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synced 2026-07-09 12:18:54 +08:00
Introduced the connectivity parameter, regrouped some code
This commit is contained in:
Matěj Týč
+111
-75
@@ -267,19 +267,49 @@ cdef inline void join_trees(DTYPE_t *forest, DTYPE_t n, DTYPE_t m):
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set_root(forest, m, root)
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def _norm_connectivity(connectivity, ndim):
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"""
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Takes the value of the connectivity parameter, validates it and converts
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it to a value that the subsequent algorithm may use as-is safely.
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Parameters
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----------
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connectivity : int
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The following should be true: -ndim < connectivity < 0, or
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0 < connectivity <= ndim.
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Returns
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-------
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connectivity : int
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Connectivity, 0 < connectivity < ndim
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"""
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if connectivity == 0 or connectivity > ndim:
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raise ValueError(
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"Connectivity of 0 or above %d doesn't make sense" % ndim)
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res = connectivity
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if res < 0:
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res = res % ndim
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# we want -1 to be normed to ndim, -2 to (ndim - 1) etc.
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res += 1
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return res
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# Connected components search as described in Fiorio et al.
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def label(input, DTYPE_t neighbors=8, background=None, return_num=False):
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def label(input, DTYPE_t neighbors=8, background=None, return_num=False,
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connectivity=None):
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"""Label connected regions of an integer array.
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Two pixels are connected when they are neighbors and have the same value.
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They can be neighbors either in a 4- or 8-connected sense::
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In 2D, they can be neighbors either in a 1- or 2-connected sense.
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The value refers to the greatest number of orthogonal hops between the
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starting point and the neighbor.
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4-connectivity 8-connectivity
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1-connectivity 2-connectivity
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[ ] [ ] [ ] [ ]
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| \ | /
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[ ]--[ ]--[ ] [ ]--[ ]--[ ]
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| / | \\
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[ ] [ ] [ ] [ ] [ ]
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| \\ | / | <- hop 2
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[ ]--[x]--[ ] [ ]--[x]--[ ] [x]--[ ]
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| / | \\ hop 1
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[ ] [ ] [ ] [ ]
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Parameters
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@@ -290,12 +320,21 @@ def label(input, DTYPE_t neighbors=8, background=None, return_num=False):
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Whether to use 4- or 8-connectivity.
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In 3D, 4-connectivity means connected pixels have to share face,
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whereas with 8-connectivity, they have to share only edge or vertex.
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**Depreceated, use ``connectivity`` instead.**
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background : int, optional
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Consider all pixels with this value as background pixels, and label
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them as -1. (Note: background pixels will be labeled as 0 starting with
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version 0.12).
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return_num : bool, optional
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Whether to return the number of assigned labels.
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connectivity : int
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Number of orthogonal hops
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For the 2D case, 1 considers horizontal and vertical neighbors, whereas
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2 adds the diagonals (you hop once vertically and once horizontally).
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1 is the lowest value of connection (4 neighbors in 2D, 6 in 3D).
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Moreover, the value of -1 specifies the highest connectivity available.
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So for example in 2D, -1 is equivalent of 2, resulting in considering
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all 8 neighbors.
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Returns
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-------
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@@ -352,15 +391,32 @@ def label(input, DTYPE_t neighbors=8, background=None, return_num=False):
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get_shape_info(input.shape, &shapeinfo)
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get_bginfo(background, &bg)
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if neighbors != 4 and neighbors != 8:
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raise ValueError('Neighbors must be either 4 or 8.')
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if neighbors is None and connectivity is None:
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# Pure default
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connectivity = -1
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elif neighbors is not None:
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# Pure fail
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if neighbors != 4 and neighbors != 8:
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msg = "Neighbors must be either 4 or 8, got '%d'.\n" % neighbors
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msg += "Moreover, this arg is depreceated, use 'connectivity' instead"
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raise ValueError(msg)
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else:
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# backwards-compatible neighbors recalc to connectivity,
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# depreciation warning
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nei2conn = {4: 1, 8: -1}
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connectivity = nei2conn[neighbors]
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msg = "Argument 'neighbors' is depreceated, use 'connectivity' "
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msg += "instead. Its coresponing value is likely '%d'" % connectivity
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DeprecationWarning(msg)
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scanBG(data_p, forest_p, & shapeinfo, & bg)
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scan3D(data_p, forest_p, & shapeinfo, & bg, neighbors)
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connectivity = _norm_connectivity(connectivity, shapeinfo.ndim)
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scanBG(data_p, forest_p, &shapeinfo, &bg)
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scan3D(data_p, forest_p, &shapeinfo, &bg, connectivity)
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# Label output
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cdef DTYPE_t ctr
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ctr = resolve_labels(data_p, forest_p, & shapeinfo, & bg)
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ctr = resolve_labels(data_p, forest_p, &shapeinfo, &bg)
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# Work around a bug in ndimage's type checking on 32-bit platforms
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if data.dtype == np.int32:
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@@ -429,12 +485,12 @@ cdef void scanBG(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# D E
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#
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# So if I am in the point E and want to take a look to A, I take the index of
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# E and add shapeinfo.Dea to it and teg the index of A.
