From 281e5c6cd19752d720048dee10041d4f118b6434 Mon Sep 17 00:00:00 2001
From: Giovanni La Mura <giovanni.lamura@inaf.it>
Date: Fri, 19 Apr 2024 15:38:34 +0200
Subject: [PATCH] Implement static output for single sphere TM
---
src/include/TransitionMatrix.h | 77 +++++++++++++++++++--
src/libnptm/TransitionMatrix.cpp | 111 +++++++++++++++++++++++++++++--
2 files changed, 178 insertions(+), 10 deletions(-)
diff --git a/src/include/TransitionMatrix.h b/src/include/TransitionMatrix.h
index 54903a95..0e51f1d8 100644
--- a/src/include/TransitionMatrix.h
+++ b/src/include/TransitionMatrix.h
@@ -60,8 +60,8 @@ class TransitionMatrix {
*
* This function takes care of the specific task of writing the transition
* matrix memory data structure to a binary output file formatted according
- * to the HDF5 standard. It is designed to work for the case of clusters of
- * spheres.
+ * to the HDF5 standard without a pre-existing instance. It is designed to
+ * work for the case of a cluster of spheres.
*
* \param file_name: `string` Name of the binary configuration data file.
* \param _nlemt: `np_int` Size of the matrix (2 * LE * (LE + 2)).
@@ -75,13 +75,33 @@ class TransitionMatrix {
double _exri, dcomplex **_am0m
);
+ /*! \brief Write transition matrix data to HDF5 binary output.
+ *
+ * This function takes care of the specific task of writing the transition
+ * matrix memory data structure to a binary output file formatted according
+ * to the HDF5 standard without a pre-existing instance. It is designed to
+ * work for the case of a single sphere.
+ *
+ * \param file_name: `string` Name of the binary configuration data file.
+ * \param _lm: `int` Maximum field expansion order.
+ * \param _vk: `double` Wave number in scale units.
+ * \param _exri: `double` External medium refractive index.
+ * \param _rmi: `complex double **`
+ * \param _rei: `complex double **`
+ * \param _sphere_radius: `double` Radius of the sphere.
+ */
+ static void write_hdf5(
+ std::string file_name, int _lm, double _vk, double _exri,
+ dcomplex **_rmi, dcomplex **_rei, double _sphere_radius
+ );
+
/*! \brief Write the Transition Matrix to legacy binary output.
*
* \param file_name: `string` Name of the binary configuration data file.
*/
void write_legacy(std::string file_name);
- /*! \brief Write transition matrix data to HDF5 binary output.
+ /*! \brief Write transition matrix data to binary output using legacy format.
*
* This function takes care of the specific task of writing the transition
* matrix memory data structure to a binary output file formatted according
@@ -100,6 +120,26 @@ class TransitionMatrix {
double _exri, dcomplex **_am0m
);
+ /*! \brief Write transition matrix data to binary output using legacy format.
+ *
+ * This function takes care of the specific task of writing the transition
+ * matrix memory data structure to a binary output file formatted according
+ * to the original code structure without a pre-existing instance. It is designed
+ * to work for the case of a single sphere.
+ *
+ * \param file_name: `string` Name of the binary configuration data file.
+ * \param _lm: `int` Maximum field expansion order.
+ * \param _vk: `double` Wave number in scale units.
+ * \param _exri: `double` External medium refractive index.
+ * \param _rmi: `complex double **`
+ * \param _rei: `complex double **`
+ * \param _sphere_radius: `double` Radius of the sphere.
+ */
+ static void write_legacy(
+ std::string file_name, int _lm, double _vk, double _exri,
+ dcomplex **_rmi, dcomplex **_rei, double _sphere_radius
+ );
+
public:
/*! \brief Default Transition Matrix instance constructor.
*
@@ -181,7 +221,7 @@ class TransitionMatrix {
*/
void write_binary(std::string file_name, std::string mode="LEGACY");
- /*! \brief Write a Transition Matrix to a binary file without instanciating it.
+ /*! \brief Write a cluster Transition Matrix to a binary file without instanciating it.
*
* Transition Matrix data can take a large amount of memory. For such reason, attempts
* to create TransitionMatrix instances only for writing purposes can create
@@ -208,6 +248,35 @@ class TransitionMatrix {
double _exri, dcomplex **_am0m, std::string mode="LEGACY"
);
+ /*! \brief Write a single sphere Transition Matrix to a binary file without instanciating it.
