initial upload

2024-09-10 20:25:18 +08:00
parent b8de03ee4f
commit f1cc876972
377 changed files with 2721267 additions and 34 deletions
--- a/lki/CMakeLists.txt
+++ b/lki/CMakeLists.txt
@@ -0,0 +1,24 @@
+set(TOOL_NAME lki)
+set(BIN_DIR bin)
+set(INSTALL_DIR sbin)
+
+find_package(GCTL_OPTIMIZATION REQUIRED)
+include_directories(${GCTL_OPTIMIZATION_INC_DIR})
+
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
+if(WIN32)
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
+else()
+	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
+endif()
+
+set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/${BIN_DIR})
+
+aux_source_directory(. TOOL_SRC)
+add_executable(${TOOL_NAME} ${TOOL_SRC})
+set_target_properties(${TOOL_NAME} PROPERTIES INSTALL_RPATH /usr/local/lib)
+set_target_properties(${TOOL_NAME} PROPERTIES CXX_STANDARD 17 CXX_STANDARD_REQUIRED ON)
+
+target_link_libraries(${TOOL_NAME} PUBLIC ${GCTL_OPTIMIZATION_LIB})
+
+install(TARGETS ${TOOL_NAME} RUNTIME DESTINATION ${INSTALL_DIR})
--- a/lki/lki.cpp
+++ b/lki/lki.cpp
@@ -0,0 +1,96 @@
+/********************************************************
+ *  ██████╗  ██████╗████████╗██╗
+ * ██╔════╝ ██╔════╝╚══██╔══╝██║
+ * ██║  ███╗██║        ██║   ██║
+ * ██║   ██║██║        ██║   ██║
+ * ╚██████╔╝╚██████╗   ██║   ███████╗
+ *  ╚═════╝  ╚═════╝   ╚═╝   ╚══════╝
+ * Geophysical Computational Tools & Library (GCTL)
+ *
+ * Copyright (c) 2022  Yi Zhang (yizhang-geo@zju.edu.cn)
+ *
+ * GCTL is distributed under a dual licensing scheme. You can redistribute 
+ * it and/or modify it under the terms of the GNU Lesser General Public 
+ * License as published by the Free Software Foundation, either version 2 
+ * of the License, or (at your option) any later version. You should have 
+ * received a copy of the GNU Lesser General Public License along with this 
+ * program. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * If the terms and conditions of the LGPL v.2. would prevent you from using 
+ * the GCTL, please consider the option to obtain a commercial license for a 
+ * fee. These licenses are offered by the GCTL's original author. As a rule, 
+ * licenses are provided "as-is", unlimited in time for a one time fee. Please 
+ * send corresponding requests to: yizhang-geo@zju.edu.cn. Please do not forget 
+ * to include some description of your company and the realm of its activities. 
+ * Also add information on how to contact you by electronic and paper mail.
+ ******************************************************/
+
+#include "lki.h"
+
+int main(int argc, char *argv[]) try
+{
+	gctl::flags_parser fp;
+	fp.set_proname("lki");
+	fp.set_proinfo("Limited memory Kriging Interpolation of 2D arbitrary located data. \
+This program is a toolkit of the GCTL package. The GCTL comes with ABSOLUTE NO WARRANTY. \
+Please see instructions or contact the author for more information.");
+	fp.add_opt('i', "in-table", required_argument, NULL, "Input table name of the constraint locations and data.", "<file-name>", true);
+	fp.add_opt('t', "target-table", required_argument, NULL, "Input table name of the target locations or parameters of output grid locations.", "<file-name>|<xmin>/<dx>/<xmax>/<ymin>/<dx>/<ymax>", true);
+	fp.add_opt('o', "out-table", required_argument, NULL, "Output table name of the interpolated data.", "<file-name>", true);
+	fp.add_opt('k', "kernel-size", required_argument, NULL, "Kernel size for solving the linear system of the Variogram functions (default is 200).", "<size>", false);
+	fp.add_opt('e', "epsilon", required_argument, NULL, "Threshold for solving the linear system of the Variogram functions (default is 1e-10).", "<value>", false);
+	fp.add_opt('b', "box-dimension", required_argument, NULL, "2D boxes' dimensions used for pre-processing the constraint data (default is 10).", "<size>", false);
