Setup initial cpp unittests

gigony · gigony · commit 8a7dd7d42220 · 2021-10-29T18:07:07.000-07:00
diff --git a/benchmarks/config.h b/benchmarks/config.h
@@ -1,6 +1,6 @@
 /*
  * Apache License, Version 2.0
- * Copyright 2020 NVIDIA Corporation
+ * Copyright 2020-2021 NVIDIA Corporation
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -21,7 +21,8 @@
 
 struct AppConfig
 {
-    std::string input_file = "test_data/private/generic_tiff_000.tif";
+    std::string test_folder;
+    std::string test_file;
     bool discard_cache = false;
     int random_seed = 0;
     bool random_start_location = false;
@@ -42,6 +43,38 @@ struct AppConfig
     std::string benchmark_color; //  {auto|true|false}
     std::string benchmark_counters_tabular;
     std::string v; // <verbosity>
+
+    std::string get_input_path(const std::string default_value = "generated/tiff_stripe_4096x4096_256.tif") const
+    {
+        // If `test_file` is absolute path
+        if (!test_folder.empty() && test_file.substr(0, 1) == "/")
+        {
+            return test_file;
+        }
+        else
+        {
+            std::string test_data_folder = test_folder;
+            if (test_data_folder.empty())
+            {
+                if (const char* env_p = std::getenv("CUCIM_TESTDATA_FOLDER"))
+                {
+                    test_data_folder = env_p;
+                }
+                else
+                {
+                    test_data_folder = "test_data";
+                }
+            }
+            if (test_file.empty())
+            {
+                return test_data_folder + "/" + default_value;
+            }
+            else
+            {
+                return test_data_folder + "/" + test_file;
+            }
+        }
+    }
 };
 
 #endif // CUCIM_CONFIG_H
diff --git a/benchmarks/main.cpp b/benchmarks/main.cpp
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2020, NVIDIA CORPORATION.
+ * Copyright (c) 2020-2021, NVIDIA CORPORATION.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -32,6 +32,8 @@ static AppConfig g_config;
 
 static void test_cucim(benchmark::State& state)
 {
+    std::string input_path = g_config.get_input_path();
+
     int arg = -1;
     for (auto state_item : state)
     {
@@ -46,7 +48,7 @@ static void test_cucim(benchmark::State& state)
 
             if (g_config.discard_cache)
             {
-                int fd = open(g_config.input_file.c_str(), O_RDONLY);
+                int fd = open(input_path.c_str(), O_RDONLY);
                 fdatasync(fd);
                 posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED);
                 close(fd);
@@ -61,7 +63,7 @@ static void test_cucim(benchmark::State& state)
             request_location[1] = rand() % (g_config.image_height - state.range(0));
         }
 
-        cucim::CuImage image = cucim::CuImage(g_config.input_file.c_str());
+        cucim::CuImage image = cucim::CuImage(input_path.c_str());
         cucim::CuImage region =
             image.read_region({ request_location[0], request_location[1] }, { state.range(0), state.range(0) }, 0,
                               cucim::DimIndices{}, "cpu", nullptr, "");
@@ -70,6 +72,8 @@ static void test_cucim(benchmark::State& state)
 
 static void test_openslide(benchmark::State& state)
 {
+    std::string input_path = g_config.get_input_path();
+
     int arg = -1;
     for (auto _ : state)
     {
@@ -84,15 +88,15 @@ static void test_openslide(benchmark::State& state)
 
             if (g_config.discard_cache)
             {
-                int fd = open(g_config.input_file.c_str(), O_RDONLY);
+                int fd = open(input_path.c_str(), O_RDONLY);
                 fdatasync(fd);
                 posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED);
                 close(fd);
             }
         }
         state.ResumeTiming();
 
-        openslide_t* slide = openslide_open(g_config.input_file.c_str());
+        openslide_t* slide = openslide_open(input_path.c_str());
         uint32_t* buf = static_cast<uint32_t*>(cucim_malloc(state.range(0) * state.range(0) * 4));
         int64_t request_location[2] = { 0, 0 };
         if (g_config.random_start_location)
@@ -131,10 +135,12 @@ static bool remove_help_option(int* argc, char** argv)
 
 static bool setup_configuration()
 {
-    openslide_t* slide = openslide_open(g_config.input_file.c_str());
+    std::string input_path = g_config.get_input_path();
+
+    openslide_t* slide = openslide_open(input_path.c_str());
     if (slide == nullptr)
     {
-        fmt::print("[Error] Cannot load {}!\n", g_config.input_file);
+        fmt::print("[Error] Cannot load {}!\n", input_path);
         return false;
     }
     int64_t w, h;
@@ -159,7 +165,8 @@ int main(int argc, char** argv)
     //        return 1;
 
