diff --git a/README.md b/README.md
index 867d5e8ff1a5456e7e496e6fcfd16236cae53097..54cf9efea3019f72b0f49990cc639a8e753f1e2f 100644
--- a/README.md
+++ b/README.md
@@ -8,10 +8,10 @@
- [ ] Feed binary data to existing compressors and produce results (tables, graphs)
- Try both data in their order and in `Z-order`
- Compressors to try:
- - gZip
- - bzip2
- - deflate
- - *B3D cuda library*
+ - [x] gZip (zLib, huffman deflate combination)
+ - [ ] bzip2
+ - [ ] deflate
+ - [ ] *B3D cuda library*
- [ ] Look at *Image difference*
- Negative values can be mapped to odd/even numbers. But the difference must be saved in more than one byte.
- Save difference in different type than byte (`short`, `uint`, `ulong`)
diff --git a/czi-format/czi-parser/CMakeLists.txt b/czi-format/czi-parser/CMakeLists.txt
index f6fab4b2aa55f2abeb712e401f546771e6ea836a..d3d9d45051d2a7587b57226aa8584fc4fdbb8e0c 100644
--- a/czi-format/czi-parser/CMakeLists.txt
+++ b/czi-format/czi-parser/CMakeLists.txt
@@ -20,6 +20,9 @@ endif()
find_package (Threads)
target_link_libraries (czi-parser ${CMAKE_THREAD_LIBS_INIT})
+find_package(ZLIB)
+target_link_libraries(czi-parser ${ZLIB_LIBRARIES})
+
set(CPACK_PROJECT_NAME ${PROJECT_NAME})
set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
include(CPack)
\ No newline at end of file
diff --git a/czi-format/czi-parser/compression/compressors.h b/czi-format/czi-parser/compression/compressors.h
index 69e5975eec12199528775ce55a40020449912613..cb4488dd26313f3b69975da35221a17a5e4230cb 100644
--- a/czi-format/czi-parser/compression/compressors.h
+++ b/czi-format/czi-parser/compression/compressors.h
@@ -3,10 +3,40 @@
#include "../utilities/vector_utilities.h"
#include "../image/z_order.h"
+namespace library_zlib
+{
+#include <zlib.h>
+};
+
enum CompressionMethod
{
CompressionMethod_RLE,
- CompressionMethod_LZ
+ CompressionMethod_LZ,
+ CompressionMethod_GZIP
+};
+
+struct CompressionResult
+{
+ size_t originalSize;
+ size_t compressedSize;
+ float compressionRatio;
+ float percentageOfOriginalSize;
+
+ CompressionResult()
+ {
+ originalSize = 0;
+ compressedSize = 0;
+ compressionRatio = 0.0f;
+ percentageOfOriginalSize = 0.0f;
+ }
+
+ void divide(float x)
+ {
+ originalSize /= x;
+ compressedSize /= x;
+ compressionRatio /= x;
+ percentageOfOriginalSize /= x;
+ }
};
constexpr size_t MAX_LITERAL_COUNT = 255;
@@ -18,6 +48,38 @@ inline float compression_ratio(float uncompressedSize, float compressedSize)
return (uncompressedSize / compressedSize);
}
+ByteArray gzip_encode(const std::vector<byte> &data)
+{
+ size_t compressedSize = library_zlib::compressBound(data.size());
+ ByteArray compressedBuffer;
+ // Maybe try reserve or normal array.
+ compressedBuffer.resize(compressedSize);
+
+ //int compressionResult = library_zlib::compress(compressedBuffer.data(), &compressedSize, data.data(), data.size());
+ int compressionResult = library_zlib::compress2(compressedBuffer.data(), &compressedSize, data.data(), data.size(), Z_BEST_COMPRESSION);
+
+ switch (compressionResult)
+ {
+ case Z_OK:
+ break;
+ case Z_MEM_ERROR:
+ printf(RED "There wasn't enaugh memory!\n" RESET);
+ break;
+ case Z_BUF_ERROR:
+ printf(RED "Output buffer was too small!\n" RESET);
+ break;
+ default:
+ INVALID_CASE;
+ }
+ always_assert(compressionResult == Z_OK);
+
+ ByteArray actualCompressedData(compressedBuffer.begin(), compressedBuffer.begin() + compressedSize);
+
+ always_assert(actualCompressedData.size() == compressedSize);
+
+ return actualCompressedData;
+}
+
// Run-Length encode bytes and return compressed bytes.