+	fp.add_opt('v', "variogram", required_argument, NULL, "Variogram function used for interpolation. Available functions are spherical (default), gaussian, \
+wave, rational, circular and linear.", "<function>", false);
+	fp.add_opt('p', "parameter", required_argument, NULL, "Parameters of the variogram function. The default values are 0.1, 10 and 100, respectively.", "<nugget>/<sill>/<range>", false);
+	fp.add_opt('c', "column", required_argument, NULL, "Column index of x, y and data. The defaults are 0,1,2", "<col-x>,<col-y>,<col-data>", false);
+	fp.add_opt('h', "head-record", required_argument, NULL, "Input file has [0] Header record(s).", "<size>", false);
+	fp.add_opt('a', "annotate", required_argument, NULL, "The starting symbol of an annotate line.", "<sym>", false);
+	fp.add_opt('d', "delimeter", required_argument, NULL, "Delimeter between different columns.", "<sym>", false);
+	fp.configure(argc, argv);
+
+	if (argc == 1)
+	{
+		fp.show_help_page();
+		return 0;
+	}
+
+	std::string in_name, out_name, tar_name, kernel_str, eps_str, box_str, variogram_str, para_str, col_str, head_str, ant_str, del_str;
+	fp.get_argv({'i', 't', 'o', 'k', 'e', 'b', 'v', 'p', 'c'}, 
+		{&in_name, &tar_name, &out_name, &kernel_str, &eps_str, &box_str, &variogram_str, &para_str, &col_str, &head_str, &ant_str, &del_str});
+	// 查看是否通过强制参数检查
+	if (!fp.pass_mandatory()) return 0;
+
+	int kernel_size, box_size;
+	double epsilon;
+	std::string variogram_type, variogram_para;
+	if (kernel_str == "NULL") kernel_size = 200; 
+	else gctl::str2type(kernel_str, kernel_size);
+
+	if (eps_str == "NULL") epsilon = 1e-10;
+	else gctl::str2type(eps_str, epsilon);
+
+	if (box_str == "NULL") box_size = 10;
+	else gctl::str2type(box_str, box_size);
+
+	if (variogram_str == "NULL")  variogram_type = "spherical";
+	else variogram_type = variogram_str;
+
+	if (para_str == "NULL") variogram_para = "0.1/10/100";
+	else variogram_para = para_str;
+
+	if (col_str == "NULL") col_str = "0,1,2";
+
+	gctl::text_descriptor desc;
+	if (head_str != "NULL") gctl::str2type(head_str, desc.head_num_);
+	if (ant_str != "NULL") gctl::str2type(ant_str, desc.att_sym_);
+	if (del_str != "NULL") gctl::str2type(del_str, desc.delimiter_);
+
+	LKI ki;
+	ki.Routine(in_name, tar_name, out_name, col_str, desc, kernel_size, box_size, epsilon, variogram_type, variogram_para);
+	return 0;
+}
+catch (std::exception &e)
+{
+	GCTL_ShowWhatError(e.what(), GCTL_ERROR_ERROR, 0, 0, 0);
+}
--- a/lki/lki.h
+++ b/lki/lki.h
@@ -0,0 +1,357 @@
+/********************************************************
+ *  ██████╗  ██████╗████████╗██╗
+ * ██╔════╝ ██╔════╝╚══██╔══╝██║
+ * ██║  ███╗██║        ██║   ██║
+ * ██║   ██║██║        ██║   ██║
+ * ╚██████╔╝╚██████╗   ██║   ███████╗
+ *  ╚═════╝  ╚═════╝   ╚═╝   ╚══════╝
+ * Geophysical Computational Tools & Library (GCTL)
+ *
+ * Copyright (c) 2022  Yi Zhang (yizhang-geo@zju.edu.cn)
+ *
+ * GCTL is distributed under a dual licensing scheme. You can redistribute 
+ * it and/or modify it under the terms of the GNU Lesser General Public 
+ * License as published by the Free Software Foundation, either version 2 
+ * of the License, or (at your option) any later version. You should have 
+ * received a copy of the GNU Lesser General Public License along with this 
+ * program. If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * If the terms and conditions of the LGPL v.2. would prevent you from using 
+ * the GCTL, please consider the option to obtain a commercial license for a 
+ * fee. These licenses are offered by the GCTL's original author. As a rule, 
+ * licenses are provided "as-is", unlimited in time for a one time fee. Please 
+ * send corresponding requests to: yizhang-geo@zju.edu.cn. Please do not forget 
+ * to include some description of your company and the realm of its activities. 