+ *
+ * Transition Matrix data can take a large amount of memory. For such reason, attempts
+ * to create TransitionMatrix instances only for writing purposes can create
+ * unnecessary resource consumption and computing time to duplicate the data into
+ * the output buffer. This function offers output to file as a static method. It
+ * takes the arguments of a constructor together with the usual arguments to specify
+ * the output file name and format, to write the required data directly to a file,
+ * without creating a new TransitionMatrix instance. The implementation works for
+ * TransitionMatrix objects built for the single sphere case. It belongs to the public
+ * class interface and it calls the proper versions of `write_legacy()` and `write_hdf5()`,
+ * depending on the requested output format.
+ *
+ * \param file_name: `string` Name of the file to be written.
+ * \param _lm: `int` Maximum field expansion order.
+ * \param _vk: `double` Wave number in scale units.
+ * \param _exri: `double` External medium refractive index.
+ * \param _rmi: `complex double **`
+ * \param _rei: `complex double **`
+ * \param _sphere_radius: `double` Radius of the sphere.
+ * \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"] . Optional
+ * (default is "LEGACY").
+ */
+ static void write_binary(
+ std::string file_name, int _lm, double _vk, double _exri,
+ dcomplex **_rmi, dcomplex **_rei, double _sphere_radius,
+ std::string mode="LEGACY"
+ );
+
/*! \brief Test whether two instances of TransitionMatrix are equal.
*
* Transition matrices can be the result of a calculation or of a file input operation,
diff --git a/src/libnptm/TransitionMatrix.cpp b/src/libnptm/TransitionMatrix.cpp
index 7468ec8d..477264ef 100644
--- a/src/libnptm/TransitionMatrix.cpp
+++ b/src/libnptm/TransitionMatrix.cpp
@@ -94,7 +94,7 @@ TransitionMatrix::TransitionMatrix(
}
}
-TransitionMatrix* TransitionMatrix::from_binary(string file_name, string mode) {
+TransitionMatrix* TransitionMatrix::from_binary(std::string file_name, std::string mode) {
TransitionMatrix *tm = NULL;
if (mode.compare("LEGACY") == 0) {
tm = TransitionMatrix::from_legacy(file_name);
@@ -107,7 +107,7 @@ TransitionMatrix* TransitionMatrix::from_binary(string file_name, string mode) {
return tm;
}
-TransitionMatrix* TransitionMatrix::from_hdf5(string file_name) {
+TransitionMatrix* TransitionMatrix::from_hdf5(std::string file_name) {
TransitionMatrix *tm = NULL;
unsigned int flags = H5F_ACC_RDONLY;
HDFFile *hdf_file = new HDFFile(file_name, flags);
@@ -160,7 +160,7 @@ TransitionMatrix* TransitionMatrix::from_hdf5(string file_name) {
return tm;
}
-TransitionMatrix* TransitionMatrix::from_legacy(string file_name) {
+TransitionMatrix* TransitionMatrix::from_legacy(std::string file_name) {
fstream ttms;
TransitionMatrix *tm = NULL;
ttms.open(file_name, ios::binary | ios::in);
@@ -207,7 +207,7 @@ TransitionMatrix* TransitionMatrix::from_legacy(string file_name) {
return tm;
}
-void TransitionMatrix::write_binary(string file_name, string mode) {
+void TransitionMatrix::write_binary(std::string file_name, std::string mode) {
if (mode.compare("LEGACY") == 0) {
write_legacy(file_name);
} else if (mode.compare("HDF5") == 0) {
@@ -232,7 +232,22 @@ void TransitionMatrix::write_binary(
}
}
-void TransitionMatrix::write_hdf5(string file_name) {
+void TransitionMatrix::write_binary(
+ std::string file_name, int _lm, double _vk, double _exri,
+ dcomplex **_rmi, dcomplex **_rei, double _sphere_radius,
+ std::string mode
+) {
+ if (mode.compare("LEGACY") == 0) {
+ write_legacy(file_name, _lm, _vk, _exri, _rmi, _rei, _sphere_radius);
+ } else if (mode.compare("HDF5") == 0) {
+ write_hdf5(file_name, _lm, _vk, _exri, _rmi, _rei, _sphere_radius);
+ } else {
