added 8bit and 16bit integer export to mrc and ccp4 io

modules/io/pymod/export_map_io.cc

@@ -112,8 +112,10 @@ void export_map_io()
     .def("GetEndianessOnSave", &Spider::GetEndianessOnSave)
   ;
 
-  class_<MRC, bases<ImageFormatBase> >("MRC", init<bool,Subformat,Endianess>
-           ((arg("normalize_on_save") = false,arg("subformat")=MRC_AUTO_FORMAT,arg("endianess_on_save")=OST_LOCAL_ENDIAN)))
+  class_<MRC, bases<ImageFormatBase> >("MRC", init<bool,Subformat,Endianess,Format>
+           ((arg("normalize_on_save") = false,arg("subformat")=MRC_AUTO_FORMAT,arg("endianess_on_save")=OST_LOCAL_ENDIAN,arg("format")=OST_DEFAULT_FORMAT)))
+    .def("SetBitDepth", &MRC::SetBitDepth)
+    .def("GetBitDepth", &MRC::GetBitDepth)
     .def("SetNormalizeOnSave", &MRC::SetNormalizeOnSave)
     .def("GetNormalizeOnSave", &MRC::GetNormalizeOnSave)
     .def("SetSubformat", &MRC::SetSubformat)
@@ -122,8 +124,8 @@ void export_map_io()
     .def("GetEndianessOnSave", &MRC::GetEndianessOnSave)
   ;
 
-  class_<CCP4, bases<MRC> >("CCP4", init<bool,Endianess>
-           ((arg("normalize_on_save") = false,arg("endianess_on_save")=OST_LOCAL_ENDIAN)))
+  class_<CCP4, bases<MRC> >("CCP4", init<bool,Endianess,Format>
+           ((arg("normalize_on_save") = false,arg("endianess_on_save")=OST_LOCAL_ENDIAN,arg("format")=OST_DEFAULT_FORMAT)))
   ;
 
   class_<DM3, bases<ImageFormatBase> >("DM3", init<>())

modules/io/src/img/map_io_mrc_handler.cc

@@ -94,13 +94,24 @@ namespace ost { namespace io {
 String MRC::FORMAT_STRING = "defined_mrc";
 
 
-MRC::MRC(bool normalize_on_save, Subformat subformat,Endianess endianess_on_save):
+MRC::MRC(bool normalize_on_save, Subformat subformat,Endianess endianess_on_save, Format bit_depth):
   ImageFormatBase(FORMAT_STRING),
   subformat_(subformat),
   normalize_on_save_(normalize_on_save),
-  endianess_on_save_(endianess_on_save)
+  endianess_on_save_(endianess_on_save),
+  bit_depth_(bit_depth)
 {
 }
+Format MRC::GetBitDepth() const
+{
+  return bit_depth_;
+}
+
+void MRC::SetBitDepth (Format bitdepth)
+{
+  bit_depth_ = bitdepth;
+}
+
 
 Endianess MRC::GetEndianessOnSave() const
 {
@@ -132,8 +143,8 @@ void MRC::SetNormalizeOnSave(bool normalize_on_save)
   normalize_on_save_ = normalize_on_save;
 }
 
-CCP4::CCP4(bool normalize_on_save, Endianess endianess_on_save):
-  MRC(normalize_on_save,MRC_NEW_FORMAT,endianess_on_save)
+CCP4::CCP4(bool normalize_on_save, Endianess endianess_on_save, Format bit_depth):
+  MRC(normalize_on_save,MRC_NEW_FORMAT,endianess_on_save,bit_depth)
 {}
 