+ * Also add information on how to contact you by electronic and paper mail.
+ ******************************************************/
+
+// linear conjugate gradient solver library
+//#include "lcg/solver.h"
+// GCTL library
+#include "gctl/core.h"
+#include "gctl/algorithm.h"
+#include "gctl/geometry.h"
+#include "gctl/io.h"
+#include "gctl/utility.h"
+#include "gctl/optimization.h"
+
+#if defined _WINDOWS || __WIN32__
+#include "io.h"
+// Test for file existence
+#define F_OK 0
+#endif
+
+class LKI : public gctl::lcg_solver
+{
+public:
+	LKI(){}
+	virtual ~LKI(){}
+	void LCG_Ax(const gctl::array<double> &a, gctl::array<double> &b);
+	void LCG_Mx(const gctl::array<double> &a, gctl::array<double> &b){}
+
+	void Routine(std::string inname, std::string tarname, std::string outname, std::string col_str, 
+		gctl::text_descriptor &desc, int kernel_size, int box_size, double epsilon, 
+		std::string variogram_type, std::string variogram_para);
+	void ReadConstrainNodes(std::string filename, gctl::text_descriptor &desc);
+	void WriteTargetNodes(std::string filename, const gctl::text_descriptor &desc);
+	void InitTargetNodes(std::string para);
+	void CalKernel();
+	void CalKernel(const gctl::point3dc &tar_node);
+	void set_kernel_size(unsigned int k){MatSize = k+1;}
+
+public:
+	gctl::array<gctl::point3dc> ConsNodes;
+	gctl::array<gctl::point3dc> TargNodes;
+	std::vector<gctl::point3dc*> LocalNodes;
+	gctl::boxes2d<gctl::point3dc> PntBoxes;
+
+	int ConsSize, MatSize;
+	gctl::matrix<double> Kernel;
+	gctl::array<double> Wgts;
+	gctl::array<double> MidPdt;
+	gctl::array<double> B;
+
+	//gctl::array<double> GK;
+	//gctl::array<double> DK;
+	//gctl::array<double> ADK;
+
+	gctl::variogram_model VarModel;
+	gctl::variogram_type_e VarType;
+
+	gctl::getoption gopt;
+
+	gctl::_1i_vector col_index;
+};
+
+void LKI::Routine(std::string inname, std::string tarname, std::string outname, std::string col_str, gctl::text_descriptor &desc, 
+	int kernel_size, int box_size, double epsilon, std::string variogram_type, std::string variogram_para)
+{
+	if (variogram_type == "spherical") VarType = gctl::SPHERICAL;
+	else if (variogram_type == "exponential") VarType = gctl::EXPONENTIAL;
+	else if (variogram_type == "gaussian") VarType = gctl::GAUSSIAN;
+	else if (variogram_type == "wave") VarType = gctl::WAVE;
+	else if (variogram_type == "rational") VarType = gctl::RATIONAL_Q;
+	else if (variogram_type == "circular") VarType = gctl::CIRCULAR;
+	else if (variogram_type == "linear") VarType = gctl::LINEAR;
+	else throw gctl::runtime_error("Invalid variogram function type. From LKI::Routine(...)");
+
+	gctl::parse_string_to_value(variogram_para, '/', true, VarModel.nugget, VarModel.sill, VarModel.range);
+	if (!VarModel.valid()) throw gctl::runtime_error("Invalid variogram parameters. From LKI::Routine(...)");
+
+	gctl::parse_string_to_vector(col_str, ',', col_index);
+	if (col_index.size() < 3)
+	{
+		throw gctl::runtime_error("Invalid column index. From LKI::Routine(...)");
+	}
+
