 0, 0, 1, 0, 0],
                    [0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
    result = mark_boundaries(image, label_image, color=(1, 1, 1)).mean(axis=2)
    assert_array_equal(result, ref)

    ref = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 1, 1, 1, 1, 1, 1, 2, 0],
                    [0, 0, 1, 2, 2, 2, 2, 1, 2, 0],
                    [0, 0, 1, 2, 0, 0, 0, 1, 2, 0],
                    [0, 0, 1, 2, 0, 0, 0, 1, 2, 0],
                    [0, 0, 1, 2, 0, 0, 0, 1, 2, 0],
                    [0, 0, 1, 1, 1, 1, 1, 2, 2, 0],
                    [0, 0, 2, 2, 2, 2, 2, 2, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
    result = mark_boundaries(image, label_image, color=(1, 1, 1),
                             outline_color=(2, 2, 2)).mean(axis=2)
    assert_array_equal(result, ref)

def test_mark_boundaries():
    image = np.zeros((10, 10))
    label_image = np.zeros((10, 10), dtype=np.uint8)
    label_image[2:7, 2:7] = 1

    ref = np.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
                    [0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
                    [0, 1, 1, 0, 0, 0, 1, 1, 0, 0],
                    [0, 1, 1, 0, 0, 0, 1, 1, 0, 0],
                    [0, 1, 1, 0, 0, 0, 1, 1, 0, 0],
                    [0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
                    [0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])

    marked = mark_boundaries(image, label_image, color=white, mode='thick')
    result = np.mean(marked, axis=-1)
    assert_array_equal(result, ref)

    ref = np.array([[0, 2, 2, 2, 2, 2, 2, 2, 0, 0],
                    [2, 2, 1, 1, 1, 1, 1, 2, 2, 0],
                    [2, 1, 1, 1, 1, 1, 1, 1, 2, 0],
                    [2, 1, 1, 2, 2, 2, 1, 1, 2, 0],
                    [2, 1, 1, 2, 0, 2, 1, 1, 2, 0],
                    [2, 1, 1, 2, 2, 2, 1, 1, 2, 0],
                    [2, 1, 1, 1, 1, 1, 1, 1, 2, 0],
                    [2, 2, 1, 1, 1, 1, 1, 2, 2, 0],
                    [0, 2, 2, 2, 2, 2, 2, 2, 0, 0],
                    [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
    marked = mark_boundaries(image, label_image, color=white,
                             outline_color=(2, 2, 2), mode='thick')
    result = np.mean(marked, axis=-1)
    assert_array_equal(result, ref)

def updateParametros(val):
    global p_segmentos, p_sigma, p_compactness, segments, image, cuda_python

    if(val == "Python SLIC"):
	cuda_python = 0
    elif(val == "CUDA gSLICr"):
	cuda_python = 1

    p_segmentos = int("%d" % (slider_segmentos.val))
    p_sigma = slider_sigma.val
    p_compactness = slider_compactness.val
    
    image = c_image.copy()

    if(cuda_python == 0):
	start_time = time.time()
    	segments = slic(img_as_float(image), n_segments=p_segmentos, sigma=p_sigma, compactness=p_compactness)
	print("--- Tempo Python skikit-image SLIC: %s segundos ---" % (time.time() - start_time))
    else:
	start_time = time.time()
	gSLICrInterface.process( p_segmentos)
	print("--- Tempo C++/CUDA gSLICr:          %s segundos ---" % (time.time() - start_time))
	segments = cuda_seg

    obj.set_data(mark_boundaries(img_as_float(cv2.cvtColor(image, cv2.COLOR_BGR2RGB)), segments, outline_color=p_outline))
    draw()

def overlay_cells(cells, image, colors):
    "Overlay the edges of each individual cell in the provided image"

    tmp = color.gray2rgb(image)

    for k in cells.keys():
        c = cells[k]
        if c.selection_state == 1:
            col = colors[c.color_i][:3]

            for px in c.outline:
                x, y = px
                tmp[x, y] = col

            if c.sept_mask is not None:
                try:
                    x0, y0, x1, y1 = c.box
                    tmp[x0:x1, y0:y1] = mark_boundaries(tmp[x0:x1, y0:y1],
                                                        img_as_int(
                                                            c.sept_mask),
                                                        color=col)
                except IndexError:
                    c.selection_state = -1

