orthanc: OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp comparison

comparison OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp @ 4834:bec432ee1094

download of numpy arrays from the REST API

author	Sebastien Jodogne <s.jodogne@gmail.com>
date	Fri, 26 Nov 2021 19:03:32 +0100
parents	7053502fbf97
children	ec1e9571b645

comparison

equal deleted inserted replaced

-:970092a67897
+:bec432ee1094
 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
 #include "../../../OrthancFramework/Sources/DicomParsing/Internals/DicomImageDecoder.h"
 #include "../../../OrthancFramework/Sources/HttpServer/HttpContentNegociation.h"
 #include "../../../OrthancFramework/Sources/Images/Image.h"
 #include "../../../OrthancFramework/Sources/Images/ImageProcessing.h"
+#include "../../../OrthancFramework/Sources/Images/NumpyWriter.h"
 #include "../../../OrthancFramework/Sources/Logging.h"
 #include "../../../OrthancFramework/Sources/MultiThreading/Semaphore.h"
 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
 #include "../OrthancConfiguration.h"
 if (windowWidth <= 1.0f)
 {
 windowWidth = 1;
 }
-if (std::abs(rescaleSlope) <= 0.1)
+if (std::abs(rescaleSlope) <= 0.0001)
 {
-rescaleSlope = 0.1;
+rescaleSlope = 0.0001;
 }
 const double scaling = 255.0 * rescaleSlope / windowWidth;
 const double offset = (rescaleIntercept - windowCenter + windowWidth / 2.0) / rescaleSlope;
 {
 Semaphore::Locker locker(throttlingSemaphore_);
 RenderedFrameHandler handler;
 IDecodedFrameHandler::Apply(call, handler, ImageExtractionMode_Preview /* arbitrary value */, true);
+}
+static void DocumentSharedNumpy(RestApiGetCall& call)
+{
+call.GetDocumentation()
+.SetUriArgument("id", "Orthanc identifier of the DICOM resource of interest")
+.SetHttpGetArgument("compress", RestApiCallDocumentation::Type_Boolean, "Compress the file as `.npz`", false)
+.SetHttpGetArgument("rescale", RestApiCallDocumentation::Type_Boolean,
+"On grayscale images, apply the rescaling and return floating-point values", false)
+.AddAnswerType(MimeType_PlainText, "Numpy file: https://numpy.org/devdocs/reference/generated/numpy.lib.format.html");
+}
+namespace
+{
+class NumpyVisitor : public boost::noncopyable
+{
+private:
+bool           rescale_;
+unsigned int   depth_;
+unsigned int   currentDepth_;
+unsigned int   height_;
+unsigned int   width_;
+PixelFormat    format_;
+ChunkedBuffer  buffer_;
+public:
+NumpyVisitor(unsigned int depth /* can be zero if 2D frame */,
+bool rescale) :
+rescale_(rescale),
+depth_(depth),
+currentDepth_(0)
+{
+}
+void WriteFrame(ParsedDicomFile& dicom,
+unsigned int frame)
+{
+std::unique_ptr<ImageAccessor> decoded(dicom.DecodeFrame(frame));
+if (decoded.get() == NULL)
+{
+throw OrthancException(ErrorCode_NotImplemented, "Cannot decode DICOM instance");
+}
+if (currentDepth_ == 0)
+{
+width_ = decoded->GetWidth();
+height_ = decoded->GetHeight();
+format_ = decoded->GetFormat();
+}
+else if (width_ != decoded->GetWidth() ||
+height_ != decoded->GetHeight())
+{
+throw OrthancException(ErrorCode_IncompatibleImageSize, "The size of the frames varies across the instance(s)");
+}
+else if (format_ != decoded->GetFormat())
+{
+throw OrthancException(ErrorCode_IncompatibleImageFormat, "The pixel format of the frames varies across the instance(s)");