+	ReadConstrainNodes(inname, desc);
+	InitTargetNodes(tarname);
+
+	unsigned int k_size = kernel_size;
+	if (k_size <= 1)
+	{
+		throw gctl::runtime_error("Invalid local size. From LBSI::Routine(...)");
+	}
+
+	if (k_size >= ConsNodes.size())
+	{
+		GCTL_ShowWhatError("The local size is equal to or bigger than the input node's size. Reduced to the global algorithm.", GCTL_WARNING_ERROR, 0, 0, 0);
+
+		ConsSize = ConsNodes.size();
+		MatSize = ConsSize + 1;
+		Kernel.resize(MatSize, MatSize);
+		Wgts.resize(MatSize);
+		B.resize(MatSize);
+
+		CalKernel();
+
+		gctl::lu lu_k(Kernel);
+		lu_k.decompose();
+
+		double dist, sum;
+		for (int i = 0; i < TargNodes.size(); ++i)
+		{
+			for (int j = 0; j < ConsSize; ++j)
+			{
+				dist = sqrt((ConsNodes[j].x - TargNodes[i].x)*(ConsNodes[j].x - TargNodes[i].x) 
+					+ (ConsNodes[j].y - TargNodes[i].y)*(ConsNodes[j].y - TargNodes[i].y));
+
+				B[j] = variogram(dist, VarModel, VarType);	
+			}
+			B[ConsSize] = 1.0;
+
+			lu_k.solve(B, Wgts);
+
+			sum = 0.0;
+			for (int j = 0; j < ConsSize; ++j)
+			{
+				sum += ConsNodes[j].z*Wgts[j];	
+			}
+			TargNodes[i].z = sum;
+		}
+		
+		WriteTargetNodes(outname, desc);
+		return;
+	}
+
+	set_kernel_size(k_size);
+	LocalNodes.resize(MatSize-1);
+	Kernel.resize(MatSize, MatSize);
+	Wgts.resize(MatSize);
+	MidPdt.resize(MatSize);
+	B.resize(MatSize);
+	//GK.resize(MatSize);
+	//DK.resize(MatSize);
+	//ADK.resize(MatSize);
+
+	gctl::lcg_para my_para = default_lcg_para();
+	//my_para.max_iterations = 1000;
+	my_para.epsilon = epsilon;
+	set_lcg_para(my_para);
+
+	gctl::array<double> xs(ConsNodes.size());
+	gctl::array<double> ys(ConsNodes.size());
+	for (int i = 0; i < ConsNodes.size(); ++i)
+	{
+		xs[i] = ConsNodes[i].x;
+		ys[i] = ConsNodes[i].y;
+	}
+
+	PntBoxes.init(xs, ys, ConsNodes, box_size, box_size);
+
+	double dist, sum;
+	gctl::progress_bar bar(TargNodes.size());
+	for (int i = 0; i < TargNodes.size(); ++i)
+	{
+		bar.progressed(i);
+
+		Kernel.assign_all(0.0);
+		Wgts.assign_all(0.0);
+
+		CalKernel(TargNodes[i]);
+
+		// run the inversion process in factory mode
+		//lcg(_AxProduct, nullptr, Wgts.get(), B.get(), MatSize, &my_para, this, GK.get(), DK.get(), ADK.get());
+		lcg(Wgts, B);
+
+		sum = 0.0;
+		for (int j = 0; j < MatSize-1; ++j)
+		{
+			sum += LocalNodes[j]->z*Wgts[j];
+		}
+		TargNodes[i].z = sum;
+	}
+
+	WriteTargetNodes(outname, desc);
+	return;
+}
+
+void LKI::ReadConstrainNodes(std::string filename, gctl::text_descriptor &desc)
+{
+	//read_text2array(filename, ConsNodes);
+
+	gctl::_2d_vector table_data;
+	gctl::read_text2vector2d(filename, table_data, desc);
+
+	if (table_data.size() <= 1)
+	{
+		throw gctl::runtime_error("Not enough constraint points. From LBSI::ReadConstrainNodes(...)");
+	}
+
+	ConsNodes.resize(table_data.size());
+	for (int i = 0; i < table_data.size(); ++i)
+	{
+		ConsNodes[i].x = table_data[i][col_index[0]];
+		ConsNodes[i].y = table_data[i][col_index[1]];
+		ConsNodes[i].z = table_data[i][col_index[2]];
+	}
+
+	gctl::destroy_vector(table_data);
