Merge pull request #147 from Zncl2222/release/v1.2.3

Release/v1.2.3

.gitignore

@@ -12,3 +12,5 @@ cbuild/
 randomfield*
 variogram*
 .coverage
+*.o
+*.exe

.pre-commit-config.yaml

@@ -14,6 +14,7 @@ repos:
     rev: v2.2.0
     hooks:
     -   id: setup-cfg-fmt
+        args: [--include-version-classifiers]
 -   repo: https://github.com/asottile/add-trailing-comma
     rev: v2.3.0
     hooks:

CMakeLists.txt

@@ -3,8 +3,9 @@ enable_testing()
 
 project(c_example)
 set(CMAKE_VERBOSE_MAKEFILE ON)
-# set true to compile the executable file (win -> .exe, linux -> .out)
-set(IS_EXECUTE true)
+
+# Set the option to compile the executable file
+option(IS_EXECUTE "Compile the executable file" ON)
 
 # set output directory
 if(IS_EXECUTE)
@@ -52,7 +53,6 @@ if(IS_EXECUTE)
     endif()
 endif()
 
-
 # unittest
 if(IS_EXECUTE)
     project(unittest)
@@ -62,11 +62,11 @@ if(IS_EXECUTE)
     set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/test)
 
     set(CTEST_COVERAGE_EXCLUDE
-    '/usr/include/*' # Exclude system headers
-    '${CMAKE_CURRENT_SOURCE_DIR}/test/utest.h' # Exclude a specific file
-    '${CMAKE_CURRENT_SOURCE_DIR}/src/c_array.c'
-    '${CMAKE_CURRENT_SOURCE_DIR}/src/c_array_mt.c'
-    '${CMAKE_CURRENT_SOURCE_DIR}/include/c_array.h'
+        '/usr/include/*' # Exclude system headers
+        '${CMAKE_CURRENT_SOURCE_DIR}/test/utest.h' # Exclude a specific file
+        '${CMAKE_CURRENT_SOURCE_DIR}/src/c_array.c'
+        '${CMAKE_CURRENT_SOURCE_DIR}/src/c_array_mt.c'
+        '${CMAKE_CURRENT_SOURCE_DIR}/include/c_array.h'
     )
     add_custom_target(
         coverage

README.md

@@ -111,8 +111,8 @@ if __name__ == '__main__':
     cov_model = Gaussian(bw_l, bw_s, k_range, sill)
 
     # Create simulation and input the Cov model
-    sgsim_py = uc.UCSgsim(x, cov_model, nR) # run sgsim with python
-    sgsim_c = uc.UCSgsimDLL(x, cov_model, nR) # run sgsim with c
+    sgsim_py = uc.UCSgsim(x, nR, cov_model) # run sgsim with python
+    sgsim_c = uc.UCSgsimDLL(x, nR, cov_model) # run sgsim with c
 
     # Start compute with n CPUs
     sgsim_c.compute(n_process=2, randomseed=randomseed)
@@ -124,7 +124,7 @@ if __name__ == '__main__':
     sgsim_c.hist_plot(x_location=10)  # Hist
     sgsim_c.variogram_compute(n_process=2)  # Compute variogram before plotting
     # Plot variogram and mean variogram for validation
-    sgsim_c.vario_plot()
+    sgsim.variogram_plot()
     # Save random_field and variogram
     sgsim_c.save_random_field('randomfields.csv', save_single=True)
     sgsim_c.save_variogram('variograms.csv', save_single=True)

cmake_build.sh

@@ -1,6 +1,30 @@
+#!/bin/bash
+
+is_execute=true
+
+# Parse command-line arguments
+while getopts ":s" opt; do
+    case $opt in
+        s)
+            is_execute=false
+            ;;
+        \?)
+            echo "Invalid option: -$OPTARG" >&2
+            ;;
+    esac
+done
+
 mkdir cmake_build
 cd cmake_build
-cmake ..
+
+if [ "$is_execute" = true ]; then
+    echo "Compile the code into an executable file !"
+    cmake -DIS_EXECUTE=ON ..
+else
+    echo "Compile the code into a shared library (dynamic library) !"
+    cmake -DIS_EXECUTE=OFF ..
+fi
+
 make
 make test
 make memcheck

python_example.py

@@ -22,8 +22,8 @@
     cov_model = Gaussian(bw_l, bw_s, k_range, sill)
 
