def test_magnitude():
"""function expects an array of N 3D vectors"""
# test bordercases and other arbitrary shapes
for vf in vfshapes:
array = np.random.random_sample((vf, 3))
# to include negative + larger values
newarray = (array - 0.5) * 1000
# ensure array of required shape
shape = [int(dimension) for dimension in newarray.shape]
assert shape == [vf, 3]
# compute expected result
newarraysq = newarray ** 2
exp = newarraysq.sum(1) ** 0.5
# compute actual result
act = ana.magnitude(newarray)
# ensure result is a numpy array
assert isinstance(act, np.ndarray)
# code works?
assert exp.all() == act.all()
def test_magnitude():
"""function expects an array of N 3D vectors"""
# test bordercases and other arbitrary shapes
for vf in vfshapes:
array = np.random.random_sample((vf, 3))
# to include negative + larger values
newarray = (array - 0.5) * 1000
# ensure array of required shape
shape = [int(dimension) for dimension in newarray.shape]
assert shape == [vf, 3]
# compute expected result
newarraysq = newarray**2
exp = newarraysq.sum(1)**0.5
# compute actual result
act = ana.magnitude(newarray)
# ensure result is a numpy array
assert isinstance(act, np.ndarray)
# code works?
assert exp.all() == act.all()
def ovf2vtk_main():
start_time = time.time()
banner_doc = 70 * "-" + \
"\novf2vtk --- converting ovf files to vtk files" + "\n" + \
"Hans Fangohr, Richard Boardman, University of Southampton\n"""\
+ 70 * "-"
# extracts command line arguments
# If any of the arguments given appear in the command line, a list of...
# ...these args and corresponding values (if any) is returned -> ('args').
# Any arguments that dont dont match the given ones are retuned in a...
# ...separate list -> ('params')
# Note (fangohr 30/12/2006 20:52): the use of getopt is historic,
args, params = getopt.getopt(sys.argv[1:], 'Vvhbta:', [
"verbose", "help", "add=", "binary", "text", "ascii",
"surface-effects", "version", "datascale=", "posscale="
])
# default value
surfaceEffects = False
datascale = 0.0 # 0.0 has special meaning -- see help text
posscale = 0.0 # 0.0 has special meaning -- see help text
# provide data from getopt.getopt (args) in form of dictionary
options = {}
for item in args:
if item[1] == '':
options[item[0]] = None
else:
options[item[0]] = item[1]
keys = options.keys()
# set system responses to arguments given
if "--surface-effects" in keys:
surfaceEffects = True
if "--posscale" in keys:
posscale = float(options["--posscale"])
if "--datascale" in keys:
datascale = float(options["--datascale"])
if "-v" in keys or "--verbose" in keys:
print("running in verbose mode")
debug = True
else:
debug = False
if "-h" in keys or "--help" in keys:
print(__doc__)
sys.exit(0)
if "-V" in keys or "--version" in keys:
print("This is version {:s}.".format(version))
sys.exit(0)
if len(params) == 0:
print(__doc__)
print("ERROR: An input file (and an output file need to be "
"specified).")
sys.exit(1)
else:
infile = params[0]
if len(params) == 1:
print(__doc__)
print("ERROR: An input file AND an output file need to be specified.")
print("specify output file")
sys.exit(1)
else:
outfile = params[1]
# okay: it seems the essential parameters are given.
# Let's check for others:
print(banner_doc)
if debug:
print("infile = {}".format(infile))
print("outfile = {}".format(outfile))
print("args = {}".format(args))
print("options = {}".format(options))
print("datascale = {}".format(datascale))
print("posscale = {}".format(posscale))
# read data from infile
vf = omf.read_structured_omf_file(infile, debug)
# compute magnitude for all cells
Ms = ana.magnitude(vf)
# Compute number of cells with non-zero Ms (rpb01r)
Ms_num_of_nonzeros = Numeric.sum(Numeric.not_equal(Ms, 0.0))
print("({:5.2f}% of {:d} cells filled)".format(
100.0 * Ms_num_of_nonzeros / len(Ms), len(Ms)))
# scale magnetisation data as required:
if datascale == 0.0:
scale = max(Ms)
print("Will scale data down by {:f}".format(scale))
else:
scale = datascale
# normalise vectorfield by scale
vf = Numeric.divide(vf, scale)
# read metadata in data file
ovf_run = omf.analyze(infile)
datatitle = ovf_run["Title:"] + "/{:g}".format(scale)
