Merge branch 'develop' into ldt

modules/base/src/string_ref.cc

@@ -18,6 +18,7 @@
 //------------------------------------------------------------------------------
 
 #include <ost/string_ref.hh>
+#include <math.h>
 
 namespace ost {
   
@@ -53,6 +54,11 @@ std::pair<bool, float> StringRef::to_float() const
   int sig=1;
   bool after_dot=false;
   float factor=0.1;
+  bool after_exponent=false;
+  float exponent=0.0;
+  int exponent_sig=1;
+  bool after_exponent_sign=false;
+
   for (const char* c=begin_; c!=end_; ++c) {
     if (*c=='-' && empty) {
       empty=false;
@@ -71,17 +77,41 @@ std::pair<bool, float> StringRef::to_float() const
       if (after_dot==true) {
         n+=factor*int(*c-'0');
         factor*=0.1;
+      } else if (after_exponent==true) {
+        exponent=exponent*10+int(*c-'0');
       } else {
         n=n*10+int(*c-'0');
       }
       continue;
     }
+    if ((*c=='+' || *c=='-') && after_exponent==true) {
+      if (after_exponent_sign==true) {
+        return std::make_pair(false, 0.0f);
+      }
+      if (*c=='-') {
+        exponent_sig=-1;
+      }
+      after_exponent_sign=true;
+      continue;
+    }
+    if (*c=='e' || *c=='E') {
+      if (after_exponent==true) {
+        return std::make_pair(false, 0.0f);
+      }
+      after_exponent=true;
+      after_dot=false;
+      continue;
+    }
     return std::make_pair(false, 0.0f);
   }
   if (empty) {
     return std::make_pair(false, 0.0f);
   }
-  return std::make_pair(true, sig*n);
+  if (after_exponent==false) {
+    return std::make_pair(true, sig*n);
+  } else {
+    return std::make_pair(true, sig*n*float(pow(10,exponent_sig*exponent)));
+  }
 }
 
 std::ostream& operator<<(std::ostream& stream, const StringRef& strref)

modules/base/tests/test_string_ref.cc

@@ -84,6 +84,55 @@ BOOST_AUTO_TEST_CASE( test_string_ref)
   BOOST_CHECK(r2.first==false);
   r2=StringRef("12.34.", 6).to_float();
   BOOST_CHECK(r2.first==false);
+
+  // to_float_with_exp
+  std::pair<bool, Real> r3=StringRef("1", 1).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK(r3.second=1.0);
+  r3=StringRef("1.5", 3).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK(r3.second=1.5);
+  r3=StringRef("x", 1).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("12.3.4", 6).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("12.34.", 6).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("12.34e5", 7).to_float();
+  BOOST_CHECK(r3.first==true);
+  r3=StringRef("12e4", 4).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK_CLOSE(Real(120000), Real(r3.second), Real(1e-4));
+  r3=StringRef("2e+4", 4).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK_CLOSE(Real(20000), Real(r3.second), Real(1e-4));
+  r3=StringRef("2.3E+4", 6).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK_CLOSE(Real(23000), Real(r3.second), Real(1e-4));
+  r3=StringRef("2.3E-4", 6).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK_CLOSE(Real(0.00023), Real(r3.second), Real(1e-4));
+  r3=StringRef("2.010000e+00", 12).to_float();
+  BOOST_CHECK(r3.first==true);
+  BOOST_CHECK_CLOSE(Real(2.01), Real(r3.second), Real(1e-4));
+  r3=StringRef("5e-34", 5).to_float();
+  BOOST_CHECK(r3.first==true);
+  r3=StringRef("5E-34", 5).to_float();
+  BOOST_CHECK(r3.first==true);
+  r3=StringRef("5.34e-34", 8).to_float();
+  BOOST_CHECK(r3.first==true);
+  r3=StringRef("5.34e-34e", 9).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("5.34ee34", 8).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("5.34e--34e", 10).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("5.34e+3+4", 9).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("5.34e-+34e", 10).to_float();
+  BOOST_CHECK(r3.first==false);
+  r3=StringRef("5.34e-3-4", 9).to_float();
+  BOOST_CHECK(r3.first==false);
 }
 
