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Commit e4dca3a3 authored by Edwin Carlinet's avatar Edwin Carlinet
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Merge branch 'development/extinction' into 'development/ranges' 

Extinction and dynamic filters.

See merge request !80
parents 766beb75 64fee302
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doc/source/figures/morpho/extinction.svg 0 → 100644
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doc/source/figures/morpho/extinction.tex 0 → 100644
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\documentclass[svgnames,tikz]{standalone}
\usepackage{pgfplots}
\begin{document}
\begin{tikzpicture}[yscale=1]
\def\signalA{3,1,4,3,6,4,5,3,4,2,3,3,7,7}
\def\signalB{0,6,0,1,0,1,0,1,0,4,0,0,0,0}
\begin{axis}[
x=1cm,y=1cm,
xmin=0,xmax=14,
ymin=0,ymax=10,
xtick={\empty},ytick={},
]
\end{axis}
\draw[blue] (0,0) foreach[count=\x] \y in \signalA { |- (\x,\y) } -- (\x,0);
\foreach[evaluate=\i as \yA using {{\signalA}[\i]},
evaluate=\i as \yB using {{\signalB}[\i]}] \i in {0,...,13}
{
\draw[red,ultra thick] (\i,\yA) ++(+.5,0) edge[<->] ++(0,\yB);
}
\draw[dashed,red,thin] (4,6) -- (12,6);
\draw[dashed,red,thin] (0,7) -- (12,7);
\end{tikzpicture}
\end{document}
doc/source/figures/morpho/hextrema.svg 0 → 100644
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<path style="fill:none;stroke-width:0.3985;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,100%);stroke-opacity:1;stroke-miterlimit:10;" d="M 0.0016875 -0.00109375 L 0.0016875 85.041875 L 28.345437 85.041875 L 28.345437 170.080937 L 56.693094 170.080937 L 56.693094 141.733281 L 85.04075 141.733281 L 85.04075 198.428594 L 113.388406 198.428594 L 113.388406 85.041875 L 170.079813 85.041875 L 170.079813 113.385625 L 198.427469 113.385625 L 198.427469 141.733281 L 226.775125 141.733281 L 226.775125 226.77625 L 255.122781 226.77625 L 255.122781 141.733281 L 311.814188 141.733281 L 311.814188 226.77625 L 340.161844 226.77625 L 340.161844 141.733281 L 396.857156 141.733281 L 396.857156 85.041875 L 425.200906 85.041875 L 425.200906 28.346562 L 453.548563 28.346562 L 453.548563 -0.00109375 " transform="matrix(1,0,0,-1,16.803,289.995)"/>
</g>
</g>
</svg>
doc/source/figures/morpho/hextrema.tex 0 → 100644
View file @ e4dca3a3
\documentclass[svgnames,tikz]{standalone}
\usepackage{pgfplots}
\begin{document}
\begin{tikzpicture}[yscale=1]
\def\signalA{3,6,5,7,3,3,4,5,8,5,5,8,5,5,3,1}
\def\signalB{3,4,4,4,3,3,4,5,5,5,5,5,5,5,3,1}
\begin{axis}[
x=1cm,y=1cm,
xmin=0,xmax=16,
ymin=0,ymax=10,
xtick={\empty},ytick={},
]
\end{axis}
\draw[fill=gray!40,draw=red] (0,0) foreach[count=\x] \y in \signalB { |- (\x,\y) } -- (\x,0);
\draw[blue] (0,0) foreach[count=\x] \y in \signalA { |- (\x,\y) } -- (\x,0);
\end{tikzpicture}
\end{document}
doc/source/labeling/local_extrema.rst
View file @ e4dca3a3
......@@ -5,20 +5,25 @@ Include :file:`<mln/labeling/local_extrema.hpp>`
.. cpp:namespace:: mln::labeling
#. .. cpp:function:: \
.. cpp:function:: \
template <class Label_t, class I, class N> \
image_ch_value_t<I, Label_t> local_minima(const Image<I>& input, const Neighborhood<N>& nbh, int& nlabel)
#. .. cpp:function:: \
image_ch_value_t<I, Label_t> local_minima(I input, Neighborhood nbh, int& nlabel)
template <class Label_t, class I, class N> \
image_ch_value_t<I, Label_t> local_maxima(const Image<I>& input, const Neighborhood<N>& nbh, int& nlabel)
#. .. cpp:function:: \
image_ch_value_t<I, Label_t> local_maxima(I input, Neighborhood nbh, int& nlabel)
template <class Label_t, class I, class N, class Compare> \
image_ch_value_t<I, Label_t> local_minima(const Image<I>& input, const Neighborhood<N>& nbh, int& nlabel, Compare cmp)
image_ch_value_t<I, Label_t> local_minima(I input, Neighborhood nbh, int& nlabel, Compare cmp)
Labelize the regional minima (1) or maxima (2) of an image with an
optional comparaison function ``cmp`` (3). According to [Soi13]_, a
*regional minimum* `M` of an image `f` at elevation `t` is a connected
component of pixels with the value `t` whose external boundary pixels have
a value strictly greater than `t`. Similarly, a *regional maximum* `M` of an
image `f` at elevation `t` is a connected component of pixels with the value `t`
whose external boundary pixels have a value strictly less than `t`.
