def __init__(self):
"""
Default values
"""
# Input
self.file = None
self.data = Data1D(x=[], y=[], dx=None, dy=None)
self.theory_lowQ = Data1D(x=[], y=[], dy=None)
self.theory_lowQ.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
self.theory_highQ = Data1D(x=[], y=[], dy=None)
self.theory_highQ.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
# self.is_time_machine = False
self.saved_state = DEFAULT_STATE
self.state_list = state_list
self.bookmark_list = bookmark_list
self.input_list = input_list
self.output_list = output_list
self.compute_num = 0
self.state_num = 0
self.timestamp = ('00:00:00', '00/00/0000')
self.container = None
# plot image
self.wximbmp = None
# report_html strings
import sas.sasgui.perspectives.invariant as invariant
path = invariant.get_data_path(media='media')
path_report_html = os.path.join(path, "report_template.html")
html_template = open(path_report_html, "r")
self.template_str = html_template.read()
self.report_str = self.template_str
# self.report_str_save = None
html_template.close()
def transform_complete(self, transforms=None):
"""
Called from FourierThread when calculation has completed
"""
self._transform_btn.SetLabel("Transform")
if transforms is None:
msg = "Error calculating Transform."
if self.transform_type == 'hilbert':
msg = "Not yet implemented"
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="Error"))
self._extract_btn.Disable()
return
self._transformed_data = transforms
(transform1, transform3, idf) = transforms
plot_x = transform1.x[transform1.x <= 200]
plot_y = transform1.y[transform1.x <= 200]
self._manager.show_data(Data1D(plot_x, plot_y), TRANSFORM_LABEL1)
# No need to shorten gamma3 as it's only calculated up to x=200
self._manager.show_data(transform3, TRANSFORM_LABEL3)
plot_x = idf.x[idf.x <= 200]
plot_y = idf.y[idf.x <= 200]
self._manager.show_data(Data1D(plot_x, plot_y), IDF_LABEL)
# Only enable extract params button if a fourier trans. has been done
if self.transform_type == 'fourier':
self._extract_btn.Enable()
else:
self._extract_btn.Disable()
def show_pr(self, out, pr, cov=None):
"""
"""
# Show P(r)
x = pylab.arange(0.0, pr.d_max, pr.d_max / self._pr_npts)
y = np.zeros(len(x))
dy = np.zeros(len(x))
y_true = np.zeros(len(x))
total = 0.0
pmax = 0.0
cov2 = np.ascontiguousarray(cov)
for i in range(len(x)):
if cov2 is None:
value = pr.pr(out, x[i])
else:
(value, dy[i]) = pr.pr_err(out, cov2, x[i])
total += value * pr.d_max / len(x)
# keep track of the maximum P(r) value
if value > pmax:
pmax = value
y[i] = value
if self._normalize_output:
y = y / total
dy = dy / total
elif self._scale_output_unity:
y = y / pmax
dy = dy / pmax
if cov2 is None:
new_plot = Data1D(x, y)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
else:
new_plot = Data1D(x, y, dy=dy)
new_plot.name = PR_FIT_LABEL
new_plot.xaxis("\\rm{r}", 'A')
new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
new_plot.title = "P(r) fit"
new_plot.id = PR_FIT_LABEL
# Make sure that the plot is linear
new_plot.xtransform = "x"
new_plot.ytransform = "y"
new_plot.group_id = GROUP_ID_PR_FIT
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot,
title="P(r) fit"))
return x, pr.d_max
def plot_theory(self, data=None, name=None):
"""
Receive a data set and post a NewPlotEvent to parent.
:param data: extrapolated data to be plotted
:param name: Data's name to use for the legend
"""
# import copy
if data is None:
id = str(self.__data.id) + name
group_id = self.__data.group_id
wx.PostEvent(
self.parent,
NewPlotEvent(id=id, group_id=group_id, action='Remove'))
return
new_plot = Data1D(x=[], y=[], dy=None)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
scale = self.invariant_panel.get_scale()
background = self.invariant_panel.get_background()
if scale != 0:
# Put back the sacle and bkg for plotting
data.y = (data.y + background) / scale
new_plot = Data1D(x=data.x, y=data.y, dy=None)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
else:
msg = "Scale can not be zero."
