fix cli bug

src/FileConnector.cpp

@@ -46,6 +46,7 @@ void FileConnector::close_file()
 void FileConnector::read_data(char *buffer, size_t data_size)
 {
  stream.read(buffer, data_size);
+
  pos += data_size;
  // Reset file to the beginning for repeat reading
  if (file_size - pos < data_size)

src/Ricom.cpp

@@ -226,7 +226,7 @@ Ricom::Ricom() : stem_max(-FLT_MAX), stem_min(FLT_MAX),
  ricom_mutex(), stem_mutex(), counter_mutex(), e_field_mutex(),
  socket(), file_path(""),
  camera(),
- mode(RICOM::FILE),
+ mode(0),
  b_print2file(false),
  redraw_interval(50),
  last_y(0),
@@ -239,7 +239,7 @@ Ricom::Ricom() : stem_max(-FLT_MAX), stem_min(FLT_MAX),
  b_recompute_kernel(false), detector(),
  kernel(),
  offset{128, 128}, com_public{0.0, 0.0},
- com_map_x(), com_map_y(),
+ comx_data(), comy_data(),
  ricom_data(),
  stem_data(),
  nx(1024), ny(1024), nxy(0),
@@ -479,16 +479,12 @@ void Ricom::process_data()
  size_t first_frame = img_num * nxy;
  size_t end_frame = (img_num + 1) * nxy;
  size_t fr_total_u = (size_t)fr_total;
- int processor_line = 0;
- int preprocessor_line = 0;
 
  ProgressMonitor prog_mon(fr_total, !b_print2file, redraw_interval);
  p_prog_mon = &prog_mon;
 
  reinit_vectors_limits();
 
- std::clock_t start_time = std::clock();
-
  while (processor_line != -1)
  {
  line_processor(
@@ -497,13 +493,9 @@ void Ricom::process_data()
  end_frame, 
  p_prog_mon, 
  fr_total_u, 
- &pool,
- processor_line, 
- preprocessor_line
+ &pool
  );
  }
- std::clock_t end_time = std::clock();
- double time_taken = static_cast<double>(end_time - start_time) / CLOCKS_PER_SEC;
  p_prog_mon = nullptr;
 }
 
@@ -513,12 +505,9 @@ void Ricom::line_processor(
  size_t &end_frame,
  ProgressMonitor *prog_mon,
  size_t &fr_total_u,
- BoundedThreadPool *pool,
- int &processor_line,
- int &preprocessor_line
+ BoundedThreadPool *pool
 )
 {
- int delay_update = (kernel.kernel_size+1)*2*nx;
  int idxx = 0;
  // process newly finished lines, if there are any
  if ((int)(prog_mon->fr_count / nx) < preprocessor_line)
@@ -529,33 +518,33 @@ void Ricom::line_processor(
 
  std::array<float, 2> com_xy = {0.0, 0.0};
  std::array<float, 2> com_xy_sum = {0.0, 0.0};
- for (size_t i = 0; i < nx; i++)
+ for (size_t i = 0; i < (size_t)nx; i++)
  {
  int idxx_p_i = idxx + i;
  if ((idxx_p_i >= 0) | (nx > 1))
  {
- if (dose_map[idxx_p_i] == 0)
+ if (dose_data[idxx_p_i] == 0)
  {
- com_map_x[idxx_p_i] = offset[0];
- com_map_y[idxx_p_i] = offset[1];
+ comx_data[idxx_p_i] = offset[0];
+ comy_data[idxx_p_i] = offset[1];
  }
  else
  {
- com_map_x[idxx_p_i] = sumx_map[idxx_p_i] / dose_map[idxx_p_i];
- com_map_y[idxx_p_i] = sumy_map[idxx_p_i] / dose_map[idxx_p_i];
+ comx_data[idxx_p_i] = sumx_data[idxx_p_i] / dose_data[idxx_p_i];
+ comy_data[idxx_p_i] = sumy_data[idxx_p_i] / dose_data[idxx_p_i];
  }
- com_xy_sum[0] += com_map_x[idxx_p_i];
- com_xy_sum[1] += com_map_y[idxx_p_i];
+ com_xy_sum[0] += comx_data[idxx_p_i];
+ com_xy_sum[1] += comy_data[idxx_p_i];
  if (!b_cumulative) {
- sumx_map[idxx_p_i] = 0;
- sumy_map[idxx_p_i] = 0;
- dose_map[idxx_p_i] = 0;
+ sumx_data[idxx_p_i] = 0;
+ sumy_data[idxx_p_i] = 0;
+ dose_data[idxx_p_i] = 0;
  }
  }
  if (b_e_mag)
  {
- com_xy[0] = com_map_x[idxx_p_i];
- com_xy[1] = com_map_y[idxx_p_i];
+ com_xy[0] = comx_data[idxx_p_i];
+ com_xy[1] = comy_data[idxx_p_i];
  compute_electric_field(com_xy, idxx_p_i);
  }
  }
@@ -632,8 +621,6 @@ void Ricom::icom_group_classical(int idxx)
 
