Updated macro to account for new Paraview threshold behaviour in >v.5.10

tools/Paraview macros/gprMax_info.py

@@ -1,5 +1,5 @@
-# Copyright (C) 2015-2021: The University of Edinburgh
-#                 Authors: Craig Warren and Antonis Giannopoulos
+# Copyright (C) 2015-2022: The University of Edinburgh
+#                 Authors: Craig Warren, Antonis Giannopoulos, and John Hartley
 #
 # This file is part of gprMax.
 #
@@ -16,11 +16,146 @@
 # You should have received a copy of the GNU General Public License
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
-from paraview.simple import *
+import json
+import mmap
+import os
 from xml.etree import ElementTree as ET
 
-# Disable automatic camera reset on 'Show'
-paraview.simple._DisableFirstRenderCameraReset()
+from paraview.simple import *
+
+# Read Paraview version number to set threshold filter method
+pvv = GetParaViewVersion()
+if pvv.major == 5 and pvv.minor < 10:
+    new_thres = False
+else:
+    new_thres = True
+
+def threshold_filt(input, lt, ut, scalars):
+    """Create threshold filter according to Paraview version.
+    
+    Args:
+        input (array): input data to threshold filter
+        lt, ut (int): lower and upper bounds of thresholding operation
+        scalars (list/str): name of scalar array to perform thresholding
+
+    Returns:
+        threshold (object): threshold filter
+    """
+
+    threshold = Threshold(Input=input)
+    threshold.Scalars = scalars
+
+    if new_thres:
+        threshold.LowerThreshold = lt
+        threshold.UpperThreshold = ut
+    else:
+        threshold.ThresholdRange = [lt, ut]
+
+    return threshold
+
+
+def display_src_rx(srcs_rxs, dl):
+    """Display sources and receivers as Paraview box sources.
+        Only suitable for gprMax >= v4
+
+    Args:
+        srcs_rxs (list): source/receiver names and positions
+        dl (tuple): spatial discretisation
+    """
+
+    for item in srcs_rxs:
+        pos = item['position']
+        name = item['name']
+        src_rx = Box(Center=[pos[0] + dl[0]/2,
+                             pos[1] + dl[1]/2,
+                             pos[2] + dl[2]/2],
+                     XLength=dl[0], YLength=dl[1], ZLength=dl[2])
+        RenameSource(name, src_rx)
+        Show(src_rx)
+
+
+def display_pmls(pmlthick, dx_dy_dz, nx_ny_nz):
+    """Display PMLs as box sources using PML thickness values.
+        Only suitable for gprMax >= v4
+
+    Args:
+        pmlthick (tuple): PML thickness values for each slab (cells)
+        dx_dy_dz (tuple): Spatial resolution (m)
+        nx_ny_dz (tuple): Domain size (cells)
+    """
+
+    pml_names = ['x0', 'y0', 'z0', 'xmax', 'ymax', 'zmax']
+    pmls = dict.fromkeys(pml_names, None)
+
+    if pmlthick[0] != 0:
+        x0 = Box(Center=[pmlthick[0] * dx_dy_dz[0] / 2,
+                         nx_ny_nz[1] * dx_dy_dz[1] / 2,
+                         nx_ny_nz[2] * dx_dy_dz[2] / 2],
+                 XLength=pmlthick[0] * dx_dy_dz[0],
+                 YLength=nx_ny_nz[1] * dx_dy_dz[1],
+                 ZLength=nx_ny_nz[2] * dx_dy_dz[2])
+        pmls['x0'] = x0
+
+    if pmlthick[3] != 0:
+        xmax = Box(Center=[dx_dy_dz[0] * (nx_ny_nz[0] - pmlthick[3] / 2),
+                           nx_ny_nz[1] * dx_dy_dz[1] / 2,
+                           nx_ny_nz[2] * dx_dy_dz[2] / 2],
+                   XLength=pmlthick[3] * dx_dy_dz[0],
+                   YLength=nx_ny_nz[1] * dx_dy_dz[1],
+                   ZLength=nx_ny_nz[2] * dx_dy_dz[2])
+        pmls['xmax'] = xmax
+
+    if pmlthick[1] != 0:
+        y0 = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
+                         pmlthick[1] * dx_dy_dz[1] / 2,
+                         nx_ny_nz[2] * dx_dy_dz[2] / 2],
+                 XLength=nx_ny_nz[0] * dx_dy_dz[0],
+                 YLength=pmlthick[1] * dx_dy_dz[1],
+                 ZLength=nx_ny_nz[2] * dx_dy_dz[2])
+        pmls['y0'] = y0
+
+    if pmlthick[4] != 0:
+        ymax = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
+                           dx_dy_dz[1] * (nx_ny_nz[1] - pmlthick[4] / 2),
+                           nx_ny_nz[2] * dx_dy_dz[2] / 2],
+                   XLength=nx_ny_nz[0] * dx_dy_dz[0],
+                   YLength=pmlthick[4] * dx_dy_dz[1],
+                   ZLength=nx_ny_nz[2] * dx_dy_dz[2])
+        pmls['ymax'] = ymax
+
+    if pmlthick[2] != 0:
+        z0 = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
+                         nx_ny_nz[1] * dx_dy_dz[1] / 2,
+                         pmlthick[2] * dx_dy_dz[2] / 2],
+                 XLength=nx_ny_nz[0] * dx_dy_dz[0],
+                 YLength=nx_ny_nz[1] * dx_dy_dz[1],
+                 ZLength=pmlthick[2] * dx_dy_dz[2])
+        pmls['z0'] = z0
+
+    if pmlthick[5] != 0:
+        zmax = Box(Center=[nx_ny_nz[0] * dx_dy_dz[0] / 2,
+                           nx_ny_nz[1] * dx_dy_dz[1] / 2,
+                           dx_dy_dz[2] * (nx_ny_nz[2] - pmlthick[5] / 2)],
+                   XLength=nx_ny_nz[0] * dx_dy_dz[0],
+                   YLength=nx_ny_nz[1] * dx_dy_dz[1],
+                   ZLength=pmlthick[5] * dx_dy_dz[2])
+        pmls['zmax'] = zmax
+
+    # Name PML sources and set opacity
+    tmp = []
+    for pml in pmls:
+        if pmls[pml]:
+            RenameSource('PML - ' + pml, pmls[pml])
+            Hide(pmls[pml], renderview)
+            tmp.append(pmls[pml])
+
+    # Create a group of PMLs to switch on/off easily
+    if tmp:
+        pml_gp = AppendDatasets(Input=tmp)
+        RenameSource('PML - All', pml_gp)
+        pml_view = Show(pml_gp)
+        pml_view.Opacity = 0.5
+
 
