Improvement in benchmark code and more results.

czi-format/benchmark_results/16_bit_z_stack/cont2.csv

+filename;subblock;pixel;width;height;compression;level;originalSize;compressedSize;compressedZ;compressionRatio;compressionRatioZ;compressionTime;compressionTimeZ
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;1;31457280;21706534;21415370;1.44921;1.46891;11678.00000;13538.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;1;31457280;18234356;17989964;1.72517;1.74860;83573.00000;83512.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;1;31457280;16811950;17070792;1.87113;1.84275;56895.00000;55434.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;2;31457280;21591821;21323216;1.45691;1.47526;12449.00000;11485.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;2;31457280;18204064;18028864;1.72804;1.74483;104041.00000;105380.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;2;31457280;16651274;16889420;1.88918;1.86254;55824.00000;54975.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;4;31457280;21596789;21318920;1.45657;1.47556;26670.00000;19498.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;4;31457280;17228332;17036472;1.82590;1.84647;129261.00000;128921.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;4;31457280;16562542;16762954;1.89930;1.87660;56634.00000;56815.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;3;31457280;21442671;21217301;1.46704;1.48262;14582.00000;15215.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;3;31457280;18188892;18055964;1.72948;1.74221;131293.00000;129141.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;3;31457280;16592079;16803872;1.89592;1.87203;56129.00000;56221.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;5;31457280;21534975;21269344;1.46075;1.47900;32021.00000;26092.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;5;31457280;17217048;17049480;1.82710;1.84506;132761.00000;132771.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;5;31457280;16528830;16719271;1.90318;1.88150;56316.00000;57042.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;6;31457280;21320230;21074519;1.47547;1.49267;41487.00000;48189.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;6;31457280;17216344;17046576;1.82718;1.84537;133741.00000;134992.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;6;31457280;16505227;16698103;1.90590;1.88388;56457.00000;57019.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;7;31457280;21313059;21067513;1.47596;1.49317;44391.00000;46510.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;7;31457280;17217068;17058500;1.82710;1.84408;136071.00000;135122.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;7;31457280;16482554;16672843;1.90852;1.88674;57403.00000;58249.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;9;31457280;21313063;21067526;1.47596;1.49316;47200.00000;49093.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;9;31457280;17217716;17057428;1.82703;1.84420;137389.00000;137355.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;9;31457280;16456890;16645416;1.91150;1.88985;58076.00000;58180.00000
+16Bit-ZStack.czi;999;Gray16;0;0;GZIP;8;31457280;21313063;21067526;1.47596;1.49316;48028.00000;46358.00000
+16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;8;31457280;17217716;17057428;1.82703;1.84420;139170.00000;137580.00000
+16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;8;31457280;16466766;16661084;1.91035;1.88807;57603.00000;57905.00000

czi-format/benchmark_results/16bit_z_stack_continuous_sorted.csv → czi-format/benchmark_results/artemia_at_z_sect/cont2.csv

 filename;subblock;pixel;width;height;compression;level;originalSize;compressedSize;compressedZ;compressionRatio;compressionRatioZ;compressionTime;compressionTimeZ
-16Bit-ZStack.czi;999;Gray16;0;0;GZIP;8;31457280;21313063;21067526;1.47596;1.49316;2014.00000;1985.00000
-16Bit-ZStack.czi;999;Gray16;0;0;LZMA2;8;31457280;17217716;17057428;1.82703;1.84420;15858.00000;21924.00000
-16Bit-ZStack.czi;999;Gray16;0;0;BZIP2;8;31457280;16466766;16661084;1.91035;1.88807;2958.00000;3136.00000
+AxioZoom_Artemia_AT-1Ch-Z_sect.czi;999;Gray16;0;0;GZIP;9;112594560;41693860;39222947;2.70051;2.87063;117712.00000;161881.00000
+AxioZoom_Artemia_AT-1Ch-Z_sect.czi;999;Gray16;0;0;LZMA2;9;112594560;31991164;31405776;3.51955;3.58515;205168.00000;199336.00000
+AxioZoom_Artemia_AT-1Ch-Z_sect.czi;999;Gray16;0;0;BZIP2;9;112594560;31016055;31077959;3.63020;3.62297;9036.00000;8966.00000

