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Commit 339d6e2f authored by Baptiste Esteban's avatar Baptiste Esteban
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Merge branch 'development/fix-canonization' into 'next' 

Fix canonization of the alphatree and watershed hierarchy

See merge request !124
parents 7be565cb c65ff69c
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doc/source/conf.py
View file @ 339d6e2f
......@@ -99,13 +99,8 @@ pygments_style = 'sphinx'
# a list of builtin themes.
html_theme = 'sphinx_rtd_theme'
html_context = {
'css_files': [
'_static/code.css',
'_static/theme_overrides.css', # override wide tables in RTD theme
],
}
html_static_path = ['_static']
html_css_files = ['code.css', 'theme_overrides.css']
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
......
doc/source/morpho/component_tree.rst
View file @ 339d6e2f
......@@ -148,15 +148,16 @@ A :cpp:class:`component_tree` `t` has the following methods.
.. cpp:namespace-push:: template <class V> component_tree
.. cpp:function:: auto compute_attribute_on_points(Image node_map, Accumulator accu) const
auto compute_attribute_on_values(Image node_map, Image values, Accumulator accu) const
auto compute_attribute_on_pixels(Image node_map, Image values, Accumulator accu) const
.. cpp:function:: auto compute_attribute_on_points(Image node_map, Accumulator accu, bool propagate) const
auto compute_attribute_on_values(Image node_map, Image values, Accumulator accu, bool propagate) const
auto compute_attribute_on_pixels(Image node_map, Image values, Accumulator accu, bool propagate) const
Accumulate the points of each component.
:param node_map: An image thats maps: point -> node id
:param values: An image where values to accumlate are taken from
:param accu: The feature to compute
:param propagate: Option to propagate the values to the parent (default: true)
:return: A vector mapping for each node the result of accumulation.
......
doc/source/morpho/multivariate_component_tree.rst
View file @ 339d6e2f
......@@ -44,26 +44,6 @@ This example computes a grain filter, which removes all the node having an area
// Function to get the median of the border values
mln::rgb8 get_median_on_border(mln::image2d<mln::rgb8> ima);
// Accumulator to compute the mean of the pixel values of each node, without taking into account the values of the holes
struct mean_node_accu : mln::Accumulator<mean_node_accu>
{
using result_type = decltype(std::declval<mln::rgb8>() + std::declval<mln::rgb8>());
public:
void take(const mln::rgb8& v)
{
m_sum += v;
m_count++;
}
void take(const mean_node_accu&) {}
result_type to_result() const { return m_count > 1 ? static_cast<result_type>(m_sum / m_count) : m_sum; }
private:
result_type m_sum = {0, 0, 0};
int m_count = 0;
};
int main(void)
{
mln::image2d<mln::rgb8> ima;
......@@ -92,7 +72,7 @@ This example computes a grain filter, which removes all the node having an area
t.filter(mln::morpho::CT_FILTER_DIRECT, nm, [&area](int n) { return area[n] >= 100; });
// Compute the mean of the connected component of each nodes
auto mean = t.compute_attribute_on_values(nm, ima, mean_node_accu());
auto mean = t.compute_attribute_on_values(nm, ima, mln::accu::features::mean<>(), false);
// Reconstruct the tree
auto rec = t.reconstruct_from(nm, ranges::make_span(mean.data(), mean.size()));
......
doc/source/snippets/mtos_example.cpp
View file @ 339d6e2f
#include <mln/accu/accumulators/count.hpp>
#include <mln/accu/accumulators/max.hpp>
#include <mln/accu/accumulators/mean.hpp>
#include <mln/core/algorithm/accumulate.hpp>
#include <mln/core/colors.hpp>
#include <mln/core/extension/padding.hpp>
......@@ -20,26 +21,6 @@
namespace
{
struct mean_node_accu : mln::Accumulator<mean_node_accu>
{
using result_type = decltype(std::declval<mln::rgb8>() + std::declval<mln::rgb8>());
public:
void take(const mln::rgb8& v)
{
m_sum += v;
m_count++;
}
void take(const mean_node_accu&) {}
result_type to_result() const { return m_count > 1 ? static_cast<result_type>(m_sum / m_count) : m_sum; }
private:
result_type m_sum = {0, 0, 0};
int m_count = 0;
};
mln::rgb8 get_median_on_border(mln::image2d<mln::rgb8> ima)
{
std::vector<mln::rgb8> border;
......@@ -134,7 +115,7 @@ int main(int argc, char* argv[])
auto area = t.compute_attribute_on_points(nm, mln::accu::accumulators::count<int>());
t.filter(mln::morpho::CT_FILTER_DIRECT, nm, [&area](int n) { return area[n] >= 100; });
auto mean = t.compute_attribute_on_values(nm, ima, mean_node_accu());
auto mean = t.compute_attribute_on_values(nm, ima, mln::accu::features::mean<>(), false);
auto rec = t.reconstruct_from(nm, ranges::make_span(mean.data(), mean.size()));
mln::io::imsave(mln::view::cast<mln::rgb8>(rec), argv[3]);
......
