gprMax/gprMax/geometry_outputs.py

# Copyright (C) 2015-2017: The University of Edinburgh
#                 Authors: Craig Warren and Antonis Giannopoulos
#
# This file is part of gprMax.
#
# gprMax is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# gprMax is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with gprMax.  If not, see <http://www.gnu.org/licenses/>.

import os
import sys

import h5py
import numpy as np
from struct import pack

from gprMax._version import __version__
from gprMax.utilities import round_value


class GeometryView(object):
    """Views of the geometry of the model."""

    if sys.byteorder == 'little':
        byteorder = 'LittleEndian'
    else:
        byteorder = 'BigEndian'

    def __init__(self, xs=None, ys=None, zs=None, xf=None, yf=None, zf=None, dx=None, dy=None, dz=None, filename=None, fileext=None):
        """
        Args:
            xs, xf, ys, yf, zs, zf (int): Extent of the volume in cells.
            dx, dy, dz (int): Spatial discretisation in cells.
            filename (str): Filename to save to.
            fileext (str): File extension of VTK file - either '.vti' for a per cell geometry view, or '.vtp' for a per cell edge geometry view.
        """

        self.xs = xs
        self.ys = ys
        self.zs = zs
        self.xf = xf
        self.yf = yf
        self.zf = zf
        self.nx = self.xf - self.xs
        self.ny = self.yf - self.ys
        self.nz = self.zf - self.zs
        self.dx = dx
        self.dy = dy
        self.dz = dz
        self.basefilename = filename
        self.fileext = fileext

        if self.fileext == '.vti':
            # Calculate number of cells according to requested sampling for geometry view
            self.vtk_xscells = round_value(self.xs / self.dx)
            self.vtk_xfcells = round_value(self.xf / self.dx)
            self.vtk_yscells = round_value(self.ys / self.dy)
            self.vtk_yfcells = round_value(self.yf / self.dy)
            self.vtk_zscells = round_value(self.zs / self.dz)
            self.vtk_zfcells = round_value(self.zf / self.dz)
            self.vtk_nxcells = self.vtk_xfcells - self.vtk_xscells
            self.vtk_nycells = self.vtk_yfcells - self.vtk_yscells
            self.vtk_nzcells = self.vtk_zfcells - self.vtk_zscells
            self.datawritesize = int(np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells) + 2 * (int(np.dtype(np.int8).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells))

        elif self.fileext == '.vtp':
            self.vtk_numpoints = (self.nx + 1) * (self.ny + 1) * (self.nz + 1)
            self.vtk_numpoint_components = 3
            self.vtk_numlines = 2 * self.nx * self.ny + 2 * self.ny * self.nz + 2 * self.nx * self.nz + 3 * self.nx * self.ny * self.nz + self.nx + self.ny + self.nz
            self.vtk_numline_components = 2
            self.vtk_connectivity_offset = round_value((self.vtk_numpoints * self.vtk_numpoint_components * np.dtype(np.float32).itemsize) + np.dtype(np.uint32).itemsize)
            self.vtk_offsets_offset = round_value(self.vtk_connectivity_offset + (self.vtk_numlines * self.vtk_numline_components * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
            self.vtk_materials_offset = round_value(self.vtk_offsets_offset + (self.vtk_numlines * np.dtype(np.uint32).itemsize) + np.dtype(np.uint32).itemsize)
            self.datawritesize = np.dtype(np.float32).itemsize * self.vtk_numpoints * self.vtk_numpoint_components + np.dtype(np.uint32).itemsize * self.vtk_numlines * self.vtk_numline_components + np.dtype(np.uint32).itemsize * self.vtk_numlines + np.dtype(np.uint32).itemsize * self.vtk_numlines

    def set_filename(self, modelrun, numbermodelruns, G):
        """Construct filename from user-supplied name and model run number.

        Args:
            modelrun (int): Current model run number.
            numbermodelruns (int): Total number of model runs.
            G (class): Grid class instance - holds essential parameters describing the model.
        """

        if numbermodelruns == 1:
            self.filename = os.path.abspath(os.path.join(G.inputdirectory, self.basefilename))
        else:
            self.filename = os.path.abspath(os.path.join(G.inputdirectory, self.basefilename + str(modelrun)))
        self.filename += self.fileext

    def write_vtk(self, modelrun, numbermodelruns, G, pbar):
        """Writes the geometry information to a VTK file. Either ImageData (.vti) for a per-cell geometry view, or PolygonalData (.vtp) for a per-cell-edge geometry view.

