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## Automatically adapted for scipy Oct 31, 2005 by
# 1998 - 2003
# Author: Travis Oliphant
# Copyright: SciPy
import gist
import pl3d, plwf
import numpy as Numeric
numpy = Numeric
from numpy import ravel, reshape, repeat, arange, transpose, compress, \
where, ones, newaxis, asarray
import numpy.lib.mlab as MLab
from numpy.lib.mlab import pi, cos, sin, arctan2, array, angle
import types
import write_style
points = 0.0013000
inches = 72.27*points
import scipy
import scipy.signal as signal
from __init__ import maxwidth as _maxwidth
from __init__ import maxheight as _maxheight
_dpi = 75
_hold = 0
_maxcolors=256
_textcolor=None
gist.pldefault(dpi=_dpi,maxcolors=_maxcolors)
# Get a directory that the user has write access to for
# storing temporary *.gp and *.gs files
import tempfile
import os
import sys
# functions copied from weave.catalog
def whoami():
"""return a string identifying the user."""
return os.environ.get("USER") or os.environ.get("USERNAME") or "unknown"
def create_dir(p):
""" Create a directory and any necessary intermediate directories."""
if not os.path.exists(p):
try:
os.mkdir(p)
except OSError:
# perhaps one or more intermediate path components don't exist
# try to create them
base,dir = os.path.split(p)
create_dir(base)
# don't enclose this one in try/except - we want the user to
# get failure info
os.mkdir(p)
def is_writable(dir):
dummy = os.path.join(dir, "dummy")
try:
open(dummy, 'w')
except IOError:
return 0
os.unlink(dummy)
return 1
# end functions copied from weave.catalog
def _getdir(name='scipy_xplt'):
try:
path = os.path.join(os.environ['HOME'],'.' + name)
except KeyError:
path = os.path.join(tempfile.gettempdir(),"%s"%whoami(),
name)
if not os.path.exists(path):
create_dir(path)
os.chmod(path,0700)
if not is_writable(path):
print "warning: default directory is not write accessible."
print "default:", path
return path
_user_path = _getdir()
try:
import Scientific.Statistics.Histogram
SSH = Scientific.Statistics.Histogram
def histogram(data,nbins=80,range=None,ntype=0,bar=1,bwidth=0.8,bcolor=0):
"""Plot a histogram. ntype is the normalization type.
Use ntype == 2 to compare with probability density function.
"""
h = SSH.Histogram(data,nbins,range)
if ntype == 1:
h.normalize()
elif ntype == 2:
h.normalizeArea()
if bar:
barplot(h[:,0],h[:,1],width=bwidth,color=bcolor)
else:
plot(h[:,0],h[:,1])
return h
except ImportError:
try:
import Statistics
SSH = Statistics
def histogram(data,nbins=80,range=None,ntype=0,bar=1,bwidth=0.8,bcolor=0):
"""Plot a histogram. ntype is the normalization type.
Use ntype == 2 to compare with probability density function.
"""
h = SSH.histogram(data,nbins,range)
if ntype == 1:
h.normalize()
elif ntype == 2:
h.normalizeArea()
if bar:
barplot(h[:,0],h[:,1],width=bwidth,color=bcolor)
else:
plot(h[:,0],h[:,1])
return h
except ImportError:
from scipy.stats import histogram2 as hist
def histogram(data,nbins=80,range=None,ntype=0,bar=1,bwidth=0.8,bcolor=0):
"""Plot a histogram. ntype is the normalization type.
Use ntype == 2 to compare with probability density function.
"""
if range is None:
dmin = Numeric.minimum.reduce(data)
dmax = Numeric.maximum.reduce(data)
else:
dmin, dmax = range
dmin = dmin + 0.0
dmax = dmax + 0.0
bin_width = (dmax - dmin)/nbins
darray = Numeric.zeros((nbins,2),Numeric.Float)
darray[:,0] = dmin + bin_width*(Numeric.arange(nbins)+0.5)
bins = dmin + bin_width*(Numeric.arange(nbins))
darray[:,1] = hist(data,bins)
if ntype == 1:
darray[:,1] = 1.0*darray[:,1] / Numeric.add.reduce(darray[:,1])
elif ntype == 2:
darray[:,1] = 1.0/bin_width*darray[:,1] / \
Numeric.add.reduce(darray[:,1])
if bar:
barplot(darray[:,0],darray[:,1],width=bwidth,color=bcolor)
else:
plot(darray[:,0],darray[:,1])
return darray
def textcolor(color=None):
global _textcolor
if color is not None:
_textcolor = color
return _textcolor
def reverse_dict(dict):
newdict = {}
for key in dict.keys():
newdict[dict[key]] = key
return newdict
_colornum = {'black':-3, 'white':-4,'red':-5,'green':-6,'blue':-7,'cyan':-8,'magenta':-9,'yellow':-10}
_types = {'-':'solid','|':'dash',':':'dot','-.':'dashdot','-:':'dashdotdot'}
_corder = ['B','r','m','g','c','k','y']
_colors = {'k':'black','r':'red','B':'blue','m':'magenta','g':'green','y':'yellow','c':'cyan','w':'white'}
_markers = { '+':'\2','.':'\1','*':'\3','o':'\4','x':'\5'}
_current_style='work.gs'
_rtypes = reverse_dict(_types)
_rtypes['none'] = ''
_rcolors = reverse_dict(_colors)
_rmarkers = reverse_dict(_markers)
def _find_and_set(dict, str, default):
import string
value = default
for k in dict.keys():
if string.find(str,k) >= 0:
value = dict[k]
break
return value
def barplot(x,y,width=0.8,color=0):
"""Plot a barplot.
Description:
Plot a barplot with centers at x and heights y with given color
Inputs:
x, y -- Centers and heights of bars
width -- Relative width of the bars.
color -- A number from the current palette.
