How to use the histomicstk.preprocessing.color_normalization function in histomicstk

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github DigitalSlideArchive / HistomicsTK / histomicstk / cli / SuperpixelSegmentation / CreateDataset.py View on Github external
# get scale for the tile and adjust centroids points
    ts_metadata = ts.getMetadata()
    scale = ts_metadata['magnification'] / args.superpixel_mag
    x_centroids = [x / scale for x in x_centroids]
    y_centroids = [y / scale for y in y_centroids]

    # get requested tile
    tile_info = \
        ts.getSingleTile(tile_position=tile_position,
                         format=large_image.tilesource.TILE_FORMAT_NUMPY,
                         **superpixel_kwargs)

    im_tile = tile_info['tile'][:, :, :3]

    # perform color normalization
    im_nmzd = htk_cnorm.reinhard(im_tile, args.reference_mu_lab,
                                 args.reference_std_lab, src_mu=src_mu_lab,
                                 src_sigma=src_sigma_lab)

    im_height, im_width = im_nmzd.shape[:2]

    left = tile_info['gx'] / scale
    top = tile_info['gy'] / scale
    patch_size = int(args.patchSize / scale)

    # get width and height
    width = tile_info['width']
    height = tile_info['height']

    n_superpixels = len(x_centroids)

    tile_features = []
github DigitalSlideArchive / CNNCellDetection / cli / FasterNuclieDetectionCPU / FasterNuclieDetectionCPU.py View on Github external
tile_position=tile_position,
        format=large_image.tilesource.TILE_FORMAT_NUMPY,
        **it_kwargs)
    im_tile = tile_info['tile'][:, :, :3]
    csv_dict['ROIShape'] = im_tile.shape[:2]

    prep_time = time.time() - start_time
    csv_dict['PreparationTime'] = round(prep_time, 3)

    # =========================================================================
    # =================Img Normalization & Color Deconv========================
    # =========================================================================
    print('\n>> Color Deconvolving ... \n')
    start_time = time.time()

    im_nmzd = htk_cnorm.reinhard(
        im_tile,
        REFERENCE_MU_LAB,
        REFERENCE_STD_LAB,
        src_mu=src_mu_lab,
        src_sigma=src_sigma_lab
    )

    # perform color decovolution
    if args.deconv_method == 'ruifrok':

        w = cli_utils.get_stain_matrix(args)
        im_stains = htk_cdeconv.color_deconvolution(
            im_nmzd, w).Stains.astype(np.float)[:, :, :2]

    elif args.deconv_method == 'macenko':
github DigitalSlideArchive / HistomicsTK / histomicstk / cli / NucleiDetection / NucleiDetection.py View on Github external
src_mu_lab=None, src_sigma_lab=None):

    # get slide tile source
    ts = large_image.getTileSource(slide_path)

    # get requested tile
    tile_info = ts.getSingleTile(
        tile_position=tile_position,
        format=large_image.tilesource.TILE_FORMAT_NUMPY,
        **it_kwargs)

    # get tile image
    im_tile = tile_info['tile'][:, :, :3]

    # perform color normalization
    im_nmzd = htk_cnorm.reinhard(im_tile,
                                 args.reference_mu_lab,
                                 args.reference_std_lab,
                                 src_mu=src_mu_lab,
                                 src_sigma=src_sigma_lab)

    # perform color decovolution
    w = cli_utils.get_stain_matrix(args)

    im_stains = htk_cdeconv.color_deconvolution(im_nmzd, w).Stains

    im_nuclei_stain = im_stains[:, :, 0].astype(np.float)

    # segment nuclear foreground
    im_nuclei_fgnd_mask = im_nuclei_stain < args.foreground_threshold

    # segment nuclei