#
# need x, y and z vectors for vtk format
#
# taking actual spacings for dx, dy and dz results generally in
# poor visualisation results (in particular for thin films, one
# would like to have some magnification in z-direction). Also:vtk
# is not happy with positions on the 10e-9 scale, so one better
# scales this to something closer to unity.
# extract dimensions from file
dimensions = (int(ovf_run["xnodes:"]), int(ovf_run["ynodes:"]),
int(ovf_run["znodes:"]))
# scale data by given factor
if posscale != 0.0:
# find range between max and min values of components
xrange = abs(float(ovf_run["xmax:"]) - float(ovf_run["xmin:"]))
yrange = abs(float(ovf_run["ymax:"]) - float(ovf_run["ymin:"]))
zrange = abs(float(ovf_run["zmax:"]) - float(ovf_run["zmin:"]))
# define no. of x,y,z nodes
xnodes = float(ovf_run["xnodes:"])
ynodes = float(ovf_run["ynodes:"])
znodes = float(ovf_run["znodes:"])
# define stepsizes
xstepsize = float(ovf_run["xstepsize:"])
ystepsize = float(ovf_run["ystepsize:"])
zstepsize = float(ovf_run["zstepsize:"])
# define bases
xbase = float(ovf_run["xbase:"])
ybase = float(ovf_run["ybase:"])
zbase = float(ovf_run["zbase:"])
# find dx, dy, dz in SI units:
dx = xrange / xnodes
dy = yrange / ynodes
dz = zrange / znodes
# find scale factor that OOMMF uses for xstepsize and xnodes,
# etc. (Don't know how to get this directly.)
xscale = dx * xstepsize
yscale = dy * ystepsize
zscale = dz * zstepsize
# extract x, y and z positions from ovf file.
xbasevector = [None] * dimensions[0] # create empty vector
for i in range(dimensions[0]):
# data is stored for 'centre' of each cuboid, therefore (i+0.5)
xbasevector[i] = xbase + (i + 0.5) * xstepsize * xscale
ybasevector = [None] * dimensions[1]
for i in range(dimensions[1]):
ybasevector[i] = ybase + (i + 0.5) * ystepsize * yscale
zbasevector = [None] * dimensions[2]
for i in range(dimensions[2]):
zbasevector[i] = zbase + (i + 0.5) * zstepsize * zscale
# finally, convert list to numeric (need to have this consistent)
xbasevector = Numeric.array(xbasevector) / float(posscale)
ybasevector = Numeric.array(ybasevector) / float(posscale)
zbasevector = Numeric.array(zbasevector) / float(posscale)
else:
# posscale == 0.0
# this generally looks better:
xbasevector = Numeric.arange(dimensions[0])
ybasevector = Numeric.arange(dimensions[1])
zbasevector = Numeric.arange(dimensions[2])
#
# write ascii or binary vtk-file (default is binary)
#
vtk_data = 'binary'
if '--ascii' in keys or '-t' in keys or '--text' in keys:
vtk_data = 'ascii'
if debug:
print("switching to ascii vtk-data")
if '--binary' in keys or '-b' in keys:
vtk_data = 'binary'
if debug:
print("switching to binary vtk-data")
#
# and now open vtk-file
#
vtkfilecomment = "Output from ovf2vtk (version {:s}), {:s}, infile={:s}. "\
.format(version, time.asctime(), infile)
vtkfilecomment += "Calling command line was '{:s}' executed in '{:s}'"\
.format(" ".join(sys.argv), os.getcwd())
# define inputs
RecGrid = pyvtk.RectilinearGrid(xbasevector.tolist(), ybasevector.tolist(),
zbasevector.tolist())
PData = pyvtk.PointData(pyvtk.Vectors(vf.tolist(), datatitle))
