name changed MeshData -> PixelData

docs/lib_guide/lib_guide.tex

@@ -183,7 +183,7 @@ \subsection{Particle Transforms}
 apr.particle_intensities.map(apr,absolute_value_of_intensities,[](const uint16_t &a) { return abs(a); });
 \end{lstlisting}
 \section{Pixel Images and Reconstruction}
-Pixel images are handled using the MeshData class and tiff library is used for input-output.
+Pixel images are handled using the PixelData class and tiff library is used for input-output.
 \subsection{Reconstruction}
 Any particle property, stored using ExtraParticleData class, can be interpolated to reconstruct an image, allowing both a piecewise constant and smooth reconstruction. For examples see Example\_reconstruct\_image.
 \subsection{Sampling particles from an image}

examples/Example_compress_apr.cpp

@@ -70,7 +70,7 @@ int main(int argc, char **argv) {
     apr.read_apr(options.directory + name + "_compress_apr.h5");
     timer.stop_timer();
 
-    MeshData<uint16_t> img;
+    PixelData<uint16_t> img;
     apr.interp_img(img,apr.particles_intensities);
     std::string output = options.directory + name + "_compress.tif";
     TiffUtils::saveMeshAsTiff(output, img);

examples/Example_compute_gradient.cpp

@@ -79,7 +79,7 @@ int main(int argc, char **argv) {
     gradient.map(apr,gradient_magnitude,[](const std::vector<float> &a) { return 20.0f*sqrt(pow(a[0], 2.0f) + pow(a[1], 2.0f) + pow(a[2], 2.0f)); });
 
     // write result to image
-    MeshData<float> gradient_magnitude_image;
+    PixelData<float> gradient_magnitude_image;
     apr.interp_img(gradient_magnitude_image,gradient_magnitude);
     //apr.interp_img(gradient_magnitude_image,apr.particles_intensities);
 
@@ -96,9 +96,9 @@ int main(int argc, char **argv) {
     if(options.original_image.size() > 0) {
 
         TiffUtils::TiffInfo inputTiff(options.directory + options.original_image);
-        MeshData<uint16_t> original_image = TiffUtils::getMesh<uint16_t>(inputTiff);
+        PixelData<uint16_t> original_image = TiffUtils::getMesh<uint16_t>(inputTiff);
 
-        std::vector<MeshData<float>> gradient_mesh;
+        std::vector<PixelData<float>> gradient_mesh;
 
         MeshNumerics::compute_gradient(original_image, gradient_mesh);
 

examples/Example_get_apr.cpp

@@ -82,7 +82,7 @@ int main(int argc, char **argv) {
 
         timer.verbose_flag = true;
 
-        MeshData<uint16_t> level;
+        PixelData<uint16_t> level;
 
         apr.interp_depth_ds(level);
 
@@ -125,14 +125,14 @@ int main(int argc, char **argv) {
             unsigned int blosc_comp_level = options.compress_level;
             unsigned int blosc_shuffle = 1;
 
-            MeshData<uint16_t> recon_image;
+            PixelData<uint16_t> recon_image;
 
             apr.interp_img(recon_image, apr.particles_intensities);
 
             TiffUtils::TiffInfo inputTiff(options.directory + options.input);
-            MeshData<uint16_t> inputImage = TiffUtils::getMesh<uint16_t>(inputTiff);
+            PixelData<uint16_t> inputImage = TiffUtils::getMesh<uint16_t>(inputTiff);
 
-            MeshData<int16_t> diff_image(inputImage.y_num,inputImage.x_num,inputImage.z_num,0);
+            PixelData<int16_t> diff_image(inputImage.y_num,inputImage.x_num,inputImage.z_num,0);
 
 #ifdef HAVE_OPENMP
 #pragma omp parallel for schedule(static)

examples/Example_get_apr.h

@@ -5,7 +5,7 @@
 #include <string>
 
 #include "algorithm/APRParameters.hpp"
-#include "data_structures/Mesh/MeshData.hpp"
+#include "data_structures/Mesh/PixelData.hpp"
 #include "algorithm/APRConverter.hpp"
 #include "data_structures/APR/APR.hpp"
 

examples/Example_ray_cast.cpp

@@ -68,7 +68,7 @@ int main(int argc, char **argv) {
 
     apr_raycaster.name = apr.name;
 
