sdfr 200001.1.1__py3-none-win_amd64.whl

sdfr/sdf_helper.py

@@ -0,0 +1,2084 @@
+import os
+import re
+try:
+    import numpy as np
+    import matplotlib.pyplot as plt
+    from matplotlib.transforms import Bbox
+    from matplotlib.offsetbox import HPacker, VPacker, TextArea, \
+        AnchoredOffsetbox
+except:
+    pass
+try:
+    from mpl_toolkits.axes_grid1 import make_axes_locatable
+except:
+    try:
+        # Workaround for broken macOS installation
+        import sys
+        import matplotlib
+        sys.path.append(os.path.join(matplotlib.__path__[0],
+                                     '..', 'mpl_toolkits'))
+        from axes_grid1 import make_axes_locatable
+    except:
+        pass
+try:
+    import builtins
+except:
+    import __builtin__ as builtins
+
+try:
+    import sdf
+    got_sdf = True
+except ImportError:
+    got_sdf = False
+
+try:
+    from matplotlib.pyplot import *  # NOQA
+    got_mpl = True
+except ImportError:
+    got_mpl = False
+
+
+# mpl.rcParams['interactive'] = True
+# hold()
+
+global data, t, step, p, ppi, ppe, rho, ei, ee, vx, vy, vz, bx, by, bz
+global x, y, z, xc, yc, zc, grid, grid_mid, mult_x, mult_y
+global old_mtime, wkdir, verbose, fig, im, cbar
+
+verbose = True
+
+wkdir = 'Data'
+old_mtime = 0
+old_size = 0
+old_filename = ''
+cached = False
+fig = None
+im = None
+cbar = None
+mult_x = 1
+mult_y = 1
+
+
+class ic_type():
+    NEW = 1
+    RESTART = 2
+    SOD = 3
+    SALTZMAN = 4
+    NOH = 5
+    SEDOV = 6
+    BRIO = 7
+    WAVE = 8
+    ADVECT = 9
+
+
+def get_si_prefix(scale, full_units=False):
+    scale = abs(scale)
+    mult = 1
+    sym = ''
+
+    if scale < 1e-24:
+        full_units = True
+    elif scale < 1e-21:
+        # yocto
+        mult = 1e24
+        sym = 'y'
+    elif scale < 1e-19:
+        # zepto
+        mult = 1e21
+        sym = 'z'
+    elif scale < 1e-16:
+        # atto
+        mult = 1e18
+        sym = 'a'
+    elif scale < 1e-13:
+        # femto
+        mult = 1e15
+        sym = 'f'
+    elif scale < 1e-10:
+        # pico
+        mult = 1e12
+        sym = 'p'
+    elif scale < 1e-7:
+        # nano
+        mult = 1e9
+        sym = 'n'
+    elif scale < 1e-4:
+        # micro
+        mult = 1e6
+        sym = '{\mu}'
+    elif scale < 1e-1:
+        # milli
+        mult = 1e3
+        sym = 'm'
+    elif scale >= 1e27:
+        full_units = True
+    elif scale >= 1e24:
+        # yotta
+        mult = 1e-24
+        sym = 'Y'
+    elif scale >= 1e21:
+        # zetta
+        mult = 1e-21
+        sym = 'Z'
+    elif scale >= 1e18:
+        # exa
+        mult = 1e-18
+        sym = 'E'
+    elif scale >= 1e15:
+        # peta
+        mult = 1e-15
+        sym = 'P'
+    elif scale >= 1e12:
+        # tera
+        mult = 1e-12
+        sym = 'T'
+    elif scale >= 1e9:
+        # giga
+        mult = 1e-9
+        sym = 'G'
+    elif scale >= 1e6:
+        # mega
+        mult = 1e-6
+        sym = 'M'
+    elif scale >= 1e3:
+        # kilo
+        mult = 1e-3
+        sym = 'k'
+
+    if full_units:
+        scale = scale * mult
+        if scale <= 0:
+            pwr = 0
+        else:
+            pwr = (-np.floor(np.log10(scale)))
+        mult = mult * np.power(10.0, pwr)
+        if np.rint(pwr) != 0:
+            sym = "(10^{%.0f})" % (-pwr) + sym
+
+    return mult, sym
+
+
+def get_title(var=None, geom=False, extra_info=True):
+    global data
+
+    if var is not None:
+        if hasattr(var, 'blocklist'):
+            data = var.blocklist
+
+    t = data.Header['time']
+    mult, sym = get_si_prefix(t)
+
+    stitle = r'$t = {:.3}{}s$'.format(mult * t, sym)
+
+    if not extra_info:
+        return stitle
+
+    if hasattr(data, 'Logical_flags'):
+        if hasattr(data.Logical_flags, 'use_szp') \
+                and data.Logical_flags.use_szp:
+            stitle += r', $m_f = {:.1}$'.format(data.Real_flags.m_f)
+        if hasattr(data.Logical_flags, 'use_tts') \
+                and data.Logical_flags.use_tts:
+            stitle += r', TTS'
+        if hasattr(data.Logical_flags, 'use_tav') \
+                and data.Logical_flags.use_tav:
+            stitle += r', Tensor viscosity'
+        else:
+            if hasattr(data.Logical_flags, 'use_qmono') \
+                    and data.Logical_flags.use_qmono:
+                stitle += r', Edge viscosity'
+            if hasattr(data.Logical_flags, 'use_edge') \
+                    and data.Logical_flags.use_edge:
+                stitle += r', Edge viscosity'
+
+    if hasattr(data, 'Real_flags'):
+        if hasattr(data.Real_flags, 'visc1'):
+            stitle += r', $c_1 = ' + str(data.Real_flags.visc1) + '$'
+        if hasattr(data.Real_flags, 'visc2'):
+            stitle += r'$,\,c_2 = ' + str(data.Real_flags.visc2) + '$'
+
+    if geom:
+        if hasattr(data, 'Logical_flags'):
+            if hasattr(data.Logical_flags, 'use_rz') \
+                    and data.Logical_flags.use_rz:
+                stitle += r', R-Z'
+            else:
+                stitle += r', Cartesian'
+
+            if hasattr(data.Logical_flags, 'polar_grid') \
+                    and data.Logical_flags.polar_grid:
+                stitle += r' Polar'
+
+    return stitle
+
+
+def get_default_iso(data):
+    iso = True
+    if hasattr(data, 'Integer_flags') \
+            and hasattr(data.Integer_flags, 'ic_type'):
+        ic = data.Integer_flags.ic_type
+        if ic == ic_type.NOH or ic == ic_type.SEDOV:
+            iso = True
+    return iso
+
+
+def get_file_list(wkd=None, base=None, block=None):
+    """Get a list of SDF filenames containing sequence numbers
+
+       Parameters
+       ----------
+       wkd : str
+           The directory in which to search
+           If no other keyword arguments are passed, then the code will
+           automatically attempt to detect if this field is base or block
+       base : str
+           A representative filename or directory
+       block : sdf.Block or sdf.BlockList
+           A representative sdf dataset or block
+
+       Returns
+       -------
+       file_list : str array
+           An array of filenames
+    """
+    import os.path
+    import glob
+    global wkdir
+
+    if wkd is not None:
+        if os.path.isdir(wkd):
+            wkdir = wkd
+        elif os.path.exists(wkd):
+            base = wkd
+        elif isinstance(wkd, sdf.BlockList) \
+                or isinstance(wkd, sdf.Block) or type(wkd) is dict:
+            block = wkd
+
+    if base is None and block is not None:
+        if hasattr(block, 'blocklist'):
+            bl = block.blocklist
+            if hasattr(bl, 'Header') and 'filename' in bl.Header:
+                base = bl.Header['filename']
+        elif hasattr(block, 'Header') and 'filename' in block.Header:
+            base = block.Header['filename']
+
+    if base is not None:
+        if os.path.isfile(base[0]):
+            apath = os.path.abspath(base[0])
+        else:
+            apath = os.path.abspath(base)
+        wkdir = os.path.dirname(apath)
+        flist = glob.glob(wkdir + "/*.sdf")
+        flist.remove(apath)
+        flist = [apath] + sorted(flist)
+    else:
+        flist = glob.glob(wkdir + "/*[0-9][0-9]*.sdf")
+        if len(flist) == 0:
+            flist = glob.glob("*[0-9][0-9]*.sdf")
+        flist = sorted(flist)
+
+    return flist
+
+
+def get_job_id(file_list=None, base=None, block=None):
+    """Get a representative job ID for a list of files
+
+       Parameters
+       ----------
+       file_list : str list
+           A list of filenames to search
+           If no other keyword arguments are passed, then the code will
+           automatically attempt to detect if this field is base or block
+       base : str
+           A representative filename or directory
+       block : sdf.Block or sdf.BlockList
+           A representative sdf dataset or block
+
+       Returns
+       -------
+       job_id : str
+           The job ID
+    """
+
+    if file_list is not None and type(file_list) is not list:
+        if os.path.exists(file_list):
