Scripts: lineplot.py

# -----------------------------------------------------------------------------
# Make a matplotlib plot of density values along a ray from center of a map.
# Use the current view direction and update plot as models are rotated.
# For Yong Zi Tan for 3D FSC plotting.
#
# This script registers command "fscplot" which takes one argument, the density
# map for which the plot is made.  For example,
#
#    fscplot #0
#
def ray_values(v, direction):
    d = v.data
    center = [0.5*(s+1) for s in d.size]
    radius = 0.5*min([s*t for s,t in zip(d.size, d.step)])
    steps = max(d.size)
    from Matrix import norm
    dn = norm(direction)
    from numpy import array, arange, float32, outer
    dir = array(direction)/dn
    spacing = radius/dn
    radii = arange(0, steps, dtype = float32)*(radius/steps)
    ray_points = outer(radii, dir)
    values = v.interpolated_values(ray_points)
    return radii, values

# -----------------------------------------------------------------------------
#
def plot(x, y, xlabel, ylabel, title, fig = None):
    import matplotlib.pyplot as plt
    if fig is None:
        fig = plt.figure()
        fig.plot = ax = fig.add_subplot(1,1,1)
    else:
        ax = fig.plot
        ax.clear()
    ax.plot(x, y, linewidth=1.0)
    ax.set_xlabel(xlabel)
    ax.set_ylabel(ylabel)
    ax.set_ylim(ymin = -0.2, ymax = 1.01)
    ax.set_title(title)
    ax.grid(True)
    fig.canvas.manager.show()
    return fig

# -----------------------------------------------------------------------------
#
def update_plot(fsc_map, fig = None):
    xf = fsc_map.openState.xform
    from chimera import Vector
    direction = xf.inverse().apply(Vector(0,0,-1)).data()
    radii, values = ray_values(fsc_map, direction)
    title = '3D FSC plotted on axis %.3g,%.3g,%.3g' % direction
    fig = plot(radii, values, xlabel = 'Radius', ylabel = 'Correlation', title = title, fig = fig)
    return fig

# -----------------------------------------------------------------------------
#
def fsc_plot(fscMap):
    fig = update_plot(fscMap)
    from chimera import triggers
    h = triggers.addHandler('OpenState', motion_cb, (fscMap, fig))

# -----------------------------------------------------------------------------
#
   
def motion_cb(trigger_name, mf, trigger_data):
    if 'transformation change' in trigger_data.reasons:
        fsc_map, fig = mf
        update_plot(fsc_map, fig)

# -----------------------------------------------------------------------------
#
def fscplot_cmd(cmdname, args):
    from Commands import volume_arg, parse_arguments
    req_args = [('fscMap', volume_arg)]
    kw = parse_arguments(cmdname, args, req_args)
    fsc_plot(**kw)

# -----------------------------------------------------------------------------
#
from Midas.midas_text import addCommand
addCommand('fscplot', fscplot_cmd)