add isotropic binary morphology functions (#421)

related to #419

These are based on the distance transform and are a faster way of computing binary morphological operations for large diameter disk or ball footprints. Unlike the sequence footprint decomposition methods, the footprint is exactly circular (spherical).

One test case `test_isotropic_erosion_spacing` will require #407 to be merged first. 

#406 will also improve the performance of this implementation

Authors:
  - Gregory Lee (https://github.com/grlee77)

Approvers:
  - Gigon Bae (https://github.com/gigony)

URL: #421

benchmarks/skimage/cucim_morphology_bench.py

@@ -53,7 +53,15 @@ def __init__(
         )
 
     def set_args(self, dtype):
-        imaged = cp.random.standard_normal(self.shape).astype(dtype) > 0
+        imaged = (cp.random.standard_normal(self.shape) > 0).astype(dtype)
+        image = cp.asnumpy(imaged)
+        self.args_cpu = (image,)
+        self.args_gpu = (imaged,)
+
+
+class IsotropicMorphologyBench(ImageBench):
+    def set_args(self, dtype):
+        imaged = (cp.random.standard_normal(self.shape) > 0).astype(dtype)
         image = cp.asnumpy(imaged)
         self.args_cpu = (image,)
         self.args_gpu = (imaged,)
@@ -127,6 +135,10 @@ def main(args):
         ("binary_dilation", dict(), dict(), False, True),
         ("binary_opening", dict(), dict(), False, True),
         ("binary_closing", dict(), dict(), False, True),
+        ("isotropic_erosion", dict(), dict(radius=[5, 10, 20]), False, True),
+        ("isotropic_dilation", dict(), dict(radius=[5, 10, 20]), False, True),
+        ("isotropic_opening", dict(), dict(radius=[5, 10, 20]), False, True),
+        ("isotropic_closing", dict(), dict(radius=[5, 10, 20]), False, True),
         # misc.py
         ("remove_small_objects", dict(), dict(), False, True),
         ("remove_small_holes", dict(), dict(), False, True),
@@ -149,6 +161,10 @@ def main(args):
         if function_name != args.func_name:
             continue
 
+        if not allow_color:
+            if len(shape) > 2 and shape[-1] == 3:
+                continue
+
         ndim = len(shape)
         if function_name in ['thin', 'medial_axis']:
             if ndim != 2:
@@ -168,9 +184,7 @@ def main(args):
                 run_cpu=run_cpu,
             )
 
-            results = B.run_benchmark(duration=args.duration)
-            all_results = pd.concat([all_results, results["full"]])
-        elif function_name.startswith('binary_'):
+        if function_name.startswith('binary'):
 
             if not allow_nd and ndim > 2:
                 continue
@@ -191,9 +205,22 @@ def main(args):
                     module_gpu=cucim.skimage.morphology,
                     run_cpu=run_cpu,
                 )
-                results = B.run_benchmark(duration=args.duration)
-                all_results = pd.concat([all_results, results["full"]])
 
+        elif function_name.startswith('isotropic'):
+
+            if not allow_nd and ndim > 2:
+                continue
+
+            B = IsotropicMorphologyBench(
+                function_name=function_name,
+                shape=shape,
+                dtypes=[bool],
+                fixed_kwargs=fixed_kwargs,
+                var_kwargs=var_kwargs,
+                module_cpu=skimage.morphology,
+                module_gpu=cucim.skimage.morphology,
+                run_cpu=run_cpu,
+            )
 
         elif function_name in ['remove_small_holes', 'remove_small_objects']:
             if not allow_nd and ndim > 2:
@@ -216,9 +243,6 @@ def main(args):
                 module_gpu=cucim.skimage.morphology,
                 run_cpu=run_cpu,
             )
-            results = B.run_benchmark(duration=args.duration)
-            all_results = pd.concat([all_results, results["full"]])
-
         else:
 
             if not allow_nd:
@@ -247,8 +271,8 @@ def main(args):
                 module_gpu=cucim.skimage.morphology,
                 run_cpu=run_cpu,
             )
-            results = B.run_benchmark(duration=args.duration)
-            all_results = pd.concat([all_results, results["full"]])
+        results = B.run_benchmark(duration=args.duration)
+        all_results = pd.concat([all_results, results["full"]])
 
     fbase = os.path.splitext(pfile)[0]
     all_results.to_csv(fbase + ".csv")
@@ -264,7 +288,15 @@ def main(args):
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Benchmarking cuCIM morphology functions')
-    func_name_choices = ['binary_erosion', 'binary_dilation', 'binary_opening', 'binary_closing', 'remove_small_objects', 'remove_small_holes', 'erosion', 'dilation', 'opening', 'closing', 'white_tophat', 'black_tophat', 'thin', 'medial_axis', 'reconstruction']
+    # fmt: off
+    func_name_choices = [
+        'binary_erosion', 'binary_dilation', 'binary_opening',
+        'binary_closing', 'isotropic_erosion', 'isotropic_dilation',
+        'isotropic_opening', 'isotropic_closing','remove_small_objects',
+        'remove_small_holes', 'erosion', 'dilation', 'opening', 'closing',
+        'white_tophat', 'black_tophat', 'thin', 'medial_axis', 'reconstruction'
+    ]
+    # fmt: on
     dtype_choices = ['float16', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']
     parser.add_argument('-i','--img_size', type=str, help='Size of input image (omit color channel, it will be appended as needed)', required=True)
     parser.add_argument('-d','--dtype', type=str, help='Dtype of input image', choices = dtype_choices, required=True)

benchmarks/skimage/run-nv-bench-morphology.sh

@@ -1,12 +1,11 @@
 #!/bin/bash
 param_shape=(512,512 3840,2160 3840,2160,3 192,192,192)
-param_filt=(binary_erosion binary_dilation binary_opening binary_closing remove_small_objects remove_small_holes erosion dilation opening closing white_tophat black_tophat medial_axis thin reconstruction)
-
+param_filt=(binary_erosion binary_dilation binary_opening binary_closing isotropic_erosion isotropic_dilation isotropic_opening isotropic_closing remove_small_objects remove_small_holes erosion dilation opening closing white_tophat black_tophat medial_axis thin reconstruction)
 param_dt=(uint8)
 for shape in "${param_shape[@]}"; do
     for filt in "${param_filt[@]}"; do
         for dt in "${param_dt[@]}"; do
-            python cucim_morphology_bench.py -f $filt -i $shape -d $dt -t 10
+            python cucim_morphology_bench.py -f $filt -i $shape -d $dt -t 4
         done
     done
 done
@@ -18,7 +17,7 @@ param_dt=(float32)
 for shape in "${param_shape[@]}"; do
     for filt in "${param_filt[@]}"; do
         for dt in "${param_dt[@]}"; do
-            python cucim_morphology_bench.py -f $filt -i $shape -d $dt -t 10
+            python cucim_morphology_bench.py -f $filt -i $shape -d $dt -t 4
         done
     done
 done

python/cucim/src/cucim/skimage/morphology/__init__.py

@@ -6,13 +6,19 @@
 from .gray import (black_tophat, closing, dilation, erosion, opening,
                    white_tophat)
 from .grayreconstruct import reconstruction
+from .isotropic import (isotropic_dilation, isotropic_erosion,
+                        isotropic_opening, isotropic_closing)
 from .misc import remove_small_holes, remove_small_objects
 
 __all__ = [
     "binary_erosion",
     "binary_dilation",
     "binary_opening",
     "binary_closing",
+    "isotropic_dilation",
+    "isotropic_erosion",
+    "isotropic_opening",
+    "isotropic_closing",
     "erosion",
     "dilation",
     "opening",