Ejemplo n.º 1
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def grey_processing(inputImg):
#    fp = [[0, 1, 0], [1, 1, 1], [0, 1, 0]]
    fp = np.ones((3, 3))
    data = nd.median_filter(inputImg, size=7)
    data = nd.grey_closing(data, footprint=fp)
    data = nd.grey_opening(data,footprint=fp)
    return data
Ejemplo n.º 2
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def segment_lungs(pixel_array):

    img_gray_open = ndi.grey_opening(pixel_array, size=10, mode='wrap')
    if DEBUG:
        plot(img_gray_open, 'Gray Opening')

    elavation_map = sobel(img_gray_open)
    if DEBUG:
        plot(elavation_map, 'Elevation Map')

    markers = extract_markers(img_gray_open)
    if DEBUG:
        plot(markers, 'Markers')

    watersheded = morphology.watershed(elavation_map, markers)
    if DEBUG:
        plot(watersheded, 'Watershed')

    external_contour = ndi.binary_fill_holes(watersheded - 1)
    if DEBUG:
        plot(external_contour, 'External Contour')

    watersheded_no_contour = (watersheded - external_contour)
    if DEBUG:
        plot(watersheded_no_contour, 'Watershed (No Contour)')

    holes_filled = ndi.binary_fill_holes(watersheded_no_contour - 1)
    if DEBUG:
        plot(holes_filled, 'Watershed (No Contour + Holes Filled)')

    removed_noise = morphology.remove_small_objects(holes_filled, 300)
    if DEBUG:
        plot(removed_noise, 'Removed Noise')

    return removed_noise
Ejemplo n.º 3
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def mpls_baseline(intensities,
                  smoothness_param=100,
                  deriv_order=1,
                  window_length=100):
    '''Perform morphological weighted penalized least squares baseline removal.
  * paper: DOI: 10.1039/C3AN00743J (Paper) Analyst, 2013, 138, 4483-4492
  * Matlab code: https://code.google.com/p/mpls/

  smoothness_param: Relative importance of smoothness of the predicted response.
  deriv_order: Polynomial order of the difference of penalties.
  window_length: size of the structuring element for the open operation.
  '''
    Xbg = grey_opening(intensities, window_length)
    # find runs of equal values in Xbg
    flat = (np.diff(Xbg) != 0).astype(np.int8)
    run_idx, = np.where(np.diff(flat))
    # local minimums between flat runs
    bounds = run_idx[1:-1] if len(run_idx) % 2 == 0 else run_idx[1:]
    bounds = bounds.reshape((-1, 2)) + (1, 2)
    min_idxs = np.array([np.argmin(Xbg[s:t]) for s, t in bounds], dtype=int)
    min_idxs += bounds[:, 0]
    # create the weight vector by setting 1 at each local min
    w = np.zeros_like(intensities)
    w[min_idxs] = 1
    # make sure we stick to the ends
    w[0] = 5
    w[-1] = 5
    # run one iteration of smoothing
    smoother = WhittakerSmoother(Xbg,
                                 smoothness_param,
                                 deriv_order=deriv_order)
    return smoother.smooth(w)
Ejemplo n.º 4
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def open_image(image_filtered):
    """open_image example ndimage.grey_opening
    """
    c = ndimage.grey_opening(np.abs(image_filtered), size=(5, 5, 5))
    new_image = nib.Nifti1Image(normalise(c), affine)
    new_image.set_data_dtype(np.float32)
    nib.save(new_image, 'image_open.nii.gz')
Ejemplo n.º 5
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 def test_opening(self):
     self.image.opening(3)
     original_image = retina_grayscale.Retina_grayscale(
         None, _image_path, 1)
     assert_array_equal(
         self.image.np_image,
         ndimage.grey_opening(original_image.np_image, size=(3, 3)))
Ejemplo n.º 6
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def MMF(Y,rn,bg):
    stru_len_op = int(bg)
    stru_len_clo = int(bg*1.5)
    
    stru_ele_op = np.linspace(0,0,stru_len_op)
    stru_ele_clo = np.linspace(0,0,stru_len_clo)
    
    #triangular wave
    tri_wave = []
    amp = 1.0
    width = 1
    samp = rn
    asym = 0.5
    points = 1
    
    while points <= samp:
    
        Xi = 0.1*points
        if 0 <= Xi and Xi <= width*asym:
            tri_wave.append(amp*Xi/(width*asym))
        elif Xi > width*asym and Xi <width:
            tri_wave.append(amp*(width-Xi)/(width*(1-asym)))
        else:
            tri_wave.append(0)
        points += 1

    #low-pass
    op_flat = nd.grey_opening(Y,size = (stru_len_op),structure = stru_ele_op)
    clo_flat = nd.grey_closing(op_flat,size = (stru_len_clo),structure = stru_ele_clo)
    
    reducing = []
    for reduce in range(len(Y)):
        reducing.append(Y[reduce] - clo_flat[reduce])
    
    op_tri = nd.grey_opening(reducing,size = (rn),structure = tri_wave)
    clo_tri = nd.grey_closing(reducing,size = (rn),structure = tri_wave)

    after_stru_ele =np.linspace(0,0,rn) 
    
    op_than_clo = nd.grey_closing(op_tri,size = (rn),structure = after_stru_ele)
    clo_than_op = nd.grey_opening(clo_tri,size = (rn),structure = after_stru_ele)

    plusing = []
    for plus in range(len(op_than_clo)):
        plusing.append((op_than_clo[plus]+clo_than_op[plus])/2.0)
    
    return plusing, clo_flat
Ejemplo n.º 7
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def run_FreeCAD_ImageT(self):

    from scipy import ndimage
    fn = self.getData('image')
    import matplotlib.image as mpimg

    img = mpimg.imread(fn)
    (sa, sb, sc) = img.shape
    red = 0.005 * (self.getData("red") + 100)
    green = 0.005 * (self.getData("green") + 100)
    blue = 0.005 * (self.getData("blue") + 100)
    #blue=0
    say("rgb", red, green, blue)

    # andere filtre
    #img = ndimage.sobel(img)
    #img = ndimage.laplace(img)

    im2 = img[:, :, 0] * red + img[:, :, 1] * green + img[:, :, 2] * blue
    im2 = np.round(im2)

    if self.getData('invert'):
        im2 = 1 - im2

    #im2 = ndimage.sobel(im2)

    ss = int((self.getData('maskSize') + 100) / 20)
    say("ss", ss)
    if ss != 0:
        mode = self.getData('mode')
        say("mode", mode)
        if mode == 'closing':
            im2 = ndimage.grey_closing(im2, size=(ss, ss))
        elif mode == 'opening':
            im2 = ndimage.grey_opening(im2, size=(ss, ss))
        elif mode == 'erosion':
            im2 = ndimage.grey_erosion(im2, size=(ss, ss))
        elif mode == 'dilitation':
            im2 = ndimage.grey_dilation(im2, footprint=np.ones((ss, ss)))
        else:
            say("NO MODE")

    nonzes = np.where(im2 == 0)
    pts = [
        FreeCAD.Vector(sb + -x, sa - y)
        for y, x in np.array(nonzes).swapaxes(0, 1)
    ]

    h = 10
    pts = [
        FreeCAD.Vector(
            sb + -x, sa - y,
            (red * img[y, x, 0] + green * img[y, x, 1] + blue * img[y, x, 2]) *
            h) for y, x in np.array(nonzes).swapaxes(0, 1)
    ]
    colors = [img[y, x] for y, x in np.array(nonzes).swapaxes(0, 1)]
    say("len pts", len(pts))
    self.setData("Points_out", pts)
 def test_grey_opening_operation_sparse_input_struct_zeros(self):
     struct = np.zeros((3, 3, 3))
     print("\n test_grey_opening_operation_sparse_input_struct_zeros...")
     v_output = vc.grey_opening(input_svar,
                                structure=struct,
                                make_float32=False)
     d_output = ndimage.grey_opening(input_svar, structure=struct)
     msgs = "test_grey_opening_operation_sparse_input_struct_zeros"
     self.assertTrue((d_output == v_output).all(), msg=msgs)
Ejemplo n.º 9
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def apply(array, **kwargs):
    """
    Apply a set of standard filter to array data: 
    
