Refactor Python unit/perf test cases

python/cucim/requirements-test.txt

@@ -0,0 +1,8 @@
+GPUtil==1.4.0
+imagecodecs==2021.6.8
+openslide-python==1.1.2
+psutil==5.8.0
+pytest==6.2.4
+pytest-cov==2.12.1
+pytest-lazy-fixture==0.6.3
+tifffile==2021.7.2

python/cucim/tests/performance/clara/test_read_region_memory_usage.py

@@ -14,12 +14,7 @@
 #
 
 import pytest
-
-
-def open_image_cucim(file_path):
-    from cucim import CuImage
-    img = CuImage(file_path)
-    return img
+from ...util.io import open_image_cucim
 
 
 def test_read_region_cuda_memleak(testimg_tiff_stripe_4096x4096_256):
@@ -69,9 +64,9 @@ def test_read_region_cpu_memleak(testimg_tiff_stripe_4096x4096_256):
 
 
 def test_read_random_region_cpu_memleak(testimg_tiff_stripe_4096x4096_256):
-    import random
     import os
     import psutil
+    import random
     process = psutil.Process(os.getpid())
 
     img = open_image_cucim(testimg_tiff_stripe_4096x4096_256)

python/cucim/tests/unit/clara/test_load_image.py

@@ -14,12 +14,7 @@
 #
 
 import pytest
-
-
-def open_image_cucim(file_path):
-    from cucim import CuImage
-    img = CuImage(file_path)
-    return img
+from ...util.io import open_image_cucim
 
 
 def test_load_non_existing_image():

python/cucim/tests/unit/clara/test_load_image_metadata.py

@@ -13,11 +13,7 @@
 # limitations under the License.
 #
 
-
-def open_image_cucim(file_path):
-    from cucim import CuImage
-    img = CuImage(file_path)
-    return img
+from ...util.io import open_image_cucim
 
 
 def test_load_image_metadata(testimg_tiff_stripe_32x24_16):

python/cucim/tests/unit/clara/test_tiff_read_region.py

@@ -15,12 +15,7 @@
 
 import numpy as np
 import pytest
-
-
-def open_image_cucim(file_path):
-    from cucim import CuImage
-    img = CuImage(file_path)
-    return img
+from ...util.io import open_image_cucim
 
 
 def test_tiff_stripe_inner(testimg_tiff_stripe_32x24_16):
@@ -39,11 +34,9 @@ def test_tiff_stripe_inner(testimg_tiff_stripe_32x24_16):
     for (start_pos, size) in region_list:
         cucim_arr = np.asarray(cucim_img.read_region(start_pos, size))
 
-        # Not channel values are zero, so we need to check that.
-        channel_value_count = np.apply_along_axis(np.count_nonzero, 2,
-                                                  cucim_arr)
-        count_all_zero = np.count_nonzero(channel_value_count == 0)
-        assert count_all_zero == 0
+        # Not all channel values are zero, so we need to check that.
+        channel_value_count = np.count_nonzero(cucim_arr, axis=2)
+        assert np.all(channel_value_count > 0)
 
 
 def test_tiff_stripe_boundary(testimg_tiff_stripe_32x24_16):
@@ -64,9 +57,8 @@ def test_tiff_stripe_boundary(testimg_tiff_stripe_32x24_16):
 
     for (start_pos, size) in region_list:
         cucim_arr = np.asarray(cucim_img.read_region(start_pos, size))
-        # Not channel values are zero, so we need to check that.
-        channel_value_count = np.apply_along_axis(np.count_nonzero, 2,
-                                                  cucim_arr)
+        # Not all channel values are zero, so we need to check that.
+        channel_value_count = np.count_nonzero(cucim_arr, axis=2)
         count_all_zero = np.count_nonzero(channel_value_count == 0)
         # 75% of the pixels would be all zero
         assert count_all_zero - (tile_width * tile_height * 0.75) < 5
@@ -87,8 +79,7 @@ def test_tiff_stripe_outside(testimg_tiff_stripe_32x24_16):
     for (start_pos, size) in region_list:
         cucim_arr = np.asarray(cucim_img.read_region(start_pos, size))
         # All channel values should be zero, so we need to check that.
-        channel_value_count = np.apply_along_axis(np.count_nonzero, 2,
-                                                  cucim_arr)
+        channel_value_count = np.count_nonzero(cucim_arr, axis=2)
         count_all_zero = np.count_nonzero(channel_value_count == 0)
         # All pixels would be zero.
         assert count_all_zero == (tile_width * tile_height)
@@ -112,9 +103,8 @@ def test_tiff_stripe_multiresolution(testimg_tiff_stripe_4096x4096_256):
     start_pos, size = ((0, 0), (256, 256))
     for level in range(level_count):
         cucim_arr = np.asarray(cucim_img.read_region(start_pos, size, level))
-        # Not channel values are zero, so we need to check that.
-        channel_value_count = np.apply_along_axis(np.count_nonzero, 2,
-                                                  cucim_arr)
+        # Not all channel values are zero, so we need to check that.
+        channel_value_count = np.count_nonzero(cucim_arr, axis=2)
         count_all_zero = np.count_nonzero(channel_value_count == 0)
         img_size = cucim_img.resolutions['level_dimensions'][level]
         # Only outside of the box is zero.
@@ -137,21 +127,22 @@ def test_array_interface_support(testimg_tiff_stripe_32x24_16_jpeg):
     assert array_interface['shape'] == tuple(whole_img.shape)
     assert array_interface['version'] == 3
 
