def plot(self, filename=None):
import gist
gist.window(self.id, wait=1)
gist.pltitle(self.title)
gist.animate(1)
var = self.vars[0]
if isinstance(var, FaceVariable):
x, y = var.mesh.faceCenters
elif isinstance(var, CellVariable):
x, y = var.mesh.cellCenters
gist.plmesh(numerix.array([y, y]), numerix.array([x, y]))
vx = numerix.array(var[0])
vy = numerix.array(var[1])
maxVec = var.mag.max().value
maxGrid = var.mesh._cellDistances.max()
gist.plv(numerix.array([vy, vy]),
numerix.array([vx, vx]),
scale=maxGrid / maxVec * 3,
hollow=1,
aspect=0.25) #,scale=0.002)
if filename is not None:
gist.hcp_file(filename)
gist.hcp()
gist.fma()
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 plot(self, filename=None):
import gist
gist.window(self.id, wait = 1)
gist.pltitle(self.title)
gist.animate(1)
var = self.vars[0]
if isinstance(var, FaceVariable):
x, y = var.getMesh().getFaceCenters()
elif isinstance(var, CellVariable):
x, y = var.getMesh().getCellCenters()
gist.plmesh(numerix.array([y, y]), numerix.array([x, y]))
vx = numerix.array(var[0])
vy = numerix.array(var[1])
maxVec = var.getMag().max().getValue()
maxGrid = var.getMesh()._getCellDistances().max()
gist.plv(numerix.array([vy,vy]), numerix.array([vx,vx]), scale=maxGrid / maxVec * 3, hollow=1, aspect=0.25) #,scale=0.002)
if filename is not None:
gist.hcp_file(filename)
gist.hcp()
gist.fma()
def __init__(self, vars, title=None, dpi=75, **kwlimits):
"""
Create a `_GistViewer` object.
:Parameters:
vars
a `CellVariable` or tuple of `CellVariable` objects to plot
title
displayed at the top of the `Viewer` window
dpi
the dot-per-inch resolution of the display
xmin, xmax, ymin, ymax, datamin, datamax
displayed range of data. A 1D `Viewer` will only use `xmin` and
`xmax`, a 2D viewer will also use `ymin` and `ymax`. All
viewers will use `datamin` and `datamax`. Any limit set to a
(default) value of `None` will autoscale.
"""
if self.__class__ is _GistViewer:
raise NotImplementedError, "can't instantiate abstract base class"
_Viewer.__init__(self, vars=vars, title=title, **kwlimits)
self.mesh = self.vars[0].getMesh()
self.id = _GistViewer._id
_GistViewer._id += 1
import gist
gist.window(self.id, wait = 1, dpi = dpi, display = '')
def __init__(self, vars, title=None, dpi=75, **kwlimits):
"""
Create a `_GistViewer` object.
:Parameters:
vars
a `CellVariable` or tuple of `CellVariable` objects to plot
title
displayed at the top of the `Viewer` window
dpi
the dot-per-inch resolution of the display
xmin, xmax, ymin, ymax, datamin, datamax
displayed range of data. A 1D `Viewer` will only use `xmin` and
`xmax`, a 2D viewer will also use `ymin` and `ymax`. All
viewers will use `datamin` and `datamax`. Any limit set to a
(default) value of `None` will autoscale.