    Call: apply(array-data, <list of key=value arguments>)

    The list of key-value define the filtering to be done and should be given in
    the order to be process. Possible key-value are:
    
      * smooth:  gaussian filtering, value is the sigma parameter (scalar or tuple)
      * uniform: uniform  filtering (2)
      * max:     maximum  filtering (1)
      * min:     minimum  filtering (1)
      * median:  median   filtering (1)
      
      * dilate: grey dilatation (1)
      * erode:  grey erosion    (1)
      * close:  grey closing    (1)
      * open:   grey opening    (1)
      
      * linear_map: call linear_map(), value is the tuple (min,max)   (3)
      * normalize:  call normalize(),  value is the method            (3)
      * adaptive:   call adaptive(),   value is the sigma             (3)
      * adaptive_:  call adaptive(),   with uniform kernel            (3)
          
    The filtering is done using standard scipy.ndimage functions.
    
    (1) The value given (to the key) is the width of the the filter: 
        the distance from the center pixel (the size of the filter is thus 2*value+1)
        The neighborhood is an (approximated) boolean circle (up to discretization)
    (2) Same as (*) but the neighborhood is a complete square
    (3) See doc of respective function
    """
    for key in kwargs:
        value = kwargs[key]
        if key not in ('smooth','uniform'):
            fp = _kernel.distance(array.ndim*(2*value+1,))<=value  # circular filter
            
        if   key=='smooth' : array = _nd.gaussian_filter(array, sigma=value)
        elif key=='uniform': array = _nd.uniform_filter( array, size=2*value+1)
        elif key=='max'    : array = _nd.maximum_filter( array, footprint=fp)
        elif key=='min'    : array = _nd.minimum_filter( array, footprint=fp)
        elif key=='median' : array = _nd.median_filter(  array, footprint=fp)

        elif key=='dilate' : array = _nd.grey_dilation(  array, footprint=fp)
        elif key=='erode'  : array = _nd.grey_erosion(   array, footprint=fp)
        elif key=='open'   : array = _nd.grey_opening(   array, footprint=fp)
        elif key=='close'  : array = _nd.grey_closing(   array, footprint=fp)
        
        elif key=='linear_map': array = linear_map(array, min=value[0], max=value[1])
        elif key=='normalize' : array = normalize( array, method = value)
        elif key=='adaptive'  : array = adaptive(  array, sigma  = value, kernel='gaussian')
        elif key=='adaptive_' : array = adaptive(  array, sigma  = value, kernel='uniform')
        else: 
            print '\033[031mUnrecognized filter :', key
            
    return array
Ejemplo n.º 10
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 def opening(self, size_structure):
     """
     dilates and erodes the stored image, by default the structure is a cross
     :param size_structure: size of kernel to apply in the filter
     """
     self._copy()
     self.np_image = ndimage.grey_opening(self.np_image,
                                          size=(size_structure,
                                                size_structure))
Ejemplo n.º 11
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    def __call__(self, 
                 img: np.ndarray, 
                 mode: Optional[str]=None,
                 radius: Optional[int]=None,
                 binary: Optional[bool]=None) -> np.ndarray:
        """
        Apply the transform to `img`.

        """
        self.mode = self.mode if mode is None else mode
        self.radius = self.radius if radius is None else radius
        self.binary = self.binary if binary is None else binary

        input_ndim = img.squeeze().ndim # spatial ndim
        if input_ndim == 2:
            structure = ndi.generate_binary_structure(2, 1)
        elif input_ndim == 3:
            structure = ndi.generate_binary_structure(3, 1)
        else:
            raise ValueError('Currently only support 2D&3D data')
        
        channel_dim = None
        if input_ndim != img.ndim:
            channel_dim = img.shape.index(1)
            img = img.squeeze()

        if self.mode == 'closing':
            if self.binary:
                img = ndi.binary_closing(img, structure=structure, iterations=self.radius)
            else:
                for _ in range(self.radius):
                    img = ndi.grey_closing(img, footprint=structure)        
        elif self.mode == 'dilation':
            if self.binary:
                img = ndi.binary_dilation(img, structure=structure, iterations=self.radius)
            else:
                for _ in range(self.radius):
                    img = ndi.grey_dilation(img, footprint=structure)
        elif self.mode == 'erosion':
            if self.binary:
                img = ndi.binary_erosion(img, structure=structure, iterations=self.radius)
            else:
                for _ in range(self.radius):
                    img = ndi.grey_erosion(img, footprint=structure)
        elif self.mode == 'opening':
            if self.binary:
                img = ndi.binary_opening(img, structure=structure, iterations=self.radius)
            else:
                for _ in range(self.radius):
                    img = ndi.grey_opening(img, footprint=structure)
        else:
            raise ValueError(f'Unexpected keyword {self.mode}')
        
        if channel_dim is not None:
            return np.expand_dims(img, axis=channel_dim)
        else:
            return img
Ejemplo n.º 12
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def remove_background(profiles, radius=20, light_background=True):
    """
    Uses port of ImageJ rolling ball background subtraction
    to estimate background and removes the background from the image

    Parameters
    ------
    profiles : Dictionary
        Key is the well number and the value is a ndarray (2D) of the well
    radius : float, optional
        The radius of the rolling ball (default : 20)
    light_background : Boolean
        Whether the background is light or not (default : True)

    Returns
    ------
    newprofiles : Dictionary
        Key is the well number and the value is a ndarray (2D) of the
        background subtracted well
    """
    # Make "spherical" structuring element
    sz_ = 2 * radius + (radius + 1) % 2
    xco, yco = np.meshgrid(range(sz_), range(sz_))
    ballheight = float(radius**2) - (xco - radius)**2 - (yco - radius)**2
    ballheight[ballheight < 0] = 0
    ballheight = np.ma.masked_where(ballheight < 0, ballheight)
    ballheight = np.sqrt(ballheight)
    newprofiles = {}
    if light_background:
        for k, im1 in profiles.items():
            imax = im1.max()
            im2 = imax - im1
            bg1 = ndi.grey_opening(im2, structure=ballheight, mode="reflect")
            im2 -= bg1
            newprofiles[k] = (im2 - imax)
    else:
        for k, im1 in profiles.items():
            imin = im1.min()
            im2 = im1 - imin
            bg1 = ndi.grey_opening(im2, structure=ballheight, mode="reflect")
            im2 -= bg1
            newprofiles[k] = im2 - im2.min()
    return newprofiles
 def test_grey_opening_operation_sparse_input_default_value(self):
     print("\n test_grey_opening_operation_sparse_input_default_value...")
     v_output = vc.grey_opening(input_svar,
                                structure=structure,
                                make_float32=False)
     d_output = ndimage.grey_opening(
         input_svar,
         structure=structure,
     )
     msgs = "test_grey_opening_operation_sparse_input_default_value"
     self.assertTrue((d_output == v_output).all(), msg=msgs)
	def __test_grey_opening_operation(self,input_var):		
		print("\n grey_opening Voxel testing...")
		start_time = t.time()
		v_output = vc.grey_opening(input_var,structure=structure,no_of_blocks=PL[0],fakeghost=PL[1],make_float32=False)
		print("grey_opening Voxel testing time taken: ",(t.time() - start_time)," sec")
		#print("\n grey_opening Default testing...")
		start_time = t.time()
		d_output = ndimage.grey_opening(input_var,structure=structure)
		print("grey_opening Default testing time taken: ",(t.time() - start_time)," sec")		
		msgs = "grey_opening_operation_FAIL_with parameters: ",PL
		self.assertTrue((d_output==v_output).all(), msg=msgs)
 def test_grey_opening_operation_dense_input_fakeghost_four(self):
     print("\n test_grey_opening_operation_dense_input_fakeghost_four...")
     v_output = vc.grey_opening(input_dvar,
                                structure=structure,
                                fakeghost=4,
                                make_float32=False)
     d_output = ndimage.grey_opening(
         input_dvar,
         structure=structure,
     )
     msgs = "test_grey_opening_operation_dense_input_fakeghost_four"
     self.assertTrue((d_output == v_output).all(), msg=msgs)
 def test_grey_opening_operation_sparse_input_blocks_ten(self):
     print("\n test_grey_opening_operation_sparse_input_blocks_ten...")
     v_output = vc.grey_opening(input_svar,
                                structure=structure,
                                no_of_blocks=10,
                                make_float32=False)
     d_output = ndimage.grey_opening(
         input_svar,
         structure=structure,
     )
     msgs = "test_grey_opening_operation_sparse_input_blocks_ten"
     self.assertTrue((d_output == v_output).all(), msg=msgs)
def getROI(image):
    image_resized = resize(image)
    b, g, r = cv2.split(image_resized)
    g = cv2.GaussianBlur(g, (15, 15), 0)
    kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (15, 15))
    g = ndimage.grey_opening(g, structure=kernel)
    (minVal, maxVal, minLoc, maxLoc) = cv2.minMaxLoc(g)

