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add odeint function
This commit is contained in:
wyq
parent
7423d8dfb9
commit
7fac130689
7
.idea/inspectionProfiles/Project_Default.xml
generated
7
.idea/inspectionProfiles/Project_Default.xml
generated
@ -336,6 +336,13 @@
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</option>
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</inspection_tool>
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<inspection_tool class="PyInterpreterInspection" enabled="false" level="WARNING" enabled_by_default="false" />
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<inspection_tool class="PyPep8NamingInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
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<option name="ignoredErrors">
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<list>
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<option value="N802" />
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</list>
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</option>
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</inspection_tool>
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<inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
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<option name="ignoredIdentifiers">
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<list>
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@ -1239,8 +1239,6 @@ public class GLPlot extends Plot {
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this.updateMatrix(gl);
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//gl.glColor3f(0.0f, 0.0f, 0.0f);
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//Draw base
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if (this.drawBase) {
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this.drawBase(gl);
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@ -67,7 +67,7 @@ import java.util.zip.ZipInputStream;
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public static String getVersion(){
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String version = GlobalUtil.class.getPackage().getImplementationVersion();
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if (version == null || version.equals("")) {
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version = "3.5.4";
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version = "3.5.5";
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}
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return version;
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}
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@ -1,30 +1,34 @@
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<MeteoInfo File="milconfig.xml" Type="configurefile">
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<Path OpenPath="D:\Working\MIScript\Jython\mis\plot_types\wind">
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\test"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\io"/>
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<Path OpenPath="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\bar">
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\io\radar"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\scatter"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\quiver"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\common_math"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\surf"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\3d_earth"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\common_math\interpolate"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\isosurface"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\particles"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\wind"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\3d_earth"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\contour"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\common_math"/>
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<RecentFolder Folder="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\bar"/>
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</Path>
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<File>
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<OpenedFiles>
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<OpenedFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\surf\surf_pumpkin_1.py"/>
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<OpenedFile File="D:\Working\MIScript\Jython\mis\common_math\interpolate\nearest_2d_radius.py"/>
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<OpenedFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\3d_earth\scatter_sphere.py"/>
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<OpenedFile File="D:\Working\MIScript\Jython\mis\common_math\integrate\odeint_1.py"/>
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<OpenedFile File="D:\Working\MIScript\Jython\mis\common_math\integrate\odeint_lorenz.py"/>
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</OpenedFiles>
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<RecentFiles>
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<RecentFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\jogl\surf\surf_pumpkin_1.py"/>
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<RecentFile File="D:\Working\MIScript\Jython\mis\common_math\interpolate\nearest_2d_radius.py"/>
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<RecentFile File="D:\Working\MIScript\Jython\mis\plot_types\3d\3d_earth\scatter_sphere.py"/>
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<RecentFile File="D:\Working\MIScript\Jython\mis\common_math\integrate\odeint_1.py"/>
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<RecentFile File="D:\Working\MIScript\Jython\mis\common_math\integrate\odeint_lorenz.py"/>
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</RecentFiles>
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</File>
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<Font>
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@ -32,5 +36,5 @@
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</Font>
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<LookFeel DockWindowDecorated="true" LafDecorated="true" Name="FlatDarkLaf"/>
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<Figure DoubleBuffering="true"/>
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<Startup MainFormLocation="-7,-7" MainFormSize="1293,685"/>
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<Startup MainFormLocation="-7,0" MainFormSize="1367,792"/>
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</MeteoInfo>
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Binary file not shown.
@ -12,11 +12,12 @@ from .basic import coriolis_parameter
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from .. import constants
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__all__ = [
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'cdiff','divergence','vorticity','advection','absolute_vorticity','potential_vorticity_barotropic',
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'ageostrophic_wind','frontogenesis','geostrophic_wind','montgomery_streamfunction',
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'potential_vorticity_baroclinic','shearing_deformation','storm_relative_helicity',
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'stretching_deformation','total_deformation','inertial_advective_wind','q_vector'
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]
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'cdiff', 'divergence', 'vorticity', 'advection', 'absolute_vorticity', 'potential_vorticity_barotropic',
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'ageostrophic_wind', 'frontogenesis', 'geostrophic_wind', 'montgomery_streamfunction',
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'potential_vorticity_baroclinic', 'shearing_deformation', 'storm_relative_helicity',
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'stretching_deformation', 'total_deformation', 'inertial_advective_wind', 'q_vector'
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]
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def cdiff(a, dimidx):
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"""
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@ -33,6 +34,7 @@ def cdiff(a, dimidx):
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else:
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return NDArray(r)
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def vorticity(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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r"""Calculate the vertical vorticity of the horizontal wind.