+}
+if (rescale_ &&
+decoded->GetFormat() != PixelFormat_RGB24)
+{
+if (currentDepth_ == 0)
+{
+NumpyWriter::WriteHeader(buffer_, depth_, width_, height_, PixelFormat_Float32);
+}
+double rescaleIntercept, rescaleSlope;
+dicom.GetRescale(rescaleIntercept, rescaleSlope, frame);
+Image converted(PixelFormat_Float32, decoded->GetWidth(), decoded->GetHeight(), false);
+ImageProcessing::Convert(converted, *decoded);
+ImageProcessing::ShiftScale2(converted, static_cast<float>(rescaleIntercept), static_cast<float>(rescaleSlope), false);
+NumpyWriter::WritePixels(buffer_, converted);
+}
+else
+{
+if (currentDepth_ == 0)
+{
+NumpyWriter::WriteHeader(buffer_, depth_, width_, height_, format_);
+}
+NumpyWriter::WritePixels(buffer_, *decoded);
+}
+currentDepth_ ++;
+}
+void Answer(RestApiOutput& output,
+bool compress)
+{
+if ((depth_ == 0 && currentDepth_ != 1) ||
+(depth_ != 0 && currentDepth_ != depth_))
+{
+throw OrthancException(ErrorCode_BadSequenceOfCalls);
+}
+else
+{
+std::string answer;
+NumpyWriter::Finalize(answer, buffer_, compress);
+output.AnswerBuffer(answer, MimeType_Binary);
+}
+}
+};
+}
+static void GetNumpyFrame(RestApiGetCall& call)
+{
+if (call.IsDocumentation())
+{
+DocumentSharedNumpy(call);
+call.GetDocumentation()
+.SetTag("Instances")
+.SetSummary("Decode frame for numpy")
+.SetDescription("Decode one frame of interest from the given DICOM instance, for use with numpy in Python")
+.SetUriArgument("frame", RestApiCallDocumentation::Type_Number, "Index of the frame (starts at `0`)");
+}
+else
+{
+const std::string instanceId = call.GetUriComponent("id", "");
+const bool compress = call.GetBooleanArgument("compress", false);
+const bool rescale = call.GetBooleanArgument("rescale", true);
+uint32_t frame;
+if (!SerializationToolbox::ParseUnsignedInteger32(frame, call.GetUriComponent("frame", "0")))
+{
+throw OrthancException(ErrorCode_ParameterOutOfRange, "Expected an unsigned integer for the \"frame\" argument");
+}
+NumpyVisitor visitor(0 /* no depth, 2D frame */, rescale);
+{
+Semaphore::Locker throttling(throttlingSemaphore_);
+ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), instanceId);
+visitor.WriteFrame(locker.GetDicom(), frame);
+}
+visitor.Answer(call.GetOutput(), compress);
+}
+}
+static void GetNumpyInstance(RestApiGetCall& call)
+{
+if (call.IsDocumentation())
+{
+DocumentSharedNumpy(call);
+call.GetDocumentation()
+.SetTag("Instances")
+.SetSummary("Decode instance for numpy")
+.SetDescription("Decode the given DICOM instance, for use with numpy in Python");
+}
+else
+{
+const std::string instanceId = call.GetUriComponent("id", "");
+const bool compress = call.GetBooleanArgument("compress", false);
+const bool rescale = call.GetBooleanArgument("rescale", true);
+{
+Semaphore::Locker throttling(throttlingSemaphore_);
+ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), instanceId);
+const unsigned int depth = locker.GetDicom().GetFramesCount();
+if (depth == 0)
+{
+throw OrthancException(ErrorCode_BadFileFormat, "Empty DICOM instance");
+}
+NumpyVisitor visitor(depth, rescale);
+for (unsigned int frame = 0; frame < depth; frame++)
+{
+visitor.WriteFrame(locker.GetDicom(), frame);
+}
+visitor.Answer(call.GetOutput(), compress);
+}
+}
+}