+            base = file_list
+            file_list = None
+        elif isinstance(file_list, sdf.BlockList) \
+                or isinstance(file_list, sdf.Block) or type(file_list) is dict:
+            block = file_list
+            file_list = None
+
+    if block is not None and base is None:
+        if hasattr(block, 'blocklist'):
+            bl = block.blocklist
+            if hasattr(bl, 'Header') and 'filename' in bl.Header:
+                base = bl.Header['filename']
+        elif hasattr(block, 'Header') and 'filename' in block.Header:
+            base = block.Header['filename']
+
+    if base is not None:
+        try:
+            data = sdf.read(base, mmap=0)
+            if len(data.__dict__) > 1:
+                return data.Header['jobid1']
+        except:
+            pass
+
+    # Find the job id
+    if file_list is not None:
+        for f in file_list:
+            try:
+                data = sdf.read(f, mmap=0)
+                if len(data.__dict__) < 2:
+                    continue
+                return data.Header['jobid1']
+            except:
+                pass
+
+    return None
+
+
+def get_files(wkd=None, base=None, block=None, varname=None, fast=True):
+    """Get a list of SDF filenames belonging to the same run
+
+       Parameters
+       ----------
+       wkd : str
+           The directory in which to search
+           If no other keyword arguments are passed, then the code will
+           automatically attempt to detect if this field is base or block
+       base : str
+           A representative filename or directory
+       block : sdf.Block or sdf.BlockList
+           A representative sdf dataset or block
+       varname : str
+           A variable name that must be present in the file
+       fast : bool
+           Assume that files follow strict datestamp ordering and exit once
+           the first file that doesn't match the job ID
+
+       Returns
+       -------
+       file_list : str array
+           An array of filenames
+    """
+
+    if wkd is not None:
+        if os.path.isdir(wkd):
+            pass
+        elif os.path.exists(wkd):
+            base = wkd
+        elif isinstance(wkd, sdf.BlockList) \
+                or isinstance(wkd, sdf.Block) or type(wkd) is dict:
+            block = wkd
+
+    if block is not None and base is None:
+        if hasattr(block, 'blocklist'):
+            bl = block.blocklist
+            if hasattr(bl, 'Header') and 'filename' in bl.Header:
+                base = bl.Header['filename']
+        elif hasattr(block, 'Header') and 'filename' in block.Header:
+            base = block.Header['filename']
+
+    flist = get_file_list(wkd=wkd, base=base)
+    flist.sort(key=lambda x: os.path.getmtime(x))
+
+    job_id = get_job_id(flist, base=base, block=block)
+
+    # Add all files matching the job id
+    file_list = []
+    for f in reversed(flist):
+        try:
+            data = sdf.read(f, mmap=0, dict=True)
+            if len(data) < 2:
+                continue
+            file_job_id = data['Header']['jobid1']
+            if file_job_id == job_id:
+                if varname is None:
+                    file_list.append(f)
+                elif varname in data:
+                    file_list.append(f)
+            elif len(file_list) > 0:
+                break
+        except:
+            pass
+
+    return list(reversed(file_list))
+
+
+def get_time(time=0, first=False, last=False, wkd=None, base=None, block=None,
+             fast=True):
+    """Get an SDF dataset that matches a given time
+
+       Parameters
+       ----------
+       time : float
+           The time to search for. If specified then the dateset that is
+           closest to this time will be returned
+       first : bool
+           If set to True then the dataset with the earliest simulation time
+           will be returned
+       last : bool
+           If set to True then the dataset with the latest simulation time
+           will be returned
+       wkd : str
+           The directory in which to search
+       base : str
+           A representative filename or directory
+       block : sdf.Block or sdf.BlockList
+           A representative sdf dataset or block
+       fast : bool
+           Use a faster but less thorough method for returning first/last
+
+       Returns
+       -------
+       data : sdf.BlockList
+           An SDF dataset
+    """
+    global data, wkdir
+
+    flist = get_file_list(wkd=wkd, base=base, block=block)
+
+    if len(flist) == 0:
+        print("No SDF files found")
+        return
+
+    flist.sort(key=lambda x: os.path.getmtime(x))
+    job_id = get_job_id(flist, base=base, block=block)
+
+    if time is None and not first:
+        last = True
+
+    t = None
+    fname = None
+    if last:
+        flist = list(reversed(flist))
+        t_old = -1e90
+    else:
+        t_old = 1e90
+
+    for f in flist:
+        dat_tmp = sdf.read(f)
+        if len(dat_tmp.__dict__) < 2:
+            continue
+        if job_id != dat_tmp.Header['jobid1']:
+            continue
+
+        t = dat_tmp.Header['time']
+        if last:
+            if fast:
+                fname = f
+                break
+            if t > t_old:
+                fname = f
+                t_old = t
+        elif first:
+            if fast:
+                fname = f
+                break
+            if t < t_old:
+                fname = f
+                t_old = t
+        else:
+            td = abs(t - time)
+            if td < t_old:
+                t_old = td
+                fname = f
+                if td < 1e-30:
+                    # Exact match found. No need to search further
+                    break
+
+    if fname is None:
+        raise Exception("No valid file found in directory: " + wkdir)
+
+    data = getdata(fname, verbose=False)
+    return data
+
+
+def get_step(step=0, first=False, last=False, wkd=None, base=None, block=None,
+             fast=True):
+    """Get an SDF dataset that matches a given step
+
+       Parameters
+       ----------
+       step : int
+           The time to search for. If specified then the dateset that is
+           closest to this time will be returned
+       first : bool
+           If set to True then the dataset with the earliest simulation step
+           will be returned
+       last : bool
+           If set to True then the dataset with the latest simulation step
+           will be returned
+       wkd : str
+           The directory in which to search
+       base : str
+           A representative filename or directory
+       block : sdf.Block or sdf.BlockList
+           A representative sdf dataset or block
+       fast : bool
+           Use a faster but less thorough method for returning first/last
+
+       Returns
+       -------
+       data : sdf.BlockList
+           An SDF dataset
+    """
+    global data, wkdir
+
+    flist = get_file_list(wkd=wkd, base=base, block=block)
+
+    if len(flist) == 0:
+        print("No SDF files found")
+        return
+
+    flist.sort(key=lambda x: os.path.getmtime(x))
+    job_id = get_job_id(flist, base=base, block=block)
+
+    if step is None and not first:
+        last = True
+
+    t = None
+    fname = None
+    if last:
+        flist = list(reversed(flist))
+        t_old = -1e90
+    else:
+        t_old = 1e90
+
+    for f in flist:
+        dat_tmp = sdf.read(f)
+        if len(dat_tmp.__dict__) < 2:
+            continue
+        if job_id != dat_tmp.Header['jobid1']:
+            continue
+
+        t = dat_tmp.Header['step']
+        if last:
+            if fast:
+                fname = f
+                break
+            if t > t_old:
+                fname = f
+                t_old = t
+        elif first:
+            if fast:
+                fname = f
+                break
+            if t < t_old:
+                fname = f
+                t_old = t
+        else:
+            td = abs(t - step)
+            if td < t_old:
+                t_old = td