"""
if self.__class__ is _GistViewer:
raise NotImplementedError, "can't instantiate abstract base class"
AbstractViewer.__init__(self, vars=vars, title=title, **kwlimits)
self.mesh = self.vars[0].mesh
self.id = _GistViewer._id
_GistViewer._id += 1
import gist
gist.window(self.id, wait=1, dpi=dpi, display='')
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 _plot(self):
import gist
gist.window(self.id, wait=1)
gist.animate(1)
gist.pltitle(self.title)
gist.palette(self.palette)
gist.gridxy(self.grid)
if self.limits != None:
gist.limits(self._getLimit('xmin'), self._getLimit('xmax'),
self._getLimit('ymin'), self._getLimit('ymax'))
def _plot(self):
import gist
gist.window(self.id, wait = 1)
gist.animate(1)
gist.pltitle(self.title)
gist.palette(self.palette)
gist.gridxy(self.grid)
if self.limits != None:
gist.limits(self._getLimit('xmin'),
self._getLimit('xmax'),
self._getLimit('ymin'),
self._getLimit('ymax'))
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 plot(self, filename=None):
import gist
gist.window(self.id, wait=1, style=self.style)
gist.pltitle(self.title)
gist.animate(1)
if self.limits != None:
gist.limits(self._getLimit('xmin'), self._getLimit('xmax'),
self._getLimit(('datamin', 'ymin')),
self._getLimit(('datamax', 'ymax')))
self._plotArrays()
_GistViewer.plot(self, filename=filename)
def plot(self, filename = None):
import gist
gist.window(self.id, wait = 1, style = self.style)
gist.pltitle(self.title)
gist.animate(1)
if self.limits != None:
gist.limits(self._getLimit('xmin'),
self._getLimit('xmax'),
self._getLimit(('datamin', 'ymin')),
self._getLimit(('datamax', 'ymax')))
self._plotArrays()
_GistViewer.plot(self, filename = filename)
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 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 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 matview(A,cmax=None,cmin=None,palette=None,color='black'):
"""Plot an image of a matrix.
"""
A = numpy.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 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
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=1,wait=0,**kwd):
# 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
# kwd for window (... , parent=None,xpos=None,ypos=None)
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),wait=wait,**kwd)
def full_page(win):
gist.window(win,style=_current_style,width=int(_dpi*8.5),height=_dpi*11)
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 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 full_page(win):
gist.window(win,style=_current_style,width=int(_dpi*8.5),height=_dpi*11)
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))
def doit(zernlist=None,
nact=9,
cents=None,
avphase=None,
readnoise=10.,
usePoisson=1,
sig=1000.,
fullpupil=0,
monteNoiseCovariance=0,
phaseCov="bccb",
diagonaliseinvChatReordered=1,
diagonaliseA=0.5,
useChatFromDiagonalisedA=1,
oversampleFFT=0,
fft2d=1,
oversampleAndBinFFTofr=0,
removeHiFreqZ=0,
removeHiFreqP=0,
removeHiFreqX=0,
convToPxl=1):
"""Create a zernike mode and get the centroids for this. Put these centroids into the PCG algorithm, and recreate the phase, and then compare with the original input phase
defaultOptions are:
diagonaliseinvChatReordered:1#should we diagonlise C-1, or use whole MX?
diagonaliseA:0#should we diagonalise A or use the whole MX.
useChatFromDiagonalisedA:1#should we compute invChat using a diagonalised chat or not?
zernlist can be a dict of zernikes eg {3:1} would be focus, amplitude 1...
or it can be the phase, or it can be none (in which case a phasescreen is
created).
This now seems to be working fairly well, iterates to an exact solution after about 10 iters, and 4-5 should be sufficient for a good solution.
"""
options = {
"diagonaliseinvChatReordered": diagonaliseinvChatReordered,
"diagonaliseA": diagonaliseA,
"useChatFromDiagonalisedA": useChatFromDiagonalisedA,
"oversampleFFT": oversampleFFT,
"2dfft": fft2d,
"oversampleAndBinFFTofr": oversampleAndBinFFTofr,
"removeHiFreqZ": removeHiFreqZ,
"removeHiFreqP": removeHiFreqP,
"removeHiFreqX": removeHiFreqX
}
gist.window(0)
gist.palette("gray.gp")
pupfn = util.tel.Pupil(nact - 1, (nact - 1) / 2., 0).fn
actfn = util.tel.Pupil(nact, nact / 2., 0).fn
noiseCov = None
if type(cents) == type(None):
if type(zernlist) in [type(1), type(1.)]:
zernlist = {zernlist: 1.}
elif type(zernlist) == type([]):
tmp = {}
for i in zernlist:
tmp[i] = 1.
