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@ptahmose
ptahmose committed Oct 6, 2024
1 parent 5ce7657 commit a6a6ae0
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Showing 3 changed files with 29 additions and 24 deletions.
2 changes: 1 addition & 1 deletion AppModel/include/app_api.h
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ struct IAppExtensionFunctions

Parameter* (*pfn_GetField)(const Parameter* parameter, const char* field_name);

Parameter* (*pfn_CreateNumericArrayReal)(size_t ndim, const size_t* dims, enum AppExtensionClassId class_id); //*
Parameter* (*pfn_CreateNumericArrayReal)(size_t ndim, const size_t* dims, enum AppExtensionClassId class_id);
};

#ifdef __cplusplus
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43 changes: 24 additions & 19 deletions lib/src/implementation/CziReader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -125,7 +125,7 @@ Parameter* CziReader::GetDefaultDisplaySettingsAsMxArray(IAppExtensionFunctions*
return CziReader::ConvertToMatlabStruct(*displaySettings, app_functions);
}

Parameter* CziReader::GetSubBlockImage(int sbBlkNo)
Parameter* CziReader::GetSubBlockImage(int sbBlkNo, IAppExtensionFunctions* app_functions)
{
auto sbBlk = this->reader->ReadSubBlock(sbBlkNo);
if (!sbBlk)
Expand All @@ -136,7 +136,7 @@ Parameter* CziReader::GetSubBlockImage(int sbBlkNo)
}

auto bm = sbBlk->CreateBitmap();
return ConvertToMxArray(bm.get());
return ConvertToMxArray(bm.get(), app_functions);
}

Parameter* CziReader::GetMultiChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const char* displaySettingsJson, IAppExtensionFunctions* app_functions)
Expand Down Expand Up @@ -169,7 +169,7 @@ Parameter* CziReader::GetMultiChannelScalingTileComposite(const libCZI::IntRect&
// we need to deal with the pathological case that all channels are disabled
if (activeChannels.empty())
{
return CziReader::GetMultiChannelScalingTileCompositeAllChannelsDisabled(roi, zoom);
return CziReader::GetMultiChannelScalingTileCompositeAllChannelsDisabled(roi, zoom, app_functions);
}

IntSize sizeResult;
Expand Down Expand Up @@ -234,13 +234,13 @@ Parameter* CziReader::GetMultiChannelScalingTileCompositeAllChannelsDisabled(con
return arr;
}

Parameter* CziReader::GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom)
Parameter* CziReader::GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, IAppExtensionFunctions* app_functions)
{
const RgbFloatColor backgndCol{ 0,0,0 };
return this->GetSingleChannelScalingTileComposite(roi, planeCoordinate, zoom, backgndCol);
return this->GetSingleChannelScalingTileComposite(roi, planeCoordinate, zoom, backgndCol, app_functions);
}

Parameter* CziReader::GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const libCZI::RgbFloatColor& backgroundColor)
Parameter* CziReader::GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const libCZI::RgbFloatColor& backgroundColor, IAppExtensionFunctions* app_functions)
{
auto scsta = this->reader->CreateSingleChannelScalingTileAccessor();
libCZI::IntSize size = scsta->CalcSize(roi, zoom);
Expand All @@ -263,7 +263,7 @@ Parameter* CziReader::GetSingleChannelScalingTileComposite(const libCZI::IntRect
accessorGetOptions.backGroundColor = backgroundColor;
auto bitmap = scsta->Get(pixeltype, roi, planeCoordinate, zoom, &accessorGetOptions);

auto* mxarray = ConvertToMxArray(bitmap.get());
auto* mxarray = ConvertToMxArray(bitmap.get(), app_functions);
return mxarray;
}

Expand All @@ -273,49 +273,54 @@ std::shared_ptr<libCZI::IDisplaySettings> CziReader::GetDisplaySettingsFromCzi()
return this->displaySettingsFromCzi;
}