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@ -106,6 +108,7 @@ def vorticity(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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else:
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return r
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def vorticity_bak(u, v, x=None, y=None):
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"""
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Calculates the vertical component of the curl (ie, vorticity). The data should be lon/lat projection.
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@ -141,6 +144,7 @@ def vorticity_bak(u, v, x=None, y=None):
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else:
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return NDArray(r)
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def divergence(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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r"""Calculate the horizontal divergence of the horizontal wind.
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@ -251,6 +255,7 @@ def divergence_bak(u, v, x=None, y=None):
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else:
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return NDArray(r)
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def shearing_deformation(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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r"""Calculate the shearing deformation of the horizontal wind.
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@ -288,6 +293,7 @@ def shearing_deformation(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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dvdx = first_derivative(v, delta=dx, axis=x_dim)
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return dvdx + dudy
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def stretching_deformation(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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r"""Calculate the stretching deformation of the horizontal wind.
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@ -325,6 +331,7 @@ def stretching_deformation(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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dvdy = first_derivative(v, delta=dy, axis=y_dim)
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return dudx - dvdy
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def total_deformation(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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r"""Calculate the total deformation of the horizontal wind.
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@ -365,10 +372,11 @@ def total_deformation(u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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"""
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dudy, dudx = gradient(u, deltas=(dy, dx), axes=(y_dim, x_dim))
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dvdy, dvdx = gradient(v, deltas=(dy, dx), axes=(y_dim, x_dim))
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return np.sqrt((dvdx + dudy)**2 + (dudx - dvdy)**2)
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return np.sqrt((dvdx + dudy) ** 2 + (dudx - dvdy) ** 2)
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def advection(scalar, u=None, v=None, w=None, dx=None, dy=None, dz=None, x_dim=-1,
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y_dim=-2, vertical_dim=-3):
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y_dim=-2, vertical_dim=-3):
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r"""
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Calculate the advection of a scalar field by the wind.
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@ -416,6 +424,7 @@ def advection(scalar, u=None, v=None, w=None, dx=None, dy=None, dz=None, x_dim=-
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if wind is not None
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)
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def frontogenesis(potential_temperature, u, v, dx=None, dy=None, x_dim=-1, y_dim=-2):
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r"""Calculate the 2D kinematic frontogenesis of a temperature field.
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@ -468,7 +477,7 @@ def frontogenesis(potential_temperature, u, v, dx=None, dy=None, x_dim=-1, y_dim
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ddx_theta = first_derivative(potential_temperature, delta=dx, axis=x_dim)
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# Compute the magnitude of the potential temperature gradient
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mag_theta = np.sqrt(ddx_theta**2 + ddy_theta**2)
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mag_theta = np.sqrt(ddx_theta ** 2 + ddy_theta ** 2)
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# Get the shearing, stretching, and total deformation of the wind field
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shrd = shearing_deformation(u, v, dx, dy, x_dim=x_dim, y_dim=y_dim)
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@ -484,6 +493,7 @@ def frontogenesis(potential_temperature, u, v, dx=None, dy=None, x_dim=-1, y_dim
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return 0.5 * mag_theta * (tdef * np.cos(2 * beta) - div)
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def geostrophic_wind(height, dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2):
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r"""Calculate the geostrophic wind given from the height or geopotential.
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@ -525,6 +535,7 @@ def geostrophic_wind(height, dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2
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dhdx = first_derivative(height, delta=dx, axis=x_dim)
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return -norm_factor * dhdy, norm_factor * dhdx
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def ageostrophic_wind(height, u, v, dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2):
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r"""Calculate the ageostrophic wind given from the height or geopotential.
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@ -571,6 +582,7 @@ def ageostrophic_wind(height, u, v, dx=None, dy=None, latitude=None, x_dim=-1, y
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)
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return u - u_geostrophic, v - v_geostrophic
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def montgomery_streamfunction(height, temperature):
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r"""Compute the Montgomery Streamfunction on isentropic surfaces.