pylene/include/mln/morpho/alphatree.hpp
View file @ 339d6e2f
......@@ -16,7 +16,6 @@
#include <range/v3/functional/concepts.hpp>
namespace mln::morpho
{
......@@ -237,14 +236,12 @@ namespace mln::morpho
return node_count;
}
template <class W>
template <class W, class I>
std::pair<std::vector<int>, std::vector<W>> canonize_component_tree(const std::vector<int>& par, //
const std::vector<W>& levels, //
std::size_t node_count, //
std::size_t nb_leaves)
I node_map
)
{
assert(node_count >= nb_leaves);
std::vector<int> canonized_par;
std::vector<W> canonized_levels;
......@@ -253,16 +250,13 @@ namespace mln::morpho
canonized_par.push_back(0);
canonized_levels.push_back(levels[0]);
std::vector<int> translation_map(node_count);
std::vector<int> translation_map(par.size());
translation_map[0] = 0;
int count = 1;
std::size_t begin_leaves = node_count - nb_leaves;
// Build canonized component tree
for (std::size_t i = 1; i < begin_leaves; ++i)
for (std::size_t i = 1; i < par.size(); ++i)
{
if (levels[i] != levels[par[i]]) // Keep the node: Update tree
{
......@@ -274,12 +268,7 @@ namespace mln::morpho
translation_map[i] = translation_map[par[i]];
}
for (std::size_t i = begin_leaves; i < node_count; ++i)
{
translation_map[i] = count++;
canonized_par.push_back(translation_map[par[i]]);
canonized_levels.push_back(levels[i]);
}
mln::for_each(node_map, [&translation_map, node_count=par.size()](int& id) { id = translation_map[static_cast<int>(node_count) - id - 1]; });
return {canonized_par, canonized_levels};
}
......@@ -298,20 +287,19 @@ namespace mln::morpho
// Parent / levels are ordered from leaves to root, we need to reverse
internal::alphatree_reorder_nodes(par.data(), levels.data(), node_count);
component_tree<W> t;
if (canonize_tree)
{
auto [canonized_par, canonized_levels] = internal::canonize_component_tree(par, levels, node_count, nb_leaves);
par = canonized_par;
levels = canonized_levels;
auto [canonized_par, canonized_levels] = internal::canonize_component_tree(par, levels, node_map);
t.parent = std::move(canonized_par);
t.values = std::move(canonized_levels);
}
component_tree<W> t;
t.parent = par;
t.values = levels;
node_count = t.parent.size();
// Update the node map according to the component tree representation
else
{
t.parent = std::move(par);
t.values = std::move(levels);
mln::for_each(node_map, [node_count](int& id) { id = static_cast<int>(node_count) - id - 1; });
}
return {std::move(t), std::move(node_map)};
}
......