    return tmp

def grabcut(img, targetness):
    u"""
    Segmenting the best target-like region from an targetness map.
    """

    mask = np.ones(img.shape[:2], np.uint8) * cv2.GC_BGD
    score_th = scoreatpercentile(targetness, 95)
    mask[targetness >= score_th] = cv2.GC_PR_FGD
    score_th = scoreatpercentile(targetness, 99)
    mask[targetness >= score_th] = cv2.GC_FGD
    mask = cv2.medianBlur(mask, 15)

    bgdModel = np.zeros((1, 65), np.float64)
    fgdModel = np.zeros((1, 65), np.float64)

    cv2.grabCut(img, mask, None, bgdModel, fgdModel, 5, cv2.GC_INIT_WITH_MASK)

    mask2 = np.where((mask == 2) | (mask == 0), 0, 1).astype('uint8')
    lab_mask2 = bwlabel(mask2)
    lab_list = np.unique(lab_mask2.flatten())[1:]
    lab_argmax = np.argmax(
        [np.max(targetness[lab_mask2 == i]) for i in lab_list])
    mask2[lab_mask2 != lab_list[lab_argmax]] = 0
    img2 = img.copy()
    img2[mask2 < 1, :] = [0, 43, 54]
    img2 = mark_boundaries(img2, mask2)

    return img2, mask2

    def update_slic(self):
        sec = self.auto_submasks_gscene.active_section

        t = time.time()
        self.slic_labelmaps[sec] = slic(self.contrast_stretched_images[sec].astype(np.float),
                                    sigma=SLIC_SIGMA, compactness=SLIC_COMPACTNESS,
                                    n_segments=SLIC_N_SEGMENTS, multichannel=False, max_iter=SLIC_MAXITER)
        sys.stderr.write('SLIC: %.2f seconds.\n' % (time.time() - t)) # 10 seconds, iter=100, nseg=1000;

        self.slic_boundary_images[sec] = img_as_ubyte(mark_boundaries(self.contrast_stretched_images[sec],
                                            label_img=self.slic_labelmaps[sec],
                                            background_label=-1, color=(1,0,0)))

        self.slic_image_feeder.set_image(sec=sec, numpy_image=self.slic_boundary_images[sec])
        self.gscene_slic.update_image(sec=sec)

        ####

        # self.ncut_labelmaps[sec] = normalized_cut_superpixels(self.contrast_stretched_images[sec], self.slic_labelmaps[sec])

        self.ncut_labelmaps[sec] = self.slic_labelmaps[sec]
        self.sp_dissim_maps[sec] = compute_sp_dissims_to_border(self.contrast_stretched_images[sec], self.ncut_labelmaps[sec])
        # self.sp_dissim_maps[sec] = compute_sp_dissims_to_border(self.thresholded_images[sec], self.ncut_labelmaps[sec])
        # self.border_dissim_images[sec] = generate_dissim_viz(self.sp_dissim_maps[sec], self.ncut_labelmaps[sec])
        # self.dissim_image_feeder.set_image(sec=sec, numpy_image=self.border_dissim_images[sec])
        # self.gscene_dissimmap.update_image(sec=sec)

        self.selected_dissim_thresholds[sec] = determine_dissim_threshold(self.sp_dissim_maps[sec], self.ncut_labelmaps[sec])
        self.ui.slider_dissimThresh.setValue(int(self.selected_dissim_thresholds[sec]/0.01))

        ######################################################

        self.update_init_submasks_image()

def intensity_range2superpixels(im, superpixels, intMinT=0.95, intMaxT=1.05, debug=False, intMin=0, intMax=255):#, fromInt=0, toInt=255):

    superseeds = np.zeros_like(superpixels)

    #if not intMin and not intMax:
    #    hist, bins = skexp.histogram(im)
    #
    #    #zeroing values that are lower/higher than fromInt/toInt
    #    toLow = np.where(bins < fromInt)
    #    hist[toLow] = 0
    #    toHigh = np.where(bins > toInt)
    #    hist[toHigh] = 0
    #
    #    max_peakIdx = hist.argmax()
    #    intMin = intMinT * bins[max_peakIdx]
    #    intMax = intMaxT * bins[max_peakIdx]

    sp_means = np.zeros(superpixels.max()+1)
    for sp in range(superpixels.max()+1):
        values = im[np.where(superpixels==sp)]
        mean = np.mean(values)
        sp_means[sp] = mean

