sdfr 1.1.0__py3-none-win32.whl → 1.2.1__py3-none-win32.whl

sdfr/sdf_helper.py

@@ -1,11 +1,16 @@
 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
+    from matplotlib.offsetbox import (
+        HPacker,
+        VPacker,
+        TextArea,
+        AnchoredOffsetbox,
+    )
 except:
     pass
 try:
@@ -15,8 +20,10 @@ except:
         # Workaround for broken macOS installation
         import sys
         import matplotlib
-        sys.path.append(os.path.join(matplotlib.__path__[0],
-                                     '..', 'mpl_toolkits'))
+
+        sys.path.append(
+            os.path.join(matplotlib.__path__[0], "..", "mpl_toolkits")
+        )
         from axes_grid1 import make_axes_locatable
     except:
         pass
@@ -26,13 +33,15 @@ except:
     import __builtin__ as builtins
 
 try:
-    import sdf
+    import sdfr as sdf
+
     got_sdf = True
 except ImportError:
     got_sdf = False
 
 try:
     from matplotlib.pyplot import *  # NOQA
+
     got_mpl = True
 except ImportError:
     got_mpl = False
@@ -47,10 +56,10 @@ global old_mtime, wkdir, verbose, fig, im, cbar
 
 verbose = True
 
-wkdir = 'Data'
+wkdir = "Data"
 old_mtime = 0
 old_size = 0
-old_filename = ''
+old_filename = ""
 cached = False
 fig = None
 im = None
@@ -59,7 +68,7 @@ mult_x = 1
 mult_y = 1
 
 
-class ic_type():
+class ic_type:
     NEW = 1
     RESTART = 2
     SOD = 3
@@ -74,83 +83,83 @@ class ic_type():
 def get_si_prefix(scale, full_units=False):
     scale = abs(scale)
     mult = 1
-    sym = ''
+    sym = ""
 
     if scale < 1e-24:
         full_units = True
     elif scale < 1e-21:
         # yocto
         mult = 1e24
-        sym = 'y'
+        sym = "y"
     elif scale < 1e-19:
         # zepto
         mult = 1e21
-        sym = 'z'
+        sym = "z"
     elif scale < 1e-16:
         # atto
         mult = 1e18
-        sym = 'a'
+        sym = "a"
     elif scale < 1e-13:
         # femto
         mult = 1e15
-        sym = 'f'
+        sym = "f"
     elif scale < 1e-10:
         # pico
         mult = 1e12
-        sym = 'p'
+        sym = "p"
     elif scale < 1e-7:
         # nano
         mult = 1e9
-        sym = 'n'
+        sym = "n"
     elif scale < 1e-4:
         # micro
         mult = 1e6
-        sym = '{\mu}'
+        sym = r"{\mu}"
     elif scale < 1e-1:
         # milli
         mult = 1e3
-        sym = 'm'
+        sym = "m"
     elif scale >= 1e27:
         full_units = True
     elif scale >= 1e24:
         # yotta
         mult = 1e-24
-        sym = 'Y'
+        sym = "Y"
     elif scale >= 1e21:
         # zetta
         mult = 1e-21
-        sym = 'Z'
+        sym = "Z"
     elif scale >= 1e18:
         # exa
         mult = 1e-18
-        sym = 'E'
+        sym = "E"
     elif scale >= 1e15:
         # peta
         mult = 1e-15
-        sym = 'P'
+        sym = "P"
     elif scale >= 1e12:
         # tera
         mult = 1e-12
-        sym = 'T'
+        sym = "T"
     elif scale >= 1e9:
         # giga
         mult = 1e-9
-        sym = 'G'
+        sym = "G"
     elif scale >= 1e6:
         # mega
         mult = 1e-6
-        sym = 'M'
+        sym = "M"
     elif scale >= 1e3:
         # kilo
         mult = 1e-3
-        sym = 'k'
+        sym = "k"
 
     if full_units:
         scale = scale * mult
         if scale <= 0:
             pwr = 0
         else:
-            pwr = (-np.floor(np.log10(scale)))
+            pwr = -np.floor(np.log10(scale))
         mult = mult * np.power(10.0, pwr)
         if np.rint(pwr) != 0:
             sym = "(10^{%.0f})" % (-pwr) + sym
@@ -162,60 +171,75 @@ def get_title(var=None, geom=False, extra_info=True):
     global data
 
     if var is not None:
-        if hasattr(var, 'blocklist'):
+        if hasattr(var, "blocklist"):
             data = var.blocklist
 
