def calculate_properties(self):
self.average = self.data.mean()
self.median = numpy.median(self.data)
self.stdev = numpy.sqrt(sum((self.data - self.data.mean())**2) / (len(self.data) - 1))
request_bins = int(numpy.sqrt(len(self.data)))
num_bins = request_bins
while True:
probs, bins = numpy.histogram(
to_unit[self.unit](self.data),
bins=num_bins,
normed=False,
)
used_bins = sum(probs > 0)
if used_bins >= request_bins:
break
num_bins = max([(request_bins*num_bins)/used_bins, num_bins+1])
self.probs = probs*(100.0/len(self.data))
self.bins = bins
self.decimals = max([
0,
-int(numpy.floor(numpy.log10(
abs(to_unit[self.unit](self.stdev))
)))
])+2
self.comments.append("Samples: %s" % len(self.data))
self.comments.append("Bins: %i (%i)" % (num_bins, used_bins))
self.comments.append("Average: %s" % express_measure(self.average, self.measure, self.decimals))
self.comments.append("Median: %s" % express_measure(self.median, self.measure, self.decimals))
self.comments.append("Stdev (N-1): %s" % express_measure(self.stdev, self.measure, self.decimals))
def fill_menu(self):
Default.fill_menu(self)
representation = self.field.read_from_widget()
from mixin import ambiguous
if representation == ambiguous:
return
self.add_separator()
try:
value = self.field.convert_to_value(representation)
if isinstance(value, numpy.ndarray):
value = value.ravel()
for unit in units_by_measure[self.field.measure]:
if isinstance(value, numpy.ndarray):
alternative_representation = tuple(
express_measure(item, self.field.measure, self.field.
decimals, self.field.scientific, unit)
for item in value)
else:
alternative_representation = express_measure(
value, self.field.measure, self.field.decimals,
self.field.scientific, unit)
self.add_item(
"Convert to '%s'" % str(alternative_representation), None,
self.write_to_widget, alternative_representation)
except ValueError:
self.add_item(
"Convert to ... (invalid entries)",
None,
None,
)
def convert_to_representation(self, value):
if value.corners is None:
return "<span foreground=\"red\">NO BBOX INFO FOUND. THIS SHOULD NEVER HAPPEN.</span>"
else:
return (
express_measure(value.corners[1][0] - value.corners[0][0], "Length"),
express_measure(value.corners[1][1] - value.corners[0][1], "Length"),
express_measure(value.corners[1][2] - value.corners[0][2], "Length")
)
def convert_to_representation(self, value):
if value.corners is None:
return "<span foreground=\"red\">NO BBOX INFO FOUND. THIS SHOULD NEVER HAPPEN.</span>"
else:
return (express_measure(value.corners[1][0] - value.corners[0][0],
"Length"),
express_measure(value.corners[1][1] - value.corners[0][1],
"Length"),
express_measure(value.corners[1][2] - value.corners[0][2],
"Length"))
def fill_ring_store(self):
self.ring_store.clear()
filter_index = self.filter_store.get_value(self.cb_filter.get_active_iter(), 1)
for ring in self.rings:
if filter_index == -1 or filter_index in ring.reverse:
self.ring_store.append([
len(ring),
express_measure(ring.av_diameter, "Length"),
express_measure(ring.min_diameter, "Length"),
ring.label,
ring,
])
self.ring_store.set_sort_column_id(0, gtk.SORT_ASCENDING)
def fill_ring_store(self):
self.ring_store.clear()
filter_index = self.filter_store.get_value(
self.cb_filter.get_active_iter(), 1)
for ring in self.rings:
if filter_index == -1 or filter_index in ring.reverse:
self.ring_store.append([
len(ring),
express_measure(ring.av_diameter, "Length"),
express_measure(ring.min_diameter, "Length"),
ring.label,
ring,
])
self.ring_store.set_sort_column_id(0, gtk.SORT_ASCENDING)
def express_distance_between_lines(index1, index2, index3, index4):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index3] - self.vectors[index4]
normal = numpy.cross(delta1, delta2)
normal /= numpy.sqrt(numpy.dot(normal, normal))
delta3 = self.vectors[index1] - self.vectors[index3]
return express_measure(abs(numpy.dot(delta3, normal)), measure="Length")
def express_out_of_plane_angle(index1, index2, index3, index4):
delta = self.vectors[index1] - self.vectors[index2]
normal = numpy.cross(
self.vectors[index4] - self.vectors[index3],
self.vectors[index2] - self.vectors[index3]
)
return express_measure(0.5*numpy.pi - angle(normal, delta), measure="Angle")
def run(self, minimize, auto_close, involved_frames, update_interval, update_steps, num_springs):
self.la_num_iter.set_text("0")