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# E and add shapeinfo.DEX[D_ea] to it and get the index of A.
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# The 1D indices are "raveled" or "linear", that's where "rindex" comes from.
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cdef void scan1D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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bginfo *bg, DTYPE_t neighbors, DTYPE_t y, DTYPE_t z):
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bginfo *bg, DTYPE_t connectivity, DTYPE_t y, DTYPE_t z):
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"""
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Perform forward scan on a 1D object, usually the first row of an image
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"""
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@@ -455,13 +511,13 @@ cdef void scan1D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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bginfo *bg, DTYPE_t neighbors, DTYPE_t z):
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bginfo *bg, DTYPE_t connectivity, DTYPE_t z):
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"""
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Perform forward scan on a 2D array.
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"""
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cdef DTYPE_t x, y, rindex, bgval = bg.background_val
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cdef INTS_t *DEX = shapeinfo.DEX
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scan1D(data_p, forest_p, shapeinfo, bg, neighbors, 0, z)
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scan1D(data_p, forest_p, shapeinfo, bg, connectivity, 0, z)
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for y in range(1, shapeinfo.y):
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rindex = shapeinfo.ravel_index(0, y, 0, shapeinfo)
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# Handle the first column
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@@ -470,7 +526,7 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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if neighbors == 8:
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if connectivity >= 2:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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# Handle the rest of columns
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@@ -483,27 +539,24 @@ cdef void scan2D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# Nothing to do if we are background
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continue
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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if neighbors == 8:
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if connectivity >= 2:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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bginfo *bg, DTYPE_t neighbors):
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bginfo *bg, DTYPE_t connectivity):
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"""
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Perform forward scan on a 2D array.
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"""
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cdef DTYPE_t x, y, z, rindex, bgval = bg.background_val
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cdef INTS_t *DEX = shapeinfo.DEX
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# Handle first plane
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scan2D(data_p, forest_p, shapeinfo, bg, neighbors, 0)
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scan2D(data_p, forest_p, shapeinfo, bg, connectivity, 0)
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for z in range(1, shapeinfo.z):
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# Handle first row in 3D manner
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rindex = shapeinfo.ravel_index(0, 0, z, shapeinfo)
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@@ -513,10 +566,11 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# Now we have pixels below
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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if connectivity >= 2:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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if connectivity >= 3:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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for x in range(1, shapeinfo.x):
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rindex += 1
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@@ -525,22 +579,18 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# Nothing to do if we are background
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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if connectivity >= 2:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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if connectivity >= 3:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex,
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DEX[D_en])
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for y in range(1, shapeinfo.y):
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rindex = shapeinfo.ravel_index(0, y, z, shapeinfo)
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@@ -549,20 +599,20 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# Nothing to do if we are background
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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if connectivity >= 2:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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if y + 1 < shapeinfo.y:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_en])
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if connectivity >= 3:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
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if y + 1 < shapeinfo.y:
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join_trees_wrapper(data_p, forest_p, rindex,
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DEX[D_en])
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# Handle the rest of columns
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for x in range(1, shapeinfo.x):
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@@ -571,39 +621,25 @@ cdef void scan3D(DTYPE_t *data_p, DTYPE_t *forest_p, shape_info *shapeinfo,
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# Nothing to do if we are background
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continue
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eb])
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if neighbors == 8:
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ed])
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# Now pixels below:
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if neighbors == 8:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ej])
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if neighbors == 8:
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if connectivity >= 2:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ea])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eg])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ei])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ec])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ek])
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if y + 1 < shapeinfo.y:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_em])
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if connectivity >= 3:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_ef])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p,
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rindex, DEX[D_en])
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_eh])
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if y + 1 < shapeinfo.y:
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join_trees_wrapper(data_p, forest_p, rindex, DEX[D_el])
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if x + 1 < shapeinfo.x:
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join_trees_wrapper(data_p, forest_p,
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rindex, DEX[D_en])
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