czi-format/benchmark_results/llc_emerald/llc_emarald_cherry_cont.csv

 filename;subblock;pixel;width;height;compression;level;originalSize;compressedSize;compressedZ;compressionRatio;compressionRatioZ;compressionTime;compressionTimeZ
+LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;GZIP;6;109051904;77916943;76868930;1.3996;1.4187;;
+LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;GZIP;8;109051904;77917145;76861800;1.3996;1.4188;;
+LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;GZIP;9;109051904;77917145;76861800;1.3996;1.4188;;
 LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;LZMA;5;109051904;66187466;65277759;1.64762;1.67060;59000;54000
 LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;LZMA;6;109051904;66179814;65281171;1.64780;1.67050;;
+LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;LZMA;9;109051904;66192740;65375130;1.6475;1.6681;;
 LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;BZIP2;5;109051904;64453164;64496632;1.692;1.6908;;
 LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;BZIP2;6;109051904;64442979;64488307;1.6922;1.691;;
 LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;BZIP2;8;109051904;64399634;64472449;1.6934;1.6914;;
-LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;BZIP2;8;109051904;64381885;64458062;1.6938;1.6918;;
+LLC-PK1_TubX-emerald_H2B-mCherry-2chZ(SD).czi;999;Gray16;0;0;BZIP2;9;109051904;64381885;64458062;1.6938;1.6918;;
+
+
+

czi-format/czi-parser/compression/benchmark.h

@@ -3,6 +3,7 @@
 #include "../czi_file.h"
 #include "../file_system.h"
 #include <iomanip>
+#include <thread>
 
 struct BenchmarkRecord
 {
@@ -69,29 +70,77 @@ void write_report(const std::vector<BenchmarkRecord> &results, const std::string
     }
 }
 
+static void compression_thread_work(const ByteArray &data, CompressionMethod method, int compressionLevel, CompressionResult &result, const char *info)
+{
+    auto compResult = test_compression_method(data, method, compressionLevel);
+    result = compResult;
+    printf("Completed: %s\n", info);
+}
+
 static std::vector<BenchmarkRecord> benchmark_continuos_compression_one_level(const ByteArray &data, const ByteArray &zOrderedData, int compressionLevel)
 {
+    // // CompressionMethod_GZIP
+    // CompressionResult gzipResult = test_compression_method(data, CompressionMethod_GZIP, compressionLevel);
+    // CompressionResult gzipZResult = test_compression_method(zOrderedData, CompressionMethod_GZIP, compressionLevel);
+
+    // BenchmarkRecord gzipRecord(gzipResult, gzipZResult);
+    // gzipRecord.compressionLevel = compressionLevel;
+    // gzipRecord.compressionMethod = GZIP_NAME;
+
+    // // CompressionMethod_LZMA
+    // CompressionResult lzmaResult = test_compression_method(data, CompressionMethod_LZMA, compressionLevel);
+    // CompressionResult lzmaZResult = test_compression_method(zOrderedData, CompressionMethod_LZMA, compressionLevel);
+
+    // BenchmarkRecord lzmaRecord(lzmaResult, lzmaZResult);
+    // lzmaRecord.compressionLevel = compressionLevel;
+    // lzmaRecord.compressionMethod = LZMA2_NAME;
+
+    // // CompressionMethod_BZIP2
+    // CompressionResult bzip2Result = test_compression_method(data, CompressionMethod_BZIP2, compressionLevel);
+    // CompressionResult bzip2ZResult = test_compression_method(zOrderedData, CompressionMethod_BZIP2, compressionLevel);
+
+    // BenchmarkRecord bzip2Record(bzip2Result, bzip2ZResult);
+    // bzip2Record.compressionLevel = compressionLevel;
+    // bzip2Record.compressionMethod = BZIP2_NAME;
 