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@ -608,6 +620,7 @@ def montgomery_streamfunction(height, temperature):
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from . import dry_static_energy
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return dry_static_energy(height, temperature)
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def storm_relative_helicity(height, u, v, depth, bottom=None, storm_u=None, storm_v=None):
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r"""Calculate storm relative helicity.
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@ -671,6 +684,7 @@ def storm_relative_helicity(height, u, v, depth, bottom=None, storm_u=None, stor
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return positive_srh, negative_srh, positive_srh + negative_srh
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def absolute_vorticity(u, v, dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2):
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"""Calculate the absolute vorticity of the horizontal wind.
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@ -708,8 +722,9 @@ def absolute_vorticity(u, v, dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2
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relative_vorticity = vorticity(u, v, dx=dx, dy=dy, x_dim=x_dim, y_dim=y_dim)
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return relative_vorticity + f
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def potential_vorticity_baroclinic(potential_temperature, pressure, u, v,
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dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2, vertical_dim=-3):
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dx=None, dy=None, latitude=None, x_dim=-1, y_dim=-2, vertical_dim=-3):
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r"""Calculate the baroclinic potential vorticity.
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.. math:: PV = -g \left(\frac{\partial u}{\partial p}\frac{\partial \theta}{\partial y}
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@ -795,8 +810,9 @@ def potential_vorticity_baroclinic(potential_temperature, pressure, u, v,
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return -constants.g * (dudp * dthetady - dvdp * dthetadx
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+ avor * dthetadp)
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def potential_vorticity_barotropic(height, u, v, dx=None, dy=None, latitude=None,
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x_dim=-1, y_dim=-2):
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x_dim=-1, y_dim=-2):
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r"""Calculate the barotropic (Rossby) potential vorticity.
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.. math:: PV = \frac{f + \zeta}{H}
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@ -837,8 +853,9 @@ def potential_vorticity_barotropic(height, u, v, dx=None, dy=None, latitude=None
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avor = absolute_vorticity(u, v, dx, dy, latitude, x_dim=x_dim, y_dim=y_dim)
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return avor / height
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def inertial_advective_wind(u, v, u_geostrophic, v_geostrophic, dx=None, dy=None,
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latitude=None, x_dim=-1, y_dim=-2):
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latitude=None, x_dim=-1, y_dim=-2):
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r"""Calculate the inertial advective wind.
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.. math:: \frac{\hat k}{f} \times (\vec V \cdot \nabla)\hat V_g
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@ -906,8 +923,9 @@ def inertial_advective_wind(u, v, u_geostrophic, v_geostrophic, dx=None, dy=None
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return u_component, v_component
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def q_vector(u, v, temperature, pressure, dx=None, dy=None,
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static_stability=1, x_dim=-1, y_dim=-2):
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static_stability=1, x_dim=-1, y_dim=-2):
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r"""Calculate Q-vector at a given pressure level using the u, v winds and temperature.
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.. math:: \vec{Q} = (Q_1, Q_2)
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@ -969,4 +987,4 @@ def q_vector(u, v, temperature, pressure, dx=None, dy=None,
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q1 = -mpconsts.Rd / (pressure * static_stability) * (dudx * dtempdx + dvdx * dtempdy)
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q2 = -mpconsts.Rd / (pressure * static_stability) * (dudy * dtempdx + dvdy * dtempdy)
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return q1.to_base_units(), q2.to_base_units()
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return q1.to_base_units(), q2.to_base_units()
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@ -9,8 +9,9 @@ from mipylib.geolib import Geod
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from ..interpolate import interpolate_1d
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from ..cbook import broadcast_indices
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__all__ = ['resample_nn_1d','nearest_intersection_idx','first_derivative','gradient',
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'lat_lon_grid_deltas','get_layer_heights', 'find_bounding_indices']
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__all__ = ['resample_nn_1d', 'nearest_intersection_idx', 'first_derivative', 'gradient',
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'lat_lon_grid_deltas', 'get_layer_heights', 'find_bounding_indices']
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def resample_nn_1d(a, centers):
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"""Return one-dimensional nearest-neighbor indexes based on user-specified centers.
