Add JPEG XL Lossless format to czi file

.gitignore

@@ -299,7 +299,7 @@ __pycache__/
 # exclude "cmake-build-directory"
 /cmake-build-*/
 
-/build
+/build*
 /Src/Build/VS
 /out/Src/Build/Doxygen/
 /out/

CMakeLists.txt

@@ -132,6 +132,9 @@ option(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_EIGEN3 "Prefer an Eigen3-package pres
 #  See here: https://discourse.cmake.org/t/findzstd/3506
 option(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_ZSTD "Prefer a ZSTD-package present on the system" OFF)
 
+# When this option is ON, libCZI is built with libjxl (JPEG XL) for provisional subblock compression id 7 (lossless).
+option(LIBCZI_BUILD_WITH_LIBJXL "Build with libjxl for JPEG XL lossless subblocks (experimental)" OFF)
+
 # When this option is ON, we try to use an existing RapidJSON-library. Otherwise, we download a private
 #  copy of RapidJSON during the CMake-run. This option is only relevant if building CZICmd.
 option(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_RAPIDJSON "Prefer an RapidJSON-package present on the system" ON)

Src/CZICmd/CMakeLists.txt

@@ -50,6 +50,8 @@ set (CZICMDSRCFILES
          BitmapGenFreeType.h    
          cmdlineoptions.h    
          executeCreateCzi.cpp     
+         executeReEncodeCzi.cpp
+         executeReEncodeCzi.h
          IBitmapGen.h         
          SaveBitmap.h    
          utils.h
@@ -67,6 +69,8 @@ set (CZICMDSRCFILES
          CZIcmd.cpp          
          executePlaneScan.h
          executePlaneScan.cpp
+         executeCompareImages.h
+         executeCompareImages.cpp
          executeBase.h
          executeBase.cpp
          CZIcmd.manifest    # the manifest is needed to allow long paths on windows, see https://docs.microsoft.com/en-us/windows/win32/fileio/maximum-file-path-limitation?tabs=cmd

Src/CZICmd/cmdlineoptions.cpp

@@ -539,7 +539,9 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
         { "ScalingChannelComposite",            Command::ScalingChannelComposite },
         { "ExtractAttachment",                  Command::ExtractAttachment},
         { "CreateCZI",                          Command::CreateCZI },
+        { "ReEncodeCZI",                        Command::ReEncodeCZI },
         { "PlaneScan",                          Command::PlaneScan },
+        { "CompareImages",                      Command::CompareImages },
     };
 
     const static PlaneCoordinateValidator plane_coordinate_validator;
@@ -567,6 +569,7 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
     Command argument_command;
     string argument_source_filename;
     string argument_output_filename;
+    string argument_compare_filename;
     string argument_plane_coordinate;
     string argument_rect;
     string argument_display_settings;
@@ -602,7 +605,7 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
     // editorconfig-checker-disable
     cli_app.add_option("-c,--command", argument_command,
         R"(COMMAND can be one of 'PrintInformation', 'ExtractSubBlock', 'SingleChannelTileAccessor', 'ChannelComposite',
-           'SingleChannelPyramidTileAccessor', 'SingleChannelScalingTileAccessor', 'ScalingChannelComposite', 'ExtractAttachment' and 'CreateCZI'.
+           'SingleChannelPyramidTileAccessor', 'SingleChannelScalingTileAccessor', 'ScalingChannelComposite', 'ExtractAttachment', 'CreateCZI', 'ReEncodeCZI' and 'CompareImages'.
            \N'PrintInformation' will print information about the CZI-file to the console. The argument 'info-level' can be used
            to specify which information is to be printed.
            \N'ExtractSubBlock' will write the bitmap contained in the specified sub-block to the OUTPUTFILE.
@@ -618,7 +621,9 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
            \N'ScalingChannelComposite' operates like the previous command, but in addition gets all channels and creates a multi-channel-composite from them
            using display-settings.
            \N'ExtractAttachment' allows to extract (and save to a file) the contents of attachments.)
-           \N'CreateCZI' is used to demonstrate the CZI-creation capabilities of libCZI.)
+           \N'CreateCZI' is used to demonstrate the CZI-creation capabilities of libCZI (synthetic tiles; use --createbounds; -s is not used for pixels).
+           \N'ReEncodeCZI' reads the CZI given with -s and writes a new CZI to -o with the same metadata, attachments, subblock layout, and per-subblock metadata/attachments; only the pixel payload is re-encoded per --compressionopts (e.g. jxl:, zstd1:, uncompressed:).)
+           \N'CompareImages' reads two CZIs (-s and --compare), pairs subblocks by tile layout (dimension coordinate, logical rect, physical size, pixel type, M-index), decodes each pair, and reports RMSD over all scalar samples. Directory index order may differ between files.)
            \N'PlaneScan' does the following: over a ROI given with the --rect option a rectangle of size given with 
            the --tilesize-for-plane-scan option is moved, and the image content of this rectangle is written out to
            files. The operation takes place on a plane which is given with the --plane-coordinate option. The filenames of the
@@ -641,6 +646,9 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
     cli_app.add_option("-o,--output", argument_output_filename,
         "Specifies the output-filename. A suffix will be appended to the name given here depending on the type of the file.")
         ->option_text("OUTPUTFILE");
+    cli_app.add_option("--compare", argument_compare_filename,
+        "Second CZI file for 'CompareImages' (decoded pixels are compared to -s in subblock order). Uses the same stream class and property bag as -s when set.")
+        ->option_text("COMPAREFILE");
     // editorconfig-checker-disable
     cli_app.add_option("-p,--plane-coordinate", argument_plane_coordinate,
         R"(Uniquely select a 2D-plane from the document. It is given in the form [DimChar][number], where 'DimChar' specifies a dimension and 
@@ -715,7 +723,8 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
         ->option_text("CHANNELCOMPOSITIONFORMAT")
         ->check(channelcompositionformat_validator);
     cli_app.add_option("--createbounds", arguments_createbounds,
-        "Only used for 'CreateCZI': specify the range of coordinates used to create a CZI. Format is e.g. 'T0:3Z0:3C0:2'.")
+        "Required for 'CreateCZI': dimension ranges for which synthetic tiles are written. Format is e.g. 'T0:3Z0:3C0:2' "
+        "(dimension letter, start index, colon, count). CreateCZI does not copy image data from -s.")
         ->option_text("BOUNDS")
         ->check(createbounds_validator);
     cli_app.add_option("--createsubblocksize", arguments_createsubblocksize,
@@ -752,9 +761,10 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
         ->option_text("KEY_VALUE_SUBBLOCKMETADATA")
         ->check(createsubblockmetadata_validator);
     cli_app.add_option("--compressionopts", argument_compressionoptions,
-        "Only used for 'CreateCZI': a string in a defined format which states the compression-method and (compression-method specific) "
+        "Used for 'CreateCZI' and 'ReEncodeCZI': a string in a defined format which states the compression-method and (compression-method specific) "
         "parameters. The format is \"compression_method: key=value; ...\". It starts with the name of the compression-method, followed by a colon, "
-        "then followed by a list of key-value pairs which are separated by a semicolon. Examples: \"zstd0:ExplicitLevel=3\", \"zstd1:ExplicitLevel=2;PreProcess=HiLoByteUnpack\".")
+        "then followed by a list of key-value pairs which are separated by a semicolon. Examples: \"zstd0:ExplicitLevel=3\", \"zstd1:ExplicitLevel=2;PreProcess=HiLoByteUnpack\", "
+        "\"jxl:\" or \"jxl:Effort=7;Modular=true;DecodingSpeed=0;Responsive=0\" for JPEG XL (requires LIBCZI_BUILD_WITH_LIBJXL), \"uncompressed:\" for raw pixels on ReEncodeCZI.")
         ->option_text("COMPRESSIONDESCRIPTION")
         ->check(compressionoptions_validator);
     cli_app.add_option("--generatorpixeltype", argument_generatorpixeltype,
@@ -836,6 +846,11 @@ CCmdLineOptions::ParseResult CCmdLineOptions::Parse(int argc, char** argv)
             this->SetOutputFilename(convertUtf8ToWide(argument_output_filename));
         }
 
+        if (!argument_compare_filename.empty())
+        {
+            this->compareCziFilename = convertUtf8ToWide(argument_compare_filename);
+        }
+
         if (!argument_plane_coordinate.empty())
         {
             this->planeCoordinate = libCZI::CDimCoordinate::Parse(argument_plane_coordinate.c_str());
@@ -1023,7 +1038,7 @@ bool CCmdLineOptions::CheckArgumentConsistency() const
         return false;
     }
 
-    if (cmd != Command::PrintInformation)
+    if (cmd != Command::PrintInformation && cmd != Command::CompareImages)
     {
         auto str = this->MakeOutputFilename(nullptr, nullptr);
         if (str.empty())
@@ -1034,6 +1049,13 @@ bool CCmdLineOptions::CheckArgumentConsistency() const
         }
     }
 
+    if (cmd == Command::CompareImages && this->compareCziFilename.empty())
+    {
+        ss << ERRORPREFIX << "CompareImages requires --compare <second CZI file>";
+        this->GetLog()->WriteLineStdErr(ss.str());
+        return false;
+    }
+
     switch (cmd)
     {
     case Command::ScalingChannelComposite:
@@ -1084,6 +1106,22 @@ bool CCmdLineOptions::CheckArgumentConsistency() const
         break;
     }
 
