Merge pull request #257 from clEsperanto/update-clic-0.13.4

Update to [email protected]

.github/workflows/build.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.11"]
         platform: [ubuntu-latest, macos-latest] #, windows-latest]
     defaults:
       run:
@@ -31,7 +31,6 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python-version }}
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           activate-environment: test
           use-mamba: true

pyclesperanto/_tier5.py

@@ -164,8 +164,8 @@ def reduce_labels_to_centroids(
 def filter_label_by_size(
     input_image: Image,
     output_image: Optional[Image] =None,
-    min_size: float =0,
-    max_size: float =100,
+    minimum_size: float =0,
+    maximum_size: float =100,
     device: Optional[Device] =None
 ) -> Image:
     """Filter labelled objects outside of the min/max size range value.
@@ -176,9 +176,9 @@ def filter_label_by_size(
         Input label image.
     output_image: Optional[Image] (= None)
         Output label image.
-    min_size: float (= 0)
+    minimum_size: float (= 0)
         Minimum size of labels to keep.
-    max_size: float (= 100)
+    maximum_size: float (= 100)
         Maximum size of labels to keep.
     device: Optional[Device] (= None)
         Device to perform the operation on.
@@ -191,14 +191,14 @@ def filter_label_by_size(
     ----------
     [1] https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
     """
-    return clic._filter_label_by_size(device, input_image, output_image, float(min_size), float(max_size))
+    return clic._filter_label_by_size(device, input_image, output_image, float(minimum_size), float(maximum_size))
 
 @plugin_function(categories=["label processing", "in assistant"])
 def exclude_labels_outside_size_range(
     input_image: Image,
     output_image: Optional[Image] =None,
-    min_size: float =0,
-    max_size: float =100,
+    minimum_size: float =0,
+    maximum_size: float =100,
     device: Optional[Device] =None
 ) -> Image:
     """Filter labelled objects outside of the min/max size range value.
@@ -209,9 +209,9 @@ def exclude_labels_outside_size_range(
         Input label image.
     output_image: Optional[Image] (= None)
         Output label image.
-    min_size: float (= 0)
+    minimum_size: float (= 0)
         Minimum size of labels to keep.
-    max_size: float (= 100)
+    maximum_size: float (= 100)
         Maximum size of labels to keep.
     device: Optional[Device] (= None)
         Device to perform the operation on.
@@ -224,4 +224,4 @@ def exclude_labels_outside_size_range(
     ----------
     [1] https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
     """
-    return clic._exclude_labels_outside_size_range(device, input_image, output_image, float(min_size), float(max_size))
+    return clic._exclude_labels_outside_size_range(device, input_image, output_image, float(minimum_size), float(maximum_size))

pyclesperanto/_tier6.py

@@ -174,7 +174,7 @@ def voronoi_labeling(
 def remove_small_labels(
     input_image: Image,
     output_image: Optional[Image] =None,
-    min_size: float =100,
+    minimum_size: float =100,
     device: Optional[Device] =None
 ) -> Image:
     """Removes labelled objects small than a given size (in pixels) from a label map.
@@ -185,7 +185,7 @@ def remove_small_labels(
         Label image to filter.
     output_image: Optional[Image] (= None)
         Output label image fitlered.
-    min_size: float (= 100)
+    minimum_size: float (= 100)
         Smallest size object allowed.
     device: Optional[Device] (= None)
         Device to perform the operation on.
@@ -198,13 +198,13 @@ def remove_small_labels(
     ----------
     [1] https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
     """
-    return clic._remove_small_labels(device, input_image, output_image, float(min_size))
+    return clic._remove_small_labels(device, input_image, output_image, float(minimum_size))
 
 @plugin_function(categories=["label processing", "in assistant"])
 def exclude_small_labels(
     input_image: Image,
     output_image: Optional[Image] =None,
-    max_size: float =100,
+    maximum_size: float =100,
     device: Optional[Device] =None
 ) -> Image:
     """Removes labels from a label map which are below a given maximum size.
@@ -215,7 +215,7 @@ def exclude_small_labels(
         Label image to filter.
     output_image: Optional[Image] (= None)
         Output label image fitlered.
-    max_size: float (= 100)
+    maximum_size: float (= 100)
         Largest size object to exclude.
     device: Optional[Device] (= None)
         Device to perform the operation on.
@@ -228,13 +228,13 @@ def exclude_small_labels(
     ----------
     [1] https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
     """
-    return clic._exclude_small_labels(device, input_image, output_image, float(max_size))
+    return clic._exclude_small_labels(device, input_image, output_image, float(maximum_size))
 
 @plugin_function(categories=["label processing", "in assistant", "bia-bob-suggestion"])
 def remove_large_labels(
     input_image: Image,
     output_image: Optional[Image] =None,
-    max_size: float =100,
+    maximum_size: float =100,
     device: Optional[Device] =None
 ) -> Image:
     """Removes labelled objects bigger than a given size (in pixels) from a label map.
@@ -245,7 +245,7 @@ def remove_large_labels(
         Label image to filter.
     output_image: Optional[Image] (= None)
         Output label image fitlered.
-    max_size: float (= 100)
+    maximum_size: float (= 100)
         Biggest size object allowed.
     device: Optional[Device] (= None)
         Device to perform the operation on.
@@ -258,13 +258,13 @@ def remove_large_labels(
     ----------
     [1] https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
     """
-    return clic._remove_large_labels(device, input_image, output_image, float(max_size))
+    return clic._remove_large_labels(device, input_image, output_image, float(maximum_size))
 