"""
N = 4*Numeric.ones(len(x))
hw = width * (x[1]-x[0])/ 2.0
Xa = x-hw
Xb = x+hw
Ya = Numeric.zeros(len(y),'d')
Yb = y
X = Numeric.array((Xa,Xa,Xb,Xb))
Y = Numeric.array((Ya,Yb,Yb,Ya))
X = Numeric.reshape(Numeric.transpose(X),(4*len(N),))
Y = Numeric.reshape(Numeric.transpose(Y),(4*len(N),))
try:
override = 1
savesys = gist.plsys(2)
gist.plsys(savesys)
except:
override = 0
if _hold or override:
pass
else:
gist.fma()
Z = color * Numeric.ones(len(N))
gist.plfp(Z.astype('B'),Y,X,N)
return
def hold(state):
"""Draw subsequent plots over the current plot.
Inputs:
state -- If 'on' or 'yes' hold the current plot.
Otherwise refresh screen when drawing new plot.
"""
global _hold
if state in ['on', 'yes']:
_hold = 1
elif state in ['off', 'no']:
_hold = 0
else:
raise ValueError, 'holds argument can be "on","off",'\
'"yes","no". Not ' + state
return
def errorbars(x,y,err,ptcolor='r',linecolor='B',pttype='o',linetype='-',fac=0.25):
"""Draw connected points with errorbars.
Description:
Plot connected points with errorbars.
Inputs:
x, y -- The points to plot.
err -- The error in the y values.
ptcolor -- The color for the points.
linecolor -- The color of the connecting lines and error bars.
pttype -- The type of point ('o', 'x', '+', '.', 'x', '*')
linetype -- The type of line ('-', '|', ':', '-.', '-:')
fac -- Adjusts how long the horizontal lines are which make the
top and bottom of the error bars.
"""
# create line arrays
yb = y - err
ye = y + err
try:
override = 1
savesys = gist.plsys(2)
gist.plsys(savesys)
except:
override = 0
if _hold or override:
pass
else:
gist.fma()
y = where(numpy.isfinite(y),y,0)
gist.plg(y,x,color=_colors[ptcolor],marker=_markers[pttype],type='none')
gist.pldj(x,yb,x,ye,color=_colors[linecolor],type=_types[linetype])
viewp = gist.viewport()
plotlims = gist.limits()
conv_factorx = (viewp[1] - viewp[0]) / (plotlims[1]-plotlims[0])
conv_factory = (viewp[3] - viewp[2]) / (plotlims[3]-plotlims[2])
width = fac*(x[1]-x[0])
x0 = x-width/2.0
x1 = x+width/2.0
gist.pldj(x0,ye,x1,ye,color=_colors[linecolor],type=_types[linetype])
gist.pldj(x0,yb,x1,yb,color=_colors[linecolor],type=_types[linetype])
return
def legend(text,linetypes=None,lleft=None,color=None,tfont='helvetica',fontsize=14,nobox=0):
"""Construct and place a legend.
Description:
Build a legend and place it on the current plot with an interactive
prompt.
Inputs:
text -- A list of strings which document the curves.
linetypes -- If not given, then the text strings are associated
with the curves in the order they were originally
drawn. Otherwise, associate the text strings with the
corresponding curve types given. See plot for description.
"""
global _hold
global _textcolor
if color is None:
color = _textcolor
else:
_textcolor = color
if color is None:
color = 'black'
sys = gist.plsys()
if sys == 0:
gist.plsys(1)
viewp = gist.viewport()
gist.plsys(sys)
DX = viewp[1] - viewp[0]
DY = viewp[3] - viewp[2]
width = DY / 10.0;
if lleft is None:
lleft = gist.mouse(0,0,"Click on point for lower left coordinate.")
llx = lleft[0]
lly = lleft[1]
else:
llx,lly = lleft[:2]
savesys = gist.plsys()
dx = width / 3.0
legarr = Numeric.arange(llx,llx+width,dx)
legy = Numeric.ones(legarr.shape)
dy = fontsize*points*1.2
deltay = fontsize*points / 2.8
deltax = fontsize*points / 2.6 * DX / DY
ypos = lly + deltay;
if linetypes is None:
linetypes = _GLOBAL_LINE_TYPES[:] # copy them out
gist.plsys(0)
savehold = _hold
_hold = 1
for k in range(len(text)):
plot(legarr,ypos*legy,linetypes[k])
print linetypes[k], text[k]
print llx+width+deltax, ypos-deltay
if text[k] != "":
gist.plt(text[k],llx+width+deltax,ypos-deltay,
color=color,font=tfont,height=fontsize,tosys=0)
ypos = ypos + dy
_hold = savehold
if nobox:
pass
else:
gist.plsys(0)
maxlen = MLab.max(map(len,text))
c1 = (llx-deltax,lly-deltay)
c2 = (llx + width + deltax + fontsize*points* maxlen/1.8 + deltax,
lly + len(text)*dy)
linesx0 = [c1[0],c1[0],c2[0],c2[0]]
linesy0 = [c1[1],c2[1],c2[1],c1[1]]
linesx1 = [c1[0],c2[0],c2[0],c1[0]]
linesy1 = [c2[1],c2[1],c1[1],c1[1]]
gist.pldj(linesx0,linesy0,linesx1,linesy1,color=color)
gist.plsys(savesys)
return
def ispointtype(linetype):
if len(linetype) > 2:
return 0
if (len(linetype) == 1):
if linetype[0] in _markers.keys():
return 1
else:
return 0
if linetype[0] in _markers.keys():
if linetype[1] in _colors.keys():
return 1
else:
return 0
if linetype[0] in _colors.keys():
if linetype[1] in _markers.keys():
return 1
else:
return 0
return 0
##def legend(text,linetypes=None,lleft=None,color='black',tfont='helvetica',fontsize=14,nobox=0):