Labelize the local minima (1) or maxima (2) of an image with an optional
comparaison function ``cmp`` (3).
:tparam Label_t: The type of label (must be :cpp:concept:`Integral` and
not boolean)
......@@ -42,3 +47,7 @@ Complexity
The algorithm is quasi-linear and requires :math:`n` extra-memory space.
References
----------
.. [Soi13] Soille, P. (2013). Morphological image analysis: principles and applications. Springer Science & Business Media.
doc/source/morpho.rst
View file @ e4dca3a3
......@@ -24,6 +24,8 @@ Geodesic transformations
morpho/opening_by_reconstruction
morpho/area_filter
morpho/dynamic_filter
morpho/extinction_transform
Segmentation
......
doc/source/morpho/dynamic_filter.rst 0 → 100644
View file @ e4dca3a3
Opening and Closing by Dynamic
==============================
Include :file:`<mln/morpho/area_filter.hpp>`
.. cpp:namespace:: mln::morpho
.. cpp:function:: \
Image{I} concrete_t<I> dynamic_opening(I f, Neighborhood nbh, int h)
Image{I} concrete_t<I> dynamic_closing(I f, Neighborhood nbh, int h)
On grayscale images, the dynamic connected opening removes maxima whose
*dynamic* is below a given value where the dynamic stands for the difference
between the lowest and highest value of the component. In [Soi13]_, it
refers to the notion of h-extrema filtering that suppresses all maxima whose
depth is lower or equal to a given threshold level *h*. This is achieved by
performing the reconstruction by dilation of *f* from :math:`f - h`.
.. figure:: /figures/morpho/hextrema.svg
Dynamic opening with a depth *h=3*. The blue function is the original image *f* and is light gray is the opening.
:param f: Input image 𝑓
:param nbh: Elementary structuring element.
:param h: The minimal dynamic to preserve a component
:return: An image whose type is deduced from the input image
:exception: N/A
Notes
-----
Complexity
----------
References
----------
.. [Soi13] Soille, P. (2013). Morphological image analysis: principles and applications. Springer Science & Business Media.
\ No newline at end of file
doc/source/morpho/extinction_transform.rst 0 → 100644
View file @ e4dca3a3
Extinction transform
====================
Include :file:`<mln/morpho/extinction_transform.hpp>`
.. cpp:namespace:: mln::morpho
.. cpp:function:: \
Image{I} concrete_t<I> minima_extinction_transform(I ima, Neighborhood nbh)
Image{I} concrete_t<I> maxima_extinction_transform(I ima, Neighborhood nbh)
The notion of *extinction* of a local extremum is based on the h-extrema (see. :doc:`dynamic_filter`).
The extinction value of a bassin corresponds its *dynamic* when it merges with another basin.
By definition, the lowest image minima / highest image maxima, have an *extinction* equal to the difference
between the highest and lowest image grey scale values.
Let Mₜ be a regional maximum at level *t* of an image *f*, and 𝓟 any path
linking a pixel *p* of Mₜ to a pixel *q* of a regional maximum Mₜ' higher
than Mₜ. In [Soi13]_, its *extinction* of Mₜ is defined as:
.. math::
\min_{\mathcal{P} = \{p, \cdots, q\}} \left\{ \max_{x \in \mathcal{P}} (f(p) - f(x)) \right\}
.. note::
Pixels that do not belong to a local extremum are set to 0.
.. figure:: /figures/morpho/extinction.svg
Extinction transform of a 1D signal. Red arrows show the extinction value of each minima.
:param f: Input image 𝑓
:param nbh: Elementary structuring element.
:return: An image whose type is deduced from the input image
:exception: N/A
Notes
-----
Complexity
----------
References
----------
.. [Soi13] Soille, P. (2013). Morphological image analysis: principles and applications. Springer Science & Business Media.