+                fname = f
+                if td == 0:
+                    # Exact match found. No need to search further
+                    break
+
+    if fname is None:
+        raise Exception("No valid file found in directory: " + wkdir)
+
+    data = getdata(fname, verbose=False)
+    return data
+
+
+def get_latest(wkd=None, base=None, block=None):
+    """Get the latest SDF dataset in a directory
+
+       Parameters
+       ----------
+       wkd : str
+           The directory in which to search
+           If no other keyword arguments are passed, then the code will
+           automatically attempt to detect if this field is base or block
+       base : str
+           A representative filename or directory
+       block : sdf.Block or sdf.BlockList
+           A representative sdf dataset or block
+
+       Returns
+       -------
+       data : sdf.BlockList
+           An SDF dataset
+    """
+    return get_step(last=True, wkd=wkd, base=base, block=base)
+
+
+def get_first(every=False, wkd=None, base=None, block=None):
+    if not every and not base:
+        base = get_newest_file(wkd=wkd, block=block)
+    return get_step(first=True, wkd=wkd, base=base, block=base)
+
+
+def get_last(every=False, wkd=None, base=None, block=None):
+    if not every and not base:
+        base = get_newest_file(wkd=wkd, block=block)
+    return get_step(last=True, wkd=wkd, base=base, block=base)
+
+
+def get_oldest_file(wkd=None, base=None, block=None):
+    import os.path
+
+    flist = get_file_list(wkd=wkd, base=base, block=block)
+    flist.sort(key=lambda x: os.path.getmtime(x))
+    for n in range(len(flist)):
+        f = flist[n]
+        data = sdf.read(f, mmap=0, dict=True)
+        if len(data) > 1:
+            return f
+
+    return None
+
+
+def get_newest_file(wkd=None, base=None, block=None):
+    import os.path
+
+    flist = get_file_list(wkd=wkd, base=base, block=block)
+    flist.sort(key=lambda x: os.path.getmtime(x))
+    for n in range(len(flist)):
+        f = flist[-n-1]
+        data = sdf.read(f, mmap=0, dict=True)
+        if len(data) > 1:
+            return f
+
+    return None
+
+
+def get_oldest(**kwargs):
+    return getdata(get_oldest_file(**kwargs), verbose=False)
+
+
+def get_newest(**kwargs):
+    return getdata(get_newest_file(**kwargs), verbose=False)
+
+
+def set_wkdir(wkd):
+    global wkdir
+    wkdir = wkd
+
+
+def get_wkdir():
+    global wkdir
+    return wkdir
+
+
+def sdfr(filename):
+    return sdf.read(filename)
+
+
+def plot_auto(*args, **kwargs):
+    try:
+        dims = args[0].dims
+    except:
+        print('error: Variable cannot be auto determined. '
+              + 'Use plot1d or plot2d')
+        return
+    if (len(dims) == 1):
+        if type(args[0]) is sdf.BlockStitchedPath:
+            plot_rays(*args, **kwargs)
+        elif (len(args[0].grid.dims) == 1):
+            plot1d(*args, **kwargs)
+        else:
+            plot_path(*args, **kwargs)
+    elif (len(dims) == 2):
+        k = 'set_ylabel'
+        if k in kwargs:
+            del kwargs[k]
+        plot2d(*args, **kwargs)
+    elif len(dims) == 3 and \
+            ('ix' in kwargs or 'iy' in kwargs or 'iz' in kwargs):
+        k = 'set_ylabel'
+        if k in kwargs:
+            del kwargs[k]
+        plot2d(*args, **kwargs)
+    else:
+        print('error: Unable to plot variables of this dimensionality')
+
+
+def oplot_auto(*args, **kwargs):
+    kwargs['set_ylabel'] = False
+    kwargs['hold'] = True
+    plot_auto(*args, **kwargs)
+
+
+def oplot1d(*args, **kwargs):
+    kwargs['set_ylabel'] = False
+    kwargs['hold'] = True
+    plot1d(*args, **kwargs)
+
+
+def plot1d(var, fmt=None, xdir=None, idx=-1, xscale=0, yscale=0, scale=0,
+           cgs=False, title=True, sym=True, set_ylabel=True, hold=True,
+           subplot=None, figure=None, **kwargs):
+    global data
+    global x, y, mult_x, mult_y
+
+    if len(var.dims) != 1 and len(var.dims) != 2:
+        print("error: Not a 1d dataset")
+        return
+
+    if subplot is None:
+        if figure is None:
+            figure = plt.gcf()
+            if len(figure.get_axes()) == 0:
+                hold = False
+            # Only clear the figure if one isn't supplied by the user
+            if not hold:
+                try:
+                    figure.clf()
+                except:
+                    pass
+        elif not hold:
+            figure.clf()
+        # Have to add subplot after clearing figure
+        subplot = plt.subplot(111)
+    elif figure is None:
+        figure = subplot.figure
+        if not hold:
+            subplot.clear()
+            if hasattr(subplot, 'colorbar'):
+                subplot.colorbar.remove()
+
+    if var.dims[0] == var.grid.dims[0]:
+        grid = var.grid
+    else:
+        grid = var.grid_mid
+
+    if len(var.dims) > 1:
+        if xdir is None:
+            if var.dims[1] < var.dims[0]:
+                xdir = 0
+            else:
+                xdir = 1
+        if xdir == 0:
+            if idx == -1:
+                idx = int(var.dims[1] / 2)
+            s = (slice(None), idx)
+        else:
+            if idx == -1:
+                idx = int(var.dims[0] / 2)
+            s = (idx, slice(None))
+        Y = var.data[s]
+    else:
+        xdir = 0
+        Y = var.data
+
+    if np.ndim(var.grid.data[0]) == 1:
+        X = grid.data[xdir]
+    else:
+        X = grid.data[xdir][s]
+
+    if xdir is None:
+        xdir = 0
+
+    if scale > 0:
+        xscale = scale
+        yscale = scale
+
+    # This is an attempt to get both axes to use the same scale
+    # I'm not at all confident that it always does the right thing
+    if xscale == 0 and yscale == 0:
+        xlen = max(abs(X[0]), abs(X[-1]))
+        ylen = max(abs(Y[0]), abs(Y[-1]))
+        ratio1 = ylen / xlen
+        ratio2 = xlen / ylen
+        if ratio1 >= 1 and ratio1 < 1e3:
+            xscale = xlen
+            yscale = xlen
+        elif ratio2 >= 1 and ratio2 < 1e3:
+            xscale = ylen
+            yscale = ylen
+
+    if xscale == 0:
+        length = max(abs(X[0]), abs(X[-1]))
+        mult_x, sym_x = get_si_prefix(length)
+    else:
+        mult_x, sym_x = get_si_prefix(xscale)
+
+    if yscale == 0:
+        length = max(abs(Y[0]), abs(Y[-1]))
+        mult_y, sym_y = get_si_prefix(length)
+    else:
+        mult_y, sym_y = get_si_prefix(yscale)
+
+    X = mult_x * X
+    Y = mult_y * Y
+
+    if fmt:
+        subplot.plot(X, Y, fmt, **kwargs)
+    else:
+        subplot.plot(X, Y, **kwargs)
+
+    subplot.set_xlabel(grid.labels[xdir] + ' $('
+                       + escape_latex(sym_x + grid.units[xdir]) + ')$')
+    if set_ylabel:
+        subplot.set_ylabel(var.name + ' $('
+                           + escape_latex(sym_y + var.units) + ')$')
+
+    if title:
+        subplot.set_title(get_title(var), fontsize='large', y=1.03)
+
+    figure.set_tight_layout(True)
+    figure.canvas.draw()
+
+
+def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
+              title=True, hold=True, subplot=None, figure=None, iso=True,
+              add_cbar=True, cbar_label=True, cbar_wd=5, cbar_top=False,
+              svar=None, update=True, axis_only=False, clip_reflect=False,
+              power=(-3,3), **kwargs):
+    """Plot an SDF path variable (eg. a laser ray)
+
+       Parameters
+       ----------
+       var : sdf.Block
+           The SDF block for the path to plot
+       xdir : integer
+           The dimension to use for the x-direction. If the path is 2D then
+           ydir will automatically be selected.
+       ydir : integer
+           The dimension to use for the y-direction. If the path is 2D then
+           xdir will automatically be selected.
+       xscale : real
+           Value to use for scaling the x-axis. If not set then the x-axis will
+           be scaled automatically. Set this to 1 to disable scaling.
+       yscale : real
+           Value to use for scaling the y-axis. If not set then the x-axis will
+           be scaled automatically. Set this to 1 to disable scaling.