-    t = data.Header['time']
+    t = data.Header["time"]
     mult, sym = get_si_prefix(t)
 
-    stitle = r'$t = {:.3}{}s$'.format(mult * t, sym)
+    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'
+    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 (
+                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'
+        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'
+                stitle += r", Cartesian"
 
-            if hasattr(data.Logical_flags, 'polar_grid') \
-                    and data.Logical_flags.polar_grid:
-                stitle += r' Polar'
+            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'):
+    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
@@ -225,24 +249,25 @@ def get_default_iso(data):
 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
+    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:
@@ -250,17 +275,20 @@ def get_file_list(wkd=None, base=None, block=None):
             wkdir = wkd
         elif os.path.exists(wkd):
             base = wkd
-        elif isinstance(wkd, sdf.BlockList) \
-                or isinstance(wkd, sdf.Block) or type(wkd) is dict:
+        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'):
+        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 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]):
@@ -283,45 +311,48 @@ def get_file_list(wkd=None, base=None, block=None):
 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
+    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 file_list is not None and not isinstance(file_list, 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:
+        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'):
+        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 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']
+                return data.Header["jobid1"]
         except:
             pass
 
@@ -332,7 +363,7 @@ def get_job_id(file_list=None, base=None, block=None):
                 data = sdf.read(f, mmap=0)
                 if len(data.__dict__) < 2:
                     continue
-                return data.Header['jobid1']
+                return data.Header["jobid1"]
             except:
                 pass
 
@@ -342,26 +373,26 @@ def get_job_id(file_list=None, base=None, block=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
+    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:
@@ -369,17 +400,20 @@ def get_files(wkd=None, base=None, block=None, varname=None, fast=True):
             pass
         elif os.path.exists(wkd):
             base = wkd
-        elif isinstance(wkd, sdf.BlockList) \
-                or isinstance(wkd, sdf.Block) or type(wkd) is dict:
+        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'):
+        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 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))
@@ -393,7 +427,7 @@ def get_files(wkd=None, base=None, block=None, varname=None, fast=True):
             data = sdf.read(f, mmap=0, dict=True)
             if len(data) < 2:
                 continue
-            file_job_id = data['Header']['jobid1']
+            file_job_id = data["Header"]["jobid1"]
             if file_job_id == job_id:
                 if varname is None:
                     file_list.append(f)
@@ -407,34 +441,35 @@ def get_files(wkd=None, base=None, block=None, varname=None, fast=True):
     return list(reversed(file_list))
 
 
-def get_time(time=0, first=False, last=False, wkd=None, base=None, block=None,
-             fast=True):
+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
+    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
 
@@ -462,10 +497,10 @@ def get_time(time=0, first=False, last=False, wkd=None, base=None, block=None,
         dat_tmp = sdf.read(f)
         if len(dat_tmp.__dict__) < 2:
             continue
-        if job_id != dat_tmp.Header['jobid1']:
+        if job_id != dat_tmp.Header["jobid1"]:
             continue
 
-        t = dat_tmp.Header['time']
+        t = dat_tmp.Header["time"]
         if last:
             if fast:
                 fname = f
@@ -496,34 +531,35 @@ def get_time(time=0, first=False, last=False, wkd=None, base=None, block=None,
     return data
 
 
-def get_step(step=0, first=False, last=False, wkd=None, base=None, block=None,
-             fast=True):
+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
+    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
 
@@ -551,10 +587,10 @@ def get_step(step=0, first=False, last=False, wkd=None, base=None, block=None,
         dat_tmp = sdf.read(f)
         if len(dat_tmp.__dict__) < 2:
             continue
-        if job_id != dat_tmp.Header['jobid1']:
+        if job_id != dat_tmp.Header["jobid1"]:
             continue
 
-        t = dat_tmp.Header['step']
+        t = dat_tmp.Header["step"]
         if last:
             if fast:
                 fname = f
@@ -588,21 +624,21 @@ def get_step(step=0, first=False, last=False, wkd=None, base=None, block=None,
 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
+    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)
 