            N.B. No Python 3 support for VTK at time of writing (03/2015)

        Args:
            modelrun (int): Current model run number.
            numbermodelruns (int): Total number of model runs.
            G (class): Grid class instance - holds essential parameters describing the model.
            pbar (class): Progress bar class instance.
        """

        if self.fileext == '.vti':
            # Create arrays and add numeric IDs for PML, sources and receivers (0 is not set, 1 is PML, srcs and rxs numbered thereafter)
            self.srcs_pml = np.zeros((G.nx + 1, G.ny + 1, G.nz + 1), dtype=np.int8)
            self.rxs = np.zeros((G.nx + 1, G.ny + 1, G.nz + 1), dtype=np.int8)
            for pml in G.pmls:
                self.srcs_pml[pml.xs:pml.xf, pml.ys:pml.yf, pml.zs:pml.zf] = 1
            for index, src in enumerate(G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
                self.srcs_pml[src.xcoord, src.ycoord, src.zcoord] = index + 2
            for index, rx in enumerate(G.rxs):
                self.rxs[rx.xcoord, rx.ycoord, rx.zcoord] = index + 1

            vtk_srcs_pml_offset = round_value((np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells) + np.dtype(np.uint32).itemsize)
            vtk_rxs_offset = round_value((np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells) + np.dtype(np.uint32).itemsize + (np.dtype(np.int8).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells) + np.dtype(np.uint32).itemsize)

            with open(self.filename, 'wb') as f:
                f.write('<?xml version="1.0"?>\n'.encode('utf-8'))
                f.write('<VTKFile type="ImageData" version="1.0" byte_order="{}">\n'.format(GeometryView.byteorder).encode('utf-8'))
                f.write('<ImageData WholeExtent="{} {} {} {} {} {}" Origin="0 0 0" Spacing="{:.3} {:.3} {:.3}">\n'.format(self.vtk_xscells, self.vtk_xfcells, self.vtk_yscells, self.vtk_yfcells, self.vtk_zscells, self.vtk_zfcells, self.dx * G.dx, self.dy * G.dy, self.dz * G.dz).encode('utf-8'))
                f.write('<Piece Extent="{} {} {} {} {} {}">\n'.format(self.vtk_xscells, self.vtk_xfcells, self.vtk_yscells, self.vtk_yfcells, self.vtk_zscells, self.vtk_zfcells).encode('utf-8'))
                f.write('<CellData Scalars="Material">\n'.encode('utf-8'))
                f.write('<DataArray type="UInt32" Name="Material" format="appended" offset="0" />\n'.encode('utf-8'))
                f.write('<DataArray type="Int8" Name="Sources_PML" format="appended" offset="{}" />\n'.format(vtk_srcs_pml_offset).encode('utf-8'))
                f.write('<DataArray type="Int8" Name="Receivers" format="appended" offset="{}" />\n'.format(vtk_rxs_offset).encode('utf-8'))
                f.write('</CellData>\n'.encode('utf-8'))
                f.write('</Piece>\n</ImageData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))

                # Write material IDs
                datasize = int(np.dtype(np.uint32).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
                # Write number of bytes of appended data as UInt32
                f.write(pack('I', datasize))
                for k in range(self.zs, self.zf, self.dz):
                    for j in range(self.ys, self.yf, self.dy):
                        for i in range(self.xs, self.xf, self.dx):
                            pbar.update(n=4)
                            f.write(pack('I', G.solid[i, j, k]))

                # Write source/PML IDs
                datasize = int(np.dtype(np.int8).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
                f.write(pack('I', datasize))
                for k in range(self.zs, self.zf, self.dz):
                    for j in range(self.ys, self.yf, self.dy):
                        for i in range(self.xs, self.xf, self.dx):
                            pbar.update()
                            f.write(pack('b', self.srcs_pml[i, j, k]))

                # Write receiver IDs
                datasize = int(np.dtype(np.int8).itemsize * self.vtk_nxcells * self.vtk_nycells * self.vtk_nzcells)
                f.write(pack('I', datasize))
                for k in range(self.zs, self.zf, self.dz):
                    for j in range(self.ys, self.yf, self.dy):
                        for i in range(self.xs, self.xf, self.dx):
                            pbar.update()
                            f.write(pack('b', self.rxs[i, j, k]))

                f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))

                self.write_gprmax_info(f, G)

        elif self.fileext == '.vtp':
            with open(self.filename, 'wb') as f:
                f.write('<?xml version="1.0"?>\n'.encode('utf-8'))
                f.write('<VTKFile type="PolyData" version="1.0" byte_order="{}">\n'.format(GeometryView.byteorder).encode('utf-8'))
                f.write('<PolyData>\n<Piece NumberOfPoints="{}" NumberOfVerts="0" NumberOfLines="{}" NumberOfStrips="0" NumberOfPolys="0">\n'.format(self.vtk_numpoints, self.vtk_numlines).encode('utf-8'))