+       scale : real
+           Value to use for scaling both axes. If not set then the axes will
+           be scaled automatically. Set this to 1 to disable scaling.
+       title : logical or string
+           If set to False, don't add a title to the plot.
+           Otherwise, add the specified value if it is a string or
+           automatically generate one if it is just True.
+       hold : logical
+           If True, do not clear the figure before plotting.
+       subplot :
+           The subplot to use for plotting
+       figure :
+           The figure to use for plotting
+       iso : logical
+           If True, generate an isotropic plot (x/y axis equal).
+       add_cbar : logical
+           Add a colorbar if true
+       cbar_label : logical or string
+           If set to False, don't add a label to the colorbar.
+           Otherwise, add the specified value if it is a string or
+           automatically generate one if it is just True.
+       cbar_wd : integer
+           The width of the colorbar
+       cbar_top : logical
+           If set to true, the colorbar is plotted along the top of the figure
+           instead of the right-hand side
+       update : logical
+           If set to true then update the axis limits for this path
+       axis_only : logical
+           If set to true then only update the axis limits for this path
+       svar : sdf.Block
+           If set, use the extents of this variable to set the axis range for
+           this plot
+       clip_reflect : logical
+           If set to true, then rays are clipped at the point where the path
+           gradient is either zero or huge
+       power : sequence
+           Sets size thresholds for scientific notation.
+           Two-element sequence passed throuth to set_powerlimits()
+
+       **kwargs : dict
+           All other keyword arguments are passed to matplotlib plotting
+           routine
+    """
+    import matplotlib.pyplot as plt
+    from matplotlib.collections import LineCollection
+    global data
+    global x, y, mult_x, mult_y
+
+    if 'norm_values' not in plot_path.__dict__:
+        plot_path.norm_values = None
+        plot_path.axis = None
+
+    if axis_only:
+        if plot_path.axis is None:
+            return
+        if subplot is None:
+            if figure is None:
+                figure = plt.gcf()
+            subplot = plt.subplot(111)
+        elif figure is None:
+            figure = subplot.figure
+        subplot.axis(plot_path.axis)
+        figure.set_tight_layout(True)
+        figure.canvas.draw()
+        return
+
+    if len(var.dims) != 1:
+        print("error: Not a 1d dataset")
+        return
+
+    if len(plt.get_fignums()) == 0:
+        hold = False
+
+    if subplot is None:
+        if figure is None:
+            figure = plt.gcf()
+            if len(figure.get_axes()) == 0:
+                hold = False
+            # Only clear the figure if one isn't supplied by the user
+            if not hold:
+                try:
+                    figure.clf()
+                except:
+                    pass
+        elif not hold:
+            figure.clf()
+        # Have to add subplot after clearing figure
+        subplot = plt.subplot(111)
+    elif figure is None:
+        figure = subplot.figure
+        if not hold:
+            subplot.clear()
+            if hasattr(subplot, 'colorbar'):
+                subplot.colorbar.remove()
+
+    if not hold:
+        plot_path.norm_values = None
+        plot_path.axis = None
+
+    #if var.dims[0] == var.grid.dims[0]:
+    #    grid = var.grid
+    #else:
+    #    grid = var.grid_mid
+    grid = var.grid
+
+    test_dir = False
+    if xdir is None:
+        xdir = 0
+    else:
+        test_dir = True
+
+    if ydir is None:
+        ydir = 1
+    else:
+        test_dir = True
+
+    if test_dir:
+        dimensions = np.shape(grid.data)[0]
+        xdir = xdir % dimensions
+        ydir = ydir % dimensions
+        if xdir == ydir:
+            ydir = (xdir + 1) % dimensions
+
+    X = grid.data[xdir]
+    Y = grid.data[ydir]
+
+    if not hold:
+        if scale > 0:
+            xscale = scale
+            yscale = scale
+
+        # This is an attempt to get both axes to use the same scale
+        # I'm not at all confident that it always does the right thing
+        if xscale == 0 and yscale == 0:
+            xlen = max(abs(X[0]), abs(X[-1]))
+            ylen = max(abs(Y[0]), abs(Y[-1]))
+            ratio1 = ylen / xlen
+            ratio2 = xlen / ylen
+            if ratio1 >= 1 and ratio1 < 1e3:
+                xscale = xlen
+                yscale = xlen
+            elif ratio2 >= 1 and ratio2 < 1e3:
+                xscale = ylen
+                yscale = ylen
+
+        if xscale == 0:
+            length = max(abs(X[0]), abs(X[-1]))
+            mult_x, sym_x = get_si_prefix(length)
+        else:
+            mult_x, sym_x = get_si_prefix(xscale)
+
+        if yscale == 0:
+            length = max(abs(Y[0]), abs(Y[-1]))
+            mult_y, sym_y = get_si_prefix(length)
+        else:
+            mult_y, sym_y = get_si_prefix(yscale)
+
+    X = mult_x * X
+    Y = mult_y * Y
+    c = var.data
+
+    if clip_reflect:
+        g = (X[0] - X[1]) / (Y[0] - Y[1])
+        for i in range(len(c) - 1):
+            ddx = X[i] - X[i+1]
+            ddy = Y[i] - Y[i+1]
+            if abs(ddy) < 1e-16:
+                grad = 100
+            else:
+                grad = ddx / ddy / g
+            if abs(grad) > 10 or grad < 0:
+                X = np.copy(X[:i+1])
+                Y = np.copy(Y[:i+1])
+                c = np.copy(c[:i+1])
+                break
+
+    points = np.array([X, Y]).T.reshape(-1, 1, 2)
+    segments = np.concatenate([points[:-1], points[1:]], axis=1)
+
+    if not hold or plot_path.norm_values is None:
+        k = 'vmin'
+        k1 = 'vrange'
+        if k in kwargs:
+            vmin = kwargs[k]
+        elif k1 in kwargs:
+            vmin = kwargs[k1][0]
+        else:
+            vmin = c.min()
+
+        k = 'vmax'
+        if k in kwargs:
+            vmax = kwargs[k]
+        elif k1 in kwargs:
+            vmax = kwargs[k1][1]
+        else:
+            vmax = c.max()
+
+        plot_path.norm_values = plt.Normalize(vmin, vmax)
+
+    kk = {}
+    k = 'lw'
+    if k in kwargs:
+        kk[k] = kwargs[k]
+    k = 'linewidth'
+    if k in kwargs:
+        kk[k] = kwargs[k]
+    lc = LineCollection(segments, norm=plot_path.norm_values, **kk)
+    lc.set_array(c)
+    im = subplot.add_collection(lc)
+
+    if not hold:
+        subplot.set_xlabel(grid.labels[xdir] + ' $('
+                           + escape_latex(sym_x + grid.units[xdir]) + ')$')
+        subplot.set_ylabel(grid.labels[ydir] + ' $('
+                           + escape_latex(sym_y + grid.units[ydir]) + ')$')
+
+        if title:
+            if type(title) is str:
+                title_label = title
+            else:
+                title_label = get_title(var, extra_info=False)
+            subplot.set_title(title_label, fontsize='large', y=1.03)
+
+        subplot.axis('tight')
+        if iso:
+            subplot.axis('image')
+
+        plot_path.axis = subplot.axis()