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@ -33,6 +34,7 @@ def resample_nn_1d(a, centers):
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ix.append(index)
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return ix
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def nearest_intersection_idx(a, b):
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"""Determine the index of the point just before two lines with common x values.
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Parameters
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@ -55,6 +57,7 @@ def nearest_intersection_idx(a, b):
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return sign_change_idx
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def _remove_nans(*variables):
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"""Remove NaNs from arrays that cause issues with calculations.
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Takes a variable number of arguments and returns masked arrays in the same
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@ -73,6 +76,7 @@ def _remove_nans(*variables):
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ret.append(v[~mask])
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return ret
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def get_layer_heights(height, depth, *args, **kwargs):
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"""Return an atmospheric layer from upper air data with the requested bottom and depth.
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@ -162,6 +166,7 @@ def get_layer_heights(height, depth, *args, **kwargs):
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ret.append(datavar)
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return ret
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def find_bounding_indices(arr, values, axis, from_below=True):
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"""Find the indices surrounding the values within arr along axis.
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@ -242,6 +247,7 @@ def find_bounding_indices(arr, values, axis, from_below=True):
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return above, below, good
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def _greater_or_close(a, value, **kwargs):
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r"""Compare values for greater or close to boolean masks.
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@ -283,13 +289,17 @@ def _less_or_close(a, value, **kwargs):
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"""
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return (a < value) | np.isclose(a, value, **kwargs)
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def make_take(ndims, slice_dim):
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"""Generate a take function to index in a particular dimension."""
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def take(indexer):
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return tuple(indexer if slice_dim % ndims == i else slice(None) # noqa: S001
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for i in range(ndims))
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return take
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def _broadcast_to_axis(arr, axis, ndim):
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"""Handle reshaping coordinate array to have proper dimensionality.
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This puts the values along the specified axis.
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@ -300,6 +310,7 @@ def _broadcast_to_axis(arr, axis, ndim):
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arr = arr.reshape(*new_shape)
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return arr
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def lat_lon_grid_deltas(longitude, latitude, x_dim=-1, y_dim=-2, geod=None):
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r"""
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Calculate the actual delta between grid points that are in latitude/longitude format.
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@ -362,6 +373,7 @@ def lat_lon_grid_deltas(longitude, latitude, x_dim=-1, y_dim=-2, geod=None):
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return dx, dy
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def _process_gradient_args(f, axes, coordinates, deltas):
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"""Handle common processing of arguments for gradient and gradient-like functions."""
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axes_given = axes is not None
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@ -389,6 +401,7 @@ def _process_gradient_args(f, axes, coordinates, deltas):
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raise ValueError('Must specify either "coordinates" or "deltas" for value positions '
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'when "f" is not a DataArray.')
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||||
def _process_deriv_args(f, axis, x, delta):
|
||||
"""Handle common processing of arguments for derivative functions."""
|
||||
n = f.ndim
|
||||
@ -416,6 +429,7 @@ def _process_deriv_args(f, axis, x, delta):
|
||||
|
||||
return n, axis, delta
|
||||
|
||||
|
||||
def first_derivative(f, axis=None, x=None, delta=None):
|
||||
"""Calculate the first derivative of a grid of values.
|
||||
Works for both regularly-spaced data and grids with varying spacing.
|
||||
@ -497,6 +511,7 @@ def first_derivative(f, axis=None, x=None, delta=None):
|
||||
|
||||
return data
|
||||
|
||||
|
||||
def gradient(f, axes=None, coordinates=None, deltas=None):
|
||||
"""Calculate the gradient of a grid of values.
|
||||
Works for both regularly-spaced data, and grids with varying spacing.
|
||||
@ -535,4 +550,4 @@ def gradient(f, axes=None, coordinates=None, deltas=None):
|
||||
"""
|
||||
pos_kwarg, positions, axes = _process_gradient_args(f, axes, coordinates, deltas)
|
||||
return tuple(first_derivative(f, axis=axis, **{pos_kwarg: positions[ind]})
|
||||
for ind, axis in enumerate(axes))
|
||||
for ind, axis in enumerate(axes))
|
||||
|
||||
Binary file not shown.
