Source code for sas.qtgui.Plotting.Plotter2D
import copy
import numpy
import functools
from PyQt5 import QtGui
from PyQt5 import QtWidgets
from mpl_toolkits.mplot3d import Axes3D
from sas.sascalc.dataloader.manipulations import CircularAverage
from sas.qtgui.Plotting.PlotterData import Data1D
from sas.qtgui.Plotting.PlotterData import Data2D
import sas.qtgui.Plotting.PlotUtilities as PlotUtilities
import sas.qtgui.Utilities.GuiUtils as GuiUtils
from sas.qtgui.Plotting.PlotterBase import PlotterBase
from sas.qtgui.Plotting.ColorMap import ColorMap
from sas.qtgui.Plotting.BoxSum import BoxSum
from sas.qtgui.Plotting.SlicerParameters import SlicerParameters
# TODO: move to sas.qtgui namespace
from sas.qtgui.Plotting.Slicers.BoxSlicer import BoxInteractorX
from sas.qtgui.Plotting.Slicers.BoxSlicer import BoxInteractorY
from sas.qtgui.Plotting.Slicers.AnnulusSlicer import AnnulusInteractor
from sas.qtgui.Plotting.Slicers.SectorSlicer import SectorInteractor
from sas.qtgui.Plotting.Slicers.BoxSum import BoxSumCalculator
import matplotlib as mpl
DEFAULT_CMAP = mpl.cm.jet
# Minimum value of Z for which we will present data.
MIN_Z = -32
[docs]class Plotter2DWidget(PlotterBase):
"""
2D Plot widget for use with a QDialog
"""
[docs] def __init__(self, parent=None, manager=None, quickplot=False, dimension=2):
self.dimension = dimension
super(Plotter2DWidget, self).__init__(parent, manager=manager, quickplot=quickplot)
self.cmap = DEFAULT_CMAP.name
# Default scale
self.scale = 'log_{10}'
# to set the order of lines drawn first.
self.slicer_z = 5
# Reference to the current slicer
self.slicer = None
self.slicer_widget = None
self.vmin = None
self.vmax = None
self.im = None
self.manager = manager
@property
def data(self):
return self._data
@property
def data0(self):
return self._data[0]
@data.setter
def data(self, data=None):
""" data setter """
if self._data:
self._data[0] = data
else:
self._data.append(data)
self.qx_data = data.qx_data
self.qy_data = data.qy_data
self.xmin = data.xmin
self.xmax = data.xmax
self.ymin = data.ymin
self.ymax = data.ymax
self.zmin = data.zmin
self.zmax = data.zmax
self.label = data.name
self.xLabel = "%s(%s)"%(data._xaxis, data._xunit)
self.yLabel = "%s(%s)"%(data._yaxis, data._yunit)
self.title(title=data.title)
[docs] def plot(self, data=None, marker=None, show_colorbar=True, update=False):
"""
Plot 2D self._data
marker - unused
"""
# Assing data
if isinstance(data, Data2D):
# no append, since there can only be one data in Data2D plot
self.data = data
if not self._data:
return
# Toggle the scale
zmin_2D_temp, zmax_2D_temp = self.calculateDepth()
# Prepare and show the plot
self.showPlot(data=self.data0.data,
qx_data=self.qx_data,
qy_data=self.qy_data,
xmin=self.xmin,
xmax=self.xmax,
ymin=self.ymin, ymax=self.ymax,
cmap=self.cmap, zmin=zmin_2D_temp,
zmax=zmax_2D_temp, show_colorbar=show_colorbar,
update=update)
self.updateCircularAverage()
[docs] def calculateDepth(self):
"""
Re-calculate the plot depth parameters depending on the scale
"""
