Fill holes in mask

Thiago Franco de Moraes
1 parent f0faf9e1
Showing 5 changed files with 326 additions and 1 deletions Show diff stats
invesalius/constants.py
invesalius/data/floodfill.pyx
invesalius/data/styles.py
invesalius/gui/frame.py
setup.py
@@ -481,6 +481,7 @@ ID_BOOLEAN_MASK = wx.NewId()
 ID_CLEAN_MASK = wx.NewId()
  
 ID_REORIENT_IMG = wx.NewId()
+ID_FLOODFILL_MASK = wx.NewId()
  
 #---------------------------------------------------------
 STATE_DEFAULT = 1000
@@ -498,6 +499,7 @@ SLICE_STATE_SCROLL = 3007
 SLICE_STATE_EDITOR = 3008
 SLICE_STATE_WATERSHED = 3009
 SLICE_STATE_REORIENT = 3010
+SLICE_STATE_MASK_FFILL = 3011
  
 VOLUME_STATE_SEED = 2001
 #  STATE_LINEAR_MEASURE = 3001
@@ -515,6 +517,7 @@ SLICE_STYLES = TOOL_STATES + TOOL_SLICE_STATES
 SLICE_STYLES.append(STATE_DEFAULT)
 SLICE_STYLES.append(SLICE_STATE_EDITOR)
 SLICE_STYLES.append(SLICE_STATE_WATERSHED)
+SLICE_STYLES.append(SLICE_STATE_MASK_FFILL)
  
 VOLUME_STYLES = TOOL_STATES + [VOLUME_STATE_SEED, STATE_MEASURE_DISTANCE,
         STATE_MEASURE_ANGLE]
@@ -523,6 +526,7 @@ VOLUME_STYLES.append(STATE_DEFAULT)
  
