示例#1
0
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
示例#2
0
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
示例#3
0
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
示例#4
0
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
示例#5
0
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)
示例#6
0
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)
示例#7
0
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)
示例#8
0
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)