raise ValueError(msg)
if len(new_plot.x) == 0:
return
new_plot.name = name
new_plot.xaxis(self.__data._xaxis, self.__data._xunit)
new_plot.yaxis(self.__data._yaxis, self.__data._yunit)
new_plot.group_id = self.__data.group_id
new_plot.id = str(self.__data.id) + name
new_plot.title = self.__data.title
# Save theory_data in a state
if data is not None:
name_head = name.split('-')
if name_head[0] == 'Low':
self.invariant_panel.state.theory_lowQ = copy.deepcopy(
new_plot)
elif name_head[0] == 'High':
self.invariant_panel.state.theory_highQ = copy.deepcopy(
new_plot)
self.parent.update_theory(data_id=self.__data.id, theory=new_plot)
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title=self.__data.title))
def setUp(self):
# Create two data sets to play with
x_0 = np.ones(5)
for i in range(5):
x_0[i] = x_0[i]*(i+1.0)
y_0 = 2.0*np.ones(5)
dy_0 = 0.5*np.ones(5)
self.data = Data1D(x_0, y_0, dy=dy_0)
x = self.data.x
y = np.ones(5)
dy = np.ones(5)
self.data2 = Data1D(x, y, dy=dy)
def _on_scale_unity(self, evt):
"""
Scale the maximum P(r) value on each displayed plot to 1.
:param evt: Menu event
"""
self._scale_output_unity = True
self._normalize_output = False
self.show_pr(self._last_out, self._last_pr, self._last_cov)
# Now scale the added plots too
for plot in self._added_plots:
_max = 0
for y in self._added_plots[plot].y:
if y > _max:
_max = y
y = self._added_plots[plot].y / _max
new_plot = Data1D(self._added_plots[plot].x, y)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
new_plot.name = self._added_plots[plot].name
new_plot.xaxis("\\rm{r}", 'A')
new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
wx.PostEvent(
self.parent,
NewPlotEvent(plot=new_plot,
update=True,
title=self._added_plots[plot].name))
def _on_normalize(self, evt):
"""
Normalize the area under the P(r) curve to 1.
This operation is done for all displayed plots.
:param evt: Menu event
"""
self._normalize_output = True
self._scale_output_unity = False
self.show_pr(self._last_out, self._last_pr, self._last_cov)
# Now scale the added plots too
for plot in self._added_plots:
total = np.sum(self._added_plots[plot].y)
npts = len(self._added_plots[plot].x)
total *= self._added_plots[plot].x[npts - 1] / npts
y = self._added_plots[plot].y / total
new_plot = Data1D(self._added_plots[plot].x, y)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
new_plot.group_id = self._added_plots[plot].group_id
new_plot.id = self._added_plots[plot].id
new_plot.title = self._added_plots[plot].title
new_plot.name = self._added_plots[plot].name
new_plot.xaxis("\\rm{r}", 'A')
new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
wx.PostEvent(
self.parent,
NewPlotEvent(plot=new_plot,
update=True,
title=self._added_plots[plot].name))
def show_shpere(self, x, radius=70.0, x_range=70.0):
"""
"""
# Show P(r)
y_true = np.zeros(len(x))
sum_true = 0.0
for i in range(len(x)):
y_true[i] = self.pr_theory(x[i], radius)
sum_true += y_true[i]
y_true = y_true / sum_true * x_range / len(x)
# Show the theory P(r)
new_plot = Data1D(x, y_true)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
new_plot.name = "P_{true}(r)"
new_plot.xaxis("\\rm{r}", 'A')
new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
new_plot.id = "P_{true}(r)"
new_plot.group_id = "P_{true}(r)"
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
#Put this call in plottables/guitools
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title="Sphere P(r)"))
def create_gui_data(self, data, path=None):
"""
Receive data from loader and create a data to use for guiframe
"""
if issubclass(Data2D, data.__class__):
new_plot = Data2D(
image=None, err_image=None
) # For now, isSesans for 2D data is always false
else:
new_plot = Data1D(x=[],
y=[],
dx=None,
dy=None,
lam=None,
dlam=None,
isSesans=data.isSesans)
#elif data.meta_data['loader'] == 'SESANS':
# new_plot = Data1D(x=[], y=[], dx=None, dy=None, lam=None, dlam=None, isSesans=True)
#else:
# new_plot = Data1D(x=[], y=[], dx=None, dy=None, lam=None, dlam=None) #SESANS check???
new_plot.copy_from_datainfo(data)
data.clone_without_data(clone=new_plot)
#creating a name for data
title = ""
file_name = os.path.basename(
path) if path is not None else data.filename
if file_name:
name = file_name
elif data.run:
name = data.run[0]
else:
name = "data"
name = self.rename(name)
#find title
if data.title.strip():
title = data.title
if title.strip() == "":
title = file_name
if new_plot.filename.strip() == "":
new_plot.filename = file_name
new_plot.name = name
new_plot.title = title
## allow to highlight data when plotted
new_plot.interactive = True
## when 2 data have the same id override the 1 st plotted
self.time_stamp += 1
new_plot.id = str(name) + str(self.time_stamp)
##group_id specify on which panel to plot this data
new_plot.group_id = str(name) + str(self.time_stamp)
new_plot.is_data = True
new_plot.path = path
new_plot.list_group_id = []
##post data to plot
# plot data
return new_plot
def write(self, filename, datainfo=None, state=None):
"""
Write the content of a Data1D as a CanSAS file.
