Code formatting;

docs/bundle_adjustment.rst

@@ -278,7 +278,7 @@ If desired, these csv files can be converted to a DEM with
      --csv-format 1:lon,2:lat,4:height_above_datum
 
 then one can look at their statistics, also have them colorized, and
-viewed in ``stereo_gui``.
+viewed in ``stereo_gui`` (:numref:`plot_csv`).
 
 This file also shows how often each feature is seen in the images, so,
 if three images are present, hopefully many features will be seen three
@@ -804,6 +804,7 @@ documentation of all options above.
    some ridges having been missed). Those do not affect the optimization. Using
    mapprojected images would have helped with this. The ultimate check will be
    the comparison with LOLA RDR (:numref:`kaguya_intrinsics_alignment_diff`).
+   Plotted with ``stereo_gui`` (:numref:`plot_csv`).
 
 Recreation of the stereo DEMs
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -872,7 +873,7 @@ KaguyaTC is already reasonably well-aligned.
    The signed difference between aligned stereo DEMs and LOLA RDR before (top)
    and after (bottom) refinement of distortion. (Blue = -20 meters, red = 20
    meters.) It can be seen that the warping of the DEMs due to distortion is much
-   reduced.
+   reduced. Plotted with ``stereo_gui`` (:numref:`plot_csv`).
 
 .. _custom_ip:
 

docs/tools/stereo_gui.rst

@@ -145,9 +145,11 @@ Hillshaded images can also be created with the ``hillshade`` tool
 Displaying colorized images, with a colorbar and axes
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-``stereo_gui`` can have images be colorized on-the-fly
-by mapping intensities to colors of a given colormap. The results
-are be plotted with a colorbar and axes (with ticks). 
+``stereo_gui`` can have images be colorized on-the-fly by mapping intensities to
+colors of a given colormap. The results are plotted with a colorbar and axes
+(with ticks). 
+
+CSV files can be shown with a colorbar as well.
 
 An example invocation is as follows::
 

src/asp/Sessions/StereoSession.cc

@@ -297,9 +297,11 @@ StereoSession::camera_model(std::string const& image_file, std::string const& ca
                                                  image_file);
 
   if (camera_file == "") // No camera file provided, use the image file.
-    m_camera_model[image_cam_pair] = load_camera_model(image_file, image_file, pixel_offset);
+    m_camera_model[image_cam_pair]
+     = load_camera_model(image_file, image_file, pixel_offset);
   else // Camera file provided
-    m_camera_model[image_cam_pair] = load_camera_model(image_file, camera_file, pixel_offset);
+    m_camera_model[image_cam_pair] 
+    = load_camera_model(image_file, camera_file, pixel_offset);
 
   return m_camera_model[image_cam_pair];
 }
@@ -368,7 +370,8 @@ void StereoSession::preprocessing_hook(bool adjust_left_image_size,
 
   // Generate aligned versions of the input images according to the
   // options.
-  vw_out() << "\t--> Applying alignment method: " << stereo_settings().alignment_method << "\n";
+  vw_out() << "\t--> Applying alignment method: "
+           << stereo_settings().alignment_method << "\n";
   if (stereo_settings().alignment_method == "epipolar") {
 
     epipolar_alignment(left_masked_image, right_masked_image, ext_nodata,  
@@ -689,7 +692,7 @@ shared_preprocessing_hook(vw::GdalWriteOptions & options,
   return false; // don't exit early
 }
 
-void StereoSession::read_bathy_masks(float & left_bathy_nodata,  float & right_bathy_nodata, 
+void StereoSession::read_bathy_masks(float & left_bathy_nodata, float & right_bathy_nodata, 
                                      vw::ImageViewRef<vw::PixelMask<float>> & left_bathy_mask,
                                      vw::ImageViewRef<vw::PixelMask<float>> & right_bathy_mask) {
 

src/asp/Tools/stereo_corr.cc

@@ -72,7 +72,8 @@ SemiGlobalMatcher::SgmSubpixelMode get_sgm_subpixel_mode() {
 }
 
 // Read the search range from D_sub, and scale it to the full image
-void read_search_range_from_D_sub(std::string const& d_sub_file, ASPGlobalOptions const& opt){
+void read_search_range_from_D_sub(std::string const& d_sub_file, 
+                                  ASPGlobalOptions const& opt){
 
   // No D_sub is generated or should be used for seed mode 0.
   if (stereo_settings().seed_mode == 0)
@@ -621,7 +622,8 @@ void lowres_correlation(ASPGlobalOptions & opt) {
 