    idxs = np.argwhere(np.logical_and(sp_means>=intMin, sp_means<=intMax))
    for i in idxs:
        superseeds = np.where(superpixels==i[0], 1, superseeds)

    if debug:
        plt.figure(), plt.gray()
        plt.imshow(im), plt.hold(True), plt.imshow(mark_boundaries(im, superseeds, color=(1,0,0)))
        plt.axis('image')
        plt.show()

    return superseeds

def createFigure4(list_file, list_param, corpus_meta, prob_topic_doc, segment_dir, n_topic, output_dir):    
    for file_item in list_file:
        print file_item
        for topic in range(n_topic):
            print topic
            fig = plt.figure()
            img = img_as_float(io.imread(img_dir+file_item+'.ppm'))
            ax1 = fig.add_subplot(4,4, 1, axisbg='grey')
            ax1.set_xticks(()), ax1.set_yticks(())
            ax1.imshow(img)
            index=2
            for param in list_param:

                if 'slic' in param:
                    # print 'test', index
                    # print corpus_meta[0][1].split('-')[0]
                    segment_in_file = [item_corpus for item_corpus in corpus_meta if file_item == item_corpus[1].split('-')[0]]
                    print len(segment_in_file)
                    segments_res = csv2Array(segment_dir+'/'+file_item+'/'+file_item+'-'+param+'.sup')
                    img = img_as_float(io.imread(img_dir+file_item+'.ppm'))
                    output = np.zeros( (len(img), len(img[0])) )
                    for segment in segment_in_file:
                        # print prob_topic_doc[int(segment[0])][topic]
                        output[segments_res == int(segment[2])] = prob_topic_doc[int(segment[0])][topic]
                    output = mark_boundaries(output, segments_res)
                    ax1 = fig.add_subplot(4,4, index, axisbg='grey')
                    # ax1 = fig.add_subplot(5,10, index, axisbg='grey')
                    ax1.set_xticks(()), ax1.set_yticks(())
                    ax1.imshow(output)
                    index += 1 
            ensure_path(output_dir+'/'+file_item+'/')
            plt.savefig(output_dir+'/'+file_item+'/topic-'+str(topic)+'-'+file_item+'.pdf')
            plt.clf()
            plt.close()

def superpixels(image):
    """ given an input image, create super pixels on it
    """
    # we could try to limit the problem of holes in boundary by first over segmenting the image
    import matplotlib.pyplot as plt
    from skimage.segmentation import felzenszwalb, slic, quickshift
    from skimage.segmentation import mark_boundaries
    from skimage.util import img_as_float
    
    jac_float = img_as_float(image)
    plt.imshow(jac_float)
    #segments_fz = felzenszwalb(jac_float, scale=100, sigma=0.5, min_size=50)
    segments_slic = slic(jac_float, n_segments=600, compactness=0.01, sigma=0.001
        #, multichannel = False
        , max_iter=50) 
      
    fig, ax = plt.subplots(1, 1, sharex=True, sharey=True, subplot_kw={'adjustable':'box-forced'})
    fig.set_size_inches(8, 3, forward=True)
    fig.subplots_adjust(0.05, 0.05, 0.95, 0.95, 0.05, 0.05)
    
    #ax[0].imshow(mark_boundaries(jac, segments_fz))
    #ax[0].set_title("Felzenszwalbs's method")
    ax.imshow(mark_boundaries(jac_float, segments_slic))
    ax.set_title("SLIC")           
    return segments_slic                     

    def plot(self):
        self.ax.cla()
        if self.segment_label is None:
            self.ax.imshow(self.new_image)
        else:
            boundary_image = segmentation.mark_boundaries(self.new_image, self.segment_label)
            self.ax.imshow(boundary_image)
            self.ax.imshow(self.background_mask.astype(float), alpha=0.3)
            mask = 1 - self.background_mask
            content_on_canvas = np.zeros(list(mask.shape) + [4], np.uint8)    # Prepare the canvas
            for stitch_image in self.stitch_images:
                content = stitch_image['content']
                x = stitch_image['x']
                y = stitch_image['y']
                size = stitch_image['size']
                print(x, y, size)
                resized = misc.imresize(content, size)                      # Resize the image