     // CompressionMethod_GZIP
-    CompressionResult gzipResult = test_compression_method(data, CompressionMethod_GZIP, compressionLevel);
-    CompressionResult gzipZResult = test_compression_method(zOrderedData, CompressionMethod_GZIP, compressionLevel);
+    CompressionResult gzipResult = {};
+    CompressionResult gzipZResult = {};
+
+    // CompressionMethod_LZMA
+    CompressionResult lzmaResult = {};
+    CompressionResult lzmaZResult = {};
+
+    // CompressionMethod_BZIP2
+    CompressionResult bzip2Result = {};
+    CompressionResult bzip2ZResult = {};
+
+    std::vector<std::thread> workers;
+    workers.resize(6);
+    // We know that lzma is slowest, let's run all three in threads.
+    workers[0] = std::thread(compression_thread_work, std::ref(data), CompressionMethod_GZIP, compressionLevel, std::ref(gzipResult), "Gzip normal order");
+    workers[1] = std::thread(compression_thread_work, std::ref(zOrderedData), CompressionMethod_GZIP, compressionLevel, std::ref(gzipZResult), "Gzip Z order");
+
+    workers[2] = std::thread(compression_thread_work, std::ref(data), CompressionMethod_LZMA, compressionLevel, std::ref(lzmaResult), "LZMA normal order");
+    workers[3] = std::thread(compression_thread_work, std::ref(zOrderedData), CompressionMethod_LZMA, compressionLevel, std::ref(lzmaZResult), "LZMA Z order");
+
+    workers[4] = std::thread(compression_thread_work, std::ref(data), CompressionMethod_BZIP2, compressionLevel, std::ref(bzip2Result), "Bzip2 normal order");
+    workers[5] = std::thread(compression_thread_work, std::ref(zOrderedData), CompressionMethod_BZIP2, compressionLevel, std::ref(bzip2ZResult), "Bzip2 Z order");
+
+    for (size_t i = 0; i < workers.size(); i++)
+    {
+        workers[i].join();
+    }
+    printf("All threads completed.\n");
 
     BenchmarkRecord gzipRecord(gzipResult, gzipZResult);
     gzipRecord.compressionLevel = compressionLevel;
     gzipRecord.compressionMethod = GZIP_NAME;
 
-    // CompressionMethod_LZMA
-    CompressionResult lzmaResult = test_compression_method(data, CompressionMethod_LZMA, compressionLevel);
-    CompressionResult lzmaZResult = test_compression_method(zOrderedData, CompressionMethod_LZMA, compressionLevel);
-
     BenchmarkRecord lzmaRecord(lzmaResult, lzmaZResult);
     lzmaRecord.compressionLevel = compressionLevel;
     lzmaRecord.compressionMethod = LZMA2_NAME;
 
-    // CompressionMethod_BZIP2
-    CompressionResult bzip2Result = test_compression_method(data, CompressionMethod_BZIP2, compressionLevel);
-    CompressionResult bzip2ZResult = test_compression_method(zOrderedData, CompressionMethod_BZIP2, compressionLevel);
-
     BenchmarkRecord bzip2Record(bzip2Result, bzip2ZResult);
     bzip2Record.compressionLevel = compressionLevel;
     bzip2Record.compressionMethod = BZIP2_NAME;

czi-format/czi-parser/czi_file.cpp

@@ -365,7 +365,8 @@ ByteArray CziFile::get_continuous_image_data(const bool ZCurveOrdered) const
     size_t bufferEnd = 0;
 
     // Rather than simply putting images one after the other, order them by channels.
-#if 1
+    // Compression ratios aren't better, so we won't waste time with sorting right now.
+#if 0
     int loaded = 0;
     for (size_t channel = 0; channel < subBlockDirectory.channelCount; channel++)
     {

czi-format/czi-parser/main.cpp

@@ -18,6 +18,7 @@ int main(int argc, char **argv)
     args::HelpFlag helpMethod(mainMethodGroup, "help", "Print help", {'h', "help"});
     args::Flag reportMethod(mainMethodGroup, "report", "Basic information about CZI file. [verbose]", {"report"});
     args::Flag compressionTestMethod(mainMethodGroup, "compression-test", "Compress subblocks and output compression ratios <compression method>", {"compression-test"});
+    args::Flag versionMethod(mainMethodGroup, "Version test", "Check version", {"version", 'V'});
     args::Flag benchmarkMethod(mainMethodGroup, "Compression benchmark", "Start compression benchmark for selected CZI file. <report-file> [continuos] [verbose].", {"benchmark"});
     args::Flag exportDataMethod(mainMethodGroup, "Export binary dat", "Export raw image data <folder> [continuos]", {"dump-data"});
     args::Flag exportImagesMethod(mainMethodGroup, "Export images", "Export images to ppm files <folder>", {"dump-images"});
@@ -54,6 +55,16 @@ int main(int argc, char **argv)
         return 1;
     }
 
+    if (versionMethod)
+    {
+#if DEBUG
+        printf("DEBUG\n");
+#else
+        printf("RELEASE\n");
+#endif
+        return 0;
+    }
+
     CziParser parser(dontParseMetadataOption.Get());
     auto parsedFile = parser.parse_czi_file(cziFile.Get());