def nth_power_scale(dataarray, nth_power):
"""
set nth_power to appropriate number between 0 and 1 for dampening the
difference between the smallest and the largest values.
If nth_power < 0 then an automatic value is computed that maps the smallest
values to 0.1 of the largest values
"""
absdat = flex.abs(dataarray).as_double()
absdat2 = graphics_utils.NoNansArray(absdat) # much faster than flex.double([e for e in absdat if not math.isnan(e)])
maxdat = flex.max(absdat2)
mindat = max(1e-10*maxdat, flex.min(absdat2) )
# only autoscale for sensible values of maxdat and mindat
if nth_power < 0.0 and maxdat > mindat : # amounts to automatic scale
nth_power = math.log(0.2)/(math.log(mindat) - math.log(maxdat))
datascaled = flex.pow(absdat, nth_power)
return datascaled, nth_power
def nth_power_scale(dataarray, nth_power):
"""
set nth_power to a number for dampening or enhancing the
difference between the smallest and the largest values.
A negative number means that a large data value is rendered with a smaller radius than
a small data value. For nth_power=0 all data values are rendered with the same radius
For nth_power=1 data values are rendered with radii proportional to the data values.
If nth_power=NaN then an automatic value is computed that maps the smallest
values to 0.1 of the largest values
"""
absdat = flex.abs(dataarray).as_double()
absdat2 = graphics_utils.NoNansArray(
absdat
) # much faster than flex.double([e for e in absdat if not math.isnan(e)])
maxdat = flex.max(absdat2)
mindat = max(1e-10 * maxdat, flex.min(absdat2))
# only autoscale for sensible values of maxdat and mindat
if math.isnan(nth_power) and maxdat > mindat: # amounts to automatic scale
nth_power = math.log(0.2) / (math.log(mindat) - math.log(maxdat))
datascaled = flex.pow(absdat, nth_power)
return datascaled, nth_power
def generate_view_data(self):
from scitbx.array_family import flex
#from scitbx import graphics_utils
settings = self.settings
data_for_colors = data_for_radii = None
if not self.fullprocessarray:
return
data = self.data #self.work_array.data()
sigmas = self.sigmas
if (isinstance(data, flex.double) and data.all_eq(0)):
data = flex.double(data.size(), 1)
if ((self.multiplicities is not None)
and (settings.scale_colors_multiplicity)):
data_for_colors = self.multiplicities.data().as_double()
assert data_for_colors.size() == data.size()
elif (settings.sqrt_scale_colors) and (isinstance(data, flex.double)):
data_for_colors = flex.sqrt(flex.abs(data))
elif isinstance(data, flex.complex_double):
data_for_colors = self.radians
foms_for_colours = self.foms
# assuming last part of the labels indicates the phase label as in ["FCALC","PHICALC"]
self.colourlabel = self.miller_array.info().labels[-1]
elif (settings.sigma_color) and sigmas is not None:
data_for_colors = sigmas.as_double()
self.colourlabel = self.miller_array.info().labels[-1]
else:
data_for_colors = flex.abs(data.deep_copy())
uc = self.work_array.unit_cell()
self.min_dist = min(uc.reciprocal_space_vector(
(1, 1, 1))) * self.renderscale
min_radius = 0.05 * self.min_dist
max_radius = 0.5 * self.min_dist
if ((self.multiplicities is not None)
and (settings.scale_radii_multiplicity)):
data_for_radii = self.multiplicities.data().as_double()
if (settings.sigma_radius) and sigmas is not None:
data_for_radii = sigmas * self.multiplicities.as_double()
assert data_for_radii.size() == data.size()
elif (settings.sigma_radius) and sigmas is not None:
