Merge branch 'config' of https://github.com/gprMax/gprMax into config

gprMax/cmds_multiuse.py

@@ -1156,10 +1156,12 @@ class GeometryView(UserObjectMulti):
         except KeyError:
             logger.exception(self.params_str() + ' requires exactly eleven parameters')
             raise
-
         GeometryViewUser = self.geometry_view_constructor(grid, output_type)
-
-        p1, p2 = uip.check_box_points(p1, p2, self.params_str())
+        try:
+            p1, p2 = uip.check_box_points(p1, p2, self.params_str())
+        except ValueError:
+            logger.exception(self.params_str() + ' point is outside the domain')
+            raise
         xs, ys, zs = p1
         xf, yf, zf = p2
 

gprMax/geometry_outputs.py

@@ -113,6 +113,9 @@ class GeometryView:
                                  np.dtype(np.uint32).itemsize * self.vtk_numlines +
                                  np.dtype(np.uint32).itemsize * vtk_cell_offsets +
                                  np.dtype(np.uint32).itemsize * 4)
+    
+    def initialise(self):
+        pass
 
     def set_filename(self):
         """Construct filename from user-supplied name and model run number."""
@@ -466,6 +469,16 @@ class GeometryViewFineMultiGrid:
         self.additional_lines = 0
         self.additional_points = 0
 
+    def set_filename(self):
+        """Construct filename from user-supplied name and model run number."""
+        parts = config.get_model_config().output_file_path.parts
+        self.filename = Path(*parts[:-1], self.filename + config.get_model_config().appendmodelnumber)
+        self.filename = self.filename.with_suffix(self.fileext)
+    
+    def initialise(self):
+
+        G = self.G
+    
         for sg in G.subgrids:
             # create an object to contain data relevant to the geometry processing
             sg_gv = SubgridGeometryView(sg)
@@ -484,11 +497,6 @@ class GeometryViewFineMultiGrid:
         self.vtk_materials_offset = round_value(int(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):
-        """Construct filename from user-supplied name and model run number."""
-        parts = config.get_model_config().output_file_path.parts
-        self.filename = Path(*parts[:-1], self.filename + config.get_model_config().appendmodelnumber)
-        self.filename = self.filename.with_suffix(self.fileext)
 
     def write_vtk(self, *args):
         """Writes the geometry information to a VTK file.
@@ -612,7 +620,73 @@ class GeometryViewFineMultiGrid:
                 f.write(sg_v.z_s_materials.tostring())
 
             f.write('\n</AppendedData>\n</VTKFile>'.encode('utf-8'))
-            #self.write_gprmax_info(f, G, materialsonly=True)
+            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 (FDTDGrid): Parameters describing a grid in a model.
+            materialsonly (bool): Only write information on materials
+        """
+
+        root = ET.Element('gprMax')
+        root.set('Version', __version__)
+        root.set('dx_dy_dz', (G.dx, G.dy, G.dz))
+        root.set('nx_ny_nz', (G.nx, G.ny, G.nz))
+
+        # Write the name and numeric ID for each material
+        mats_el = ET.SubElement(root, 'Materials')
+        for material in G.materials:
+            mat_el = ET.SubElement(mats_el, 'Material')
+            mat_el.set('ID', material.ID)
+            mat_el.set('numID', str(material.numID))
+
+        # Write information on PMLs, sources, and receivers
+        if not materialsonly:
+            # Information on PML thickness
+            if G.pmls:
+                # Only render PMLs if they are in the geometry view
+                pmlstorender = dict.fromkeys(G.pmlthickness, 0)
+                xmax = G.nx - self.vtk_xfcells
+                ymax = G.ny - self.vtk_yfcells
+                zmax = G.nz - self.vtk_zfcells
+                if G.pmlthickness['x0'] - self.vtk_xscells > 0:
+                    pmlstorender['x0'] = G.pmlthickness['x0']
+                if G.pmlthickness['y0'] - self.vtk_yscells > 0:
+                    pmlstorender['y0'] = G.pmlthickness['y0']
+                if G.pmlthickness['z0'] - self.vtk_zscells > 0:
+                    pmlstorender['z0'] = G.pmlthickness['z0']
+                if self.vtk_xfcells > G.nx - G.pmlthickness['xmax']:
+                    pmlstorender['xmax'] = G.pmlthickness['xmax']
+                if self.vtk_yfcells > G.ny - G.pmlthickness['ymax']:
+                    pmlstorender['ymax'] = G.pmlthickness['ymax']
+                if self.vtk_zfcells > G.nz - G.pmlthickness['zmax']:
+                    pmlstorender['zmax'] = G.pmlthickness['zmax']
+                root.set('PMLthickness', list(pmlstorender.values()))
+            # Location of sources and receivers
+            srcs = G.hertziandipoles + G.magneticdipoles + G.voltagesources + G.transmissionlines
+            if srcs:
+                srcs_el = ET.SubElement(root, 'Sources')
+                for src in srcs:
+                    src_el = ET.SubElement(srcs_el, 'Source')
+                    src_el.set('name', src.ID)
+                    src_el.set('position', (src.xcoord * G.dx,
+                                            src.ycoord * G.dy,
+                                            src.zcoord * G.dz))                          
+            if G.rxs:
+                rxs_el = ET.SubElement(root, 'Receivers')
+                for rx in G.rxs:
+                    rx_el = ET.SubElement(rxs_el, 'Receiver')
+                    rx_el.set('name', rx.ID)
+                    rx_el.set('position', (rx.xcoord * G.dx,
+                                           rx.ycoord * G.dy,
+                                           rx.zcoord * G.dz))
+
+        xml_string = pretty_xml(ET.tostring(root))
+        f.write(str.encode(xml_string))
 