  if (((idxx / nx - 2*kernel.kernel_size) >= 0))
  {
-
-
  for (int i_line = 0, idr_delay = idxx - kernel.kernel_size * nx;
  i_line < nx;
  i_line++, idr_delay++)
@@ -653,11 +640,11 @@ void Ricom::icom_group_classical(int idxx)
  {
  if (((idr_x + ix) >= 0) & ((idr_x + ix) < nx))
  {
- // ricom_data[idr] += ((com_map_x[idc + ix] - offset[0]) * -kernel.kernel_x[idk] +
- // (com_map_y[idc + ix] - offset[1]) * -kernel.kernel_y[idk]);
+ // ricom_data[idr] += ((comx_data[idc + ix] - offset[0]) * -kernel.kernel_x[idk] +
+ // (comy_data[idc + ix] - offset[1]) * -kernel.kernel_y[idk]);
 
- ricom_data[idr_delay] += ((com_map_x[idc + ix] - offset[0]) * -kernel.kernel_x[idk] +
- (com_map_y[idc + ix] - offset[1]) * -kernel.kernel_y[idk]);
+ ricom_data[idr_delay] += ((comx_data[idc + ix] - offset[0]) * -kernel.kernel_x[idk] +
+ (comy_data[idc + ix] - offset[1]) * -kernel.kernel_y[idk]);
  }
  ++idk;
  }
@@ -670,8 +657,9 @@ void Ricom::icom_group_classical(int idxx)
 }
 
 // Entrance function for Ricom_reconstructinon
-void Ricom::run_reconstruction()
+void Ricom::run(int mode)
 {
+ this->mode = mode;
  reset();
  b_busy = true;
  // Initializations
@@ -705,16 +693,13 @@ void Ricom::run_reconstruction()
  switch (camera)
  {
  // Merlin not implemented
- case RICOM::ADVAPIX
+ case RICOM::ADVAPIX:
  { 
- std::vector<std::vector<ADVAPIX_ADDITIONAL::event>> buffer(
- ADVAPIX_ADDITIONAL::n_buffer, 
- std::vector<ADVAPIX_ADDITIONAL::event>>(ADVAPIX_ADDITIONAL::buffer_size));
- ADVAPIX<ADVAPIX_ADDITIONAL::event> cam(
+ using namespace ADVAPIX_ADDITIONAL;
+ ADVAPIX cam(
  nx, 
  ny, 
  n_cam, 
- n_cam, 
  dt,
  b_vSTEM,
  b_ricom,
@@ -735,24 +720,20 @@ void Ricom::run_reconstruction()
  &preprocessor_line,
  mode,
  file_path,
- &socket,
- ADVAPIX_ADDITIONAL::buffer_size,
- ADVAPIX_ADDITIONAL::n_buffer,
- &buffer,
+ &socket
  );
  cam.run();
+ process_data();
+ cam.terminate();
  break;
  }
- case RICOM::CHEETAH
+ case RICOM::CHEETAH:
  {
- std::vector<std::vector<CHEETAH_ADDITIONAL::event>> buffer(
- CHEETAH_ADDITIONAL::n_buffer, 
- std::vector<CHEETAH_ADDITIONAL::event>>(CHEETAH_ADDITIONAL::buffer_size));
- CHEETAH<CHEETAH_ADDITIONAL::event> cam(
+ using namespace CHEETAH_ADDITIONAL;
+ CHEETAH cam(
  nx, 
  ny, 
  n_cam, 
- n_cam, 
  dt,
  b_vSTEM,
  b_ricom,
@@ -773,17 +754,18 @@ void Ricom::run_reconstruction()
  &preprocessor_line,
  mode,
  file_path,
- &socket,
- CHEETAH_ADDITIONAL::buffer_size,
- CHEETAH_ADDITIONAL::n_buffer,
- &buffer,
+ &socket
  );
  cam.run();
+ process_data();
+ cam.terminate();
  break;
  }
  }
 
- process_data();
+
+ // std::this_thread::sleep_for(std::chrono::milliseconds(10*1000));
+
 
  // close the reading and preprocess threads ??
 