 STYLE_LEVEL = {SLICE_STATE_EDITOR: 1,
                SLICE_STATE_WATERSHED: 1,
+               SLICE_STATE_MASK_FFILL: 1,
                SLICE_STATE_CROSS: 2,
                SLICE_STATE_SCROLL: 2,
                SLICE_STATE_REORIENT: 2,
@@ -0,0 +1,214 @@
+import numpy as np
+cimport numpy as np
+cimport cython
+
+from collections import deque
+
+from libc.math cimport floor, ceil
+from libcpp.deque cimport deque as cdeque
+
+from cy_my_types cimport image_t, mask_t
+
+@cython.boundscheck(False) # turn of bounds-checking for entire function
+@cython.wraparound(False)
+@cython.nonecheck(False)
+@cython.cdivision(True)
+cdef inline void append_queue(cdeque[int]& stack, int x, int y, int z, int d, int h, int w) nogil:
+    stack.push_back(z*h*w + y*w + x)
+
+
+@cython.boundscheck(False) # turn of bounds-checking for entire function
+@cython.wraparound(False)
+@cython.nonecheck(False)
+@cython.cdivision(True)
+cdef inline void pop_queue(cdeque[int]& stack, int* x, int* y, int* z, int d, int h, int w) nogil:
+    cdef int i = stack.front()
+    stack.pop_front()
+    x[0] = i % w
+    y[0] = (i / w) % h
+    z[0] = i / (h * w)
+
+
+@cython.boundscheck(False) # turn of bounds-checking for entire function
+def floodfill(np.ndarray[image_t, ndim=3] data, int i, int j, int k, int v, int fill, np.ndarray[mask_t, ndim=3] out):
+
+    cdef int to_return = 0
+    if out is None:
+        out = np.zeros_like(data)
+        to_return = 1
+
+    cdef int x, y, z
+    cdef int w, h, d
+
+    d = data.shape[0]
+    h = data.shape[1]
+    w = data.shape[2]
+
+    stack = [(i, j, k), ]
+    out[k, j, i] = fill
+
+    while stack:
+        x, y, z = stack.pop()
+
+        if z + 1 < d and data[z + 1, y, x] == v and out[z + 1, y, x] != fill:
+            out[z + 1, y, x] =  fill
+            stack.append((x, y, z + 1))
+
+        if z - 1 >= 0 and data[z - 1, y, x] == v and out[z - 1, y, x] != fill:
+            out[z - 1, y, x] = fill
+            stack.append((x, y, z - 1))
+
+        if y + 1 < h and data[z, y + 1, x] == v and out[z, y + 1, x] != fill:
+            out[z, y + 1, x] = fill
+            stack.append((x, y + 1, z))
+
+        if y - 1 >= 0 and data[z, y - 1, x] == v and out[z, y - 1, x] != fill:
+            out[z, y - 1, x] = fill
+            stack.append((x, y - 1, z))
+
+        if x + 1 < w and data[z, y, x + 1] == v and out[z, y, x + 1] != fill:
+            out[z, y, x + 1] = fill
+            stack.append((x + 1, y, z))
+
+        if x - 1 >= 0 and data[z, y, x - 1] == v and out[z, y, x - 1] != fill:
+            out[z, y, x - 1] = fill
+            stack.append((x - 1, y, z))
+
+    if to_return:
+        return out
+
+
+@cython.boundscheck(False) # turn of bounds-checking for entire function
+@cython.wraparound(False)
+@cython.nonecheck(False)
+def floodfill_threshold(np.ndarray[image_t, ndim=3] data, list seeds, int t0, int t1, int fill, np.ndarray[mask_t, ndim=3] out):
+
+    cdef int to_return = 0
+    if out is None:
+        out = np.zeros_like(data)
+        to_return = 1
+
+    cdef int x, y, z
+    cdef int w, h, d
+    cdef int xo, yo, zo
+
+    d = data.shape[0]
+    h = data.shape[1]
+    w = data.shape[2]
+
+    stack = deque()
+
+    for i, j, k in seeds:
+        if data[k, j, i] >= t0 and data[k, j, i] <= t1:
+            stack.append((i, j, k))
+            out[k, j, i] = fill
+
+    while stack:
+        x, y, z = stack.pop()
+
+        xo = x
+        yo = y
+        zo = z
+
+        if z + 1 < d and data[z + 1, y, x] >= t0 and data[z + 1, y, x] <= t1 and out[zo + 1, yo, xo] != fill:
+            out[zo + 1, yo, xo] =  fill
+            stack.append((x, y, z + 1))
+
+        if z - 1 >= 0 and data[z - 1, y, x] >= t0 and data[z - 1, y, x] <= t1 and out[zo - 1, yo, xo] != fill:
+            out[zo - 1, yo, xo] = fill
+            stack.append((x, y, z - 1))
+
+        if y + 1 < h and data[z, y + 1, x] >= t0 and data[z, y + 1, x] <= t1 and out[zo, yo + 1, xo] != fill:
+            out[zo, yo + 1, xo] = fill
+            stack.append((x, y + 1, z))
+
+        if y - 1 >= 0 and data[z, y - 1, x] >= t0 and data[z, y - 1, x] <= t1 and out[zo, yo - 1, xo] != fill:
+            out[zo, yo - 1, xo] = fill
+            stack.append((x, y - 1, z))
+
+        if x + 1 < w and data[z, y, x + 1] >= t0 and data[z, y, x + 1] <= t1 and out[zo, yo, xo + 1] != fill:
+            out[zo, yo, xo + 1] = fill
+            stack.append((x + 1, y, z))
+
+        if x - 1 >= 0 and data[z, y, x - 1] >= t0 and data[z, y, x - 1] <= t1 and out[zo, yo, xo - 1] != fill:
+            out[zo, yo, xo - 1] = fill
+            stack.append((x - 1, y, z))
+
+    if to_return:
+        return out
+
+
+@cython.boundscheck(False) # turn of bounds-checking for entire function
+@cython.wraparound(False)
+@cython.nonecheck(False)
+def floodfill_auto_threshold(np.ndarray[image_t, ndim=3] data, list seeds, float p, int fill, np.ndarray[mask_t, ndim=3] out):
+
+    cdef int to_return = 0
+    if out is None:
+        out = np.zeros_like(data)
+        to_return = 1
+
+    cdef cdeque[int] stack
+    cdef int x, y, z
+    cdef int w, h, d
+    cdef int xo, yo, zo
+    cdef int t0, t1
+
+    cdef int i, j, k
+
+    d = data.shape[0]
+    h = data.shape[1]
+    w = data.shape[2]
+
+
+    #  stack = deque()
+
+    x = 0
+    y = 0
+    z = 0
+
+
+    for i, j, k in seeds:
+        append_queue(stack, i, j, k, d, h, w)
+        out[k, j, i] = fill
+        print i, j, k, d, h, w
+
+    with nogil:
+        while stack.size():
+            pop_queue(stack, &x, &y, &z, d, h, w)
+
+            #  print x, y, z, d, h, w
+
+            xo = x
+            yo = y
+            zo = z
+
+            t0 = <int>ceil(data[z, y, x] * (1 - p))
+            t1 = <int>floor(data[z, y, x] * (1 + p))
+
+            if z + 1 < d and data[z + 1, y, x] >= t0 and data[z + 1, y, x] <= t1 and out[zo + 1, yo, xo] != fill:
+                out[zo + 1, yo, xo] =  fill
+                append_queue(stack, x, y, z+1, d, h, w)
+
+            if z - 1 >= 0 and data[z - 1, y, x] >= t0 and data[z - 1, y, x] <= t1 and out[zo - 1, yo, xo] != fill:
+                out[zo - 1, yo, xo] = fill
+                append_queue(stack, x, y, z-1, d, h, w)
+
+            if y + 1 < h and data[z, y + 1, x] >= t0 and data[z, y + 1, x] <= t1 and out[zo, yo + 1, xo] != fill:
+                out[zo, yo + 1, xo] = fill
+                append_queue(stack, x, y+1, z, d, h, w)
+
+            if y - 1 >= 0 and data[z, y - 1, x] >= t0 and data[z, y - 1, x] <= t1 and out[zo, yo - 1, xo] != fill:
+                out[zo, yo - 1, xo] = fill
+                append_queue(stack, x, y-1, z, d, h, w)
+
+            if x + 1 < w and data[z, y, x + 1] >= t0 and data[z, y, x + 1] <= t1 and out[zo, yo, xo + 1] != fill:
+                out[zo, yo, xo + 1] = fill
+                append_queue(stack, x+1, y, z, d, h, w)
+
+            if x - 1 >= 0 and data[z, y, x - 1] >= t0 and data[z, y, x - 1] <= t1 and out[zo, yo, xo - 1] != fill:
+                out[zo, yo, xo - 1] = fill
+                append_queue(stack, x-1, y, z, d, h, w)
+
+    if to_return:
+        return out
@@ -42,6 +42,8 @@ from skimage import filter
  