+        if update:
+            subplot.axis([X.min(), X.max(), Y.min(), Y.max()])
+            plot_path.axis = [X.min(), X.max(), Y.min(), Y.max()]
+
+    if not hold and add_cbar:
+        ax = subplot.axes
+        ca = subplot
+        divider = make_axes_locatable(ca)
+        pad = int(0.6 * cbar_wd + 0.5)
+        if cbar_top:
+            cax = divider.append_axes("top", "%i%%" % cbar_wd,
+                                      pad="%i%%" % pad)
+            cbar = figure.colorbar(im, orientation='horizontal',
+                                   cax=cax, ax=ax)
+            cax.xaxis.set_ticks_position('top')
+        else:
+            cax = divider.append_axes("right", "%i%%" % cbar_wd,
+                                      pad="%i%%" % pad)
+            cbar = figure.colorbar(im, cax=cax, ax=ax)
+        try:
+            cbar.formatter.set_powerlimits(power)
+            cbar.update_ticks()
+        except:
+            pass
+        subplot.colorbar = cax
+        plt.sca(ax)
+        if cbar_label:
+            if type(cbar_label) is str:
+                var_label = cbar_label
+            else:
+                var_label = var.name + ' $(' + escape_latex(var.units) + ')$'
+            if cbar_top:
+                cbar.set_label(var_label, fontsize='large')
+                cax.xaxis.set_label_position('top')
+            else:
+                cbar.set_label(var_label, fontsize='large', x=1.2)
+
+    if not hold and svar is not None:
+        lim = np.array(svar.grid.extents)
+        lim[0] *= mult_x
+        lim[1] *= mult_x
+        lim[2] *= mult_y
+        lim[3] *= mult_y
+        subplot.axis([lim[0], lim[2], lim[1], lim[3]])
+    elif hold:
+        if plot_path.axis is None:
+            plot_path.axis = [X.min(), X.max(), Y.min(), Y.max()]
+        lims = plot_path.axis
+        if lims is None:
+            lim = [X.min(), X.max(), Y.min(), Y.max()]
+        else:
+            lim = list(lims)
+            v = X.min()
+            if v < lim[0]:
+                lim[0] = v
+            v = X.max()
+            if v > lim[1]:
+                lim[1] = v
+            v = Y.min()
+            if v < lim[2]:
+                lim[2] = v
+            v = Y.max()
+            if v > lim[3]:
+                lim[3] = v
+        plot_path.axis = lim
+        if update:
+            subplot.axis(lim)
+
+    if update:
+        figure.set_tight_layout(True)
+        figure.canvas.draw()
+
+
+def plot_rays(var, skip=1, rays=None, **kwargs):
+    """Plot all rays found in an SDF file
+
+       Parameters
+       ----------
+       var : sdf.Block
+           The SDF variable for the rays to plot
+       skip : integer
+           Number of rays to skip before selecting the next one to plot
+    """
+
+    ray_start = -1
+    l = 'ray_start'
+    if l in kwargs:
+        ray_start = kwargs[l]
+
+    ray_stop = 1e9
+    l = 'ray_stop'
+    if l in kwargs:
+        ray_stop = kwargs[l]
+
+    if type(var) is sdf.BlockStitchedPath:
+        v = var.data[0]
+        l = '_label'
+        if l not in kwargs:
+            kwargs[l] = var.name
+
+        if type(v) is sdf.BlockStitchedPath:
+            for v in var.data:
+                plot_rays(v, skip=skip, rays=rays, **kwargs)
+                kwargs['hold'] = True
+            return
+
+        k = 'cbar_label'
+        if k not in kwargs or (kwargs[k] and type(kwargs[k]) != str):
+            kwargs[k] = kwargs[l] + ' $(' + escape_latex(v.units) + ')$'
+            del kwargs[l]
+
+        k0 = 'vmin'
+        k1 = 'vmax'
+        k = 'vrange'
+        if k not in kwargs and not (k0 in kwargs and k1 in kwargs):
+            v = var.data[0]
+            vmin = v.data.min()
+            vmax = v.data.max()
+            for iray, v in enumerate(var.data):
+                if iray < ray_start:
+                    continue
+                if iray > ray_stop:
+                    break
+                if iray%skip == 0:
+                    vmin = min(vmin, v.data.min())
+                    vmax = max(vmax, v.data.max())
+            if k0 not in kwargs:
+                kwargs[k0] = vmin
+            if k1 not in kwargs:
+                kwargs[k1] = vmax
+
+        for iray, v in enumerate(var.data):
+            if iray < ray_start:
+                continue
+            if iray > ray_stop:
+                break
+            if iray%skip == 0:
+                plot_auto(v, update=False, **kwargs)
+                kwargs['hold'] = True
+
+        plot_auto(var.data[0], axis_only=True, **kwargs)
+        kwargs['hold'] = True
+
+        return
+
+    split_name = var.name.split('/')
+    start = split_name[0] + '_'
+    end = '_' + split_name[-1]
+    data = var.blocklist.__dict__
+
+    k0 = 'vmin'
+    k1 = 'vmax'
+    k = 'vrange'
+    if k not in kwargs and not (k0 in kwargs and k1 in kwargs):
+        vmin = var.data.min()
+        vmax = var.data.max()
+        iray = -1
+        for k in data.keys():
+            if k.startswith(start) and k.endswith(end):
+                iray += 1
+                if iray < ray_start:
+                    continue
+                if iray > ray_stop:
+                    break
+                if iray%skip == 0:
+                    vmin = min(vmin, data[k].data.min())
+                    vmax = max(vmax, data[k].data.max())
+        if k0 not in kwargs:
+            kwargs[k0] = vmin
+        if k1 not in kwargs:
+            kwargs[k1] = vmax
+
+    k = 'cbar_label'
+    if k not in kwargs or (kwargs[k] and type(kwargs[k]) != str):
+        # Remove /Ray[1-9]+ from the name
+        kwargs[k] = '/'.join([split_name[0]] + split_name[2:]) \
+                     + ' $(' + escape_latex(var.units) + ')$'
+
+    iray = -1
+    for k in data.keys():
+        if k.startswith(start) and k.endswith(end):
+            iray += 1
+            if iray < ray_start:
+                continue
+            if iray > ray_stop:
+                break
+            if iray%skip == 0:
+                plot_auto(data[k], hold=True, update=False, **kwargs)
+                kwargs['hold'] = True
+
+    plot_auto(var, axis_only=True, **kwargs)
+    kwargs['hold'] = True
+
+
+def oplot2d(*args, **kwargs):
+    kwargs['hold'] = True
+    plot2d(*args, **kwargs)
+
+
+def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
+                 iso=None, fast=None, title=True, full=True, vrange=None,
+                 reflect=0, norm=None, hold=True, xscale=0, yscale=0, scale=0,
+                 figure=None, subplot=None, add_cbar=True, cbar_label=True,
+                 cbar_wd=5, cbar_top=False, power=(-3,3), **kwargs):
+    import matplotlib as mpl
+    global data, fig, im, cbar
+    global mult_x, mult_y
+
+    if idx is None:
+        i0 = 0
+        i1 = 1
+        i2 = 2
+        i3 = 3
+    else:
+        i0 = idx[0]
+        i1 = idx[1]
+        i2 = idx[2]
+        i3 = idx[3]
+
+    cmap = plt.get_cmap()
+
+    if norm is not None:
+        v0 = np.min(array) - norm
+        v1 = np.max(array) - norm
+
+        if abs(v0/v1) > 1:
+            low = 0
+            high = 0.5 * (1 - v1/v0)
+        else:
+            low = 0.5 * (1 + v0/v1)
+            high = 1.0
+
+        cmap = mpl.colors.LinearSegmentedColormap.from_list(