@ -13,10 +13,11 @@ from . import optimize
|
||||
from . import signal
|
||||
from . import spatial
|
||||
from . import special
|
||||
from . import integrate
|
||||
|
||||
__all__ = ['linalg', 'fitting', 'random', 'ma', 'stats', 'interpolate', 'optimize', 'signal', 'spatial',
|
||||
'special']
|
||||
'special', 'integrate']
|
||||
__all__.extend(['__version__'])
|
||||
__all__.extend(core.__all__)
|
||||
__all__.extend(lib.__all__)
|
||||
__all__.extend(['griddata'])
|
||||
__all__.extend(['griddata'])
|
||||
|
||||
@ -0,0 +1,3 @@
|
||||
from ._ode import *
|
||||
|
||||
__all__ = _ode.__all__
|
||||
52
meteoinfo-lab/pylib/mipylib/numeric/integrate/_ode.py
Normal file
52
meteoinfo-lab/pylib/mipylib/numeric/integrate/_ode.py
Normal file
@ -0,0 +1,52 @@
|
||||
# coding=utf-8
|
||||
|
||||
from org.meteoinfo.math.integrate import ODEEquations, IntegrateUtil
|
||||
from ..core import numeric as np
|
||||
|
||||
__all__ = ['odeint']
|
||||
|
||||
|
||||
class ODE(ODEEquations):
|
||||
|
||||
def __init__(self, f):
|
||||
"""
|
||||
Initialize
|
||||
|
||||
:param f: Jython function
|
||||
"""
|
||||
self.f = f
|
||||
self._args = list(f.__code__.co_varnames)[2:]
|
||||
self._args = tuple(self._args)
|
||||
self.order = len(self._args)
|
||||
|
||||
def doComputeDerivatives(self, y, t):
|
||||
args = tuple(self.getParameters())
|
||||
return self.f(y, t, *args)
|
||||
|
||||
|
||||
def odeint(func, y0, t, args=()):
|
||||
"""
|
||||
Integrate a system of ordinary differential equations.
|
||||
|
||||
:param func: (callable(y, t, …) ) Computes the derivative of y at t.
|
||||
:param y0: (*array*) Initial condition on y (can be a vector).
|
||||
:param t: (*array*) A sequence of time points for which to solve for y. The initial value point should
|
||||
be the first element of this sequence.
|
||||
:param args: (*tuple*) Extra arguments to pass to function.
|
||||
:return: Array containing the value of y for each desired time in t.
|
||||
"""
|
||||
func = ODE(func)
|
||||
if len(args) > 0:
|
||||
func.setParameters(args)
|
||||
|
||||
if isinstance(y0, (tuple, list)):
|
||||
y0 = np.array(y0)
|
||||
ndim = len(y0)
|
||||
func.setDimension(ndim)
|
||||
|
||||
if isinstance(t, (tuple, list)):
|
||||
t = np.array(t)
|
||||
|
||||
r = IntegrateUtil.odeIntegrate(func, y0.asarray(), t.asarray())
|
||||
|
||||
return np.NDArray(r)
|
||||
Binary file not shown.
@ -1,20 +1,18 @@
|
||||
from org.meteoinfo.math.optimize import OptimizeUtil, ParamUnivariateFunction
|
||||
from org.apache.commons.math4.legacy.fitting.leastsquares import LeastSquaresBuilder
|
||||
from org.apache.commons.math4.legacy.fitting.leastsquares import LevenbergMarquardtOptimizer
|
||||
|
||||
import warnings
|
||||
from ..core import numeric as np
|
||||
from ..linalg import cholesky, solve_triangular, svd
|
||||
from ..lib._util import _lazywhere
|
||||
from ..linalg import solve_triangular
|
||||
|
||||
# __all__ = ['fsolve', 'leastsq', 'fixed_point', 'curve_fit']
|
||||
__all__ = ['curve_fit', 'fixed_point']
|
||||
|
||||
#__all__ = ['fsolve', 'leastsq', 'fixed_point', 'curve_fit']
|
||||
__all__ = ['curve_fit','fixed_point']
|
||||
|
||||
def _check_func(checker, argname, thefunc, x0, args, numinputs,
|
||||
output_shape=None):
|
||||
res = np.atleast_1d(thefunc(*((x0[:numinputs],) + args)))
|
||||
if (output_shape is not None) and (np.shape(res) != output_shape):
|
||||
if (output_shape[0] != 1):
|
||||
if output_shape[0] != 1:
|
||||
if len(output_shape) > 1:
|
||||
if output_shape[1] == 1:
|
||||
return shape(res)
|
||||