pylene/include/mln/morpho/component_tree.hpp
View file @ 339d6e2f
......@@ -88,9 +88,10 @@ namespace mln::morpho
/// \param node_map Image point -> node_id mapping
/// \param values Image point -> value mapping
/// \param acc Accumulator to apply on values
/// \param propagate Boolean to propagate the values to the parent
template <class I, class J, class Accu>
std::vector<typename accu::result_of<Accu, image_value_t<J>>::type> //
compute_attribute_on_values(I node_map, J values, Accu acc) const;
compute_attribute_on_values(I node_map, J values, Accu acc, bool propagate = true) const;
/// \brief Compute attribute on values
///
......@@ -99,9 +100,10 @@ namespace mln::morpho
/// \param node_map Image point -> node_id mapping
/// \param values Image point -> value mapping
/// \param acc Accumulator to apply on points
/// \param propagate Boolean to propagate the values to the parent
template <class I, class Accu>
std::vector<typename accu::result_of<Accu, image_point_t<I>>::type> //
compute_attribute_on_points(I node_map, Accu acc) const;
compute_attribute_on_points(I node_map, Accu acc, bool propagate = true) const;
/// \brief Compute attribute on pixels
......@@ -111,9 +113,10 @@ namespace mln::morpho
/// \param node_map Image point -> node_id mapping
/// \param values Image point -> value mapping
/// \param acc Accumulator to apply on values
/// \param propagate Boolean to propagate the values to the parent
template <class I, class J, class Accu>
std::vector<typename accu::result_of<Accu, image_pixel_t<J>>::type> //
compute_attribute_on_pixels(I node_map, J values, Accu acc) const;
compute_attribute_on_pixels(I node_map, J values, Accu acc, bool propagate = true) const;
/// \brief Compute the horizontal cut of a hierarchie at level `threshold` and return a nodemap
/// valued with the node indices of the lowest nodes satisfying levels[n] > threshold
......@@ -297,7 +300,7 @@ namespace mln::morpho
template <class I, class Accu>
std::vector<typename accu::result_of<Accu, image_point_t<I>>::type>
component_tree<void>::compute_attribute_on_points(I node_map, Accu acc) const
component_tree<void>::compute_attribute_on_points(I node_map, Accu acc, bool propagate) const
{
mln_entering("mln::morpho::component_tree::compute_attribute_on_points");
......@@ -313,12 +316,13 @@ namespace mln::morpho
mln_foreach (auto px, node_map.pixels())
attr[px.val()].take(px.point());
const std::size_t n = parent.size();
if (propagate)
{
// Propgate to parent
std::size_t n = parent.size();
for (std::size_t i = n - 1; i > 0; --i)
attr[parent[i]].take(attr[i]);
}
// Extract values
std::vector<R> out(n);
......@@ -330,7 +334,7 @@ namespace mln::morpho
template <class I, class J, class Accu>
std::vector<typename accu::result_of<Accu, image_value_t<J>>::type> //
component_tree<void>::compute_attribute_on_values(I node_map, J input, Accu acc) const
component_tree<void>::compute_attribute_on_values(I node_map, J input, Accu acc, bool propagate) const
{
mln_entering("mln::morpho::component_tree::compute_attribute_on_values");
......@@ -347,12 +351,13 @@ namespace mln::morpho
mln_foreach ((auto [node_id, val]), zz.values())
attr[node_id].take(val);
const std::size_t n = parent.size();
if (propagate)
{
// Propgate to parent
std::size_t n = parent.size();
for (std::size_t i = n - 1; i > 0; --i)
attr[parent[i]].take(attr[i]);
}
// Extract values
std::vector<R> out(n);
......@@ -364,7 +369,7 @@ namespace mln::morpho
template <class I, class J, class Accu>
std::vector<typename accu::result_of<Accu, image_pixel_t<J>>::type> //
component_tree<void>::compute_attribute_on_pixels(I node_map, J values, Accu acc) const
component_tree<void>::compute_attribute_on_pixels(I node_map, J values, Accu acc, bool propagate) const
{
mln_entering("mln::morpho::component_tree::compute_attribute_on_pixels");
......@@ -380,12 +385,13 @@ namespace mln::morpho
mln_foreach (auto px, values.pixels())
attr[node_map(px.point())].take(px);
const std::size_t n = parent.size();
if (propagate)
{
// Propgate to parent
std::size_t n = parent.size();
for (std::size_t i = n - 1; i > 0; --i)
attr[parent[i]].take(attr[i]);
}
// Extract values
std::vector<R> out(n);
......