\ No newline at end of file
pylene/include/mln/morpho/experimental/area_filter.hpp
View file @ e4dca3a3
......@@ -40,7 +40,11 @@ namespace mln::morpho::experimental
void on_make_set(P p) noexcept { m_count(p) = 1; }
void on_union(P p, P q) noexcept { m_count(q) += m_count(p); }
P on_union(dontcare_t, P rp, dontcare_t, P rq) noexcept
{
m_count(rp) += m_count(rq);
return rp;
}
void on_finish(P p, P root) noexcept { m_ima(p) = m_ima(root); }
......@@ -85,22 +89,22 @@ namespace mln::morpho::experimental
impl::area_opening_inplace(out, nbh, area, std::move(cmp));
return out;
}
}
template <class InputImage, class N>
image_concrete_t<std::remove_reference_t<InputImage>> //
area_closing(InputImage&& ima, const N& nbh, int area)
{
using I = std::remove_reference_t<InputImage>;
template <class InputImage, class N>
image_concrete_t<std::remove_reference_t<InputImage>> //
area_closing(InputImage&& ima, const N& nbh, int area)
{
using I = std::remove_reference_t<InputImage>;
static_assert(mln::is_a<I, mln::experimental::Image>());
static_assert(mln::is_a<N, mln::experimental::Neighborhood>());
static_assert(mln::is_a<I, mln::experimental::Image>());
static_assert(mln::is_a<N, mln::experimental::Neighborhood>());
mln_entering("mln::morpho::area_closing");
image_concrete_t<I> out = clone(ima);
impl::area_opening_inplace(out, nbh, area, std::greater<image_value_t<I>>());
mln_entering("mln::morpho::area_closing");
image_concrete_t<I> out = clone(ima);
impl::area_opening_inplace(out, nbh, area, std::greater<image_value_t<I>>());
return out;
}
return out;
}
} // namespace mln::moprho::experimental
pylene/include/mln/morpho/experimental/canvas/unionfind.hpp
View file @ e4dca3a3
......@@ -22,10 +22,15 @@ namespace mln::morpho::experimental::canvas
void on_make_set([[maybe_unused]] ignore_t p) {}
/// \brief Called during the merge-step.
/// It returns the new root of the component (either p or q).
///
/// Called when a component rooted in \p p merges with a
/// component rooted in \p q, \p q becomes the new root.
void on_union([[maybe_unused]] ignore_t p, [[maybe_unused]] ignore_t q) {}
/// Called when a component rooted in \p p merges with a component rooted in \p q through the point \p x.
/// The component rooted in p is the last that has been updated (it is initially the current point being process).
///
/// IF YOU WANT THE ROOT TO BE A POINT THAT HAS THE MINIMUM VALUE OF THE COMPONENT: RETURN p (it is usually what you
/// want). You want the root to be defined in another way (e.g. to a local maximum or using a rank criterion)
ignore_t on_union([[maybe_unused]] ignore_t p, [[maybe_unused]] ignore_t rp,
[[maybe_unused]] ignore_t q, [[maybe_unused]] ignore_t rq) { return {}; }
/// \brief Called at the end of the algorithm for each point
///
......@@ -103,34 +108,37 @@ namespace mln::morpho::experimental::canvas
// Forward pass
{
mln_entering("Uniion-find forward pass");
mln_entering("Union-find forward pass");
for (auto p : ::ranges::view::reverse(S))
{
par(p) = p;
viz.on_make_set(p);
status(p) = static_cast<ufstatus>(viz.test(p));
auto rp = p;
ufstatus st = static_cast<ufstatus>(viz.test(p));
for (auto n : nbh(p))
{
if (status.at(n) == ufstatus::NONE) // Out-of-range neighbor
continue;
auto r = zfindroot(par, n);
if (p == r) // Already the root
auto rn = zfindroot(par, n);
if (rn == rp) // Already the root
continue;
if (status(r) == ufstatus::PASS) // Merging with a PASS component => so PASS
{
status(p) = ufstatus::PASS;
}
else
// Merging with a PASS component => so PASS (no need to merge)
if (status(rn) == ufstatus::PASS)
{
par(r) = p;
viz.on_union(r, p);
st = ufstatus::PASS;
continue;
}
auto new_root = viz.on_union(p, rp, n, rn);
par(rp) = new_root;
par(rn) = new_root;
rp = new_root;
}
if (status(p) == ufstatus::FAIL && viz.test(p))
status(p) = ufstatus::PASS;
status(p) = static_cast<ufstatus>((bool)(st) || (bool)(viz.test(p)));
}
}
......
pylene/include/mln/morpho/experimental/dynamic_filter.hpp 0 → 100644
View file @ e4dca3a3
#pragma once
#include <mln/core/concept/new/images.hpp>
#include <mln/core/concept/new/neighborhoods.hpp>
#include <mln/morpho/experimental/canvas/unionfind.hpp>
namespace mln::morpho::experimental
{
/// \brief Compute the dynamic algebraic opening of an image.