@@ -639,7 +675,7 @@ def get_newest_file(wkd=None, base=None, block=None):
     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]
+        f = flist[-n - 1]
         data = sdf.read(f, mmap=0, dict=True)
         if len(data) > 1:
             return f
@@ -673,46 +709,72 @@ def plot_auto(*args, **kwargs):
     try:
         dims = args[0].dims
     except:
-        print('error: Variable cannot be auto determined. '
-              + 'Use plot1d or plot2d')
+        print(
+            "error: Variable cannot be auto determined. "
+            + "Use plot1d or plot2d"
+        )
         return
-    if (len(dims) == 1):
-        if type(args[0]) is sdf.BlockStitchedPath:
+    if len(dims) == 1:
+        if isinstance(args[0], sdf.BlockStitchedPath):
             plot_rays(*args, **kwargs)
-        elif (len(args[0].grid.dims) == 1):
+        elif isinstance(args[0], sdf.BlockStitched):
+            newargs = list(args[:])
+            for block in args[0].data:
+                newargs[0] = block
+                plot_auto(*newargs, **kwargs)
+        elif len(args[0].grid.dims) == 1:
             plot1d(*args, **kwargs)
         else:
             plot_path(*args, **kwargs)
-    elif (len(dims) == 2):
-        k = 'set_ylabel'
+    elif isinstance(args[0], sdf.BlockLagrangianMesh) and dims[1] == 1:
+        plot_path(*args, **kwargs)
+    elif isinstance(args[0], sdf.BlockStitchedPath):
+        plot_rays(*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'
+    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')
+        print("error: Unable to plot variables of this dimensionality")
 
 
 def oplot_auto(*args, **kwargs):
-    kwargs['set_ylabel'] = False
-    kwargs['hold'] = True
+    kwargs["set_ylabel"] = False
+    kwargs["hold"] = True
     plot_auto(*args, **kwargs)
 
 
 def oplot1d(*args, **kwargs):
-    kwargs['set_ylabel'] = False
-    kwargs['hold'] = True
+    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):
+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
 
@@ -739,7 +801,7 @@ def plot1d(var, fmt=None, xdir=None, idx=-1, xscale=0, yscale=0, scale=0,
         figure = subplot.figure
         if not hold:
             subplot.clear()
-            if hasattr(subplot, 'colorbar'):
+            if hasattr(subplot, "colorbar"):
                 subplot.colorbar.remove()
 
     if var.dims[0] == var.grid.dims[0]:
@@ -812,92 +874,116 @@ def plot1d(var, fmt=None, xdir=None, idx=-1, xscale=0, yscale=0, scale=0,
     else:
         subplot.plot(X, Y, **kwargs)
 
-    subplot.set_xlabel(grid.labels[xdir] + ' $('
-                       + escape_latex(sym_x + grid.units[xdir]) + ')$')
+    subplot.set_xlabel(
+        grid.labels[xdir]
+        + " $("
+        + escape_latex(sym_x + grid.units[xdir])
+        + ")$"
+    )
     if set_ylabel:
-        subplot.set_ylabel(var.name + ' $('
-                           + escape_latex(sym_y + var.units) + ')$')
+        subplot.set_ylabel(
+            var.name + " $(" + escape_latex(sym_y + var.units) + ")$"
+        )
 
     if title:
-        subplot.set_title(get_title(var), fontsize='large', y=1.03)
+        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):
+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
+    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__:
+    if "norm_values" not in plot_path.__dict__:
         plot_path.norm_values = None
         plot_path.axis = None
 
@@ -915,7 +1001,12 @@ def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
         figure.canvas.draw()
         return
 
-    if len(var.dims) != 1:
+    isvar = True
+    if isinstance(var, sdf.BlockLagrangianMesh):
+        isvar = False
+        add_cbar = False
+
+    if isvar and len(var.dims) != 1:
         print("error: Not a 1d dataset")
         return
 
@@ -941,18 +1032,21 @@ def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
         figure = subplot.figure
         if not hold:
             subplot.clear()
-            if hasattr(subplot, 'colorbar'):
+            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]:
+    # if var.dims[0] == var.grid.dims[0]:
     #    grid = var.grid
-    #else:
+    # else:
     #    grid = var.grid_mid
-    grid = var.grid
+    if isvar:
+        grid = var.grid
+    else:
+        grid = var
 
     test_dir = False
     if xdir is None:
@@ -1008,73 +1102,85 @@ def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
 
