Added extractDX to convert Born output to DX

scripts/apbs-bornprofile-extractDX.py

@@ -0,0 +1,90 @@
+import numpy as np
+import pandas as pd
+from gridData import Grid
+
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    '--input', help='input filename')
+parser.add_argument(
+    '--output', help='output filename. .dx is auto added to name')
+parser.add_argument(
+    'grid', type=float, help='grid interval')
+parser.add_argument(
+    'gridL', type=float, help='loose grid interval')
+
+args = parser.parse_args()
+
+filename = args.input
+outname = args.output
+
+# Grid interval
+grid_int= args.grid
+
+# Edge offset for Grid
+offset = grid_int/2.0
+
+# For losse edge
+grid_intL = args.gridL
+offsetL = grid_intL/2.0
+
+df = pd.read_csv(filename,delim_whitespace=True)
+df = df.to_numpy()
+
+data = df[:,0:4]
+samples = data[:, 0:3]
+
+coord = data[:, 0:3].T
+weight = data[:,3]
+weight = weight
+
+# get dimensions
+xmin = np.min(data[:,0])
+ymin = np.min(data[:,1])
+zmin = np.min(data[:,2])
+xmax = np.max(data[:,0])
+ymax = np.max(data[:,1])
+zmax = np.max(data[:,2])
+
+# get grid dimensions
+xlen = int((xmax-xmin)/grid_int) + 1
+ylen = int((ymax-ymin)/grid_int) + 1
+zlen = int((zmax-zmin)/grid_int) + 1
+
+# get edge.
+xedge = np.linspace(xmin-offset, xmax+offset, xlen+1)
+yedge = np.linspace(ymin-offset, ymax+offset, ylen+1)
+zedge = np.linspace(zmin-offset, zmax+offset, zlen+1)
+edges = [xedge, yedge, zedge]
+
+# get loose edge.
+xedge_L = np.arange(xmin-offsetL, xmax+offsetL, grid_intL)
+yedge_L = np.arange(ymin-offsetL, ymax+offsetL, grid_intL)
+zedge_L = np.arange(zmin-offsetL, zmax+offsetL, grid_intL)
+edges_L = [xedge_L, yedge_L, zedge_L]
+
+# Filling empty points with high value
+filling_value = 2* weight.max()
+grid = np.full([xlen, ylen, zlen], filling_value)
+
+def get_ind(x, xmin, xint):
+    ind = int((x-xmin)/xint)
+    return ind
+
+for i, c in enumerate(coord.T):
+    xind = get_ind(c[0], xmin, grid_int)
+    yind = get_ind(c[1], ymin, grid_int)
+    zind = get_ind(c[2], zmin, grid_int)
+    grid[xind, yind, zind] = weight[i]
+
+# resample
+g = Grid(grid, edges=edges)
+
+# Needs GridDataFormat 0.6 or higher
+g.interpolation_spline_order = 3
+g_L = g.resample(edges_L)
+
+# export
+g.export(outname+'.dx')
+g_L.export(outname+'-loose.dx')