Made threaded triangulation and transforming standard. Also added an …

…option for normalizing the images on input.

src/Isis/StereoSessionIsis.cc

@@ -249,6 +249,7 @@ void StereoSessionIsis::pre_preprocessing_hook(std::string const& input_file1, s
     min_max_channel_values(create_mask(right_disk_image), right_lo, right_hi);
   }
   vw_out(InfoMessage) << "\t    Right: [" << right_lo << " " << right_hi << "]\n";
+
   float lo = std::min (left_lo, right_lo);
   float hi = std::min (left_hi, right_hi);
 
@@ -268,9 +269,17 @@ void StereoSessionIsis::pre_preprocessing_hook(std::string const& input_file1, s
     // Create the geotransform objects and determine the common size
     // of the output images and apply it to the right image.
     GeoTransform trans2(input_georef2, common_georef);
-    ImageViewRef<PixelGray<float> > Limg = normalize(remove_isis_special_pixels(left_disk_image, lo), lo, hi, 0, 1.0);
-    ImageViewRef<PixelGray<float> > Rimg = crop(transform(normalize(remove_isis_special_pixels(right_disk_image, lo),lo,hi,0.0,1.0),trans2),common_bbox);
-
+    ImageViewRef<PixelGray<float> > Limg;
+    ImageViewRef<PixelGray<float> > Rimg;
+    if (stereo_settings().individually_normalize == 0 ) {
+      Limg = normalize(remove_isis_special_pixels(left_disk_image, lo), lo, hi, 0, 1.0);
+      Rimg = crop(transform(normalize(remove_isis_special_pixels(right_disk_image, lo), lo, hi, 0, 1.0),trans2),common_bbox);
+    } else {
+      vw_out(0) << "\t--> Individually normalizing.\n";
+      Limg = normalize(remove_isis_special_pixels(left_disk_image, left_lo));
+      Rimg = crop(transform(normalize(remove_isis_special_pixels(right_disk_image, right_lo)),trans2),common_bbox);
+    }
+
     // Write the results to disk.
     write_image(output_file1, channel_cast_rescale<uint8>(Limg), TerminalProgressCallback(ErrorMessage, "Left map-projected image: " ));
     write_image(output_file2, channel_cast_rescale<uint8>(Rimg), TerminalProgressCallback(ErrorMessage, "Right map-projected image: ")); 
@@ -284,19 +293,36 @@ void StereoSessionIsis::pre_preprocessing_hook(std::string const& input_file1, s
     Matrix<double> align_matrix(3,3);
     align_matrix.set_identity();
     if (stereo_settings().keypoint_alignment)
-      align_matrix = determine_image_alignment(input_file1, input_file2, lo, hi);
+      align_matrix = determine_image_alignment(input_file1, input_file2, 
+					       lo, hi);
     ::write_matrix(m_out_prefix + "-align.exr", align_matrix);
 
     // Apply the alignment transformation to the right image.
-    ImageViewRef<PixelGray<float> > Limg = normalize(remove_isis_special_pixels(left_disk_image, lo),lo,hi,0.0,1.0);
-    ImageViewRef<PixelGray<float> > Rimg = transform(normalize(remove_isis_special_pixels(right_disk_image,lo),lo,hi,0.0,1.0), 
-                                                     HomographyTransform(align_matrix),
-                                                     left_disk_image.cols(), left_disk_image.rows());
+    ImageViewRef<PixelGray<uint8> > Limg;
+    ImageViewRef<PixelGray<uint8> > Rimg;
+    if (stereo_settings().individually_normalize == 0 ) {
+      Limg = channel_cast_rescale<uint8>(normalize(remove_isis_special_pixels(left_disk_image, lo),lo,hi,0.0,1.0));
+      Rimg = channel_cast_rescale<uint8>(transform(normalize(remove_isis_special_pixels(right_disk_image,lo),lo,hi,0.0,1.0), 
+						   HomographyTransform(align_matrix),
+						   left_disk_image.cols(), left_disk_image.rows()));
+    } else {
+      vw_out(0) << "\t--> Individually normalizing.\n";
+      Limg = channel_cast_rescale<uint8>(normalize(remove_isis_special_pixels(left_disk_image, left_lo)));
+      Rimg = channel_cast_rescale<uint8>(transform(normalize(remove_isis_special_pixels(right_disk_image,right_lo)), 
+						   HomographyTransform(align_matrix),
+						   left_disk_image.cols(), left_disk_image.rows()));
+    }
 
