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feat(image-io): Add --information-only flag
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Support only reading and writing image metadata as opposed to pixel
data.

Also output whether an IO can read or write a image with a json output
that contains a boolean.
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@thewtex
thewtex committed Oct 3, 2023
1 parent 34d9762 commit 564e678
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Showing 5 changed files with 125 additions and 81 deletions.
11 changes: 7 additions & 4 deletions include/itkInputImageIO.h
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Original file line number Diff line number Diff line change
Expand Up @@ -92,10 +92,13 @@ bool lexical_cast(const std::string &input, InputImageIO &inputImageIO)
const rapidjson::Value & dataJson = document["data"];
const std::string dataString( dataJson.GetString() );
const char * dataPtr = reinterpret_cast< char * >( std::strtoull(dataString.substr(35).c_str(), nullptr, 10) );
WasmImageIOBase::PixelDataContainerType * pixelDataContainer = wasmImageIOBase->GetPixelDataContainer();
const size_t pixelDataBytes = wasmImageIO->GetImageSizeInBytes();
pixelDataContainer->resize(pixelDataBytes);
pixelDataContainer->assign(dataPtr, dataPtr + pixelDataBytes);
if (dataPtr != nullptr)
{
WasmImageIOBase::PixelDataContainerType * pixelDataContainer = wasmImageIOBase->GetPixelDataContainer();
const size_t pixelDataBytes = wasmImageIO->GetImageSizeInBytes();
pixelDataContainer->resize(pixelDataBytes);
pixelDataContainer->assign(dataPtr, dataPtr + pixelDataBytes);
}
wasmImageIOBase->SetImageIO(wasmImageIO, false);
wasmImageIOBase->SetJSON(json);

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29 changes: 25 additions & 4 deletions include/itkOutputImageIO.h
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,12 @@ namespace wasm
class OutputImageIO
{
public:

/** Set whether to only read image metadata. Do not read the pixel data. */
void SetInformationOnly(bool informationOnly) {
this->m_InformationOnly = informationOnly;
}

void Set(ImageIOBase * imageIO) {
this->m_ImageIO = imageIO;
}
Expand Down Expand Up @@ -76,13 +82,19 @@ class OutputImageIO
wasmImageIOBase->SetImageIO(this->m_ImageIO);
setMemoryStoreOutputDataObject(0, index, wasmImageIOBase);

const auto directionAddress = reinterpret_cast< size_t >( &(wasmImageIOBase->GetDirectionContainer()->at(0)) );
const auto directionSize = wasmImageIOBase->GetDirectionContainer()->size() * sizeof(double);
setMemoryStoreOutputArray(0, index, 1, directionAddress, directionSize);

if (this->m_InformationOnly)
{
return;
}

const auto dataAddress = reinterpret_cast< size_t >( &(wasmImageIOBase->GetPixelDataContainer()->at(0)) );
const auto dataSize = wasmImageIOBase->GetPixelDataContainer()->size();
setMemoryStoreOutputArray(0, index, 0, dataAddress, dataSize);

const auto directionAddress = reinterpret_cast< size_t >( &(wasmImageIOBase->GetDirectionContainer()->at(0)) );
const auto directionSize = wasmImageIOBase->GetDirectionContainer()->size() * sizeof(double);
setMemoryStoreOutputArray(0, index, 1, directionAddress, directionSize);
}
#else
std::cerr << "Memory IO not supported" << std::endl;
Expand Down Expand Up @@ -117,12 +129,19 @@ class OutputImageIO
{
ioRegion.SetSize(dim, this->m_ImageIO->GetDimensions( dim ));
}

this->m_ImageIO->SetIORegion( ioRegion );
this->m_ImageIO->SetUseStreamedReading(false);
this->m_ImageIO->Read(reinterpret_cast< void * >( &(pixelData.at(0)) ));

wasmImageIO->SetFileName(this->m_Identifier);
wasmImageIO->WriteImageInformation();

if (this->m_InformationOnly)
{
return;
}

this->m_ImageIO->Read(reinterpret_cast< void * >( &(pixelData.at(0)) ));
wasmImageIO->SetIORegion( ioRegion );
wasmImageIO->Write(reinterpret_cast< void * >( &(pixelData.at(0)) ));
}
Expand All @@ -136,6 +155,8 @@ class OutputImageIO
typename ImageIOBase::Pointer m_ImageIO;

std::string m_Identifier;

bool m_InformationOnly{ false };
};

bool lexical_cast(const std::string &input, OutputImageIO &outputImageIO)
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2 changes: 1 addition & 1 deletion package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@
"build:wasi:dicom": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/dicom -b wasi-build build",
"build:wasi:compare-images": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/compare-images -b wasi-build build",
"build:wasi:image-io": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/image-io -b wasi-build build",
"build:wasi:packages": "npm run build:wasi:compress-stringify && npm run build:bindgen:python:compress-stringify && npm run build:wasi:compare-images && npm run build:bindgen:python:compare-images && npm run build:wasi:dicom && npm run build:bindgen:python:dicom && npm run build:wasi:dicom && npm run build:bindgen:python:image-io",
"build:wasi:packages": "npm run build:wasi:compress-stringify && npm run build:bindgen:python:compress-stringify && npm run build:wasi:compare-images && npm run build:bindgen:python:compare-images && npm run build:wasi:dicom && npm run build:bindgen:python:dicom && npm run build:wasi:image-io && npm run build:bindgen:python:image-io",
"cypress:open": "npx cypress open",
"cypress:run": "npx cypress run --config defaultCommandTimeout=8000",
"cypress:install": "npx cypress install",
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79 changes: 44 additions & 35 deletions packages/image-io/read-image.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
#include "itkImageIOBase.h"
#include "itkImage.h"
#include "itkOutputImageIO.h"
#include "itkOutputTextStream.h"