+ string message = "Unknown format mode: \"" + mode + "\"";
+ throw UnrecognizedFormatException(message);
+ }
+}
+
+void TransitionMatrix::write_hdf5(std::string file_name) {
if (is == 1 || is == 1111) {
List<string> rec_name_list(1);
List<string> rec_type_list(1);
@@ -328,7 +343,58 @@ void TransitionMatrix::write_hdf5(
delete hdf_file;
}
-void TransitionMatrix::write_legacy(string file_name) {
+void TransitionMatrix::write_hdf5(
+ std::string file_name, int _lm, double _vk, double _exri,
+ dcomplex **_rmi, dcomplex **_rei, double _sphere_radius
+) {
+ int is = 1111;
+ List<string> rec_name_list(1);
+ List<string> rec_type_list(1);
+ List<void *> rec_ptr_list(1);
+ string str_type, str_name;
+ rec_name_list.set(0, "IS");
+ rec_type_list.set(0, "INT32_(1)");
+ rec_ptr_list.set(0, &is);
+ rec_name_list.append("L_MAX");
+ rec_type_list.append("INT32_(1)");
+ rec_ptr_list.append(&_lm);
+ rec_name_list.append("VK");
+ rec_type_list.append("FLOAT64_(1)");
+ rec_ptr_list.append(&_vk);
+ rec_name_list.append("EXRI");
+ rec_type_list.append("FLOAT64_(1)");
+ rec_ptr_list.append(&_exri);
+ dcomplex *_elements = new dcomplex[2 * _lm]();
+ for (int ei = 0; ei < _lm; ei++) {
+ _elements[2 * ei] = -1.0 / _rmi[ei][0];
+ _elements[2 * ei + 1] = -1.0 / _rei[ei][0];
+ }
+ rec_name_list.append("ELEMENTS");
+ str_type = "COMPLEX128_(" + to_string(_lm) + "," + to_string(2) + ")";
+ rec_type_list.append(str_type);
+ rec_ptr_list.append(_elements);
+ rec_name_list.append("RADIUS");
+ rec_type_list.append("FLOAT64_(1)");
+ rec_ptr_list.append(&_sphere_radius);
+
+ string *rec_names = rec_name_list.to_array();
+ string *rec_types = rec_type_list.to_array();
+ void **rec_pointers = rec_ptr_list.to_array();
+ const int rec_num = rec_name_list.length();
+ FileSchema schema(rec_num, rec_types, rec_names);
+ HDFFile *hdf_file = HDFFile::from_schema(schema, file_name, H5F_ACC_TRUNC);
+ for (int ri = 0; ri < rec_num; ri++)
+ hdf_file->write(rec_names[ri], rec_types[ri], rec_pointers[ri]);
+ hdf_file->close();
+
+ delete[] _elements;
+ delete[] rec_names;
+ delete[] rec_types;
+ delete[] rec_pointers;
+ delete hdf_file;
+}
+
+void TransitionMatrix::write_legacy(std::string file_name) {
fstream ttms;
if (is == 1111 || is == 1) {
ttms.open(file_name, ios::binary | ios::out);
@@ -388,6 +454,39 @@ void TransitionMatrix::write_legacy(
}
}
+void TransitionMatrix::write_legacy(
+ std::string file_name, int _lm, double _vk, double _exri,
+ dcomplex **_rmi, dcomplex **_rei, double _sphere_radius
+) {
+ fstream ttms;
+ int is = 1111;
+ ttms.open(file_name, ios::binary | ios::out);
+ if (ttms.is_open()) {
+ ttms.write(reinterpret_cast<char *>(&is), sizeof(int));
+ ttms.write(reinterpret_cast<char *>(&_lm), sizeof(int));
+ ttms.write(reinterpret_cast<char *>(&_vk), sizeof(double));
+ ttms.write(reinterpret_cast<char *>(&_exri), sizeof(double));
+ double rval, ival;
+ dcomplex element;
+ for (int ei = 0; ei < _lm; ei++) {
+ element = -1.0 / _rmi[ei][0];
+ rval = real(element);
+ ival = imag(element);
+ ttms.write(reinterpret_cast<char *>(&rval), sizeof(double));
+ ttms.write(reinterpret_cast<char *>(&ival), sizeof(double));
+ element = -1.0 / _rei[ei][0];
+ rval = real(element);
+ ival = imag(element);
+ ttms.write(reinterpret_cast<char *>(&rval), sizeof(double));
+ ttms.write(reinterpret_cast<char *>(&ival), sizeof(double));
+ }
+ ttms.write(reinterpret_cast<char *>(&_sphere_radius), sizeof(double));
+ ttms.close();
+ } else { // Failed to open output file. Should never happen.
+ printf("ERROR: could not open Transition Matrix file for writing.\n");
+ }
+}
+
bool TransitionMatrix::operator ==(TransitionMatrix &other) {
if (is != other.is) {
return false;
--
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