std::vector<byte> rle_encode(const std::vector<byte> &bytes)
{
@@ -264,4 +326,31 @@ void comp_test()
bool same = vecUtil::vector_eq(data, uncompressed);
always_assert(same && "Error in compression!");
-}
\ No newline at end of file
+}
+
+CompressionResult test_compression_method(const ByteArray &data, CompressionMethod method)
+{
+ ByteArray compressedData;
+ switch (method)
+ {
+ case CompressionMethod_RLE:
+ compressedData = rle_encode(data);
+ break;
+ case CompressionMethod_LZ:
+ compressedData = lz_encode(data);
+ break;
+ case CompressionMethod_GZIP:
+ compressedData = gzip_encode(data);
+ break;
+ default:
+ INVALID_CASE;
+ }
+
+ CompressionResult result = {};
+ result.originalSize = data.size();
+ result.compressedSize = compressedData.size();
+ result.compressionRatio = compression_ratio((float)result.originalSize, (float)result.compressedSize);
+ result.percentageOfOriginalSize = ((float)result.compressedSize / (float)result.originalSize) * 100.0f;
+
+ return result;
+}
diff --git a/czi-format/czi-parser/custom_types.h b/czi-format/czi-parser/custom_types.h
index f35dae1254fa46aec6f30b94cc22a4ba6d4a73ba..d29883dc64bc399aea582e99b1173dabc4714e52 100644
--- a/czi-format/czi-parser/custom_types.h
+++ b/czi-format/czi-parser/custom_types.h
@@ -23,6 +23,8 @@ typedef unsigned long ulong;
#define TagType std::string, std::string
typedef std::pair<TagType> Tag;
+typedef std::vector<byte> ByteArray;
+
// Terminal colors
#define RESET "\033[0m"
#define RED "\033[31m" /* Red */
diff --git a/czi-format/czi-parser/czi_file.cpp b/czi-format/czi-parser/czi_file.cpp
index 2d03417fc319a8a369a5f9a092381b7ddcfde7a8..40e95c07425c305eec2a6009b88dc1ba03a8cede 100644
--- a/czi-format/czi-parser/czi_file.cpp
+++ b/czi-format/czi-parser/czi_file.cpp
@@ -411,6 +411,7 @@ void CziFile::dump_image_data(const std::string &baseName) const
void CziFile::test_compression(CompressionMethod method, bool verbose) const
{
+
switch (method)
{
case CompressionMethod_LZ:
@@ -419,71 +420,49 @@ void CziFile::test_compression(CompressionMethod method, bool verbose) const
case CompressionMethod_RLE:
printf("Selected compression: RLE\n");
break;
+ case CompressionMethod_GZIP:
+ printf("Selected compression: GZIP (zlib)\n");
+ break;
default:
INVALID_CASE;
return;
}
- float dataSize, dataZSize, compressedDataSize, compressedDataZSize, ratio, ratioZ;
- float overall = 0;
- float overallZ = 0;
- size_t totalSize = 0;
- size_t totalRleSize = 0;
- size_t totalRleSizeZ = 0;
+ CompressionResult overallN;
+ CompressionResult overallZ;
+
for (size_t i = 0; i < subBlockDirectory.entries.size(); i++)
{
auto data = get_image_data(i, false);
auto dataZ = get_image_data(i, true);
- std::vector<byte> compressedData;
- std::vector<byte> compressedDataZ;
+ CompressionResult nResult = test_compression_method(data, method);
+ CompressionResult zResult = test_compression_method(dataZ, method);
- switch (method)
- {
- case CompressionMethod_LZ:
- {
- compressedData = lz_encode(data);
- compressedDataZ = lz_encode(dataZ);
- }
- break;
- case CompressionMethod_RLE:
- {
- compressedData = rle_encode(data);
- compressedDataZ = rle_encode(dataZ);
- }
- break;
- default:
- INVALID_CASE;
- return;
- }
-
- dataSize = (float)data.size();
- dataZSize = (float)dataZ.size();
- compressedDataSize = (float)compressedData.size();
- compressedDataZSize = (float)compressedDataZ.size();
+ overallN.compressionRatio += nResult.compressionRatio;
+ overallZ.compressionRatio += zResult.compressionRatio;
