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Nov 3, 2021
Merged

Update initial cpp unittests #128

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37 changes: 35 additions & 2 deletions benchmarks/config.h
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Original file line number Diff line number Diff line change
@@ -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.
Expand All @@ -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;
Comment on lines -24 to +25
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@jakirkham jakirkham Oct 29, 2021

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We may want to revisit at some point and look at using std::filesystem::path. Though that requires C++17 and we were already using std::string. So just a future note

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@gigony gigony Oct 30, 2021

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Thanks!
Created a issue for following up:

bool discard_cache = false;
int random_seed = 0;
bool random_start_location = false;
Expand All @@ -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
23 changes: 15 additions & 8 deletions benchmarks/main.cpp
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Original file line number Diff line number Diff line change
@@ -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.
Expand Down Expand Up @@ -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)
{
Expand All @@ -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);
Expand All @@ -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, "");
Expand All @@ -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)
{
Expand All @@ -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)
Expand Down Expand Up @@ -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;
Expand All @@ -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(
Expand Down
37 changes: 35 additions & 2 deletions cpp/plugins/cucim.kit.cuslide/benchmarks/config.h
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Original file line number Diff line number Diff line change
@@ -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.
Expand All @@ -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;
Expand All @@ -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
20 changes: 13 additions & 7 deletions cpp/plugins/cucim.kit.cuslide/benchmarks/main.cpp
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Expand Up @@ -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)
{
Expand All @@ -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);
Expand All @@ -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());
Expand Down Expand Up @@ -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)
{
Expand All @@ -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)
Expand Down Expand Up @@ -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;
}

Expand All @@ -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(
Expand Down
4 changes: 2 additions & 2 deletions cpp/plugins/cucim.kit.cuslide/tests/config.h
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@@ -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.
Expand All @@ -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) == "/")
Expand Down
7 changes: 5 additions & 2 deletions cpp/tests/config.h
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Expand Up @@ -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) == "/")
Expand Down Expand Up @@ -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"))
Expand Down
15 changes: 15 additions & 0 deletions cpp/tests/test_read_region.cpp
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Expand Up @@ -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();
Expand Down
2 changes: 1 addition & 1 deletion cucim.code-workspace
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Expand Up @@ -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": {
Expand Down
1 change: 1 addition & 0 deletions python/cucim/tests/util/gen_image.py
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Expand Up @@ -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')
Expand Down
11 changes: 9 additions & 2 deletions test_data/README.md
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Expand Up @@ -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/)
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