     // Load IP from disk if they exist, or else compute them.
     std::string match_filename;
-    load_or_compute_ip(opt.session->left_cropped_image(), opt.session->right_cropped_image(),
+    load_or_compute_ip(opt.session->left_cropped_image(), 
+                       opt.session->right_cropped_image(),
                        opt.cam_file1, opt.cam_file2, opt.out_prefix, opt.session,
                        // Output
                        match_filename);

src/asp/Tools/stereo_pprc.cc

@@ -39,7 +39,7 @@ using namespace vw;
 using namespace asp;
 
 // Invalidate pixels < threshold
-struct MaskAboveThreshold: public ReturnFixedType< PixelMask<uint8> > {
+struct MaskAboveThreshold: public ReturnFixedType<PixelMask<uint8>> {
   double m_threshold;
   MaskAboveThreshold(double threshold): m_threshold(threshold){}
   PixelMask<uint8> operator() (PixelGray<float> const& pix) const {
@@ -51,9 +51,9 @@ struct MaskAboveThreshold: public ReturnFixedType< PixelMask<uint8> > {
 };
 template <class ImageT>
 UnaryPerPixelView<ImageT, MaskAboveThreshold>
-inline mask_above_threshold( ImageViewBase<ImageT> const& image, double threshold ) {
-  return UnaryPerPixelView<ImageT, MaskAboveThreshold>( image.impl(),
-                                                        MaskAboveThreshold(threshold) );
+inline mask_above_threshold(ImageViewBase<ImageT> const& image, double threshold) {
+  return UnaryPerPixelView<ImageT, MaskAboveThreshold>(image.impl(),
+                                                        MaskAboveThreshold(threshold));
 }
 
 struct BlobHolder {
@@ -63,16 +63,16 @@ struct BlobHolder {
   boost::shared_ptr<vw::BlobIndexThreaded> m_blobPtr;
 
   // Member function which does the hole-filling.
-  ImageViewRef< PixelMask<uint8> > mask_and_fill_holes( ImageViewRef< PixelGray<float> > const& img,
-                                                        double threshold );
+  ImageViewRef<PixelMask<uint8>> 
+  mask_and_fill_holes(ImageViewRef<PixelGray<float>> const& img, double threshold);
 };
 
 /// Create the mask of pixels above threshold. Fix any holes in it.
-ImageViewRef< PixelMask<uint8> >
-BlobHolder::mask_and_fill_holes( ImageViewRef< PixelGray<float> > const& img,
+ImageViewRef<PixelMask<uint8>>
+BlobHolder::mask_and_fill_holes( ImageViewRef<PixelGray<float>> const& img,
                                  double threshold ){
 
-  ImageViewRef< PixelMask<uint8> > thresh_mask = mask_above_threshold(img, threshold);
+  ImageViewRef<PixelMask<uint8>> thresh_mask = mask_above_threshold(img, threshold);
   int max_area = 0; // fill arbitrarily big holes
   bool use_grassfire = false; // fill with default value
   PixelMask<uint8> default_inpaint_val = uint8(255);
@@ -141,7 +141,8 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
   // It could be made to work, but it is an obscure scenario not
   // worth testing.
   if (skip_img_norm && opt.session->do_bathymetry()) 
-    vw_throw( ArgumentErr() << "\nCannot do bathymery when skipping image normalization.\n");
+    vw_throw( ArgumentErr() 
+             << "\nCannot do bathymetry when skipping image normalization.\n");
 
   // Need to also write the transformed bathy masks to disk, those
   // will be used in stereo_tri.
@@ -150,15 +151,15 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
                      left_image_file, right_image_file);
   else // Perform image normalization
     opt.session->preprocessing_hook(adjust_left_image_size,
-                                        opt.in_file1,    opt.in_file2,
-                                        left_image_file, right_image_file);
+                                    opt.in_file1,    opt.in_file2,
+                                    left_image_file, right_image_file);
 
   boost::shared_ptr<DiskImageResource>
     left_rsrc (vw::DiskImageResourcePtr(left_image_file)),
     right_rsrc(vw::DiskImageResourcePtr(right_image_file));
 
   // Load the normalized images.
-  DiskImageView<PixelGray<float>> left_image (left_rsrc ),
+  DiskImageView<PixelGray<float>> left_image (left_rsrc),
                                   right_image(right_rsrc);
 
   // If we crop the images, we must always rebuild the masks
@@ -187,8 +188,8 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
       rebuild = true;
     }else{
       vw_log().console_log().rule_set().add_rule(-1,"fileio");
-      DiskImageView<PixelGray<uint8> > testa(left_mask_file );
-      DiskImageView<PixelGray<uint8> > testb(right_mask_file);
+      DiskImageView<PixelGray<uint8>> testa(left_mask_file );
+      DiskImageView<PixelGray<uint8>> testb(right_mask_file);
       vw_settings().reload_config();
     }
   } catch (vw::IOErr const& e) {
@@ -208,21 +209,20 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
   bool  has_nodata    = true;
   float output_nodata = -32768.0;
 
