Changeset 1750

Timestamp:

01/11/10 23:38:27 (2 years ago)

Author:

andreas

Message:

backported big/little endian mrc export from dng

Files:

• branches/qt_gui/src/io/lib/SConscript (modified) (2 diffs)
• branches/qt_gui/src/io/lib/convert.cc (added)
• branches/qt_gui/src/io/lib/convert.hh (added)
• branches/qt_gui/src/io/lib/converting_streams.hh (added)
• branches/qt_gui/src/io/lib/image_format.cc (modified) (3 diffs)
• branches/qt_gui/src/io/lib/image_format.hh (modified) (3 diffs)
• branches/qt_gui/src/io/lib/io_mrc.cc (modified) (8 diffs)
• branches/qt_gui/src/io/lib/io_mrc.hh (modified) (2 diffs)

branches/qt_gui/src/io/lib/SConscript

@@ -8 +8 @@
-image_format_conversion.cc
-convert_vax_data.h
+converting_streams.hh
+convert.hh
-""")
-
@@ -24 +26 @@
-io_nanoscope.cc
-convert_vax_data.c
+convert.cc
-""")
-

branches/qt_gui/src/io/lib/image_format.cc

@@ -30 +30 @@
-  encoding_(IEEE),
-  format_("auto"),
-
+
+
-{
-  string lformatstring=formatstring;
-  std::transform(lformatstring.begin(),lformatstring.end(),lformatstring.begin(),tolower);
-  bool set_depth_=false;
-  string subformat("");
@@ -89 +89 @@
-  if(subformat.find("v")!=string::npos) {
-    encoding_=VAX;
+    byte_order_=IPLT_VAX_DATA;
+  }
+  if(subformat.find("e")!=string::npos) {
+    byte_order_=IPLT_LITTLE_ENDIAN;
+  }
+  if(subformat.find("E")!=string::npos) {
+    byte_order_=IPLT_BIG_ENDIAN;
-  }
-
@@ -109 +116 @@
-}
-
+unsigned int ImageFormat::GetByteOrder() const
+{
+  return byte_order_;;
+}
+ 
-unsigned int ImageFormat::GetBitDepth() const
-{

branches/qt_gui/src/io/lib/image_format.hh

@@ -20 +20 @@
-
-#include <iplt/base.hh>
-
+
-
-namespace iplt { namespace io {
@@ -35 +35 @@
-  unsigned int GetBitDepth() const;
-  unsigned int GetEncoding() const;
+  unsigned int GetByteOrder() const;
-  string GetFormat() const;
-  int GetSubImage() const;
@@ -51 +52 @@
-  string format_;
-  int subimage_;
+  unsigned int byte_order_;
-};
-

