Merge pull request #1712 from pace-neutrons/1700_bin_writer

1700 bin writer

CMakeLists.txt

@@ -8,8 +8,9 @@ project("Horace" VERSION "${_version}")
 #
 cmake_host_system_information(RESULT CMAKE_HOST_SYSTEM_NAME QUERY OS_NAME)
 
-# C++11 is required for GTest
-set(CMAKE_CXX_STANDARD 11)
+# C++11 is required for GTest but 17 for some plugins
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED TRUE)
 
 # Sort our targets into folders
 set_property(GLOBAL PROPERTY USE_FOLDERS ON)

_LowLevelCode/cpp/CMakeLists.txt

@@ -19,6 +19,8 @@ set(MEX_FUNCTIONS
     "compute_pix_sums"
     "mtimesx_horace"
     "sort_pixels_by_bins"
+    "mex_bin_plugin"
+    "file_parameters"
      ${HDF_READER}
 )
 foreach(_mex_func ${MEX_FUNCTIONS})

_LowLevelCode/cpp/combine_sqw/CMakeLists.txt

@@ -2,19 +2,19 @@ set(
     SRC_FILES
     "combine_sqw.cpp"
     "exchange_buffer.cpp"
-    "fileParameters.cpp"
     "nsqw_pix_reader.cpp"
     "pix_mem_map.cpp"
     "sqw_pix_writer.cpp"
     "sqw_reader.cpp"
+    "../file_parameters/fileParameters.cpp"
 )
 
 set(
     HDR_FILES
     "../CommonCode.h"
+    "../file_parameters/fileParameters.h"
     "combine_sqw.h"
     "exchange_buffer.h"
-    "fileParameters.h"
     "nsqw_pix_reader.h"
     "pix_mem_map.h"
     "sqw_pix_writer.h"

_LowLevelCode/cpp/combine_sqw/TestCombineSQW/TestCombineSQW.h

@@ -103,7 +103,7 @@ class TestCombineSQW : public CxxTest::TestSuite {
             sqw_reader reader;
             fileParameters file_par;
             file_par.fileName = test_file_name;
-            file_par.file_id = 0;
+            file_par.run_id = 0;
             file_par.nbin_start_pos = bin_pos_in_file;
             file_par.pix_start_pos = pix_pos_in_file;
             file_par.total_NfileBins = num_bin_in_file;

_LowLevelCode/cpp/combine_sqw/combine_sqw.cpp

@@ -3,6 +3,7 @@
 #include "nsqw_pix_reader.h"
 #include "sqw_pix_writer.h"
 #include "../utility/version.h"
+#include "../file_parameters/fileParameters.h"
 
 #include <memory>
 #include <stdio.h>
@@ -37,16 +38,16 @@ enum OutputArguments { // unique output arguments,
     "npix_start_pos"    -- the location of the beginning of the npix data in the binary file
                            (output of ftellg(fid) or of fseek(fid, npix_start_pos)
     "pix_start_pos"     -- the location of the beginning of the pix data in the binary file. Similar to npix
-    "file_id"           -- number of pixel (pixel ID) distinguishing the pixels, obtained from this run from
-                           all other pixels in combined sqw file.
+    "run_id"            -- the number (pixel ID) distinguishing the pixels, obtained from a particular run from
+                           pixels generated retrieved from other runs in combined sqw file.
     "nbins_total"       -- number of bins stored in single data file
 %
 % 2) outFileParams -- structure, which defines the parameters for the pixels to write.
     The structure is similar to the one used for inFileParams but some fields are undefined.
     The fields need to be defined are file_name, npix_start_pos and pix_start_pos.
-    The undefined fields are file_id and nbins_total
+    The undefined fields are run_id and nbins_total
     nbins_total is calculated from nbins_total of the input files and file id
-    is the combination of file_ids of input files to can not be unique or defined.
+    is the combination of run_ids of input files to can not be unique or defined.
 %
 % 3) programSettings -- array of parameters defining the file combine process, namely:
 % n_bin        -- number of bins in the image array
@@ -269,7 +270,7 @@ void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
     std::vector<sqw_reader> fileReader(n_files);
     for (size_t i = 0; i < n_files; i++) {
         if (change_fileno && !fileno_provided) { // renumbering pixel id-s with file number
-            fileParam[i].file_id = int(i + 1); // file numbers in Matlab start from 1 so adhere to this convention
+            fileParam[i].run_id = int(i + 1); // file numbers in Matlab start from 1 so adhere to this convention
         }
         fileReader[i].init(fileParam[i], change_fileno,read_buf_size, read_files_multitreaded);
     }
@@ -314,4 +315,3 @@ void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
     }
     fileReader.clear();
 }
-

_LowLevelCode/cpp/combine_sqw/combine_sqw.h

@@ -1,5 +1,4 @@
-#ifndef H_COMBINE_SQW
-#define H_COMBINE_SQW
+#pragma once
 #include "nsqw_pix_reader.h"
 #include "sqw_pix_writer.h"
 