-
   if (!rebuild) {
     vw_out() << "\t--> Using cached masks.\n";
   }else{
 
-    vw_out() << "\t--> Generating image masks... \n";
+    vw_out() << "\t--> Generating image masks.\n";
 
     Stopwatch sw;
     sw.start();
 
-    ImageViewRef< PixelMask<uint8> > left_mask
+    ImageViewRef<PixelMask<uint8>> left_mask
       = copy_mask(constant_view(uint8(255),
                                 left_image.cols(), left_image.rows()),
                   asp::threaded_edge_mask(left_image,0,0,1024));
-    ImageViewRef< PixelMask<uint8> > right_mask
+    ImageViewRef<PixelMask<uint8>> right_mask
       = copy_mask(constant_view(uint8(255),
                                 right_image.cols(), right_image.rows() ),
                   asp::threaded_edge_mask(right_image,0,0,1024));
@@ -262,7 +262,7 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
     }
     if (!std::isnan(nodata_fraction)){
       // Declare a fixed proportion of low-value pixels to be no-data.
-      math::CDFAccumulator< PixelGray<float> > left_cdf (1024, 1024),
+      math::CDFAccumulator<PixelGray<float>> left_cdf (1024, 1024),
                                                right_cdf(1024, 1024);
       for_each_pixel(left_image,  left_cdf );
       for_each_pixel(right_image, right_cdf);
@@ -274,9 +274,9 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
     BlobHolder LB, RB;
     // TODO(oalexan1): Wipe this code.
     if ( !std::isnan(left_threshold) && !std::isnan(right_threshold) ){
-      ImageViewRef< PixelMask<uint8> > left_thresh_mask
+      ImageViewRef<PixelMask<uint8>> left_thresh_mask
         = LB.mask_and_fill_holes(left_image,  left_threshold);
-      ImageViewRef< PixelMask<uint8> > right_thresh_mask
+      ImageViewRef<PixelMask<uint8>> right_thresh_mask
         = RB.mask_and_fill_holes(right_image, right_threshold);
       left_mask  = intersect_mask(left_mask,  left_thresh_mask );
       right_mask = intersect_mask(right_mask, right_thresh_mask);
@@ -321,14 +321,14 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
     vw_out() << "Writing masks: " << left_mask_file << ' ' << right_mask_file << ".\n";
     if (has_left_georef && has_right_georef && !opt.input_dem.empty()){
       // Left image mask transformed into right coordinates
-      ImageViewRef< PixelMask<uint8> > warped_left_mask
+      ImageViewRef<PixelMask<uint8>> warped_left_mask
         = crop(vw::cartography::geo_transform
                (left_mask, left_georef, right_georef,
                 ConstantEdgeExtension(),NearestPixelInterpolation()
                ),
                bounding_box(right_mask));
       // Right image mask transformed into left coordinates
-      ImageViewRef< PixelMask<uint8> > warped_right_mask
+      ImageViewRef<PixelMask<uint8>> warped_right_mask
         = crop(vw::cartography::geo_transform
                (right_mask, right_georef, left_georef,
                 ConstantEdgeExtension(), NearestPixelInterpolation()
@@ -387,8 +387,8 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
       rebuild = true;
     }else{
       // This confusing try catch is to see if the subsampled images actually have content.
-      DiskImageView<PixelGray<float> > testl (lsub );
-      DiskImageView<PixelGray<float> > testr (rsub );
+      DiskImageView<PixelGray<float>> testl (lsub );
+      DiskImageView<PixelGray<float>> testr (rsub );
       DiskImageView<uint8>             testlm(lmsub);
       DiskImageView<uint8>             testrm(rmsub);
       vw_out() << "\t--> Using cached subsampled images.\n";
@@ -523,7 +523,7 @@ void stereo_preprocessing(bool adjust_left_image_size, ASPGlobalOptions& opt) {
 
     ImageViewRef<PixelMask<PixelGray<float>>> left_masked_image
       = create_mask_less_or_equal(left_image, left_no_data_value);
-    ImageViewRef< PixelMask<PixelGray<float>>> right_masked_image
+    ImageViewRef<PixelMask<PixelGray<float>>> right_masked_image
       = create_mask_less_or_equal(right_image, right_no_data_value); 
 
     Vector6f left_stats  = gather_stats(pixel_cast<PixelMask<float>>(left_masked_image),