zernlist = tmp
elif type(zernlist) == type(None):
zernlist = science.infScrn.makeInitialScreen(dpix=(nact - 1) * 8,
Dtel=4.2,
L0=30.,
scrnXPxls=None,
scrnYPxls=None,
seed=None,
tstep=0.05,
globR0=0.2,
strLayer=1.,
natype=numpy.float64,
windDirection=0.,
vWind=10.)[:-1,
1:].copy()
c, phase, avphase = getFocusCents(zernlist,
nact=nact,
readnoise=readnoise,
usePoisson=usePoisson,
sig=sig,
plot=1,
fullpupil=fullpupil)
print phase.shape
cents = c.cent
if monteNoiseCovariance:
noiseCov = c.computeNoiseCovariance(20, convertToRad=1)
if convToPxl: #convert from radians to pixel values for the noises...
radToPxlFactor = 1. / c.convFactor**2
else:
radToPxlFactor = 1.
Pcg = testfull(fromdisk=0,
nact=nact,
pupfn=pupfn,
actfn=actfn,
fullpmx=1,
noiseCov=noiseCov,
phaseCov=phaseCov,
options=options,
radToPxlFactor=radToPxlFactor) #agbhome
Pcg.newCentroids(cents)
Pcg.initialise()
#now inverse A, multiply with b, to get the MVM reconstructed phase...
invA = numpy.linalg.inv(Pcg.A)
gist.fma()
gist.pli(invA)
raw_input("Displaying inverse of A... press return")
gist.fma()
gist.pli(phase)
raw_input("The phase... press a key")
recphase = quick.dot(invA, Pcg.b)
print "Reconstructed phase min/max:", min(recphase.flat), max(
recphase.flat)
recphase.shape = (9, 9)
gist.window(4)
gist.palette("gray.gp")
gist.fma()
gist.pli(recphase)
gist.palette("gray.gp")
gist.window(0)
chires = numpy.zeros((100, ), "d")
#also compute what a traditional MVM with pokemx would give...
#invpokemx=numpy.linalg.pinv(Pcg.pokemx)#same as generalised_inverse
#pmphase=quick.dot(invpokemx,cents)
print "Press return for next iteration or key+return to quit"
#gist.fma()
#gist.pli(numpy.reshape(pmphase,(nact,nact)))
if type(avphase) != type(None):
print "press a key"
raw_input()
gist.fma()
gist.pli(avphase)
actphase = phase2acts(avphase)
actphase -= numpy.average(actphase.flat) #remove piston
smallpupfn = util.tel.Pupil(nact, nact / 2. - 2, 0).fn
raw_input("press return (min, max actphase is %g %g" %
(min(actphase.flat), max(actphase.flat)))
gist.fma()
gist.pli(actphase)
gist.window(1)
gist.palette("gray.gp")
gist.window(2)
gist.palette("gray.gp")
niter = 0
while len(raw_input()) == 0:
niter += 1
gist.window(1)
gist.fma()
img = numpy.reshape(Pcg.x.real, (nact, nact))
gist.pli(img)
gist.window(2)
gist.fma()
img = smallpupfn * img
#gist.pli(numpy.where(img==0,min(img.flat),img))
gist.pli(numpy.reshape(Pcg.p, (nact, nact)))
gist.window(3)
gist.fma()
fftimg = numpy.fft.fft2(numpy.reshape(Pcg.x, (nact, nact)))
gist.pli(fftimg.real)
Pcg.nextIter()
chirespos = niter - 1
if chirespos > 99:
chirespos = 99
chires[chirespos] = chi2(Pcg.x, recphase,
scale=0) #changed from actphase
Pcg.alphaHist[chirespos] = Pcg.alpha
Pcg.betaHist[chirespos] = Pcg.beta
Pcg.tolerance[chirespos] = max(numpy.fabs(Pcg.xprev - Pcg.x))
print niter, Pcg.tolerance[chirespos], chires[chirespos], min(
Pcg.x.real), max(Pcg.x.real), min(Pcg.p), max(
Pcg.p), Pcg.alphaHist[chirespos], Pcg.betaHist[chirespos]
print "Press return for next iteration or key+return to quit"
gist.fma()
gist.plg(chires[:chirespos])
gist.window(2)
gist.fma()
gist.plg(Pcg.tolerance[:niter])
gist.window(0)
return Pcg, actphase, phase, recphase, c
def handle(self, data):
"""Handle data returned from the simulation"""
if data[1] == "warning" or data[1] == "error":
print "Error retrieving data", data[1:], data[0]
elif len(self.gettype()) == 0: #not doing anything with it...