                f.write('<Points>\n<DataArray type="Float32" NumberOfComponents="3" format="appended" offset="0" />\n</Points>\n'.encode('utf-8'))
                f.write('<Lines>\n<DataArray type="UInt32" Name="connectivity" format="appended" offset="{}" />\n'.format(self.vtk_connectivity_offset).encode('utf-8'))
                f.write('<DataArray type="UInt32" Name="offsets" format="appended" offset="{}" />\n</Lines>\n'.format(self.vtk_offsets_offset).encode('utf-8'))

                f.write('<CellData Scalars="Material">\n'.encode('utf-8'))
                f.write('<DataArray type="UInt32" Name="Material" format="appended" offset="{}" />\n'.format(self.vtk_materials_offset).encode('utf-8'))
                f.write('</CellData>\n'.encode('utf-8'))

                f.write('</Piece>\n</PolyData>\n<AppendedData encoding="raw">\n_'.encode('utf-8'))

                # Write points
                datasize = np.dtype(np.float32).itemsize * self.vtk_numpoints * self.vtk_numpoint_components
                f.write(pack('I', datasize))
                for i in range(self.xs, self.xf + 1):
                    for j in range(self.ys, self.yf + 1):
                        for k in range(self.zs, self.zf + 1):
                            pbar.update(n=12)
                            f.write(pack('fff', i * G.dx, j * G.dy, k * G.dz))

                # Write cell type (line) connectivity for x components
                datasize = np.dtype(np.uint32).itemsize * self.vtk_numlines * self.vtk_numline_components
                f.write(pack('I', datasize))
                vtk_x2 = (self.ny + 1) * (self.nz + 1)
                for vtk_x1 in range(self.nx * (self.ny + 1) * (self.nz + 1)):
                    pbar.update(n=8)
                    f.write(pack('II', vtk_x1, vtk_x2))
                    # print('x {} {}'.format(vtk_x1, vtk_x2))
                    vtk_x2 += 1

                # Write cell type (line) connectivity for y components
                vtk_ycnt1 = 1
                vtk_ycnt2 = 0
                for vtk_y1 in range((self.nx + 1) * (self.ny + 1) * (self.nz + 1)):
                    if vtk_y1 >= (vtk_ycnt1 * (self.ny + 1) * (self.nz + 1)) - (self.nz + 1) and vtk_y1 < vtk_ycnt1 * (self.ny + 1) * (self.nz + 1):
                        vtk_ycnt2 += 1
                    else:
                        vtk_y2 = vtk_y1 + self.nz + 1
                        pbar.update(n=8)
                        f.write(pack('II', vtk_y1, vtk_y2))
                        # print('y {} {}'.format(vtk_y1, vtk_y2))
                    if vtk_ycnt2 == self.nz + 1:
                        vtk_ycnt1 += 1
                        vtk_ycnt2 = 0

                # Write cell type (line) connectivity for z components
                vtk_zcnt = self.nz
                for vtk_z1 in range((self.nx + 1) * (self.ny + 1) * self.nz + (self.nx + 1) * (self.ny + 1)):
                    if vtk_z1 != vtk_zcnt:
                        vtk_z2 = vtk_z1 + 1
                        pbar.update(n=8)
                        f.write(pack('II', vtk_z1, vtk_z2))
                        # print('z {} {}'.format(vtk_z1, vtk_z2))
                    else:
                        vtk_zcnt += self.nz + 1

                # Write cell type (line) offsets
                vtk_cell_pts = 2
                datasize = np.dtype(np.uint32).itemsize * self.vtk_numlines
                f.write(pack('I', datasize))
                for vtk_offsets in range(vtk_cell_pts, (self.vtk_numline_components * self.vtk_numlines) + vtk_cell_pts, vtk_cell_pts):
                    pbar.update(n=4)
                    f.write(pack('I', vtk_offsets))

                # Write material IDs per-cell-edge, i.e. from ID array
                datasize = np.dtype(np.uint32).itemsize * self.vtk_numlines
                f.write(pack('I', datasize))
                for i in range(self.xs, self.xf):
                    for j in range(self.ys, self.yf + 1):
                        for k in range(self.zs, self.zf + 1):
                            pbar.update(n=4)
                            f.write(pack('I', G.ID[0, i, j, k]))

                for i in range(self.xs, self.xf + 1):
                    for j in range(self.ys, self.yf):
                        for k in range(self.zs, self.zf + 1):
                            pbar.update(n=4)
                            f.write(pack('I', G.ID[1, i, j, k]))

                for i in range(self.xs, self.xf + 1):
                    for j in range(self.ys, self.yf + 1):
                        for k in range(self.zs, self.zf):
                            pbar.update(n=4)
                            f.write(pack('I', G.ID[2, i, j, k]))

                f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))

                self.write_gprmax_info(f, G, materialsonly=True)

    def write_gprmax_info(self, f, G, materialsonly=False):
        """Writes gprMax specific information relating material, source, and receiver names to numeric identifiers.