# define vtk file.
vtk = pyvtk.VtkData(RecGrid, vtkfilecomment, PData, format=vtk_data)
# now compute all the additional data such as angles, etc
# check whether we should do all
keys = map(lambda x: x[1], args)
if "all" in keys:
args = []
for add_arg in add_features:
args.append(("--add", add_arg))
# when ovf2vtk was re-written using Numeric, I had to group
# certain operations to make them fast. Now some switches are
# unneccessary. (fangohr 25/08/2003 01:35)
# To avoid executing the
# same code again, we remember what we have computed already:
done_angles = 0
done_comp = 0
for arg in args:
if arg[0] == "-a" or arg[0] == "--add":
print("working on {}".format(arg))
data = []
lookup_table = 'default'
# compute observables that need more than one field value
# i.e. div, rot
if arg[1][0:6] == "divrot": # rotation = vorticity, curl
(div, rot, rotx, roty, rotz, rotmag) = \
ana.divergence_and_curl(vf, surfaceEffects, ovf_run)
# change order of observables for upcoming loop
observables = (rotx, roty, rotz, rotmag, rot, div)
comments = [
"curl, x-comp", "curl, y-comp", "curl, z-comp",
"curl, magnitude", "curl", "divergence"
]
# append data to vtk file
for obs, comment in zip(observables, comments):
# for rotx, roty, rotz, rotmag, div
if comment != "curl":
vtk.point_data.append(
pyvtk.Scalars(obs.tolist(), comment, lookup_table))
# for rot
else:
vtk.point_data.append(
pyvtk.Vectors(obs.tolist(), comment))
# components
elif arg[1] in ["Mx", "My", "Mz", "Ms"]:
if done_comp == 0:
done_comp = 1
comments = "x-component", "y-component", "z-component"
for data, comment in zip(ana.components(vf), comments):
vtk.point_data.append(
pyvtk.Scalars(data.tolist(), comment,
lookup_table))
# magnitude of magnitisation
Mmag = ana.magnitude(vf)
vtk.point_data.append(
pyvtk.Scalars(Mmag.tolist(), "Magnitude",
lookup_table))
elif arg[1] in ["xy", "xz", "yz"]:
if done_angles == 0:
done_angles = 1
# in-plane angles
comments = ("xy in-plane angle", "yz in-plane angle",
"xz in-plane angle")
for data, comment in zip(ana.plane_angles(vf), comments):
vtk.point_data.append(
pyvtk.Scalars(data.tolist(), comment,
lookup_table))
else:
print("only xy, xz, Mx, My, Mz, divergence, Ms, or 'all' \
allowed after -a or --add")
print("Current choice is {}".format(arg))
print(__doc__)
sys.exit(1)
#
# eventually, write the file
#
print("saving file ({:s})".format(outfile))
vtk.tofile(outfile, format=vtk_data)
print("finished conversion (execution time {:5.3s} seconds)".format(
str(time.time() - start_time)))
def ovf2vtk_main():
start_time = time.time()
banner_doc = 70 * "-" + \
"\novf2vtk --- converting ovf files to vtk files" + "\n" + \
"Hans Fangohr, Richard Boardman, University of Southampton\n"""\
+ 70 * "-"
# extract command line arguments
additions, params = getopt.getopt(sys.argv[1:], 'Vvhbta:',
["verbose", "help", "add=", "binary",
"text", "ascii", "surface-effects",
"version", "datascale=", "posscale="])
# Note (fangohr 30/12/2006 20:52): the use of getopt is historic,
# and so is the use of the name 'additions'.
# default value
surfaceEffects = False
datascale = 0.0 # 0.0 has special meaning -- see help text
posscale = 0.0 # 0.0 has special meaning -- see help text
# provide data from getopt.getopt (additions) in form of hash table
options = {}
for item in additions:
if item[1] == '':
options[item[0]] = None
else:
options[item[0]] = item[1]
keys = options.keys()
if "--surface-effects" in keys:
surfaceEffects = True
if "--posscale" in keys:
posscale = float(options["--posscale"])
if "--datascale" in keys:
datascale = float(options["--datascale"])
if "-v" in keys or "--verbose" in keys:
print "running in verbose mode"
debug = True
else:
debug = False
if "-h" in keys or "--help" in keys:
print __doc__
sys.exit(0)
if "-V" in keys or "--version" in keys:
print "This is version {:s}.".format(ovf2vtk.__version__)
sys.exit(0)
if len(params) == 0:
print __doc__
print "ERROR: An input file (and an output file need to be specified)."
sys.exit(1)
else:
infile = params[0]
if len(params) == 1:
print __doc__
print "ERROR: An input file AND an output file need to be specified."
print "specify output file"
sys.exit(1)
else:
outfile = params[1]
# okay: it seems the essential parameters are given.
# Let's check for others:
print banner_doc
if debug:
print "infile = ", infile
print "outfile = ", outfile
print "additions= ", additions
print "options = ", options
print "datascale=", datascale
print "posscale=", posscale
# read data from infile
vf = read_structured_omf_file(infile, debug)
# compute magnitude for all cells
Ms = magnitude(vf)
# Compute number of cells with non-zero Ms (rpb01r)
Ms_num_of_nonzeros = Numeric.sum(Numeric.not_equal(Ms, 0.0))
print "({:5.2f}% of {:d} cells filled)"\
.format(100.0*Ms_num_of_nonzeros/len(Ms), len(Ms))
# read metadata in data file
ovf_run = analyze(infile)
# scale magnetisation data as required:
if datascale == 0.0:
scale = max(Ms)
print "Will scale data down by {:f}".format(scale)
else:
scale = datascale
vf = Numeric.divide(vf, scale)
datatitle = ovf_run["Title:"]+"/{:g}".format(scale)