: param filename: Name of the file to write
: param datainfo: Data1D object
: param state: CorfuncState object
"""
# Prepare datainfo
if datainfo is None:
datainfo = Data1D(x=[], y=[])
elif not (isinstance(datainfo, Data1D)
or isinstance(datainfo, LoaderData1D)):
msg = ("The CanSAS writer expects a Data1D instance. {} was "
"provided").format(datainfo.__class__.__name__)
raise RuntimeError, msg
if datainfo.title is None or datainfo.title == '':
datainfo.title = datainfo.name
if datainfo.run_name is None or datainfo.run_name == '':
datainfo.run = [str(datainfo.name)]
datainfo.run_name[0] = datainfo.name
# Create the XMl doc
doc, sasentry = self._to_xml_doc(datainfo)
if state is not None:
doc = state.toXML(doc=doc, entry_node=sasentry)
# Write the XML doc to a file
fd = open(filename, 'w')
fd.write(doc.toprettyxml())
fd.close()
def _post_data(self, nbins=None):
"""
compute sector averaging of data2D into data1D
:param nbins: the number of point to plot for the average 1D data
"""
## get the data2D to average
data = self.base.data2D
# If we have no data, just return
if data == None:
return
## Averaging
from sas.sascalc.dataloader.manipulations import SectorQ
radius = self.qmax
phimin = -self.left_line.phi + self.main_line.theta
phimax = self.left_line.phi + self.main_line.theta
if nbins == None:
nbins = 20
sect = SectorQ(r_min=0.0,
r_max=radius,
phi_min=phimin + math.pi,
phi_max=phimax + math.pi,
nbins=nbins)
sector = sect(self.base.data2D)
##Create 1D data resulting from average
if hasattr(sector, "dxl"):
dxl = sector.dxl
else:
dxl = None
if hasattr(sector, "dxw"):
dxw = sector.dxw
else:
dxw = None
new_plot = Data1D(x=sector.x, y=sector.y, dy=sector.dy, dx=sector.dx)
new_plot.dxl = dxl
new_plot.dxw = dxw
new_plot.name = "SectorQ" + "(" + self.base.data2D.name + ")"
new_plot.source = self.base.data2D.source
#new_plot.info=self.base.data2D.info
new_plot.interactive = True
new_plot.detector = self.base.data2D.detector
## If the data file does not tell us what the axes are, just assume...
new_plot.xaxis("\\rm{Q}", "A^{-1}")
new_plot.yaxis("\\rm{Intensity}", "cm^{-1}")
if hasattr(data, "scale") and data.scale == 'linear' and \
self.base.data2D.name.count("Residuals") > 0:
new_plot.ytransform = 'y'
new_plot.yaxis("\\rm{Residuals} ", "/")
new_plot.group_id = "2daverage" + self.base.data2D.name
new_plot.id = "SectorQ" + self.base.data2D.name
new_plot.is_data = True
self.base.parent.update_theory(data_id=data.id, theory=new_plot)
wx.PostEvent(
self.base.parent,
NewPlotEvent(plot=new_plot,
title="SectorQ" + self.base.data2D.name))
def onCircular(self, event, ismask=False):
"""
perform circular averaging on Data2D
:param event: wx.menu event
"""
# Find the best number of bins
npt = math.sqrt(len(self.data2D.data[np.isfinite(self.data2D.data)]))
npt = math.floor(npt)
from sas.sascalc.dataloader.manipulations import CircularAverage
# compute the maximum radius of data2D
self.qmax = max(math.fabs(self.data2D.xmax),
math.fabs(self.data2D.xmin))
self.ymax = max(math.fabs(self.data2D.ymax),
math.fabs(self.data2D.ymin))
self.radius = math.sqrt(
math.pow(self.qmax, 2) + math.pow(self.ymax, 2))
# Compute beam width
bin_width = (self.qmax + self.qmax) / npt
# Create data1D circular average of data2D
Circle = CircularAverage(r_min=0,
r_max=self.radius,
bin_width=bin_width)
circ = Circle(self.data2D, ismask=ismask)
from sas.sasgui.guiframe.dataFitting import Data1D
if hasattr(circ, "dxl"):
dxl = circ.dxl
else:
dxl = None
if hasattr(circ, "dxw"):
dxw = circ.dxw
else:
dxw = None
new_plot = Data1D(x=circ.x, y=circ.y, dy=circ.dy, dx=circ.dx)