        Args:
            f (filehandle): VTK file.
            G (class): Grid class instance - holds essential parameters describing the model.
            materialsonly (boolean): Only write information on materials
        """

        f.write('\n\n<gprMax>\n'.encode('utf-8'))
        for material in G.materials:
            f.write('<Material name="{}">{}</Material>\n'.format(material.ID, material.numID).encode('utf-8'))
        if not materialsonly:
            f.write('<PML name="PML boundary region">1</PML>\n'.encode('utf-8'))
            for index, src in enumerate(G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines):
                f.write('<Sources name="{}">{}</Sources>\n'.format(src.ID, index + 2).encode('utf-8'))
            for index, rx in enumerate(G.rxs):
                f.write('<Receivers name="{}">{}</Receivers>\n'.format(rx.ID, index + 1).encode('utf-8'))
        f.write('</gprMax>\n'.encode('utf-8'))


class GeometryObjects(object):
    """Geometry objects to be written to file."""

    def __init__(self, xs=None, ys=None, zs=None, xf=None, yf=None, zf=None, basefilename=None):
        """
        Args:
            xs, xf, ys, yf, zs, zf (int): Extent of the volume in cells.
            filename (str): Filename to save to.
        """

        self.xs = xs
        self.ys = ys
        self.zs = zs
        self.xf = xf
        self.yf = yf
        self.zf = zf
        self.nx = self.xf - self.xs
        self.ny = self.yf - self.ys
        self.nz = self.zf - self.zs
        self.filename = basefilename + '.h5'
        self.materialsfilename = basefilename + '_materials.txt'
        self.solidsize = (self.nx + 1) * (self.ny + 1) * (self.nz + 1) * np.dtype(np.int16).itemsize
        self.rigidsize = 18 * (self.nx + 1) * (self.ny + 1) * (self.nz + 1) * np.dtype(np.int8).itemsize
        self.IDsize = 6 * (self.nx + 1) * (self.ny + 1) * (self.nz + 1) * np.dtype(np.uint32).itemsize
        self.datawritesize = self.solidsize + self.rigidsize + self.IDsize

    def write_hdf5(self, G, pbar):
        """Write a geometry objects file in HDF5 format.

        Args:
            G (class): Grid class instance - holds essential parameters describing the model.
            pbar (class): Progress bar class instance.
        """

        # Write the geometry objects to a HDF5 file
        fdata = h5py.File(os.path.abspath(os.path.join(G.inputdirectory, self.filename)), 'w')
        fdata.attrs['gprMax'] = __version__
        fdata.attrs['Title'] = G.title
        fdata.attrs['dx, dy, dz'] = (G.dx, G.dy, G.dz)

        # Get minimum and maximum integers of materials in geometry objects volume
        minmat = np.amin(G.ID[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1])
        maxmat = np.amax(G.ID[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1])
        fdata['/data'] = G.solid[self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1].astype('int16') - minmat
        pbar.update(self.solidsize)
        fdata['/rigidE'] = G.rigidE[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1]
        fdata['/rigidH'] = G.rigidH[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1]
        pbar.update(self.rigidsize)
        fdata['/ID'] = G.ID[:, self.xs:self.xf + 1, self.ys:self.yf + 1, self.zs:self.zf + 1] - minmat
        pbar.update(self.IDsize)

        # Write materials list to a text file
        # This includes all materials in range whether used in volume or not; also append a 6-digit random number to the material ID to make it unique
        fmaterials = open(os.path.abspath(os.path.join(G.inputdirectory, self.materialsfilename)), 'w')
        for numID in range(minmat, maxmat + 1):
            for material in G.materials:
                if material.numID == numID:
                    fmaterials.write('#material: {:g} {:g} {:g} {:g} {}\n'.format(material.er, material.se, material.mr, material.sm, material.ID))
                    if material.poles > 0:
                        if 'debye' in material.type:
                            dispersionstr = '#add_dispersion_debye: {:g} '.format(material.poles)
                            for pole in range(material.poles):
                                dispersionstr += '{:g} {:g} '.format(material.deltaer[pole], material.tau[pole])
                        elif 'lorenz' in material.type:
                            dispersionstr = '#add_dispersion_lorenz: {:g} '.format(material.poles)
                            for pole in range(material.poles):
                                dispersionstr += '{:g} {:g} {:g} '.format(material.deltaer[pole], material.tau[pole], material.alpha[pole])
                        elif 'drude' in material.type:
                            dispersionstr = '#add_dispersion_drude: {:g} '.format(material.poles)
                            for pole in range(material.poles):
                                dispersionstr += '{:g} {:g} '.format(material.tau[pole], material.alpha[pole])
                        dispersionstr += material.ID
                        fmaterials.write(dispersionstr + '\n')