Source code for instaseis.database_interfaces.reciprocal_merged_instaseis_db

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Python library to extract seismograms from a set of wavefields generated by
AxiSEM.

:copyright:
    Martin van Driel (Martin@vanDriel.de), 2014
    Lion Krischer (krischer@geophysik.uni-muenchen.de), 2014
:license:
    GNU Lesser General Public License, Version 3 [non-commercial/academic use]
    (http://www.gnu.org/copyleft/lgpl.html)
"""
from __future__ import (absolute_import, division, print_function,
                        unicode_literals)

import collections
import numpy as np

from .base_netcdf_instaseis_db import BaseNetCDFInstaseisDB
from . import mesh
from .. import rotations, sem_derivatives, spectral_basis
from ..source import Source, ForceSource


[docs]class ReciprocalMergedInstaseisDB(BaseNetCDFInstaseisDB): """ Reciprocal Merged Instaseis Database. """ def __init__(self, db_path, netcdf_file, buffer_size_in_mb=100, read_on_demand=False, *args, **kwargs): """ :param db_path: Path to the Instaseis Database. :type db_path: str :param netcdf_file: The path to the actual netcdf4 file. :type netcdf_file: str :param buffer_size_in_mb: Strain and displacement are buffered to avoid repeated disc access. Depending on the type of database and the number of components of the database, the total buffer memory can be up to four times this number. The optimal value is highly application and system dependent. :type buffer_size_in_mb: int, optional :param read_on_demand: Read several global fields on demand (faster initialization) or on initialization (slower initialization, faster in individual seismogram extraction, useful e.g. for finite sources, default). :type read_on_demand: bool, optional """ BaseNetCDFInstaseisDB.__init__( self, db_path=db_path, buffer_size_in_mb=buffer_size_in_mb, read_on_demand=read_on_demand, *args, **kwargs) self._parse_mesh(netcdf_file) def _parse_mesh(self, filename): MeshCollection_merged = collections.namedtuple( "MeshCollection_merged", ["merged"]) self.meshes = MeshCollection_merged(mesh.Mesh( filename, full_parse=True, strain_buffer_size_in_mb=self.buffer_size_in_mb, displ_buffer_size_in_mb=self.buffer_size_in_mb, read_on_demand=self.read_on_demand)) self.parsed_mesh = self.meshes.merged self._is_reciprocal = True def _get_data(self, source, receiver, components, coordinates, element_info): ei = element_info # Collect data arrays and mu in a dictionary. data = {} mesh = self.parsed_mesh.f["Mesh"] # Get mu. if not self.read_on_demand: mesh_mu = self.parsed_mesh.mesh_mu else: mesh_mu = mesh["mesh_mu"] if self.info.dump_type == "displ_only": npol = self.info.spatial_order mu = mesh_mu[ei.gll_point_ids[npol // 2, npol // 2]] else: # pragma: no cover # Merged databases currently not implemented for # non-displacement databases. raise NotImplementedError # XXX: Is this correct? mu = mesh_mu[ei.id_elem] data["mu"] = mu fac_1_map = {"N": np.cos, "E": np.sin} fac_2_map = {"N": lambda x: - np.sin(x), "E": np.cos} if isinstance(source, Source): if self.info.dump_type == 'displ_only': if ei.axis: G = self.parsed_mesh.G2 GT = self.parsed_mesh.G1T else: G = self.parsed_mesh.G2 GT = self.parsed_mesh.G2T if self.info.dump_type == 'displ_only': strain_x, strain_z = self._get_strain_interp( ei.id_elem, ei.gll_point_ids, G, GT, ei.col_points_xi, ei.col_points_eta, ei.corner_points, ei.eltype, ei.axis, ei.xi, ei.eta) elif (self.info.dump_type == 'fullfields' or