#ifndef IMAGE_IO_CLASS
#error "IMAGE_IO_CLASS definition must be provided"
Expand Down Expand Up @@ -74,24 +75,28 @@
#endif
#include "itkWasmImageIO.h"

#define PIPELINE_NAME (#IMAGE_IO_KEBAB_NAME "read-image")
#define VALUE(string) #string
#define TO_LITERAL(string) VALUE(string)

#include "itkPipeline.h"
#include "itkOutputImage.h"

template <typename TImageIO>
int readImage(const std::string & inputFileName, itk::wasm::OutputImageIO & outputImageIO, bool quiet)
int readImage(const std::string & inputFileName, itk::wasm::OutputTextStream & couldRead, itk::wasm::OutputImageIO & outputImageIO, bool informationOnly)
{
using ImageIOType = TImageIO;

auto imageIO = ImageIOType::New();

if(!imageIO->CanReadFile(inputFileName.c_str()))
outputImageIO.SetInformationOnly(informationOnly);

if (imageIO->CanReadFile(inputFileName.c_str()))
{
couldRead.Get() << "true\n";
}
else
{
if(!quiet)
{
std::cerr << "Could not read file: " << inputFileName << std::endl;
}
couldRead.Get() << "false\n";
return EXIT_FAILURE;
}

Expand All @@ -103,65 +108,69 @@ int readImage(const std::string & inputFileName, itk::wasm::OutputImageIO & outp

int main (int argc, char * argv[])
{
itk::wasm::Pipeline pipeline("PIPELINE_NAME", "Read an image file format and convert it to the itk-wasm file format", argc, argv);
const char * pipelineName = TO_LITERAL(IMAGE_IO_KEBAB_NAME) "-read-image";
itk::wasm::Pipeline pipeline(pipelineName, "Read an image file format and convert it to the itk-wasm file format", argc, argv);

std::string inputFileName;
pipeline.add_option("input-image", inputFileName, "Input image")->required()->check(CLI::ExistingFile)->type_name("INPUT_BINARY_FILE");
pipeline.add_option("serialized-image", inputFileName, "Input image serialized in the file format")->required()->check(CLI::ExistingFile)->type_name("INPUT_BINARY_FILE");

itk::wasm::OutputTextStream couldRead;
pipeline.add_option("could-read", couldRead, "Whether the input could be read. If false, the output image is not valid.")->type_name("OUTPUT_JSON");

itk::wasm::OutputImageIO outputImageIO;
pipeline.add_option("output-image", outputImageIO, "Output image")->required()->type_name("OUTPUT_IMAGE");
pipeline.add_option("image", outputImageIO, "Output image")->required()->type_name("OUTPUT_IMAGE");

bool quiet = false;
pipeline.add_flag("-q,--quiet", quiet, "Less verbose output");
bool informationOnly = false;
pipeline.add_flag("-i,--information-only", informationOnly, "Only read image metadata -- do not read pixel data.");

ITK_WASM_PARSE(pipeline);

#if IMAGE_IO_CLASS == 0
return readImage<itk::PNGImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::PNGImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 1
return readImage<itk::MetaImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::MetaImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 2
return readImage<itk::TIFFImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::TIFFImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 3
return readImage<itk::NiftiImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::NiftiImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 4
return readImage<itk::JPEGImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::JPEGImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 5
return readImage<itk::NrrdImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::NrrdImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 6
return readImage<itk::VTKImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::VTKImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 7
return readImage<itk::BMPImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::BMPImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 8
return readImage<itk::HDF5ImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::HDF5ImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 9
return readImage<itk::MINCImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::MINCImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 10
return readImage<itk::MRCImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::MRCImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 11
return readImage<itk::LSMImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::LSMImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 12
return readImage<itk::MGHImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::MGHImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 13
return readImage<itk::BioRadImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::BioRadImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 14
return readImage<itk::GiplImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::GiplImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 15
return readImage<itk::GE4ImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::GE4ImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 16
return readImage<itk::GE5ImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::GE5ImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 17
return readImage<itk::GEAdwImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::GEAdwImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 18
return readImage<itk::GDCMImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::GDCMImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 19
return readImage<itk::ScancoImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::ScancoImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 20
return readImage<itk::FDFImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::FDFImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 21
return readImage<itk::WasmImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::WasmImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#elif IMAGE_IO_CLASS == 22
return readImage<itk::WasmZstdImageIO>(inputFileName, outputImageIO, quiet);
return readImage<itk::WasmZstdImageIO>(inputFileName, couldRead, outputImageIO, informationOnly);
#else
#error "Unsupported IMAGE_IO_CLASS"
#endif
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