tests/morpho/watershed_hierarchy.cpp
View file @ 339d6e2f
......@@ -87,11 +87,8 @@ TEST(Morpho, AreaWatershedHierarchyGray)
{121, 112, 121, 112, 163}, //
};
std::vector<int> expected_parent = {0, 0, 1, 1, 0, 4, 5, 6, 7, 1, 9, 10, 2, 8, 12,
14, 15, 16, 2, 14, 3, 20, 17, 18, 3, 24, 21, 22, 14};
std::vector<unsigned long> expected_values = {6, 3, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 1, 1, 0, 1, 2, 2, 3, 3};
std::vector<unsigned long> expected_values = {6, 3, 2, 2, 0, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
......@@ -121,16 +118,12 @@ TEST(Morpho, DynamicWatershedHierarchyGray)
{121, 112, 121, 112, 163}, //
};
std::vector<int> expected_parent = {0, 0, 1, 0, 3, 4, 5, 6, 1, 8, 9, 2, 7, 11, 13,
14, 15, 1, 13, 2, 19, 16, 17, 0, 23, 20, 21, 13};
std::vector<unsigned long> expected_values = {70, 38, 29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 1, 0, 1, 2, 1, 2, 0};
std::vector<unsigned long> expected_values = {70, 38, 29, 0, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
mln::morpho::WatershedAttribute::DYNAMIC,
mln::c4, [](const auto& a, const auto& b) -> float { return mln::functional::l2dist(a, b); });
input, mln::morpho::WatershedAttribute::DYNAMIC, mln::c4,
[](const auto& a, const auto& b) -> float { return mln::functional::l2dist(a, b); });
ASSERT_EQ(expected_parent.size(), tree.parent.size());
ASSERT_EQ(expected_values.size(), tree.values.size());
......@@ -153,15 +146,12 @@ TEST(Morpho, HeightWatershedHierarchyGray)
{121, 112, 121, 112, 163}, //
};
std::vector<int> expected_parent = {0, 0, 1, 0, 3, 4, 5, 6, 1, 8, 9, 2, 7, 11, 13, 14, 15, 1, 13, 2, 19, 16, 17, 0, 23, 20, 21, 13};
std::vector<unsigned long> expected_values = {70, 38, 29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 1, 0, 1, 2, 1, 2, 0};
std::vector<unsigned long> expected_values = {70, 38, 29, 0, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
mln::morpho::WatershedAttribute::HEIGHT,
mln::c4, [](const auto& a, const auto& b) -> float { return mln::functional::l2dist(a, b); });
input, mln::morpho::WatershedAttribute::HEIGHT, mln::c4,
[](const auto& a, const auto& b) -> float { return mln::functional::l2dist(a, b); });
ASSERT_EQ(expected_parent.size(), tree.parent.size());
ASSERT_EQ(expected_values.size(), tree.values.size());
......@@ -184,11 +174,8 @@ TEST(Morpho, AreaWatershedHierarchyGrayHQ)
{121, 112, 121, 112, 163}, //
};
std::vector<int> expected_parent = {0, 0, 1, 1, 0, 4, 5, 6, 7, 1, 9, 10, 2, 8, 12,
14, 15, 16, 2, 14, 3, 20, 17, 18, 3, 24, 21, 22, 14};
std::vector<unsigned long> expected_values = {6, 3, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 1, 1, 0, 1, 2, 2, 3, 3};
std::vector<unsigned long> expected_values = {6, 3, 2, 2, 0, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
......@@ -218,11 +205,8 @@ TEST(Morpho, AreaWatershedHierarchyRGB)
{{255, 75, 0}, {31, 174, 0}, {255, 75, 0}, {31, 174, 0}, {255, 146, 0}}, //
};
std::vector<int> expected_parent = {0, 0, 0, 0, 3, 2, 5, 6, 3, 4, 3, 3, 7, 3,
9, 12, 12, 16, 3, 1, 19, 2, 5, 1, 23, 20, 21, 26};
std::vector<unsigned long> expected_values = {3, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 0, 0, 2, 1, 2, 1};
std::vector<unsigned long> expected_values = {3, 2, 2, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
......@@ -252,11 +236,8 @@ TEST(Morpho, AreaWatershedHierarchyGrayC8)
{107, 73, 125, 157, 117}, //
};
std::vector<int> expected_parent = {0, 0, 0, 0, 1, 3, 2, 3, 1, 4, 6, 5, 7, 8, 9,
2, 11, 4, 13, 4, 5, 15, 21, 17, 19, 5, 21, 22, 17, 23};
std::vector<unsigned long> expected_values = {7, 3, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 0, 0, 1, 3, 2, 3, 1, 4, 2, 4, 4};
std::vector<unsigned long> expected_values = {7, 3, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
......@@ -284,11 +265,8 @@ TEST(Morpho, AreaWatershedHierarchy3DImage)
{{11, 18, 0}, {25, 17, 11}, {9, 0, 5}} //
};
std::vector<int> expected_parent = {0, 0, 1, 0, 3, 3, 2, 2, 6, 1, 5, 8, 8, 7, 9, 9,
4, 10, 12, 8, 9, 18, 9, 8, 1, 17, 25, 24, 26, 28, 27};
std::vector<unsigned long> expected_values = {9, 3, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
std::vector<int> expected_parent = {0, 0, 1, 0, 3, 3, 2, 2, 1, 1};
std::vector<unsigned long> expected_values = {9, 3, 2, 2, 0, 0, 0, 0, 0, 0};
auto [tree, _] = mln::morpho::watershed_hierarchy(
input,
......
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