data_for_radii = sigmas.as_double()
else:
data_for_radii, self.nth_power_scale_radii = nth_power_scale(
flex.abs(data.deep_copy()), settings.nth_power_scale_radii)
if (settings.slice_mode):
data = data.select(self.slice_selection)
if (not settings.keep_constant_scale):
data_for_radii = data_for_radii.select(self.slice_selection)
data_for_colors = data_for_colors.select(self.slice_selection)
foms_for_colours = foms_for_colours.select(
self.slice_selection)
if isinstance(data, flex.complex_double):
if self.isUsingFOMs():
colors = graphics_utils.colour_by_phi_FOM(
data_for_colors, foms_for_colours)
else:
colors = graphics_utils.colour_by_phi_FOM(
data_for_colors, None)
elif (settings.color_scheme in ["rainbow", "heatmap", "redblue"]):
colors = graphics_utils.color_by_property(
properties=data_for_colors,
selection=flex.bool(data_for_colors.size(), True),
color_all=False,
gradient_type=settings.color_scheme)
elif (settings.color_scheme == "grayscale"):
colors = graphics_utils.grayscale_by_property(
properties=data_for_colors,
selection=flex.bool(data_for_colors.size(), True),
shade_all=False,
invert=settings.black_background)
else:
if (settings.black_background):
base_color = (1.0, 1.0, 1.0)
else:
base_color = (0.0, 0.0, 0.0)
colors = flex.vec3_double(data_for_colors.size(), base_color)
if (settings.slice_mode) and (settings.keep_constant_scale):
colors = colors.select(self.slice_selection)
data_for_radii = data_for_radii.select(self.slice_selection)
#if (settings.sqrt_scale_radii) and (not settings.scale_radii_multiplicity):
# data_for_radii = flex.sqrt(flex.abs(data_for_radii))
if len(data_for_radii):
#dat2 = flex.abs(flex.double([e for e in data_for_radii if not math.isnan(e)]))
dat2 = flex.abs(
flex.double(graphics_utils.NoNansArray(data_for_radii, 0.1)))
# don't divide by 0 if dealing with selection of Rfree array where all values happen to be zero
scale = max_radius / (flex.max(dat2) + 0.001)
radii = data_for_radii * (self.settings.scale * scale)
assert radii.size() == colors.size()
else:
radii = flex.double()
max_radius = 0
self.radii = radii
self.max_radius = max_radius
self.min_radius = min_radius
self.colors = colors
if isinstance(data, flex.complex_double):
self.foms = foms_for_colours
def __init__(self, millarr, wrap_labels=0):
from cctbx.miller import display2
from cctbx.array_family import flex
from scitbx import graphics_utils
from libtbx.math_utils import roundoff
import math
nan = float("nan")
self.wrap_labels = wrap_labels
if millarr.space_group() is None:
self.spginf = "?"
else:
self.spginf = millarr.space_group_info().symbol_and_number()
if millarr.unit_cell() is None:
self.ucell = (nan, nan, nan, nan, nan, nan)
else:
self.ucell = millarr.unit_cell().parameters()
self.ucellinf = "({:.6g}Å, {:.6g}Å, {:.6g}Å, {:.6g}°, {:.6g}°, {:.6g}°)".format(
*self.ucell)
data = millarr.deep_copy().data()
self.maxdata = self.mindata = self.maxsigmas = self.minsigmas = nan
self.minmaxdata = (nan, nan)
self.minmaxsigs = (nan, nan)
self.data_sigdata_max = nan
self.data_sigdata = nan
self.desc = ""
self.arrsize = data.size()
if not isinstance(data, flex.std_string):
if isinstance(data, flex.hendrickson_lattman):
data = graphics_utils.NoNansHL(data)
# estimate minmax values of HL coefficients as a simple sum
if self.arrsize:
self.maxdata = max(
[e[0] + e[1] + e[2] + e[3] for e in data])
self.mindata = min(
[e[0] + e[1] + e[2] + e[3] for e in data])
self.arrsize = len([