+            'tr', cmap(np.linspace(low, high, 256)))
+
+    if subplot is None:
+        if figure is None:
+            figure = plt.gcf()
+            if len(figure.get_axes()) == 0:
+                hold = False
+            # Only clear the figure if one isn't supplied by the user
+            if not hold:
+                try:
+                    figure.clf()
+                except:
+                    pass
+        elif not hold:
+            figure.clf()
+        # Have to add subplot after clearing figure
+        subplot = plt.subplot(111)
+    elif figure is None:
+        figure = subplot.figure
+        if not hold:
+            subplot.clear()
+            if hasattr(subplot, 'colorbar'):
+                subplot.colorbar.remove()
+
+    if iso is None:
+        iso = get_default_iso(data)
+
+    if scale > 0:
+        xscale = scale
+        yscale = scale
+
+    ext = extents[:]
+    # This is an attempt to get both axes to use the same scale
+    # I'm not at all confident that it always does the right thing
+    if xscale == 0 and yscale == 0:
+        xlen = max(abs(extents[i2]), abs(extents[i0]))
+        ylen = max(abs(extents[i3]), abs(extents[i1]))
+        ratio1 = ylen / xlen
+        ratio2 = xlen / ylen
+        if ratio1 >= 1 and ratio1 < 1e3:
+            xscale = xlen
+            yscale = xlen
+        elif ratio2 >= 1 and ratio2 < 1e3:
+            xscale = ylen
+            yscale = ylen
+
+    if xscale == 0:
+        length = max(abs(extents[i2]), abs(extents[i0]))
+        mult_x, sym_x = get_si_prefix(length)
+    else:
+        mult_x, sym_x = get_si_prefix(xscale)
+
+    if yscale == 0:
+        length = max(abs(extents[i3]), abs(extents[i1]))
+        mult_y, sym_y = get_si_prefix(length)
+    else:
+        mult_y, sym_y = get_si_prefix(yscale)
+
+    if vrange == 1:
+        v = np.max(abs(array))
+        vrange = [-v, v]
+
+    if fast:
+        if reflect == 1:
+            # about x=0
+            ext[i0] = 2 * extents[i0] - extents[i2]
+            array = np.vstack((np.flipud(array), array))
+        elif reflect == 2:
+            # about y=0
+            ext[i1] = 2 * extents[i1] - extents[i3]
+            array = np.hstack((np.fliplr(array), array))
+        elif reflect == 3:
+            # about x=0, y=0
+            ext[i0] = 2 * extents[i0] - extents[i2]
+            ext[i1] = 2 * extents[i1] - extents[i3]
+            array = np.vstack((np.flipud(array), array))
+            array = np.hstack((np.fliplr(array), array))
+
+    if np.ndim(x) == 1:
+        if fast is None:
+            fast = True
+
+        if not fast:
+            Y, X = np.meshgrid(y, x)
+    else:
+        if fast is None:
+            fast = False
+
+        if not fast:
+            X = x
+            Y = y
+
+    if fast:
+        ext[i0] = mult_x * ext[i0]
+        ext[i1] = mult_y * ext[i1]
+        ext[i2] = mult_x * ext[i2]
+        ext[i3] = mult_y * ext[i3]
+        e = ext[i1]
+        ext[i1] = ext[i2]
+        ext[i2] = e
+        ext = [ext[i0], ext[i1], ext[i2], ext[i3]]
+        k = 'interpolation'
+        if k not in kwargs:
+            kwargs[k] = 'none'
+        if vrange is None:
+            im = subplot.imshow(array.T, origin='lower', extent=ext, cmap=cmap,
+                                **kwargs)
+        else:
+            im = subplot.imshow(array.T, origin='lower', extent=ext, cmap=cmap,
+                                vmin=vrange[0], vmax=vrange[1], **kwargs)
+    else:
+        X = np.multiply(mult_x, X)
+        Y = np.multiply(mult_y, Y)
+        if vrange is None:
+            im = subplot.pcolormesh(X, Y, array, cmap=cmap, **kwargs)
+        else:
+            im = subplot.pcolormesh(X, Y, array, cmap=cmap,
+                                    vmin=vrange[0], vmax=vrange[1], **kwargs)
+
+    subplot.set_xlabel(xlabel)
+    subplot.set_ylabel(ylabel)
+
+    title_text = None
+    if full:
+        if add_cbar and cbar_label:
+            title_text = get_title()
+        else:
+            title_text = var_label + ', ' + get_title()
+    elif title:
+        if not (add_cbar and cbar_label):
+            title_text = var_label
+
+    if title and title_text:
+        subplot.set_title(title_text, fontsize='large', y=1.03)
+
+    subplot.axis('tight')
+    if iso:
+        subplot.axis('image')
+
+    if not hold and add_cbar:
+        ax = subplot.axes
+        ca = subplot
+        divider = make_axes_locatable(ca)
+        pad = int(0.6 * cbar_wd + 0.5)
+        if cbar_top:
+            cax = divider.append_axes("top", "%i%%" % cbar_wd,
+                                      pad="%i%%" % pad)
+            cbar = figure.colorbar(im, orientation='horizontal',
+                                   cax=cax, ax=ax)
+            cax.xaxis.set_ticks_position('top')
+        else:
+            cax = divider.append_axes("right", "%i%%" % cbar_wd,
+                                      pad="%i%%" % pad)
+            cbar = figure.colorbar(im, cax=cax, ax=ax)
+        try:
+            cbar.formatter.set_powerlimits(power)
+            cbar.update_ticks()
+        except:
+            pass
+        subplot.colorbar = cax
+        plt.sca(ax)
+        if cbar_label:
+            if type(cbar_label) is str:
+                var_label = cbar_label
+            if cbar_top:
+                cbar.set_label(var_label, fontsize='large')
+                cax.xaxis.set_label_position('top')
+            else:
+                cbar.set_label(var_label, fontsize='large', x=1.2)
+    figure.canvas.draw()
+
+    figure.set_tight_layout(True)
+    figure.canvas.draw()
+
+
+def plot2d(var, iso=None, fast=None, title=True, full=True, vrange=None,
+           ix=None, iy=None, iz=None, reflect=0, norm=None, irange=None,
+           jrange=None, hold=True, xscale=0, yscale=0, scale=0, figure=None,
+           subplot=None, add_cbar=True, cbar_label=True, cbar_top=False,
+           **kwargs):
+    global data, fig, im, cbar
+    global x, y, mult_x, mult_y
+
+    if type(irange) is list or type(irange) is tuple:
+        si = slice(*irange)
+    else:
+        si = slice(None, irange)
+
+    if type(jrange) is list or type(jrange) is tuple:
+        sj = slice(*jrange)
+    else:
+        sj = slice(None, jrange)
+
+    i0 = 0
+    i1 = 1
+    if len(var.dims) == 3:
+        if ix is not None:
+            if iz is None:
+                if ix < 0:
+                    ix = int(var.dims[0] / 2)
+                i0 = 1
+                i1 = 2
+                ss = ix, si, sj
+            else:
+                if ix < 0:
+                    ix = int(var.dims[2] / 2)
+                i0 = 0
+                i1 = 2
+                ss = si, sj, ix
+        elif iy is not None:
+            if iy < 0:
+                iy = int(var.dims[1] / 2)
+            i0 = 0
+            i1 = 2
+            ss = si, iy, sj
+            if iz is not None:
+                i0 = 0
+                i1 = 1
+                ss = si, iy, sj
+        elif iz is not None:
+            if iz < 0:
+                iz = int(var.dims[2] / 2)
+            i0 = 0
+            i1 = 1
+            ss = si, sj, iz
+        else:
+            print("error: Not a 2d dataset")
+            return
+        i2 = i0 + 3