     // Write the results to disk.
     vw_out(0) << "\t--> Writing pre-aligned images.\n";
-    write_image(output_file1, channel_cast_rescale<uint8>(Limg), TerminalProgressCallback(ErrorMessage, "\t    Left:  "));
-    write_image(output_file2, channel_cast_rescale<uint8>(Rimg), TerminalProgressCallback(ErrorMessage, "\t    Right: ")); 
+    { 
+      DiskImageResourceGDAL left_rsrc( output_file1, Limg.format() ); 
+      block_write_image( left_rsrc, Limg, TerminalProgressCallback(ErrorMessage, "\t    Left:  "));
+    }
+    {
+      DiskImageResourceGDAL right_rsrc( output_file2, Rimg.format() );
+      block_write_image( right_rsrc, Rimg, TerminalProgressCallback(ErrorMessage, "\t    Right: ")); 
+    }
   }
 }
 

src/Isis/StereoSessionIsis.h

@@ -105,7 +105,9 @@ class StereoSessionIsis: public StereoSession {
   static StereoSession* construct() { return new StereoSessionIsis; }
 
 private:
-  vw::math::Matrix<double> determine_image_alignment(std::string const& input_file1, std::string const& input_file2, float lo, float hi);
+  vw::math::Matrix<double> determine_image_alignment(std::string const& input_file1, 
+						     std::string const& input_file2, 
+						     float lo, float hi );
 
 };
 

src/StereoSettings.cc

@@ -98,6 +98,7 @@ StereoSettings::StereoSettings() {
   ASSOC_INT("DO_EPIPOLAR_ALIGNMENT", epipolar_alignment, 1, "Align images using epipolar constraints");
   ASSOC_INT("DO_INTERESTPOINT_ALIGNMENT", keypoint_alignment, 0, "Align images using the keypoint alignment method");
   ASSOC_INT("INTERESTPOINT_ALIGNMENT_SUBSAMPLING", keypoint_align_subsampling, 1, "Image sub-sampling factor for keypoint alignment.");
+  ASSOC_INT("DO_INDIVIDUAL_NORMALIZATION", individually_normalize, 0, "Normalize each image individually before processsing.");
 
   // Correlation Options
   ASSOC_INT("DO_SLOG", slog, 1, "perform an slog (relpace the emboss)");

src/StereoSettings.h

@@ -46,6 +46,7 @@ class StereoSettings {
   int epipolar_alignment;     /* Align images using the epipolar constraints */
   int keypoint_alignment;     /* Align images using the keypoint alignment method */
   int keypoint_align_subsampling;	   // if > 1, image sub-sampling factor for keypoint aligment (to speed things up)
+  int individually_normalize; // if > 1, normalize the images individually with their own hi's and low. Default = 0 means we pick a global high and low.
 
   // Correlation Options
   int slog;		/* perform an slog (relpace the emboss) */

src/stereo.cc

@@ -766,7 +766,7 @@ int main(int argc, char* argv[]) {
       point_cloud_rsrc.set_block_size(Vector2i(std::min(1024,point_cloud.cols()),
 					       std::min(1024, point_cloud.rows())));
 
-      write_image(point_cloud_rsrc, point_cloud, TerminalProgressCallback(ErrorMessage, "\t--> Triangulating: "));
+      block_write_image(point_cloud_rsrc, point_cloud, TerminalProgressCallback(ErrorMessage, "\t--> Triangulating: "));
       vw_out(0) << "\t--> " << universe_radius_func;
     } catch (IOErr &e) { 
       cout << "\nUnable to start at point cloud stage -- could not read input files.\n" << e.what() << "\nExiting.\n\n";