## viewp = gist.viewport()
## plotlims = gist.limits()
## gist.limits(plotlims)
## conv_factorx = (viewp[1] - viewp[0]) / (plotlims[1]-plotlims[0])
## conv_factory = (viewp[3] - viewp[2]) / (plotlims[3]-plotlims[2])
## width = (plotlims[1] - plotlims[0]) / 10.0;
## if lleft is None:
## lleft = gist.mouse(-1,0,"Click on point for lower left coordinate.")
## llx = lleft[0]
## lly = lleft[1]
## else:
## llx,lly = lleft[:2]
## dx = width / 3.0
## legarr = Numeric.arange(llx,llx+width,dx)
## legy = Numeric.ones(legarr.shape)
## dy = fontsize*points/conv_factory*1.15
## deltay = fontsize*points / conv_factory / 2.8
## deltax = fontsize*points / conv_factorx / 2.8
## ypos = lly + deltay;
## if linetypes is None:
## linetypes = _GLOBAL_LINE_TYPES[:] # copy them out
## for k in range(len(text)):
## if ispointtype(linetypes[k]):
## pt = len(legarr)/2
## plot([legarr[pt]],[ypos*legy[pt]],linetypes[k], hold=1)
## else:
## plot(legarr,ypos*legy,linetypes[k],hold=1)
## print llx+width+deltax, ypos-deltay
## if text[k] != "":
## gist.plt(text[k],llx+width+deltax,ypos-deltay,
## color=color,font=tfont,height=fontsize,tosys=1)
## ypos = ypos + dy
## if nobox:
## pass
## else:
## maxlen = MLab.max(map(len,text))
## c1 = (llx-deltax,lly-deltay)
## c2 = (llx + width + deltax + fontsize*points/conv_factorx * maxlen/1.8 + deltax,
## lly + len(text)*dy)
## linesx0 = [c1[0],c1[0],c2[0],c2[0]]
## linesy0 = [c1[1],c2[1],c2[1],c1[1]]
## linesx1 = [c1[0],c2[0],c2[0],c1[0]]
## linesy1 = [c2[1],c2[1],c1[1],c1[1]]
## gist.pldj(linesx0,linesy0,linesx1,linesy1,color=color)
## return
import operator
def arrow(x0,y0,x1,y1,color=0,ang=45.0,height=6,width=1.5,lc=None):
"""Draw an arrow.
Description:
Draw an arrow from (x0,y0) to (x1,y1) in the current coordinate system.
Inputs:
x0, y0 -- The beginning point.
x1, y1 -- Then ending point.
color -- The color of the arrowhead. Number represents an index
in the current palette or a negative number or a spelled
out basic color.
lc -- The color of the line (same as color by default).
ang -- The angle of the arrowhead.
height -- The height of the arrowhead in points.
width -- The width of the arrow line in points.
"""
if lc is None:
lc = color
if type(lc) is types.StringType:
lc = _colornum[lc]
if type(color) is types.StringType:
color = _colornum[color]
vp = gist.viewport()
plotlims = gist.limits()
gist.limits(plotlims)
conv_factorx = (vp[1]-vp[0]) / (plotlims[1]-plotlims[0])
conv_factory = (vp[3]-vp[2]) / (plotlims[3]-plotlims[2])
ang = ang*pi/180
height = height*points
hypot = height / cos(ang)
difx = (x1 - x0) * conv_factorx
dify = (y1 - y0) * conv_factory
theta = arctan2(dify,difx) + pi
tha = theta + ang
thb = theta - ang
x1a = x1 + hypot*cos(tha) / conv_factorx
x1b = x1 + hypot*cos(thb) / conv_factorx
y1a = y1 + hypot*sin(tha) / conv_factory
y1b = y1 + hypot*sin(thb) / conv_factory
gist.pldj([x0],[y0],[x1],[y1],color=lc,width=width)
gist.plfp(array([color],'B'),[y1,y1a,y1b],[x1,x1a,x1b],[3])
return
def _parse_type_arg(thearg,nowplotting):
indx = nowplotting % len(_corder)
if type(thearg) is type(''):
tomark = 1
thetype = _find_and_set(_types,thearg,'none')
thecolor = _find_and_set(_colors,thearg,_colors[_corder[indx]])
themarker = _find_and_set(_markers,thearg,None)
if (themarker is None):
tomark = 0
if thetype == 'none':
thetype = 'solid'
return (thetype, thecolor, themarker, tomark)
else: # no string this time
return ('solid',_colors[_corder[indx]],'Z',0)
_GLOBAL_LINE_TYPES=[]
def clear_global_linetype():
for k in range(len(_GLOBAL_LINE_TYPES)):
_GLOBAL_LINE_TYPES.pop()
def append_global_linetype(arg):
_GLOBAL_LINE_TYPES.append(arg)
def _minsqueeze(arr,min=1):
# eliminate extra dimensions above min
arr = asarray(arr)
arr = numpy.squeeze(arr)
n = len(arr.shape)
if n < min:
arr.shape = arr.shape + (1,)*(min-n)
return arr
def plot(x,*args,**keywds):
"""Plot curves.
Description:
Plot one or more curves on the same graph.
Inputs:
There can be a variable number of inputs which consist of pairs or
triples. The second variable is plotted against the first using the
linetype specified by the optional third variable in the triple. If
only two plots are being compared, the x-axis does not have to be
repeated.
"""
try:
override = 1
savesys = gist.plsys(2)
gist.plsys(savesys)
except:
override = 0
global _hold
try: _hold=keywds['hold']
except KeyError: pass
try: linewidth=float(keywds['width'])
except KeyError: linewidth=1.0
try: msize = float(keywds['msize'])
except KeyError: msize=1.0
if _hold or override:
pass
else:
gist.fma()
gist.animate(0)
savesys = gist.plsys()
winnum = gist.window()
if winnum < 0:
gist.window(0)
if savesys >= 0:
gist.plsys(savesys)
nargs = len(args)
if nargs == 0:
y = _minsqueeze(x)
x = Numeric.arange(0,len(y))
if numpy.iscomplexobj(y):
print "Warning: complex data plotting real part."
y = y.real
y = where(numpy.isfinite(y),y,0)
gist.plg(y,x,type='solid',color='blue',marks=0,width=linewidth)
return
y = args[0]
argpos = 1
nowplotting = 0
clear_global_linetype()
while 1:
try:
thearg = args[argpos]
except IndexError:
thearg = 0
thetype,thecolor,themarker,tomark = _parse_type_arg(thearg,nowplotting)
if themarker == 'Z': # args[argpos] was data or non-existent.