-    def test_cuda_array_interface_support(testimg_tiff_stripe_32x24_16_jpeg):
-        img = open_image_cucim(testimg_tiff_stripe_32x24_16_jpeg)
-        whole_img = img.read_region(device='cuda')
-        array_interface = whole_img.__cuda_array_interface__
-        print(array_interface)
-
-        # {'data': (81888083968, False), 'strides': None,
-        #  'descr': [('', '|u1')], 'typestr': '|u1', 'shape': (24, 32, 3),
-        #  'version': 3, 'mask': None, 'stream': 1}
-        assert array_interface['data'][0] is not None
-        assert not array_interface['data'][1]
-        assert array_interface['strides'] is None
-        assert array_interface['descr']
-        assert array_interface['typestr']
-        assert array_interface['shape'] == tuple(whole_img.shape)
-        assert array_interface['version'] == 3
-        assert array_interface['mask'] is None
-        assert array_interface['stream'] == 1
+
+def test_cuda_array_interface_support(testimg_tiff_stripe_32x24_16_jpeg):
+    img = open_image_cucim(testimg_tiff_stripe_32x24_16_jpeg)
+    whole_img = img.read_region(device='cuda')
+    array_interface = whole_img.__cuda_array_interface__
+    print(array_interface)
+
+    # {'data': (81888083968, False), 'strides': None,
+    #  'descr': [('', '|u1')], 'typestr': '|u1', 'shape': (24, 32, 3),
+    #  'version': 3, 'mask': None, 'stream': 1}
+    assert array_interface['data'][0] is not None
+    assert not array_interface['data'][1]
+    assert array_interface['strides'] is None
+    assert array_interface['descr']
+    assert array_interface['typestr']
+    assert array_interface['shape'] == tuple(whole_img.shape)
+    assert array_interface['version'] == 3
+    assert array_interface['mask'] is None
+    assert array_interface['stream'] == 1

python/cucim/tests/util/io.py

@@ -0,0 +1,19 @@
+#
+# Copyright (c) 2021, NVIDIA CORPORATION.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+def open_image_cucim(file_path):
+    from cucim import CuImage
+    img = CuImage(file_path)
+    return img

run

@@ -679,60 +679,23 @@ test() {
     fi
 }
 
-check_install_python_dep_() {
-    local package_names="$@"
-
-    [ -z "$package_names" ] && c_echo_err R "Please specify package names to check!" && return 1
-
-    local packages_to_install=""
-    local has_all_packages=true
-
-    for package_name in $package_names; do
-        # `package_name` has '<package name>[:<conda package name>]' format.
-        if [ -n "${CONDA_PREFIX}" ]; then
-            # abc:def => def
-            # abc => abc
-            package_name="${package_name##*:}"
-            if ! conda list | grep -i -c "${package_name} " > /dev/null; then
-                c_echo G "${package_name}" W " doesn't exists. Installing " G "${package_name}" W "..."
-                has_all_packages=false
-
-                # Workaround for `openslide-python`
-                # (See https://github.com/conda-forge/openslide-python-feedstock/issues/4)
-                [ "${package_name}" = "openslide-python" ] && package_name="conda-forge/linux-64::openslide-python"
-
-                packages_to_install="${packages_to_install} ${package_name}"
-            fi
-        else
-            # abc:def => abc
-            # abc => abc
-            package_name="${package_name%%:*}"
-            if ! pip3 list | grep -i -c "${package_name} " > /dev/null; then
-                c_echo G "${package_name}" W " doesn't exists. Installing " G "${package_name}" W "..."
-                has_all_packages=false
-                packages_to_install="${packages_to_install} ${package_name}"
-            fi
-        fi
-    done
-    if [ "$has_all_packages" != "true" ]; then
-        if [ -n "${CONDA_PREFIX}" ]; then
-            run_command conda install -c conda-forge -y ${packages_to_install}
+install_python_test_deps_() {
+    if [ -n "${CONDA_PREFIX}" ]; then
+        # Cannot use 'conda install' until
+        #   https://github.com/conda-forge/openslide-python-feedstock/issues/4
+        # is fixed.
+        # (run_command conda install -c conda-forge -y --file ${TOP}/python/cucim/requirements-test.txt)
+        run_command pip3 install -r ${TOP}/python/cucim/requirements-test.txt
+    else
+        if [ -n "${VIRTUAL_ENV}" ]; then
+            run_command pip3 install -r ${TOP}/python/cucim/requirements-test.txt
         else
-            if [ -n "${VIRTUAL_ENV}" ]; then
-                run_command pip3 install ${packages_to_install}
-            else
-                run_command pip3 install --user ${packages_to_install}
-            fi
+            run_command pip3 install --user -r ${TOP}/python/cucim/requirements-test.txt
         fi
     fi
     hash -r
 }
 
-install_python_test_deps_() {
-    # Package name has '<package name>[:<conda package name>]' format.
-    check_install_python_dep_ pytest pytest-cov pytest-lazy-fixture psutil GPUtil tifffile imagecodecs openslide-python
-}
-
 test_python_desc() { echo 'Execute Python test cases
 
 Arguments: