Add CZI writer functions and update CMakeLists.txt

Updated CMakeLists.txt to include new source files and headers for `func_createcziwriter`, `func_addsubblock`, and `func_closecziwriter`. Included new headers and removed commented-out includes in `mexFunctions.cpp`. Uncommented `CreateCziWriter`, `AddSubBlock`, and `CloseCziWriter` entries in `CMexFunctions::funcItems`. Added `func_addsubblock.cpp` and `func_addsubblock.h` for `MexFunction_AddSubBlock_CheckArguments` and `MexFunction_AddSubBlock_Execute`. Added `func_closecziwriter.cpp` and `func_closecziwriter.h` for `MexFunction_CloseCziWriter_CheckArguments` and `MexFunction_CloseCziWriter_Execute`. Added `func_createcziwriter.cpp` and `func_createcziwriter.h` for `MexFunction_CreateCziWriter_CheckArguments` and `MexFunction_CreateCziWriter_Execute`.
ptahmose · Oct 6, 2024 · 241da33 · 241da33
1 parent 27580c9
commit 241da33
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Showing 8 changed files with 309 additions and 7 deletions.
diff --git a/lib/CMakeLists.txt b/lib/CMakeLists.txt
@@ -1,6 +1,6 @@
 set (libSourceFiles
-			include/function.h
-			src/function.cpp
+			"include/function.h"
+			"src/function.cpp"
 			"src/mexFunctions.h" 
 			"src/errorcodes.h" 
 			"src/errorcodes.cpp" 
@@ -45,8 +45,16 @@ set (libSourceFiles
 			"src/functions/func_getsinglechannelscalingtilecomposite.cpp"
 			"src/functions/func_close.cpp" 
 			"src/functions/func_close.h"
-
- "src/functions/func_getdefaultdisplaysettings.cpp" "src/functions/func_getdefaultdisplaysettings.h" "src/functions/func_getsubblock.cpp" "src/functions/func_getsubblock.h")
+			"src/functions/func_getdefaultdisplaysettings.cpp" 
+			"src/functions/func_getdefaultdisplaysettings.h" 
+			"src/functions/func_getsubblock.cpp" 
+			"src/functions/func_getsubblock.h" 
+			"src/functions/func_createcziwriter.cpp" 
+			"src/functions/func_createcziwriter.h" 
+			"src/functions/func_addsubblock.cpp" 
+			"src/functions/func_addsubblock.h" 
+			"src/functions/func_closecziwriter.cpp" 
+			"src/functions/func_closecziwriter.h")
 
 if(CMAKE_BUILD_TYPE MATCHES Debug)
  set(lib_ENABLE_LOGGING 1)

diff --git a/lib/src/functions/func_addsubblock.cpp b/lib/src/functions/func_addsubblock.cpp
@@ -0,0 +1,157 @@
+#include "func_addsubblock.h"
+//#include "libraryInfo.h"
+#include "../implementation/CziWriterManager.h"
+#include <limits>
+#include <memory>
+#include <optional>
+
+#include "../implementation/argsutils.h"
+#include "../implementation/dbgprint.h"
+//#include "mexapi.h"
+#include "../implementation/utils.h"
+
+using namespace std;
+
+
+void MexFunction_AddSubBlock_CheckArguments(MatlabArgs* args)
+{
+    // argument 1 : [int] handle
+    // argument 2 : [string] coordinate, e.g. 'C1Z23T4'
+    // argument 3 : [array of 4 numbers] logical position and size of the subblock
+    // argument 4 : [int or string] Pixeltype
+    // argument 5 : [array] data
+    // argument 6 : [struct] optional information (e.g. M-index or metadata-xml)
+    if (args->nrhs < 6)
+    {
+        throw invalid_argument("not enough arguments");
+    }
+
+    if (!CArgsUtils::IsNumericArrayOfMinSize(args->prhs[1], 1, args->app_functions))
+    {
+        throw invalid_argument("1st argument must be an integer");
+    }
+
+    //if (!MexApi::GetInstance().MxIsChar(args->prhs[2]))
+    if (args->app_functions->pfn_IsChar(args->prhs[2]))
+    {
+        throw invalid_argument("2nd argument must be a string");
+    }
+
+    if (!CArgsUtils::IsNumericArrayOfMinSize(args->prhs[3], 4, args->app_functions))
+    {
+        throw invalid_argument("3nd argument must be a ROI");
+    }
+
+    //if (!CArgsUtils::IsNumericArrayOfMinSize(args->prhs[4], 1, args->app_functions) && !MexApi::GetInstance().MxIsChar(args->prhs[4]))
+    if (!CArgsUtils::IsNumericArrayOfMinSize(args->prhs[4], 1, args->app_functions) && !args->app_functions->pfn_IsChar(args->prhs[4]))
+    {
+        throw invalid_argument("4th argument must be an integer or a string");
+    }
+
+    CArgsUtils::ArrayInfo array_info;
+    if (!CArgsUtils::TryGetArrayInfo(args->prhs[5], &array_info, args->app_functions))
+    {
+        throw invalid_argument("5th argument must be an array");
+    }
+
+    if (array_info.number_of_dimensions != 2 && array_info.number_of_dimensions != 3)
+    {
+        throw invalid_argument("5th argument must be a 2D array or a 3D array");
+    }
+
+    if (array_info.number_of_dimensions==3 && array_info.dimensions[2] != 3)
+    {
+        throw invalid_argument("If the 5th argument is a 3D array, the 3rd dimension must be 3");
+    }
+
+    if (args->nrhs >= 7)
+    {
+        if (!CArgsUtils::IsStructure(args->prhs[6], args->app_functions))
+        {
+            throw invalid_argument("6th argument must be a structure");
+        }
+    }
+}
+
+void MexFunction_AddSubBlock_Execute(MatlabArgs* args)
+{
+    int id;
+    bool b = CArgsUtils::TryGetInt32(args->prhs[1], &id, args->app_functions);
+    if (!b)
+    {
+        throw invalid_argument("1st argument must be an integer");
+    }
+
+    // get the coordinate of the subblock
+    libCZI::CDimCoordinate coord;
+    b = CArgsUtils::TryGetDimCoordinate(args->prhs[2], &coord, args->app_functions);
+    if (!b)
+    {
+        throw invalid_argument("2nd argument must be a string defining the coordinate");
+    }
+
+    // get the logical position/size
+    libCZI::IntRect rect;
+    b = CArgsUtils::TryGetIntRect(args->prhs[3], &rect, args->app_functions);
+    if (!b)
+    {
+        throw invalid_argument("3rd argument must be an array of 4 numbers");
+    }
+
+    // determine the pixel type for the subblock
+    libCZI::PixelType pixel_type;
+    b = CArgsUtils::TryGetPixelType(args->prhs[4], &pixel_type, args->app_functions);
+    if (!b)
+    {
+        throw invalid_argument("4th argument must be an integer or a string identifying a valid pixel type");
+    }
+
+    CArgsUtils::ArrayInfo array_info;
+    b = CArgsUtils::TryGetArrayInfo(args->prhs[5], &array_info, args->app_functions);
+    if (!b)
+    {
+        throw invalid_argument("5th argument must be an array");
+    }
+
+    std::optional<int> m_index;
+    string metadata_xml;
+    libCZI::Utils::CompressionOption compression_option = make_pair(libCZI::CompressionMode::UnCompressed, nullptr);
+    if (args->nrhs >= 7)
+    {
+        int i;
+        if (CArgsUtils::TryGetIntValueOfField(args->prhs[6], "M", &i, args->app_functions))
+        {
+            m_index = i;
+        }
+
+        CArgsUtils::TryGetStringValueOfField(args->prhs[6], "metadata_xml", &metadata_xml, args->app_functions);
+
+        string compression_options_text;
+        if (CArgsUtils::TryGetStringValueOfField(args->prhs[6], "compression", &compression_options_text, args->app_functions))
+        {
+            compression_option = libCZI::Utils::ParseCompressionOptions(compression_options_text);
+        }
+    }
+
+    if (array_info.dimensions[1] > (numeric_limits<int>::max)() || array_info.dimensions[0] > (numeric_limits<int>::max)())
+    {
+        throw invalid_argument("Array dimensions are too large");
+    }
+
+    std::shared_ptr<CziWriter> writer = ::Utils::GetWriterOrThrow(id);
+    libCZI::AddSubBlockInfoBase add_sub_block_info_base;
+    add_sub_block_info_base.Clear();
+    add_sub_block_info_base.coordinate = coord;
+    add_sub_block_info_base.x = rect.x;
+    add_sub_block_info_base.y = rect.y;
+    add_sub_block_info_base.logicalWidth = rect.w;
+    add_sub_block_info_base.logicalHeight = rect.h;
+    add_sub_block_info_base.physicalWidth = static_cast<int>(array_info.dimensions[1]);
+    add_sub_block_info_base.physicalHeight = static_cast<int>(array_info.dimensions[0]);
+    add_sub_block_info_base.PixelType = pixel_type;
+    add_sub_block_info_base.mIndex = m_index.value_or(0);
+    add_sub_block_info_base.mIndexValid = m_index.has_value();
+
+    auto bitmap_data = Utils::ConvertToBitmapData(array_info, pixel_type);
+    writer->AddSubBlock(add_sub_block_info_base, bitmap_data, metadata_xml, compression_option);
+}
diff --git a/lib/src/functions/func_addsubblock.h b/lib/src/functions/func_addsubblock.h
@@ -0,0 +1,6 @@
+#pragma once
+
+#include "../mexFunctions.h"
+
+void MexFunction_AddSubBlock_CheckArguments(MatlabArgs* args);
+void MexFunction_AddSubBlock_Execute(MatlabArgs* args);
diff --git a/lib/src/functions/func_closecziwriter.cpp b/lib/src/functions/func_closecziwriter.cpp
@@ -0,0 +1,48 @@
+#include "func_open.h"
+//#include "libraryInfo.h"
+//#include <vector>
+#include <memory>
+
+#include "../implementation/CziWriterManager.h"
+#include "../implementation/dbgprint.h"
+//#include "mexapi.h"
+#include "../implementation/utils.h"
+
+using namespace std;
+
+
+void MexFunction_CloseCziWriter_CheckArguments(MatlabArgs* args)
+{
+    // argument 1 : [int] handle
+    if (args->nrhs < 2)
+    {
+        throw invalid_argument("not enough arguments");
+    }
+
+    if (!CArgsUtils::IsNumericArrayOfMinSize(args->prhs[1], 1, args->app_functions))
+    {
+        throw invalid_argument("1st argument must be an integer");
+    }
+}
+
+void MexFunction_CloseCziWriter_Execute(MatlabArgs* args)
+{
+    int id;
+    bool b = CArgsUtils::TryGetInt32(args->prhs[1], &id, args->app_functions);
+    if (!b)
+    {
+        throw invalid_argument("1st argument must be an integer");
+    }
+
+    std::shared_ptr<CziWriter> writer = ::Utils::GetWriterOrThrow(id);
+    writer->Close();
+    writer.reset();
+
+    VDBGPRINT((CDbg::Level::Trace, "MexFunction_CloseCziWriter_Execute: trying to remove instance with id=%i.", id));
+    b = CziWriterManager::GetInstance().RemoveInstance(id);
+    if (!b)
+    {
+        VDBGPRINT((CDbg::Level::Trace, "MexFunction_CloseCziWriter_Execute: removing instance with id=%i failed.", id));
+        throw invalid_argument("invalid handle specified");
+    }
+}
diff --git a/lib/src/functions/func_closecziwriter.h b/lib/src/functions/func_closecziwriter.h
@@ -0,0 +1,6 @@
+#pragma once
+
+#include "../mexFunctions.h"
+
+void MexFunction_CloseCziWriter_CheckArguments(MatlabArgs* args);
+void MexFunction_CloseCziWriter_Execute(MatlabArgs* args);
diff --git a/lib/src/functions/func_createcziwriter.cpp b/lib/src/functions/func_createcziwriter.cpp
@@ -0,0 +1,70 @@
+#include "func_open.h"
+//#include "libraryInfo.h"
+#include "../implementation/CziWriterManager.h"
+#include <vector>
+#include <memory>
+
+#include "../implementation/CziReaderManager.h"
+#include "../implementation/dbgprint.h"
+#include "../implementation/utils.h"
+
+using namespace std;
+
+
+void MexFunction_CreateCziWriter_CheckArguments(MatlabArgs* args)
+{
+    // 2nd argument : [string] filename
+    // 3rd argument : [string] -optional- 'x' or 'overwrite' 
+    if (args->nrhs < 2)
+    {
+        throw invalid_argument("not enough arguments");
+    }
+
+    //if (!MexApi::GetInstance().MxIsChar(args->prhs[1], args->app_functions))
+    if (args->app_functions->pfn_IsChar(args->prhs[1]))
+    {
+        throw invalid_argument("Expecting a string as 2nd argument");
+    }
+
+    if (args->nrhs >= 2)
+    {
+        //if (!MexApi::GetInstance().MxIsChar(args->prhs[1], args->app_functions))
+        if (args->app_functions->pfn_IsChar(args->prhs[2]))
+        {
+            throw invalid_argument("Expecting a string as 3rd argument");
+        }
+    }
+}
+
+void MexFunction_CreateCziWriter_Execute(MatlabArgs* args)
+{
+    //const auto filename = MexApi::GetInstance().UpMxArrayToMatlabAllocatedUtf8String(args->prhs[1]);
+    const auto filename = CArgsUtils::GetAsUtf8String(args->prhs[1], args->app_functions);
+
+    bool overwrite_existing_file = false;
+    if (args->nrhs >= 2)
+    {
+        //const auto option = MexApi::GetInstance().UpMxArrayToMatlabAllocatedUtf8String(args->prhs[2]);
+        const auto option = CArgsUtils::GetAsUtf8String(args->prhs[2], args->app_functions);
+        if (option == "x" || option == "overwrite")
+        {
+            overwrite_existing_file = true;
+        }
+    }
+
+    int id = CziWriterManager::GetInstance().CreateNewInstance();
+    auto reader = CziWriterManager::GetInstance().GetInstance(id);
+    try
+    {
+        VDBGPRINT((CDbg::Level::Trace, "MexFunction_CreateCziWriter_Execute: attempting to create file \"%s\".", filename.c_str()));
+        reader->Create(filename, overwrite_existing_file);
+    }
+    catch (exception& excp)
+    {
+        VDBGPRINT((CDbg::Level::Warn, "MexFunction_CreateCziWriter_Execute: Open failed -> %s.", excp.what()));
+        CziReaderManager::GetInstance().RemoveInstance(id);
+        throw;
+    }
+
+    args->plhs[0] = MexUtils::Int32To1x1Matrix(id, args->app_functions);
+}
diff --git a/lib/src/functions/func_createcziwriter.h b/lib/src/functions/func_createcziwriter.h
@@ -0,0 +1,6 @@
+#pragma once
+
+#include "../mexFunctions.h"
+
+void MexFunction_CreateCziWriter_CheckArguments(MatlabArgs* args);
+void MexFunction_CreateCziWriter_Execute(MatlabArgs* args);
diff --git a/lib/src/mexFunctions.cpp b/lib/src/mexFunctions.cpp
@@ -12,8 +12,10 @@
 #include "functions/func_close.h"
 #include "functions/func_getdefaultdisplaysettings.h"
 #include "functions/func_getsubblock.h"
+#include "functions/func_createcziwriter.h"
+#include "functions/func_addsubblock.h"
+#include "functions/func_closecziwriter.h"
 /*
-#include "src/func_createcziwriter.h"
 #include "src/func_addsubblock.h"
 #include "src/func_closecziwriter.h"
 */
@@ -35,11 +37,10 @@
     {u8"GetBitmapFromSubBlock", {MexFunction_GetBitmapFromSubBlock_CheckArguments,MexFunction_GetBitmapFromSubBlock_Execute}},
     {u8"GetMetadataFromSubBlock", {MexFunction_GetMetadataFromSubBlock_CheckArguments,MexFunction_GetMetadataFromSubBlock_Execute}},
     {u8"ReleaseSubBlock", {MexFunction_ReleaseSubBlock_CheckArguments,MexFunction_ReleaseSubBlock_Execute}},
-    /*
     {u8"CreateCziWriter", {MexFunction_CreateCziWriter_CheckArguments, MexFunction_CreateCziWriter_Execute}},
     {u8"AddSubBlock", {MexFunction_AddSubBlock_CheckArguments, MexFunction_AddSubBlock_Execute}},
     {u8"CloseCziWriter", {MexFunction_CloseCziWriter_CheckArguments, MexFunction_CloseCziWriter_Execute}},
-    */
+    /* */
 };
 
 /*static*/CMexFunctions CMexFunctions::instance;