     # Create simulation and input the Cov model
-    # sgsim = uc.UCSgsim(x, cov_model, nR)
-    sgsim = uc.UCSgsimDLL(x, cov_model, nR)
+    # sgsim = uc.UCSgsim(x, nR, cov_model)
+    sgsim = uc.UCSgsimDLL(x, nR, cov_model)
 
     # Start compute with n CPUs
     sgsim.compute(n_process=2, randomseed=randomseed)
@@ -37,7 +37,7 @@
     sgsim.hist_plot(x_location=10)  # Hist
     sgsim.variogram_compute(n_process=2)  # Compute variogram before plotting
     # Plot variogram and mean variogram for validation
-    sgsim.vario_plot()
+    sgsim.variogram_plot()
     # Save random_field and variogram
     sgsim.save_random_field('randomfields.csv', save_single=True)
     sgsim.save_variogram('variograms.csv', save_single=True)

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = uc_sgsim
-version = 1.2.2
+version = 1.2.3
 description = Random Field Generation
 long_description = file: README.md
 long_description_content_type = text/markdown
@@ -12,8 +12,12 @@ license_file = LICENSE.md
 classifiers =
     Development Status :: 5 - Production/Stable
     License :: OSI Approved :: MIT License
+    Programming Language :: C
     Programming Language :: Python :: 3
     Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
     Topic :: Scientific/Engineering :: Mathematics
 
 [options]

tests/uc_sgsim_test.py

@@ -36,71 +36,71 @@ def sgsim_save(self, sgsim: uc.UCSgsim) -> None:
         sgsim.save_variogram('variogram/', save_single=False)
 
     def test_uc_sgsim_gaussian_py_single_process(self):
-        sgsim = uc.UCSgsim(self.X, self.gaussian, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
         sgsim.compute(n_process=1, randomseed=454)
         sgsim.variogram_compute(n_process=1)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_gaussian_py_multi_process(self):
-        sgsim = uc.UCSgsim(self.X, self.gaussian, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_gaussian_nugget_py(self):
         model = Gaussian(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, model, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, model)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_spherical_py(self):
-        sgsim = uc.UCSgsim(self.X, self.spherical, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, self.spherical)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_spherical_nugget_py(self):
         model = Spherical(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, model, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, model)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_exponential_py(self):
-        sgsim = uc.UCSgsim(self.X, self.exponential, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, self.exponential)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_exponential_nugget_py(self):
         model = Exponential(35, 1, 17.32, 1, 0.01)
-        sgsim = uc.UCSgsim(self.X, model, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, model)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_gaussian_c(self):
-        sgsim = uc.UCSgsimDLL(self.X, self.gaussian, self.nR)
+        sgsim = uc.UCSgsimDLL(self.X, self.nR, self.gaussian)
         sgsim.compute(n_process=2, randomseed=454)
         sgsim.variogram_compute(n_process=2)
         self.sgsim_plot(sgsim)
         self.sgsim_save(sgsim)
 
     def test_uc_sgsim_varigram_exception(self):
-        sgsim = uc.UCSgsimDLL(self.X, self.gaussian, self.nR)
+        sgsim = uc.UCSgsimDLL(self.X, self.nR, self.gaussian)
         sgsim.compute(n_process=1, randomseed=454)
         with pytest.raises(VariogramDoesNotCompute):
             sgsim.variogram_plot()
 
-        sgsim = uc.UCSgsim(self.X, self.gaussian, self.nR)
+        sgsim = uc.UCSgsim(self.X, self.nR, self.gaussian)
         sgsim.compute(n_process=1, randomseed=454)
         with pytest.raises(VariogramDoesNotCompute):
             sgsim.variogram_plot()

uc_sgsim/c_core/CMakeLists.txt

@@ -13,6 +13,9 @@ endif()
 # Include header files
 include_directories(include/)
 