     X = mult_x * X
     Y = mult_y * Y
-    c = var.data
+    if isvar:
+        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]
+            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])
+                X = np.copy(X[: i + 1])
+                Y = np.copy(Y[: i + 1])
+                if isvar:
+                    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()
+    if isvar:
+        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()
+            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)
+            plot_path.norm_values = plt.Normalize(vmin, vmax)
 
     kk = {}
-    k = 'lw'
+    k = "lw"
     if k in kwargs:
         kk[k] = kwargs[k]
-    k = 'linewidth'
+    k = "linewidth"
     if k in kwargs:
         kk[k] = kwargs[k]
     lc = LineCollection(segments, norm=plot_path.norm_values, **kk)
-    lc.set_array(c)
+    if isvar:
+        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] + ' $('
-                           + escape_latex(sym_y + grid.units[ydir]) + ')$')
+        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:
+            if isinstance(title, str):
                 title_label = title
             else:
                 title_label = get_title(var, extra_info=False)
-            subplot.set_title(title_label, fontsize='large', y=1.03)
+            subplot.set_title(title_label, fontsize="large", y=1.03)
 
-        subplot.axis('tight')
+        subplot.axis("tight")
         if iso:
-            subplot.axis('image')
+            subplot.axis("image")
 
         plot_path.axis = subplot.axis()
         if update:
@@ -1087,14 +1193,13 @@ def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
         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')
+            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)
+            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)
@@ -1104,15 +1209,15 @@ def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
         subplot.colorbar = cax
         plt.sca(ax)
         if cbar_label:
-            if type(cbar_label) is str:
+            if isinstance(cbar_label, str):
                 var_label = cbar_label
             else:
-                var_label = var.name + ' $(' + escape_latex(var.units) + ')$'
+                var_label = var.name + " $(" + escape_latex(var.units) + ")$"
             if cbar_top:
-                cbar.set_label(var_label, fontsize='large')
-                cax.xaxis.set_label_position('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)
+                cbar.set_label(var_label, fontsize="large", x=1.2)
 
     if not hold and svar is not None:
         lim = np.array(svar.grid.extents)
@@ -1153,83 +1258,86 @@ def plot_path(var, xdir=None, ydir=None, xscale=0, yscale=0, scale=0,
 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
+    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'
+    l = "ray_start"
     if l in kwargs:
         ray_start = kwargs[l]
 
     ray_stop = 1e9
-    l = 'ray_stop'
+    l = "ray_stop"
     if l in kwargs:
         ray_stop = kwargs[l]
 
-    if type(var) is sdf.BlockStitchedPath:
+    if isinstance(var, sdf.BlockStitchedPath):
         v = var.data[0]
-        l = '_label'
+        l = "_label"
         if l not in kwargs:
             kwargs[l] = var.name
 
-        if type(v) is sdf.BlockStitchedPath:
+        if isinstance(v, sdf.BlockStitchedPath):
             for v in var.data:
                 plot_rays(v, skip=skip, rays=rays, **kwargs)
-                kwargs['hold'] = True
+                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
+        if not isinstance(v, sdf.BlockLagrangianMesh):
+            k = "cbar_label"
+            if k not in kwargs or (
+                kwargs[k] and not isinstance(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:
+            if iray % skip == 0:
                 plot_auto(v, update=False, **kwargs)
-                kwargs['hold'] = True
+                kwargs["hold"] = True
 
         plot_auto(var.data[0], axis_only=True, **kwargs)
-        kwargs['hold'] = True
+        kwargs["hold"] = True
 
         return
 
-    split_name = var.name.split('/')
-    start = split_name[0] + '_'
-    end = '_' + split_name[-1]
+    split_name = var.name.split("/")
+    start = split_name[0] + "_"
+    end = "_" + split_name[-1]
     data = var.blocklist.__dict__
 
-    k0 = 'vmin'
-    k1 = 'vmax'
-    k = 'vrange'
+    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()
@@ -1241,7 +1349,7 @@ def plot_rays(var, skip=1, rays=None, **kwargs):
                     continue
                 if iray > ray_stop:
                     break
-                if iray%skip == 0:
+                if iray % skip == 0:
                     vmin = min(vmin, data[k].data.min())
                     vmax = max(vmax, data[k].data.max())
         if k0 not in kwargs:
@@ -1249,11 +1357,15 @@ def plot_rays(var, skip=1, rays=None, **kwargs):
         if k1 not in kwargs:
             kwargs[k1] = vmax
 
