From 608181a4f3157f838bb93bdd682a036f389ed3c3 Mon Sep 17 00:00:00 2001
From: andreas <andreas@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Wed, 18 Aug 2010 22:26:32 +0000
Subject: [PATCH] extended dat io handler to accept different bit depths
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2653 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/io/pymod/export_map_io.cc | 12 +-
modules/io/src/img/map_io_dat_handler.cc | 360 ++++++++++++++++++++--
modules/io/src/img/map_io_dat_handler.hh | 10 +-
modules/io/src/img/map_io_tiff_handler.cc | 20 +-
4 files changed, 357 insertions(+), 45 deletions(-)
diff --git a/modules/io/pymod/export_map_io.cc b/modules/io/pymod/export_map_io.cc
index 6f30e2961..e2b10e158 100644
--- a/modules/io/pymod/export_map_io.cc
+++ b/modules/io/pymod/export_map_io.cc
@@ -132,6 +132,8 @@ void export_map_io()
.def("GetFormat", &TIF::GetFormat)
.def("SetSigned", &TIF::SetSigned)
.def("GetSigned", &TIF::GetSigned)
+ .def("SetBitDepth", &TIF::SetBitDepth)
+ .def("GetBitDepth", &TIF::GetBitDepth)
.def("GetPhasecolor", &TIF::GetPhasecolor)
.def("SetPhasecolor", &TIF::SetPhasecolor)
.def("SetSubimage", &TIF::SetSubimage)
@@ -143,9 +145,13 @@ void export_map_io()
.def("GetNormalizeOnSave", &PNG::GetNormalizeOnSave)
;
- class_<DAT, bases<ImageFormatBase> >("DAT", init<bool,Endianess>((arg("normalize_on_save") = false,arg("endianess") = OST_LOCAL_ENDIAN)))
- .def("SetNormalizeOnSave", &PNG::SetNormalizeOnSave)
- .def("GetNormalizeOnSave", &PNG::GetNormalizeOnSave)
+ class_<DAT, bases<ImageFormatBase> >("DAT", init<bool,Format,bool,Endianess>((arg("normalize_on_save") = false,arg("format")=OST_DEFAULT_FORMAT,arg("signed")=false,arg("endianess") = OST_LOCAL_ENDIAN)))
+ .def("SetNormalizeOnSave", &DAT::SetNormalizeOnSave)
+ .def("GetNormalizeOnSave", &DAT::GetNormalizeOnSave)
+ .def("SetSigned", &DAT::SetSigned)
+ .def("GetSigned", &DAT::GetSigned)
+ .def("SetBitDepth", &DAT::SetBitDepth)
+ .def("GetBitDepth", &DAT::GetBitDepth)
;
class_<JPK, bases<TIF> >("JPK", init<boost::logic::tribool,Format,bool,bool,int>
diff --git a/modules/io/src/img/map_io_dat_handler.cc b/modules/io/src/img/map_io_dat_handler.cc
index 988d590e5..c2503261e 100644
--- a/modules/io/src/img/map_io_dat_handler.cc
+++ b/modules/io/src/img/map_io_dat_handler.cc
@@ -17,6 +17,7 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+#include <ost/stdint.hh>
#include <boost/shared_array.hpp>
#include <boost/filesystem/operations.hpp>
#include <boost/filesystem/fstream.hpp>
@@ -34,11 +35,33 @@ namespace ost { namespace io {
String DAT::FORMAT_STRING = "defined_dat";
-DAT::DAT(bool normalize_on_save, Endianess end):
- ImageFormatBase(FORMAT_STRING)
+DAT::DAT(bool normalize_on_save, Format bit_depth, bool sign, Endianess end):
+ ImageFormatBase(FORMAT_STRING),
+ normalize_on_save_(normalize_on_save),
+ bit_depth_(bit_depth),
+ signed_(sign),
+ endianness_(end)
{
- normalize_on_save_ = normalize_on_save;
- endianness_ = end;
+}
+
+Format DAT::GetBitDepth() const
+{
+ return bit_depth_;
+}
+
+void DAT::SetBitDepth (Format bitdepth)
+{
+ bit_depth_ = bitdepth;
+}
+
+bool DAT::GetSigned () const
+{
+ return signed_;
+}
+
+void DAT::SetSigned (bool sign)
+{
+ signed_ = sign;
}
Endianess DAT::GetEndianess() const
@@ -92,7 +115,7 @@ void MapIODatHandler::Import(img::MapHandle& sh, const boost::filesystem::path&
infile.close();
}
-template <int CONVERSIONTYPE>
+template <int CONVERSIONTYPE,typename DATATYPE>
void real_filler(img::MapHandle& sh, std::istream& file)
{
BinaryIStream<CONVERSIONTYPE> file_bin(file);
@@ -101,7 +124,7 @@ void real_filler(img::MapHandle& sh, std::istream& file)
img::Progress::Instance().Register(&this_dummy,size[1],100);
for(unsigned int row=0;row<size[1];row++) {
for(unsigned int column=0;column<size[0];column++) {
- short value;
+ DATATYPE value;
file_bin >> value;
sh.SetReal(img::Point(column,row),static_cast<Real>(value));
}
@@ -110,7 +133,7 @@ void real_filler(img::MapHandle& sh, std::istream& file)
img::Progress::Instance().DeRegister(&this_dummy);
}
-template <int CONVERSIONTYPE>
+template <int CONVERSIONTYPE,typename DATATYPE>
void real_dumper(const img::MapHandle& sh, std::ostream& file, const DAT& formatdat)
{
BinaryOStream<CONVERSIONTYPE> file_bin(file);
@@ -124,7 +147,7 @@ void real_dumper(const img::MapHandle& sh, std::ostream& file, const DAT& format
for(unsigned int row=0;row<size[1];row++) {
for(unsigned int column=0;column<size[0];column++)
{
- file_bin << static_cast<short>(norm.Convert(sh.GetReal(img::Point(column,row))));