+# Set compiler optimization flags
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3")
+
 # Link each file
 add_library(
     uc_sgsim ${LIB_TYPE}

uc_sgsim/c_core/src/krige.c

@@ -69,7 +69,7 @@ void simple_kriging(double* array, sampling_state* _sampling, mt19937_state* rng
     }
 
     if (_sampling->neighbor >= 2) {
-        quicksort2d(array2d_temp.data, 0, _sampling->currlen - 1);
+        quickselect2d(array2d_temp.data, 0, _sampling->currlen - 1, _sampling->neighbor);
     }
 
     for (int j = 0; j < _sampling->neighbor; j++) {

uc_sgsim/c_core/src/sort_tools.c

@@ -40,3 +40,17 @@ void quicksort2d(double** array, int front, int end) {
         quicksort2d(array, pivot + 1, end);
     }
 }
+
+void quickselect2d(double** array, int front, int end, int k) {
+    if (front < end) {
+        int pivot = partition2d(array, front, end);
+
+        if (pivot == k - 1) {
+            return;
+        } else if (pivot > k - 1) {
+            quickselect2d(array, front, pivot, k);
+        } else {
+            quickselect2d(array, pivot + 1, end, k);
+        }
+    }
+}

uc_sgsim/random_field.py

@@ -5,14 +5,11 @@
 
 
 class RandomField:
-    def __init__(self, x: int, model: CovModel, realization_number: int):
-        self.__model = model
+    def __init__(self, x: int, realization_number: int):
         self.__realization_number = realization_number
-        self.__bandwidth_step = model.bandwidth_step
-        self.__bandwidth = model.bandwidth
-        self.__create_grid(x)
+        self._create_grid(x)
 
-    def __create_grid(self, x: int, y: int = 0) -> None:
+    def _create_grid(self, x: int, y: int = 0) -> None:
         self.__x = range(x)
         self.__y = range(y)
         self.__x_size = len(self.__x)
@@ -36,10 +33,6 @@ def y(self) -> int:
     def y_size(self) -> int:
         return self.__y_size
 
-    @property
-    def model(self) -> CovModel:
-        return self.__model
-
     @property
     def realization_number(self) -> int:
         return self.__realization_number
@@ -48,14 +41,6 @@ def realization_number(self) -> int:
     def realization_number(self, val: int):
         self.__realization_number = val
 
-    @property
-    def bandwidth(self) -> np.array:
-        return self.__bandwidth
-
-    @property
-    def bandwidth_step(self) -> int:
-        return self.__bandwidth_step
-
     def save_random_field(
         self,
         path: str,
@@ -106,3 +91,28 @@ def save_variogram(self, path: str, file_type: str = 'csv', save_single: bool =
                 )
         else:
             save_as_one_file(path, self.variogram)
+
+
+class SgsimField(RandomField):
+    def __init__(
+        self,
+        x: int,
+        realization_number: int,
+        model: CovModel,
+    ):
+        super().__init__(x, realization_number)
+        self.__model = model
+        self.__bandwidth_step = model.bandwidth_step
+        self.__bandwidth = model.bandwidth
+
+    @property
+    def model(self) -> CovModel:
+        return self.__model
+
+    @property
+    def bandwidth(self) -> np.array:
+        return self.__bandwidth
+
+    @property
+    def bandwidth_step(self) -> int:
+        return self.__bandwidth_step

uc_sgsim/sgsim.py

@@ -7,15 +7,15 @@
 import numpy as np
 from uc_sgsim.exception import VariogramDoesNotCompute
 from uc_sgsim.krige import SimpleKrige
-from uc_sgsim.random_field import RandomField
+from uc_sgsim.random_field import SgsimField
 from uc_sgsim.plot.plot import Visualize
 from uc_sgsim.cov_model.base import CovModel
 from uc_sgsim.utils import CovModelStructure, SgsimStructure
 
 BASE_DIR = Path(__file__).resolve().parent
 
 
-class UCSgsim(RandomField):
+class UCSgsim(SgsimField):
     def __init__(
         self,
         x: int,