-    MeshData<uint16_t> views;
+    PixelData<uint16_t> views;
 
     /////////////
     ///
@@ -92,9 +92,9 @@ int main(int argc, char **argv) {
     if(options.original_image.size() > 0){
 
         TiffUtils::TiffInfo inputTiff(options.directory + options.original_image);
-        MeshData<uint16_t> original_image = TiffUtils::getMesh<uint16_t>(inputTiff);
+        PixelData<uint16_t> original_image = TiffUtils::getMesh<uint16_t>(inputTiff);
 
-        MeshData<uint16_t> mesh_views;
+        PixelData<uint16_t> mesh_views;
 
         apr_raycaster.perpsective_mesh_raycast(original_image,mesh_views);
 

examples/Example_reconstruct_image.cpp

@@ -127,7 +127,7 @@ int main(int argc, char **argv) {
 
         if(options.output_pc_recon) {
             //create mesh data structure for reconstruction
-            MeshData<uint16_t> recon_pc;
+            PixelData<uint16_t> recon_pc;
 
             timer.start_timer("pc interp");
             //perform piece-wise constant interpolation
@@ -179,7 +179,7 @@ int main(int argc, char **argv) {
 
         // Intentionaly block-scoped since local type_recon will be destructed when block ends and release memory.
         {
-            MeshData<uint16_t> type_recon;
+            PixelData<uint16_t> type_recon;
 
             apr.interp_img(type_recon, type);
             TiffUtils::saveMeshAsTiff(options.directory + apr.name + "_type.tif", type_recon);
@@ -205,7 +205,7 @@ int main(int argc, char **argv) {
     if(options.output_smooth_recon) {
 
         //smooth reconstruction - requires float
-        MeshData<float> recon_smooth;
+        PixelData<float> recon_smooth;
         std::vector<float> scale_d = {2, 2, 2};
 
         timer.start_timer("smooth reconstrution");

examples/Example_reconstruct_patch.cpp

@@ -191,7 +191,7 @@ int main(int argc, char **argv) {
 
         if(options.output_pc_recon) {
             //create mesh data structure for reconstruction
-            MeshData<uint16_t> recon_pc;
+            PixelData<uint16_t> recon_pc;
 
 
 
@@ -245,7 +245,7 @@ int main(int argc, char **argv) {
 
         // Intentionaly block-scoped since local type_recon will be destructed when block ends and release memory.
         {
-            MeshData<uint16_t> type_recon;
+            PixelData<uint16_t> type_recon;
 
             aprReconstruction.interp_image_patch(apr,type_recon, type,reconPatch);
             TiffUtils::saveMeshAsTiff(options.directory + apr.name + "_type.tif", type_recon);
@@ -291,7 +291,7 @@ int main(int argc, char **argv) {
 
         // Intentionaly block-scoped since local type_recon will be destructed when block ends and release memory.
         {
-            MeshData<uint8_t> type_recon;
+            PixelData<uint8_t> type_recon;
 
             //level
             aprReconstruction.interp_image_patch(apr,type_recon, level,reconPatch);

libapr.i

@@ -68,7 +68,7 @@ namespace std {
 #include "src/numerics/APRNumerics.hpp"
 %}
 
-%include "src/data_structures/Mesh/MeshData.hpp"
+%include "src/data_structures/Mesh/PixelData.hpp"
 %include "src/data_structures/APR/APR.hpp"
 %include "src/data_structures/APR/APRIterator.hpp"
 %include "src/numerics/APRNumerics.hpp"

src/algorithm/APRConverter.hpp

@@ -9,7 +9,7 @@
 #ifndef PARTPLAY_APR_CONVERTER_HPP
 #define PARTPLAY_APR_CONVERTER_HPP
 
-#include "../data_structures/Mesh/MeshData.hpp"
+#include "data_structures/Mesh/PixelData.hpp"
 #include "../io/TiffUtils.hpp"
 #include "../data_structures/APR/APR.hpp"
 
@@ -51,30 +51,30 @@ class APRConverter: public LocalIntensityScale, public ComputeGradient, public L
 private:
     //get apr without setting parameters, and with an already loaded image.
     template<typename T>
-    bool get_apr_method(APR<ImageType> &aAPR, MeshData<T> &input_image);
+    bool get_apr_method(APR<ImageType> &aAPR, PixelData<T> &input_image);
 