 
 class SubgridGeometryView:
@@ -659,7 +733,6 @@ class SubgridGeometryView:
         """Label is the starting label. 0 if no other grids are present but
             +1 the last label used for a multigrid view.
         """
-
         sg = self.sg
         self.label = label
 

gprMax/model_build_run.py

@@ -114,6 +114,7 @@ class ModelBuildRun:
                 G.geometryviews[0].write_vtk_pvd(G.geometryviews)
                 logger.info(f'Written wrapper for geometry files: {G.geometryviews[0].pvdfile.name}')
             for i, gv in enumerate(G.geometryviews):
+                gv.initialise()
                 gv.set_filename()
                 pbar = tqdm(total=gv.datawritesize, unit='byte', unit_scale=True,
                             desc=f'Writing geometry view file {i + 1}/{len(G.geometryviews)}, {gv.filename.name}',

user_models/sub-gridding/subgrid_basic.py

@@ -0,0 +1,94 @@
+# Copyright (C) 2015-2020, John Hartley
+#
+# This module is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
+# To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.
+
+from pathlib import Path
+import sys
+import gprMax
+from user_libs.antennas.GSSI import antenna_like_GSSI_400
+
+import numpy as np
+
+# file path step
+fn = Path(__file__)
+parts = fn.parts
+
+# subgrid Discretisation is 1 mm in x, y, z directions. This allows us
+# to model the geometry of the antenna
+dl_s = 1e-3
+# subgridding ratio. This must always be an odd integer multiple. In this case
+# the main grid discrestisation is 9e-3 m.
+ratio = 5
+dl = dl_s * ratio
+
+# cells
+# default number of pml cells
+pml_cells = 10
+# distance between model and pml cells
+pml_gap = 15
+# number of cells between the Inner Surface and the Outer Surface of the sub-grid
+is_os_gap = 4
+# size of the sub-gridded region
+sub_gridded_region = 3
+# domain size
+extent = sub_gridded_region + 2 * (pml_cells + pml_gap + is_os_gap)
+
+# domain extent
+x = dl * extent
+y = x
+z = x
+
+tw = 1e-9
+
+scene = gprMax.Scene()
+
+title_gpr = gprMax.Title(name=fn.name)
+dxdydz = gprMax.Discretisation(p1=(dl, dl, dl))
+domain = gprMax.Domain(p1=(x, y, z))
+time_window = gprMax.TimeWindow(time=tw)
+
+scene.add(domain)
+scene.add(title_gpr)
+scene.add(dxdydz)
+scene.add(time_window)
+
+sg_x0 = (pml_cells + pml_gap + is_os_gap) * dl
+sg_y0 = sg_x0
+sg_z0 = sg_x0
+
+sg_x1 = sg_x0 + sub_gridded_region * dl
+sg_y1 = sg_x1
+sg_z1 = sg_x1
+
+sg_p0 = [sg_x0, sg_y0, sg_z0]
+sg_p1 = [sg_x1, sg_y1, sg_z1]
+
+sg = gprMax.SubGridHSG(p1=sg_p0, p2=sg_p1, ratio=ratio, id='mysubgrid')
+scene.add(sg)
+
+# plastic box in sub grid
+material = gprMax.Material(er=3, mr=1, se=0, sm=0, id='plastic')
+scene.add(material)
+plastic_box = gprMax.Box(p1=(30*dl, 30*dl, 30*dl), p2=(31*dl, 31*dl, 31*dl), material_id='plastic')
+sg.add(plastic_box)
+
+# create a geometry view of the main grid and the sub grid stitched together
+gv = gprMax.GeometryView(p1=(0, 0, 0),
+                         p2=domain.props.p1,
+                         dl=dl,
+                         filename=fn.with_suffix('').parts[-1],
+                         output_type='f',
+                         multi_grid=True)
+
+
+# create a geometry view of the main grid and the sub grid stitched together
+gv_normal = gprMax.GeometryView(p1=(0, 0, 0),
+                         p2=domain.props.p1,
+                         dl=dl,
+                         filename=fn.with_suffix('').parts[-1] + '_voxels',
+                         output_type='n')
+scene.add(gv)
+#scene.add(gv_normal)
+
+gprMax.run(scenes=[scene], n=1, geometry_only=False, outputfile=fn, subgrid=True, autotranslate=True)