self.la_rms_error.set_text(express_measure(0.0, "Length"))
self.progress_bar.set_fraction(0.0)
self.progress_bar.set_text("0%")
self.minimize = minimize
self.involved_frames = [frame for frame in involved_frames if frame is not None]
self.update_interval = update_interval
self.update_steps = update_steps
self.num_springs = num_springs
self.last_time = time.time()
self.last_step = 0
self.status = None
result = ChildProcessDialog.run(self,
[context.get_share_filename("helpers/iterative")],
self.minimize, auto_close, pickle=True
)
# just to avoid confusion
del self.minimize
del self.involved_frames
del self.update_interval
del self.update_steps
del self.last_time
del self.last_step
del self.num_springs
del self.status
return result
def express_distance_to_plane(index1, index2, index3, index4):
delta = self.vectors[index1] - self.vectors[index2]
normal = numpy.cross(
self.vectors[index2] - self.vectors[index3], self.vectors[index4] - self.vectors[index3]
)
normal /= math.sqrt(numpy.dot(normal, normal))
return express_measure(abs(numpy.dot(delta, normal)), measure="Length")
def express_distance_to_line(index1, index2, index3):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index2] - self.vectors[index3]
delta2 /= numpy.sqrt(numpy.dot(delta2, delta2))
normal = delta1 - delta2 * numpy.dot(delta1, delta2)
return express_measure(numpy.sqrt(numpy.dot(normal, normal)),
measure="Length")
def run(self, minimize, involved_frames, update_interval, update_steps,
num_springs):
self.la_num_iter.set_text("0")
self.la_rms_error.set_text(express_measure(0.0, "Length"))
self.progress_bar.set_fraction(0.0)
self.progress_bar.set_text("0%")
self.minimize = minimize
self.involved_frames = [
frame for frame in involved_frames if frame is not None
]
self.update_interval = update_interval
self.update_steps = update_steps
self.num_springs = num_springs
self.last_time = time.time()
self.last_step = 0
self.status = None
result = ChildProcessDialog.run(
self, [context.get_share_filename("helpers/iterative")],
self.minimize,
pickle=True)
# just to avoid confusion
del self.minimize
del self.involved_frames
del self.update_interval
del self.update_steps
del self.last_time
del self.last_step
del self.num_springs
del self.status
return result
def express_distance_to_plane(index1, index2, index3, index4):
delta = self.vectors[index1] - self.vectors[index2]
normal = numpy.cross(self.vectors[index2] - self.vectors[index3],
self.vectors[index4] - self.vectors[index3])
normal /= numpy.sqrt(numpy.dot(normal, normal))
return express_measure(abs(numpy.dot(delta, normal)),
measure="Length")
def express_dihedral_angle(index1, index2, index3, index4):
normal1 = numpy.cross(
self.vectors[index1] - self.vectors[index2], self.vectors[index3] - self.vectors[index2]
)
normal2 = numpy.cross(
self.vectors[index2] - self.vectors[index3], self.vectors[index4] - self.vectors[index3]
)
return express_measure(angle(normal1, normal2), measure="Angle")
def express_distance_between_lines(index1, index2, index3, index4):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index3] - self.vectors[index4]
normal = numpy.cross(delta1, delta2)
normal /= numpy.sqrt(numpy.dot(normal, normal))
delta3 = self.vectors[index1] - self.vectors[index3]
return express_measure(abs(numpy.dot(delta3, normal)),
measure="Length")
def fill_menu(self):
Default.fill_menu(self)
representation = self.field.read_from_widget()
from mixin import ambiguous
if representation == ambiguous:
return
self.add_separator()
try:
value = self.field.convert_to_value(representation)
if isinstance(value, numpy.ndarray):
value = value.ravel()
for unit in units_by_measure[self.field.measure]:
if isinstance(value, numpy.ndarray):
alternative_representation = tuple(
express_measure(
item,
self.field.measure,
self.field.decimals,
self.field.scientific,
unit
)
for item in value
)
else:
alternative_representation = express_measure(
value,
self.field.measure,
self.field.decimals,
self.field.scientific,
unit
)
self.add_item(
"Convert to '%s'" % str(alternative_representation),
None,
self.write_to_widget,
alternative_representation
)
except ValueError:
self.add_item(
"Convert to ... (invalid entries)",
None,
None,
)
def create_widgets(self):
Edit.create_widgets(self)
self.buttons = {}
ta_elements = gtk.Table(11, 19, homogeneous=True)
ta_elements.set_row_spacings(0)
ta_elements.set_col_spacings(0)