pass
append_global_linetype(_rtypes[thetype]+_rcolors[thecolor])
else: # args[argpos] was a string
argpos = argpos + 1
if tomark:
append_global_linetype(_rtypes[thetype]+_rcolors[thecolor]+_rmarkers[themarker])
else:
append_global_linetype(_rtypes[thetype]+_rcolors[thecolor])
if numpy.iscomplexobj(x) or numpy.iscomplexobj(y):
print "Warning: complex data provided, using only real part."
x = numpy.real(x)
y = numpy.real(y)
y = where(numpy.isfinite(y),y,0)
y = _minsqueeze(y)
x = _minsqueeze(x)
gist.plg(y,x,type=thetype,color=thecolor,marker=themarker,marks=tomark,msize=msize,width=linewidth)
nowplotting = nowplotting + 1
## Argpos is pointing to the next potential triple of data.
## Now one of four things can happen:
##
## 1: argpos points to data, argpos+1 is a string
## 2: argpos points to data, end
## 3: argpos points to data, argpos+1 is data
## 4: argpos points to data, argpos+1 is data, argpos+2 is a string
if argpos >= nargs: break # no more data
if argpos == nargs-1: # this is a single data value.
x = x
y = args[argpos]
argpos = argpos+1
elif type(args[argpos+1]) is types.StringType:
x = x
y = args[argpos]
argpos = argpos+1
else: # 3
x = args[argpos]
y = args[argpos+1]
argpos = argpos+2
return
def matplot(x,y=None,axis=-1):
if y is None: # no axis data
y = x
x = Numeric.arange(0,y.shape[axis])
x,y = Numeric.asarray(x), Numeric.asarray(y)
assert(len(y.shape)==2)
assert(len(x)==y.shape[axis])
otheraxis = (1+axis) % 2
sliceobj = [slice(None)]*2
if not _hold and gist.plsys() < 2:
gist.fma()
clear_global_linetype()
for k in range(y.shape[otheraxis]):
thiscolor = _colors[_corder[k % len(_corder)]]
sliceobj[otheraxis] = k
ysl = where(numpy.isfinite(y[sliceobj]),y[sliceobj],0)
gist.plg(ysl,x,type='solid',color=thiscolor,marks=0)
append_global_linetype(_rcolors[thiscolor]+'-')
def addbox(x0,y0,x1,y1,color='black',width=1,type='-'):
if not isinstance(color,types.IntType):
color = _colornum[color]
wordtype = _types[type]
gist.pldj([x0,x1,x1,x0],[y0,y0,y1,y1],[x1,x1,x0,x0],[y0,y1,y1,y0],
color=color,type=wordtype,width=width)
def write_palette(tofile,pal):
pal = Numeric.asarray(pal)
if pal.dtype.char not in ['B','b','s','i','l']:
raise ValueError, "Palette data must be integer data."
palsize = pal.shape
if len(palsize) > 2:
raise TypeError, "Input must be a 1-d or 2-d array"
if len(palsize) == 2:
if palsize[0] == 1 and palsize[1] > 1:
pal = pal[0]
if palsize[1] == 1 and palsize[0] > 1:
pal = pal[:,0]
palsize = pal.shape
if len(palsize) == 1:
pal = Numeric.multiply.outer(pal,ones((3,),pal.dtype.char))
palsize = pal.shape
if not (palsize[1] == 3 or palsize[0] == 3):
raise TypeError, "If input is 2-d, the length of at least one dimension must be 3."
if palsize[0] == 3 and palsize[1] != 3:
pal = Numeric.transpose(pal)
palsize = pal.shape
if palsize[0] > 256:
raise ValueError, "Palettes should be no longer than 256."
fid = open(tofile,'w')
fid.write("ncolors=%d\n\n# r g b\n" % palsize[0])
for k in range(palsize[0]):
fid.write("%4d%4d%4d\n" % tuple(pal[k]))
fid.close()
def list_palettes():
import os, glob
direc = os.environ['GISTPATH']
files = glob.glob1(direc,"*.gp")
lengths = map(len,files)
maxlen = numpy.amax(lengths)
print "Available palettes..."
print "=====================\n"
for file in files:
print file[:-3] + ' '*(maxlen-len(file[:-3])-3) + ' --- ',
k = 0
fid = open(direc+"/"+file)
while 1:
line = fid.readline()
if line[0] != '#':
fid.close()
if k == 0:
print
break
if k > 0:
print ' '*(maxlen+3) + line[1:-1]
else:
print line[1:-1]
k = k + 1
def change_palette(pal):
if pal is not None:
if isinstance(pal, types.StringType):
try:
gist.palette('%s.gp' % pal)
except gist.error:
if len(pal) > 3 and pal[-2:] == 'gp':
gist.palette(pal)
else:
raise ValueError, "Palette %s not found." % pal
else:
data = Numeric.transpose(Numeric.asarray(pal))
data = data.astype('B')
gist.palette(*transpose(data))
#filename = os.path.join(_user_path,'_temp.gp')
#write_palette(filename,data)
#gist.palette(filename)
chpal = change_palette
def matview(A,cmax=None,cmin=None,palette=None,color='black'):
"""Plot an image of a matrix.
"""
A = Numeric.asarray(A)
if A.dtype.char in ['D','F']:
print "Warning: complex array given, plotting magnitude."