 from .measures import MeasureData
  
+from . import floodfill
+
 import watershed_process
  
 import utils
@@ -1747,6 +1749,92 @@ class ReorientImageInteractorStyle(DefaultInteractorStyle):
             buffer_.discard_vtk_image()
             buffer_.discard_image()
  
+
+class FlooFillMaskInteractorStyle(DefaultInteractorStyle):
+    def __init__(self, viewer):
+        DefaultInteractorStyle.__init__(self, viewer)
+
+        self.viewer = viewer
+        self.orientation = self.viewer.orientation
+
+        self.picker = vtk.vtkWorldPointPicker()
+        self.slice_actor = viewer.slice_data.actor
+        self.slice_data = viewer.slice_data
+
+        self.viewer.slice_.do_threshold_to_all_slices()
+
+        self.AddObserver("LeftButtonPressEvent", self.OnFFClick)
+
+    def OnFFClick(self, obj, evt):
+        if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
+            return
+
+
+        viewer = self.viewer
+        iren = viewer.interactor
+
+        mouse_x, mouse_y = iren.GetEventPosition()
+        render = iren.FindPokedRenderer(mouse_x, mouse_y)
+        slice_data = viewer.get_slice_data(render)
+
+        self.picker.Pick(mouse_x, mouse_y, 0, render)
+
+        coord = self.get_coordinate_cursor()
+        position = slice_data.actor.GetInput().FindPoint(coord)
+
+        if position != -1:
+            coord = slice_data.actor.GetInput().GetPoint(position)
+
+        if position < 0:
+            position = viewer.calculate_matrix_position(coord)
+
+        x, y, z = self.calcultate_scroll_position(position)
+        mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
+
+        cp_mask = mask.copy()
+
+        floodfill.floodfill_threshold(cp_mask, [[x, y, z]], 0, 1, 254, mask)
+
+        viewer.OnScrollBar()
+
+    def get_coordinate_cursor(self):
+        # Find position
+        x, y, z = self.picker.GetPickPosition()
+        bounds = self.viewer.slice_data.actor.GetBounds()
+        if bounds[0] == bounds[1]:
+            x = bounds[0]
+        elif bounds[2] == bounds[3]:
+            y = bounds[2]
+        elif bounds[4] == bounds[5]:
+            z = bounds[4]
+        return x, y, z
+
+    def calcultate_scroll_position(self, position):
+        # Based in the given coord (x, y, z), returns a list with the scroll positions for each
+        # orientation, being the first position the sagital, second the coronal
+        # and the last, axial.
+
+        if self.orientation == 'AXIAL':
+            image_width = self.slice_actor.GetInput().GetDimensions()[0]
+            axial = self.slice_data.number
+            coronal = position / image_width
+            sagital = position % image_width
+
+        elif self.orientation == 'CORONAL':
+            image_width = self.slice_actor.GetInput().GetDimensions()[0]
+            axial = position / image_width
+            coronal = self.slice_data.number
+            sagital = position % image_width
+
+        elif self.orientation == 'SAGITAL':
+            image_width = self.slice_actor.GetInput().GetDimensions()[1]
+            axial = position / image_width
+            coronal = position % image_width
+            sagital = self.slice_data.number
+
+        return sagital, coronal, axial
+
+
 def get_style(style):
     STYLES = {
         const.STATE_DEFAULT: DefaultInteractorStyle,
@@ -1762,5 +1850,8 @@ def get_style(style):
         const.SLICE_STATE_EDITOR: EditorInteractorStyle,
         const.SLICE_STATE_WATERSHED: WaterShedInteractorStyle,
         const.SLICE_STATE_REORIENT: ReorientImageInteractorStyle,
+        const.SLICE_STATE_MASK_FFILL: FlooFillMaskInteractorStyle,
     }
     return STYLES[style]
+
+
@@ -439,6 +439,9 @@ class Frame(wx.Frame):
         elif id == const.ID_REORIENT_IMG:
             self.OnReorientImg()
  
