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 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(numpy.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 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 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 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 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 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 stem(m, y, linetype='b-', mtype='mo', shift=0.013):
y0 = numpy.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(numpy.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 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 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*numpy.ones(len(x), dtype=numpy.int32)
hw = width * (x[1]-x[0])/ 2.0
Xa = x-hw
Xb = x+hw
Ya = numpy.zeros(len(y),'d')
Yb = y
X = numpy.array((Xa,Xa,Xb,Xb))
Y = numpy.array((Ya,Yb,Yb,Ya))
X = numpy.reshape(numpy.transpose(X),(4*len(N),))
Y = numpy.reshape(numpy.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 * numpy.ones(len(N))
gist.plfp(Z.astype(numpy.uint8),Y,X,N)
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 matplot(x,y=None,axis=-1):
if y is None: # no axis data
y = x
x = numpy.arange(0,y.shape[axis])
x,y = numpy.asarray(x), numpy.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 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 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 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 = numpy.arange(llx,llx+width,dx)
legy = numpy.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 = numpy.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 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,axis=-1)
xb1 = compress(getdx1,xb,axis=-1)
xe1 = compress(getdx1,xe,axis=-1)
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,axis=-1)
xb2 = compress(getdx2,xb,axis=-1)
xe2 = compress(getdx2,xe,axis=-1)
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 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,axis=-1)
xb1 = compress(getdx1,xb,axis=-1)
xe1 = compress(getdx1,xe,axis=-1)
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,axis=-1)
xb2 = compress(getdx2,xb,axis=-1)
xe2 = compress(getdx2,xe,axis=-1)
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:
import scipy.signal
img1 = scipy.signal.medfilt(img1,[medfilt,medfilt])
img2 = scipy.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 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 = numpy.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