new_plot.dxl = dxl
new_plot.dxw = dxw
new_plot.name = "Circ avg " + self.data2D.name
new_plot.source = self.data2D.source
# new_plot.info = self.data2D.info
new_plot.interactive = True
new_plot.detector = self.data2D.detector
# If the data file does not tell us what the axes are, just assume...
new_plot.xaxis("\\rm{Q}", "A^{-1}")
if hasattr(self.data2D, "scale") and \
self.data2D.scale == 'linear':
new_plot.ytransform = 'y'
new_plot.yaxis("\\rm{Residuals} ", "normalized")
else:
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
new_plot.group_id = "2daverage" + self.data2D.name
new_plot.id = "Circ avg " + self.data2D.name
new_plot.is_data = True
self.parent.update_theory(data_id=self.data2D.id, theory=new_plot)
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title=new_plot.name))
def show_data(self, path=None, data=None, reset=False):
"""
Show data read from a file
:param path: file path
:param reset: if True all other plottables will be cleared
"""
#if path is not None:
if data is not None:
try:
pr = self._create_file_pr(data)
except:
status = "Problem reading data: %s" % sys.exc_value
wx.PostEvent(self.parent, StatusEvent(status=status))
raise RuntimeError, status
# If the file contains nothing, just return
if pr is None:
raise RuntimeError, "Loaded data is invalid"
self.pr = pr
# Make a plot of I(q) data
if self.pr.err is None:
new_plot = Data1D(self.pr.x, self.pr.y)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
else:
new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err)
new_plot.name = IQ_DATA_LABEL
new_plot.xaxis("\\rm{Q}", 'A^{-1}')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
new_plot.interactive = True
new_plot.group_id = GROUP_ID_IQ_DATA
new_plot.id = self.data_id
new_plot.title = "I(q)"
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title="I(q)", reset=reset))
self.current_plottable = new_plot
# Get Q range
self.control_panel.q_min = min(self.pr.x)
self.control_panel.q_max = max(self.pr.x)
def show_data(self, data, label, reset=False, active_ctrl=None):
"""
Show data read from a file
:param data: The data to plot (Data1D)
:param label: What to label the plot. Also used as the plot ID
:param reset: If True, all other plottables will be cleared
"""
new_plot = Data1D(data.x, copy.deepcopy(data.y), dy=data.dy)
group_id = ""
if label == IQ_DATA_LABEL or label == IQ_EXTRAPOLATED_DATA_LABEL:
new_plot.xaxis("\\rm{Q}", 'A^{-1}')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
new_plot.y -= self.corfunc_panel.background
# Show data on a log(Q)/I scale
new_plot.ytransform = 'y'
group_id = GROUP_ID_IQ_DATA
if label == IQ_EXTRAPOLATED_DATA_LABEL:
# Show the extrapolation as a curve instead of points
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
elif label == TRANSFORM_LABEL1 or label == TRANSFORM_LABEL3:
new_plot.xaxis("{x}", 'A')
new_plot.yaxis("{\\Gamma}", '')
# Show transform on a linear scale
new_plot.xtransform = 'x'
new_plot.ytransform = 'y'
group_id = GROUP_ID_TRANSFORM
# Show the transformation as a curve instead of points
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
elif label == IDF_LABEL:
new_plot.xaxis("{x}", 'A')
new_plot.yaxis("{g_1}", '')
# Linear scale
new_plot.xtransform = 'x'
new_plot.ytransform = 'y'
group_id = GROUP_ID_IDF
# Show IDF as a curve instead of points
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
new_plot.id = label
new_plot.name = label
new_plot.group_id = group_id
new_plot.interactive = True
new_plot.title = group_id.replace('$', '').replace('\\', '')
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title=new_plot.title,
reset=reset))
if label == IQ_DATA_LABEL or label == IQ_EXTRAPOLATED_DATA_LABEL:
wx.CallAfter(self.corfunc_panel.plot_qrange, active=active_ctrl,
leftdown=True)
if label == IQ_EXTRAPOLATED_DATA_LABEL:
# Zoom in to the region we're interested in
xlim = (min(self.corfunc_panel._extrapolated_data.x), self.corfunc_panel.qmax[1]*1.2)
wx.CallAfter(wx.PostEvent, self.parent, PlotLimitEvent(id=IQ_DATA_LABEL, group_id=GROUP_ID_IQ_DATA, xlim=xlim))
def post_data(self, new_sector):
""" post data averaging in Q"""
if self.inner_circle.get_radius() < self.outer_circle.get_radius():
rmin = self.inner_circle.get_radius()
rmax = self.outer_circle.get_radius()
else:
rmin = self.outer_circle.get_radius()
rmax = self.inner_circle.get_radius()
if self.right_edge.get_angle() < self.left_edge.get_angle():
phimin = self.right_edge.get_angle()
phimax = self.left_edge.get_angle()
else:
phimin = self.left_edge.get_angle()
phimax = self.right_edge.get_angle()
# print "phimin, phimax, rmin ,rmax",math.degrees(phimin),
# math.degrees(phimax), rmin ,rmax
# from sas.sascalc.dataloader.manipulations import SectorQ
sect = new_sector(r_min=rmin,
r_max=rmax,
phi_min=phimin,
phi_max=phimax)
sector = sect(self.base.data2D)
from sas.sasgui.guiframe.dataFitting import Data1D
if hasattr(sector, "dxl"):
dxl = sector.dxl
else:
dxl = None
if hasattr(sector, "dxw"):
dxw = sector.dxw
else:
dxw = None
new_plot = Data1D(x=sector.x,
y=sector.y,
dy=sector.dy,
dxl=dxl,
dxw=dxw)
new_plot.name = str(new_sector.__name__) + \
"(" + self.base.data2D.name + ")"