#
# need x, y and z vectors for vtk format
#
# taking actual spacings for dx, dy and dz results generally in
# poor visualisation results (in particular for thin films, one
# would like to have some magnification in z-direction). Also:vtk
# is not happy with positions on the 10e-9 scale, so one better
# scales this to something closer to unity.
# extract dimensions from file
dimensions = (int(ovf_run["xnodes:"]),
int(ovf_run["ynodes:"]),
int(ovf_run["znodes:"]))
if posscale != 0.0: # scale data by given factor
# find dx, dy, dz in SI units:
Lx = abs(float(ovf_run["xmax:"])-float(ovf_run["xmin:"]))
Ly = abs(float(ovf_run["ymax:"])-float(ovf_run["ymin:"]))
Lz = abs(float(ovf_run["zmax:"])-float(ovf_run["zmin:"]))
dx = Lx / float(ovf_run["xnodes:"])
dy = Ly / float(ovf_run["ynodes:"])
dz = Lz / float(ovf_run["znodes:"])
# find scale factor that OOMMF uses for xstepsize and xnodes,
# etc. (Don't know how to get this directly.)
xscale = dx * float(ovf_run["xstepsize:"])
yscale = dy * float(ovf_run["ystepsize:"])
zscale = dz * float(ovf_run["zstepsize:"])
# extract x, y and z positions from ovf file.
xbasevector = [None] * dimensions[0] # create empty vector
for i in range(dimensions[0]):
# data is stored for 'centre' of each cuboid, therefore (i+0.5)
xbasevector[i] = float(ovf_run["xbase:"]) +\
(i+0.5) * float(ovf_run["xstepsize:"])*xscale
ybasevector = [None] * dimensions[1]
for i in range(dimensions[1]):
ybasevector[i] = float(ovf_run["ybase:"]) + (i+0.5) * \
float(ovf_run["ystepsize:"]) * yscale
zbasevector = [None] * dimensions[2]
for i in range(dimensions[2]):
zbasevector[i] = float(ovf_run["zbase:"]) + (i+0.5) *\
float(ovf_run["zstepsize:"]) * zscale
# finally, convert list to numerix (need to have this consistent)
xbasevector = Numeric.array(xbasevector)/float(posscale)
ybasevector = Numeric.array(ybasevector)/float(posscale)
zbasevector = Numeric.array(zbasevector)/float(posscale)
else: # posscale == 0.0
#
# this generally looks better:
#
xbasevector = Numeric.arange(dimensions[0])
ybasevector = Numeric.arange(dimensions[1])
zbasevector = Numeric.arange(dimensions[2])
#
# write ascii or binary vtk-file (default is binary)
#
vtk_data = 'binary'
if '--ascii' in keys or '-t' in keys or '--text' in keys:
vtk_data = 'ascii'
if debug:
print "switching to ascii vtk-data"
if '--binary' in keys or '-b' in keys:
vtk_data = 'binary'
if debug:
print "switching to binary vtk-data"
#
# and now open vtk-file
#
vtkfilecomment = "Output from ovf2vtk (version {:s}), {:s}, infile={:s}. "\
.format(ovf2vtk.__version__, time.asctime(), infile)
vtkfilecomment += "Calling command line was '{:s}' executed in '{:s}'"\
.format(" ".join(sys.argv), os.getcwd())
vtk = pyvtk.VtkData(pyvtk.RectilinearGrid(xbasevector.tolist(),
ybasevector.tolist(),
zbasevector.tolist()),
vtkfilecomment,
pyvtk.PointData(pyvtk.Vectors(vf.tolist(), datatitle)),
format=vtk_data)
#
# now compute all the additional data such as angles, etc
#
# check whether we should do all
keys = map(lambda x: x[1], additions)
if "all" in keys:
additions = []
for add in add_features:
additions.append(("--add", add))
# when ovf2vtk was re-written using Numeric, I had to group
# certain operations to make them fast. Now some switches are
# unneccessary. (fangohr 25/08/2003 01:35)
# To avoid executing the
# same code again, we remember what we have computed already:
done_angles = 0
done_comp = 0
for add in additions:
if add[0] == "-a" or add[0] == "--add":
print "working on", add
data = []