///
/// Also called h-maxima transformation. The dynamic represents the difference between the maximum and the minimum of
/// the connected component.
///
/// \param ima The input image
/// \param nbh The neighborhood
/// \param area The grain size
/// \param cmp A strict total ordering on values
template <class I, class N, class Compare = std::less<image_value_t<std::remove_reference_t<I>>>>
image_concrete_t<std::remove_reference_t<I>> //
dynamic_opening(I&& ima, const N& nbh, int dynamic, Compare cmp = {});
/// \brief Compute the dynamic algebraic closing of an image.
///
/// Also called h-minima transformation. The dynamic represents the difference between the maximum and the minimum of
/// the connected component.
///
/// \param ima The input image
/// \param nbh The neighborhood
/// \param area The grain size
template <class I, class N>
image_concrete_t<std::remove_reference_t<I>> //
dynamic_closing(I&& ima, const N& nbh, int dynamic);
/******************************/
/*** Implementation **/
/******************************/
namespace impl
{
template <class I, class Compare>
struct dynamic_filter_ufind_visitor
{
using P = image_point_t<I>;
void on_make_set(P p) noexcept { m_max(p) = m_ima(p); }
void on_finish(P p, P root) noexcept { m_ima(p) = m_ima(root); }
bool test(P p) const noexcept { return std::abs(m_max(p) - m_ima(p)) >= m_dynamic; }
P on_union(dontcare_t, P rp, dontcare_t, P rq) noexcept
{
auto a = m_max(rp);
auto b = m_max(rq);
m_max(rp) = m_cmp(a,b) ? b : a;
return rp;
}
dynamic_filter_ufind_visitor(I& input, Compare cmp, int dynamic)
: m_ima(input)
, m_cmp(cmp)
, m_dynamic(dynamic)
{
m_max = imconcretize(input);
}
private:
I& m_ima;
Compare m_cmp;
int m_dynamic;
image_concrete_t<I> m_max;
};
template <class I, class N, class Compare>
void dynamic_opening_inplace(I& ima, const N& nbh, int dynamic, Compare cmp)
{
dynamic_filter_ufind_visitor viz(ima, cmp, dynamic);
mln::morpho::experimental::canvas::union_find(ima, nbh, viz, cmp);
}
}
template <class InputImage, class N, class Compare>
image_concrete_t<std::remove_reference_t<InputImage>> //
dynamic_opening(InputImage&& ima, const N& nbh, int dynamic, Compare cmp)
{
using I = std::remove_reference_t<InputImage>;
static_assert(mln::is_a<I, mln::experimental::Image>());
static_assert(mln::is_a<N, mln::experimental::Neighborhood>());
mln_entering("mln::morpho::dynamic_opening");
image_concrete_t<I> out = clone(ima);
impl::dynamic_opening_inplace(out, nbh, dynamic, std::move(cmp));
return out;
}
template <class InputImage, class N>
image_concrete_t<std::remove_reference_t<InputImage>> //
dynamic_closing(InputImage&& ima, const N& nbh, int dynamic)
{
using I = std::remove_reference_t<InputImage>;
static_assert(mln::is_a<I, mln::experimental::Image>());
static_assert(mln::is_a<N, mln::experimental::Neighborhood>());
mln_entering("mln::morpho::dynamic_closing");
image_concrete_t<I> out = clone(ima);
impl::dynamic_opening_inplace(out, nbh, dynamic, std::greater<image_value_t<I>>());
return out;
}
} // namespace mln::moprho::experimental
pylene/include/mln/morpho/experimental/extinction_transform.hpp 0 → 100644
View file @ e4dca3a3
#pragma once
#include <mln/core/concept/new/images.hpp>
#include <mln/core/concept/new/neighborhoods.hpp>
#include <mln/core/trace.hpp>
#include <mln/morpho/experimental/canvas/unionfind.hpp>
namespace mln::morpho::experimental
{
/// \brief Compute the dynamic algebraic opening of an image.
///
/// Also called h-maxima transformation
///
/// \param ima The input image
/// \param nbh The neighborhood
/// \param area The grain size
/// \param cmp A strict total ordering on values
template <class I, class N>
image_concrete_t<std::remove_reference_t<I>> //
maxima_extinction_transform(I&& ima, const N& nbh);
template <class I, class N>
image_concrete_t<std::remove_reference_t<I>> //
minima_extinction_transform(I&& ima, const N& nbh);
/******************************/
/*** Implementation **/
/******************************/