new_plot.source = self.base.data2D.source
new_plot.interactive = True
# print "loader output.detector",output.source
new_plot.detector = self.base.data2D.detector
# If the data file does not tell us what the axes are, just assume...
new_plot.xaxis("\\rm{Q}", 'rad')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
new_plot.group_id = str(new_sector.__name__) + self.base.data2D.name
self.base.parent.update_theory(data_id=self.base.data2D.id, \
theory=new_plot)
wx.PostEvent(
self.base.parent,
NewPlotEvent(plot=new_plot, title=str(new_sector.__name__)))
def _simulation_completed_1D(self, output, elapsed, error=None):
"""
Called by the computation thread when the simulation is complete.
This method processes the simulation output, plots it, and updates
the simulation time estimate.
@param output: simulated distribution I(q)
@param elapsed: simulation time, in seconds
@param error: standard deviation on the I(q) points
"""
# Create the plotting event to pop up the I(Q) plot.
new_plot = Data1D(x=self.x, y=output, dy=error)
new_plot.name = "I(Q) Simulation"
new_plot.group_id = "simulation_output"
new_plot.xaxis("\\rm{Q}", 'A^{-1}')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title="Simulation I(Q)"))
# Create the plotting event to pop up the P(r) plot.
r, pr = self.volCanvas.getPrData()
new_plot = Data1D(x=r, y=pr, dy=[0] * len(r))
new_plot.name = "P(r) Simulation"
new_plot.group_id = "simulated_pr"
new_plot.xaxis("\\rm{r}", 'A')
new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
wx.PostEvent(self.parent,
NewPlotEvent(plot=new_plot, title="Simulated P(r)"))
# Notify the user of the simlation time and update the basic
# simulation estimate that will allow us to estimate simulation time
# next time we are asked to simulate.
msg = "Calculation completed in %g secs! [%g points]" % (
elapsed, self.volCanvas.npts)
wx.PostEvent(self.parent, StatusEvent(status=msg))
if self.volCanvas.npts > 0:
self.speed = elapsed / self.volCanvas.npts**2
def __init__(self,
parent=None,
base=None,
data=None,
dimension=1,
id=ID,
*args,
**kwds):
kwds["style"] = wx.DEFAULT_DIALOG_STYLE
kwds["size"] = wx.Size(PANEL_SIZE * 1.5, PANEL_SIZE * 1.5)
wx.Dialog.__init__(self, parent, id=id, *args, **kwds)
if data is not None:
# Font size
kwds = []
self.SetWindowVariant(variant=FONT_VARIANT)
self.SetTitle("Plot " + data.name)
self.parent = base
self.data = data
self.str = self.data.__str__()
# # when 2 data have the same id override the 1 st plotted
self.name = self.data.name
self.dimension = dimension
# Panel for 2D plot
self.plotpanel = Maskplotpanel(self,
-1,
dimension,
style=wx.TRANSPARENT_WINDOW)
self.plotpanel._SetInitialSize()
self.plotpanel.prevXtrans = "x"
self.plotpanel.prevYtrans = "y"
self.cmap = DEFAULT_CMAP
# # Create Artist and bind it
self.subplot = self.plotpanel.subplot
self._setup_layout()
if self.dimension == 1:
self.newplot = Data1D(x=data.x,
y=data.y,
dx=data.dx,
dy=data.dy)
self.newplot.name = data.name
else:
self.newplot = Data2D(image=self.data.data)
self.newplot.setValues(self.data)
# Compute and get the image plot
self.get_plot()
# self.plotpanel.add_image(self.newplot)
self.Centre()
self.Layout()
def _fit_pr(self, evt):
"""
"""
# Generate P(r) for sphere
radius = 60.0
d_max = 2 * radius
r = pylab.arange(0.01, d_max, d_max / 51.0)
M = len(r)
y = np.zeros(M)
pr_err = np.zeros(M)
total = 0.0
for j in range(M):