# compute observables that need more than one field value
# i.e. div, rot
if add[1][0:6] == "divrot": # rotation = vorticity, curl
(div, rot, rotx, roty, rotz, rotmag) = \
divergence_and_curl(vf, surfaceEffects, ovf_run)
comment = "curl, x-comp"
vtk.point_data.append(pyvtk.Scalars(rotx.tolist(), comment,
lookup_table='default'))
comment = "curl, y-comp"
vtk.point_data.append(pyvtk.Scalars(roty.tolist(), comment,
lookup_table='default'))
comment = "curl, z-comp"
vtk.point_data.append(pyvtk.Scalars(rotz.tolist(), comment,
lookup_table='default'))
comment = "curl, magnitude"
vtk.point_data.append(pyvtk.Scalars(rotmag.tolist(), comment,
lookup_table='default'))
comment = "curl"
vtk.point_data.append(pyvtk.Vectors(rot.tolist(), comment))
comment = "divergence"
vtk.point_data.append(pyvtk.Scalars(div.tolist(), comment,
lookup_table='default'))
elif add[1] in ["Mx", "My", "Mz", "Ms"]: # components
if not done_comp:
done_comp = 1
comments = "x-component", "y-component", "z-component"
for data, comment in zip(components(vf), comments):
vtk.point_data.append(pyvtk.Scalars(data.tolist(),
comment,
lookup_table='\
default'))
# magnitude of magnitisation
Mmag = magnitude(vf)
vtk.point_data.append(pyvtk.Scalars(Mmag.tolist(),
"Magnitude",
lookup_table='\
default'))
elif add[1] in ["xy", "xz", "yz"]:
if not done_angles:
done_angles = 1
# in-plane angles
comments = ("xy in-plane angle", "yz in-plane angle",
"xz in-plane angle")
for data, comment in zip(plane_angles(vf), comments):
vtk.point_data.append(pyvtk.Scalars(data.tolist(),
comment,
lookup_table='\
default'))
else:
print "only xy, xz, Mx, My, Mz, divergence, Ms, or 'all' \
allowed after -a or --add"
print "Current choice is", add
print __doc__
sys.exit(1)
#
# eventually, write the file
#
print "saving file ({:s})".format(outfile)
vtk.tofile(outfile, format=vtk_data)
print "finished conversion (execution time {:5.3s} seconds)"\
.format(str(time.time()-start_time))
def test_divergence_and_curl():
"""function takes inputs vf (a Nx3 array), SurfaceEffects (a boolean), and
ovf_run (a dictionary of keyword pairs)"""
# takes the filename and connects to the product of the files' Nx, Ny, Nz
node_products = {os.path.join('..', 'Examples', 'cantedvortex.omf'):
32768,
os.path.join('..', 'Examples', 'ellipsoidwrap.omf'):
768,
os.path.join('..', 'Examples', 'h2hleftedge.ohf'):
25600,
os.path.join('..', 'Examples', 'yoyoleftedge.ohf'):
6000}
filenames = (os.path.join('..', 'Examples', 'cantedvortex.omf'),
os.path.join('..', 'Examples', 'ellipsoidwrap.omf'),
os.path.join('..', 'Examples', 'h2hleftedge.ohf'),
os.path.join('..', 'Examples', 'yoyoleftedge.ohf'))
# test that final shapes of returned objects are correct.
# 'divflat' shape should be Nx x Ny x Nz whereas...
# ...rotflat should be Nx x Ny x Nz x 3
for filename in filenames:
# 'vf' and 'ovf_run' are returned in functions within omfread.py
divflat = ana.divergence_and_curl(
omf.read_structured_omf_file(filename), False,
omf.analyze(filename))[0]
rotflat = ana.divergence_and_curl(
omf.read_structured_omf_file(filename), False,
omf.analyze(filename))[1]
rotmag = ana.magnitude(rotflat)
assert [int(i) for i in divflat.shape] == [node_products[filename]]
assert [int(i) for i in rotflat.shape] == [node_products[filename], 3]
assert [int(i) for i in rotmag.shape] == [node_products[filename]]
for i in range(3):
shape = rotflat[:, i].shape
assert [int(j) for j in shape] == [node_products[filename]]
# test the return types are numpy arrays.
objects = [divflat, rotflat, rotflat[:, 0], rotflat[:, 1],
rotflat[:, 2], rotmag]
for obj in objects:
assert isinstance(obj, np.ndarray)