     //pointer to the APR structure so member functions can have access if they need
     const APR<ImageType> *apr;
 
     template<typename T>
-    void init_apr(APR<ImageType>& aAPR, MeshData<T>& input_image);
+    void init_apr(APR<ImageType>& aAPR, PixelData<T>& input_image);
 
     template<typename T>
-    void auto_parameters(const MeshData<T> &input_img);
+    void auto_parameters(const PixelData<T> &input_img);
 
     template<typename T>
     bool get_apr_method_from_file(APR<ImageType> &aAPR, const TiffUtils::TiffInfo &aTiffFile);
 
-    void get_gradient(MeshData<ImageType> &image_temp, MeshData<ImageType> &grad_temp, MeshData<float> &local_scale_temp, MeshData<float> &local_scale_temp2, float bspline_offset);
-    void get_local_intensity_scale(MeshData<float> &local_scale_temp, MeshData<float> &local_scale_temp2);
-    void get_local_particle_cell_set(MeshData<ImageType> &grad_temp, MeshData<float> &local_scale_temp, MeshData<float> &local_scale_temp2);
+    void get_gradient(PixelData<ImageType> &image_temp, PixelData<ImageType> &grad_temp, PixelData<float> &local_scale_temp, PixelData<float> &local_scale_temp2, float bspline_offset);
+    void get_local_intensity_scale(PixelData<float> &local_scale_temp, PixelData<float> &local_scale_temp2);
+    void get_local_particle_cell_set(PixelData<ImageType> &grad_temp, PixelData<float> &local_scale_temp, PixelData<float> &local_scale_temp2);
 };
 
 template <typename T>
 struct MinMax{T min; T max; };
 
 template <typename T>
-MinMax<T> getMinMax(const MeshData<T>& input_image) {
+MinMax<T> getMinMax(const PixelData<T>& input_image) {
     T minVal = std::numeric_limits<T>::max();
     T maxVal = std::numeric_limits<T>::min();
 
@@ -96,7 +96,7 @@ MinMax<T> getMinMax(const MeshData<T>& input_image) {
 template<typename ImageType> template<typename T>
 bool APRConverter<ImageType>::get_apr_method_from_file(APR<ImageType> &aAPR, const TiffUtils::TiffInfo &aTiffFile) {
     allocation_timer.start_timer("read tif input image");
-    MeshData<T> inputImage = TiffUtils::getMesh<T>(aTiffFile);
+    PixelData<T> inputImage = TiffUtils::getMesh<T>(aTiffFile);
     allocation_timer.stop_timer();
 
     method_timer.start_timer("calculate automatic parameters");
@@ -141,7 +141,7 @@ bool APRConverter<ImageType>::get_apr_method_from_file(APR<ImageType> &aAPR, con
  * Main method for constructing the APR from an input image
  */
 template<typename ImageType> template<typename T>
-bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, MeshData<T>& input_image) {
+bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, PixelData<T>& input_image) {
     apr = &aAPR; // in case it was called directly
 
     total_timer.start_timer("Total_pipeline_excluding_IO");
@@ -155,12 +155,12 @@ bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, MeshData<T>&
     //assuming uint16, the total memory cost shoudl be approximately (1 + 1 + 1/8 + 2/8 + 2/8) = 2 5/8 original image size in u16bit
     //storage of the particle cell tree for computing the pulling scheme
     allocation_timer.start_timer("init and copy image");
-    MeshData<ImageType> image_temp(input_image, false /* don't copy */); // global image variable useful for passing between methods, or re-using memory (should be the only full sized copy of the image)
-    MeshData<ImageType> grad_temp; // should be a down-sampled image
+    PixelData<ImageType> image_temp(input_image, false /* don't copy */); // global image variable useful for passing between methods, or re-using memory (should be the only full sized copy of the image)
+    PixelData<ImageType> grad_temp; // should be a down-sampled image
     grad_temp.initDownsampled(input_image.y_num, input_image.x_num, input_image.z_num, 0);
-    MeshData<float> local_scale_temp; // Used as down-sampled images for some averaging steps where it is useful to not lose precision, or get over-flow errors
+    PixelData<float> local_scale_temp; // Used as down-sampled images for some averaging steps where it is useful to not lose precision, or get over-flow errors
     local_scale_temp.initDownsampled(input_image.y_num, input_image.x_num, input_image.z_num);
-    MeshData<float> local_scale_temp2;
+    PixelData<float> local_scale_temp2;
     local_scale_temp2.initDownsampled(input_image.y_num, input_image.x_num, input_image.z_num);
     allocation_timer.stop_timer();
 