value = self.pr_theory(r[j], radius)
total += value
y[j] = value
pr_err[j] = math.sqrt(y[j])
y = y / total * d_max / len(r)
# Perform fit
pr = Invertor()
pr.d_max = d_max
pr.alpha = 0
pr.x = r
pr.y = y
pr.err = pr_err
out, cov = pr.pr_fit()
for i in range(len(out)):
print("%g +- %g" % (out[i], math.sqrt(cov[i][i])))
# Show input P(r)
title = "Pr"
new_plot = Data1D(pr.x, pr.y, dy=pr.err)
new_plot.name = "P_{obs}(r)"
new_plot.xaxis("\\rm{r}", 'A')
new_plot.yaxis("\\rm{P(r)} ", "cm^{-3}")
new_plot.group_id = "P_{obs}(r)"
new_plot.id = "P_{obs}(r)"
new_plot.title = title
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))
# Show P(r) fit
self.show_pr(out, pr)
# Show I(q) fit
q = pylab.arange(0.001, 0.1, 0.01 / 51.0)
self.show_iq(out, pr, q)
def test_clone_theory1D(self):
"""
Test basic cloning
"""
theory = Data1D(x=[], y=[], dy=None)
theory.clone_without_data(clone=self.data)
theory.copy_from_datainfo(data1d=self.data)
for i in range(len(self.data.detector)):
self.assertEqual(
self.data.detector[i].distance, theory.detector[i].distance)
for i in range(len(self.data.x)):
self.assertEqual(self.data.x[i], theory.x[i])
self.assertEqual(self.data.y[i], theory.y[i])
self.assertEqual(self.data.dy[i], theory.dy[i])
def convert_1d_data(self, qdata, iqdata):
"""
Formats a 1D array of q_axis data and a 2D array of I axis data (where
each row of iqdata is a separate row), into an array of Data1D objects
"""
frames = []
increment = 1
single_file = True
n_frames = iqdata.shape[0]
# Standard file has 3 frames: SAS, calibration and WAS
if n_frames > 3:
# File has multiple frames - ask the user which ones they want to
# export
params = self.ask_frame_range(n_frames)
frames = params['frames']
increment = params['inc']
single_file = params['file']
if frames == []: return
else: # Only interested in SAS data
frames = [0]
output_path = self.output.GetPath()
metadata = self.get_metadata()
frame_data = {}
for i in frames:
data = Data1D(x=qdata, y=iqdata[i])
frame_data[i] = data
if single_file:
# Only need to set metadata on first Data1D object
frame_data = frame_data.values(
) # Don't need to know frame numbers
frame_data[0].filename = output_path.split('\\')[-1]
for key, value in metadata.iteritems():
setattr(frame_data[0], key, value)
else:
# Need to set metadata for all Data1D objects
for datainfo in frame_data.values():
datainfo.filename = output_path.split('\\')[-1]
for key, value in metadata.iteritems():
setattr(datainfo, key, value)
_, ext = os.path.splitext(output_path)
if ext == '.xml':
self.convert_to_cansas(frame_data, output_path, single_file)
else: # ext == '.h5'
w = NXcanSASWriter()
w.write(frame_data, output_path)
def write_toXML(self, datainfo=None, state=None):
"""
Write toXML, a helper for write()
: return: xml doc
"""
if datainfo is None:
datainfo = Data1D(x=[], y=[])
elif not issubclass(datainfo.__class__, Data1D):
msg = "The cansas writer expects a Data1D "
msg += "instance: %s" % str(datainfo.__class__.__name__)
raise RuntimeError(msg)
# Create basic XML document
doc, sasentry = self._to_xml_doc(datainfo)
# Add the invariant information to the XML document
if state is not None:
doc = state.toXML(doc=doc, entry_node=sasentry)
return doc
def transform_complete(self, transform=None):
"""
Called from FourierThread when calculation has completed
"""
self._transform_btn.SetLabel("Transform")
if transform is None:
msg = "Error calculating Transform."