branches/qt_gui/src/io/lib/io_mrc.cc

@@ -16 +16 @@
-#include <boost/scoped_array.hpp>
-#include <iplt/progress.hh>
+#include <boost/algorithm/string.hpp>
+#include <boost/format.hpp>
-
-#include <cstdio>
@@ -22 +24 @@
-
-#include <iplt/normalizer_impl.hh>
+#include <iplt/alg/normalizer_factory.hh>
-#include <iplt/util.hh>
-
@@ -28 +31 @@
-
-#include "io_mrc.hh"
+#include "converting_streams.hh"
+#include <boost/filesystem/operations.hpp>
-
-namespace iplt { namespace io {
@@ -70 +75 @@
-*/
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-void complex_filler(image_state::ComplexHalfFrequencyImageState& isi,
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-    throw Error("Only EVENxEVEN MRC half-complex format supported");
-  }
-  // always assume hcomplex (!)
-x-1)*2 == header.ny
+c-1)*2 == header.nr
-    char this_dummy; //create dummy variable to give to Progress as this
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-      // first half
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-          // complex conjugate
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-        }
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-        }
- 
-
-y starts at header.ny
-y>0;--sy,++cy
-fread(rawp.get(),sizeof(B)*2,header.nx,fhandle)
-f(swap_flag)
-  util::swap_buf<B>(rawp.get(),header.nx*2);
-int sx=0
-for(;sx<header.nx-1;++sx) {
-Point(sx,header.ny/2-sy,sz))=Complex(scale*double(rawp.get()[sx*2]),scale*double(rawp.get()[sx*2+1]
-//mlog(5) << " " << Point(sx,header.ny/2-sy,sz) << " <- " << Point(sx,cy,sz) << " " << isi.Value(Point(sx,header.ny/2-sy,sz)) << std::endl
+
+
+r starts at header.nr
+r>0;--sr,++cr
+p[mapr]=header.nr/2-sr
+nt sc=0;
+for(;sc<header.nc-1;++sc) {
+  p[mapc]=sc
+  fhandle >> real >> imag;
+p)=Complex(Real(real),Real(imag
+mlog(5) << " " << p << " " << isi.Value(p) << std::endl 
-        }
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-      }
-    }
-    Progress::Instance().DeRegister(&this_dummy);
-x*2 == header.ny
+c*2 == header.nr
-    throw Error("Half Complex Format NX = (NY+1)/2 not supported");
-  } else {
@@ -140 +568 @@
-  }
-}
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-  }
@@ -173 +599 @@
-}
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-    }
-  }
@@ -196 +653 @@
-}
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-  if(header.mode==5) header.mode=0;
-
-  if(Verbosity::GetLevel()>=4) {
-    dump_header(header);
-  }
-  
-  if(header.nz>1) {
-    throw(Error("3D mrc format not implemented yet"));
-  }
-  
-  if(header.mode==3 || header.mode==4) {
-    // always assume half-complex mode
-    image.Reset(Size((header.nx-1)*2,header.ny,header.nz),COMPLEX,HALF_FREQUENCY);
-    
-    if(image_state::ComplexHalfFrequencyImageState *cs=dynamic_cast<image_state::ComplexHalfFrequencyImageState*>(image.ImageStatePtr().get())) {
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-    } else {
@@ -324 +673 @@
-    }
-  } else if (header.mode>=0 && header.mode<=2) {
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-    if(image_state::RealSpatialImageState *rs=dynamic_cast<image_state::RealSpatialImageState*>(image.ImageStatePtr().get())) {
-      if(header.mode==0) {
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-      }
-    } else {
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-  } else {
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-    throw Error(mesg.str());
-  }
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-  if(image.GetType()==REAL) {
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-    if(image.GetDomain()==HALF_FREQUENCY){
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-
-double mrc_plugin::GetMinimum(const ImageFormat& format) const

branches/qt_gui/src/io/lib/io_mrc.hh

@@ -22 +22 @@
-namespace iplt { namespace io {
-
-namespace {
-
-struct mrc_header {
-  int nx,ny,nz; // nr of columns, rows and sections
-  int mode; // data format
-  int nxstart,nystart,nzstart;  // column, row and section offset
-  int mx,my,mz;  // logical size, used for hcomplex format
-  float x,y,z,alpha,beta,gamma; // cell constans
-  int mapc,mapr,maps; // axis to column/row/section
-  float amin,amax,amean; // min, max and mean data value
-  int ispg; // spacegroup (should be 0 for images)
-  int nsymbt; // number of bytes used for symmetry op
-  int extra[29]; // extra stuff
-  float xorigin,yorigin;
-  int nlabel;
-  char label[800];
-};
-
-} // anon ns
-
-class mrc_plugin: public ImageIOPlugin {
@@ -49 +30 @@
-  virtual bool Import(const path& location, ImageHandle& i, const ImageFormat& format);
-  virtual bool Export(const path& location, const ConstImageHandle& i, const ImageFormat& format,const  NormalizerPtr& nptr);
+  virtual void Import(std::istream& loc, ImageHandle& i, const ImageFormat& format);
+  virtual void Export(std::ostream& loc, const ConstImageHandle& i, const ImageFormat& format,const  NormalizerPtr& nptr);
-  virtual double GetMinimum(const ImageFormat& format) const;
-  virtual double GetMaximum(const ImageFormat& format) const;
-private:
-
-void fill_header(mrc_header& header,const ConstImageHandle& image, int mode, bool hcomplex_flag,const  NormalizerPtr& nptr)
-void dump_header(const mrc_header& h)
+
+mutable bool is_file_
+mutable string extension_
-};
-