Adding labels_centers (deprecating pos2img and center_of_mass)

tdegeus · Dec 5, 2023 · 3a00e1d · 3a00e1d
1 parent 6856dfe
commit 3a00e1d
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Showing 4 changed files with 115 additions and 105 deletions.
diff --git a/include/GooseEYE/GooseEYE.h b/include/GooseEYE/GooseEYE.h
@@ -1282,8 +1282,11 @@ array_type::array<int> clusters(const T& f, bool periodic = true)
  * @return The image, with labels inserted (overwritten) at the positions.
  */
 template <typename T, typename U, typename V>
+[[deprecated("Will not be supported in the future. See Python warning for new API.")]]
 inline T pos2img(const T& img, const U& positions, const V& labels)
 {
+    GOOSEEYE_WARNING_PYTHON("pos2img(img, positions, labels) deprecated, use: "
+                            "i = ravel_multi_index(positions.T, img.shape); img.flat[i] = labels")
     GOOSEEYE_ASSERT(img.dimension() > 0, std::out_of_range);
     GOOSEEYE_ASSERT(img.dimension() <= 3, std::out_of_range);
     GOOSEEYE_ASSERT(img.dimension() == positions.shape(1), std::out_of_range);
@@ -1319,11 +1322,13 @@ inline T pos2img(const T& img, const U& positions, const V& labels)
  *      https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions
  *
  * @param labels An image with labels [0..N].
+ * @param weights Weights for each pixel.
  * @param periodic Switch to assume image periodic.
  * @return The position of the center of each label.
  */
-template <class T>
-array_type::tensor<double, 2> center_of_mass(const T& labels, bool periodic = true)
+template <class T, class W = decltype(nullptr)>
+array_type::tensor<double, 2>
+labels_centers(const T& labels, const W& weights = nullptr, bool periodic = true)
 {
     static_assert(std::is_integral<typename T::value_type>::value, "Integral labels required.");
 
@@ -1364,6 +1369,20 @@ array_type::tensor<double, 2> center_of_mass(const T& labels, bool periodic = tr
     return xt::view(ret, xt::all(), xt::keep(axes));
 }
 
+/**
+ * @brief Get the position of the center of each label.
+ * @param labels An image with labels [0..N].
+ * @param periodic Switch to assume image periodic.
+ * @return The position of the center of each label (in array-index).
+ */
+template <class T>
+[[deprecated("Use labels_centers() instead.")]] array_type::tensor<double, 2>
+center_of_mass(const T& labels, bool periodic = true)
+{
+    GOOSEEYE_WARNING_PYTHON("center_of_mass() is deprecated, use labels_centers() instead");
+    return labels_centers(labels, nullptr, periodic);
+}
+
 /**
  * Compute ensemble averaged statistics, by repetitively calling the member-function of a certain
  * statistical measure with different data.

diff --git a/python/main.cpp b/python/main.cpp
@@ -212,10 +212,17 @@ PYBIND11_MODULE(_GooseEYE, m)
 
     m.def(
         "center_of_mass",
-        &GooseEYE::center_of_mass<xt::pyarray<size_t>>,
+        &GooseEYE::center_of_mass<xt::pyarray<ptrdiff_t>>,
         py::arg("labels"),
         py::arg("periodic") = true);
 
+    m.def(
+        "labels_centers",
+        &GooseEYE::labels_centers<xt::pyarray<ptrdiff_t>, xt::pyarray<double>>,
+        py::arg("labels"),
+        py::arg("weights").none(true) = nullptr,
+        py::arg("periodic") = true);
+
     py::class_<GooseEYE::Ensemble>(m, "Ensemble")
 
         // Constructors

diff --git a/tests/clusters.cpp b/tests/clusters.cpp
diff --git a/tests/test_clusters.py b/tests/test_clusters.py
@@ -216,6 +216,92 @@ def test_labels_sizes():
     )
 
 
+def test_labels_centers():
+    labels = np.array(
+        [
+            [0, 0, 0, 0, 0],
+            [0, 0, 1, 0, 0],
+            [0, 1, 1, 1, 0],
+            [0, 0, 1, 0, 0],
+            [0, 0, 0, 0, 0],
+        ]
+    )
+    centers = np.array(
+        [
+            [2.0, 2.0],  # background (0)
+            [2.0, 2.0],  # label (1)
+        ]
+    )
+    assert np.allclose(eye.labels_centers(labels, periodic=False), centers)
+
+
+def test_labels_centers2():
+    labels = np.array(
+        [
+            [0, 0, 0, 0, 0],
+            [0, 0, 1, 0, 0],
+            [0, 1, 1, 1, 0],
+            [0, 0, 1, 0, 0],
+            [0, 0, 0, 0, 0],
+        ]
+    )
+    centers = np.array(
+        [
+            [4.5, 4.5],  # background (0)
+            [2.0, 2.0],  # label (1)
+        ]
+    )
+
+    for i in range(labels.shape[0]):
+        for j in range(labels.shape[1]):
+            assert np.allclose(eye.labels_centers(labels, periodic=True), centers)
+            labels = np.roll(labels, 1, 1)
+            y = centers[:, 1] + 1
+            centers[:, 1] = np.where(y > labels.shape[1], y - labels.shape[1], y)
+
+        labels = np.roll(labels, 1, 0)
+        x = centers[:, 0] + 1
+        centers[:, 0] = np.where(x > labels.shape[0], x - labels.shape[0], x)
+
+
+def test_labels_centers3():
+    labels = np.array(
+        [
+            [2, 3, 3, 3, 2],
+            [0, 0, 1, 0, 0],
+            [0, 1, 1, 1, 0],
+            [0, 0, 1, 0, 0],
+            [2, 4, 4, 4, 2],
+        ]
+    )
+
+    c = np.array(
+        [
+            [0, 0, 3, 0, 0],
+            [0, 0, 0, 0, 0],
+            [0, 0, 1, 0, 0],
+            [0, 0, 0, 0, 0],
+            [0, 0, 4, 0, 2],
+        ]
+    )
+
+    centers = np.array(
+        [
+            [2.0, 4.5],
+            [2.0, 2.0],
+            [4.5, 4.5],
+            [0.0, 2.0],
+            [4.0, 2.0],
+        ]
+    )
+
+    res_centers = eye.labels_centers(labels)
+    assert np.allclose(res_centers, centers)
+
+    centers_flat = np.ravel_multi_index(np.floor(centers).astype(int).T, c.shape)
+    assert np.all(np.equal(np.sort(np.flatnonzero(c)), np.sort(centers_flat[1:])))
+
+
 def test_prune():
     segmenter = eye.ClusterLabeller(shape=(4, 4))
     segmenter.add_points([0, 2, 8, 10, 1])