     CLI::App app{ "cuCIM Benchmark" };
-    app.add_option("--test_file", g_config.input_file, "An input .tif/.svs file path");
+    app.add_option("--test_folder", g_config.test_folder, "An input test folder path");
+    app.add_option("--test_file", g_config.test_file, "An input test image file path");
     app.add_option("--discard_cache", g_config.discard_cache, "Discard page cache for the input file for each iteration");
     app.add_option("--random_seed", g_config.random_seed, "A random seed number");
     app.add_option(
diff --git a/cpp/plugins/cucim.kit.cuslide/benchmarks/config.h b/cpp/plugins/cucim.kit.cuslide/benchmarks/config.h
@@ -1,6 +1,6 @@
 /*
  * Apache License, Version 2.0
- * Copyright 2020 NVIDIA Corporation
+ * Copyright 2020-2021 NVIDIA Corporation
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -21,7 +21,8 @@
 
 struct AppConfig
 {
-    std::string input_file = "test_data/private/generic_tiff_000.tif";
+    std::string test_folder;
+    std::string test_file;
     bool discard_cache = false;
     int random_seed = 0;
     bool random_start_location = false;
@@ -42,6 +43,38 @@ struct AppConfig
     std::string benchmark_color; //  {auto|true|false}
     std::string benchmark_counters_tabular;
     std::string v; // <verbosity>
+
+    std::string get_input_path(const std::string default_value = "generated/tiff_stripe_4096x4096_256.tif") const
+    {
+        // If `test_file` is absolute path
+        if (!test_folder.empty() && test_file.substr(0, 1) == "/")
+        {
+            return test_file;
+        }
+        else
+        {
+            std::string test_data_folder = test_folder;
+            if (test_data_folder.empty())
+            {
+                if (const char* env_p = std::getenv("CUCIM_TESTDATA_FOLDER"))
+                {
+                    test_data_folder = env_p;
+                }
+                else
+                {
+                    test_data_folder = "test_data";
+                }
+            }
+            if (test_file.empty())
+            {
+                return test_data_folder + "/" + default_value;
+            }
+            else
+            {
+                return test_data_folder + "/" + test_file;
+            }
+        }
+    }
 };
 
 #endif // CUSLIDE_CONFIG_H
diff --git a/cpp/plugins/cucim.kit.cuslide/benchmarks/main.cpp b/cpp/plugins/cucim.kit.cuslide/benchmarks/main.cpp
@@ -43,6 +43,8 @@ static AppConfig g_config;
 
 static void test_basic(benchmark::State& state)
 {
+    std::string input_path = g_config.get_input_path();
+
     int arg = -1;
     for (auto state_item : state)
     {
@@ -57,7 +59,7 @@ static void test_basic(benchmark::State& state)
 
             if (g_config.discard_cache)
             {
-                int fd = open(g_config.input_file.c_str(), O_RDONLY);
+                int fd = open(input_path.c_str(), O_RDONLY);
                 fdatasync(fd);
                 posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED);
                 close(fd);
@@ -83,7 +85,7 @@ static void test_basic(benchmark::State& state)
             return;
         }
 
-        auto handle = image_format->formats[0].image_parser.open(g_config.input_file.c_str());
+        auto handle = image_format->formats[0].image_parser.open(input_path.c_str());
 
         cucim::io::format::ImageMetadata metadata{};
         image_format->formats[0].image_parser.parse(&handle, &metadata.desc());
@@ -118,6 +120,8 @@ static void test_basic(benchmark::State& state)
 
 static void test_openslide(benchmark::State& state)
 {
+    std::string input_path = g_config.get_input_path();
+
     int arg = -1;
     for (auto _ : state)
     {
@@ -132,15 +136,15 @@ static void test_openslide(benchmark::State& state)
 
             if (g_config.discard_cache)
             {
-                int fd = open(g_config.input_file.c_str(), O_RDONLY);
+                int fd = open(input_path.c_str(), O_RDONLY);
                 fdatasync(fd);
                 posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED);
                 close(fd);
             }
         }
         state.ResumeTiming();
 
