--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancFramework/Sources/Images/NumpyWriter.cpp	Fri Nov 26 19:03:32 2021 +0100
@@ -0,0 +1,236 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2021 Osimis S.A., Belgium
+ * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation, either version 3 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "NumpyWriter.h"
+
+#if ORTHANC_ENABLE_ZLIB == 1
+#  include "../Compression/ZipWriter.h"
+#endif
+
+#if ORTHANC_SANDBOXED == 0
+#  include "../SystemToolbox.h"
+#endif
+
+#include "../OrthancException.h"
+#include "../Toolbox.h"
+
+#include <boost/lexical_cast.hpp>
+
+namespace Orthanc
+{
+  void NumpyWriter::WriteHeader(ChunkedBuffer& target,
+                                unsigned int depth,
+                                unsigned int width,
+                                unsigned int height,
+                                PixelFormat format)
+  {
+    // https://numpy.org/devdocs/reference/generated/numpy.lib.format.html
+    static const unsigned char VERSION[] = {
+      0x93, 'N', 'U', 'M', 'P', 'Y',
+      0x01 /* major version: 1 */,
+      0x00 /* minor version: 0 */
+    };
+
+    std::string datatype;
+
+    switch (Toolbox::DetectEndianness())
+    {
+      case Endianness_Little:
+        datatype = "<";
+        break;
+        
+      case Endianness_Big:
+        datatype = ">";
+        break;
+
+      default:
+        throw OrthancException(ErrorCode_InternalError);
+    }
+    
+    unsigned int channels;
+
+    switch (format)
+    {
+      case PixelFormat_Grayscale8:
+        datatype += "u1";
+        channels = 1;
+        break;
+
+      case PixelFormat_Grayscale16:
+        datatype += "u2";
+        channels = 1;
+        break;
+
+      case PixelFormat_SignedGrayscale16:
+        datatype += "s2";
+        channels = 1;
+        break;
+
+      case PixelFormat_RGB24:
+        datatype += "u1";
+        channels = 3;
+        break;
+
+      case PixelFormat_Float32:
+        datatype += "f4";
+        channels = 1;
+        break;
+
+      default:
+        throw OrthancException(ErrorCode_NotImplemented);
+    }
+
+    std::string depthString;
+    if (depth != 0)
+    {
+      depthString = boost::lexical_cast<std::string>(depth) + ", ";
+    }
+    
+    const std::string info = ("{'descr': '" + datatype + "', 'fortran_order': False, " +
+                              "'shape': (" + depthString + boost::lexical_cast<std::string>(height) +
+                              "," + boost::lexical_cast<std::string>(width) +
+                              "," + boost::lexical_cast<std::string>(channels) + "), }");
+
+    const uint16_t minimumLength = sizeof(VERSION) + sizeof(uint16_t) + info.size() + 1 /* trailing '\n' */;
+
+    // The length of the header must be evenly divisible by 64. This
+    // loop could be optimized by a "ceil()" operation, but we keep
+    // the code as simple as possible
+    uint16_t length = 64;
+    while (length < minimumLength)
+    {
+      length += 64;
+    }
+
+    uint16_t countZeros = length - minimumLength;
+    uint16_t headerLength = info.size() + countZeros + 1 /* trailing '\n' */;
+    uint8_t highByte = headerLength / 256;
+    uint8_t lowByte = headerLength % 256;
+    
+    target.AddChunk(VERSION, sizeof(VERSION));
+    target.AddChunk(&lowByte, 1);
+    target.AddChunk(&highByte, 1);
+    target.AddChunk(info);
+    target.AddChunk(std::string(countZeros, ' '));
+    target.AddChunk("\n");
+  }
+
+
+  void NumpyWriter::WritePixels(ChunkedBuffer& target,
+                                const ImageAccessor& image)
+  {
+    size_t rowSize = image.GetBytesPerPixel() * image.GetWidth();
+
+    for (unsigned int y = 0; y < image.GetHeight(); y++)
+    {
+      target.AddChunk(image.GetConstRow(y), rowSize);
+    }
+  }
+  
+
+  void NumpyWriter::Finalize(std::string& target,
+                             ChunkedBuffer& source,
+                             bool compress)
+  {
+    if (compress)
+    {
+#if ORTHANC_ENABLE_ZLIB == 1
+      // This is the default name of the first array if arrays are
+      // specified as positional arguments in "numpy.savez()"
+      // https://numpy.org/doc/stable/reference/generated/numpy.savez.html
+      const char* ARRAY_NAME = "arr_0";
+      
+      std::string uncompressed;
+      source.Flatten(uncompressed);
+
+      const bool isZip64 = (uncompressed.size() >= 1lu * 1024lu * 1024lu * 1024lu);
+
+      ZipWriter writer;
+      writer.SetMemoryOutput(target, isZip64);
+      writer.Open();
+      writer.OpenFile(ARRAY_NAME);
+      writer.Write(uncompressed);
+      writer.Close();
+#else
+      throw OrthancException(ErrorCode_InternalError, "Orthanc was compiled without support for zlib");
+#endif
+    }
+    else
+    {
+      source.Flatten(target);
+    }
+  }
+
+
+#if ORTHANC_SANDBOXED == 0
+  void NumpyWriter::WriteToFileInternal(const std::string& filename,
+                                        unsigned int width,
+                                        unsigned int height,
+                                        unsigned int pitch,
+                                        PixelFormat format,
+                                        const void* buffer)
+  {
+    std::string content;
+    WriteToMemoryInternal(content, width, height, pitch, format, buffer);
+    
+    SystemToolbox::WriteFile(content, filename);
+  }
+#endif
+
+  
+  void NumpyWriter::WriteToMemoryInternal(std::string& content,
+                                          unsigned int width,
+                                          unsigned int height,
+                                          unsigned int pitch,
+                                          PixelFormat format,
+                                          const void* buffer)
+  {
+    ChunkedBuffer chunks;
+    WriteHeader(chunks, 0 /* no depth */, width, height, format);
+
+    ImageAccessor image;
+    image.AssignReadOnly(format, width, height, pitch, buffer);
+    WritePixels(chunks, image);
+
+    Finalize(content, chunks, compressed_);
+  }
+
+
+  NumpyWriter::NumpyWriter()
+  {
+    compressed_ = false;
+  }
+
+  
+  void NumpyWriter::SetCompressed(bool compressed)
+  {
+#if ORTHANC_ENABLE_ZLIB == 1
+    compressed_ = compressed;
+#else
+    if (compressed)
+    {
+      throw OrthancException(ErrorCode_InternalError, "Orthanc was compiled without support for zlib");
+    }
+#endif
+  }
+}