A = abs(A)
M,N = A.shape
A = A[::-1,:]
if cmax is None:
cmax = max(ravel(A))
if cmin is None:
cmin = min(ravel(A))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(A,cmin=cmin,cmax=cmax)
change_palette(palette)
gist.window(style='nobox.gs')
_current_style='nobox.gs'
gist.pli(byteimage)
old_vals = gist.limits(square=1)
vals = gist.limits(square=1)
if color is None:
return
vp = gist.viewport()
axv,bxv,ayv,byv = vp
axs,bxs,ays,bys = vals[:4]
# bottom left corner column
posy = -ays*(byv-ayv)/(bys-ays) + ayv
posx = -axs*(bxv-axv)/(bxs-axs) + axv
gist.plt('b',posx,posy-0.005,justify='LT',color=color)
# bottom left corner row
gist.plt(str(M),posx-0.005,posy,justify='RB',color=color)
# top left corner row
posy = (M-ays)*(byv-ayv)/(bys-ays) + ayv
gist.plt('b',posx-0.005,posy,justify='RT',color=color)
# bottom right column
posy = -ays*(byv-ayv)/(bys-ays) + ayv
posx = (N-axs)*(bxv-axv)/(bxs-axs) + axv
gist.plt(str(N),posx,posy-0.005,justify='RT',color=color)
def imagesc(z,cmin=None,cmax=None,xryr=None,_style='default', palette=None,
color='black',colormap=None):
"""Plot an image on axes.
z -- The data
cmin -- Value to map to lowest color in palette (min(z) if None)
cmax -- Value to map to highest color in palette (max(z) if None)
xryr -- (xmin, ymin, xmax, ymax) coordinates to print
(0, 0, z.shape[1], z.shape[0]) if None
_style -- A 'style-sheet' to use if desired (a default one will be used
if 'default'). If None, then no style will be imposed.
palette -- A string for a palette previously saved in a file (see write_palette)
or an array specifying the red-green-blue values (2-d array N x 3) or
gray-scale values (2-d array N x 1 or 1-d array).
color -- The color to use for the axes.
"""
if xryr is None:
xryr = (0,0,z.shape[1],z.shape[0])
try:
_style = None
saveval = gist.plsys(2)
gist.plsys(saveval)
except:
_style = 'default'
if not _hold:
gist.fma()
gist.animate(0)
if _style is not None:
if _style == "default":
_style=os.path.join(_user_path,'image.gs')
system = write_style.getsys(hticpos='below',vticpos='left',frame=1,
color=color)
fid = open(_style,'w')
fid.write(write_style.style2string(system))
fid.close()
gist.window(style=_style)
_current_style=_style
if cmax is None:
cmax = max(ravel(z))
if cmin is None:
cmin = min(ravel(z))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(z,cmin=cmin,cmax=cmax)
if (colormap is not None): palette=colormap
change_palette(palette)
gist.pli(byteimage,xryr[0],xryr[1],xryr[2],xryr[3])
return
def movie(data,aslice,plen,loop=1,direc='z',cmax=None,cmin=None):
"movie(data,slice,pause,loop=1,direc='z')"
gist.animate(1)
if type(aslice) is types.IntType:
num = aslice
aslice = [slice(None)]*3
aslice[ord('x')-ord(direc)-1] = num
for num in range(loop):
for k in range(data.shape[0]):
gist.fma()
gist.pli(data[k][aslice],cmax=cmax,cmin=cmin)
gist.pause(plen)
gist.animate(0)
def setdpi(num):
""" Set the dpi for new windows """
if num in [75,100]:
_dpi = num
gist.set_default_dpi(_dpi)
else:
raise ValueError, "DPI must be 75 or 100"
def figure(n=None,style=os.path.join(_user_path,"currstyle.gs"), color=-2, frame=0, labelsize=14, labelfont='helvetica',aspect=1.618,land=0):
global _figures
if (aspect < 0.1) or (aspect > 10):
aspect = 1.618
if isinstance(color, types.StringType):
color = _colornum[color]
fid = open(style,'w')
syst = write_style.getsys(color=color,frame=frame,
labelsize=labelsize,font=labelfont)
if land:
cntr = (5.5*inches,4.25*inches) # horizontal, vertical
else:
cntr = (4.25*inches,5.5*inches)
height = 4.25*inches
width = aspect*height
syst['viewport'] = [cntr[0]-width/2.0,cntr[0]+width/2.0,cntr[1]-height/2.0,cntr[1]+height/2.0]
fid.write(write_style.style2string(syst,landscape=land))
fid.close()
if n is None:
winnum = gist.window(style=style,width=int(width*1.25/inches*_dpi),height=int(height*1.4/inches*_dpi))
if winnum < 0:
gist.window(style=style,width=int(width*1.25/inches*_dpi),height=int(height*1.4/inches*_dpi))
else:
gist.window(n,style=style,width=int(width*1.25/inches*_dpi),height=int(height*1.4/inches*_dpi))
_current_style = style
return
def full_page(win):
gist.window(win,style=_current_style,width=int(_dpi*8.5),height=_dpi*11)
def _add_color(system, color, frame=0):
try:
system['ticks']['horiz']['tickStyle'] = {'color':color}
system['ticks']['horiz']['gridStyle'] = {'color':color}
except KeyError:
system['ticks']['horiz'] = {}
system['ticks']['horiz']['tickStyle'] = {'color':color}
system['ticks']['horiz']['gridStyle'] = {'color':color}
try:
text = system['ticks']['horiz']['textStyle']
except KeyError:
system['ticks']['horiz']['textStyle'] = {}
text = system['ticks']['horiz']['textStyle']
text['color'] = color
try:
system['ticks']['vert']['tickStyle'] = {'color':color}
system['ticks']['vert']['gridStyle'] = {'color':color}
except KeyError:
system['ticks']['vert'] = {}
system['ticks']['vert']['tickStyle'] = {'color':color}
system['ticks']['vert']['gridStyle'] = {'color':color}
try:
text = system['ticks']['vert']['textStyle']
except KeyError:
system['ticks']['vert']['textStyle'] = {}
text = system['ticks']['vert']['textStyle']
text['color'] = color
system['ticks']['frame'] = frame
system['ticks']['frameStyle'] = {'color':color}
def _chng_font(system, font, height):
if height is None:
height=14
if font is None:
font = 'helvetica'