@ -29,6 +27,7 @@ def _check_func(checker, argname, thefunc, x0, args, numinputs,
|
||||
raise TypeError(msg)
|
||||
return np.shape(res), res.dtype
|
||||
|
||||
|
||||
def _wrap_func(func, xdata, ydata, transform):
|
||||
if transform is None:
|
||||
def func_wrapped(params):
|
||||
@ -49,6 +48,7 @@ def _wrap_func(func, xdata, ydata, transform):
|
||||
return solve_triangular(transform, func(xdata, *params) - ydata, lower=True)
|
||||
return func_wrapped
|
||||
|
||||
|
||||
def _wrap_jac(jac, xdata, transform):
|
||||
if transform is None:
|
||||
def jac_wrapped(params):
|
||||
@ -61,6 +61,7 @@ def _wrap_jac(jac, xdata, transform):
|
||||
return solve_triangular(transform, np.asarray(jac(xdata, *params)), lower=True)
|
||||
return jac_wrapped
|
||||
|
||||
|
||||
def _initialize_feasible(lb, ub):
|
||||
p0 = np.ones_like(lb)
|
||||
lb_finite = np.isfinite(lb)
|
||||
@ -77,6 +78,7 @@ def _initialize_feasible(lb, ub):
|
||||
|
||||
return p0
|
||||
|
||||
|
||||
class UniFunc(ParamUnivariateFunction):
|
||||
def __init__(self, f):
|
||||
"""
|
||||
@ -93,6 +95,7 @@ class UniFunc(ParamUnivariateFunction):
|
||||
args = tuple(self.getParameters())
|
||||
return self.f(x, *args)
|
||||
|
||||
|
||||
def curve_fit(f, xdata, ydata, p0=None, npoint=5, step=0.1):
|
||||
"""
|
||||
Use non-linear least squares to fit a function, f, to data.
|
||||
@ -140,6 +143,7 @@ def curve_fit(f, xdata, ydata, p0=None, npoint=5, step=0.1):
|
||||
|
||||
return r
|
||||
|
||||
|
||||
# def curve_fit(f, xdata, ydata, p0=None, npoint=5, step=0.1):
|
||||
# """
|
||||
# Use non-linear least squares to fit a function, f, to data.
|
||||
@ -202,6 +206,7 @@ def _del2(p0, p1, d):
|
||||
def _relerr(actual, desired):
|
||||
return (actual - desired) / desired
|
||||
|
||||
|
||||
def _fixed_point_helper(func, x0, args, xtol, maxiter, use_accel):
|
||||
p0 = x0
|
||||
for _ in range(maxiter):
|
||||
@ -257,6 +262,6 @@ def fixed_point(func, x0, args=(), xtol=1e-8, maxiter=500, method='del2'):
|
||||
array([ 1.4920333 , 1.37228132])
|
||||
"""
|
||||
use_accel = {'del2': True, 'iteration': False}[method]
|
||||
#x0 = _asarray_validated(x0, as_inexact=True)
|
||||
# x0 = _asarray_validated(x0, as_inexact=True)
|
||||
x0 = np.asarray(x0)
|
||||
return _fixed_point_helper(func, x0, args, xtol, maxiter, use_accel)
|
||||
return _fixed_point_helper(func, x0, args, xtol, maxiter, use_accel)
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -0,0 +1,60 @@
|
||||
package org.meteoinfo.math.integrate;
|
||||
|
||||
import org.apache.commons.math4.legacy.ode.ContinuousOutputModel;
|
||||
import org.apache.commons.math4.legacy.ode.FirstOrderDifferentialEquations;
|
||||
import org.apache.commons.math4.legacy.ode.FirstOrderIntegrator;
|
||||
import org.apache.commons.math4.legacy.ode.nonstiff.DormandPrince853Integrator;
|
||||
import org.apache.commons.math4.legacy.ode.sampling.StepHandler;
|
||||
import org.apache.commons.math4.legacy.ode.sampling.StepInterpolator;
|
||||
import org.meteoinfo.ndarray.Array;
|
||||
import org.meteoinfo.ndarray.DataType;
|
||||
import org.meteoinfo.ndarray.IndexIterator;
|
||||
|
||||
import java.io.*;
|
||||
|
||||
public class IntegrateUtil {
|
||||
|
||||
/**
|
||||
* Integrate a system of ordinary differential equations
|
||||
*
|
||||
* @param equations Computes the derivative of y at t
|
||||
* @param y0 Initial condition on y
|
||||
* @param t A sequence of time points for which to solve for y
|
||||
* @return Array containing the value of y for each desired time in t, with the initial value y0 in the first row.