    x0 = int(maxLoc[0]) - 110
    y0 = int(maxLoc[1]) - 110
    x1 = int(maxLoc[0]) + 110
    y1 = int(maxLoc[1]) + 110

    return image_resized[y0:y1, x0:x1]
Ejemplo n.º 18
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def test_2d_ndimage_equivalence():
    image = np.zeros((9, 9), np.uint8)
    image[2:-2, 2:-2] = 128
    image[3:-3, 3:-3] = 196
    image[4, 4] = 255

    opened = gray.opening(image)
    closed = gray.closing(image)

    footprint = ndi.generate_binary_structure(2, 1)
    ndimage_opened = ndi.grey_opening(image, footprint=footprint)
    ndimage_closed = ndi.grey_closing(image, footprint=footprint)

    assert_array_equal(opened, ndimage_opened)
    assert_array_equal(closed, ndimage_closed)
Ejemplo n.º 19
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    def opening(self):
        """Perform a grey opening: an erosion followed by a dilation."""
        def disk(N):
            """Get circle morphology."""
            y, x = np.ogrid[-N:N + .1, -N:N + .1]
            return np.asarray(x**2 + y**2 < N**2, dtype=np.uint8)

        # obtain and subtract background lighting level
        kernel = disk(self.lsize)
        if not cv2:
            background = ndimage.grey_opening(self.im, structure=kernel)
        else:
            background = cv2.dilate(cv2.erode(self.im, kernel), kernel)
        I2 = self.im - background
        return I2
Ejemplo n.º 20
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def dtm_krauss_2015(dsm, ps, minf_r):
    nx, ny = dsm.shape
    scale = 20.0 / ps
    nnx = int(nx / scale + 0.5)
    nny = int(ny / scale + 0.5)
    scale_int = int(scale + 0.5)
    print scale
    print scale_int
    minf = filters.minimum_filter(dsm, minf_r)
    dwn = cv2.resize(minf, (nny, nnx), interpolation=cv2.INTER_NEAREST)
    #    dwn = scipy.misc.imresize(minf,(nnx,nny),interp='cubic')
    dwn_o = ndimage.grey_opening(dwn, 5)
    dwn_g = filters.gaussian_filter(dwn_o, 2.5)
    #    return scipy.misc.imresize(dwn_g,(nx,ny),interp='cubic')
    return cv2.resize(dwn_g, (ny, nx), interpolation=cv2.INTER_CUBIC)
Ejemplo n.º 21
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def test_2d_ndimage_equivalence():
    image = np.zeros((9, 9), np.uint8)
    image[2:-2, 2:-2] = 128
    image[3:-3, 3:-3] = 196
    image[4, 4] = 255

    opened = grey.opening(image)
    closed = grey.closing(image)

    selem = ndi.generate_binary_structure(2, 1)
    ndimage_opened = ndi.grey_opening(image, footprint=selem)
    ndimage_closed = ndi.grey_closing(image, footprint=selem)

    testing.assert_array_equal(opened, ndimage_opened)
    testing.assert_array_equal(closed, ndimage_closed)
Ejemplo n.º 22
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def dtm_krauss_2015(dsm,ps,minf_r):
    nx,ny = dsm.shape
    scale = 20.0/ps
    nnx = int(nx/scale+0.5)
    nny = int(ny/scale+0.5)
    scale_int = int(scale+0.5)
    print scale
    print scale_int
    minf = filters.minimum_filter(dsm,minf_r)
    dwn = cv2.resize(minf,(nny,nnx),interpolation = cv2.INTER_NEAREST)
#    dwn = scipy.misc.imresize(minf,(nnx,nny),interp='cubic')
    dwn_o = ndimage.grey_opening(dwn,5)
    dwn_g = filters.gaussian_filter(dwn_o,2.5)
#    return scipy.misc.imresize(dwn_g,(nx,ny),interp='cubic')
    return cv2.resize(dwn_g,(ny,nx),interpolation = cv2.INTER_CUBIC)
Ejemplo n.º 23
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	def __operationTask(self,input_var):
		'''
		perform respective moephological operation on input block.
        Parameters
        ----------
        input_var  	: type: 3d numpy array, ith block.		
		
        Returns
		-------
		output     : type: 3d array, output of operation, ith block array.
        '''
		
		
		D=self.__operationArgumentDic
		if self.__operation=="binary_closing":	
			return ndimage.binary_closing(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
		elif self.__operation=="binary_dilation":
			return ndimage.binary_dilation(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
		elif self.__operation=="binary_erosion":
			return ndimage.binary_erosion(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
		elif self.__operation=="binary_fill_holes": #the output might be different then scipy.ndimage  
			return ndimage.binary_fill_holes(input_var, structure=D["structure"],output=D["output"], origin=D["origin"])
		elif self.__operation=="binary_hit_or_miss":
			return ndimage.binary_hit_or_miss(input_var, structure1=D["structure1"],structure2=D["structure2"],output=D["output"], origin1=D["origin1"], origin2=D["origin2"])
		elif self.__operation=="binary_opening":
			return ndimage.binary_opening(input_var, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
		elif self.__operation=="binary_propagation":			
			return ndimage.binary_propagation(input_var, structure=D["structure"],output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"])
		elif self.__operation=="black_tophat":
			return ndimage.black_tophat(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="grey_dilation":
			return ndimage.grey_dilation(input_var, structure=D["structure"],size=D["size"], footprint=D["footprint"],output=D["output"], mode=D["mode"], cval=D["cval"], origin=D["origin"])			
		elif self.__operation=="grey_closing":
			return ndimage.grey_closing(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="grey_erosion":
			return ndimage.grey_erosion(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="grey_opening":
			return ndimage.grey_opening(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="morphological_gradient":
			return ndimage.morphological_gradient(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="morphological_laplace":
			return ndimage.morphological_laplace(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="white_tophat":
			return ndimage.white_tophat(input_var, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
		elif self.__operation=="multiply":
			return input_var*D["scalar"]		
		else:
			return input_var # no operation performed....
Ejemplo n.º 24
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def test_grey_morph():
    root = 'local_histos/'
    for datablock in get_data():
        data,x,y = datablock
        data = get_uint_image(data)
        print(x,y)
        for i in range(0,30,4):
            mdata = nd.grey_opening(data,(i,i))
            R = mahotas.thresholding.rc(mdata)
            gradient = get_grad_mag(mdata)
            fig = plt.figure(figsize=(12,12))
            ax1 = fig.add_subplot(211)
            ax1.imshow(gradient)
            ax1.set_title(str(i)+', R: '+str(R))
            ax2 = fig.add_subplot(212)
            ax2.hist(gradient.flatten(),50)
            plt.savefig(get_fname([root+'img',x,y,i,'.png']))
            plt.close(fig)
Ejemplo n.º 25
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    def forward(self, labels: Tensor, *args) -> Tensor:
        r"""Computes the Opening loss -- i.e. the MSE due to performing a greyscale opening operation.