num = write_style.tfont[font]
system['ticks'] = {
'horiz':{
'textStyle':{'font':num,
'height':height*points}
},
'vert':{
'textStyle':{'font':num,
'height':height*points}
}
}
return
def _remove_ticks(system):
system['ticks'] = {'horiz': {'flags':0},
'vert': {'flags':0},
}
return
plotframe = gist.plsys
import os
def subplot(Numy,Numx,win=0,pw=None,ph=None,hsep=100,vsep=100,color='black',frame=0,fontsize=8,font=None,ticks=1,land=0):
# Use gist.plsys to change coordinate systems
# all inputs (except fontsize) given as pixels, gist wants
# things in normalized device
# coordinate. Window is brought up with center of window at
# center of 8.5 x 11 inch page: in landscape mode (5.25, 4.25)
# or at position (4.25,6.75) for portrait mode
msg = 1
if pw is None:
pw = Numx*300
msg = 0
if ph is None:
ph = Numy*300
msg = 0
if land:
maxwidth=min(_maxwidth,11*_dpi)
maxheight=min(_maxheight,8.5*_dpi)
else:
maxwidth=min(_maxwidth,8.5*_dpi)
maxheight=min(_maxheight,11*_dpi)
printit = 0
if ph > maxheight:
ph = maxheight
printit = 1
if pw > maxwidth:
pw = maxwidth
printit = 1
if _dpi != 100:
fontsize = 12
conv = inches *1.0 / _dpi # multiply by this factor to convert pixels to
# NDC
if printit and msg:
message = "Warning: Requested height and width too large.\n"
message +="Changing to %d x %d" % (pw,ph)
print message
# Now we've got a suitable height and width
if land:
cntr = array([5.5,4.25])*_dpi # landscape
else:
if sys.platform == 'win32':
cntr = array([4.25,6.75])*_dpi # portrait
else:
cntr = array([4.25,5.5])*_dpi
Yspace = ph/float(Numy)*conv
Xspace = pw/float(Numx)*conv
hsep = hsep * conv
vsep = vsep * conv
ytop = (cntr[1]+ph/2.0)*conv
xleft = (cntr[0]-pw/2.0)*conv
if type(color) is types.StringType:
color = _colornum[color]
systems=[]
ind = -1
for nY in range(Numy):
ystart = ytop - (nY+1)*Yspace
for nX in range(Numx):
xstart = xleft + nX*Xspace
systems.append({})
systems[-1]['viewport'] = [xstart+hsep/2.0,xstart+Xspace-hsep/2.0,ystart+vsep/2.0,ystart+Yspace-vsep/2.0]
if font is not None or fontsize is not None:
_chng_font(systems[-1],font,fontsize)
if color != -3 or frame != 0:
_add_color(systems[-1],color,frame=frame)
if ticks != 1:
_remove_ticks(systems[-1])
_current_style=os.path.join(_user_path,"subplot%s.gs" % win)
fid = open(_current_style,'w')
fid.write(write_style.style2string(systems,landscape=land))
fid.close()
gist.winkill(win)
gist.window(win,style=_current_style,width=int(pw),height=int(ph))
_dwidth=6*inches
_dheight=6*inches
import colorbar
def imagesc_cb(z,cmin=None,cmax=None,xryr=None,_style='default',
zlabel=None,font='helvetica',fontsize=16,color='black',
palette=None):
"""Plot an image on axes with a colorbar on the side.
z -- The data
cmin -- Value to map to lowest color in palette (min(z) if None)
cmax -- Value to map to highest color in palette (max(z) if None)
xryr -- (xmin, ymin, xmax, ymax) coordinates to print
(0, 0, z.shape[1], z.shape[0]) if None
_style -- A 'style-sheet' to use if desired (a default one will be used
if 'default'). If None, then no style will be imposed.
palette -- A string for a palette previously saved in a file (see write_palette)
or an array specifying the red-green-blue values (2-d array N x 3) or
gray-scale values (2-d array N x 1 or 1-d array).
zlabel -- The label to attach to the colorbar (font, fontsize, and color
match this).
color -- The color to use for the ticks and frame.
"""
if xryr is None:
xryr = (0,0,z.shape[1],z.shape[0])
if not _hold:
gist.fma()
gist.animate(0)
if _style is not None:
if _style == 'default':
_style=os.path.join(_user_path,"colorbar.gs")
system = write_style.getsys(hticpos='below',vticpos='left',frame=1,color=color)
fid = open(_style,'w')
fid.write(write_style.style2string(system))
fid.close()
gist.window(style=_style)
_current_style=_style
if cmax is None:
cmax = max(ravel(z))
if cmin is None:
cmin = min(ravel(z))
cmax = float(cmax)
cmin = float(cmin)
change_palette(palette)
byteimage = gist.bytscl(z,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xryr[0],xryr[1],xryr[2],xryr[3])
colorbar.color_bar(cmin,cmax,ncol=240,zlabel=zlabel,font=font,fontsize=fontsize,color=color)
def xlabel(text,color=None,font='helvetica',fontsize=16,deltax=0.0,deltay=0.0):
"""To get symbol font for the next character precede by !. To get
superscript enclose with ^^
To get subscript enclose with _<text>_
"""
global _textcolor
if color is None:
color = _textcolor
else:
_textcolor = color
if color is None:
color = 'black'
vp = gist.viewport()
xmidpt = (vp[0] + vp[1])/2.0 + deltax
y0 = vp[2] - 0.035 + deltay
if text != "":
gist.plt(text, xmidpt, y0, color=color,
font=font, justify="CT", height=fontsize)
return xmidpt, y0
def ylabel(text,color=None,font='helvetica',fontsize=16,deltax=0.0,deltay=0.0):
"""To get symbol font for the next character precede by !. To get
superscript enclose with ^^
To get subscript enclose with _<text>_
"""
global _textcolor
if color is None:
color = _textcolor
else:
_textcolor = color
if color is None:
color = 'black'
vp = gist.viewport()
ymidpt = (vp[2] + vp[3])/2.0 + deltay
x0 = vp[0] - 0.055 + deltax
if text != "":
gist.plt(text, x0, ymidpt, color=color,
font=font, justify="CB", height=fontsize, orient=1)
return x0, ymidpt
def title(text,color=None,font='helvetica',fontsize=18,deltax=0.0,deltay=0.0):
"""Set title for plot.