|
||||
*/
|
||||
public static Array odeIntegrate(FirstOrderDifferentialEquations equations, Array y0, Array t) throws IOException, ClassNotFoundException {
|
||||
y0 = y0.copyIfView();
|
||||
t = t.copyIfView();
|
||||
|
||||
int nt = (int) t.getSize();
|
||||
int ny0 = (int) y0.getSize();
|
||||
FirstOrderIntegrator integrator = new DormandPrince853Integrator(1.0e-8, 100.0, 1.0e-10, 1.0e-10);
|
||||
double[] y0v = (double[]) y0.getStorage();
|
||||
double[] yDot = new double[ny0];
|
||||
|
||||
integrator.addStepHandler(new ContinuousOutputModel());
|
||||
integrator.integrate(equations, t.getDouble(0), y0v, t.getDouble(nt - 1), yDot);
|
||||
|
||||
ByteArrayOutputStream bos = new ByteArrayOutputStream();
|
||||
ObjectOutputStream oos = new ObjectOutputStream(bos);
|
||||
for (StepHandler handler : integrator.getStepHandlers()) {
|
||||
oos.writeObject(handler);
|
||||
}
|
||||
|
||||
ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());
|
||||
ObjectInputStream ois = new ObjectInputStream(bis);
|
||||
ContinuousOutputModel cm = (ContinuousOutputModel) ois.readObject();
|
||||
|
||||
Array r = Array.factory(DataType.DOUBLE, new int[]{nt, ny0});
|
||||
IndexIterator iter = r.getIndexIterator();
|
||||
for (int i = 0; i < nt; i++) {
|
||||
cm.setInterpolatedTime(t.getDouble(i));
|
||||
double[] interpolatedY = cm.getInterpolatedState();
|
||||
for (double v : interpolatedY) {
|
||||
iter.setDoubleNext(v);
|
||||
}
|
||||
}
|
||||
|
||||
return r;
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,54 @@
|
||||
package org.meteoinfo.math.integrate;
|
||||
|
||||
import org.apache.commons.math4.legacy.exception.DimensionMismatchException;
|
||||
import org.apache.commons.math4.legacy.exception.MaxCountExceededException;
|
||||
import org.apache.commons.math4.legacy.ode.FirstOrderDifferentialEquations;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
public class ODEEquations implements FirstOrderDifferentialEquations {
|
||||
|
||||
private List<Double> parameters = new ArrayList<>();
|
||||
private int dimension;
|
||||
|
||||
/**
|
||||
* Get parameters
|
||||
* @return Parameters
|
||||
*/
|
||||
public List<Double> getParameters() {
|
||||
return this.parameters;
|
||||
}
|
||||
|
||||
/**
|
||||
* Set parameters
|
||||
* @param value Parameters
|
||||
*/
|
||||
public void setParameters(List<Double> value) {
|
||||
this.parameters = value;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int getDimension() {
|
||||
return dimension;
|
||||
}
|
||||
|
||||
public void setDimension(int value) {
|
||||
this.dimension = value;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void computeDerivatives(double v, double[] y, double[] yDot) throws MaxCountExceededException, DimensionMismatchException {
|
||||
List<Double> yd = doComputeDerivatives(Arrays.stream(y).boxed().collect(Collectors.toList()), v);
|
||||
int n = yd.size();
|
||||
for (int i = 0; i < n; i++) {
|
||||
yDot[i] = yd.get(i);
|
||||
}
|
||||
}
|
||||
|
||||
public List<Double> doComputeDerivatives(List<Double> y, double t) {
|
||||
return Arrays.asList(0.);
|
||||
}
|
||||
}
|
||||
Loading…
x
Reference in New Issue
Block a user