-    k = 'cbar_label'
-    if k not in kwargs or (kwargs[k] and type(kwargs[k]) != str):
+    k = "cbar_label"
+    if k not in kwargs or (kwargs[k] and not isinstance(kwargs[k], str)):
         # Remove /Ray[1-9]+ from the name
-        kwargs[k] = '/'.join([split_name[0]] + split_name[2:]) \
-                     + ' $(' + escape_latex(var.units) + ')$'
+        kwargs[k] = (
+            "/".join([split_name[0]] + split_name[2:])
+            + " $("
+            + escape_latex(var.units)
+            + ")$"
+        )
 
     iray = -1
     for k in data.keys():
@@ -1263,25 +1375,50 @@ def plot_rays(var, skip=1, rays=None, **kwargs):
                 continue
             if iray > ray_stop:
                 break
-            if iray%skip == 0:
+            if iray % skip == 0:
                 plot_auto(data[k], hold=True, update=False, **kwargs)
-                kwargs['hold'] = True
+                kwargs["hold"] = True
 
     plot_auto(var, axis_only=True, **kwargs)
-    kwargs['hold'] = True
+    kwargs["hold"] = True
 
 
 def oplot2d(*args, **kwargs):
-    kwargs['hold'] = True
+    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):
+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
 
@@ -1302,15 +1439,16 @@ def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
         v0 = np.min(array) - norm
         v1 = np.max(array) - norm
 
-        if abs(v0/v1) > 1:
+        if abs(v0 / v1) > 1:
             low = 0
-            high = 0.5 * (1 - v1/v0)
+            high = 0.5 * (1 - v1 / v0)
         else:
-            low = 0.5 * (1 + v0/v1)
+            low = 0.5 * (1 + v0 / v1)
             high = 1.0
 
         cmap = mpl.colors.LinearSegmentedColormap.from_list(
-            'tr', cmap(np.linspace(low, high, 256)))
+            "tr", cmap(np.linspace(low, high, 256))
+        )
 
     if subplot is None:
         if figure is None:
@@ -1331,7 +1469,7 @@ def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
         figure = subplot.figure
         if not hold:
             subplot.clear()
-            if hasattr(subplot, 'colorbar'):
+            if hasattr(subplot, "colorbar"):
                 subplot.colorbar.remove()
 
     if iso is None:
@@ -1411,23 +1549,32 @@ def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
         ext[i1] = ext[i2]
         ext[i2] = e
         ext = [ext[i0], ext[i1], ext[i2], ext[i3]]
-        k = 'interpolation'
+        k = "interpolation"
         if k not in kwargs:
-            kwargs[k] = 'none'
+            kwargs[k] = "none"
         if vrange is None:
-            im = subplot.imshow(array.T, origin='lower', extent=ext, cmap=cmap,
-                                **kwargs)
+            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)
+            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)
+            im = subplot.pcolormesh(
+                X, Y, array, cmap=cmap, vmin=vrange[0], vmax=vrange[1], **kwargs
+            )
 
     subplot.set_xlabel(xlabel)
     subplot.set_ylabel(ylabel)
@@ -1437,17 +1584,17 @@ def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
         if add_cbar and cbar_label:
             title_text = get_title()
         else:
-            title_text = var_label + ', ' + get_title()
+            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.set_title(title_text, fontsize="large", y=1.03)
 
-    subplot.axis('tight')
+    subplot.axis("tight")
     if iso:
-        subplot.axis('image')
+        subplot.axis("image")
 
     if not hold and add_cbar:
         ax = subplot.axes
@@ -1455,14 +1602,13 @@ def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
         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')
+            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)
+            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)
@@ -1472,33 +1618,53 @@ def plot2d_array(array, x, y, extents, var_label, xlabel, ylabel, idx=None,
         subplot.colorbar = cax
         plt.sca(ax)
         if cbar_label:
-            if type(cbar_label) is str:
+            if isinstance(cbar_label, str):
                 var_label = cbar_label
             if cbar_top:
-                cbar.set_label(var_label, fontsize='large')
-                cax.xaxis.set_label_position('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)
+                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):
+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:
+    if isinstance(irange, list) or isinstance(irange, tuple):
         si = slice(*irange)
     else:
         si = slice(None, irange)
 