 @plugin_function(categories=["label processing", "in assistant"])
 def exclude_large_labels(
     input_image: Image,
     output_image: Optional[Image] =None,
-    min_size: float =100,
+    minimum_size: float =100,
     device: Optional[Device] =None
 ) -> Image:
     """Removes labels from a label map which are higher a given minimum size.
@@ -275,7 +275,7 @@ def exclude_large_labels(
         Label image to filter.
     output_image: Optional[Image] (= None)
         Output label image fitlered.
-    min_size: float (= 100)
+    minimum_size: float (= 100)
         Smallest size object to keep.
     device: Optional[Device] (= None)
         Device to perform the operation on.
@@ -288,4 +288,4 @@ def exclude_large_labels(
     ----------
     [1] https://clij.github.io/clij2-docs/reference_excludeLabelsOutsideSizeRange
     """
-    return clic._exclude_large_labels(device, input_image, output_image, float(min_size))
+    return clic._exclude_large_labels(device, input_image, output_image, float(minimum_size))

pyclesperanto/_version.py

@@ -1,3 +1,3 @@
-VERSION = "0.13.3"
-CLIC_VERSION = "0.13.3"
+VERSION = "0.13.4"
+CLIC_VERSION = "0.13.4"
 COMMON_ALIAS = "cle"

src/wrapper/tier5_.cpp

@@ -28,9 +28,9 @@ m.def("_array_equal", &cle::tier5::array_equal_func, "Call cle::tier5::array_equ
 
     m.def("_filter_label_by_size", &cle::tier5::filter_label_by_size_func, "Call cle::tier5::filter_label_by_size_func from C++ CLIc.",
     py::return_value_policy::take_ownership,
-    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("min_size"), py::arg("max_size"));
+    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("minimum_size"), py::arg("maximum_size"));
 
     m.def("_exclude_labels_outside_size_range", &cle::tier5::exclude_labels_outside_size_range_func, "Call cle::tier5::exclude_labels_outside_size_range_func from C++ CLIc.",
     py::return_value_policy::take_ownership,
-    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("min_size"), py::arg("max_size"));
+    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("minimum_size"), py::arg("maximum_size"));
 }

src/wrapper/tier6_.cpp

@@ -28,17 +28,17 @@ m.def("_dilate_labels", &cle::tier6::dilate_labels_func, "Call cle::tier6::dilat
 
     m.def("_remove_small_labels", &cle::tier6::remove_small_labels_func, "Call cle::tier6::remove_small_labels_func from C++ CLIc.",
     py::return_value_policy::take_ownership,
-    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("min_size"));
+    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("minimum_size"));
 
     m.def("_exclude_small_labels", &cle::tier6::exclude_small_labels_func, "Call cle::tier6::exclude_small_labels_func from C++ CLIc.",
     py::return_value_policy::take_ownership,
-    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("max_size"));
+    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("maximum_size"));
 
     m.def("_remove_large_labels", &cle::tier6::remove_large_labels_func, "Call cle::tier6::remove_large_labels_func from C++ CLIc.",
     py::return_value_policy::take_ownership,
-    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("max_size"));
+    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("maximum_size"));
 
     m.def("_exclude_large_labels", &cle::tier6::exclude_large_labels_func, "Call cle::tier6::exclude_large_labels_func from C++ CLIc.",
     py::return_value_policy::take_ownership,
-    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("min_size"));
+    py::arg("device"), py::arg("src"), py::arg("dst"), py::arg("minimum_size"));
 }

tests/test_filter_labels_by_size.py

@@ -28,7 +28,7 @@ def test_exclude_labels_out_of_size_range_2d():
         )
     )
 
-    gpu_output = cle.filter_label_by_size(gpu_input, min_size=4, max_size=5)
+    gpu_output = cle.filter_label_by_size(gpu_input, minimum_size=4, maximum_size=5)
 
     a = cle.pull(gpu_output)
     b = cle.pull(gpu_reference)
@@ -64,7 +64,7 @@ def test_exclude_small_labels_2d():
         )
     )
 
-    gpu_output = cle.exclude_small_labels(gpu_input, max_size=5)
+    gpu_output = cle.exclude_small_labels(gpu_input, maximum_size=5)
 
     a = cle.pull(gpu_output)
     b = cle.pull(gpu_reference)
@@ -100,7 +100,7 @@ def test_exclude_large_labels_2d():
         )
     )
 
-    gpu_output = cle.exclude_large_labels(gpu_input, min_size=3)
+    gpu_output = cle.exclude_large_labels(gpu_input, minimum_size=3)
 
     a = cle.pull(gpu_output)
     b = cle.pull(gpu_reference)

tests/test_threshold_otsu.py

@@ -30,3 +30,18 @@ def test_threshold_otsu_against_scikit_image():
 
     # compare
     assert np.allclose(binary, (cle.pull(gpu_binary) > 0))
+
+
+
+def test_threshold_otsu_low_values():
+    input = np.asarray([[0,0,0],
+             [0,0.003,0],
+             [0,0,0]])
+
+    reference = np.asarray([[0,0,0],
+             [0,1,0],
+             [0,0,0]])
+
+    result = cle.threshold_otsu(input)
+
+    assert np.allclose(reference, cle.pull(result) > 0)