-        openslide_t* slide = openslide_open(g_config.input_file.c_str());
+        openslide_t* slide = openslide_open(input_path.c_str());
         uint32_t* buf = static_cast<uint32_t*>(cucim_malloc(state.range(0) * state.range(0) * 4));
         int64_t request_location[2] = { 0, 0 };
         if (g_config.random_start_location)
@@ -177,10 +181,11 @@ static bool remove_help_option(int* argc, char** argv)
 
 static bool setup_configuration()
 {
-    openslide_t* slide = openslide_open(g_config.input_file.c_str());
+    std::string input_path = g_config.get_input_path();
+    openslide_t* slide = openslide_open(input_path.c_str());
     if (slide == nullptr)
     {
-        fmt::print("[Error] Cannot load {}!\n", g_config.input_file);
+        fmt::print("[Error] Cannot load {}!\n", input_path);
         return false;
     }
 
@@ -205,7 +210,8 @@ int main(int argc, char** argv)
     //    if (::benchmark::ReportUnrecognizedArguments(argc, argv))
     //        return 1;
     CLI::App app{ "benchmark: cuSlide" };
-    app.add_option("--test_file", g_config.input_file, "An input .tif/.svs file path");
+    app.add_option("--test_folder", g_config.test_folder, "An input test folder path");
+    app.add_option("--test_file", g_config.test_file, "An input test image file path");
     app.add_option("--discard_cache", g_config.discard_cache, "Discard page cache for the input file for each iteration");
     app.add_option("--random_seed", g_config.random_seed, "A random seed number");
     app.add_option(
diff --git a/cpp/plugins/cucim.kit.cuslide/tests/config.h b/cpp/plugins/cucim.kit.cuslide/tests/config.h
@@ -1,6 +1,6 @@
 /*
  * Apache License, Version 2.0
- * Copyright 2020 NVIDIA Corporation
+ * Copyright 2020-2021 NVIDIA Corporation
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -25,7 +25,7 @@ struct AppConfig
     std::string test_folder;
     std::string test_file;
     std::string temp_folder = "/tmp";
-    std::string get_input_path(const char* default_value = "private/generic_tiff_000.tif") const
+    std::string get_input_path(const std::string default_value = "generated/tiff_stripe_4096x4096_256.tif") const
     {
         // If `test_file` is absolute path
         if (!test_folder.empty() && test_file.substr(0, 1) == "/")
diff --git a/cpp/tests/config.h b/cpp/tests/config.h
@@ -20,12 +20,15 @@
 #include <string>
 #include <cstdlib>
 
+#define XSTR(x) STR(x)
+#define STR(x) #x
+
 struct AppConfig
 {
     std::string test_folder;
     std::string test_file;
     std::string temp_folder = "/tmp";
-    std::string get_input_path(const char* default_value = "private/generic_tiff_000.tif") const
+    std::string get_input_path(const std::string default_value = "generated/tiff_stripe_4096x4096_256.tif") const
     {
         // If `test_file` is absolute path
         if (!test_folder.empty() && test_file.substr(0, 1) == "/")
@@ -56,7 +59,7 @@ struct AppConfig
             }
         }
     }
-    std::string get_plugin_path(const char* default_value = "cucim.kit.cuslide@0.0.0.so")
+    std::string get_plugin_path(const char* default_value = "cucim.kit.cuslide@" XSTR(CUCIM_VERSION) ".so")
     {
         std::string plugin_path = default_value;
         if (const char* env_p = std::getenv("CUCIM_TEST_PLUGIN_PATH"))
diff --git a/cpp/tests/test_read_region.cpp b/cpp/tests/test_read_region.cpp
@@ -110,6 +110,21 @@ SCENARIO("Verify read_region()", "[test_read_region.cpp]")
         //        }
         printf("\ncucim count: %d\n", hash);
         cucim_free(image_data.container.data);
+        if (image_data.container.shape)
+        {
+            cucim_free(image_data.container.shape);
+            image_data.container.shape = nullptr;
+        }
+        if (image_data.container.strides)
+        {
+            cucim_free(image_data.container.strides);
+            image_data.container.strides = nullptr;
+        }
+        if (image_data.shm_name)
+        {
+            cucim_free(image_data.shm_name);
+            image_data.shm_name = nullptr;
+        }
         image_format->formats[0].image_parser.close(&handle);
 
         auto end = std::chrono::high_resolution_clock::now();
diff --git a/cucim.code-workspace b/cucim.code-workspace
@@ -161,7 +161,7 @@
 					"cwd": "${workspaceFolder}",
 					"env": {
 						// Workaround the environment variable issue: https://github.com/microsoft/vscode/issues/121470
-						"PATH": "${env:PATH}"
+						"PATH": "${env:HOME}/.local/bin:${env:PATH}"
 					}
 				},
 				"presentation": {
diff --git a/python/cucim/tests/util/gen_image.py b/python/cucim/tests/util/gen_image.py
@@ -82,6 +82,7 @@ def gen(self):
                                                   image_size=image_size,
                                                   tile_size=tile_size,
                                                   compression=compression)
+            self.logger.info('  Generated %s...', image_path)
             results.append(image_path)
 
         self.logger.info('[Finished] Dataset generation')
diff --git a/test_data/README.md b/test_data/README.md
@@ -2,12 +2,19 @@
 