if self.transform_type == 'hilbert':
msg = "Not yet implemented"
wx.PostEvent(self._manager.parent,
StatusEvent(status=msg, info="Error"))
self._extract_btn.Disable()
return
self._transformed_data = transform
import numpy as np
plot_x = transform.x[np.where(transform.x <= 200)]
plot_y = transform.y[np.where(transform.x <= 200)]
self._manager.show_data(Data1D(plot_x, plot_y), TRANSFORM_LABEL1)
# Only enable extract params button if a fourier trans. has been done
if self.transform_type == 'fourier':
self._extract_btn.Enable()
else:
self._extract_btn.Disable()
def __init__(self,
parent=None,
base=None,
data=None,
axes=['Radius'],
id=-1,
*args,
**kwds):
kwds["style"] = wx.DEFAULT_DIALOG_STYLE
kwds["size"] = wx.Size(_STATICBOX_WIDTH, PANEL_SIZE)
wx.Dialog.__init__(self, parent, id=id, *args, **kwds)
if data != None:
#Font size
kwds = []
self.SetWindowVariant(variant=FONT_VARIANT)
self.SetTitle("Scattering Length Density Profile")
self.parent = parent
self._mgr = None
self.data = data
self.str = self.data.__str__()
## when 2 data have the same id override the 1 st plotted
self.name = self.data.name
# Panel for plot
self.plotpanel = SLDplotpanel(self,
axes,
-1,
style=wx.TRANSPARENT_WINDOW)
self.cmap = DEFAULT_CMAP
## Create Artist and bind it
self.subplot = self.plotpanel.subplot
# layout
self._setup_layout()
# plot
data_plot = deepcopy(self.data)
data_plot.dy = self._set_dy_data()
# unit increase to M times for users
data_plot.y = self._set_y_data()
self.newplot = Data1D(data_plot.x, data_plot.y, data_plot.dy)
self.newplot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
self.newplot.dy = None
self.newplot.name = 'SLD'
self.newplot.is_data = False
self.newplot.id = self.newplot.name
self.plotpanel.add_image(self.newplot)
self.plotpanel.resizing = False
self.plotpanel.canvas.set_resizing(self.plotpanel.resizing)
self.plotpanel.subplot.set_ylim(
min(data_plot.y) - _Y_OFF,
max(data_plot.y) + _Y_OFF)
self.plotpanel.subplot.set_xlim(
min(data_plot.x) - _X_OFF,
max(data_plot.x) + _X_OFF)
self.plotpanel.graph.render(self.plotpanel)
self.plotpanel.canvas.draw()
def _post_data(self, nbins=None):
"""
Uses annulus parameters to plot averaged data into 1D data.
:param nbins: the number of points to plot
"""
# Data to average
data = self.base.data2D
# If we have no data, just return
if data == None:
return
from sas.sascalc.dataloader.manipulations import Ring
rmin = min(math.fabs(self.inner_circle.get_radius()),
math.fabs(self.outer_circle.get_radius()))
rmax = max(math.fabs(self.inner_circle.get_radius()),
math.fabs(self.outer_circle.get_radius()))
# if the user does not specify the numbers of points to plot
# the default number will be nbins= 36
if nbins == None:
self.nbins = 36
else:
self.nbins = nbins
# # create the data1D Q average of data2D
sect = Ring(r_min=rmin, r_max=rmax, nbins=self.nbins)
sector = sect(self.base.data2D)
if hasattr(sector, "dxl"):
dxl = sector.dxl
else:
dxl = None
if hasattr(sector, "dxw"):
dxw = sector.dxw
else:
dxw = None
new_plot = Data1D(x=(sector.x - math.pi) * 180 / math.pi,
y=sector.y,
dy=sector.dy)
new_plot.dxl = dxl
new_plot.dxw = dxw
new_plot.name = "AnnulusPhi" + "(" + self.base.data2D.name + ")"