+        elif id == const.ID_FLOODFILL_MASK:
+            self.OnFillHolesManually()
+
     def OnSize(self, evt):
         """
         Refresh GUI when frame is resized.
@@ -559,6 +562,9 @@ class Frame(wx.Frame):
         rdlg = dlg.ReorientImageDialog()
         rdlg.Show()
  
+    def OnFillHolesManually(self):
+        Publisher.sendMessage('Enable style', const.SLICE_STATE_MASK_FFILL)
+
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
 # ------------------------------------------------------------------
@@ -578,7 +584,8 @@ class MenuBar(wx.MenuBar):
         self.enable_items = [const.ID_PROJECT_SAVE,
                              const.ID_PROJECT_SAVE_AS,
                              const.ID_PROJECT_CLOSE,
-                             const.ID_REORIENT_IMG]
+                             const.ID_REORIENT_IMG,
+                             const.ID_FLOODFILL_MASK]
         self.__init_items()
         self.__bind_events()
  
@@ -689,6 +696,9 @@ class MenuBar(wx.MenuBar):
         self.clean_mask_menu = mask_menu.Append(const.ID_CLEAN_MASK, _(u"Clean Mask\tCtrl+Shift+A"))
         self.clean_mask_menu.Enable(False)
  
+        self.fill_hole_mask_menu = mask_menu.Append(const.ID_FLOODFILL_MASK, _(u"Fill mask holes manually"))
+        self.fill_hole_mask_menu.Enable(False)
+
         tools_menu.AppendMenu(-1,  _(u"Mask"), mask_menu)
  