/*static*/Parameter* CziReader::ConvertToMxArray(libCZI::IBitmapData* bitmapData)
/*static*/Parameter* CziReader::ConvertToMxArray(libCZI::IBitmapData* bitmapData, IAppExtensionFunctions* app_functions)
{
auto mexApi = MexApi::GetInstance();
//auto mexApi = MexApi::GetInstance();
switch (bitmapData->GetPixelType())
{
case PixelType::Gray8:
{
auto* arr = mexApi.MxCreateNumericMatrix(bitmapData->GetHeight(), bitmapData->GetWidth(), mxUINT8_CLASS, mxREAL);
CziReader::CopyTransposeGray8(bitmapData, mexApi.MxGetData(arr), 1 * static_cast<size_t>(bitmapData->GetHeight()));
//auto* arr = mexApi.MxCreateNumericMatrix(bitmapData->GetHeight(), bitmapData->GetWidth(), mxUINT8_CLASS, mxREAL);
auto* arr = app_functions->pfn_CreateNumericMatrixReal(bitmapData->GetHeight(), bitmapData->GetWidth(), AppExtensionClassId_Uint8);
CziReader::CopyTransposeGray8(bitmapData, app_functions->pfn_GetData(arr)/*mexApi.MxGetData(arr)*/, 1 * static_cast<size_t>(bitmapData->GetHeight()));
return arr;
}
case PixelType::Gray16:
{
auto* arr = mexApi.MxCreateNumericMatrix(bitmapData->GetHeight(), bitmapData->GetWidth(), mxUINT16_CLASS, mxREAL);
CziReader::CopyTransposeGray16(bitmapData, mexApi.MxGetData(arr), 2 * static_cast<size_t>(bitmapData->GetHeight()));
//auto* arr = mexApi.MxCreateNumericMatrix(bitmapData->GetHeight(), bitmapData->GetWidth(), mxUINT16_CLASS, mxREAL);
auto* arr = app_functions->pfn_CreateNumericMatrixReal(bitmapData->GetHeight(), bitmapData->GetWidth(), AppExtensionClassId_Uint16);
CziReader::CopyTransposeGray16(bitmapData, app_functions->pfn_GetData(arr)/*mexApi.MxGetData(arr)*/, 2 * static_cast<size_t>(bitmapData->GetHeight()));
return arr;
}
case PixelType::Bgr24:
{
size_t dims[3] = { bitmapData->GetHeight(), bitmapData->GetWidth(), 3 };
auto* arr = mexApi.MxCreateNumericArray(3, dims, mxUINT8_CLASS, mxREAL);
//auto* arr = mexApi.MxCreateNumericArray(3, dims, mxUINT8_CLASS, mxREAL);
auto* arr = app_functions->pfn_CreateNumericArrayReal(3, dims, AppExtensionClassId_Uint8);
CziReader::CopyTransposeInterleavedToPlanarBgr24(
bitmapData,
mexApi.MxGetData(arr),
app_functions->pfn_GetData(arr),//mexApi.MxGetData(arr),
static_cast<size_t>(bitmapData->GetHeight()),
static_cast<size_t>(bitmapData->GetWidth()) * static_cast<size_t>(bitmapData->GetHeight()));
return arr;
}
case PixelType::Bgr48:
{
size_t dims[3] = { bitmapData->GetHeight(), bitmapData->GetWidth() ,3 };
auto* arr = mexApi.MxCreateNumericArray(3, dims, mxUINT16_CLASS, mxREAL);
//auto* arr = mexApi.MxCreateNumericArray(3, dims, mxUINT16_CLASS, mxREAL);
auto* arr = app_functions->pfn_CreateNumericArrayReal(3, dims, AppExtensionClassId_Uint16);
CziReader::CopyTransposeInterleavedToPlanarBgr48(
bitmapData,
mexApi.MxGetData(arr),
app_functions->pfn_GetData(arr),//mexApi.MxGetData(arr),
static_cast<size_t>(bitmapData->GetHeight()) * 2,
static_cast<size_t>(bitmapData->GetWidth()) * static_cast<size_t>(bitmapData->GetHeight()) * 2);
return arr;
}
case PixelType::Gray32Float:
{
auto* arr = mexApi.MxCreateNumericMatrix(bitmapData->GetHeight(), bitmapData->GetWidth(), mxSINGLE_CLASS, mxREAL);
CziReader::CopyTransposeGrayFloat(bitmapData, mexApi.MxGetData(arr), 4 * static_cast<size_t>(bitmapData->GetHeight()));
//auto* arr = mexApi.MxCreateNumericMatrix(bitmapData->GetHeight(), bitmapData->GetWidth(), mxSINGLE_CLASS, mxREAL);
auto* arr = app_functions->pfn_CreateNumericMatrixReal(bitmapData->GetHeight(), bitmapData->GetWidth(), AppExtensionClassId_Single);
CziReader::CopyTransposeGrayFloat(bitmapData, app_functions->pfn_GetData(arr)/*mexApi.MxGetData(arr)*/, 4 * static_cast<size_t>(bitmapData->GetHeight()));
return arr;
}
default:
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8 changes: 4 additions & 4 deletions lib/src/implementation/CziReader.h
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,10 @@ class CziReader

Parameter* GetDefaultDisplaySettingsAsMxArray(IAppExtensionFunctions* app_functions);

Parameter* GetSubBlockImage(int sbBlkNo);
Parameter* GetSubBlockImage(int sbBlkNo, IAppExtensionFunctions* app_functions);
Parameter* GetMultiChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const char* displaySettingsJson, IAppExtensionFunctions* app_functions);
Parameter* GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom);
Parameter* GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const libCZI::RgbFloatColor& backgroundColor);
Parameter* GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, IAppExtensionFunctions* app_functions);
Parameter* GetSingleChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const libCZI::RgbFloatColor& backgroundColor, IAppExtensionFunctions* app_functions);

std::array<double, 3> GetScaling();
Parameter* GetScalingAsMatlabStruct(IAppExtensionFunctions* app_functions);
Expand All @@ -55,7 +55,7 @@ class CziReader
Parameter* GetMultiChannelScalingTileComposite(const libCZI::IntRect& roi, const libCZI::IDimCoordinate* planeCoordinate, float zoom, const libCZI::IDisplaySettings* displaySettings, IAppExtensionFunctions* app_functions);
Parameter* GetMultiChannelScalingTileCompositeAllChannelsDisabled(const libCZI::IntRect& roi, float zoom, IAppExtensionFunctions* app_functions);

static Parameter* ConvertToMxArray(libCZI::IBitmapData* bitmapData);
static Parameter* ConvertToMxArray(libCZI::IBitmapData* bitmapData, IAppExtensionFunctions* app_functions);
static Parameter* ConvertToMatlabStruct(const std::map<int, libCZI::BoundingBoxes>& boundingBoxMap);
static Parameter* ConvertToMatlabStruct(const libCZI::IntRect& rect);
static Parameter* ConvertToMatlabStruct(const libCZI::IntSize& size);
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