# test returned objects contain correct data values for both...
# ...surfaceeffects=true and surfaceeffects=false for each example file.
surfaceEffects = [True, False]
for filename in filenames:
for boolean in surfaceEffects:
# actual result
act = ana.divergence_and_curl(
omf.read_structured_omf_file(filename), boolean,
omf.analyze(filename))
# expected result. The original version of the function...
# ... i.e. not refactored
exp = analysis_original.divergence_and_curl(
omf.read_structured_omf_file(filename), boolean,
omf.analyze(filename))
for j in range(len(act)):
assert act[j].all() == exp[j].all()
# test special 2d case; Nz = 1
dic = {"xnodes:": 3, "ynodes:": 3, "znodes:": 1, "xstepsize:": 0.01,
"ystepsize:": 0.01, "zstepsize:": 0.01}
for boolean in surfaceEffects:
# actual result
act = ana.divergence_and_curl(vfexample2, boolean, dic)
# expected result. The original version of the function...
# ... i.e. not refactored
exp = analysis_original.divergence_and_curl(vfexample2, boolean, dic)
for j in range(len(act)):
assert act[j].all() == exp[j].all()
def ovf2vtk_main():
start_time = time.time()
banner_doc = 70*"-"+\
"\novf2vtk --- converting ovf files to vtk files"+"\n"+\
"Hans Fangohr, Richard Boardman, University of Southampton\n"""+70*"-"
#extract command line arguments
additions,params = getopt.getopt( sys.argv[1:], 'Vvhbta:', ["verbose","help","add=","binary","text","ascii","surface-effects","version","datascale=","posscale="] )
#Note (fangohr 30/12/2006 20:52): the use of getopt is historic,
#and so is the use of the name 'additions'.
#default value
surfaceEffects = False
datascale = 0.0 #0.0 has special meaning -- see help text
posscale = 0.0 #0.0 has special meaning -- see help text
#provide data from getopt.getopt (additions) in form of hash table
options = {}
for item in additions:
if item[1]=='':
options[item[0]] = None
else:
options[item[0]] = item[1]
keys = options.keys()
if "--surface-effects" in keys:
surfaceEffects = True
if "--posscale" in keys:
posscale = float(options["--posscale"])
if "--datascale" in keys:
datascale = float(options["--datascale"])
if "-v" in keys or "--verbose" in keys:
print "running in verbose mode"
debug = True
else:
debug = False
if "-h" in keys or "--help" in keys:
print __doc__
sys.exit(0)
if "-V" in keys or "--version" in keys:
print "This is version %s." % ovf2vtk.__version__
sys.exit(0)
if len( params ) == 0:
print __doc__
print "ERROR: An input file (and an output file need to be specified)."
sys.exit(1)
else:
infile = params[0]
if len( params ) == 1:
print __doc__
print "ERROR: An input file AND an output file need to be specified."
print "specify output file"
sys.exit(1)
else:
outfile = params[1]
# okay: it seems the essential parameters are given. Let's check for others:
print banner_doc
if debug:
print "infile = ", infile
print "outfile = ",outfile
print "additions= ",additions
print "options = ",options
print "datascale=",datascale
print "posscale=",posscale
#read data from infile
vf = read_structured_omf_file( infile, debug )
#compute magnitude for all cells
Ms = magnitude( vf )
# Compute number of cells with non-zero Ms (rpb01r)
Ms_num_of_nonzeros = Numeric.sum( Numeric.not_equal( Ms, 0.0 ) )
print "(%5.2f%% of %d cells filled)" % (100.0*Ms_num_of_nonzeros/len(Ms), len(Ms))
#read metadata in data file
ovf_run = analyze( infile )
#scale magnetisation data as required:
if datascale == 0.0:
scale = max( Ms )
print "Will scale data down by %f" % scale
else:
scale = datascale
vf = Numeric.divide( vf, scale )
datatitle = ovf_run["Title:"]+"/%g" % (scale)
#
#need x, y and z vectors for vtk format
#
#taking actual spacings for dx, dy and dz results generally in
#poor visualisation results (in particular for thin films, one
#would like to have some magnification in z-direction). Also:vtk
#is not happy with positions on the 10e-9 scale, so one better
#scales this to something closer to unity.