 
@@ -223,7 +234,7 @@ public:
       label[i]=' ';
     }
   }
-  header_base(const img::ConstImageHandle& im):
+  header_base(const img::ConstImageHandle& im, Format bit_depth):
     nc(),
     nr(static_cast<int>(im.GetExtent().GetSize().GetHeight())),
     ns(static_cast<int>(im.GetExtent().GetSize().GetDepth())),
@@ -247,13 +258,38 @@ public:
   {
     if(im.GetType()==img::REAL){
       nc=static_cast<int>(im.GetExtent().GetSize().GetWidth());
-      mode=2;
+      switch(bit_depth){
+      case OST_BIT8_FORMAT:
+        mode=0;
+        break;
+      case OST_BIT16_FORMAT:
+        mode=1;
+        break;
+      case OST_FLOAT_FORMAT:
+      case OST_DEFAULT_FORMAT:
+        mode=2;
+        break;
+      default:
+        throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+        break;
+      }
       x=im.GetExtent().GetSize().GetWidth()*im.GetSpatialSampling()[0];
       y=im.GetExtent().GetSize().GetHeight()*im.GetSpatialSampling()[1];
       z=im.GetExtent().GetSize().GetDepth()*im.GetSpatialSampling()[2];
     }else{
       nc=static_cast<int>(im.GetExtent().GetSize().GetWidth()/2 +1);
-      mode=4;
+      switch(bit_depth){
+      case OST_BIT16_FORMAT:
+        mode=3;
+        break;
+      case OST_FLOAT_FORMAT:
+      case OST_DEFAULT_FORMAT:
+        mode=4;
+        break;
+      default:
+        throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+        break;
+      }
       x=1.0;
       y=1.0;
       z=1.0;
@@ -342,8 +378,8 @@ public:
     yorigin(0.0)
   {
   }
-  mrc_header(const img::ConstImageHandle& im):
-    header_base(im),
+  mrc_header(const img::ConstImageHandle& im, Format bit_depth):
+    header_base(im,bit_depth),
     xorigin(0.0), // todo determine origin
     yorigin(0.0)
   {
@@ -435,8 +471,8 @@ public:
     arms()
   {
   }
-  ccp4_header(const img::ConstImageHandle& im):
-    header_base(im),
+  ccp4_header(const img::ConstImageHandle& im, Format bit_depth):
+    header_base(im,bit_depth),
     lskflag(),
     skwmat(),
     skwtrn(),
@@ -857,14 +893,39 @@ void export_helper(const img::MapHandle& image,
                                     const MRC& formatmrc)
 {
   BinaryOStream<CONVERSIONTYPE> f(out);
-  HEADER header(image);
+  HEADER header(image,formatmrc.GetBitDepth());
 
   f << header;
   if(image.GetType()==img::REAL) {
-    detail::real_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+    switch(formatmrc.GetBitDepth()){
+    case OST_BIT8_FORMAT:
+      detail::real_dumper<int8_t,CONVERSIONTYPE>(f,header,image,formatmrc);
+      break;
+    case OST_BIT16_FORMAT:
+      detail::real_dumper<int16_t,CONVERSIONTYPE>(f,header,image,formatmrc);
+      break;
+    case OST_FLOAT_FORMAT:
+    case OST_DEFAULT_FORMAT:
+      detail::real_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+      break;
+    default:
+      throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+      break;
+    }
   } else {
     if(image.GetDomain()==img::HALF_FREQUENCY){
-      detail::complex_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+      switch(formatmrc.GetBitDepth()){
+        case OST_BIT16_FORMAT:
+          detail::complex_dumper<int16_t,CONVERSIONTYPE>(f,header,image,formatmrc);
+          break;
+        case OST_FLOAT_FORMAT:
+        case OST_DEFAULT_FORMAT:
+          detail::complex_dumper<float,CONVERSIONTYPE>(f,header,image,formatmrc);
+          break;
+        default:
+          throw(IOException("MRC/CCP4 export: Bit depth not supported."));
+          break;
+      }
     } else {
       throw(IOException("MRC/CCP4 export: full complex export not supported."));
     }

modules/io/src/img/map_io_mrc_handler.hh

@@ -28,7 +28,10 @@ class DLLEXPORT_OST_IO MRC: public ImageFormatBase
 {
  public:
 
-  MRC(bool normalize_on_save = false, Subformat subformat = MRC_AUTO_FORMAT ,Endianess endianness_on_save = OST_LOCAL_ENDIAN);
+  MRC(bool normalize_on_save = false, Subformat subformat = MRC_AUTO_FORMAT ,Endianess endianness_on_save = OST_LOCAL_ENDIAN, Format bit_depth = OST_DEFAULT_FORMAT);
+
+  Format GetBitDepth() const;
+  void SetBitDepth ( Format bitdepth);
 
   Endianess GetEndianessOnSave() const;
   void SetEndianessOnSave(Endianess end);
@@ -46,12 +49,13 @@ class DLLEXPORT_OST_IO MRC: public ImageFormatBase
   Subformat subformat_;
   bool normalize_on_save_;
   Endianess endianess_on_save_;
+  Format bit_depth_;
 };
 
 class DLLEXPORT_OST_IO CCP4: public MRC
 {
  public:
-  CCP4(bool normalize_on_save = false, Endianess endianness_on_save = OST_LOCAL_ENDIAN);
+  CCP4(bool normalize_on_save = false, Endianess endianness_on_save = OST_LOCAL_ENDIAN, Format bit_depth = OST_DEFAULT_FORMAT);
 };
 
 typedef CCP4 MAP;