pass
else:
if self.when[:3] != "rpt" or self.repeating == 1: #still expecting data
if self.ret != None and data[3].has_key(self.ret):
data = data[3][self.ret]
else:
data = None
ret = self.ret
if ret == None:
ret = "None"
if self.button == None:
d = {ret: data, "button": None}
else:
d = {ret: data, "button": self.button[0]}
try:
exec self.preprocess in d
except:
pass
if self.button != None:
self.button[0] = d["button"]
data = d[ret]
dim = self.dim
xaxis = self.xaxis
if dim == None:
if type(data) == numpy.ndarray:
if len(data.shape) > 1:
dim = 2
elif len(data.shape) == 1:
dim = 1
else:
dim = 0
else:
dim = 0
if dim == 1:
if type(self.xaxis) == types.NoneType:
if len(data.shape) > 1:
xaxis = data[0]
data = data[1:]
else:
xaxis = numpy.arange(data.shape[0])
data = data
else:
if type(self.xaxis) == types.StringType:
xaxis = eval(self.xaxis)
if self.gisttype:
if type(data) == numpy.ndarray:
if not self.info.has_key("window"):
self.info["window"] = 0
if not self.info.has_key("palette"):
self.info["palette"] = "gray.gp"
if not self.info.has_key("gistdpi"):
self.info["gistdpi"] = 75
if self.gistWindow == None:
self.gistWindow = gist.window(
self.info["window"],
wait=1,
dpi=self.info["gistdpi"])
gist.animate(0)
gist.animate(1)
gist.palette(self.info["palette"])
else:
gist.window(self.gistWindow)
#gist.fma()
if dim == 1:
for i in range(data.shape[0]):
gist.plg(data[i], xaxis)
else:
gist.pli(data)
gist.fma()
else:
print "Cannot display type %s with gist" % str(
type(data))
if self.pylabtype:
if type(data) == numpy.ndarray:
if not self.info.has_key("palette"):
self.info["palette"] = "gray"
if not self.info.has_key("interp"):
self.info["interp"] = "nearest"
if not self.info.has_key("plotwin"):
self.info["plotwin"] = mypylab.plot()
p = self.info["plotwin"]
p.win.set_title(self.title)
p.newPalette(self.info["palette"])
p.newInterpolation(self.info["interp"])
p.deactivatefn = self.cancel #deactivate
p = self.info["plotwin"]
if dim == 1:
p.dims = 1
axis = xaxis
else:
p.dims = 2
axis = None
if p.active:
p.plot(data, axis=axis)
else:
if self.button != None:
self.button[0] = 0
#print "Not expecting this data any more... (simdata.handle, type=pylab)"
self.repeating = 0
else:
print "Cannot display type %s with pylab" % str(
type(data))
if self.texttype:
#self.info["texttype"]=="ownwindow, mainwindow", default own
#self.info["replace"]==1 or 0, default 0
if not self.info.has_key("wintype"):
self.info["wintype"] = "ownwindow"
if not self.info.has_key("textreplace"):
self.info["textreplace"] = 0
if self.info["wintype"] == "ownwindow":
if self.textWindow == None:
self.textWindow = textbox(self.title)
self.textWindow.closeFunc = self.cancel #deactivate
if self.textWindow.destroyed == 0:
#print "adding text",str(data)
self.textWindow.addText(
str(data) + "\n",
replace=self.info["textreplace"])
else: #tell simulation not to send...