To get symbol font for the next character precede by !. To get
superscript enclose with ^^
To get subscript enclose with _<text>_
"""
global _textcolor
if color is None:
color = _textcolor
else:
_textcolor = color
if color is None:
color = 'black'
vp = gist.viewport()
xmidpt = (vp[0] + vp[1])/2.0 + deltax
if text != "":
gist.plt(text,xmidpt,vp[3] + 0.02 + deltay, font=font, justify='CB',
height=fontsize, color=color)
def title3(text,color=None,font='helvetica',fontsize=18,deltax=0.0,deltay=0.0):
global _textcolor
if color is None:
color = _textcolor
else:
_textcolor = color
if color is None:
color = 'black'
vp = gist.viewport()
xmidpt = (vp[0] + vp[1])/2.0 + deltax
if text != "":
gist.plt(text,xmidpt,vp[3]-0.05-deltay, font=font, justify='CB',
height=fontsize, color=color)
def stem(m, y, linetype='b-', mtype='mo', shift=0.013):
y0 = Numeric.zeros(len(y),y.dtype.char)
y1 = y
x0 = m
x1 = m
try:
override = 1
savesys = gist.plsys(2)
gist.plsys(savesys)
except:
override = 0
if not (_hold or override):
gist.fma()
thetype,thecolor,themarker,tomark = _parse_type_arg(linetype,0)
lcolor = thecolor
gist.pldj(x0, y0, x1, y1, color=thecolor, type=thetype)
thetype,thecolor,themarker,tomark = _parse_type_arg(mtype,0)
if themarker not in ['o','x','.','*']:
themarker = 'o'
y = where(numpy.isfinite(y),y,0)
gist.plg(y,m,color=thecolor,marker=themarker,type='none')
gist.plg(Numeric.zeros(len(m)),m,color=lcolor,marks=0)
gist.limits()
lims = gist.limits()
newlims = [None]*4
vp = gist.viewport()
factor1 = vp[1] - vp[0]
factor2 = vp[3] - vp[2]
cfactx = factor1 / (lims[1] - lims[0])
cfacty = factor2 / (lims[3] - lims[2])
d1 = shift / cfactx
d2 = shift / cfacty
newlims[0] = lims[0] - d1
newlims[1] = lims[1] + d1
newlims[2] = lims[2] - d2
newlims[3] = lims[3] + d2
gist.limits(*newlims)
return
def makeleg(leg,pos,lenx,dd,theight=12):
# Place legend
x0,y0 = pos
dx,dy = dd
for k in range(len(leg['txt'])):
gist.plg([y0+k*dy]*2,[x0,x0+lenx],type=leg['sym'][k][1],marks=0)
if leg['sym'][k][0] is not None:
gist.plg([y0+k*dy]*2,[x0,x0+lenx],type='none',marks=1,marker=leg['sym'][k][0])
if leg['txt'][k] != "":
gist.plt(leg['txt'][k],x0+lenx+dx,y0+k*dy,height=theight,tosys=1,justify='LH')
return
def twoplane(DATA,slice1,slice2,dx=[1,1,1],cmin=None,cmax=None,xb=None,xe=None,
xlab="",ylab="",zlab="",clab="",titl="",
totalheight=0.5,space=0.02, medfilt=5,
font='helvetica',fontsize=16,color='black',lcolor='white',
fcolor='black', cb=1, line=1, palette=None):
""" Visualize a 3d volume as a two connected slices. The slices are
given in the 2-tuple slice1 and slice2.
These give the dimension and corresponding slice numbers to plot.
The unchosen slice is the common dimension in the images.
twoplane(img3d,(0,12),(2,60)) plots two images with a common "x"-axis
as the first dimension. The lower plot is img3d[12,:,:] with a line
through row 60 corresponding to the slice transpose(img3d[:,:,60])
plotted above this first plot.
"""
if xb is None:
xb = [0,0,0]
if xe is None:
xe = DATA.shape
# get two image slices
# make special style file so that pixels are square
getdx = array([1,1,1])
imgsl1 = [slice(None,None),slice(None,None),slice(None,None)]
imgsl1[slice1[0]] = slice1[1]
img1 = DATA[imgsl1]
getdx1 = getdx.__copy__()
getdx1[slice1[0]] = 0
dx1 = compress(getdx1,dx)
xb1 = compress(getdx1,xb)
xe1 = compress(getdx1,xe)
imgsl2 = [slice(None,None),slice(None,None),slice(None,None)]
imgsl2[slice2[0]] = slice2[1]
img2 = DATA[imgsl2]
getdx2 = getdx.__copy__()
getdx2[slice2[0]] = 0
dx2 = compress(getdx2,dx)
xb2 = compress(getdx2,xb)
xe2 = compress(getdx2,xe)
if (slice1[0] == slice2[0]):
raise ValueError, "Same slice dimension.."