 Symbolic links for for this folder is available under the following subfolders:
 
-- `cpp/plugins/cucim.kit.cuslide
+- `cpp/plugins/cucim.kit.cuslide`
 - `python/cucim`
 
+## Generated Test Data (`test_data/generated` folder)
+
+Generated by executing `gen_images.sh`.
+
+- tiff_stripe_32x32_16.tif
+- tiff_stripe_4096x4096_256.tif
+
 ## Private Test Data (`test_data/private` folder)
 
 - `generic_tiff_000.tif` : 256x256 multi-resolution/tiled TIF conversion of `TUPAC-TR-467.svs` from the dataset
 of [Tumor Proliferation Assessment Challenge 2016](http://tupac.tue-image.nl/node/3) (TUPAC16 | MICCAI Grand Challenge) which are publicly
 available through [The Cancer Genome Atlas (TCGA)](https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) under [CC BY 3.0 License](https://creativecommons.org/licenses/by/3.0/)
-- `philips_tiff_000.tif` : `patient_100_node_0.tif` from the [Camelyon16 challenge data](https://drive.google.com/drive/folders/0BzsdkU4jWx9BUzVXeUg0dUNOR1U) (another [link](https://camelyon17.grand-challenge.org/Data/)) which is under [CC0 License](https://choosealicense.com/licenses/cc0-1.0/)
+- `philips_tiff_000.tif` : `normal_042.tif` from the [Camelyon16 challenge data](ftp://parrot.genomics.cn/gigadb/pub/10.5524/100001_101000/100439/CAMELYON16/training/normal/normal_042.tif) (another [link](https://camelyon17.grand-challenge.org/Data/)) which is under [CC0 License](https://choosealicense.com/licenses/cc0-1.0/)
diff --git a/test_data/gen_images.sh b/test_data/gen_images.sh