@@ -206,7 +206,7 @@ bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, MeshData<T>&
     method_timer.stop_timer();
 
     method_timer.start_timer("downsample_pyramid");
-    std::vector<MeshData<T>> downsampled_img;
+    std::vector<PixelData<T>> downsampled_img;
     //Down-sample the image for particle intensity estimation
     downsamplePyrmaid(input_image, downsampled_img, aAPR.level_max(), aAPR.level_min());
     method_timer.stop_timer();
@@ -229,7 +229,7 @@ bool APRConverter<ImageType>::get_apr_method(APR<ImageType> &aAPR, MeshData<T>&
 }
 
 template<typename ImageType>
-void APRConverter<ImageType>::get_local_particle_cell_set(MeshData<ImageType> &grad_temp, MeshData<float> &local_scale_temp, MeshData<float> &local_scale_temp2) {
+void APRConverter<ImageType>::get_local_particle_cell_set(PixelData<ImageType> &grad_temp, PixelData<float> &local_scale_temp, PixelData<float> &local_scale_temp2) {
     //
     //  Computes the Local Particle Cell Set from a down-sampled local intensity scale (\sigma) and gradient magnitude
     //
@@ -274,7 +274,7 @@ void APRConverter<ImageType>::get_local_particle_cell_set(MeshData<ImageType> &g
 }
 
 template<typename ImageType>
-void APRConverter<ImageType>::get_gradient(MeshData<ImageType> &image_temp, MeshData<ImageType> &grad_temp, MeshData<float> &local_scale_temp, MeshData<float> &local_scale_temp2, float bspline_offset) {
+void APRConverter<ImageType>::get_gradient(PixelData<ImageType> &image_temp, PixelData<ImageType> &grad_temp, PixelData<float> &local_scale_temp, PixelData<float> &local_scale_temp2, float bspline_offset) {
     //  Bevan Cheeseman 2018
     //  Calculate the gradient from the input image. (You could replace this method with your own)
     //  Input: full sized image.
@@ -335,7 +335,7 @@ void APRConverter<ImageType>::get_gradient(MeshData<ImageType> &image_temp, Mesh
 }
 
 template<typename ImageType>
-void APRConverter<ImageType>::get_local_intensity_scale(MeshData<float> &local_scale_temp, MeshData<float> &local_scale_temp2) {
+void APRConverter<ImageType>::get_local_intensity_scale(PixelData<float> &local_scale_temp, PixelData<float> &local_scale_temp2) {
     //
     //  Calculate the Local Intensity Scale (You could replace this method with your own)
     //
@@ -385,7 +385,7 @@ void APRConverter<ImageType>::get_local_intensity_scale(MeshData<float> &local_s
 
 
 template<typename ImageType> template<typename T>
-void APRConverter<ImageType>::init_apr(APR<ImageType>& aAPR,MeshData<T>& input_image){
+void APRConverter<ImageType>::init_apr(APR<ImageType>& aAPR,PixelData<T>& input_image){
     //
     //  Initializing the size of the APR, min and maximum level (in the data structures it is called depth)
     //
@@ -406,7 +406,7 @@ void APRConverter<ImageType>::init_apr(APR<ImageType>& aAPR,MeshData<T>& input_i
 }
 
 template<typename ImageType> template<typename T>
-void APRConverter<ImageType>::auto_parameters(const MeshData<T>& input_img){
+void APRConverter<ImageType>::auto_parameters(const PixelData<T>& input_img){
     //
     //  Simple automatic parameter selection for 3D APR Flouresence Images
     //
@@ -484,7 +484,7 @@ void APRConverter<ImageType>::auto_parameters(const MeshData<T>& input_img){
     float proportion_flat = freq[0]/(counter*1.0f);
     float proportion_next = freq[1]/(counter*1.0f);
 
-    MeshData<T> histogram;
+    PixelData<T> histogram;
     histogram.init(num_bins, 1, 1);
     std::copy(freq.begin(),freq.end(),histogram.mesh.begin());