for k in range(3):
if k not in [slice1[0],slice2[0]]:
samedim = k
break
if samedim == 2:
pass
elif samedim == 1:
if samedim > slice1[0]:
img1 = transpose(img1)
dx1 = dx1[::-1]
xb1 = xb1[::-1]
xe1 = xe1[::-1]
if samedim > slice2[0]:
img2 = transpose(img2)
dx2 = dx2[::-1]
xb2 = xb2[::-1]
xe2 = xe2[::-1]
else:
img1 = transpose(img1)
dx1 = dx1[::-1]
xb1 = xb1[::-1]
xe1 = xe1[::-1]
img2 = transpose(img2)
dx2 = dx2[::-1]
xb2 = xb2[::-1]
xe2 = xe2[::-1]
assert(img1.shape[1] == img2.shape[1])
units = totalheight - space
totaldist = img1.shape[0]*dx1[0] + img2.shape[0]*dx2[0]
convfactor = units / float(totaldist)
height1 = img1.shape[0]*dx1[0] * convfactor
xwidth = img1.shape[1]*dx1[1]*convfactor
if xwidth > 0.6:
rescale = 0.6 / xwidth
xwidth = rescale * xwidth
height1 = rescale * height1
totalheight = totalheight * rescale
print xwidth, height1
else:
print xwidth
ystart = 0.5 - totalheight / 2
ypos1 = [ystart, ystart+height1]
ypos2 = [ystart+height1+space,ystart+totalheight]
xpos = [0.395-xwidth/2.0, 0.395+xwidth/2.0]
systems = []
system = write_style.getsys(hticpos='', vticpos='left')
system['viewport'] = [xpos[0],xpos[1],ypos2[0],ypos2[1]]
if fcolor not in ['black',None]:
_add_color(system, _colornum[color])
systems.append(system)
system = write_style.getsys(hticpos='below', vticpos='left')
system['viewport'] = [xpos[0],xpos[1],ypos1[0],ypos1[1]]
if fcolor not in ['black',None]:
_add_color(system, _colornum[color])
systems.append(system)
the_style = os.path.join(_user_path,"two-plane.gs")
write_style.writestyle(the_style,systems)
gist.window(style=the_style)
_current_style = the_style
change_palette(palette)
gist.plsys(1)
if medfilt > 1:
img1 = signal.medfilt(img1,[medfilt,medfilt])
img2 = signal.medfilt(img2,[medfilt,medfilt])
if cmax is None:
cmax = max(max(ravel(img1)),max(ravel(img2)))
if cmin is None:
cmin = min(min(ravel(img1)),min(ravel(img2)))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(img2,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xb2[1],xb2[0],xe2[1],xe2[0])
ylabel(zlab,color=color)
if titl != "":
title(titl,color=color)
if line:
xstart = xb2[1]
xstop = xe2[1]
yval = slice1[1]*(xe2[0] - xb2[0])/(img2.shape[0]) + xb2[0]
gist.pldj([xstart],[yval],[xstop],[yval],type='dash',width=2,color='white')
gist.plsys(2)
ylabel(ylab,color=color)
xlabel(xlab,color=color)
byteimage = gist.bytscl(img1,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xb1[1],xb1[0],xe1[1],xe1[0])
if line:
xstart = xb1[1]
xstop = xe1[1]
yval = slice2[1]*(xe1[0] - xb1[0])/(img1.shape[0]) + xb1[0]
gist.pldj([xstart],[yval],[xstop],[yval],type='dash',width=2,color='white')
if cb:
colorbar.color_bar(cmin,cmax,ncol=240,zlabel=clab,font=font,fontsize=fontsize,color=color,ymin=ystart,ymax=ystart+totalheight,xmin0=xpos[1]+0.02,xmax0=xpos[1]+0.04)
def surf(z,x=None,y=None,win=None,shade=0,edges=1,edge_color="black",phi=-45.0,
theta=30.0,zscale=1.0,palette=None,gnomon=0):
"""Plot a three-dimensional wire-frame (surface): z=f(x,y)
"""
if win is None:
pl3d.window3()
else:
pl3d.window3(win)
pl3d.set_draw3_(0)
phi0 = phi*pi/180.0
theta0 = theta*pi/180.0
pl3d.orient3(phi=phi0,theta=theta0)
pl3d.light3()
change_palette(palette)
sz = numpy.shape(z)
if len(sz) != 2:
raise ValueError, "Input must be a 2-d array --- a surface."
N,M = sz
if x is None:
x = arange(0,N)
if y is None:
y = arange(0,M)
x = numpy.squeeze(x)
y = numpy.squeeze(y)
if (len(numpy.shape(x)) == 1):
x = x[:,newaxis]*ones((1,M))
if (len(numpy.shape(y)) == 1):
y = ones((N,1))*y[newaxis,:]
plwf.plwf(z,y,x,shade=shade,edges=edges,ecolor=edge_color,scale=zscale)
lims = pl3d.draw3(1)
gist.limits(lims[0],lims[1],lims[2],lims[3])
pl3d.gnomon(gnomon)
def expand_limits(xpcnt,ypcnt=None):
"""Expand the limits by a certain percentage.
"""
if ypcnt is None:
ypcnt = xpcnt
if xpcnt > 1:
xpcnt = xpcnt / 100.0
if ypcnt > 1:
ypcnt = ypcnt / 100.0
xmin, xmax, ymin, ymax, flag = gist.limits()
dx = (xmax-xmin)*xpcnt/2.0
dy = (ymax-ymin)*ypcnt/2.0
gist.limits(xmin-dx,xmax+dx,ymin-dy,ymax+dy)
def axes(type='b|'):
vals = gist.limits()
v0,v1,v2,v3 = vals[:4]
x0 = numpy.r_[v0:v1:5j]
y0 = 5*[0]
x1 = 5*[0]
y1 = numpy.r_[v2:v3:5j]
plot(x0,y0,type,x1,y1,type,hold=1)
gist.limits(v0,v1,v2,v3)
def bode(w,H,win=0,frame=0,lcolor='blue',color='black',tcolor='black',freq='rad'):
"""Plot a bode plot of the transfer function H as a function of w.
"""
if freq == 'Hz':
w = w /2.0 / pi
subplot(2,1,win,hsep=120,frame=frame,color=color)
gist.plsys(1)
gist.plg(20*numpy.log10(abs(H)),w,type='solid',color=lcolor,marks=0)
gist.logxy(1,0)
gist.gridxy(1,1)
if freq == 'Hz':
xlabel('Frequency (Hz)',color=tcolor,deltay=-0.005)
else:
xlabel('Frequency (rad/s)',color=tcolor,deltay=-0.005)
ylabel('Magnitude (dB)',color=tcolor,deltax=-0.005)
title("Bode Plot",color=tcolor)
gist.plsys(2)
gist.plg(180/pi*numpy.unwrap(MLab.angle(H)),w,type='solid',color=lcolor,marks=0)
gist.logxy(1,0)
gist.gridxy(1,1)
if freq == 'Hz':
xlabel('Frequency (Hz)',color=tcolor,deltay=-0.005)
else:
xlabel('Frequency (rad/s)',color=tcolor,deltay=-0.005)
ylabel('Phase (deg.)',color=tcolor,deltax=-0.005)
def addtext(txt,xy=None,fontsize=16,font='helvetica',color='black',
orient=0,justify='LA',tosys=0):
if xy is None:
result = gist.mouse(0,0,"Click on point for lower left starting position")
if result is None:
raise ValueError, "Invalid point entered."
x,y = result[4],result[5]
tosys = 0
else:
x,y = xy
if isinstance(txt, type('')) and txt != '':
gist.plt(txt, x, y, tosys=tosys, justify=justify,
height=fontsize,font=font, color=color, orient=orient)
return
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