def _makebytes(data,top,cmin,cmax):
if data.dtype == UnsignedInt8:
return data
if cmin is None:
if cmax is None:
bytedata = gist.bytscl(data,top=255)
else:
bytedata = gist.bytscl(data,cmax=cmax,top=255)
else:
if cmax is None:
bytedata = gist.bytscl(data,cmin=cmin,top=255)
else:
bytedata = gist.bytscl(data,cmin=cmin,cmax=cmax,top=255)
return bytedata
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 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 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)