         # Image menu
@@ -25,6 +25,12 @@ if sys.platform == &#39;linux2&#39;:
                                  include_dirs=[numpy.get_include()],
                                  extra_compile_args=['-fopenmp',],
                                  extra_link_args=['-fopenmp',]),
+
+                       Extension("invesalius.data.floodfill", ["invesalius/data/floodfill.pyx"],
+                                 include_dirs=[numpy.get_include()],
+                                 extra_compile_args=['-fopenmp',],
+                                 extra_link_args=['-fopenmp',],
+                                 language='c++',),
                        ])
          )
...	...	@@ -481,6 +481,7 @@ ID_BOOLEAN_MASK = wx.NewId()
481	481	ID_CLEAN_MASK = wx.NewId()
482	482
483	483	ID_REORIENT_IMG = wx.NewId()
	484	+ID_FLOODFILL_MASK = wx.NewId()
484	485
485	486	#---------------------------------------------------------
486	487	STATE_DEFAULT = 1000
...	...	@@ -498,6 +499,7 @@ SLICE_STATE_SCROLL = 3007
498	499	SLICE_STATE_EDITOR = 3008
499	500	SLICE_STATE_WATERSHED = 3009
500	501	SLICE_STATE_REORIENT = 3010
	502	+SLICE_STATE_MASK_FFILL = 3011
501	503
502	504	VOLUME_STATE_SEED = 2001
503	505	# STATE_LINEAR_MEASURE = 3001
...	...	@@ -515,6 +517,7 @@ SLICE_STYLES = TOOL_STATES + TOOL_SLICE_STATES
515	517	SLICE_STYLES.append(STATE_DEFAULT)
516	518	SLICE_STYLES.append(SLICE_STATE_EDITOR)
517	519	SLICE_STYLES.append(SLICE_STATE_WATERSHED)
	520	+SLICE_STYLES.append(SLICE_STATE_MASK_FFILL)
518	521
519	522	VOLUME_STYLES = TOOL_STATES + [VOLUME_STATE_SEED, STATE_MEASURE_DISTANCE,
520	523	STATE_MEASURE_ANGLE]
...	...	@@ -523,6 +526,7 @@ VOLUME_STYLES.append(STATE_DEFAULT)
523	526
524	527	STYLE_LEVEL = {SLICE_STATE_EDITOR: 1,
525	528	SLICE_STATE_WATERSHED: 1,
	529	+ SLICE_STATE_MASK_FFILL: 1,
526	530	SLICE_STATE_CROSS: 2,
527	531	SLICE_STATE_SCROLL: 2,
528	532	SLICE_STATE_REORIENT: 2,
...	...
...	...	@@ -0,0 +1,214 @@
	1	+import numpy as np
	2	+cimport numpy as np
	3	+cimport cython
	4	+
	5	+from collections import deque
	6	+
	7	+from libc.math cimport floor, ceil
	8	+from libcpp.deque cimport deque as cdeque
	9	+
	10	+from cy_my_types cimport image_t, mask_t
	11	+
	12	+@cython.boundscheck(False) # turn of bounds-checking for entire function
	13	+@cython.wraparound(False)
	14	+@cython.nonecheck(False)
	15	+@cython.cdivision(True)
	16	+cdef inline void append_queue(cdeque[int]& stack, int x, int y, int z, int d, int h, int w) nogil:
	17	+ stack.push_back(zhw + y*w + x)
	18	+
	19	+
	20	+@cython.boundscheck(False) # turn of bounds-checking for entire function
	21	+@cython.wraparound(False)
	22	+@cython.nonecheck(False)
	23	+@cython.cdivision(True)
	24	+cdef inline void pop_queue(cdeque[int]& stack, int* x, int* y, int* z, int d, int h, int w) nogil:
	25	+ cdef int i = stack.front()
	26	+ stack.pop_front()
	27	+ x[0] = i % w
	28	+ y[0] = (i / w) % h
	29	+ z[0] = i / (h * w)
	30	+
	31	+
	32	+@cython.boundscheck(False) # turn of bounds-checking for entire function
	33	+def floodfill(np.ndarray[image_t, ndim=3] data, int i, int j, int k, int v, int fill, np.ndarray[mask_t, ndim=3] out):
	34	+
	35	+ cdef int to_return = 0
	36	+ if out is None:
	37	+ out = np.zeros_like(data)
	38	+ to_return = 1
	39	+
	40	+ cdef int x, y, z
	41	+ cdef int w, h, d
	42	+
	43	+ d = data.shape[0]
	44	+ h = data.shape[1]
	45	+ w = data.shape[2]
	46	+
	47	+ stack = [(i, j, k), ]
	48	+ out[k, j, i] = fill
	49	+
	50	+ while stack:
	51	+ x, y, z = stack.pop()
	52	+
	53	+ if z + 1 < d and data[z + 1, y, x] == v and out[z + 1, y, x] != fill:
	54	+ out[z + 1, y, x] = fill
	55	+ stack.append((x, y, z + 1))
	56	+
	57	+ if z - 1 >= 0 and data[z - 1, y, x] == v and out[z - 1, y, x] != fill:
	58	+ out[z - 1, y, x] = fill
	59	+ stack.append((x, y, z - 1))
	60	+
	61	+ if y + 1 < h and data[z, y + 1, x] == v and out[z, y + 1, x] != fill:
	62	+ out[z, y + 1, x] = fill
	63	+ stack.append((x, y + 1, z))
	64	+
	65	+ if y - 1 >= 0 and data[z, y - 1, x] == v and out[z, y - 1, x] != fill:
	66	+ out[z, y - 1, x] = fill
	67	+ stack.append((x, y - 1, z))
	68	+
	69	+ if x + 1 < w and data[z, y, x + 1] == v and out[z, y, x + 1] != fill:
	70	+ out[z, y, x + 1] = fill
	71	+ stack.append((x + 1, y, z))
	72	+
	73	+ if x - 1 >= 0 and data[z, y, x - 1] == v and out[z, y, x - 1] != fill:
	74	+ out[z, y, x - 1] = fill
	75	+ stack.append((x - 1, y, z))
	76	+
	77	+ if to_return:
	78	+ return out
	79	+
	80	+
	81	+@cython.boundscheck(False) # turn of bounds-checking for entire function
	82	+@cython.wraparound(False)
	83	+@cython.nonecheck(False)
	84	+def floodfill_threshold(np.ndarray[image_t, ndim=3] data, list seeds, int t0, int t1, int fill, np.ndarray[mask_t, ndim=3] out):
	85	+
	86	+ cdef int to_return = 0
	87	+ if out is None:
	88	+ out = np.zeros_like(data)
	89	+ to_return = 1
	90	+
	91	+ cdef int x, y, z
	92	+ cdef int w, h, d
	93	+ cdef int xo, yo, zo
	94	+
	95	+ d = data.shape[0]
	96	+ h = data.shape[1]
	97	+ w = data.shape[2]
	98	+
	99	+ stack = deque()
	100	+
	101	+ for i, j, k in seeds:
	102	+ if data[k, j, i] >= t0 and data[k, j, i] <= t1:
	103	+ stack.append((i, j, k))
	104	+ out[k, j, i] = fill
	105	+
	106	+ while stack:
	107	+ x, y, z = stack.pop()
	108	+
	109	+ xo = x
	110	+ yo = y
	111	+ zo = z
	112	+
	113	+ if z + 1 < d and data[z + 1, y, x] >= t0 and data[z + 1, y, x] <= t1 and out[zo + 1, yo, xo] != fill:
	114	+ out[zo + 1, yo, xo] = fill
	115	+ stack.append((x, y, z + 1))
	116	+
	117	+ if z - 1 >= 0 and data[z - 1, y, x] >= t0 and data[z - 1, y, x] <= t1 and out[zo - 1, yo, xo] != fill:
	118	+ out[zo - 1, yo, xo] = fill
	119	+ stack.append((x, y, z - 1))
	120	+
	121	+ if y + 1 < h and data[z, y + 1, x] >= t0 and data[z, y + 1, x] <= t1 and out[zo, yo + 1, xo] != fill:
	122	+ out[zo, yo + 1, xo] = fill
	123	+ stack.append((x, y + 1, z))
	124	+
	125	+ if y - 1 >= 0 and data[z, y - 1, x] >= t0 and data[z, y - 1, x] <= t1 and out[zo, yo - 1, xo] != fill:
	126	+ out[zo, yo - 1, xo] = fill
	127	+ stack.append((x, y - 1, z))
	128	+
	129	+ if x + 1 < w and data[z, y, x + 1] >= t0 and data[z, y, x + 1] <= t1 and out[zo, yo, xo + 1] != fill:
	130	+ out[zo, yo, xo + 1] = fill
	131	+ stack.append((x + 1, y, z))
	132	+
	133	+ if x - 1 >= 0 and data[z, y, x - 1] >= t0 and data[z, y, x - 1] <= t1 and out[zo, yo, xo - 1] != fill:
	134	+ out[zo, yo, xo - 1] = fill
	135	+ stack.append((x - 1, y, z))
	136	+
	137	+ if to_return:
	138	+ return out
	139	+
	140	+
	141	+@cython.boundscheck(False) # turn of bounds-checking for entire function
	142	+@cython.wraparound(False)
	143	+@cython.nonecheck(False)
	144	+def floodfill_auto_threshold(np.ndarray[image_t, ndim=3] data, list seeds, float p, int fill, np.ndarray[mask_t, ndim=3] out):
	145	+
	146	+ cdef int to_return = 0
	147	+ if out is None:
	148	+ out = np.zeros_like(data)
	149	+ to_return = 1
	150	+
	151	+ cdef cdeque[int] stack
	152	+ cdef int x, y, z
	153	+ cdef int w, h, d
	154	+ cdef int xo, yo, zo
	155	+ cdef int t0, t1
	156	+
	157	+ cdef int i, j, k
	158	+
	159	+ d = data.shape[0]
	160	+ h = data.shape[1]
	161	+ w = data.shape[2]
	162	+
	163	+
	164	+ # stack = deque()
	165	+
	166	+ x = 0
	167	+ y = 0
	168	+ z = 0
	169	+
	170	+
	171	+ for i, j, k in seeds:
	172	+ append_queue(stack, i, j, k, d, h, w)
	173	+ out[k, j, i] = fill
	174	+ print i, j, k, d, h, w
	175	+
	176	+ with nogil:
	177	+ while stack.size():