print "Not expecting this data any more... (simdata.handle, type=text)"
self.textWindow = None
self.repeating = 0
else:
print str(data)
if self.savetype:
if not self.info.has_key("filetype"):
self.info["filetype"] = "fits"
if not self.info.has_key("filename"):
self.info["filename"] = "tmp.fits"
if not self.info.has_key("filereplace"):
self.info["filereplace"] = 0
if self.info["filetype"] == "fits":
if type(data) == numpy.ndarray:
print "WARNING - depreciated - use util.FITS instead (code needs updating)"
if self.info["filereplace"]:
imghdu = util.pyfits.PrimaryHDU(
numarray.array(data))
imghdu.header.update("DATE", time.asctime())
imghdu.header.update("USER",
os.environ["USER"])
imghdu.header.update(
"CREATOR", "simctrl.py simulation control")
imghdu.header.update("TITLE", str(self.title))
imghdu.header.update("COMMAND", str(self.cmd))
imghdu.header.update("RETURN", str(self.ret))
imghdu.header.update("TYPE", self.gettype())
imghdu.header.update("PREPROC",
str(self.preprocess))
imghdu.header.update("DIMS", str(self.dim))
imghdu.header.update("XAXIS", str(self.xaxis))
imghdu.header.update("WHEN", str(self.when))
imghdu.header.update("INFO", str(self.info))
hdulist = util.pyfits.HDUList([imghdu])
hdulist.writeto(self.info["filename"],
clobber=True)
else:
f = util.pyfits.open(self.info["filename"],
mode="update")
imghdu = util.pyfits.ImageHDU(
numarray.array(data))
imghdu.header.update("DATE", time.asctime())
imghdu.header.update("USER",
os.environ["USER"])
imghdu.header.update(
"CREATOR", "simctrl.py simulation control")
imghdu.header.update("TITLE", str(self.title))
imghdu.header.update("COMMAND", str(self.cmd))
imghdu.header.update("RETURN", str(self.ret))
imghdu.header.update("TYPE", self.gettype())
imghdu.header.update("PREPROC",
str(self.preprocess))
imghdu.header.update("DIMS", str(self.dim))
imghdu.header.update("XAXIS", str(self.xaxis))
imghdu.header.update("WHEN", str(self.when))
imghdu.header.update("INFO", str(self.info))
f.append(imghdu)
f.close()
else:
print "Cannot save fits data of this format:", type(
data)
elif self.info["filetype"] == "csv":
if self.info["filereplace"]:
mode = "w"
else:
mode = "a"
f = open(self.info["filename"], mode)
f.write(
"#Date\t%s\n#User\t%s\n#Creator\tsimctrl.py simulation control\n#Title\t%s\n#Command\t%s\n#Return\t%s\n#Type\t%s\n#Preprocess\t%s\n#Dims\t%s\n#Xaxis\t%s\n#When\t%s\n#Info\t%s\n"
% (time.asctime(), os.environ["USER"],
str(self.title), str(self.cmd), str(self.ret),
self.gettype(), str(self.preprocess),
str(self.dim), str(self.xaxis), str(
self.when), str(self.info)))
if dim == 1:
try:
for i in range(xaxis.shape[0]):
f.write("%g" % float(xaxis[i]))
for j in range(data.shape[0]):
f.write("\t%g" % float(data[j][i]))
f.write("\n")
f.write("\n")
except:
print "Data not in correct 1D format - can't save as csv"
f.write(str(data))
f.write("\n\n")
else:
print "Can't save 2D data as csv... using text instead"
f.write(str(data))
f.write("\n\n")
f.close()
elif self.info["filetype"] == "text":
if self.info["filereplace"]:
mode = "w"
else:
mode = "a"
f = open(self.info["filename"], mode)
f.write(
"#Date\t%s\n#User\t%s\n#Creator\tsimctrl.py simulation control\n#Title\t%s\n#Command\t%s\n#Return\t%s\n#Type\t%s\n#Preprocess\t%s\n#Dims\t%s\n#Xaxis\t%s\n#When\t%s\n#Info\t%s\n"
% (time.asctime(), os.environ["USER"],
str(self.title), str(self.cmd), str(self.ret),
self.gettype(), str(self.preprocess),
str(self.dim), str(self.xaxis), str(
self.when), str(self.info)))
f.write(str(data))
f.write("\n\n")
f.close()
else:
print "Unrecognised filetype - not saving"
if self.feedbacktype:
try:
d = {"feedback": data}
exec self.info["feedbackmsg"] in d
msg = d["msg"]
except:
msg = "Feedback data:" + str(data)
print msg
exec self.post
else:
print "Warning: No longer expecting data for", self.cmd
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)