        :param labels: Predicted class probabilities
        :param args: Extra inputs, in case user also provides input/output image values.
        :return: Opening loss
        """
        smooth_labels = labels.clone().detach().cpu().numpy()
        for i in range(labels.shape[0]):
            for j in range(labels.shape[1]):
                smooth_labels[i, j] = grey_opening(smooth_labels[i, j],
                                                   self.radius)

        smooth_labels = torch.from_numpy(smooth_labels.astype(np.float32))
        if labels.device.type == 'cuda':
            smooth_labels = smooth_labels.cuda()

        return nn.MSELoss()(labels, smooth_labels.detach())
Ejemplo n.º 26
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def epi_mask(in_file, out_file=None):
    """Use grayscale morphological operations to obtain a quick mask of EPI data."""
    from pathlib import Path
    import nibabel as nb
    import numpy as np
    from scipy import ndimage
    from skimage.morphology import ball

    if out_file is None:
        out_file = Path("mask.nii.gz").absolute()

    img = nb.load(in_file)
    data = img.get_fdata(dtype="float32")
    # First open to blur out the skull around the brain
    opened = ndimage.grey_opening(data, structure=ball(3))
    # Second, close large vessels and the ventricles
    closed = ndimage.grey_closing(opened, structure=ball(2))

    # Window filter on percentile 30
    closed -= np.percentile(closed, 30)
    # Window filter on percentile 90 of data
    maxnorm = np.percentile(closed[closed > 0], 90)
    closed = np.clip(closed, a_min=0.0, a_max=maxnorm)
    # Calculate index of center of masses
    cm = tuple(
        np.round(ndimage.measurements.center_of_mass(closed)).astype(int))
    # Erode the picture of the brain by a lot
    eroded = ndimage.grey_erosion(closed, structure=ball(5))
    # Calculate the residual
    wshed = opened - eroded
    wshed -= wshed.min()
    wshed = np.round(1e3 * wshed / wshed.max()).astype(np.uint16)
    markers = np.zeros_like(wshed, dtype=int)
    markers[cm] = 2
    markers[0, 0, -1] = -1
    # Run watershed
    labels = ndimage.watershed_ift(wshed, markers)

    hdr = img.header.copy()
    hdr.set_data_dtype("uint8")
    nb.Nifti1Image(
        ndimage.binary_dilation(labels == 2, ball(2)).astype("uint8"),
        img.affine, hdr).to_filename(out_file)
    return out_file
Ejemplo n.º 27
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def label_fusion(label, win=3):
    """Apply a morphological filtering on the label to remove isolated labels.
    In case the input is a two channel label (2D ndarray of boolean of same 
    length) the labels of two channels are fused to remove
    overlaping segments of speech.
    
    :param label: input labels given in a 1D or 2D ndarray
    :param win: parameter or the morphological filters
    """
    channel_nb = len(label)
    if channel_nb == 2:
        overlap_label = numpy.logical_and(label[0], label[1])
        label[0] = numpy.logical_and(label[0], ~overlap_label)
        label[1] = numpy.logical_and(label[1], ~overlap_label)

    for idx, lbl in enumerate(label):
        cl = ndimage.grey_closing(lbl, size=win)
        label[idx] = ndimage.grey_opening(cl, size=win)

    return label
Ejemplo n.º 28
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def detect_growth_markers(flow, wvd):
    wvd_diff_raw = flow.diff(wvd) / get_time_diff_from_coord(
        wvd.t)[:, np.newaxis, np.newaxis]

    wvd_diff_smoothed = filtered_tdiff(flow, wvd_diff_raw)

    s_struct = ndi.generate_binary_structure(2, 1)[np.newaxis, ...]
    wvd_diff_filtered = ndi.grey_opening(
        wvd_diff_smoothed, footprint=s_struct) * get_curvature_filter(wvd)

    watershed_markers = flow.label(wvd_diff_filtered >= 0.5)

    if isinstance(wvd, xr.DataArray):
        watershed_markers = filter_labels_by_length_and_mask(
            watershed_markers, wvd.data >= -5, 3)
    else:
        watershed_markers = filter_labels_by_length_and_mask(
            watershed_markers, wvd >= -5, 3)

    # marker_regions = flow.watershed(-wvd_diff_filtered,
    #                                 watershed_markers != 0,
    #                                 mask=wvd_diff_filtered<0.25,
    #                                 structure=ndi.generate_binary_structure(3,1))
    marker_labels = flow.label(
        ndi.binary_opening(wvd_diff_filtered >= 0.25, structure=s_struct))
    # marker_labels = flow.label(ndi.binary_opening(marker_regions, structure=s_struct))
    marker_labels = filter_labels_by_length_and_mask(marker_labels,
                                                     watershed_markers != 0, 3)
    if isinstance(wvd, xr.DataArray):
        marker_labels = filter_labels_by_length_and_mask(
            marker_labels, wvd.data >= -5, 3)
    else:
        marker_labels = filter_labels_by_length_and_mask(
            marker_labels, wvd >= -5, 3)

    if isinstance(wvd, xr.DataArray):
        wvd_diff_raw = xr.DataArray(wvd_diff_raw, wvd.coords, wvd.dims)
        marker_labels = xr.DataArray(marker_labels, wvd.coords, wvd.dims)

    return wvd_diff_smoothed, marker_labels
Ejemplo n.º 29
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def grey_opening(img, params):
    if params['footprint_shape'] == 'rectangle':
        footprint = np.ones(
            (params['footprint_size_y'], params['footprint_size_x']),
            dtype=int)
    elif params['footprint_shape'] == 'ellipse':
        a = params['footprint_size_x'] / 2
        b = params['footprint_size_y'] / 2
        x, y = np.mgrid[-ceil(a):ceil(a) + 1, -ceil(b):ceil(b) + 1]
        footprint = ((x / a)**2 + (y / b)**2 < 1) * 1

    mode = params['mode']
    cval = params['cval']
    origin = params['origin']

    return ndimage.grey_opening(img,
                                size=None,
                                footprint=footprint,
                                structure=None,
                                mode=mode,
                                cval=cval,
                                origin=origin)
def operationTask(input):
	D=operationArgumentDic
	#self.M.add_mem()#.....................................................................................................
	