42 for e in millarr.data()
if not math.isnan(e[0] + e[1] + e[2] + e[3])
])
elif isinstance(data, flex.vec3_double) or isinstance(
data, flex.vec2_double):
# XDS produces 2D or 3D arrays in some of its files
if self.arrsize:
self.maxdata = max([max(e) for e in data])
self.mindata = min([min(e) for e in data])
else:
# Get a list of bools with True whenever there is a nan
selection = ~graphics_utils.IsNans(
flex.abs(millarr.data()).as_double())
# count elements that are not nan values
self.arrsize = millarr.data().select(selection).size()
if (isinstance(data, flex.int)):
data = flex.double(
[e for e in data if e != display2.inanval])
if millarr.is_complex_array():
data = flex.abs(data)
i = 0
while math.isnan(data[i]):
i += 1 # go on until we find a data[i] that isn't NaN
data = graphics_utils.NoNansArray(
data, data[i]) # assuming data[0] isn't NaN
self.maxdata = flex.max(data)
self.mindata = flex.min(data)
if millarr.sigmas() is not None:
data = millarr.sigmas().deep_copy()
i = 0
while math.isnan(data[i]):
i += 1 # go on until we find a data[i] that isn't NaN
data = graphics_utils.NoNansArray(data, data[i])
self.maxsigmas = flex.max(data)
self.minsigmas = flex.min(data)
# Inspired by Diederichs doi:10.1107/S0907444910014836 I/SigI_asymptotic
data_over_sigdata = millarr.data() / millarr.sigmas()
self.data_sigdata = flex.sum(data_over_sigdata) / len(
data_over_sigdata)
self.data_sigdata_max = flex.max(data_over_sigdata)
self.minmaxdata = (self.mindata, self.maxdata)
self.minmaxsigs = (self.minsigmas, self.maxsigmas)
self.labels = self.desc = self.wavelength = ""
if millarr.info():
self.labels = millarr.info().labels
self.desc = get_array_description(millarr)
self.wavelength = "{:.6g}".format(
millarr.info().wavelength) if millarr.info(
).wavelength is not None else float("nan")
self.span = "(?,?,?), (?,?,?)"
self.dmin = nan
self.dmax = nan
if millarr.unit_cell() is not None:
self.span = str(millarr.index_span().min()) + ", " + str(
millarr.index_span().max())
self.dmin = millarr.d_max_min()[1]
self.dmax = millarr.d_max_min()[0]
self.dminmax = roundoff((self.dmin, self.dmax))
self.issymunique = "?"
self.isanomalous = "?"
self.n_sys_abs = 0
self.n_bijvoet = self.n_singletons = 0
self.ano_mean_diff = nan
self.ano_completeness = nan
self.data_compl_infty = nan
self.data_completeness = nan
self.n_centric = nan
# computations below done as in cctbx.miller.set.show_comprehensive_summary()
if self.spginf != "?":
self.issymunique = millarr.is_unique_set_under_symmetry()
self.isanomalous = millarr.anomalous_flag()
sys_absent_flags = millarr.sys_absent_flags().data()
self.n_sys_abs = sys_absent_flags.count(True)
if (self.n_sys_abs != 0):
millarr = millarr.select(selection=~sys_absent_flags)
self.n_centric = millarr.centric_flags().data().count(True)
if not math.isnan(self.ucell[0]):
if (self.spginf != "?" and millarr.indices().size() > 0
and self.issymunique):
millarr.setup_binner(n_bins=1)
completeness_d_max_d_min = millarr.completeness(
use_binning=True)
binner = completeness_d_max_d_min.binner
assert binner.counts_given()[0] == 0
assert binner.counts_given()[2] == 0
n_obs = binner.counts_given()[1]
n_complete = binner.counts_complete()[1]
if (n_complete != 0 and self.dmax != self.dmin):
self.data_completeness = n_obs / n_complete
n_complete += binner.counts_complete()[0]
if (n_complete != 0):
self.data_compl_infty = n_obs / n_complete
if (self.isanomalous) and (millarr.is_xray_intensity_array() or