# Use periodic to fill the table with buttons.
for atom_info in periodic.atoms_by_number.itervalues():
bu_element = gtk.ToggleButton("")
bu_element.set_property("can-focus", False)
label = bu_element.get_child()
label.set_label("<small>%s</small>" % atom_info.symbol)
label.set_use_markup(True)
bu_element.connect("toggled", self.on_bu_element_toggled,
atom_info.number)
bu_element.connect("toggled", self.on_widget_changed)
tip = str(atom_info.number) + ": " + atom_info.name
if atom_info.mass is not None:
if atom_info.artificial:
tip = tip + "\nMass = *%s" % express_measure(
atom_info.mass, measure="Mass")
else:
tip = tip + "\nMass = %s" % express_measure(atom_info.mass,
measure="Mass")
if atom_info.vdw_radius is not None:
tip = tip + "\nVan der Waals radius = " + express_measure(
atom_info.vdw_radius, "Length")
bu_element.set_tooltip_text(tip)
ta_elements.attach(bu_element, int(atom_info.col),
int(atom_info.col) + 1, int(atom_info.row),
int(atom_info.row) + 1)
self.buttons[atom_info.number] = bu_element
# also add a few indicative labels
for c, r, label_text in self.mendeljev_labels:
indicative = gtk.Label("<b><small>" + label_text + "</small></b>")
indicative.set_use_markup(True)
ta_elements.attach(indicative, c, c + 1, r, r + 1)
self.bu_former = None
self.data_widget = ta_elements
def create_widgets(self):
Edit.create_widgets(self)
self.buttons = {}
ta_elements = gtk.Table(11, 19, homogeneous=True)
ta_elements.set_row_spacings(0)
ta_elements.set_col_spacings(0)
# Use periodic to fill the table with buttons.
for atom_info in periodic.atoms_by_number.itervalues():
bu_element = gtk.ToggleButton("")
bu_element.set_property("can-focus", False)
label = bu_element.get_child()
label.set_label("<small>%s</small>" % atom_info.symbol)
label.set_use_markup(True)
bu_element.connect("toggled", self.on_bu_element_toggled, atom_info.number)
bu_element.connect("toggled", self.on_widget_changed)
tip = str(atom_info.number) + ": " + atom_info.name
if atom_info.mass is not None:
if atom_info.artificial:
tip = tip + "\nMass = *%s" % express_measure(atom_info.mass, measure="Mass")
else:
tip = tip + "\nMass = %s" % express_measure(atom_info.mass, measure="Mass")
if atom_info.vdw_radius is not None:
tip = tip + "\nVan der Waals radius = " + express_measure(atom_info.vdw_radius, "Length")
bu_element.set_tooltip_text(tip)
ta_elements.attach(
bu_element,
int(atom_info.col), int(atom_info.col) + 1,
int(atom_info.row), int(atom_info.row) + 1
)
self.buttons[atom_info.number] = bu_element
# also add a few indicative labels
for c, r, label_text in self.mendeljev_labels:
indicative = gtk.Label("<b><small>" + label_text + "</small></b>")
indicative.set_use_markup(True)
ta_elements.attach(indicative, c, c+1, r, r+1)
self.bu_former = None
self.data_widget = ta_elements
def calculate_properties(self):
self.average = self.data.mean()
self.median = numpy.median(self.data)
self.stdev = numpy.sqrt(
sum((self.data - self.data.mean())**2) / (len(self.data) - 1))
request_bins = int(numpy.sqrt(len(self.data)))
num_bins = request_bins
while True:
probs, bins = numpy.histogram(
to_unit[self.unit](self.data),
bins=num_bins,
normed=False,
)
used_bins = sum(probs > 0)
if used_bins >= request_bins:
break
num_bins = max([(request_bins * num_bins) / used_bins,
num_bins + 1])
self.probs = probs * (100.0 / len(self.data))
self.bins = bins
self.decimals = max([
0,
-int(numpy.floor(numpy.log10(abs(to_unit[self.unit](self.stdev)))))
]) + 2
self.comments.append("Samples: %s" % len(self.data))
self.comments.append("Bins: %i (%i)" % (num_bins, used_bins))
self.comments.append(
"Average: %s" %
express_measure(self.average, self.measure, self.decimals))
self.comments.append(
"Median: %s" %
express_measure(self.median, self.measure, self.decimals))
self.comments.append(
"Stdev (N-1): %s" %
express_measure(self.stdev, self.measure, self.decimals))
def update_gui(self):
if self.status is not None:
self.la_num_iter.set_text("%i" % self.status.step)
self.la_rms_error.set_text(express_measure(numpy.sqrt(self.status.value/self.num_springs), "Length"))
self.progress_bar.set_text("%i%%" % int(self.status.progress*100))
self.progress_bar.set_fraction(self.status.progress)
for state_index, frame, variable in zip(self.state_indices, self.involved_frames, self.minimize.root_expression.state_variables):
if isinstance(variable, iterative.var.Frame):
r, t = variable.extract_state(state_index, self.status.state)
frame.set_transformation(Complete(r, t))
elif isinstance(variable, iterative.var.Translation):
t = variable.extract_state(state_index, self.status.state)
new_transformation = frame.transformation.copy_with(t=t)
frame.set_transformation(new_transformation)
context.application.main.drawing_area.queue_draw()
def update_gui(self):
if self.status is not None:
self.la_num_iter.set_text("%i" % self.status.step)
self.la_rms_error.set_text(
express_measure(
numpy.sqrt(self.status.value / self.num_springs),
"Length"))
self.progress_bar.set_text("%i%%" %
int(self.status.progress * 100))
self.progress_bar.set_fraction(self.status.progress)
for state_index, frame, variable in zip(
self.state_indices, self.involved_frames,
self.minimize.root_expression.state_variables):
if isinstance(variable, iterative.var.Frame):
r, t = variable.extract_state(state_index,
self.status.state)
frame.set_transformation(Complete(r, t))
elif isinstance(variable, iterative.var.Translation):
t = variable.extract_state(state_index, self.status.state)
new_transformation = frame.transformation.copy_with(t=t)
frame.set_transformation(new_transformation)
context.application.main.drawing_area.queue_draw()
def fn():
express_measure(0, "Mass")
def express_distance(index1, index2):
delta = self.vectors[index1] - self.vectors[index2]
return express_measure(numpy.sqrt(numpy.dot(delta, delta)), measure="Length")
def express_angle(index1, index2, index3):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index3] - self.vectors[index2]
return express_measure(angle(delta1, delta2), measure="Angle")
def convert_to_representation(self, value):
return express_measure(value, self.measure, self.decimals,
self.scientific)
def express_distance_to_line(index1, index2, index3):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index2] - self.vectors[index3]
delta2 /= numpy.sqrt(numpy.dot(delta2, delta2))
normal = delta1 - delta2*numpy.dot(delta1, delta2)
return express_measure(numpy.sqrt(numpy.dot(normal, normal)), measure="Length")
def fn():
express_measure(0, "Mass")
def convert_to_representation(self, value):
return express_measure(value, "Length")
def convert_to_representation(self, value):
return express_measure(value, self.measure, self.decimals, self.scientific)
def convert_to_representation(self, value):
return express_measure(value, "Length")
def express_out_of_plane_angle(index1, index2, index3, index4):
delta = self.vectors[index1] - self.vectors[index2]
normal = numpy.cross(self.vectors[index4] - self.vectors[index3],
self.vectors[index2] - self.vectors[index3])
return express_measure(0.5 * numpy.pi - angle(normal, delta),
measure="Angle")
def express_dihedral_angle(index1, index2, index3, index4):
normal1 = numpy.cross(self.vectors[index1] - self.vectors[index2],
self.vectors[index3] - self.vectors[index2])
normal2 = numpy.cross(self.vectors[index2] - self.vectors[index3],
self.vectors[index4] - self.vectors[index3])
return express_measure(angle(normal1, normal2), measure="Angle")
def express_angle(index1, index2, index3):
delta1 = self.vectors[index1] - self.vectors[index2]
delta2 = self.vectors[index3] - self.vectors[index2]
return express_measure(angle(delta1, delta2), measure="Angle")
def express_distance(index1, index2):
delta = self.vectors[index1] - self.vectors[index2]
return express_measure(numpy.sqrt(numpy.dot(delta, delta)),
measure="Length")