 # Get whatever source is loaded (should be model)
 model = GetActiveSource()
@@ -28,91 +163,184 @@ model = GetActiveSource()
 # Get active view
 renderview = GetActiveView()
 
-# Show data in view
-Show(model, renderview)
+# Show Data Axes Grid
+renderview.AxesGrid.Visibility = 1
 
-# Reset view to fit data
-renderview.ResetCamera()
+# Hide display of root data
+Hide(model)
 
-# Lists to hold material and sources/receiver identifiers written in VTK file in tags <gprMax3D> <Material> and <gprMax3D> <Sources/Receivers>
-materials = []
-srcs_pml = []
-rxs = []
-with open(model.FileName[0], 'rb') as f:
-    for line in f:
-        if line.startswith(b'<Material'):
-            line.rstrip(b'\n')
-            tmp = (int(ET.fromstring(line).text), ET.fromstring(line).attrib.get('name'))
-            materials.append(tmp)
-        elif line.startswith(b'<Sources') or line.startswith(b'<PML'):
-            line.rstrip(b'\n')
-            tmp = (int(ET.fromstring(line).text), ET.fromstring(line).attrib.get('name'))
-            srcs_pml.append(tmp)
-        elif line.startswith(b'<Receivers'):
-            line.rstrip(b'\n')
-            tmp = (int(ET.fromstring(line).text), ET.fromstring(line).attrib.get('name'))
-            rxs.append(tmp)
 
-if materials:
-    # Get range of data
-    mat_datarange = model.CellData.GetArray('Material').GetRange()
+#####################################
+# Get filename or list of filenames #
+#####################################
 
-    # Create threshold for materials (name and numeric value)
-    for x in range(0, int(mat_datarange[1]) + 1):
-        for y in range(len(materials)):
-            if materials[y][0] == x:
-                threshold = Threshold(Input=model)
-                threshold.Scalars = 'Material'
-                threshold.ThresholdRange = [materials[y][0], materials[y][0]]
+# Single .vti or .vtu file
+if len(model.FileName) == 1:
+    files = model.FileName
+    dirname = os.path.dirname(files[0])
 
-                RenameSource(materials[y][1], threshold)
+# Multiple .vti or .vtu files referenced in a .pvd file 
+else:
+    files = []
+    dirname = os.path.dirname(model.FileName)
+    tree = ET.parse(model.FileName)
+    root = tree.getroot()
+    for elem in root:
+        for subelem in elem.findall('DataSet'):
+            tmp = os.path.join(dirname, subelem.get('file'))
+            files.append(tmp)
 
-                if materials[y][0] != 1:
-                    # Show data in view
-                    thresholddisplay = Show(threshold, renderview)
-                    thresholddisplay.ColorArrayName = 'Material'
+# Dictionaries to hold data - mainly for <v4 behaviour
+materials = {}
+srcs = {}
+rxs = {}
+pmls = {}
 
-if srcs_pml:
-    # Get ranges of data
-    srcs_pml_datarange = model.CellData.GetArray('Sources_PML').GetRange()
+# To hold the maximum numerical ID for materials across multiple files
+material_ID_max = 0
 
-    # Create threshold for sources/pml (name and numeric value)
-    for x in range(1, int(srcs_pml_datarange[1]) + 1):
-        for y in range(len(srcs_pml)):
-            if srcs_pml[y][0] == x:
-                threshold = Threshold(Input=model)
-                threshold.Scalars = 'Sources_PML'
-                threshold.ThresholdRange = [srcs_pml[y][0], srcs_pml[y][0]]
+#################################################################
+# Read and display data from file(s), i.e. materials, sources,  #
+#                                           receivers, and PMLs #
+# Method depends on gprMax version                              #
+#################################################################
 