millarr.is_xray_amplitude_array()):
self.ano_completeness = millarr.anomalous_completeness()
if (self.spginf != "?" and self.isanomalous and self.issymunique):
asu, matches = millarr.match_bijvoet_mates()
self.n_bijvoet = matches.pairs().size()
self.n_singletons = matches.n_singles() - self.n_centric
if millarr.is_real_array():
self.ano_mean_diff = millarr.anomalous_signal()
# break long label into list of shorter strings
self.labelstr = ",".join(self.labels)
if self.wrap_labels > 0:
tlabels = textwrap.wrap(self.labelstr, width=self.wrap_labels)
nlabl = len(tlabels)
self.labelsformat = "{0[0]:>%d} " % (1 + self.wrap_labels)
if len(tlabels) > 1:
for i in range((len(tlabels) - 1)):
self.labelsformat += "\n{0[%d]:>%d} " % (
i + 1, self.wrap_labels + 1)
blanks = self.wrap_labels - 5
else:
self.labelsformat = "{:>16} "
if len(self.labelstr) > 15:
self.labelsformat = "{}\n "
blanks = 10
self.info_format_dict = {
# the keys here must be verbatim copies of names of phil attributes in arrayinfo_phil_str below
"labels": (" %s" % self.caption_dict["labels"][0] + " " * blanks,
self.labelstr, "{}", self.labelsformat),
"description":
(" %s " % self.caption_dict["description"][0],
self.desc, "{}", "{:>16} "),
"wavelength": (" %s " % self.caption_dict["wavelength"][0],
self.wavelength, "{}", "{:>8} "),
"n_reflections": (" %s " % self.caption_dict["n_reflections"][0],
self.arrsize, "{}", "{:>8} "),
"span": (" " * 15 + self.caption_dict["span"][0] + " " * 14,
self.span, "{}", "{:>32} "),
"minmax_data":
(" %s " % self.caption_dict["minmax_data"][0],
self.minmaxdata, "{0[0]:.6}, {0[1]:.6}",
"{0[0]:>11.5}, {0[1]:>11.5}"),
"minmax_sigmas":
(" %s " % self.caption_dict["minmax_sigmas"][0],
self.minmaxsigs, "{0[0]:.6}, {0[1]:.6}",
"{0[0]:>11.5}, {0[1]:>11.5}"),
"data_sigdata": (" %s" % self.caption_dict["data_sigdata"][0],
self.data_sigdata, "{:.4g}", "{:>9.4g} "),
"data_sigdata_max":
("%s" % self.caption_dict["data_sigdata_max"][0],
self.data_sigdata_max, "{:.4g}", "{:>11.4g} "),
"d_minmax": (" %s " % self.caption_dict["d_minmax"][0],
self.dminmax, "{0[0]:.6}, {0[1]:.6}",
"{0[0]:>8.5}, {0[1]:>8.5}"),
"unit_cell":
(" %s " % self.caption_dict["unit_cell"][0], self.ucell,
"{0[0]:>7.5g},{0[1]:>7.5g},{0[2]:>7.5g},{0[3]:>7.5g},{0[4]:>7.5g},{0[5]:>7.5g}",
"{0[0]:>7.5g},{0[1]:>7.5g},{0[2]:>7.5g},{0[3]:>7.5g},{0[4]:>7.5g},{0[5]:>7.5g} "
),
"space_group":
(" %s " % self.caption_dict["space_group"][0], self.spginf,
"{}", "{:>19} "),
"n_centrics": ("%s" % self.caption_dict["n_centrics"][0],
self.n_centric, "{}", "{:>8} "),
"n_sys_abs": ("%s" % self.caption_dict["n_sys_abs"][0],
self.n_sys_abs, "{}", "{:>9} "),
"data_completeness":
("%s" % self.caption_dict["data_completeness"][0],
self.data_completeness, "{:.5g}", "{:>10.5g} "),
"data_compl_infty":
("%s" % self.caption_dict["data_compl_infty"][0],
self.data_compl_infty, "{:.5g}", "{:>9.5g} "),
"is_anomalous": ("%s" % self.caption_dict["is_anomalous"][0],
str(self.isanomalous), "{}", "{:>8} "),
"is_symmetry_unique":
("%s" % self.caption_dict["is_symmetry_unique"][0],
str(self.issymunique), "{}", "{:>8} "),
"ano_completeness":
("%s" % self.caption_dict["ano_completeness"][0],
self.ano_completeness, "{:.5g}", "{:>11.5g} "),
"ano_mean_diff": ("%s" % self.caption_dict["ano_mean_diff"][0],
self.ano_mean_diff, "{:.5g}", "{:>8.5g} "),
"n_bijvoet": ("%s" % self.caption_dict["n_bijvoet"][0],
self.n_bijvoet, "{}", "{:>8} "),