	if operation=="binary_closing":	
		return ndimage.binary_closing(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
	elif operation=="binary_dilation":
		return ndimage.binary_dilation(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
	elif operation=="binary_erosion":
		return ndimage.binary_erosion(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
	elif operation=="binary_fill_holes":
		return ndimage.binary_fill_holes(input, structure=D["structure"],output=D["output"], origin=D["origin"])
	elif operation=="binary_hit_or_miss":
		return ndimage.binary_hit_or_miss(input, structure1=D["structure1"],structure2=D["structure2"],output=D["output"], origin1=D["origin1"], origin2=D["origin2"])
	elif operation=="binary_opening":
		return ndimage.binary_opening(input, structure=D["structure"], iterations=D["iterations"], output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"], brute_force=D["brute_force"])
	elif operation=="binary_propagation":			
		return ndimage.binary_propagation(input, structure=D["structure"],output=D["output"], origin=D["origin"], mask=D["mask"], border_value=D["border_value"])
	elif operation=="black_tophat":
		return ndimage.black_tophat(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="grey_dilation":
		return ndimage.grey_dilation(input, structure=D["structure"],size=D["size"], footprint=D["footprint"],output=D["output"], mode=D["mode"], cval=D["cval"], origin=D["origin"])
	elif operation=="grey_closing":
		return ndimage.grey_closing(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="grey_erosion":
		return ndimage.grey_erosion(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="grey_opening":
		return ndimage.grey_opening(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="morphological_gradient":
		return ndimage.morphological_gradient(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="morphological_laplace":
		return ndimage.morphological_laplace(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="white_tophat":
		return ndimage.white_tophat(input, structure=D["structure"], size=D["size"], footprint=D["footprint"],  output=D["output"], origin=D["origin"],mode=D["mode"], cval=D["cval"])
	elif operation=="intMultiply":
		return input*D["scalar"]
	
	else:
		return input
Ejemplo n.º 31
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def readImage(thigh, img):
    imgOr = cv2.imread(img, 0)

    imgTh = cv2.imread(img, 0)

    opening = ndimage.grey_opening(imgTh, size=(3, 4))

    gauss = cv2.GaussianBlur(opening, (11, 11), 0)

    imgTh[gauss < thigh] = 0
    imgTh[gauss >= thigh] = 1

    kernel = np.ones((1, 5))
    erode = cv2.erode(imgTh, kernel, iterations=1)

    kernel = np.ones((2, 15))
    dilate = cv2.dilate(erode, kernel, iterations=1)

    m.showImage6(imgOr, opening, gauss, imgTh, erode, dilate, "Original",
                 "Apertura gris", "Suav Gauss", "Th", "Erode", "Dilate")

    return imgOr, dilate
Ejemplo n.º 32
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def morphop(im, operation='open', radius='5'):
    """Perform a morphological operation with spherical structuring element.

    Parameters
    ----------
    im : array, shape (M, N[, P])
        2D or 3D grayscale image.
    operation : string, optional
        The operation to perform. Choices are 'opening', 'closing',
        'erosion', and 'dilation'. Imperative verbs also work, e.g.
        'dilate'.
    radius : int, optional
        The radius of the structuring element (disk or ball) used.

    Returns
    -------
    imout : array, shape (M, N[, P])
        The transformed image.

    Raises
    ------
    ValueError : if the image is not 2D or 3D.
    """
    if im.ndim == 2:
        selem = morphology.disk(radius)
    elif im.ndim == 3:
        selem = morphology.ball(radius)
    else:
        raise ValueError("Image input to 'morphop' should be 2D or 3D"
                         ", got %iD" % im.ndim)
    if operation.startswith('open'):
        imout = ndi.grey_opening(im, footprint=selem)
    elif operation.startswith('clos'):
        imout = ndi.grey_closing(im, footprint=selem)
    elif operation.startswith('dila'):
        imout = ndi.grey_dilation(im, footprint=selem)
    elif operation.startswith('ero'):
        imout = ndi.grey_erosion(im, footprint=selem)
    return imout
Ejemplo n.º 33
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def morphop(im, operation='open', radius='5'):
    """Perform a morphological operation with spherical structuring element.

    Parameters
    ----------
    im : array, shape (M, N[, P])
        2D or 3D grayscale image.
    operation : string, optional
        The operation to perform. Choices are 'opening', 'closing',
        'erosion', and 'dilation'. Imperative verbs also work, e.g.
        'dilate'.
    radius : int, optional
        The radius of the structuring element (disk or ball) used.

    Returns
    -------
    imout : array, shape (M, N[, P])
        The transformed image.

    Raises
    ------
    ValueError : if the image is not 2D or 3D.
    """
    if im.ndim == 2:
        selem = skmorph.disk(radius)
    elif im.ndim == 3:
        selem = skmorph.ball(radius)
    else:
        raise ValueError("Image input to 'morphop' should be 2D or 3D"
                         ", got %iD" % im.ndim)
    if operation.startswith('open'):
        imout = nd.grey_opening(im, footprint=selem)
    elif operation.startswith('clos'):
        imout = nd.grey_closing(im, footprint=selem)
    elif operation.startswith('dila'):
        imout = nd.grey_dilation(im, footprint=selem)
    elif operation.startswith('ero'):
        imout = nd.grey_erosion(im, footprint=selem)
    return imout
Ejemplo n.º 34
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 def run(self, image):
     """
     apply local otsu threshold to every z-stack and re-combine them
     image.shape = (x, y, z)
     """
     image = image.copy()
     image = np.moveaxis(image, -1, 0)
     result = []
     image *= 255
     image = image.astype(np.uint8)
     for i, stack in enumerate(image):
         local_otsu = filters.rank.otsu(stack, disk(self.radius))
         mask = stack > local_otsu
         stack = stack * mask
         if self.parameters['open_radius']:
             stack = ndimage.grey_opening(stack,
                                          self.parameters['open_radius'])
         result.append(stack)
     result = np.stack(result, axis=0)
     result = np.moveaxis(result, 0, -1)
     self.mask = result > 0
     self.image = self.apply_mask(result, self.mask)
     return self.image
Ejemplo n.º 35
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def closingFilter(image, mask):
    """ Aplica o filtro de abertura em uma imagem,
    de acordo com o tamanho da máscara passada por
    parâmetro.
    
    @param image deve ser um PIL.Image.
    @param mask string "row x cols"

    @return matriz com novos valores após aplicação do filtro
    """

    threshold = 0.8
    sumColors = numpy.float(numpy.sum(image))
    isbinary = sumColors / image.size <= 1 - threshold

    
    (row, col) = [int(dim) for dim in mask.split('x')]
    structure = [[1 for i in range(col)] for j in range(row)]

    if isbinary:
        return ndimage.binary_opening(image, structure=structure)
    else:
        return ndimage.grey_opening(image, structure=structure)
Ejemplo n.º 36
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def tophat_baseline(intensities):
    '''Perform "tophat" baseline removal, from the paper: Morphology-Based
  Automated Baseline Removal for Raman Spectra of Artistic Pigments.
  Perez-Pueyo et al., Appl. Spec. 2010'''
    # find the optimal window length
    old_b, num_equal = 0, 1
    for window_length in count(start=3, step=2):
        b1 = grey_opening(intensities, window_length)
        if np.allclose(b1, old_b):
            if num_equal == 2:
                break
            num_equal += 1
        else:
            num_equal = 1
        old_b = b1
    # use the smallest of the three equivalent window lengths
    window_length -= 4

    # compute another estimate of the baseline
    b2 = 0.5 * (grey_dilation(intensities, window_length) +
                grey_erosion(intensities, window_length))

    # combine the two estimates
    return np.minimum(b1, b2)
Ejemplo n.º 37
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 def opening(self, tissue, size=def_size):
     nd.grey_opening(self.P[tissue], size=[size,size,size], output=self.P[tissue]) 
Ejemplo n.º 38
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def opening(P, size=def_size):
    return nd.grey_opening(P, size=[size,size,size]) 
Ejemplo n.º 39
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def opening(src, r=2):
    se = ball(r)
    result = nd.grey_opening(src, footprint=se)
    return result
Ejemplo n.º 40
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				[1, 1, 1, 1, 1],
				[0, 1, 1, 1, 0]]
				
	print xorg, yorg, pres, xmax, ymax
	
	red						= get_band_data( ds, 1 ) 	
	green					= get_band_data( ds, 2 ) 	
	blue					= get_band_data( ds, 3 ) 	
	
	epsilon					= 0.0001
	norm_diff_ratio			= (red - blue) / (epsilon+blue+red)
	
	data1					= norm_diff_ratio
	data1					= speckle_filter(data1,'median', 11)
	data1					= linear_stretch(data1, max_percentile=50.0)	
	data1 					= ndimage.grey_opening(data1, size=(5,5), structure=octagon_2)
	thresh					= threshold_otsu(data1,nbins=7)
	print "otsu1", thresh
	data1[data1>=thresh] 	= 0
	data1[red==0] 			= 0
	#data1[data1>0]			= 255
	