+static void GetNumpySeries(RestApiGetCall& call)
+{
+if (call.IsDocumentation())
+{
+DocumentSharedNumpy(call);
+call.GetDocumentation()
+.SetTag("Series")
+.SetSummary("Decode series for numpy")
+.SetDescription("Decode the given DICOM series, for use with numpy in Python");
+}
+else
+{
+const std::string seriesId = call.GetUriComponent("id", "");
+const bool compress = call.GetBooleanArgument("compress", false);
+const bool rescale = call.GetBooleanArgument("rescale", true);
+Semaphore::Locker throttling(throttlingSemaphore_);
+ServerIndex& index = OrthancRestApi::GetIndex(call);
+SliceOrdering ordering(index, seriesId);
+unsigned int depth = 0;
+for (size_t i = 0; i < ordering.GetInstancesCount(); i++)
+{
+depth += ordering.GetFramesCount(i);
+}
+ServerContext& context = OrthancRestApi::GetContext(call);
+NumpyVisitor visitor(depth, rescale);
+for (size_t i = 0; i < ordering.GetInstancesCount(); i++)
+{
+const std::string& instanceId = ordering.GetInstanceId(i);
+unsigned int framesCount = ordering.GetFramesCount(i);
+{
+ServerContext::DicomCacheLocker locker(context, instanceId);
+for (unsigned int frame = 0; frame < framesCount; frame++)
+{
+visitor.WriteFrame(locker.GetDicom(), frame);
+}
+}
+}
+visitor.Answer(call.GetOutput(), compress);
+}
 }
 static void GetMatlabImage(RestApiGetCall& call)
 {
 Register("/instances/{id}/frames/{frame}/image-uint16", GetImage<ImageExtractionMode_UInt16>);
 Register("/instances/{id}/frames/{frame}/image-int16", GetImage<ImageExtractionMode_Int16>);
 Register("/instances/{id}/frames/{frame}/matlab", GetMatlabImage);
 Register("/instances/{id}/frames/{frame}/raw", GetRawFrame<false>);
 Register("/instances/{id}/frames/{frame}/raw.gz", GetRawFrame<true>);
+Register("/instances/{id}/frames/{frame}/numpy", GetNumpyFrame);  // New in Orthanc 1.9.8
 Register("/instances/{id}/pdf", ExtractPdf);
 Register("/instances/{id}/preview", GetImage<ImageExtractionMode_Preview>);
 Register("/instances/{id}/rendered", GetRenderedFrame);
 Register("/instances/{id}/image-uint8", GetImage<ImageExtractionMode_UInt8>);
 Register("/instances/{id}/image-uint16", GetImage<ImageExtractionMode_UInt16>);
 Register("/instances/{id}/image-int16", GetImage<ImageExtractionMode_Int16>);
 Register("/instances/{id}/matlab", GetMatlabImage);
 Register("/instances/{id}/header", GetInstanceHeader);
+Register("/instances/{id}/numpy", GetNumpyInstance);  // New in Orthanc 1.9.8
 Register("/patients/{id}/protected", IsProtectedPatient);
 Register("/patients/{id}/protected", SetPatientProtection);
 std::vector<std::string> resourceTypes;
 Register("/series/{id}/instances-tags", GetChildInstancesTags);
 Register("/instances/{id}/content/*", GetRawContent);
 Register("/series/{id}/ordered-slices", OrderSlices);
+Register("/series/{id}/numpy", GetNumpySeries);  // New in Orthanc 1.9.8
 Register("/patients/{id}/reconstruct", ReconstructResource<ResourceType_Patient>);
 Register("/studies/{id}/reconstruct", ReconstructResource<ResourceType_Study>);
 Register("/series/{id}/reconstruct", ReconstructResource<ResourceType_Series>);
 Register("/instances/{id}/reconstruct", ReconstructResource<ResourceType_Instance>);

Mercurial > hg > orthanc

comparison OrthancServer/Sources/OrthancRestApi/OrthancRestResources.cpp @ 4834:bec432ee1094