#extract dimensions from file
dimensions = ( int( ovf_run["xnodes:"] ), \
int( ovf_run["ynodes:"] ), \
int( ovf_run["znodes:"] ))
if posscale != 0.0: #scale data by given factor
#find dx, dy, dz in SI units:
Lx = abs(float(ovf_run["xmax:"])-float(ovf_run["xmin:"]))
Ly = abs(float(ovf_run["ymax:"])-float(ovf_run["ymin:"]))
Lz = abs(float(ovf_run["zmax:"])-float(ovf_run["zmin:"]))
dx = Lx / float( ovf_run["xnodes:"] )
dy = Ly / float( ovf_run["ynodes:"] )
dz = Lz / float( ovf_run["znodes:"] )
#find scale factor that OOMMF uses for xstepsize and xnodes,
#etc. (Don't know how to get this directly.)
xscale = Lx / (float( ovf_run["xnodes:"])*float(ovf_run["xstepsize:"]))
yscale = Ly / (float( ovf_run["ynodes:"])*float(ovf_run["ystepsize:"]))
zscale = Lz / (float( ovf_run["znodes:"])*float(ovf_run["zstepsize:"]))
#extract x, y and z positions from ovf file.
xbasevector = [None] * dimensions[0] #create empty vector
for i in range( dimensions[0] ):
#data is stored for 'centre' of each cuboid, therefore (i+0.5)
xbasevector[i] = float( ovf_run["xbase:"] ) +\
(i+0.5) *float( ovf_run["xstepsize:"] )*xscale
ybasevector = [None]* dimensions[1]
for i in range( dimensions[1] ):
ybasevector[i] = float( ovf_run["ybase:"] ) + (i+0.5) *float( ovf_run["ystepsize:"] )*yscale
zbasevector = [None]* dimensions[2]
for i in range( dimensions[2] ):
zbasevector[i] = float( ovf_run["zbase:"] ) + (i+0.5) *float( ovf_run["zstepsize:"] )*zscale
#finally, convert list to numerix (need to have this consistent)
xbasevector = Numeric.array(xbasevector)/float(posscale)
ybasevector = Numeric.array(ybasevector)/float(posscale)
zbasevector = Numeric.array(zbasevector)/float(posscale)
else: #posscale == 0.0
#
#this generally looks better:
#
xbasevector = Numeric.arange( dimensions[0] )
ybasevector = Numeric.arange( dimensions[1] )
zbasevector = Numeric.arange( dimensions[2] )
#
# write ascii or binary vtk-file (default is binary)
#
vtk_data = 'binary'
if '--ascii' in keys or '-t' in keys or '--text' in keys:
vtk_data = 'ascii'
if debug:
print "switching to ascii vtk-data"
if '--binary' in keys or '-b' in keys:
vtk_data = 'binary'
if debug:
print "switching to binary vtk-data"
#
#and now open vtk-file
#
vtkfilecomment = "Output from ovf2vtk (version %s), %s, infile=%s. " % (ovf2vtk.__version__,\
time.asctime(),\
infile)
vtkfilecomment += "Calling command line was '%s' executed in '%s'" % (" ".join(sys.argv),\
os.getcwd())
vtk = pyvtk.VtkData( pyvtk.RectilinearGrid(xbasevector.tolist(),ybasevector.tolist(),zbasevector.tolist()),
vtkfilecomment,
pyvtk.PointData(pyvtk.Vectors( vf.tolist(), datatitle ) ),
format=vtk_data)
#
# now compute all the additional data such as angles, etc
#
# check whether we should do all
keys = map(lambda x:x[1], additions)
if "all" in keys:
additions = []
for add in add_features:
additions.append(("--add",add))
# when ovf2vtk was re-written using Numeric, I had to group
# certain operations to make them fast. Now some switches are
# unneccessary. (fangohr 25/08/2003 01:35)
# To avoid executing the
# same code again, we remember what we have computed already:
done_angles = 0
done_comp = 0
for add in additions:
if add[0]=="-a" or add[0]=="--add":
print "working on",add
data=[]
#compute observables that need more than one field value, i.e. div, rot
if add[1][0:6] == "divrot": #rotation = vorticity, curl
(div, rot, rotx, roty, rotz, rotmag) = divergence_and_curl( vf, surfaceEffects, ovf_run )
comment = "curl, x-comp"
vtk.point_data.append( pyvtk.Scalars( rotx.tolist() , comment , lookup_table='default') )
Comment = "curl, y-comp"
vtk.point_data.append( pyvtk.Scalars( roty.tolist() , comment , lookup_table='default') )
comment = "curl, z-comp"
vtk.point_data.append( pyvtk.Scalars( rotz.tolist() , comment , lookup_table='default') )
comment = "curl, magnitude"
vtk.point_data.append( pyvtk.Scalars( rotmag.tolist(), comment , lookup_table='default') )
comment = "curl"
vtk.point_data.append( pyvtk.Vectors( rot.tolist() , comment ) )