- ratio = compression_ratio(dataSize, compressedDataSize);
- ratioZ = compression_ratio(dataZSize, compressedDataZSize);
-
- overall += ratio;
- overallZ += ratioZ;
-
- totalSize += dataSize;
- totalRleSize += compressedDataSize;
- totalRleSizeZ += compressedDataZSize;
+ overallN.originalSize += data.size();
+ overallN.compressedSize += nResult.compressedSize;
+ overallZ.compressedSize += zResult.compressedSize;
+ overallN.percentageOfOriginalSize += nResult.percentageOfOriginalSize;
+ overallZ.percentageOfOriginalSize += zResult.percentageOfOriginalSize;
if (verbose)
{
- if (ratio > 1 || ratioZ > 1)
- printf("Subblock %-3i Compression ratios: Normal: %8f Z-Ordered: %8f\n", (int)i, ratio, ratioZ);
+ if (nResult.compressionRatio > 1.0f || zResult.compressionRatio > 1.0f)
+ printf("Subblock %-3i Compression ratios: Normal: %8f Z-Ordered: %8f; Size(N): %5.3f%%; Size(Z): %5.3f%%\n",
+ (int)i, nResult.compressionRatio, zResult.compressionRatio, nResult.percentageOfOriginalSize, zResult.percentageOfOriginalSize);
else
- printf("Subblock %-3i Compression ratios: Normal: %8f Z-Ordered: %8f\n", (int)i, ratio, ratioZ);
+ printf(RED "Subblock %-3i Compression ratios: Normal: %8f Z-Ordered: %8f; Size(N): %5.3f%%; Size(Z): %5.3f%%\n" RESET, (int)i, nResult.compressionRatio, zResult.compressionRatio, nResult.percentageOfOriginalSize, zResult.percentageOfOriginalSize);
}
}
float dataCount = (float)subBlockDirectory.entries.size();
- overall /= dataCount;
- overallZ /= dataCount;
- printf("Overall compression ratios: Normal %8f Z-Ordered: %8f\n", overall, overallZ);
- printf("Original size: %8lu B Rle size: %8lu B RleZOrder size: %8lu B\n", totalSize, totalRleSize, totalRleSizeZ);
+ overallN.divide(dataCount);
+ overallZ.divide(dataCount);
+
+ printf("Overall compression ratios: Normal %8f Z-Ordered: %8f\n", overallN.compressionRatio, overallZ.compressionRatio);
+ printf("Original size: %8lu B Compressed size: %8lu B Compressed Z-Order size: %8lu B\n", overallN.originalSize, overallN.compressedSize, overallZ.compressedSize);
+ printf("Original size (%%): 100%% Compressed: %5.5f%% Compressed Z-Order: %5.5f%%\n", overallN.percentageOfOriginalSize, overallZ.percentageOfOriginalSize);
}
\ No newline at end of file
diff --git a/czi-format/czi-parser/main.cpp b/czi-format/czi-parser/main.cpp
index 466176b1ce25586c8ef2e7412254d5c2f34d52dd..e40c3368a177d2fed85fb9c2d72f9ffaf5b27509 100644
--- a/czi-format/czi-parser/main.cpp
+++ b/czi-format/czi-parser/main.cpp
@@ -23,6 +23,7 @@ int main(int argc, char **argv)
args::Flag verboseOption(optionsGroup, "verbose", "Extend output of method", {'v', "verbose"});
args::Flag rleCompressionOption(compressionGroup, "RLE", "RLE compression", {"rle"});
args::Flag lzCompressionOption(compressionGroup, "LZ", "LZ compression", {"lz"});
+ args::Flag gzipCompressionOption(compressionGroup, "GZIP", "GZIP (zlib) compression", {"gzip"});
try
{
@@ -36,12 +37,12 @@ int main(int argc, char **argv)
}
catch (args::ValidationError &e)
{
- printf(RED "%s\n" RESET, e.what());
+ printf(RED "%s Check help with -h or --help.\n" RESET, e.what());
return 1;
}
catch (args::ParseError &pe)
{
- printf(RED "%s\n" RESET, pe.what());
+ printf(RED "%s Check help with -h or --help.\n" RESET, pe.what());
return 1;
}
@@ -55,6 +56,8 @@ int main(int argc, char **argv)
if (lzCompressionOption)
cm = CompressionMethod_LZ;
+ else if (gzipCompressionOption)
+ cm = CompressionMethod_GZIP;
parsedFile.test_compression(cm, verboseOption.Matched());
}