"n_singletons": ("%s" % self.caption_dict["n_singletons"][0],
self.n_singletons, "{}", "{:>10} "),
}
def generate_view_data(self):
from scitbx.array_family import flex
settings = self.settings
data_for_colors = data_for_radii = None
if not self.fullprocessarray:
return
data = self.data #self.work_array.data()
sigmas = self.sigmas
if (isinstance(data, flex.double) and data.all_eq(0)):
data = flex.double(data.size(), 1)
if isinstance(data, flex.complex_double):
data_for_colors = self.phases
foms_for_colours = self.foms
# assuming last part of the labels indicates the phase label as in ["FCALC","PHICALC"]
self.colourlabel = "Phase of " + self.miller_array.info(
).label_string()
elif (settings.sigma_color_radius) and sigmas is not None:
data_for_colors = sigmas.as_double()
self.colourlabel = "Sigma of " + self.miller_array.info(
).label_string()
else:
data_for_colors = flex.abs(data.deep_copy())
uc = self.work_array.unit_cell()
self.min_dist = min(uc.reciprocal_space_vector(
(1, 1, 1))) * self.renderscale
min_radius = 0.05 * self.min_dist
max_radius = 0.5 * self.min_dist
if (settings.sigma_color_radius) and sigmas is not None:
data_for_radii, self.nth_power_scale_radii = nth_power_scale(
flex.abs(sigmas.as_double().deep_copy()),
settings.nth_power_scale_radii)
else:
data_for_radii, self.nth_power_scale_radii = nth_power_scale(
flex.abs(data.deep_copy()), settings.nth_power_scale_radii)
if (settings.slice_mode):
data = data.select(self.slice_selection)
# Computing rgb colours of each reflection is slow so make a small array
# of precomputed colours to use as a lookup table for each reflection
if isinstance(data, flex.complex_double):
COL = MplColorHelper(settings.color_scheme, 0, 360)
rgbcolarray = [COL.get_rgb(d)[0:3] for d in range(360)]
if self.isUsingFOMs():
colors = graphics_utils.map_to_rgb_colourmap(
data_for_colors=data_for_colors,
colormap=rgbcolarray,
selection=flex.bool(data_for_colors.size(), True),
attenuation=foms_for_colours,
map_directly=True,
color_all=False)
else:
colors = graphics_utils.map_to_rgb_colourmap(
data_for_colors=data_for_colors,
colormap=rgbcolarray,
selection=flex.bool(data_for_colors.size(), True),
attenuation=None,
map_directly=True,
color_all=False)
else:
# Use a colour gradient from matplotlib
COL = MplColorHelper(settings.color_scheme, 0, 199)
colorgradientarray = flex.vec3_double(
[COL.get_rgb(d)[0:3] for d in range(200)])
# Do the table lookup in C++ for speed improvement
colors = graphics_utils.map_to_rgb_colourmap(
data_for_colors=data_for_colors,
colormap=colorgradientarray,
selection=flex.bool(data_for_colors.size(), True),
powscale=settings.color_powscale,
attenuation=None,
color_all=False)
if (settings.slice_mode):
colors = colors.select(self.slice_selection)
data_for_radii = data_for_radii.select(self.slice_selection)
if len(data_for_radii):
#dat2 = flex.abs(flex.double([e for e in data_for_radii if not math.isnan(e)]))
dat2 = flex.abs(
flex.double(graphics_utils.NoNansArray(data_for_radii, 0.1)))
# don't divide by 0 if dealing with selection of Rfree array where all values happen to be zero
scale = max_radius / (flex.max(dat2) + 0.001)
radii = data_for_radii * (self.settings.scale * scale)
assert radii.size() == colors.size()
else:
radii = flex.double()
max_radius = 0
self.radii = radii
self.max_radius = max_radius
self.min_radius = min_radius
self.colors = colors
if isinstance(data, flex.complex_double):
self.foms = foms_for_colours