-                RenameSource(srcs_pml[y][1], threshold)
+for file in files:
+    with open(file, 'rb') as f:
+        #######################
+        # Read data from file #
+        #######################
+        # Determine gprMax version
+        # Read XML data
+        mm = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
+        
+        # Look for <gprMax> tag which indicates version <4
+        try:
+            xml_pos = mm.find(b'<gprMax')
+            mm.seek(xml_pos)
+            xml = mm.read(mm.size() - xml_pos)
+            root = ET.fromstring(xml)
+            # ET.dump(root)
+            v4 = False
+            print('\ngprMax version: < v.4.0.0')
+            print(file)            
+            # Read material names and numeric IDs into a dict
+            for elem in root.findall('Material'):
+                materials[elem.get('name')] = int(elem.text)
+                if int(elem.text) > material_ID_max:
+                    material_ID_max = int(elem.text)
+
+            # Read sources
+            for elem in root.findall('Sources'):
+                srcs[elem.get('name')] = int(elem.text)
+
+            # Read receivers
+            for elem in root.findall('Receivers'):
+                rxs[elem.get('name')] = int(elem.text)
+
+            # Read PMLs
+            for elem in root.findall('PML'):
+                pmls[elem.get('name')] = int(elem.text)
+
+        except:
+            v4 = True
+            # Comments () embedded in line 3 of file
+            f.readline()
+            f.readline()
+            c = f.readline().decode()
+            # Strip comment tags
+            c = c[5:-5]
+            # Model information
+            c = json.loads(c)
+            print('\ngprMax version: ' + c['gprMax_version'])
+            print(file)            
+
+    ################
+    # Display data #
+    ################
+
+    if v4:
+        # Discretisation
+        dl = c['dx_dy_dz']
+        # Number of voxels
+        nl = c['nx_ny_nz']
+
+        # Store materials
+        try:
+            mats = c['Materials']
+            for i, material in enumerate(mats):
+                materials[material] = i
+                if i > material_ID_max:
+                    material_ID_max = i
+        except KeyError:
+            print('No materials to load')
+
+        # Display any sources
+        try:
+            srcs = c['Sources']
+            display_src_rx(srcs, dl)
+        except KeyError:
+            print('No sources to load')
+
+        # Display any receivers
+        try:
+            rxs = c['Receivers']
+            display_src_rx(rxs, dl)
+        except KeyError:
+            print('No receivers to load')
+
+        # Display any PMLs
+        try:
+            pt = c['PMLthickness']
+            display_pmls(pt, dl, nl)
+        except KeyError:
+            print('No PMLs to load')
+
+    else:
+        # Display any sources and PMLs
+        srcs_pmls = dict(srcs)
+        srcs_pmls.update(pmls)
+        if srcs_pmls:
+            for k, v in srcs_pmls.items():
+                threshold = threshold_filt(model, v, v, 'Sources_PML')
+                RenameSource(k, threshold)
 
                 # Show data in view
                 thresholddisplay = Show(threshold, renderview)
                 thresholddisplay.ColorArrayName = 'Sources_PML'
-
-                if srcs_pml[y][0] == 1:
+                if v == 1:
                     thresholddisplay.Opacity = 0.5
+                threshold.UpdatePipeline()
 
+        # Display any receivers
         if rxs:
-    # Get ranges of data
-    rxs_datarange = model.CellData.GetArray('Receivers').GetRange()
-
-    # Create threshold for sources/pml (name and numeric value)
-    for x in range(1, int(rxs_datarange[1]) + 1):
-        for y in range(len(rxs)):
-            if rxs[y][0] == x:
-                threshold = Threshold(Input=model)
-                threshold.Scalars = 'Receivers'
-                threshold.ThresholdRange = [rxs[y][0], rxs[y][0]]
-
-                RenameSource(rxs[y][1], threshold)
+            for k, v in rxs.items():
+                threshold = threshold_filt(model, v, v, 'Receivers')
+                RenameSource(k, threshold)
 
                 # Show data in view
                 thresholddisplay = Show(threshold, renderview)
                 thresholddisplay.ColorArrayName = 'Receivers'
+                threshold.UpdatePipeline()
+
+# Display materials
+material_range = range(0, material_ID_max + 1)
+for k, v in sorted(materials.items(), key=lambda x: x[1]):
+    if v in material_range:
+        threshold = threshold_filt(model, v, v, ['CELLS', 'Material'])
+        RenameSource(k, threshold)
+
+        # Show data in view, except for free_space
+        if v != 1:
+            thresholddisplay = Show(threshold, renderview)
+            thresholddisplay.ColorArrayName = ['CELLS', 'Material']
+        threshold.UpdatePipeline()
+
 
-# renderview.CameraParallelProjection = 1
 RenderAllViews()
 
+# Reset view to fit data
+renderview.ResetCamera()
+
 # Show color bar/color legend
 # thresholdDisplay.SetScalarBarVisibility(renderview, False)