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STYLE: Move three internal helper functions into the unnamed namespace #72

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Sep 9, 2024
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STYLE: Move three internal helper functions into the unnamed namespace #72

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170 changes: 85 additions & 85 deletions src/itkOMEZarrNGFFImageIO.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -372,46 +372,6 @@ MakeKVStoreHTTPDriverSpec(nlohmann::json & spec, const std::string & fullPath)
spec["kvstore"]["path"] = fullPath.substr(fullPath.find_last_of("/") + 1);
}

} // namespace

struct OMEZarrNGFFImageIO::TensorStoreData
{
tensorstore::Context tsContext{ tensorstore::Context::Default() };
tensorstore::TensorStore<> store{};
};

OMEZarrNGFFImageIO::OMEZarrNGFFImageIO()
: m_TensorStoreData(std::make_unique<TensorStoreData>())
{
this->AddSupportedWriteExtension(".zarr");
this->AddSupportedWriteExtension(".zr2");
this->AddSupportedWriteExtension(".zr3");
this->AddSupportedWriteExtension(".zip");
this->AddSupportedWriteExtension(".memory");

this->AddSupportedReadExtension(".zarr");
this->AddSupportedReadExtension(".zr2");
this->AddSupportedReadExtension(".zr3");
this->AddSupportedReadExtension(".zip");
this->AddSupportedWriteExtension(".memory");

this->Self::SetCompressor("");
this->Self::SetMaximumCompressionLevel(9);
this->Self::SetCompressionLevel(2);
}

OMEZarrNGFFImageIO::~OMEZarrNGFFImageIO() = default;


void
OMEZarrNGFFImageIO::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "DatasetIndex: " << m_DatasetIndex << std::endl;
os << indent << "TimeIndex: " << m_TimeIndex << std::endl;
os << indent << "ChannelIndex: " << m_ChannelIndex << std::endl;
}

// JSON file path, e.g. "C:/Dev/ITKIOOMEZarrNGFF/v0.4/cyx.ome.zarr/.zgroup"
void
writeJson(nlohmann::json json, std::string path, std::string driver, tensorstore::Context& tsContext)
Expand Down Expand Up @@ -466,6 +426,91 @@ jsonRead(const std::string path, nlohmann::json & result, std::string driver, te
}
}

void
addCoordinateTransformations(OMEZarrNGFFImageIO * io, nlohmann::json ct)
{
itkAssertOrThrowMacro(ct.is_array(), "Failed to parse coordinate transforms");
itkAssertOrThrowMacro(ct.size() >= 1, "Expected at least one coordinate transform");
itkAssertOrThrowMacro(ct[0].at("type") == "scale",
("Expected first transform to be \"scale\" but found " +
std::string(ct[0].at("type")))); // first transformation must be scale

nlohmann::json s = ct[0].at("scale");
itkAssertOrThrowMacro(s.is_array(), "Failed to parse scale transform");
unsigned dim = s.size();
itkAssertOrThrowMacro(dim == io->GetNumberOfDimensions(), "Found dimension mismatch in scale transform");

for (unsigned d = 0; d < dim; ++d)
{
double dS = s[dim - d - 1].get<double>(); // reverse indices KJI into IJK
io->SetSpacing(d, dS * io->GetSpacing(d));
io->SetOrigin(d, dS * io->GetOrigin(d)); // TODO: should we update origin like this?
}

if (ct.size() > 1) // there is also a translation
{
itkAssertOrThrowMacro(ct[1].at("type") == "translation",
("Expected second transform to be \"translation\" but found " +
std::string(ct[1].at("type")))); // first transformation must be scale
nlohmann::json tr = ct[1].at("translation");
itkAssertOrThrowMacro(tr.is_array(), "Failed to parse translation transform");
dim = tr.size();
itkAssertOrThrowMacro(dim == io->GetNumberOfDimensions(), "Found dimension mismatch in translation transform");

for (unsigned d = 0; d < dim; ++d)
{
double dOrigin = tr[dim - d - 1].get<double>(); // reverse indices KJI into IJK
io->SetOrigin(d, dOrigin + io->GetOrigin(d));
}
}

if (ct.size() > 2)
{
itkGenericOutputMacro(<< "A sequence of more than 2 transformations is specified in '" << io->GetFileName()
<< "'. This is currently not supported. Extra transformations are ignored.");
}
}