 BOOST_AUTO_TEST_SUITE_END()

modules/gui/pymod/export_data_viewer.cc

@@ -73,6 +73,7 @@ void export_data_viewer()
     .def("AddOverlay",&DataViewer::AddOverlay,o_AddOverlay())
     .def("ClearOverlays",&DataViewer::ClearOverlays)
     .def("GetSelection",&DataViewer::GetSelection)
+    .def("SetSelection",&DataViewer::SetSelection)
     .def("UpdateView",&DataViewer::UpdateView)
     .def("Recenter",&DataViewer::Recenter)
     .def("AddDockWidget",add_dock1)

modules/gui/src/data_viewer/data_viewer.cc

@@ -118,6 +118,12 @@ Extent DataViewer::GetSelection() const
   return panel_->GetSelection();
 }
 
+void DataViewer::SetSelection(const Extent& selection)
+{
+  assert(panel_);
+  panel_->SetSelection(selection);
+}
+
 void DataViewer::SetName(const String& name)
 {
   setWindowTitle(QString::fromStdString(name));

modules/gui/src/data_viewer/data_viewer.hh

@@ -80,6 +80,9 @@ public:
   //! return currently active selection
   Extent GetSelection() const;
 
+  //! set currently active selection
+  void SetSelection(const Extent& selection);
+
   //! set the name, displayed as the window title
   void SetName(const String& name);
 

modules/gui/src/data_viewer/data_viewer_panel_base.cc

@@ -643,6 +643,18 @@ Extent DataViewerPanelBase::GetSelection() const
   return selection_;
 }
 
+void DataViewerPanelBase::SetSelection(const Extent& selection)
+{
+  selection_=selection;
+  update_rubberband_from_selection_();
+  if(selection==Extent()){
+    rubberband_->hide();
+  }else{
+    rubberband_->show();
+  }
+  UpdateView(false);
+}
+
 Real DataViewerPanelBase::GetZoomScale() const 
 {
   return zoom_scale_;

modules/gui/src/data_viewer/data_viewer_panel_base.hh

@@ -101,6 +101,9 @@ public:
   */
   Extent GetSelection() const;
 
+  //! set currently active selection
+  void SetSelection(const Extent& extent);
+
   //! convert window coordinates to image point
   Point WinToPoint(int mx, int my) const;
   Point WinToPoint(const QPoint& p) const;

modules/gui/src/messages/message_widget.cc

@@ -61,6 +61,7 @@ MessageWidget::MessageWidget(QWidget* parent) :
   view_->setDragEnabled(true);
   view_->setContextMenuPolicy(Qt::CustomContextMenu);
   view_->setFrameShape(QFrame::NoFrame);
+  view_->setVerticalScrollMode(QAbstractItemView::ScrollPerPixel);
   layout->addWidget(view_);
 
   connect(view_, SIGNAL(customContextMenuRequested(const QPoint&)), this,

modules/index.rst

@@ -93,6 +93,9 @@ Varia
 
 **Datasets:** :doc:`tabular data <table>`
 
+**File Formats:** :doc:`supported file formats <io/formats>`
+
+
 Extending OpenStructure
 --------------------------------------------------------------------------------
 
@@ -102,4 +105,4 @@ Extending OpenStructure
 
 
 
-  
\ No newline at end of file
+  

modules/io/doc/formats.rst

@@ -71,3 +71,116 @@ Promod
   
 *Format Name*
   promod
+  
+
+Image File Formats
+--------------------------------------------------------------------------------
+
+DAT
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  dat, img  
+
+*Format Name*
+  Simple binary format for square images
+
+DF3
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  df3
+
+*Format Name*
+  PovRay Density file format
+
+DM3
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  dm3
+
+*Format Name*
+  Format used by Gatan Inc.'s  Digital Micrograph software
+
+DX
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  dx  
+
+*Format Name*
+  Format used by the OpenDX software package
+
+IPL
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  ipl  
+
+*Format Name*
+  Ditabis Micron Image Plate Scanner Format
+
+JPK
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  jpk
+
+*Format Name*
+  Format used by JPK Instruments AG's software (Customized Tiff format)
+
+MRC
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  map, ccp4, mrc   
+
+*Format Name*
+  Format used by the MRC software package
+
+NanoScope
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  mod
+
+*Format Name*
+  Format used by software from Veeco
+
+PNG
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  png
+
+*Format Name*
+  Portable Network Graphic image format
+
+Situs
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  situs, sit
+
+*Format Name*
+  Format used by the Situs software package
+
+SPI
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  spi
+
+*Format Name*
+  Format used by the Spider software package
+
+TIFF
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Recognized File Extensions*
+  tif, tiff
+
+*Format Name*
+  Tagged Image File Format
+