-    if type(jrange) is list or type(jrange) is tuple:
+    if isinstance(jrange, list) or isinstance(jrange, tuple):
         sj = slice(*jrange)
     else:
         sj = slice(None, jrange)
@@ -1589,23 +1755,51 @@ def plot2d(var, iso=None, fast=None, title=True, full=True, vrange=None,
     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'):
+    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)
+    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):
@@ -1616,8 +1810,17 @@ def plot2d_update(var):
     fig.canvas.draw()
 
 
-def plot_levels(var, r0=None, r1=None, nl=10, iso=None, out=False,
-                title=True, levels=True, **kwargs):
+def plot_levels(
+    var,
+    r0=None,
+    r1=None,
+    nl=10,
+    iso=None,
+    out=False,
+    title=True,
+    levels=True,
+    **kwargs
+):
     global data
 
     try:
@@ -1626,7 +1829,7 @@ def plot_levels(var, r0=None, r1=None, nl=10, iso=None, out=False,
         pass
 
     if iso is None:
-        if hasattr(var, 'blocklist'):
+        if hasattr(var, "blocklist"):
             data = var.blocklist
         iso = get_default_iso(data)
 
@@ -1656,13 +1859,13 @@ def plot_levels(var, r0=None, r1=None, nl=10, iso=None, out=False,
     else:
         ax = plt.gca()
 
-    k = 'colors'
+    k = "colors"
     if k not in kwargs:
-        kwargs[k] = 'k'
-    k = 'linewidths'
+        kwargs[k] = "k"
+    k = "linewidths"
     if k not in kwargs:
         kwargs[k] = 0.5
-    k = 'levels'
+    k = "levels"
     if k not in kwargs:
         kwargs[k] = rl
 
@@ -1670,57 +1873,73 @@ def plot_levels(var, r0=None, r1=None, nl=10, iso=None, out=False,
 
     if levels:
         fmt = {}
-        for l, i in zip(cs.levels, range(1, len(cs.levels)+1)):
+        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)))):
+        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'))
+        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'))
+        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)
+            t = AnchoredOffsetbox(
+                loc=2,
+                child=t,
+                pad=0.4,
+                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 = AnchoredOffsetbox(
+                loc=1,
+                child=t,
+                pad=0.4,
+                bbox_to_anchor=(1, 1),
+                frameon=True,
+                bbox_transform=ax.transAxes,
+                borderpad=0.4,
+            )
         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] + ' $('
-                  + escape_latex(var.grid.units[1]) + ')$')
+    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)
+            plt.suptitle(get_title(var), fontsize="large", y=0.92)
         else:
-            plt.title(get_title(var), fontsize='large', y=1.03)
+            plt.title(get_title(var), fontsize="large", y=1.03)
 
-    plt.axis('tight')
+    plt.axis("tight")
     if iso:
-        plt.axis('image')
+        plt.axis("image")
 
     plt.draw()
     if out:
@@ -1737,8 +1956,17 @@ def plot_levels(var, r0=None, r1=None, nl=10, iso=None, out=False,
 
 
 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)
+    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):
@@ -1767,13 +1995,16 @@ def getdata(fname, wkd=None, verbose=True, squeeze=False):
             filename = "./" + fname
         try:
             st = os.stat(filename)
-            wkdir = '.'
+            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 (
+        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)
@@ -1792,7 +2023,7 @@ def getdata(fname, wkd=None, verbose=True, squeeze=False):
             try:
                 dims = []
                 for element in value.dims:
-                    dims.append([0, element-1])
+                    dims.append([0, element - 1])
                 subarray(value, dims)
             except:
                 pass
@@ -1805,8 +2036,8 @@ def getdata(fname, wkd=None, verbose=True, squeeze=False):
             sdfdict[key] = value
 
     fdict = {}
-    table = {'time': 't'}
-    k = 'Header'
+    table = {"time": "t"}
+    k = "Header"
     if k in sdfdict:
         h = sdfdict[k]
         k = list(table.keys())[0]
@@ -1814,44 +2045,46 @@ def getdata(fname, wkd=None, verbose=True, squeeze=False):
             key = table[k]
             var = h[k]
             if verbose:
-                print(key + str(np.shape(var)) + ' = ' + k)
+                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'}
+    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:
+    if "Vr" in sdfdict:
         rz = True
 
     if rz:
-        table['Vz'] = 'vy'
-        table['Bz'] = 'by'
+        table["Vz"] = "vy"
+        table["Bz"] = "by"
 
     inv_table = {}
     for k, v in table.items():
@@ -1867,68 +2100,69 @@ def getdata(fname, wkd=None, verbose=True, squeeze=False):
                 var = sdfdict[k]
             dims = str(tuple(int(i) for i in sdfdict[k].dims))
             if verbose:
-                print(key + dims + ' = ' + k)
+                print(key + dims + " = " + k)
             fdict[key] = var
             globals()[key] = var
             builtins.__dict__[key] = var
 
