def plot_from_context(context):
do_plot, x, y, options, p = context
if do_plot:
if p is None:
master = options.pop('master', None)
title = options.pop('title', '')
if master is None:
master = Tk.Toplevel()
master.title(title)
figsize = options.pop('figsize', None)
if x is None:
p = pygmyplot.xy_plot(y, master=master, figsize=figsize)
else:
p = pygmyplot.xy_plot(x, y, master=master, figsize=figsize)
options['figsize'] = figsize
options['title'] = title
options['master'] = master
else:
# xlim = p.axes.get_xlim()
# ylim = p.axes.get_ylim()
p.plot(x, y)
# p.axes.set_xlim(*xlim)
# p.axes.set_ylim(*ylim)
# p.refresh()
p.zoom_all()
p.refresh()
if 'label' in options:
p.axes.legend()
xlim = options.pop('xlim', None)
if xlim is None:
xlim = p.axes.get_xlim()
p.axes.set_xlim(xlim)
# trying to change number font
p.canvas.show()
options['xlim'] = xlim
return p
def powder_main():
if len(sys.argv) != 2:
usage()
else:
y = yaml.load(open(sys.argv[1]).read())
uicfg = y['general']
config = y['simulation']
experiment = y['experiment']
pltcfg = y['plot']
powderx_version = __version__.rsplit(".", 1)[0]
if uicfg['powderx_version'] != str(powderx_version):
tplt = "Config file should be version '%s'."
raise VersionError(tplt % powderx_version)
log_level = getattr(logging, uicfg['verbosity'])
logger = phyles.basic_logger(__name__, level=log_level)
tk = TK.Tk()
# logger.info("Reading mtz: '%s'", config['mtz_name'])
# mtz_file = mtz.object(config['mtz_name'])
# logger.info("Constructing Miller dict from mtz.")
# mtz_miller_dict = mtz_file.as_miller_arrays_dict()
# mtz_key = tuple(config['mtz_column'])
# sf_mtz = mtz_miller_dict[mtz_key]
logger.info("Reading pdb: '%s'", config['pdb_name'])
pdb_inp = pdb.input(file_name=config['pdb_name'])
logger.info("Creating structure factors from pdb.")
structure = pdb_inp.xray_structure_simple()
sf_pdb = structure.structure_factors(d_min=config['d_min']).f_calc()
ec_x = config.get("extinction_correction_x", None)
if ec_x is not None:
# sf_mtz = sf_mtz.apply_shelxl_extinction_correction(ec_x,
# experiment['WAVELENGTH'])
sf_pdb = sf_pdb.apply_shelxl_extinction_correction(ec_x,
experiment['WAVELENGTH'])
# logger.info("Plotting powder from mtz: '%s'", config['mtz_name'])
# p = plot_powder(sf_mtz, config, pltcfg, experiment, master=tk)
# logger.info("Plotting powder from pdb: '%s'", config['pdb_name'])
# p = plot_powder(sf_pdb, config, pltcfg, experiment, master=tk)
logger.info("Creating integrated intensity pattern from pdb.")
pattern = integrated_intensity(sf_pdb,
experiment['WAVELENGTH'],
config['d_max'],
config['d_min'],
v=config['v'],
w=config['w'],
B=config['B'],
apply_Lp = config['apply_Lp'],
pattern_bins=config['pattern_shells'],
peakwidths=config['peak_widths'],
bin_reflections=config['combine_reflections'])
p = pygmyplot.xy_plot(numpy.degrees(pattern[0]),
pattern[1], master=tk)
p.axes.set_xlabel("$2\\theta$ (degrees)")
p.axes.set_ylabel("Integrated Intensity")
adj = {"left": pltcfg['left'],
"right": pltcfg['right'],
"top": pltcfg['top'],
"bottom": pltcfg['bottom'],
"wspace": None,
"hspace": None}
_radialx.plot_adjust(p, adj)
tk.title(pltcfg['window_name'])
p.refresh()
_radialx.write_spectrum(config['pattern_name'],
config['pdb_name'],
pattern[0], pattern[1], False)
TK.Button(tk, text="Quit", command=tk.destroy).pack()
tk.mainloop()
def plot_powder(sf, config, pltcfg, experiment, master=None,
plot=None):
"""
Returns an instance of :class:`pygmyplot.MyXYPlot` with intensity per
detector area plotted over ``config['d_max']`` - ``config['d_min']``.
Args:
`sf`:
structure factors as a :class:`cctbx.miller.array`
`pltcfg`:
mapping object with keys of
- ``plot_points``: number of bins for the plot
- ``n_ticks``: number of ticks for the x-axis
`config`:
mapping object with keys of
- ``d_max``: maximum d-spacing in Angstroms
- ``d_min``: minimum d-spacing in Angstroms
`experiment`:
mapping object with keys of
- ``'WAVELENGTH'``: x-ray wavelength Angstroms
- ``'DISTANCE'``: detector distance in mm
`master`:
Tkinter widget
`plot`:
a :class:`pygmyplot.MyPlot` to which the plot is added
"""
if (master is not None) and (plot is not None):
msg = "Either or both of master and plot should be None."
raise GUIError(msg)
max_min = sf.d_max_min()
d_max = config['d_max']
d_min = config['d_min']
plot_bins = pltcfg['plot_points']
n_ticks = pltcfg['x_ticks']
I = sf.intensities()
borders = _radialx.make_borders_rho(plot_bins, d_max, d_min, experiment)
binner = Binner(I, borders, experiment)
values = getattr(binner, config['values'])()
x_labels = [("%4.1f" % c) for c in binner.centers_res]
tick_step = int(math.floor(plot_bins / n_ticks))
if plot is None:
plot = pygmyplot.xy_plot(binner.centers, values, master=master)
else:
plot.plot(binner.centers, values)
plot.axes.set_xticks(binner.centers[::tick_step])
plot.axes.set_xticklabels(x_labels[::tick_step])
plot.axes.set_xlabel('Resolution ($\\AA$)')
plot.axes.set_ylabel('intensity')
adj = {"left": pltcfg['left'],
"right": pltcfg['right'],
"top": pltcfg['top'],
"bottom": pltcfg['bottom']}
_radialx.plot_adjust(plot, adj)
plot.canvas.draw()
return plot