                # Compute the intersecting length between canvas and content
                x_copy_width = mask.shape[1] - stitch_image['x']
                if resized.shape[1] < x_copy_width:
                    x_copy_width = resized.shape[1]
                y_copy_width = mask.shape[0] - stitch_image['y']
                if resized.shape[0] < y_copy_width:
                    y_copy_width = resized.shape[0]
                print(x_copy_width, y_copy_width)
                # Copy content onto canvas and apply mask
                new_content = np.zeros(list(mask.shape) + [4], np.uint8)
                new_content[y:y+y_copy_width, x:x+x_copy_width, :] = resized[0:y_copy_width, 0:x_copy_width, :]
                content_on_canvas = self.merge(content_on_canvas, new_content)
            content_on_canvas[:, :, 3] = np.multiply(mask, content_on_canvas[:, :, 3])
            self.ax.imshow(content_on_canvas)
        self.ax.figure.canvas.draw()

def generateImageWithSuperPixelBoundaries(image, segmentationMask):
    # Function returns an image with superpixel boundaries displayed as lines.  It is assumed that the image was the source for the segmentation mask.
    # See [http://scikit-image.org/docs/dev/api/skimage.segmentation.html?highlight=slic#skimage.segmentation.mark_boundaries]
    # Function signature: skimage.segmentation.mark_boundaries(image, label_img, color=(1, 1, 0), outline_color=(0, 0, 0))
    
    superPixelImage = mark_boundaries(image, segmentationMask)
    return superPixelImage

def explain(model, img, topLabels, numSamples, numFeatures, hideRest, hideColor, positiveOnly):
            
    img, oldImg = transform_img_fn(img)
    img = img*(1./255)
    prediction = model.predict(img)
    explainer = lime_image.LimeImageExplainer()
    img = np.squeeze(img)
    explanation = explainer.explain_instance(img, model.predict, top_labels=topLabels, hide_color=hideColor, num_samples=numSamples)
    temp, mask = explanation.get_image_and_mask(getTopPrediction(prediction[0]), positive_only=positiveOnly, num_features=numFeatures, hide_rest=hideRest)
    tempMask = mask * 255
    temp = Image.fromarray(np.uint8(tempMask))
    temp = temp.resize((oldImg.width, oldImg.height))
    temp = image.img_to_array(temp)
    temp = temp * 1./255
    temp = temp.astype(np.int64)
    temp = np.squeeze(temp)
    oldImgArr = image.img_to_array(oldImg)
    oldImgArr = oldImgArr * (1./255)
    oldImgArr = oldImgArr.astype(np.float64)
    imgExplained = mark_boundaries(oldImgArr, temp)
    imgFinal = np.uint8(imgExplained*255)
    img = Image.fromarray(imgFinal)
    imgByteArr = io.BytesIO()
    img.save(imgByteArr, format='JPEG')
    imgByteArr = imgByteArr.getvalue()


    return imgByteArr

def visualize_pascal(plot_probabilities=False):
    data = load_pascal('val')
    ds = PascalSegmentation()
    for x, y, f, sps in zip(data.X, data.Y, data.file_names, data.superpixels):
        fig, ax = plt.subplots(2, 3)
        ax = ax.ravel()
        image = ds.get_image(f)
        y_pixel = ds.get_ground_truth(f)
        x_raw = load_kraehenbuehl(f)

        boundary_image = mark_boundaries(image, sps)

        ax[0].imshow(image)
        ax[1].imshow(y_pixel, cmap=ds.cmap)
        ax[2].imshow(boundary_image)
        ax[3].imshow(np.argmax(x_raw, axis=-1), cmap=ds.cmap, vmin=0, vmax=256)
        ax[4].imshow(y[sps], cmap=ds.cmap, vmin=0, vmax=256)
        ax[5].imshow(np.argmax(x, axis=-1)[sps], cmap=ds.cmap, vmin=0,
                     vmax=256)
        for a in ax:
            a.set_xticks(())
            a.set_yticks(())
        plt.savefig("figures_pascal_val/%s.png" % f, bbox_inches='tight')
        plt.close()
        if plot_probabilities:
            fig, ax = plt.subplots(3, 7)
            for k in range(21):
                ax.ravel()[k].matshow(x[:, :, k], vmin=0, vmax=1)
            for a in ax.ravel():
                a.set_xticks(())
                a.set_yticks(())
            plt.savefig("figures_pascal_val/%s_prob.png" % f,
                        bbox_inches='tight')
            plt.close()
    tracer()