@@ -807,8 +789,8 @@ void Ricom::reinit_vectors_limits()
 {
  std::fill(ricom_data.begin(), ricom_data.end(), 0);
  std::fill(stem_data.begin(), stem_data.end(), 0);
- std::fill(com_map_x.begin(), com_map_x.end(), 0);
- std::fill(com_map_y.begin(), com_map_y.end(), 0);
+ std::fill(comx_data.begin(), comx_data.end(), 0);
+ std::fill(comy_data.begin(), comy_data.end(), 0);
  last_y = 0;
  reset_limits();
 }
@@ -819,11 +801,3 @@ void Ricom::reset()
  fr_freq = 0;
  reinit_vectors_limits();
 }
-
-
-void RICOM::run(Ricom *r, int mode, RICOM::cameras cameras)
-{
- r->modes = mode;
- r->cameras = cameras;
- r->run_reconstruction();
-}

src/Ricom.h

@@ -43,10 +43,9 @@
 #include "fft2d.hpp"
 #include "SocketConnector.h"
 #include "ProgressMonitor.h"
-#include "MerlinInterface.h"
-#include "CheetahInterface.h"
-#include "TimepixInterface.h"
-#include "Camera.h"
+#include "Cheetah.h"
+#include "Timepix.h"
+#include "Advapix.h"
 #include "GuiUtils.h"
 
 namespace chc = std::chrono;
@@ -145,11 +144,10 @@ namespace RICOM
 {
  enum cameras
  {
- MERLIN,
+ // MERLIN,
  ADVAPIX,
  CHEETAH
  };
- void run(Ricom *r, int mode, RICOM::cameras cameras);
 }
 
 class Ricom
@@ -200,9 +198,7 @@ class Ricom
  size_t &end_frame,
  ProgressMonitor *prog_mon,
  size_t &fr_total_u,
- BoundedThreadPool *pool,
- int &processor_line,
- int &preprocessor_line
+ BoundedThreadPool *pool
  );
 
  void icom_group_decompose(int idxx);
@@ -223,7 +219,6 @@ class Ricom
 public:
  SocketConnector socket;
  std::string file_path;
- int mode; // 0: file, 1: tcp
  bool b_print2file;
  int redraw_interval;
  std::atomic<int> last_y;
@@ -304,9 +299,8 @@ class Ricom
  void draw_e_field_image();
  void draw_e_field_image(int y0, int ye);
  // template <class CameraInterface>
- void run_reconstruction();
+ void run(int mode);
  void reset();
- template <typename T>
  void process_data();
 
  // Constructor

src/RunCLI.cpp

@@ -32,7 +32,14 @@ int run_cli(int argc, char *argv[], Ricom *ricom)
  // Set filename to read from .mib file
  if (strcmp(argv[i], "-filename") == 0)
  {
- ricom->file_path = argv[i + 1];
+ if (std::filesystem::path(argv[i + 1]).extension() == ".t3p") 
+ {
+ ricom->camera = RICOM::ADVAPIX;
+ ImGui::DragInt("dwell time", &ricom->dt, 1, 1);
+ }
+ else if (std::filesystem::path(argv[i + 1]).extension() == ".tpx3") 
+ {ricom->camera = RICOM::CHEETAH;}
+ ricom->file_path = argv[i + 1]; 
  ricom->mode = 0;
  i++;
  }
@@ -185,14 +192,14 @@ int run_cli(int argc, char *argv[], Ricom *ricom)
  {
  std::vector<SdlImageWindow> image_windows;
  std::thread run_thread;
- // run_thread = std::thread(RICOM::run, ricom, ricom->mode);
+ // run_thread = std::thread(&Ricom::run, ricom, ricom->mode);
  while (ricom->srf_ricom == NULL)
  {
  SDL_Delay(ricom->redraw_interval);
  }
 
  // run_thread.detach();
- RICOM::run(ricom, ricom->mode);
+ ricom->run(ricom->mode);
 
  // // Initializing SDL
  SDL_DisplayMode DM; // To get the current display size
@@ -251,7 +258,7 @@ int run_cli(int argc, char *argv[], Ricom *ricom)
  }
  else
  {
- RICOM::run(ricom, ricom->mode);
+ ricom->run(ricom->mode);
  }
  if (save_dat != "")
  {