self.info.dump_type == 'strain_only'): # pragma: no cover # Merged databases currently not implemented for # non-displacement databases. raise NotImplementedError mij = rotations \ .rotate_symm_tensor_voigt_xyz_src_to_xyz_earth( source.tensor_voigt, np.deg2rad(source.longitude), np.deg2rad(source.colatitude)) mij = rotations \ .rotate_symm_tensor_voigt_xyz_earth_to_xyz_src( mij, np.deg2rad(receiver.longitude), np.deg2rad(receiver.colatitude)) mij = rotations.rotate_symm_tensor_voigt_xyz_to_src( mij, coordinates.phi) mij /= self.parsed_mesh.amplitude if "Z" in components: final = np.zeros(strain_z.shape[0], dtype="float64") for i in range(3): final += mij[i] * strain_z[:, i] final += 2.0 * mij[4] * strain_z[:, 4] data["Z"] = final if "R" in components: final = np.zeros(strain_x.shape[0], dtype="float64") final -= strain_x[:, 0] * mij[0] * 1.0 final -= strain_x[:, 1] * mij[1] * 1.0 final -= strain_x[:, 2] * mij[2] * 1.0 final -= strain_x[:, 4] * mij[4] * 2.0 data["R"] = final if "T" in components: final = np.zeros(strain_x.shape[0], dtype="float64") final += strain_x[:, 3] * mij[3] * 2.0 final += strain_x[:, 5] * mij[5] * 2.0 data["T"] = final for comp in ["E", "N"]: if comp not in components: continue fac_1 = fac_1_map[comp](coordinates.phi) fac_2 = fac_2_map[comp](coordinates.phi) final = np.zeros(strain_x.shape[0], dtype="float64") final += strain_x[:, 0] * mij[0] * 1.0 * fac_1 final += strain_x[:, 1] * mij[1] * 1.0 * fac_1 final += strain_x[:, 2] * mij[2] * 1.0 * fac_1 final += strain_x[:, 3] * mij[3] * 2.0 * fac_2 final += strain_x[:, 4] * mij[4] * 2.0 * fac_1 final += strain_x[:, 5] * mij[5] * 2.0 * fac_2 if comp == "N": final *= -1.0 data[comp] = final elif isinstance(source, ForceSource): if self.info.dump_type != 'displ_only': # pragma: no cover # Merged databases currently not implemented for # non-displacement databases. raise NotImplementedError raise ValueError("Force sources only in displ_only mode") displ_x, displ_z = self._get_displacement( ei.id_elem, ei.gll_point_ids, ei.col_points_xi, ei.col_points_eta, ei.xi, ei.eta) force = rotations.rotate_vector_xyz_src_to_xyz_earth( source.force_tpr, np.deg2rad(source.longitude), np.deg2rad(source.colatitude)) force = rotations.rotate_vector_xyz_earth_to_xyz_src( force, np.deg2rad(receiver.longitude), np.deg2rad(receiver.colatitude)) force = rotations.rotate_vector_xyz_to_src( force, coordinates.phi) force /= self.parsed_mesh.amplitude if "Z" in components: final = np.zeros(displ_z.shape[0], dtype="float64") final += displ_z[:, 0] * force[0] final += displ_z[:, 2] * force[2] data["Z"] = final if "R" in components: final = np.zeros(displ_x.shape[0], dtype="float64") final += displ_x[:, 0] * force[0] final += displ_x[:, 2] * force[2] data["R"] = final if "T" in components: final = np.zeros(displ_x.shape[0], dtype="float64") final += displ_x[:, 1] * force[1] data["T"] = final for comp in ["E", "N"]: if comp not in components: continue fac_1 = fac_1_map[comp](coordinates.phi) fac_2 = fac_2_map[comp](coordinates.phi) final = np.zeros(displ_x.shape[0], dtype="float64") final += displ_x[:, 0] * force[0] * fac_1 final += displ_x[:, 1] * force[1] * fac_2 final += displ_x[:, 2] * force[2] * fac_1 if comp == "N": final *= -1.0 data[comp] = final else: raise NotImplementedError return data def _get_and_reorder_utemp(self, id_elem): # We can now read it in a single go! utemp = self.meshes.merged.f["MergedSnapshots"][id_elem] # utemp is currently (nvars, jpol, ipol, npts) # 1. Roll to (npts, nvar, jpol, ipol) utemp = np.rollaxis(utemp, 3, 0) # 2. Roll to (npts, jpol, nvar, ipol) utemp = np.rollaxis(utemp, 2, 1) # 3. Roll to (npts, jpol, ipol, nvar) utemp = np.rollaxis(utemp, 3, 2) return utemp def _get_strain_interp(self, id_elem, gll_point_ids, G, GT, col_points_xi, col_points_eta, corner_points, eltype, axis, xi, eta): mesh = self.meshes.merged if id_elem not in mesh.strain_buffer: utemp = self._get_and_reorder_utemp(id_elem) strain_fct_map = { "monopole": sem_derivatives.strain_monopole_td, "dipole": sem_derivatives.strain_dipole_td, "quadpole": sem_derivatives.strain_quadpole_td} # We want the cache to work - thus we always have to # calculate both! Also I/O is the slow part here. # Horizontal component is available if we have 3 or 5 components. if utemp.shape[-1] >= 3: utemp_x = utemp[:, :, :, :3] utemp_x = np.require(utemp_x, requirements=["F"], dtype=np.float64) strain_x = strain_fct_map["dipole"]( utemp_x, G, GT, col_points_xi, col_points_eta, mesh.npol, mesh.ndumps, corner_points, eltype, axis) else: strain_x = None # Vertical component is available if we have 2 or 5 components. if utemp.shape[-1] in (2, 5): # Vertical expects disp_s at index 0 and disp_z at index 2. # Expand if only vertical. _s = list(utemp.shape) if _s[-1] == 2: _s[-1] = 3 utemp_new = np.zeros(_s, dtype=utemp.dtype) utemp_new[:, :, :, 0] = utemp[:, :, :, 0] utemp_new[:, :, :, 2] = utemp[:, :, :, 1] utemp_z = utemp_new # Reform all others. else: utemp_z = utemp[:, :, :, -3:] utemp_z[:, :, :, 0] = utemp_z[:, :, :, 1] utemp_z[:, :, :, 1][:] = 0 utemp_z = np.require(utemp_z, requirements=["F"], dtype=np.float64) strain_z = strain_fct_map["monopole"]( utemp_z, G, GT, col_points_xi, col_points_eta, mesh.npol, mesh.ndumps, corner_points, eltype, axis) else: strain_z = None mesh.strain_buffer.add(id_elem, (strain_x, strain_z)) else: strain_x, strain_z = mesh.strain_buffer.get(id_elem) all_strains = {} for name, strain in (("strain_x", strain_x), ("strain_z", strain_z)): if strain is None: all_strains[name] = None continue final_strain = np.empty((strain.shape[0], 6), order="F") for i in range(6): final_strain[:, i] = spectral_basis.lagrange_interpol_2D_td( col_points_xi, col_points_eta, strain[:, :, :, i], xi, eta) if not name == "strain_z": final_strain[:, 3] *= -1.0 final_strain[:, 5] *= -1.0 all_strains[name] = final_strain return all_strains["strain_x"], all_strains["strain_z"] def _get_displacement(self, id_elem, gll_point_ids, col_points_xi, col_points_eta, xi, eta): mesh = self.meshes.merged if id_elem not in mesh.displ_buffer: utemp = self._get_and_reorder_utemp(id_elem) mesh.displ_buffer.add(id_elem, utemp) else: utemp = mesh.displ_buffer.get(id_elem) final_displacement_x = np.empty((utemp.shape[0], 3), order="F") utemp_x = utemp[:, :, :, :3] utemp_x = np.require(utemp_x, requirements=["F"], dtype=np.float64) for i in range(3): final_displacement_x[:, i] = \ spectral_basis.lagrange_interpol_2D_td( col_points_xi, col_points_eta, utemp_x[:, :, :, i], xi, eta) utemp_z = utemp[:, :, :, -3:] utemp_z[:, :, :, 0] = utemp_z[:, :, :, 1] utemp_z[:, :, :, 1][:] = 0 utemp_z = np.require(utemp_z, requirements=["F"], dtype=np.float64) final_displacement_z = np.empty((utemp.shape[0], 3), order="F") for i in range(3): final_displacement_z[:, i] = \ spectral_basis.lagrange_interpol_2D_td( col_points_xi, col_points_eta, utemp_z[:, :, :, i], xi, eta) return final_displacement_x, final_displacement_z