new_plot.source = self.base.data2D.source
# new_plot.info=self.base.data2D.info
new_plot.interactive = True
new_plot.detector = self.base.data2D.detector
# If the data file does not tell us what the axes are, just assume...
new_plot.xaxis("\\rm{\phi}", 'degrees')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
if hasattr(data, "scale") and data.scale == 'linear' and \
self.base.data2D.name.count("Residuals") > 0:
new_plot.ytransform = 'y'
new_plot.yaxis("\\rm{Residuals} ", "/")
new_plot.group_id = "AnnulusPhi" + self.base.data2D.name
new_plot.id = "AnnulusPhi" + self.base.data2D.name
new_plot.is_data = True
new_plot.xtransform = "x"
new_plot.ytransform = "y"
self.base.parent.update_theory(data_id=data.id, theory=new_plot)
wx.PostEvent(self.base.parent,
NewPlotEvent(plot=new_plot, title="AnnulusPhi"))
def post_data(self, new_slab=None, nbins=None, direction=None):
"""
post data averaging in Qx or Qy given new_slab type
:param new_slab: slicer that determine with direction to average
:param nbins: the number of points plotted when averaging
:param direction: the direction of averaging
"""
if self.direction is None:
self.direction = direction
x_min = -1 * math.fabs(self.vertical_lines.x)
x_max = math.fabs(self.vertical_lines.x)
y_min = -1 * math.fabs(self.horizontal_lines.y)
y_max = math.fabs(self.horizontal_lines.y)
if nbins is not None:
self.nbins = nbins
if self.averager is None:
if new_slab is None:
msg = "post data:cannot average , averager is empty"
raise ValueError(msg)
self.averager = new_slab
if self.direction == "X":
if self.fold:
x_low = 0
else:
x_low = math.fabs(x_min)
bin_width = (x_max + x_low) / self.nbins
elif self.direction == "Y":
if self.fold:
y_low = 0
else:
y_low = math.fabs(y_min)
bin_width = (y_max + y_low) / self.nbins
else:
msg = "post data:no Box Average direction was supplied"
raise ValueError(msg)
# # Average data2D given Qx or Qy
box = self.averager(x_min=x_min, x_max=x_max, y_min=y_min, y_max=y_max,
bin_width=bin_width)
box.fold = self.fold
boxavg = box(self.base.data2D)
# 3 Create Data1D to plot
if hasattr(boxavg, "dxl"):
dxl = boxavg.dxl
else:
dxl = None
if hasattr(boxavg, "dxw"):
dxw = boxavg.dxw
else:
dxw = None
new_plot = Data1D(x=boxavg.x, y=boxavg.y, dy=boxavg.dy)
new_plot.dxl = dxl
new_plot.dxw = dxw
new_plot.name = str(self.averager.__name__) + \
"(" + self.base.data2D.name + ")"
new_plot.source = self.base.data2D.source
new_plot.interactive = True
new_plot.detector = self.base.data2D.detector
# # If the data file does not tell us what the axes are, just assume...
new_plot.xaxis("\\rm{Q}", "A^{-1}")
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
data = self.base.data2D
if hasattr(data, "scale") and data.scale == 'linear' and \
self.base.data2D.name.count("Residuals") > 0:
new_plot.ytransform = 'y'
new_plot.yaxis("\\rm{Residuals} ", "/")
new_plot.group_id = "2daverage" + self.base.data2D.name
new_plot.id = (self.averager.__name__) + self.base.data2D.name
new_plot.is_data = True
self.base.parent.update_theory(data_id=self.base.data2D.id, \
theory=new_plot)
wx.PostEvent(self.base.parent,
NewPlotEvent(plot=new_plot, title=str(self.averager.__name__)))
def show_iq(self, out, pr, q=None):
"""
Display computed I(q)
"""
qtemp = pr.x
if q is not None:
qtemp = q
# Make a plot
maxq = -1
for q_i in qtemp:
if q_i > maxq:
maxq = q_i
minq = 0.001
# Check for user min/max
if pr.q_min is not None:
minq = pr.q_min
if pr.q_max is not None:
maxq = pr.q_max
x = pylab.arange(minq, maxq, maxq / 301.0)
y = np.zeros(len(x))
err = np.zeros(len(x))
for i in range(len(x)):
value = pr.iq(out, x[i])
y[i] = value
try:
err[i] = math.sqrt(math.fabs(value))
except:
err[i] = 1.0
print("Error getting error", value, x[i])
new_plot = Data1D(x, y)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
new_plot.name = IQ_FIT_LABEL
new_plot.xaxis("\\rm{Q}", 'A^{-1}')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
title = "I(q)"
new_plot.title = title
# If we have a group ID, use it
if 'plot_group_id' in pr.info:
new_plot.group_id = pr.info["plot_group_id"]
new_plot.id = IQ_FIT_LABEL
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))
# If we have used slit smearing, plot the smeared I(q) too
if pr.slit_width > 0 or pr.slit_height > 0:
x = pylab.arange(minq, maxq, maxq / 301.0)
y = np.zeros(len(x))
err = np.zeros(len(x))
for i in range(len(x)):
value = pr.iq_smeared(out, x[i])
y[i] = value
try:
err[i] = math.sqrt(math.fabs(value))
except:
err[i] = 1.0
print("Error getting error", value, x[i])
new_plot = Data1D(x, y)
new_plot.symbol = GUIFRAME_ID.CURVE_SYMBOL_NUM
new_plot.name = IQ_SMEARED_LABEL
new_plot.xaxis("\\rm{Q}", 'A^{-1}')
new_plot.yaxis("\\rm{Intensity} ", "cm^{-1}")
# If we have a group ID, use it
if 'plot_group_id' in pr.info:
new_plot.group_id = pr.info["plot_group_id"]
new_plot.id = IQ_SMEARED_LABEL
new_plot.title = title
self.parent.update_theory(data_id=self.data_id, theory=new_plot)
wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title))