Original file line number	Diff line number	Diff line change
`@@ -43,6 +43,8 @@ static AppConfig g_config;`
`43`	`43`
`44`	`44`	`static void test_basic(benchmark::State& state)`
`45`	`45`	`{`
	`46`	`+ std::string input_path = g_config.get_input_path();`
	`47`	`+`
`46`	`48`	`int arg = -1;`
`47`	`49`	`for (auto state_item : state)`
`48`	`50`	`{`
`@@ -57,7 +59,7 @@ static void test_basic(benchmark::State& state)`
`57`	`59`
`58`	`60`	`if (g_config.discard_cache)`
`59`	`61`	`{`
`60`		`- int fd = open(g_config.input_file.c_str(), O_RDONLY);`
	`62`	`+ int fd = open(input_path.c_str(), O_RDONLY);`
`61`	`63`	`fdatasync(fd);`
`62`	`64`	`posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED);`
`63`	`65`	`close(fd);`
`@@ -83,7 +85,7 @@ static void test_basic(benchmark::State& state)`
`83`	`85`	`return;`
`84`	`86`	`}`
`85`	`87`
`86`		`- auto handle = image_format->formats[0].image_parser.open(g_config.input_file.c_str());`
	`88`	`+ auto handle = image_format->formats[0].image_parser.open(input_path.c_str());`
`87`	`89`
`88`	`90`	`cucim::io::format::ImageMetadata metadata{};`
`89`	`91`	`image_format->formats[0].image_parser.parse(&handle, &metadata.desc());`
`@@ -118,6 +120,8 @@ static void test_basic(benchmark::State& state)`
`118`	`120`
`119`	`121`	`static void test_openslide(benchmark::State& state)`
`120`	`122`	`{`
	`123`	`+ std::string input_path = g_config.get_input_path();`
	`124`	`+`
`121`	`125`	`int arg = -1;`
`122`	`126`	`for (auto _ : state)`
`123`	`127`	`{`
`@@ -132,15 +136,15 @@ static void test_openslide(benchmark::State& state)`
`132`	`136`
`133`	`137`	`if (g_config.discard_cache)`
`134`	`138`	`{`
`135`		`- int fd = open(g_config.input_file.c_str(), O_RDONLY);`
	`139`	`+ int fd = open(input_path.c_str(), O_RDONLY);`
`136`	`140`	`fdatasync(fd);`
`137`	`141`	`posix_fadvise(fd, 0, 0, POSIX_FADV_DONTNEED);`
`138`	`142`	`close(fd);`
`139`	`143`	`}`
`140`	`144`	`}`
`141`	`145`	`state.ResumeTiming();`
`142`	`146`
`143`		`- openslide_t* slide = openslide_open(g_config.input_file.c_str());`
	`147`	`+ openslide_t* slide = openslide_open(input_path.c_str());`
`144`	`148`	`uint32_t* buf = static_cast<uint32_t>(cucim_malloc(state.range(0) state.range(0) * 4));`
`145`	`149`	`int64_t request_location[2] = { 0, 0 };`
`146`	`150`	`if (g_config.random_start_location)`
`@@ -177,10 +181,11 @@ static bool remove_help_option(int* argc, char** argv)`
`177`	`181`
`178`	`182`	`static bool setup_configuration()`
`179`	`183`	`{`
`180`		`- openslide_t* slide = openslide_open(g_config.input_file.c_str());`
	`184`	`+ std::string input_path = g_config.get_input_path();`
	`185`	`+ openslide_t* slide = openslide_open(input_path.c_str());`
`181`	`186`	`if (slide == nullptr)`
`182`	`187`	`{`
`183`		`- fmt::print("[Error] Cannot load {}!\n", g_config.input_file);`
	`188`	`+ fmt::print("[Error] Cannot load {}!\n", input_path);`
`184`	`189`	`return false;`
`185`	`190`	`}`
`186`	`191`
`@@ -205,7 +210,8 @@ int main(int argc, char** argv)`
`205`	`210`	`// if (::benchmark::ReportUnrecognizedArguments(argc, argv))`
`206`	`211`	`// return 1;`
`207`	`212`	`CLI::App app{ "benchmark: cuSlide" };`
`208`		`- app.add_option("--test_file", g_config.input_file, "An input .tif/.svs file path");`
	`213`	`+ app.add_option("--test_folder", g_config.test_folder, "An input test folder path");`
	`214`	`+ app.add_option("--test_file", g_config.test_file, "An input test image file path");`
`209`	`215`	`app.add_option("--discard_cache", g_config.discard_cache, "Discard page cache for the input file for each iteration");`
`210`	`216`	`app.add_option("--random_seed", g_config.random_seed, "A random seed number");`
`211`	`217`	`app.add_option(`
Original file line number	Diff line number	Diff line change
`@@ -20,12 +20,15 @@`
`20`	`20`	`#include <string>`
`21`	`21`	`#include <cstdlib>`
`22`	`22`
	`23`	`+#define XSTR(x) STR(x)`
	`24`	`+#define STR(x) #x`
	`25`	`+`
`23`	`26`	`struct AppConfig`
`24`	`27`	`{`
`25`	`28`	`std::string test_folder;`
`26`	`29`	`std::string test_file;`
`27`	`30`	`std::string temp_folder = "/tmp";`
`28`		`- std::string get_input_path(const char* default_value = "private/generic_tiff_000.tif") const`
	`31`	`+ std::string get_input_path(const std::string default_value = "generated/tiff_stripe_4096x4096_256.tif") const`
`29`	`32`	`{`
`30`	`33`	// If `test_file` is absolute path
`31`	`34`	`if (!test_folder.empty() && test_file.substr(0, 1) == "/")`
`@@ -56,7 +59,7 @@ struct AppConfig`
`56`	`59`	`}`
`57`	`60`	`}`
`58`	`61`	`}`
`59`		`- std::string get_plugin_path(const char* default_value = "cucim.kit.cuslide@0.0.0.so")`
	`62`	`+ std::string get_plugin_path(const char* default_value = "cucim.kit.cuslide@" XSTR(CUCIM_VERSION) ".so")`
`60`	`63`	`{`
`61`	`64`	`std::string plugin_path = default_value;`
`62`	`65`	`if (const char* env_p = std::getenv("CUCIM_TEST_PLUGIN_PATH"))`
Original file line number	Diff line number	Diff line change
`@@ -161,7 +161,7 @@`
`161`	`161`	`"cwd": "${workspaceFolder}",`
`162`	`162`	`"env": {`
`163`	`163`	`// Workaround the environment variable issue: https://github.com/microsoft/vscode/issues/121470`
`164`		`- "PATH": "${env:PATH}"`
	`164`	`+ "PATH": "${env:HOME}/.local/bin:${env:PATH}"`
`165`	`165`	`}`
`166`	`166`	`},`
`167`	`167`	`"presentation": {`