Change the default name for particles for writing and reading across the examples to be particles from particles_intensities (#132)

Author: cheesema

examples/Example_apr_iterate.cpp

@@ -48,7 +48,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t>parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     aprFile.close();
     timer.stop_timer();

examples/Example_apr_neighbour_access.cpp

@@ -49,7 +49,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t>parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     aprFile.close();
 

examples/Example_apr_tree.cpp

@@ -58,7 +58,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t>parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     aprFile.close();
 

examples/Example_compress_apr.cpp

@@ -57,7 +57,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t>parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     aprFile.close();
 

examples/Example_compute_gradient.cpp

@@ -59,7 +59,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t>parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     std::string name = options.input;
     //remove the file extension

examples/Example_get_apr.cpp

@@ -107,7 +107,7 @@ int runAPR(cmdLineOptions options) {
         aprFile.set_read_write_tree(false); //not writing tree to file.
 
         aprFile.write_apr(apr);
-        aprFile.write_particles("particle_intensities",particle_intensities);
+        aprFile.write_particles("particles",particle_intensities);
 
         float apr_file_size = aprFile.current_file_size_MB();
 

examples/Example_random_access.cpp

@@ -50,7 +50,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t> parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     aprFile.close();
 

examples/Example_reconstruct_image.cpp

@@ -38,7 +38,7 @@ Default: Piece-wise constant reconstruction
 #include"data_structures/APR/particles/ParticleData.hpp"
 #include"io/APRFile.hpp"
 #include "numerics/APRReconstruction.hpp"
-
+#include <random>
 
 struct cmdLineOptions{
     std::string output = "output";
@@ -106,6 +106,23 @@ static cmdLineOptions read_command_line_options(int argc, char **argv) {
 
     return result;
 }
+template<typename T>
+void add_random_to_img(PixelData<T>& img,float sd){
+
+    std::default_random_engine generator;
+    std::normal_distribution<float> distribution(0.0,sd);
+
+    size_t size = (size_t)img.y_num * img.x_num * img.z_num;
+    size_t i = 0;
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(i)
+#endif
+    for(i=0; i < size; i++){
+        float number = distribution(generator);
+        img.mesh[i] += number;
+    }
+
+}
 
 int main(int argc, char **argv) {
     // INPUT PARSING
@@ -126,7 +143,7 @@ int main(int argc, char **argv) {
     aprFile.read_apr(apr);
 
     ParticleData<uint16_t>parts;
-    aprFile.read_particles(apr,"particle_intensities",parts);
+    aprFile.read_particles(apr,"particles",parts);
 
     aprFile.close();
     apr.name = options.output;
@@ -137,19 +154,25 @@ int main(int argc, char **argv) {
 
         if(options.output_pc_recon) {
             //create mesh data structure for reconstruction
+            bool add_random_gitter = true;
+
             PixelData<uint16_t> recon_pc;
 
             timer.start_timer("pc interp");
             //perform piece-wise constant interpolation
             APRReconstruction::interp_img(apr,recon_pc, parts);
             timer.stop_timer();
 
+            if(add_random_gitter){
+                add_random_to_img(recon_pc,1.0f);
+            }
+
             float elapsed_seconds = timer.t2 - timer.t1;
             std::cout << "PC recon "
                       << (recon_pc.x_num * recon_pc.y_num * recon_pc.z_num * 2) / (elapsed_seconds * 1000000.0f)
                       << " MB per second" << std::endl;
 
-            //write output as tiff
+            // write output as tiff
             TiffUtils::saveMeshAsTiff(options.directory + apr.name + "_pc.tif", recon_pc);
         }
     }