	178	+ pop_queue(stack, &x, &y, &z, d, h, w)
	179	+
	180	+ # print x, y, z, d, h, w
	181	+
	182	+ xo = x
	183	+ yo = y
	184	+ zo = z
	185	+
	186	+ t0 = <int>ceil(data[z, y, x] * (1 - p))
	187	+ t1 = <int>floor(data[z, y, x] * (1 + p))
	188	+
	189	+ if z + 1 < d and data[z + 1, y, x] >= t0 and data[z + 1, y, x] <= t1 and out[zo + 1, yo, xo] != fill:
	190	+ out[zo + 1, yo, xo] = fill
	191	+ append_queue(stack, x, y, z+1, d, h, w)
	192	+
	193	+ if z - 1 >= 0 and data[z - 1, y, x] >= t0 and data[z - 1, y, x] <= t1 and out[zo - 1, yo, xo] != fill:
	194	+ out[zo - 1, yo, xo] = fill
	195	+ append_queue(stack, x, y, z-1, d, h, w)
	196	+
	197	+ if y + 1 < h and data[z, y + 1, x] >= t0 and data[z, y + 1, x] <= t1 and out[zo, yo + 1, xo] != fill:
	198	+ out[zo, yo + 1, xo] = fill
	199	+ append_queue(stack, x, y+1, z, d, h, w)
	200	+
	201	+ if y - 1 >= 0 and data[z, y - 1, x] >= t0 and data[z, y - 1, x] <= t1 and out[zo, yo - 1, xo] != fill:
	202	+ out[zo, yo - 1, xo] = fill
	203	+ append_queue(stack, x, y-1, z, d, h, w)
	204	+
	205	+ if x + 1 < w and data[z, y, x + 1] >= t0 and data[z, y, x + 1] <= t1 and out[zo, yo, xo + 1] != fill:
	206	+ out[zo, yo, xo + 1] = fill
	207	+ append_queue(stack, x+1, y, z, d, h, w)
	208	+
	209	+ if x - 1 >= 0 and data[z, y, x - 1] >= t0 and data[z, y, x - 1] <= t1 and out[zo, yo, xo - 1] != fill:
	210	+ out[zo, yo, xo - 1] = fill
	211	+ append_queue(stack, x-1, y, z, d, h, w)
	212	+
	213	+ if to_return:
	214	+ return out
...	...
...	...	@@ -42,6 +42,8 @@ from skimage import filter
42	42
43	43	from .measures import MeasureData
44	44
	45	+from . import floodfill
	46	+
45	47	import watershed_process
46	48
47	49	import utils
...	...	@@ -1747,6 +1749,92 @@ class ReorientImageInteractorStyle(DefaultInteractorStyle):
1747	1749	buffer_.discard_vtk_image()
1748	1750	buffer_.discard_image()
1749	1751
	1752	+
	1753	+class FlooFillMaskInteractorStyle(DefaultInteractorStyle):
	1754	+ def __init__(self, viewer):
	1755	+ DefaultInteractorStyle.__init__(self, viewer)
	1756	+
	1757	+ self.viewer = viewer
	1758	+ self.orientation = self.viewer.orientation
	1759	+
	1760	+ self.picker = vtk.vtkWorldPointPicker()
	1761	+ self.slice_actor = viewer.slice_data.actor
	1762	+ self.slice_data = viewer.slice_data
	1763	+
	1764	+ self.viewer.slice_.do_threshold_to_all_slices()
	1765	+
	1766	+ self.AddObserver("LeftButtonPressEvent", self.OnFFClick)
	1767	+
	1768	+ def OnFFClick(self, obj, evt):
	1769	+ if (self.viewer.slice_.buffer_slices[self.orientation].mask is None):
	1770	+ return
	1771	+
	1772	+
	1773	+ viewer = self.viewer
	1774	+ iren = viewer.interactor
	1775	+
	1776	+ mouse_x, mouse_y = iren.GetEventPosition()
	1777	+ render = iren.FindPokedRenderer(mouse_x, mouse_y)
	1778	+ slice_data = viewer.get_slice_data(render)
	1779	+
	1780	+ self.picker.Pick(mouse_x, mouse_y, 0, render)
	1781	+
	1782	+ coord = self.get_coordinate_cursor()
	1783	+ position = slice_data.actor.GetInput().FindPoint(coord)
	1784	+
	1785	+ if position != -1:
	1786	+ coord = slice_data.actor.GetInput().GetPoint(position)
	1787	+
	1788	+ if position < 0:
	1789	+ position = viewer.calculate_matrix_position(coord)
	1790	+
	1791	+ x, y, z = self.calcultate_scroll_position(position)
	1792	+ mask = self.viewer.slice_.current_mask.matrix[1:, 1:, 1:]
	1793	+
	1794	+ cp_mask = mask.copy()
	1795	+
	1796	+ floodfill.floodfill_threshold(cp_mask, [[x, y, z]], 0, 1, 254, mask)
	1797	+
	1798	+ viewer.OnScrollBar()
	1799	+
	1800	+ def get_coordinate_cursor(self):
	1801	+ # Find position
	1802	+ x, y, z = self.picker.GetPickPosition()
	1803	+ bounds = self.viewer.slice_data.actor.GetBounds()
	1804	+ if bounds[0] == bounds[1]:
	1805	+ x = bounds[0]