comment = "divergence"
vtk.point_data.append( pyvtk.Scalars( div.tolist() , comment , lookup_table='default') )
done_div_rot = True
elif add[1] in ["Mx","My","Mz","Ms"]: # components
if not done_comp:
done_comp = 1
comments = "x-component", "y-component", "z-component"
for data, comment in zip( components( vf ), comments):
vtk.point_data.append( pyvtk.Scalars( data.tolist(), comment,lookup_table='default' ) )
# magnitude of magnitisation
Mmag = magnitude( vf )
vtk.point_data.append( pyvtk.Scalars(Mmag.tolist(), "Magnitude",lookup_table='default' ) )
elif add[1] in ["xy","xz","yz"]:
if not done_angles:
done_angles = 1
# in-plane angles
comments = "xy in-plane angle", "yz in-plane angle", "xz in-plane angle"
for data, comment in zip( plane_angles( vf ), comments):
vtk.point_data.append( pyvtk.Scalars( data.tolist(), comment, lookup_table='default' ) )
else:
print "only xy, xz, Mx, My, Mz, divergence, Ms, or 'all' allowed after -a or --add"
print "Current choice is",add
print __doc__
sys.exit(1)
#
#eventually, write the file
#
print "saving file (%s)" % (outfile)
vtk.tofile(outfile,format=vtk_data)
print "finished conversion (execution time %5.3s seconds)" % (time.time()-start_time)
def test_divergence_and_curl():
"""function takes inputs vf (a Nx3 array), SurfaceEffects (a boolean), and
ovf_run (a dictionary of keyword pairs)"""
# takes the filename and connects to the product of the files' Nx, Ny, Nz
node_products = {
os.path.join('..', 'Examples', 'cantedvortex.omf'): 32768,
os.path.join('..', 'Examples', 'ellipsoidwrap.omf'): 768,
os.path.join('..', 'Examples', 'h2hleftedge.ohf'): 25600,
os.path.join('..', 'Examples', 'yoyoleftedge.ohf'): 6000
}
filenames = (os.path.join('..', 'Examples', 'cantedvortex.omf'),
os.path.join('..', 'Examples', 'ellipsoidwrap.omf'),
os.path.join('..', 'Examples', 'h2hleftedge.ohf'),
os.path.join('..', 'Examples', 'yoyoleftedge.ohf'))
# test that final shapes of returned objects are correct.
# 'divflat' shape should be Nx x Ny x Nz whereas...
# ...rotflat should be Nx x Ny x Nz x 3
for filename in filenames:
# 'vf' and 'ovf_run' are returned in functions within omfread.py
divflat = ana.divergence_and_curl(
omf.read_structured_omf_file(filename), False,
omf.analyze(filename))[0]
rotflat = ana.divergence_and_curl(
omf.read_structured_omf_file(filename), False,
omf.analyze(filename))[1]
rotmag = ana.magnitude(rotflat)
assert [int(i) for i in divflat.shape] == [node_products[filename]]
assert [int(i) for i in rotflat.shape] == [node_products[filename], 3]
assert [int(i) for i in rotmag.shape] == [node_products[filename]]
for i in range(3):
shape = rotflat[:, i].shape
assert [int(j) for j in shape] == [node_products[filename]]
# test the return types are numpy arrays.
objects = [
divflat, rotflat, rotflat[:, 0], rotflat[:, 1], rotflat[:, 2],
rotmag
]
for obj in objects:
assert isinstance(obj, np.ndarray)
# test returned objects contain correct data values for both...
# ...surfaceeffects=true and surfaceeffects=false for each example file.
surfaceEffects = [True, False]
for filename in filenames:
for boolean in surfaceEffects:
# actual result
act = ana.divergence_and_curl(
omf.read_structured_omf_file(filename), boolean,
omf.analyze(filename))
# expected result. The original version of the function...
# ... i.e. not refactored
exp = analysis_original.divergence_and_curl(
omf.read_structured_omf_file(filename), boolean,
omf.analyze(filename))
for j in range(len(act)):
assert act[j].all() == exp[j].all()
# test special 2d case; Nz = 1
dic = {
"xnodes:": 3,
"ynodes:": 3,
"znodes:": 1,
"xstepsize:": 0.01,
"ystepsize:": 0.01,
"zstepsize:": 0.01
}
for boolean in surfaceEffects:
# actual result
act = ana.divergence_and_curl(vfexample2, boolean, dic)
# expected result. The original version of the function...
# ... i.e. not refactored
exp = analysis_original.divergence_and_curl(vfexample2, boolean, dic)
for j in range(len(act)):
assert act[j].all() == exp[j].all()