+        i3 = i1 + 3
+    elif len(var.dims) != 2:
+        print("error: Not a 2d dataset")
+        return
+    else:
+        i2 = i0 + 2
+        i3 = i1 + 2
+        ss = si, sj
+
+    array = var.data[ss]
+    if np.ndim(var.grid.data[0]) == 1:
+        x = var.grid.data[i0][si]
+        y = var.grid.data[i1][sj]
+    else:
+        x = var.grid.data[i0][ss]
+        y = var.grid.data[i1][ss]
+
+    idx = [i0, i1, i2, i3]
+
+    if scale > 0:
+        xscale = scale
+        yscale = scale
+
+    extents = list(var.grid.extents)
+    # This is an attempt to get both axes to use the same scale
+    # I'm not at all confident that it always does the right thing
+    if xscale == 0 and yscale == 0:
+        xlen = max(abs(extents[i2]), abs(extents[i0]))
+        ylen = max(abs(extents[i3]), abs(extents[i1]))
+        ratio1 = ylen / xlen
+        ratio2 = xlen / ylen
+        if ratio1 >= 1 and ratio1 < 1e3:
+            xscale = xlen
+            yscale = xlen
+        elif ratio2 >= 1 and ratio2 < 1e3:
+            xscale = ylen
+            yscale = ylen
+
+    if xscale == 0:
+        length = max(abs(extents[i2]), abs(extents[i0]))
+        mult_x, sym_x = get_si_prefix(length)
+    else:
+        mult_x, sym_x = get_si_prefix(xscale)
+
+    if yscale == 0:
+        length = max(abs(extents[i3]), abs(extents[i1]))
+        mult_y, sym_y = get_si_prefix(length)
+    else:
+        mult_y, sym_y = get_si_prefix(yscale)
+
+    xlabel = var.grid.labels[i0] \
+        + ' $(' + escape_latex(sym_x + var.grid.units[i0]) + ')$'
+    ylabel = var.grid.labels[i1] \
+        + ' $(' + escape_latex(sym_y + var.grid.units[i1]) + ')$'
+
+    var_label = var.name + ' $(' + escape_latex(var.units) + ')$'
+
+    if hasattr(var, 'blocklist'):
+        data = var.blocklist
+
+    plot2d_array(array=array, x=x, y=y, extents=extents, var_label=var_label,
+                 xlabel=xlabel, ylabel=ylabel, idx=idx, iso=iso, fast=fast,
+                 title=title, full=full, vrange=vrange, reflect=reflect,
+                 norm=norm, hold=hold, xscale=xscale, yscale=yscale,
+                 scale=scale, figure=figure, subplot=subplot,
+                 add_cbar=add_cbar, cbar_label=cbar_label, cbar_top=cbar_top,
+                 **kwargs)
+
+
+def plot2d_update(var):
+    global fig, im
+
+    im.set_array(var.ravel())
+    im.autoscale()
+    fig.canvas.draw()
+
+
+def plot_levels(var, r0=None, r1=None, nl=10, iso=None, out=False,
+                title=True, levels=True, **kwargs):
+    global data
+
+    try:
+        plt.clf()
+    except:
+        pass
+
+    if iso is None:
+        if hasattr(var, 'blocklist'):
+            data = var.blocklist
+        iso = get_default_iso(data)
+
+    if np.ndim(var.grid.data[0]) == 1:
+        X, Y = np.meshgrid(var.grid.data[1], var.grid.data[0])
+    else:
+        if tuple(var.grid.dims) == tuple(var.dims):
+            X = var.grid.data[0]
+            Y = var.grid.data[1]
+        else:
+            X = var.grid_mid.data[0]
+            Y = var.grid_mid.data[1]
+
+    if r0 is None:
+        r0 = np.min(var.data)
+        r1 = np.max(var.data)
+        dr = (r1 - r0) / (nl + 1)
+        r0 += dr
+        r1 -= dr
+
+    rl = r0 + 1.0 * (r1 - r0) * np.array(range(nl)) / (nl - 1)
+
+    fig = plt.gcf()
+    if out:
+        gs = plt.GridSpec(1, 1)  # , width_ratios=[8, 1])
+        ax = plt.subplot(gs[0])
+    else:
+        ax = plt.gca()
+
+    k = 'colors'
+    if k not in kwargs:
+        kwargs[k] = 'k'
+    k = 'linewidths'
+    if k not in kwargs:
+        kwargs[k] = 0.5
+    k = 'levels'
+    if k not in kwargs:
+        kwargs[k] = rl
+
+    cs = ax.contour(X, Y, var.data, **kwargs)
+
+    if levels:
+        fmt = {}
+        for l, i in zip(cs.levels, range(1, len(cs.levels)+1)):
+            fmt[l] = str(i)
+
+        sidx = ""
+        slvl = ""
+        for l, i in reversed(list(zip(cs.levels, range(1, len(cs.levels)+1)))):
+            # sidx += rtn + "%i" % i
+            # slvl += rtn + "%-6.4g" % l
+            # rtn = "\n"
+            sidx += "%i\n" % i
+            slvl += "%-6.4g\n" % l
+
+        t1 = TextArea('Level', textprops=dict(color='k', fontsize='small'))
+        t2 = TextArea(sidx, textprops=dict(color='k', fontsize='small'))
+        tl = VPacker(children=[t1, t2], align="center", pad=0, sep=2)
+
+        lname = var.name.replace("_node", "")
+        t3 = TextArea(lname, textprops=dict(color='k', fontsize='small'))
+        t4 = TextArea(slvl, textprops=dict(color='k', fontsize='small'))
+        tr = VPacker(children=[t3, t4], align="center", pad=0, sep=2)
+
+        t = HPacker(children=[tl, tr], align="center", pad=0, sep=8)
+
+        if out:
+            t = AnchoredOffsetbox(loc=2, child=t, pad=.4,
+                                  bbox_to_anchor=(1.01, 1), frameon=True,
+                                  bbox_transform=ax.transAxes, borderpad=0)
+        else:
+            t = AnchoredOffsetbox(loc=1, child=t, pad=.4,
+                                  bbox_to_anchor=(1, 1), frameon=True,
+                                  bbox_transform=ax.transAxes, borderpad=.4)
+        t.set_clip_on(False)
+        ax.add_artist(t)
+
+        plt.clabel(cs, cs.levels, fmt=fmt, inline_spacing=2, fontsize=8)
+
+    ax.set_xlabel(var.grid.labels[0] + ' $('
+                  + escape_latex(var.grid.units[0]) + ')$')
+    ax.set_ylabel(var.grid.labels[1] + ' $('
+                  + escape_latex(var.grid.units[1]) + ')$')
+
+    if title:
+        if out:
+            # suptitle(get_title(), fontsize='large')
+            plt.suptitle(get_title(var), fontsize='large', y=0.92)
+        else:
+            plt.title(get_title(var), fontsize='large', y=1.03)
+
+    plt.axis('tight')
+    if iso:
+        plt.axis('image')
+
+    plt.draw()
+    if out:
+        gs.tight_layout(fig, rect=[0, -0.01, 0.95, 0.92])
+        # fw = fig.get_window_extent().width
+        # tw = fw*.06+t1.get_children()[0].get_window_extent().width \
+        #     + t3.get_children()[0].get_window_extent().width
+        # print(1-tw/fw)
+        # gs.update(right=1-tw/fw)
+        # ax.set_position([box.x0, box.y0, box.width + bw, box.height])
+    else:
+        fig.set_tight_layout(True)
+    plt.draw()
+
+
+def plot_contour(var, r0=None, r1=None, nl=10, iso=None, title=True, **kwargs):
+    return plot_levels(var, r0=r0, r1=r1, nl=nl, iso=iso, out=False,
+                       title=title, levels=False, **kwargs)
+
+
+def getdata(fname, wkd=None, verbose=True, squeeze=False):
+    global data, t, step, p, ppi, ppe, rho, ei, ee, vx, vy, vz, bx, by, bz
+    global x, y, z, xc, yc, zc, grid, grid_mid
+    global old_mtime, old_filename, old_size, cached
+    global wkdir
+
+    if wkd is not None:
+        wkdir = wkd
+
+    if isinstance(fname, int):
+        try:
+            filename = wkdir + "/%0.4i.sdf" % fname
+        except:
+            filename = wkdir + "/" + fname
+    else:
+        filename = fname
+
+    try:
+        st = os.stat(filename)
+    except OSError as e:
+        try:
+            filename = "./%0.4i.sdf" % fname
+        except:
+            filename = "./" + fname
+        try:
+            st = os.stat(filename)
+            wkdir = '.'