@@ -11,7 +10,3 @@ enum readBinInfoOption {
     sumPixInfo,
     keepPixInfo
 };
-
-
-#endif
-

_LowLevelCode/cpp/combine_sqw/sqw_pix_writer.h

@@ -1,8 +1,6 @@
-#ifndef H_SQW_PIX_WRITER
-#define H_SQW_PIX_WRITER
-
+#pragma once
 //#include "pix_mem_map.h"
-#include "fileParameters.h"
+#include "../file_parameters/fileParameters.h"
 #include "exchange_buffer.h"
 
 //-----------------------------------------------------------------------------------------------------------------
@@ -37,7 +35,4 @@ class sqw_pix_writer {
     //
     static const size_t PIX_BLOCK_SIZE_BYTES = 36; //9 * 4; // size of the pixel block in bytes
 
-
 };
-
-#endif

_LowLevelCode/cpp/combine_sqw/sqw_reader.cpp

@@ -13,7 +13,7 @@ sqw_reader::sqw_reader() :
 {}
 
 sqw_reader::~sqw_reader() {
-    //mexPrintf("|MEX::COMBINE_SQW: in destructor for file N %d  |",this->fileDescr.file_id);
+    //mexPrintf("|MEX::COMBINE_SQW: in destructor for file N %d  |",this->fileDescr.run_id);
     //mexEvalString("pause(.002);");
 
     this->finish_read_job();
@@ -310,7 +310,7 @@ void sqw_reader::read_pixels_job() {
 }
 //
 void sqw_reader::finish_read_job() {
-    //mexPrintf("|MEX::COMBINE_SQW: in finish read job for file N %d  |",this->fileDescr.file_id);
+    //mexPrintf("|MEX::COMBINE_SQW: in finish read job for file N %d  |",this->fileDescr.run_id);
     //mexEvalString("pause(.002);");
 
     this->pix_map.finish_read_bin_job();
@@ -334,7 +334,7 @@ void sqw_reader::finish_read_job() {
     }
     this->read_pix_needed.notify_one();
     read_pix_job_holder.join();
-    //mexPrintf(" completed pix read job|\n",this->fileDescr.file_id);
+    //mexPrintf(" completed pix read job|\n",this->fileDescr.run_id);
     //mexEvalString("pause(.002);");
 
 }
@@ -364,7 +364,7 @@ void sqw_reader::_read_pix(size_t pix_start_num, float *const pix_buffer, size_t
 
     if (this->change_fileno) {
         for (size_t i = 0; i < num_pix_to_read; i++) {
-            *(pix_buffer + 4 + i * 9) = float(this->fileDescr.file_id);
+            *(pix_buffer + 4 + i * 9) = float(this->fileDescr.run_id);
         }
 
     }

_LowLevelCode/cpp/combine_sqw/sqw_reader.h

@@ -2,7 +2,7 @@
 #define H_SQW_READER
 
 #include "pix_mem_map.h"
-#include "fileParameters.h"
+#include "../file_parameters/fileParameters.h"
 //-----------------------------------------------------------------------------------------------------------------
 class sqw_reader
 {
@@ -54,8 +54,8 @@ class sqw_reader
     size_t PIX_BUF_SIZE;
     //Boolean indicating that the id, which specify pixel run number should be modified
     bool change_fileno;
-    // Boolean, indicating if one needs to offset pixel's run number id by fileDescr.file_id
-    // or set up its value into fileDescr.file_id;
+    // Boolean, indicating if one needs to offset pixel's run number id by fileDescr.run_id
+    // or set up its value into fileDescr.run_id;
     bool fileno;
 
     static const size_t PIX_SIZE = 9; // size of the pixel in pixel data units (float)

_LowLevelCode/cpp/cpp_communicator/cpp_communicator.h

@@ -4,4 +4,5 @@
 #include "MPI_wrapper.h"
 #include "input_parser.h"
 
-void set_numlab_and_nlabs(class_handle<MPI_wrapper> * const pCommunicatorHolder, int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]);
+void set_numlab_and_nlabs(class_handle<MPI_wrapper> * const pCommunicatorHolder,
+	int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]);

_LowLevelCode/cpp/file_parameters/CMakeLists.txt

@@ -0,0 +1,24 @@
+# The project builds tester application for fileParameters
+# The class itself is used elsewhere
+set(
+    SRC_FILES
+    "fileParameters.cpp"
+    "file_parameters_tester.cpp"
+)
+
+set(
+    HDR_FILES
+    "../CommonCode.h"
+    "fileParameters.h"
+)
+
+set(MEX_NAME "file_parameters_tester")
+pace_add_mex(
+    NAME "${MEX_NAME}"
+    SRC "${SRC_FILES}" "${HDR_FILES}"
+)
+# openmp is currently disabled here but it may be used in a future
+#if(${OPENMP_FOUND})
+#    target_compile_options("${MEX_NAME}" PRIVATE ${OpenMP_CXX_FLAGS})
+#    target_link_options("${MEX_NAME}" PRIVATE ${OpenMP_EXE_LINKER_FLAGS})
+#endif()