modules/io/src/img/map_io_dx_handler.cc

@@ -24,6 +24,9 @@
 #include <sstream>
 
 #include <ost/log.hh>
+#include <ost/string_ref.hh>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
 #include <boost/filesystem/fstream.hpp>
 #include <boost/filesystem/convenience.hpp>
 #include <boost/lexical_cast.hpp>
@@ -43,6 +46,23 @@ namespace ost { namespace io {
 
 using boost::format;
 
+namespace {
+
+bool IEquals(const StringRef& a, const StringRef& b)
+{
+  if (a.size()!=b.size()) {
+    return false;
+  }
+  for (size_t i=0; i<a.size(); ++i) {
+    if (toupper(a[i])!=b[i]) {
+      return false;
+    }
+  }
+  return true;
+}
+
+}
+
 String DX::FORMAT_STRING="defined_dx";
 
 DX::DX (bool normalize_on_save):
@@ -68,8 +88,12 @@ void MapIODxHandler::Import(img::MapHandle& mh, const bf::path& loc,const ImageF
   {
     throw IOException("could not open "+loc.string());
   }
-
-  this->Import(mh,infile,form);
+  boost::iostreams::filtering_stream<boost::iostreams::input> in;
+  if (boost::iequals(".gz", boost::filesystem::extension(loc))) {
+    in.push(boost::iostreams::gzip_decompressor());
+  }
+  in.push(infile);
+  this->Import(mh,in,form);
   infile.close();
 }
 
@@ -91,6 +115,9 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
   img::MapHandle mh2;
   std::vector<String> tokens;
   while (std::getline(infile,line)) {
+    if (line.empty()) {
+      continue;
+    }
     // read gridpoints line
     if (boost::iequals(line.substr(0,35), "object 1 class gridpositions counts")) {
       boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
@@ -183,14 +210,14 @@ void MapIODxHandler::Import(img::MapHandle& mh, std::istream& infile, const Imag
       Real value=0;
       for(int i=0; i<num_gridpoints; i+=3) {
         std::getline(infile,line);
-        boost::split(tokens, line, boost::is_any_of(" "), boost::token_compress_on);
-        for (size_t j=0; j<tokens.size()-1; j++) {  // three values per line
-          try {
-            value=boost::lexical_cast<Real>(boost::trim_copy(tokens[j]));
-          } catch(boost::bad_lexical_cast&) {
-            format fmer = format("Bad value line: Can't convert grid point value '%s' to Real constant.") % line;
-            throw IOException(fmer.str());
-          } 
+        StringRef curr_line(line.c_str(), line.size());
+        std::vector<StringRef> fields=curr_line.split(' ');
+        for (size_t j=0; j<fields.size(); j++) {
+          std::pair<bool, float> result=fields[j].trim().to_float();
+          if (!result.first) {
+            throw IOException((format("Bad value line: Can't convert grid point value '%s' to Real constant.") % line).str());
+          }
+          value=result.second;
           mh2.SetReal(img::Point(((i+j)/(v_size*w_size))%u_size,((i+j)/w_size)%v_size, (i+j)%w_size), value);
         }
       }
@@ -266,10 +293,10 @@ bool MapIODxHandler::MatchType(const ImageFormatBase& formatstruct)
 }
 bool MapIODxHandler::MatchSuffix(const String& loc)
 {
-	if(detail::FilenameEndsWith(loc,".dx") ) {
-      return true;
-    }
-    return false;
+	if(detail::FilenameEndsWith(loc,".dx") || detail::FilenameEndsWith(loc,".dx.gz")) {
+    return true;
+  }
+  return false;
 }
 
 }} // ns