+        except OSError as e:
+            print("ERROR opening file {0}: {1}".format(filename, e.strerror))
+            raise
+
+    if st.st_mtime != old_mtime or st.st_size != old_size \
+            or filename != old_filename:
+        if verbose:
+            print("Reading file " + filename)
+        data = sdf.read(filename)
+        old_mtime = st.st_mtime
+        old_size = st.st_size
+        old_filename = filename
+    else:
+        cached = True
+        return data
+
+    cached = False
+
+    if squeeze:
+        for key, value in data.__dict__.items():
+            # Remove single element dimensions
+            try:
+                dims = []
+                for element in value.dims:
+                    dims.append([0, element-1])
+                subarray(value, dims)
+            except:
+                pass
+
+    sdfdict = {}
+    for key, value in data.__dict__.items():
+        if hasattr(value, "id"):
+            sdfdict[value.id] = value
+        else:
+            sdfdict[key] = value
+
+    fdict = {}
+    table = {'time': 't'}
+    k = 'Header'
+    if k in sdfdict:
+        h = sdfdict[k]
+        k = list(table.keys())[0]
+        if k in h:
+            key = table[k]
+            var = h[k]
+            if verbose:
+                print(key + str(np.shape(var)) + ' = ' + k)
+            fdict[key] = var
+            globals()[key] = var
+            builtins.__dict__[key] = var
+
+    table = {'Pressure': 'p',
+             'Pressure_ion': 'ppi',
+             'Pressure_electron': 'ppe',
+             'Rho': 'rho',
+             'Energy_ion': 'ei',
+             'Energy_electron': 'ee',
+             'Vx': 'vx',
+             'Vy': 'vy',
+             'Vz': 'vz',
+             'Vr': 'vx',
+             'VTheta': 'vz',
+             'Bx': 'bx',
+             'By': 'by',
+             'Bz': 'bz',
+             'Br': 'bx',
+             'Bt': 'bz',
+             'bx': 'bx',
+             'by': 'by',
+             'bz': 'bz',
+             'ex': 'ex',
+             'ey': 'ey',
+             'ez': 'ez',
+             'jx': 'jx',
+             'jy': 'jy',
+             'jz': 'jz'}
+
+    rz = False
+    if 'Vr' in sdfdict:
+        rz = True
+
+    if rz:
+        table['Vz'] = 'vy'
+        table['Bz'] = 'by'
+
+    inv_table = {}
+    for k, v in table.items():
+        inv_table[v] = inv_table.get(v, [])
+        inv_table[v].append(k)
+
+    for k in table:
+        if k in sdfdict:
+            key = table[k]
+            if hasattr(sdfdict[k], "data"):
+                var = sdfdict[k].data
+            else:
+                var = sdfdict[k]
+            dims = str(tuple(int(i) for i in sdfdict[k].dims))
+            if verbose:
+                print(key + dims + ' = ' + k)
+            fdict[key] = var
+            globals()[key] = var
+            builtins.__dict__[key] = var
+
+    k = 'grid'
+    if k in sdfdict:
+        vargrid = sdfdict[k]
+        grid = vargrid
+        keys = 'x', 'y', 'z'
+        for n in range(np.size(vargrid.dims)):
+            key = keys[n]
+            var = vargrid.data[n]
+            dims = str(tuple(int(i) for i in sdfdict[k].dims))
+            if verbose:
+                print(key + dims + ' = ' + k)
+            fdict[key] = var
+            globals()[key] = var
+            builtins.__dict__[key] = var
+
+    k = 'grid_mid'
+    if k in sdfdict:
+        vargrid = sdfdict[k]
+        grid_mid = vargrid
+        keys = 'xc', 'yc', 'zc'
+        for n in range(np.size(vargrid.dims)):
+            key = keys[n]
+            var = vargrid.data[n]
+            dims = str(tuple(int(i) for i in sdfdict[k].dims))
+            if verbose:
+                print(key + dims + ' = ' + k)
+            fdict[key] = var
+            globals()[key] = var
+            builtins.__dict__[key] = var
+
+    # Export particle arrays
+    for k, value in data.__dict__.items():
+        if type(value) != sdf.BlockPointVariable \
+                and type(value) != sdf.BlockPointMesh:
+            continue
+        key = re.sub(r'[^a-z0-9]', '_', value.id.lower())
+        if hasattr(value, "data"):
+            var = value.data
+        else:
+            var = value
+        dims = str(tuple(int(i) for i in value.dims))
+        if type(value) == sdf.BlockPointVariable:
+            if verbose:
+                print(key + dims + ' = ' + value.name)
+            fdict[key] = var
+            globals()[key] = var
+            builtins.__dict__[key] = var
+        else:
+            vargrid = value
+            grid = vargrid
+            keys = 'x', 'y', 'z'
+            for n in range(np.size(value.dims)):
+                gkey = keys[n] + '_' + key
+                var = value.data[n]
+                dims = str(tuple(int(i) for i in value.dims))
+                if verbose:
+                    print(gkey + dims + ' = ' + k + ' ' + keys[n])
+                fdict[gkey] = var
+                globals()[gkey] = var
+                builtins.__dict__[gkey] = var
+
+    # X, Y = np.meshgrid(x, y)
+    return data
+
+
+def ogrid(skip=None, **kwargs):
+    global x, y, mult_x, mult_y
+    if np.ndim(x) == 1:
+        X, Y = np.meshgrid(x, y)
+    else:
+        s = slice(None, None, skip)
+        X = x[s, s]
+        Y = y[s, s]
+    X = np.multiply(mult_x, X)
+    Y = np.multiply(mult_y, Y)
+    k = 'lw'
+    if k not in kwargs and 'linewidth' not in kwargs:
+        kwargs[k] = 0.5
+    k = 'color'
+    if k not in kwargs:
+        kwargs[k] = 'k'
+    plt.plot(X, Y, **kwargs)
+    plt.plot(X.transpose(), Y.transpose(), **kwargs)
+
+
+def plotgrid(fname=None, iso=None, title=True):
+    if type(fname) is sdf.BlockList or type(fname) is dict:
+        dat = fname
+    elif fname is not None:
+        dat = getdata(fname, verbose=verbose)
+
+    if iso is None:
+        iso = get_default_iso(dat)
+
+    ogrid()
+
+    ax = plt.gca()
+
+    ax.set_xlabel(grid.labels[0] + ' $(' + escape_latex(grid.units[0]) + ')$')
+    ax.set_ylabel(grid.labels[1] + ' $(' + escape_latex(grid.units[1]) + ')$')
+
+    if title:
+        plt.title(get_title(), fontsize='large', y=1.03)
+
+    plt.axis('tight')
+    if iso:
+        plt.axis('image')
+
+    plt.draw()
+
+    fig = plt.gcf()
+    fig.set_tight_layout(True)
+    plt.draw()
+
+
+def axis_offset(boxed=False):
+    ax = plt.gca()
+    xlab = ax.get_xlabel()
+    ylab = ax.get_ylabel()
+
+    f = 1e-3
+
+    # for o in ax.findobj():
+    for l in ax.get_lines():
+        bb = l.get_clip_box()
+        bb._bbox = Bbox([[-f, -f], [1+2*f, 1+2*f]])
+        l.set_clip_box(bb)
+        # l.set_clip_on(False)
+
+    if boxed:
+        r = matplotlib.patches.Rectangle((-f, -f), 1+2*f, 1+2*f,
+                                         transform=ax.transAxes)
+        r.set_color((0, 0, 0, 0))
+        r.set_edgecolor('k')
+        r.set_clip_on(False)
+        ax.add_patch(r)
+
+    w = 1.1
+    gap = 8
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+    ax.spines['left'].set_position(('outward', gap))
+    ax.spines['left'].set_linewidth(w)
+    ax.spines['bottom'].set_position(('outward', gap))
+    ax.spines['bottom'].set_linewidth(w)
+    ax.tick_params(direction='out', width=w, length=4.5, top='off',
+                   right='off')
+    ax.set_xlabel(xlab)
+    ax.set_ylabel(ylab)
+
+    plt.draw()
+
+
+def tuple_to_slice(slices):
+    subscripts = []
+    for val in slices:
+        start = val[0]
+        end = val[1]
+        if end is not None:
+            end = end + 1
+        subscripts.append(slice(start, end, 1))
+    subscripts = tuple(subscripts)
+    return subscripts
+
+
+def subarray(base, slices):
+    if (len(slices) != len(base.dims)):
+        print("Must specify a range in all dimensions")
+        return None
+    dims = []
+    # Construct the lengths of the subarray
+    for x in range(0, len(slices)):
+        begin = slices[x][0]
+        end = slices[x][1]
+        if begin is None:
+            begin = 0
+        if end is None:
+            end = base.dims[x]
+        if (end-begin != 0):
+            dims.append(end-begin+1)
+
+    subscripts = tuple_to_slice(slices)
+    base.data = np.squeeze(base.data[subscripts])
+    base.dims = tuple(dims)
+
+
+def list_variables(data):
+    dct = data.__dict__
+    for key in sorted(dct):
+        try:
+            val = dct[key]
+            print('{} {} {}'.format(key, type(val),
+                  np.array2string(np.array(val.dims), separator=', ')))
+        except:
+            pass
+
+
+def escape_latex(string):
+    return string.replace('%', '\%')
+
+
+pi = 3.141592653589793238462643383279503
+q0 = 1.602176565e-19
+m0 = 9.10938291e-31
+c = 2.99792458e8
+kb = 1.3806488e-23
+mu0 = pi * 4e-7
+epsilon0 = 1.0 / mu0 / c**2
+h_planck = 6.62606957e-34
+h_bar = h_planck / 2.0 / pi