	#thresh2					= threshold_otsu(data1,nbins=7)
	#print "otsu2", thresh2
	#data1[data1>thresh2] 	= 0
	
	write_data(data1, outfileName, ds)
	
	#norm_diff_ratio			= (red - green) / (epsilon+green+red)
	#data2					= linear_stretch(norm_diff_ratio)
	#write_data(data2, outfileName2, ds)
Ejemplo n.º 41
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def opening(src, r=2):
    """Using the opening image algrithm to process the src image."""
    se = ball(r)
    result = nd.grey_opening(src, footprint=se)
    return result
	def hand(self):
		base_img 		= self.output_4326

		in_img 			= os.path.join(self.hand_dir, HAND_FILE)
		out_img			= self.hand_4326

		# Get a subset of HAND for particular tile
		#if self.force or not os.path.isfile(out_img):
		#print "generate hand subset:"+out_img +" from:"+in_img
		self.generate_hand_subset(base_img, in_img, out_img)

		#if not os.path.isfile(self.hand_4326) and not self.force:
		#	cmd = "gdalwarp -of GTIFF "+ out_img + " " + self.hand_4326
		#	print cmd
		#	err = os.system(cmd)
		#	print "Generating HAND Tif error:", err
		#	#sys.exit(0)

		if os.path.isfile(self.output_4326_hand) and not self.force:
			return

		if verbose:
			print "Generating ", self.output_4326_hand

		src_ds 			= gdal.Open( self.output_4326_rgb )

		driver 			= gdal.GetDriverByName( "GTiff" )
		input_dataset	= driver.CreateCopy( self.output_4326_hand, src_ds, 0,	[ 'COMPRESS=DEFLATE' ] )

		input_band 		= input_dataset.GetRasterBand(1)
		input_data 		= input_band.ReadAsArray(0, 0, input_dataset.RasterXSize, input_dataset.RasterYSize )

		alpha_band		= input_dataset.GetRasterBand(4)
		alpha_data 		= alpha_band.ReadAsArray(0, 0, input_dataset.RasterXSize, input_dataset.RasterYSize )

		hand_ds 		= gdal.Open(out_img)
		hand_band 		= hand_ds.GetRasterBand(1)
		hand_data 		= hand_band.ReadAsArray(0, 0, hand_ds.RasterXSize, hand_ds.RasterYSize )

		coastlines_ds	= gdal.Open(self.coastlines)
		coastal_band 	= coastlines_ds.GetRasterBand(1)
		coastal_data 	= coastal_band.ReadAsArray(0, 0, coastlines_ds.RasterXSize, coastlines_ds.RasterYSize )
		
		if app.verbose:
			print "hand_data:", hand_data.min(), hand_data.max()

		# HAND Masking
		mask			= hand_data==0
		input_data[mask]= 0

		mask			= hand_data==255
		input_data[mask]= 0

		mask			= coastal_data>0
		input_data[mask]= 0

		#
		# Morphing to smooth and filter the data
		#
		octagon_2 =[[0, 1, 1, 1, 0],
					[1, 1, 1, 1, 1],
					[1, 1, 1, 1, 1],
					[1, 1, 1, 1, 1],
					[0, 1, 1, 1, 0]]

		morphed = ndimage.grey_opening(input_data, size=(5,5), structure=octagon_2)

		input_band.WriteArray(morphed, 0, 0)
		input_band.SetNoDataValue(0)

		# set transparency
		alpha_data[morphed<255]=0
		alpha_data[morphed>=255]=255
		alpha_band.WriteArray(alpha_data, 0, 0)

		input_data 		= None
		morphed			= None
		input_dataset 	= None
		hand_band		= None
		hand_ds			= None
		src_ds			= None
		coastlines_ds	= None
		
		if app.verbose:
			print "Hand Morphed Done ", self.output_4326_hand
Ejemplo n.º 43
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def opening(f, b=bm.create_structure_element_cross()):
    return mm.grey_opening(f, structure=b)
Ejemplo n.º 44
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    unI = sorted(unique(im.ravel()))
    nbin = len(unI)
    h  = histogram(im, unI)
    P = h[0].astype(float)/sum(h[0])
    
    w = cumsum(P)
    nbin = len(P)
    mu = cumsum(arange(1, nbin+1) * P)
    sigma2B = (mu[-1] * w[1:-1] - mu[1:-1])** 2 / w[1:-1]/(1-w[1:-1])
    idx = where(sigma2B == max(sigma2B))[0][0]
    return h[1][idx]

# ------------------------------------------------------------------------------
    
im = array(Image.open('textures/structure/015.jpg').convert("L")) / 255.
bg = ndimage.grey_opening(im, footprint = circle(5))
pb.set_cmap(pb.cm.gray)

pb.figure()
pb.title("Original")
pb.imshow(im,vmin=0, vmax=1)
pb.savefig('result/structure/001.png', dpi=150)    

imbgadj = imadjust(im)
pb.figure()
pb.title("Normalized")
pb.imshow(imbgadj, vmin = 0, vmax=1)
pb.savefig('result/structure/002.png', dpi=150)    

t = otsu(imbgadj)
print t
def opening(f, b):
    return mm.grey_opening(f, struture=b)
Ejemplo n.º 46
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    def watershed_cube(self):
        writeVerbose = False;
        #writeVerbose = self.dpWatershedTypes_verbose
        readVerbose = False;
        #readVerbose = self.dpWatershedTypes_verbose

        # load the probability data, allocate as array of volumes instead of 4D ndarray to maintain C-order volumes
        probs = [None]*self.ntypes; bwseeds = [None]*self.nfg_types
        if self.srclabels:
            # this code path is typically not used in favor of the label checker for fully labeled 3d gt components.
            # but, some ground truth (for example, 2d ECS cases) was only labeled with voxel type,
            #   so this is used to create ground truth components from the voxel types.
            loadh5 = emLabels.readLabels(srcfile=self.srclabels, chunk=self.chunk.tolist(), offset=self.offset.tolist(),
                size=self.size.tolist(), data_type='uint16', verbose=writeVerbose)
            self.datasize = loadh5.datasize; self.chunksize = loadh5.chunksize; self.attrs = loadh5.data_attrs
            # pre-allocate for srclabels method, labeled areas are set to prob of 1 below
            for i in range(self.ntypes): probs[i] = np.zeros(self.size, dtype=emProbabilities.PROBS_DTYPE, order='C')
            if self.TminSrc < 2:
                # simple method with no "cleaning"
                for i in range(self.ntypes): probs[i][loadh5.data_cube==i] = 1
            else:
                # optionally "clean" labels by removing small bg and fg components for each foreground type
                fgbwlabels = np.zeros(self.size, dtype=np.bool)
                for i in range(self.nfg_types):
                    # background connected components and threshold
                    comps, nlbls = nd.measurements.label(loadh5.data_cube!=i+1)
                    comps, sizes = emLabels.thresholdSizes(comps, minSize=self.TminSrc)
                    # foreground connected components and threshold
                    comps, nlbls = nd.measurements.label(comps==0)
                    comps, sizes = emLabels.thresholdSizes(comps, minSize=self.TminSrc)
                    # keep track of mask for all foreground types
                    bwlabels = (comps > 0); fgbwlabels = np.logical_or(fgbwlabels, bwlabels)
                    probs[i+1][bwlabels] = 1
                # set background type as all areas that are not in foreground types after "cleaning"
                probs[0][np.logical_not(fgbwlabels)] = 1
        else:
            # check if background is in the prob file
            hdf = h5py.File(self.probfile,'r'); has_bg = self.bg_type in hdf; hdf.close()
            for i in range(0 if has_bg else 1, self.ntypes):
                loadh5 = dpLoadh5.readData(srcfile=self.probfile, dataset=self.types[i], chunk=self.chunk.tolist(),
                    offset=self.offset.tolist(), size=self.size.tolist(), data_type=emProbabilities.PROBS_STR_DTYPE,
                    verbose=readVerbose)
                self.datasize = loadh5.datasize; self.chunksize = loadh5.chunksize; self.attrs = loadh5.data_attrs
                probs[i] = loadh5.data_cube; del loadh5
            # if background was not in hdf5 then create it as 1-sum(fg type probs)
            if not has_bg:
                probs[0] = np.ones_like(probs[1])
                for i in range(1,self.ntypes): probs[0] -= probs[i]
                #assert( (probs[0] >= 0).all() ) # comment for speed
                probs[0][probs[0] < 0] = 0 # rectify