-    k = 'grid'
+    k = "grid"
     if k in sdfdict:
         vargrid = sdfdict[k]
         grid = vargrid
-        keys = 'x', 'y', 'z'
+        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)
+                print(key + dims + " = " + k)
             fdict[key] = var
             globals()[key] = var
             builtins.__dict__[key] = var
 
-    k = 'grid_mid'
+    k = "grid_mid"
     if k in sdfdict:
         vargrid = sdfdict[k]
         grid_mid = vargrid
-        keys = 'xc', 'yc', 'zc'
+        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)
+                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:
+        if not isinstance(value, sdf.BlockPointVariable) and not isinstance(
+            value, sdf.BlockPointMesh
+        ):
             continue
-        key = re.sub(r'[^a-z0-9]', '_', value.id.lower())
+        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 isinstance(value, sdf.BlockPointVariable):
             if verbose:
-                print(key + dims + ' = ' + value.name)
+                print(key + dims + " = " + value.name)
             fdict[key] = var
             globals()[key] = var
             builtins.__dict__[key] = var
         else:
             vargrid = value
             grid = vargrid
-            keys = 'x', 'y', 'z'
+            keys = "x", "y", "z"
             for n in range(np.size(value.dims)):
-                gkey = keys[n] + '_' + key
+                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])
+                    print(gkey + dims + " = " + k + " " + keys[n])
                 fdict[gkey] = var
                 globals()[gkey] = var
                 builtins.__dict__[gkey] = var
@@ -1947,18 +2181,18 @@ def ogrid(skip=None, **kwargs):
         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:
+    k = "lw"
+    if k not in kwargs and "linewidth" not in kwargs:
         kwargs[k] = 0.5
-    k = 'color'
+    k = "color"
     if k not in kwargs:
-        kwargs[k] = 'k'
+        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:
+    if isinstance(fname, sdf.BlockList) or isinstance(fname, dict):
         dat = fname
     elif fname is not None:
         dat = getdata(fname, verbose=verbose)
@@ -1970,15 +2204,15 @@ def plotgrid(fname=None, iso=None, title=True):
 
     ax = plt.gca()
 
-    ax.set_xlabel(grid.labels[0] + ' $(' + escape_latex(grid.units[0]) + ')$')
-    ax.set_ylabel(grid.labels[1] + ' $(' + escape_latex(grid.units[1]) + ')$')
+    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.title(get_title(), fontsize="large", y=1.03)
 
-    plt.axis('tight')
+    plt.axis("tight")
     if iso:
-        plt.axis('image')
+        plt.axis("image")
 
     plt.draw()
 
@@ -1997,28 +2231,28 @@ def axis_offset(boxed=False):
     # 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]])
+        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 = 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_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.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)
 
@@ -2038,7 +2272,7 @@ def tuple_to_slice(slices):
 
 
 def subarray(base, slices):
-    if (len(slices) != len(base.dims)):
+    if len(slices) != len(base.dims):
         print("Must specify a range in all dimensions")
         return None
     dims = []
@@ -2050,8 +2284,8 @@ def subarray(base, slices):
             begin = 0
         if end is None:
             end = base.dims[x]
-        if (end-begin != 0):
-            dims.append(end-begin+1)
+        if end - begin != 0:
+            dims.append(end - begin + 1)
 
     subscripts = tuple_to_slice(slices)
     base.data = np.squeeze(base.data[subscripts])
@@ -2063,14 +2297,19 @@ def list_variables(data):
     for key in sorted(dct):
         try:
             val = dct[key]
-            print('{} {} {}'.format(key, type(val),
-                  np.array2string(np.array(val.dims), separator=', ')))
+            print(
+                "{} {} {}".format(
+                    key,
+                    type(val),
+                    np.array2string(np.array(val.dims), separator=", "),
+                )
+            )
         except:
             pass
 
 
 def escape_latex(string):
-    return string.replace('%', '\%')
+    return string.replace("%", r"\%")
 
 
 pi = 3.141592653589793238462643383279503