	1806	+ elif bounds[2] == bounds[3]:
	1807	+ y = bounds[2]
	1808	+ elif bounds[4] == bounds[5]:
	1809	+ z = bounds[4]
	1810	+ return x, y, z
	1811	+
	1812	+ def calcultate_scroll_position(self, position):
	1813	+ # Based in the given coord (x, y, z), returns a list with the scroll positions for each
	1814	+ # orientation, being the first position the sagital, second the coronal
	1815	+ # and the last, axial.
	1816	+
	1817	+ if self.orientation == 'AXIAL':
	1818	+ image_width = self.slice_actor.GetInput().GetDimensions()[0]
	1819	+ axial = self.slice_data.number
	1820	+ coronal = position / image_width
	1821	+ sagital = position % image_width
	1822	+
	1823	+ elif self.orientation == 'CORONAL':
	1824	+ image_width = self.slice_actor.GetInput().GetDimensions()[0]
	1825	+ axial = position / image_width
	1826	+ coronal = self.slice_data.number
	1827	+ sagital = position % image_width
	1828	+
	1829	+ elif self.orientation == 'SAGITAL':
	1830	+ image_width = self.slice_actor.GetInput().GetDimensions()[1]
	1831	+ axial = position / image_width
	1832	+ coronal = position % image_width
	1833	+ sagital = self.slice_data.number
	1834	+
	1835	+ return sagital, coronal, axial
	1836	+
	1837	+
1750	1838	def get_style(style):
1751	1839	STYLES = {
1752	1840	const.STATE_DEFAULT: DefaultInteractorStyle,
...	...	@@ -1762,5 +1850,8 @@ def get_style(style):
1762	1850	const.SLICE_STATE_EDITOR: EditorInteractorStyle,
1763	1851	const.SLICE_STATE_WATERSHED: WaterShedInteractorStyle,
1764	1852	const.SLICE_STATE_REORIENT: ReorientImageInteractorStyle,
	1853	+ const.SLICE_STATE_MASK_FFILL: FlooFillMaskInteractorStyle,
1765	1854	}
1766	1855	return STYLES[style]
	1856	+
	1857	+
...	...
...	...	@@ -439,6 +439,9 @@ class Frame(wx.Frame):
439	439	elif id == const.ID_REORIENT_IMG:
440	440	self.OnReorientImg()
441	441
	442	+ elif id == const.ID_FLOODFILL_MASK:
	443	+ self.OnFillHolesManually()
	444	+
442	445	def OnSize(self, evt):
443	446	"""
444	447	Refresh GUI when frame is resized.
...	...	@@ -559,6 +562,9 @@ class Frame(wx.Frame):
559	562	rdlg = dlg.ReorientImageDialog()
560	563	rdlg.Show()
561	564
	565	+ def OnFillHolesManually(self):
	566	+ Publisher.sendMessage('Enable style', const.SLICE_STATE_MASK_FFILL)
	567	+
562	568	# ------------------------------------------------------------------
563	569	# ------------------------------------------------------------------
564	570	# ------------------------------------------------------------------
...	...	@@ -578,7 +584,8 @@ class MenuBar(wx.MenuBar):
578	584	self.enable_items = [const.ID_PROJECT_SAVE,
579	585	const.ID_PROJECT_SAVE_AS,
580	586	const.ID_PROJECT_CLOSE,
581		- const.ID_REORIENT_IMG]
	587	+ const.ID_REORIENT_IMG,
	588	+ const.ID_FLOODFILL_MASK]
582	589	self.__init_items()
583	590	self.__bind_events()
584	591
...	...	@@ -689,6 +696,9 @@ class MenuBar(wx.MenuBar):
689	696	self.clean_mask_menu = mask_menu.Append(const.ID_CLEAN_MASK, _(u"Clean Mask\tCtrl+Shift+A"))
690	697	self.clean_mask_menu.Enable(False)
691	698
	699	+ self.fill_hole_mask_menu = mask_menu.Append(const.ID_FLOODFILL_MASK, _(u"Fill mask holes manually"))
	700	+ self.fill_hole_mask_menu.Enable(False)
	701	+
692	702	tools_menu.AppendMenu(-1, _(u"Mask"), mask_menu)
693	703
694	704	# Image menu
...	...
...	...	@@ -25,6 +25,12 @@ if sys.platform == 'linux2':
25	25	include_dirs=[numpy.get_include()],
26	26	extra_compile_args=['-fopenmp',],
27	27	extra_link_args=['-fopenmp',]),
	28	+
	29	+ Extension("invesalius.data.floodfill", ["invesalius/data/floodfill.pyx"],
	30	+ include_dirs=[numpy.get_include()],
	31	+ extra_compile_args=['-fopenmp',],
	32	+ extra_link_args=['-fopenmp',],
	33	+ language='c++',),
28	34	])
29	35	)
30	36
...	...