+    if (cmd == Command::CreateCZI && this->createBounds.IsEmpty())
+    {
+        ss << ERRORPREFIX << "CreateCZI requires --createbounds (for example: --createbounds \"C0:1\" or \"C0:1T0:3\"). "
+              "If bounds are empty, no subblocks are written. The source file (-s) is not read for CreateCZI; "
+              "tiles are generated only by the bitmap generator for the coordinate ranges you specify.";
+        this->GetLog()->WriteLineStdErr(ss.str());
+        return false;
+    }
+
+    if (cmd == Command::ReEncodeCZI && this->compressionMode == libCZI::CompressionMode::Invalid)
+    {
+        ss << ERRORPREFIX << "ReEncodeCZI requires --compressionopts (for example: \"jxl:\", \"jxl:Effort=5\", \"zstd1:ExplicitLevel=3\", or \"uncompressed:\").";
+        this->GetLog()->WriteLineStdErr(ss.str());
+        return false;
+    }
+
     // TODO: there is probably more to be checked
 
     return true;
@@ -1092,6 +1130,7 @@ bool CCmdLineOptions::CheckArgumentConsistency() const
 void CCmdLineOptions::Clear()
 {
     this->command = Command::Invalid;
+    this->compareCziFilename.clear();
     this->useDisplaySettingsFromDocument = true;
     this->calcHashOfResult = false;
     this->drawTileBoundaries = false;

Src/CZICmd/cmdlineoptions.h

@@ -32,9 +32,13 @@ enum class Command
 
     CreateCZI,
 
+    ReEncodeCZI,
+
     ReadWriteCZI,
 
     PlaneScan,
+
+    CompareImages,
 };
 
 enum class InfoLevel : std::uint32_t
@@ -143,6 +147,7 @@ class CCmdLineOptions
 
     Command command;
     std::wstring cziFilename;
+    std::wstring compareCziFilename;
     std::string source_stream_class;
     std::map<int, libCZI::StreamsFactory::Property> property_bag_for_stream_class;
     libCZI::CDimCoordinate planeCoordinate;
@@ -224,6 +229,7 @@ class CCmdLineOptions
     std::shared_ptr<ILog> GetLog() const { return this->log; }
     Command GetCommand() const { return this->command; }
     const std::wstring& GetCZIFilename() const { return this->cziFilename; }
+    const std::wstring& GetCompareCziFilename() const { return this->compareCziFilename; }
     const std::string& GetInputStreamClassName() const { return this->source_stream_class; }
     const std::map<int, libCZI::StreamsFactory::Property>& GetInputStreamPropertyBag() const { return this->property_bag_for_stream_class; }
     const libCZI::CDimCoordinate& GetPlaneCoordinate() const { return this->planeCoordinate; }

Src/CZICmd/execute.cpp

@@ -6,7 +6,9 @@
 #include "execute.h"
 #include "executeBase.h"
 #include "executeCreateCzi.h"
+#include "executeReEncodeCzi.h"
 #include "executePlaneScan.h"
+#include "executeCompareImages.h"
 #include "inc_libCZI.h"
 #include "SaveBitmap.h"
 #include "utils.h"
@@ -1141,9 +1143,15 @@ bool execute(const CCmdLineOptions& options)
         case Command::CreateCZI:
             success = executeCreateCzi(options);
             break;
+        case Command::ReEncodeCZI:
+            success = executeReEncodeCzi(options);
+            break;
         case Command::PlaneScan:
             success = executePlaneScan(options);
             break;
+        case Command::CompareImages:
+            success = executeCompareImages(options);
+            break;
         default:
             break;
         }

Src/CZICmd/executeBase.cpp

@@ -10,16 +10,21 @@ using namespace std;
 using namespace libCZI;
 
 std::shared_ptr<ICZIReader> CExecuteBase::CreateAndOpenCziReader(const CCmdLineOptions& options)
+{
+    return CreateAndOpenCziReaderForPath(options.GetCZIFilename().c_str(), options);
+}
+
+std::shared_ptr<ICZIReader> CExecuteBase::CreateAndOpenCziReaderForPath(const wchar_t* path, const CCmdLineOptions& options)
 {
     shared_ptr<IStream> stream;
     if (options.GetInputStreamClassName().empty())
     {
-        stream = CExecuteBase::CreateStandardFileBasedStreamObject(options.GetCZIFilename().c_str());
+        stream = CExecuteBase::CreateStandardFileBasedStreamObject(path);
     }
     else
     {
         stream = CExecuteBase::CreateInputStreamObject(
-                                options.GetCZIFilename().c_str(),
+                                path,
                                 options.GetInputStreamClassName(),
                                 &options.GetInputStreamPropertyBag());
     }

Src/CZICmd/executeBase.h

@@ -16,6 +16,7 @@ class CExecuteBase
 {
 protected:
     static std::shared_ptr<libCZI::ICZIReader> CreateAndOpenCziReader(const CCmdLineOptions& options);
+    static std::shared_ptr<libCZI::ICZIReader> CreateAndOpenCziReaderForPath(const wchar_t* path, const CCmdLineOptions& options);
     static std::shared_ptr<libCZI::IStream> CreateStandardFileBasedStreamObject(const wchar_t* fileName);
     static std::shared_ptr<libCZI::IStream> CreateInputStreamObject(const wchar_t* uri, const std::string& class_name, const std::map<int, libCZI::StreamsFactory::Property>* property_bag);
     static libCZI::IntRect GetRoiFromOptions(const CCmdLineOptions& options, const libCZI::SubBlockStatistics& subBlockStatistics);