+ file_bin << static_cast<DATATYPE>(norm.Convert(sh.GetReal(img::Point(column,row))));
}
img::Progress::Instance().AdvanceProgress(&this_dummy);
}
@@ -151,21 +174,168 @@ void MapIODatHandler::Import(img::MapHandle& sh, std::istream& file, const Image
uint filesize = end-start;
file.seekg(curr_pos,std::ios::beg);
- unsigned int size=static_cast<unsigned int>(sqrt(filesize/2.0));
- // default origin is top-left
- sh.Reset(img::Extent(img::Point(0,0),img::Size(size,size)), img::REAL, img::SPATIAL);
-
- switch(formatdat.GetEndianess()) {
- case OST_BIG_ENDIAN:
- real_filler<OST_BIG_ENDIAN>(sh,file);
+ double datasize=1.0;
+ switch(formatdat.GetBitDepth()){
+ case OST_BIT8_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ datasize=1.0;
+ break;
+ case OST_BIT16_FORMAT:
+ datasize=2.0;
break;
- case OST_LITTLE_ENDIAN:
- real_filler<OST_LITTLE_ENDIAN>(sh,file);
+ case OST_BIT32_FORMAT:
+ datasize=4.0;
break;
- case OST_VAX_DATA:
- real_filler<OST_VAX_DATA>(sh,file);
+ case OST_FLOAT_FORMAT:
+ datasize=sizeof(float);
break;
- }
+ case OST_DOUBLE_FORMAT:
+ datasize=sizeof(double);
+ break;
+ }
+ unsigned int size=static_cast<unsigned int>(sqrt(filesize/datasize));
+ // default origin is top-left
+ sh.Reset(img::Extent(img::Point(0,0),img::Size(size,size)), img::REAL, img::SPATIAL);
+
+ if(formatdat.GetSigned()){
+ switch(formatdat.GetBitDepth()){
+ case OST_BIT8_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,int8_t>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,int8_t>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,int8_t>(sh,file);
+ break;
+ }
+ break;
+ case OST_BIT16_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,int16_t>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,int16_t>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,int16_t>(sh,file);
+ break;
+ }
+ break;
+ case OST_BIT32_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,int32_t>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,int32_t>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,int32_t>(sh,file);
+ break;
+ }
+ break;
+ case OST_FLOAT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,float>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,float>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,float>(sh,file);
+ break;
+ }
+ break;
+ case OST_DOUBLE_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,double>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,double>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,double>(sh,file);
+ break;
+ }
+ break;
+ }
+ }else{
+ switch(formatdat.GetBitDepth()){
+ case OST_BIT8_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,uint8_t>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,uint8_t>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,uint8_t>(sh,file);
+ break;
+ }
+ break;
+ case OST_BIT16_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,uint16_t>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,uint16_t>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,uint16_t>(sh,file);
+ break;
+ }
+ break;
+ case OST_BIT32_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,uint32_t>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,uint32_t>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,uint32_t>(sh,file);
+ break;
+ }
+ break;
+ case OST_FLOAT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,float>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,float>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,float>(sh,file);
+ break;
+ }
+ break;
+ case OST_DOUBLE_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_filler<OST_BIG_ENDIAN,double>(sh,file);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_filler<OST_LITTLE_ENDIAN,double>(sh,file);
+ break;
+ case OST_VAX_DATA:
+ real_filler<OST_VAX_DATA,double>(sh,file);
+ break;
+ }
+ break;
+ }
+ }
}
void MapIODatHandler::Export(const img::MapHandle& mh2,
@@ -197,17 +367,145 @@ void MapIODatHandler::Export(const img::MapHandle& sh, std::ostream& file,const
throw IOException("DAT IO: Dat format only supports square 2D images");
}
- switch(formatdat.GetEndianess()) {
- case OST_BIG_ENDIAN:
- real_dumper<OST_BIG_ENDIAN>(sh,file,formatdat);
- break;
- case OST_LITTLE_ENDIAN:
- real_dumper<OST_LITTLE_ENDIAN>(sh,file,formatdat);
- break;
- case OST_VAX_DATA:
- real_dumper<OST_VAX_DATA>(sh,file,formatdat);
- break;
- }
+ if(formatdat.GetSigned()){
+ switch(formatdat.GetBitDepth()){