} // namespace

struct OMEZarrNGFFImageIO::TensorStoreData
{
tensorstore::Context tsContext{ tensorstore::Context::Default() };
tensorstore::TensorStore<> store{};
};

OMEZarrNGFFImageIO::OMEZarrNGFFImageIO()
: m_TensorStoreData(std::make_unique<TensorStoreData>())
{
this->AddSupportedWriteExtension(".zarr");
this->AddSupportedWriteExtension(".zr2");
this->AddSupportedWriteExtension(".zr3");
this->AddSupportedWriteExtension(".zip");
this->AddSupportedWriteExtension(".memory");

this->AddSupportedReadExtension(".zarr");
this->AddSupportedReadExtension(".zr2");
this->AddSupportedReadExtension(".zr3");
this->AddSupportedReadExtension(".zip");
this->AddSupportedWriteExtension(".memory");

this->Self::SetCompressor("");
this->Self::SetMaximumCompressionLevel(9);
this->Self::SetCompressionLevel(2);
}

OMEZarrNGFFImageIO::~OMEZarrNGFFImageIO() = default;


void
OMEZarrNGFFImageIO::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "DatasetIndex: " << m_DatasetIndex << std::endl;
os << indent << "TimeIndex: " << m_TimeIndex << std::endl;
os << indent << "ChannelIndex: " << m_ChannelIndex << std::endl;
}

bool
OMEZarrNGFFImageIO::CanReadFile(const char * filename)
{
Expand Down Expand Up @@ -606,51 +651,6 @@ OMEZarrNGFFImageIO::ConfigureTensorstoreIORegion(const ImageIORegion & ioRegion)
return storeRegion;
}

void
addCoordinateTransformations(OMEZarrNGFFImageIO * io, nlohmann::json ct)
{
itkAssertOrThrowMacro(ct.is_array(), "Failed to parse coordinate transforms");
itkAssertOrThrowMacro(ct.size() >= 1, "Expected at least one coordinate transform");
itkAssertOrThrowMacro(ct[0].at("type") == "scale",
("Expected first transform to be \"scale\" but found " +
std::string(ct[0].at("type")))); // first transformation must be scale

nlohmann::json s = ct[0].at("scale");
itkAssertOrThrowMacro(s.is_array(), "Failed to parse scale transform");
unsigned dim = s.size();
itkAssertOrThrowMacro(dim == io->GetNumberOfDimensions(), "Found dimension mismatch in scale transform");

for (unsigned d = 0; d < dim; ++d)
{
double dS = s[dim - d - 1].get<double>(); // reverse indices KJI into IJK
io->SetSpacing(d, dS * io->GetSpacing(d));
io->SetOrigin(d, dS * io->GetOrigin(d)); // TODO: should we update origin like this?
}

if (ct.size() > 1) // there is also a translation
{
itkAssertOrThrowMacro(ct[1].at("type") == "translation",
("Expected second transform to be \"translation\" but found " +
std::string(ct[1].at("type")))); // first transformation must be scale
nlohmann::json tr = ct[1].at("translation");
itkAssertOrThrowMacro(tr.is_array(), "Failed to parse translation transform");
dim = tr.size();
itkAssertOrThrowMacro(dim == io->GetNumberOfDimensions(), "Found dimension mismatch in translation transform");

for (unsigned d = 0; d < dim; ++d)
{
double dOrigin = tr[dim - d - 1].get<double>(); // reverse indices KJI into IJK
io->SetOrigin(d, dOrigin + io->GetOrigin(d));
}
}

if (ct.size() > 2)
{
itkGenericOutputMacro(<< "A sequence of more than 2 transformations is specified in '" << io->GetFileName()
<< "'. This is currently not supported. Extra transformations are ignored.");
}
}

void
OMEZarrNGFFImageIO::ReadImageInformation()
{
Expand Down
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