        # save some of the parameters as attributes
        self.attrs['types'] = self.types; self.attrs['fg_types'] = self.fg_types
        self.attrs['fg_types_labels'] = self.fg_types_labels

        # save connnetivity structure and warping LUT because used on each iteration (for speed)
        self.bwconn = nd.morphology.generate_binary_structure(dpLoadh5.ND, self.connectivity)
        self.bwconn2d = self.bwconn[:,:,1]; self.simpleLUT = None

        # load the warpings if warping mode is enabled
        warps = None
        if self.warpfile:
            warps = [None]*self.nwarps
            for i in range(self.nwarps):
                loadh5 = dpLoadh5.readData(srcfile=self.warpfile, dataset=self.warp_datasets[i],
                    chunk=self.chunk.tolist(), offset=self.offset.tolist(), size=self.size.tolist(),
                    verbose=readVerbose)
                warps[i] = loadh5.data_cube; del loadh5

        # xxx - may need to revisit cropping, only intended to be used with warping method.
        if self.docrop: c = self.cropborder; s = self.size  # DO NOT use variables c or s below

        # optionally apply filters in attempt to fill small background (membrane) probability gaps.
        if self.close_bg > 0:
            # create structuring element
            n = 2*self.close_bg + 1; h = self.close_bg; strel = np.zeros((n,n,n),dtype=np.bool); strel[h,h,h]=1;
            strel = nd.binary_dilation(strel,iterations=self.close_bg)

            # xxx - this was the only thing tried here that helped some but didn't work well against the skeletons
            probs[0] = nd.grey_closing( probs[0], structure=strel )
            for i in range(self.nfg_types): probs[i+1] = nd.grey_opening( probs[i+1], structure=strel )
            # xxx - this gave worse results
            #probs[0] = nd.maximum_filter( probs[0], footprint=strel )
            # xxx - this had almost no effect
            #probs[0] = nd.grey_closing( probs[0], structure=strel )

        # argmax produces the winner-take-all assignment for each supervoxel.
        # background type was put first, so voxType of zero is background (membrane).
        voxType = np.concatenate([x.reshape(x.shape + (1,)) for x in probs], axis=3).argmax(axis=3)
        # write out the winning type for each voxel
        # save some params from this watershed run in the attributes
        d = self.attrs.copy(); d['thresholds'] = self.Ts; d['Tmins'] = self.Tmins
        data = voxType.astype(emVoxelType.VOXTYPE_DTYPE)
        if self.docrop: data = data[c[0]:s[0]-c[0],c[1]:s[1]-c[1],c[2]:s[2]-c[2]]
        emVoxelType.writeVoxType(outfile=self.outlabels, chunk=self.chunk.tolist(),
            offset=self.offset_crop.tolist(), size=self.size_crop.tolist(), datasize=self.datasize.tolist(),
            chunksize=self.chunksize.tolist(), verbose=writeVerbose, attrs=d,
            data=data)

        # only allow a voxel to be included in the type of component that had max prob for that voxel.
        # do this by setting the non-winning probabilities to zero.
        for i in range(self.ntypes): probs[i][voxType != i] = 0;

        # create a type mask for each foreground type to select only current voxel type (winner-take-all from network)
        voxTypeSel = [None] * self.nfg_types; voxTypeNotSel =  [None] * self.nfg_types
        for i in range(self.nfg_types):
            voxTypeSel[i] = (voxType == i+1)
            # create an inverted version, only used for complete fill not for warping (which requires C-contiguous),
            #   so apply crop here if cropping enabled
            voxTypeNotSel[i] = np.logical_not(voxTypeSel[i])
            if self.docrop: voxTypeNotSel[i] = voxTypeNotSel[i][c[0]:s[0]-c[0],c[1]:s[1]-c[1],c[2]:s[2]-c[2]]

        # need C-contiguous probabilities for binary_warping.
        for i in range(self.nfg_types):
            if not probs[i+1].flags.contiguous or np.isfortran(probs[i+1]):
                probs[i+1] = np.ascontiguousarray(probs[i+1])

        # iteratively apply thresholds, each time only keeping components that have fallen under size Tmin.
        # at last iteration keep all remaining components.
        # do this separately for foreground types.
        for k in range(self.nTmin):
            for i in range(self.nfg_types): bwseeds[i] = np.zeros(self.size, dtype=np.bool, order='C')
            for i in range(self.nthresh):
                if self.dpWatershedTypes_verbose:
                    print('creating supervoxels at threshold = %.8f with Tmin = %d' % (self.Ts[i], self.Tmins[k]))
                    t = time.time()
                types_labels = [None]*self.nfg_types; types_uclabels = [None]*self.nfg_types;
                if self.skeletonize: types_sklabels = [None]*self.nfg_types
                types_nlabels = np.zeros((self.nfg_types,),dtype=np.int64)
                types_ucnlabels = np.zeros((self.nfg_types,),dtype=np.int64)
                for j in range(self.nfg_types):
                    # run connected components at this threshold on labels
                    labels, nlabels = nd.measurements.label(probs[j+1] > self.Ts[i], self.bwconn)

                    # merge the current thresholded components with the previous seeds to get current bwlabels
                    bwlabels = np.logical_or(labels, bwseeds[j])

                    # take the current components under threshold and merge with the seeds for the next iteration
                    if i < self.nthresh-1:
                        labels, sizes = emLabels.thresholdSizes(labels, minSize=-self.Tmins[k])
                        bwseeds[j] = np.logical_or(labels, bwseeds[j])

                    # this if/elif switch determines the main method for creating the labels.
                    # xxx - make cropping to be done in more efficient way, particular to avoid filling cropped areas
                    if self.method == 'overlap':
                        # definite advantage to this method over other methods, but cost is about 2-3 times slower.
                        # labels are linked per zslice using precalculated slice to slice warpings based on the probs.
                        labels, nlabels = self.label_overlap(bwlabels, voxTypeSel[j], warps)

                        # xxx - add switches to only optionally export the unconnected labels
                        #uclabels = labels; ucnlabels = nlabels;

                        # crop right after the labels are created and stay uncropped from here.
                        # xxx - labels will be wrong unless method implicitly handled the cropping during the labeling.
                        #   currently only the warping method is doing, don't need cropping for other methods anyways.
                        if self.docrop: labels = labels[c[0]:s[0]-c[0],c[1]:s[1]-c[1],c[2]:s[2]-c[2]]

                        # this method can not create true unconnected 3d labels, but should be unconnected in 2d.
                        # NOTE: currently this only removes 6-connectivity, no matter what specified connecitity is
                        # xxx - some method of removing adjacencies with arbitrary connectivity?
                        uclabels, ucnlabels = emLabels.remove_adjacencies(labels)
                    elif self.method == 'skim-ws':
                        # xxx - still trying to evaluate if there is any advantage to this more traditional watershed.
                        #   it does not leave a non-adjacency boundary and is about 1.5 times slower than bwmorph

                        # run connected components on the thresholded labels merged with previous seeds
                        labels, nlabels = nd.measurements.label(bwlabels, self.bwconn)

                        # run a true watershed based the current foreground probs using current components as markers
                        labels = morph.watershed(probs[j+1], labels, connectivity=self.bwconn, mask=voxTypeSel[j])

                        # remove any adjacencies created during the watershed
                        # NOTE: currently this only removes 6-connectivity, no matter what specified connecitity is
                        # xxx - some method of removing adjacencies with arbitrary connectivity?
                        uclabels, ucnlabels = emLabels.remove_adjacencies(labels)
                    else:
                        if self.method == 'comps-ws' and i>1:
                            # this is an alternative to the traditional watershed that warps out only based on stepping
                            #   back through the thresholds in reverse order. has advantages of non-connectivity.
                            # may help slightly for small supervoxels but did not show much improved metrics in
                            #   terms of large-scale connectivity (against skeletons)
                            # about 4-5 times slower than regular warping method.