+ case OST_BIT8_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,int8_t>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,int8_t>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,int8_t>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_BIT16_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,int16_t>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,int16_t>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,int16_t>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_BIT32_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,int32_t>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,int32_t>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,int32_t>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_FLOAT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,float>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,float>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,float>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_DOUBLE_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,double>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,double>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,double>(sh,file,formatdat);
+ break;
+ }
+ break;
+ }
+ }else{
+ switch(formatdat.GetBitDepth()){
+ case OST_BIT8_FORMAT:
+ case OST_DEFAULT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,int8_t>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,int8_t>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,int8_t>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_BIT16_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,int16_t>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,int16_t>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,int16_t>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_BIT32_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,int32_t>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,int32_t>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,int32_t>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_FLOAT_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,float>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,float>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,float>(sh,file,formatdat);
+ break;
+ }
+ break;
+ case OST_DOUBLE_FORMAT:
+ switch(formatdat.GetEndianess()) {
+ case OST_BIG_ENDIAN:
+ real_dumper<OST_BIG_ENDIAN,double>(sh,file,formatdat);
+ break;
+ case OST_LITTLE_ENDIAN:
+ real_dumper<OST_LITTLE_ENDIAN,double>(sh,file,formatdat);
+ break;
+ case OST_VAX_DATA:
+ real_dumper<OST_VAX_DATA,double>(sh,file,formatdat);
+ break;
+ }
+ break;
+ }
+ }
}
}} // namespaces
diff --git a/modules/io/src/img/map_io_dat_handler.hh b/modules/io/src/img/map_io_dat_handler.hh
index 92335aa17..9244c705b 100644
--- a/modules/io/src/img/map_io_dat_handler.hh
+++ b/modules/io/src/img/map_io_dat_handler.hh
@@ -34,7 +34,13 @@ class DLLEXPORT_OST_IO DAT: public ImageFormatBase
public:
- DAT(bool normalize_on_save = true,Endianess endianness = OST_LOCAL_ENDIAN);
+ DAT(bool normalize_on_save = true, Format bit_depth = OST_DEFAULT_FORMAT, bool sign = false,Endianess endianness = OST_LOCAL_ENDIAN);
+
+ Format GetBitDepth() const;
+ void SetBitDepth ( Format bitdepth);
+
+ bool GetSigned () const;
+ void SetSigned (bool sign);
Endianess GetEndianess() const;
void SetEndianess(Endianess end);
@@ -45,6 +51,8 @@ class DLLEXPORT_OST_IO DAT: public ImageFormatBase
private:
bool normalize_on_save_;
+ Format bit_depth_;
+ bool signed_;
Endianess endianness_;
};
diff --git a/modules/io/src/img/map_io_tiff_handler.cc b/modules/io/src/img/map_io_tiff_handler.cc
index 10c1a5c3f..26305654b 100644
--- a/modules/io/src/img/map_io_tiff_handler.cc
+++ b/modules/io/src/img/map_io_tiff_handler.cc
@@ -47,21 +47,21 @@ namespace ost { namespace io {
String TIF::FORMAT_STRING="defined_tiff";
TIF::TIF(boost::logic::tribool normalize_on_save, Format bit_depth, bool sign, bool phasecolor, int subimage):
- ImageFormatBase(FORMAT_STRING)
+ ImageFormatBase(FORMAT_STRING),
+ normalize_on_save_(normalize_on_save),
+ bit_depth_(bit_depth),
+ signed_(sign),
+ phasecolor_(phasecolor)
{
- normalize_on_save_ = normalize_on_save;
- bit_depth_ = bit_depth;
- signed_ = sign;
- phasecolor_ = phasecolor;
}
TIF::TIF(String format_string, boost::logic::tribool normalize_on_save, Format bit_depth,bool sign, bool phasecolor, int subimage):
- ImageFormatBase(format_string)
+ ImageFormatBase(FORMAT_STRING),
+ normalize_on_save_(normalize_on_save),
+ bit_depth_(bit_depth),
+ signed_(sign),
+ phasecolor_(phasecolor)
{
- normalize_on_save_ = normalize_on_save;
- bit_depth_ = bit_depth;
- signed_ = sign;
- phasecolor_ = phasecolor;
}
Format TIF::GetBitDepth() const
--
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