From 26ea4f42bba02f9325ed9f4535f48478cbd4c82f Mon Sep 17 00:00:00 2001
From: Urs Ganse <urs.ganse@utu.fi>
Date: Tue, 3 May 2016 13:16:07 +0300
Subject: [PATCH] Added plot_timestep.py script for quick plotting.

---
 examples/plot_timestep.py | 77 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100755 examples/plot_timestep.py

diff --git a/examples/plot_timestep.py b/examples/plot_timestep.py
new file mode 100755
index 00000000..d74b1c72
--- /dev/null
+++ b/examples/plot_timestep.py
@@ -0,0 +1,77 @@
+#!/usr/bin/python
+# Plot a single vlasiator bulk file, can be used for continuous job monitoring.
+# 
+# Note: this requires python with matplotlib!
+# On hornet, do:
+#  module load tools/python/2.7.8
+# before running this.
+
+import matplotlib;
+matplotlib.use('Agg')
+
+from matplotlib.colors import LogNorm
+import numpy as np;
+import pytools as pt;
+import pylab as pl;
+import numpy.ma as ma;
+import sys
+
+if len(sys.argv) < 2:
+	print("Syntax: python plot_timestep.py bulkfile.vlsv output.png")
+	sys.exit()
+
+# Open file
+filename = sys.argv[1] 
+outputname = sys.argv[2]
+f = pt.vlsvfile.VlasiatorReader(filename)
+
+# Themis colormap, as extracted from the themis tools' IDL file
+hot_desaturated_colors=[(71./255.,71./255.,219./255.),(0,0,91./255.),(0,1,1),(0,.5,0),(1,1,0),(1,96./255,0),(107./255,0,0),(224./255,76./255,76./255)]
+hot_desaturated_colormap = matplotlib.colors.LinearSegmentedColormap.from_list("hot_desaturated",hot_desaturated_colors)
+
+# Determine sizes
+xsize = f.read_parameter("xcells_ini")
+ysize = f.read_parameter("ycells_ini")
+zsize = f.read_parameter("zcells_ini")
+cellids = f.read_variable("CellID")
+
+# Juggle fields into correct order
+rho = f.read_variable("rho")
+rho = rho[cellids.argsort()].reshape([ysize,xsize])
+
+B = f.read_variable("B")
+#B = f.read_variable("perturbed_B") + f.read_variable("B")
+B_mag = np.array([np.linalg.norm(v) for v in B])
+B_mag = B_mag[cellids.argsort()].reshape([ysize,xsize])
+
+boundary_type = f.read_variable("Boundary_type");
+boundary_type = boundary_type[cellids.argsort()].reshape([ysize,xsize])
+boundary_type = (boundary_type != 1)
+
+maskedrho = ma.masked_array(rho,mask=boundary_type)
+maskedB = ma.masked_array(B_mag,mask=boundary_type)
+
+rhomin = np.min(maskedrho)
+rhomax = np.max(maskedrho)
+Bmin = np.min(maskedB)
+Bmax = np.max(maskedB)
+
+# Plot rho and B
+pl.rcParams['figure.figsize']= 30,38
+#pl.rcParams['figure.DPI']= xcells_ini/30
+
+ax1=pl.plt.subplot(2,1,1)
+ax1.set_aspect('equal','datalim')
+ax1.set_title("Rho (min = " + ("%.3e" % rhomin)+ ", max = " +("%.3e" % rhomax)+")")
+fig1=ax1.pcolormesh(maskedrho, norm=LogNorm(vmin=1e4, vmax=1e7),cmap=hot_desaturated_colormap);
+pl.plt.colorbar(fig1)
+
+ax2=pl.plt.subplot(2,1,2,sharex=ax1, sharey=ax1)
+ax2.set_title("B(min = " +("%.3e" % Bmin)+ ", max = " +("%.3e" % Bmax)+")")
+fig2=ax2.pcolormesh(maskedB, norm=LogNorm(vmin=1e-9, vmax=1e-7),cmap=hot_desaturated_colormap);
+pl.plt.colorbar(fig2)
+
+#fig1.tight_layout()
+#fig2.tight_layout()
+pl.plt.savefig(outputname,bbox_inches='tight',dpi=xsize/30)
+