                            # make an unconnected version of bwlabels by warping out but with mask only for this type
                            # everything above current threshold is already labeled, so only need to use gray thresholds
                            #    starting below the current threshold level.
                            bwlabels, diff, self.simpleLUT = binary_warping(bwlabels, np.ones(self.size,dtype=np.bool),
                                mask=voxTypeSel[j], borderval=False, slow=True, simpleLUT=self.simpleLUT,
                                connectivity=self.connectivity, gray=probs[j+1],
                                grayThresholds=self.Ts[i-1::-1].astype(np.float32, order='C'))
                        else:
                            assert( self.method == 'comps' )     # bad method option
                            # make an unconnected version of bwlabels by warping out but with mask only for this type
                            bwlabels, diff, self.simpleLUT = binary_warping(bwlabels, np.ones(self.size,dtype=np.bool),
                                mask=voxTypeSel[j], borderval=False, slow=True, simpleLUT=self.simpleLUT,
                                connectivity=self.connectivity)

                        # run connected components on the thresholded labels merged with previous seeds (warped out)
                        uclabels, ucnlabels = nd.measurements.label(bwlabels, self.bwconn);

                        # in this case the normal labels are the same as the unconnected labels because of warping
                        labels = uclabels; nlabels = ucnlabels;

                    # optionally make a skeletonized version of the unconnected labels
                    # xxx - revisit this, currently not being used for anything, started as a method to skeletonize GT
                    if self.skeletonize:
                        # method to skeletonize using max range endpoints only
                        sklabels, sknlabels = emLabels.ucskeletonize(uclabels, mask=voxTypeSel[j],
                            sampling=self.attrs['scale'] if hasattr(self.attrs,'scale') else None)
                        assert( sknlabels == ucnlabels )

                    # fill out these labels out so that they fill in remaining voxels based on voxType.
                    # this uses bwdist method for finding nearest neighbors, so connectivity can be violoated.
                    # this is mitigated by first filling out background using the warping transformation
                    #   (or watershed) above, then this step is only to fill in remaining voxels for the
                    #   current foreground voxType.
                    labels = emLabels.nearest_neighbor_fill(labels, mask=voxTypeNotSel[j],
                        sampling=self.attrs['scale'] if hasattr(self.attrs,'scale') else None)

                    # save the components labels generated for this type
                    types_labels[j] = labels.astype(emLabels.LBLS_DTYPE, copy=False);
                    types_uclabels[j] = uclabels.astype(emLabels.LBLS_DTYPE, copy=False);
                    types_nlabels[j] = nlabels if self.fg_types_labels[j] < 0 else 1
                    types_ucnlabels[j] = ucnlabels if self.fg_types_labels[j] < 0 else 1
                    if self.skeletonize: types_sklabels[j] = sklabels.astype(emLabels.LBLS_DTYPE, copy=False)

                # merge the fg components labels. they can not overlap because voxel type is winner-take-all.
                nlabels = 0; ucnlabels = 0;
                labels = np.zeros(self.size_crop, dtype=emLabels.LBLS_DTYPE);
                uclabels = np.zeros(self.size_crop, dtype=emLabels.LBLS_DTYPE);
                if self.skeletonize: sklabels = np.zeros(self.size, dtype=emLabels.LBLS_DTYPE);
                for j in range(self.nfg_types):
                    sel = (types_labels[j] > 0); ucsel = (types_uclabels[j] > 0);
                    if self.skeletonize: sksel = (types_sklabels[j] > 0);
                    if self.fg_types_labels[j] < 0:
                        labels[sel] += (types_labels[j][sel] + nlabels);
                        uclabels[ucsel] += (types_uclabels[j][ucsel] + ucnlabels);
                        if self.skeletonize: sklabels[sksel] += (types_sklabels[j][sksel] + ucnlabels);
                        nlabels += types_nlabels[j]; ucnlabels += types_ucnlabels[j];
                    else:
                        labels[sel] = self.fg_types_labels[j];
                        uclabels[ucsel] = self.fg_types_labels[j];
                        if self.skeletonize: sklabels[sksel] = self.fg_types_labels[j]
                        nlabels += 1; ucnlabels += 1;

                if self.dpWatershedTypes_verbose:
                    print('\tnlabels = %d' % (nlabels,))
                    #print('\tnlabels = %d %d' % (nlabels,labels.max())) # for debug only
                    #assert(nlabels == labels.max()) # sanity check for non-overlapping voxTypeSel, comment for speed
                    print('\tdone in %.4f s' % (time.time() - t,))

                # make a fully-filled out version using bwdist nearest foreground neighbor
                wlabels = emLabels.nearest_neighbor_fill(labels, mask=None,
                    sampling=self.attrs['scale'] if hasattr(self.attrs,'scale') else None)

                # write out the results
                if self.nTmin == 1: subgroups = ['%.8f' % (self.Ts[i],)]
                else: subgroups = ['%d' % (self.Tmins[k],), '%.8f' % (self.Ts[i],)]
                d = self.attrs.copy(); d['threshold'] = self.Ts[i];
                d['types_nlabels'] = types_nlabels; d['Tmin'] = self.Tmins[k]
                emLabels.writeLabels(outfile=self.outlabels, chunk=self.chunk.tolist(),
                    offset=self.offset_crop.tolist(), size=self.size_crop.tolist(), datasize=self.datasize.tolist(),
                    chunksize=self.chunksize.tolist(), data=labels, verbose=writeVerbose,
                    attrs=d, strbits=self.outlabelsbits, subgroups=['with_background']+subgroups )
                emLabels.writeLabels(outfile=self.outlabels, chunk=self.chunk.tolist(),
                    offset=self.offset_crop.tolist(), size=self.size_crop.tolist(), datasize=self.datasize.tolist(),
                    chunksize=self.chunksize.tolist(), data=wlabels, verbose=writeVerbose,
                    attrs=d, strbits=self.outlabelsbits, subgroups=['zero_background']+subgroups )
                d['type_nlabels'] = types_ucnlabels;
                emLabels.writeLabels(outfile=self.outlabels, chunk=self.chunk.tolist(),
                    offset=self.offset_crop.tolist(), size=self.size_crop.tolist(), datasize=self.datasize.tolist(),
                    chunksize=self.chunksize.tolist(), data=uclabels, verbose=writeVerbose,
                    attrs=d, strbits=self.outlabelsbits, subgroups=['no_adjacencies']+subgroups )
                if self.skeletonize:
                    emLabels.writeLabels(outfile=self.outlabels, chunk=self.chunk.tolist(),
                        offset=self.offset_crop.tolist(), size=self.size_crop.tolist(), datasize=self.datasize.tolist(),
                        chunksize=self.chunksize.tolist(), data=sklabels, verbose=writeVerbose,
                        attrs=d, strbits=self.outlabelsbits, subgroups=['skeletonized']+subgroups )