+	return;
+}
+
+void LKI::WriteTargetNodes(std::string filename, const gctl::text_descriptor &desc)
+{
+	save_array2text(filename, TargNodes, desc);
+	return;
+}
+
+void LKI::InitTargetNodes(std::string para)
+{
+	// try to use the para as a file name
+	if (access(para.c_str(), F_OK) != -1)
+	{
+		std::vector<gctl::point2dc> tmp_vec;
+		gctl::read_text2vector(para, tmp_vec);
+
+		TargNodes.resize(tmp_vec.size());
+		for (int i = 0; i < tmp_vec.size(); ++i)
+		{
+			TargNodes[i].x = tmp_vec[i].x;
+			TargNodes[i].y = tmp_vec[i].y;
+			TargNodes[i].z = 0.0;
+		}
+
+		gctl::destroy_vector(tmp_vec);
+		return;
+	}
+
+	double dx, dy, xmin, xmax, ymin, ymax, ele = 0.0;
+	gctl::parse_string_to_value(para, '/', true, xmin, dx, xmax, ymin, dy, ymax);
+	gctl::get_grid_point3c(TargNodes, xmin, xmax, ymin, ymax, dx, dy, ele);
+	return;
+}
+
+void LKI::CalKernel()
+{
+	// 计算出所有成对的协方差函数值 成对的
+	double dist;
+	for (int i = 0; i < ConsSize; ++i)
+	{
+		Kernel[i][i] = variogram(0.0, VarModel, VarType);
+		for (int j = i+1; j < ConsSize; ++j)
+		{
+			dist = sqrt((ConsNodes[i].x - ConsNodes[j].x)*(ConsNodes[i].x - ConsNodes[j].x) 
+				+ (ConsNodes[i].y - ConsNodes[j].y)*(ConsNodes[i].y - ConsNodes[j].y));
+
+			Kernel[i][j] = Kernel[j][i] = variogram(dist, VarModel, VarType);
+		}
+	}
+
+	// 最后一行系数全为1
+	for (int i = 0; i < ConsSize; ++i)
+	{
+		Kernel[ConsSize][i] = Kernel[i][ConsSize] = 1.0;
+	}
+
+	Kernel[ConsSize][ConsSize] = 0.0;
+	return;
+}
+
+void LKI::CalKernel(const gctl::point3dc &tar_node)
+{
+	// 找出距离tar_node最近的一组控制点
+	PntBoxes.get_by_number(tar_node.x, tar_node.y, MatSize-1, LocalNodes);
+	
+	// 计算出所有成对的格林函数值
+	double dist;
+	for (int j = 0; j < MatSize-1; ++j)
+	{
+		Kernel[j][j] = variogram(0.0, VarModel, VarType);
+		for (int k = j+1; k < MatSize-1; ++k)
+		{
+			dist = sqrt((LocalNodes[j]->x - LocalNodes[k]->x)*(LocalNodes[j]->x - LocalNodes[k]->x) 
+				+ (LocalNodes[j]->y - LocalNodes[k]->y)*(LocalNodes[j]->y - LocalNodes[k]->y));
+
+			Kernel[j][k] = Kernel[k][j] = variogram(dist, VarModel, VarType);
+		}
+	}
+
+	// 最后一行系数全为1
+	for (int i = 0; i < MatSize-1; ++i)
+	{
+		Kernel[MatSize-1][i] = Kernel[i][MatSize-1] = 1.0;
+	}
+	Kernel[MatSize-1][MatSize-1] = 0.0;
+
+	for (int j = 0; j < MatSize-1; ++j)
+	{
+		dist = sqrt((LocalNodes[j]->x - tar_node.x)*(LocalNodes[j]->x - tar_node.x) 
+			+ (LocalNodes[j]->y - tar_node.y)*(LocalNodes[j]->y - tar_node.y));
+
+		MidPdt[j] = variogram(dist, VarModel, VarType);	
+	}
+	MidPdt[MatSize-1] = 1.0;
+
+	for (int i = 0; i < MatSize; ++i)
+	{
+		B[i] = 0;
+		for (int j = 0; j < MatSize; ++j)
+		{
+			B[i] += Kernel[j][i] * MidPdt[j];
+		}
+	}
+	return;
+}
+
+void LKI::LCG_Ax(const gctl::array<double> &a, gctl::array<double> &b)
+{
+	for (int i = 0; i < MatSize; ++i)
+	{
+		MidPdt[i] = 0;
+		for (int j = 0; j < MatSize; ++j)
+		{
+			MidPdt[i] += a[j] * Kernel[i][j];
+		}
+	}
+
+	for (int i = 0; i < MatSize; ++i)
+	{
+		b[i] = 0;
+		for (int j = 0; j < MatSize; ++j)
+		{
+			b[i] += MidPdt[j] * Kernel[j][i];
+		}
+	}
+	return;
+}