# Toggle the scale
zmin_temp = self.zmin
zmax_temp = self.zmax
# self.scale predefined in the baseclass
# in numpy > 1.12 power(int, -int) raises ValueException
# "Integers to negative integer powers are not allowed."
if self.scale == 'log_{10}':
if self.zmin is not None:
zmin_temp = numpy.power(10.0, self.zmin)
if self.zmax is not None:
zmax_temp = numpy.power(10.0, self.zmax)
else:
if self.zmin is not None:
# min log value: no log(negative)
zmin_temp = MIN_Z if self.zmin <= 0 else numpy.log10(self.zmin)
if self.zmax is not None:
zmax_temp = numpy.log10(self.zmax)
return (zmin_temp, zmax_temp)
[docs] def createContextMenu(self):
"""
Define common context menu and associated actions for the MPL widget
"""
self.defaultContextMenu()
self.contextMenu.addSeparator()
self.actionDataInfo = self.contextMenu.addAction("&DataInfo")
self.actionDataInfo.triggered.connect(
functools.partial(self.onDataInfo, self.data0))
self.actionSavePointsAsFile = self.contextMenu.addAction("&Save Points as a File")
self.actionSavePointsAsFile.triggered.connect(
functools.partial(self.onSavePoints, self.data0))
self.contextMenu.addSeparator()
self.actionCircularAverage = self.contextMenu.addAction("&Perform Circular Average")
self.actionCircularAverage.triggered.connect(self.onCircularAverage)
self.actionSectorView = self.contextMenu.addAction("&Sector [Q View]")
self.actionSectorView.triggered.connect(self.onSectorView)
self.actionAnnulusView = self.contextMenu.addAction("&Annulus [Phi View]")
self.actionAnnulusView.triggered.connect(self.onAnnulusView)
self.actionBoxSum = self.contextMenu.addAction("&Box Sum")
self.actionBoxSum.triggered.connect(self.onBoxSum)
self.actionBoxAveragingX = self.contextMenu.addAction("&Box Averaging in Qx")
self.actionBoxAveragingX.triggered.connect(self.onBoxAveragingX)
self.actionBoxAveragingY = self.contextMenu.addAction("&Box Averaging in Qy")
self.actionBoxAveragingY.triggered.connect(self.onBoxAveragingY)
# Additional items for slicer interaction
if self.slicer:
self.actionClearSlicer = self.contextMenu.addAction("&Clear Slicer")
self.actionClearSlicer.triggered.connect(self.onClearSlicer)
self.actionEditSlicer = self.contextMenu.addAction("&Edit Slicer Parameters")
self.actionEditSlicer.triggered.connect(self.onEditSlicer)
self.contextMenu.addSeparator()
self.actionColorMap = self.contextMenu.addAction("&2D Color Map")
self.actionColorMap.triggered.connect(self.onColorMap)
self.contextMenu.addSeparator()
self.actionChangeScale = self.contextMenu.addAction("Toggle Linear/Log Scale")
self.actionChangeScale.triggered.connect(self.onToggleScale)
self.contextMenu.addSeparator()
self.actionToggleMenu = self.contextMenu.addAction("Toggle Navigation Menu")
self.actionToggleMenu.triggered.connect(self.onToggleMenu)
[docs] def createContextMenuQuick(self):
"""
Define context menu and associated actions for the quickplot MPL widget
"""
self.defaultContextMenu()
if self.dimension == 2:
self.actionToggleGrid = self.contextMenu.addAction("Toggle Grid On/Off")
self.contextMenu.addSeparator()
self.actionChangeScale = self.contextMenu.addAction("Toggle Linear/Log Scale")
# Define the callbacks
self.actionChangeScale.triggered.connect(self.onToggleScale)
if self.dimension == 2:
self.actionToggleGrid.triggered.connect(self.onGridToggle)
[docs] def onToggleScale(self, event):
"""
Toggle axis and replot image
"""
# self.scale predefined in the baseclass
if self.scale == 'log_{10}':
self.scale = 'linear'
else:
self.scale = 'log_{10}'
self.plot()
[docs] def onClearSlicer(self):
"""
Remove all sclicers from the chart
"""
if self.slicer is None:
return
self.slicer.clear()
self.canvas.draw()
self.slicer = None
if self.slicer_widget:
self.slicer_widget.setModel(None)
[docs] def getActivePlots(self):
''' utility method for manager query of active plots '''
return self.manager.active_plots
[docs] def onEditSlicer(self):
"""
Present a dialog for manipulating the current slicer
"""
# Only show the dialog if not currently shown
if self.slicer_widget:
return
def slicer_closed():
# Need to disconnect the signal!!
self.slicer_widget.closeWidgetSignal.disconnect()
self.manager.parent.workspace().removeSubWindow(self.slicer_subwindow)
# reset slicer_widget on "Edit Slicer Parameters" window close
self.slicer_widget = None
self.param_model = None
validator = None
if self.slicer is not None and not isinstance(self.slicer, BoxSumCalculator):
self.param_model = self.slicer.model()
validator = self.slicer.validate
# Pass the model to the Slicer Parameters widget
self.slicer_widget = SlicerParameters(self, model=self.param_model,
active_plots=self.getActivePlots(),
validate_method=validator,
communicator=self.manager.communicator)
self.slicer_widget.closeWidgetSignal.connect(slicer_closed)
# Add the plot to the workspace
self.slicer_subwindow = self.manager.parent.workspace().addSubWindow(self.slicer_widget)
self.slicer_widget.show()
[docs] def circularAverage(self):
"""
Calculate the circular average and create the Data object for it
"""
# Find the best number of bins
npt = numpy.sqrt(len(self.data0.data[numpy.isfinite(self.data0.data)]))
npt = numpy.floor(npt)
# compute the maximum radius of data2D
self.qmax = max(numpy.fabs(self.data0.xmax),
numpy.fabs(self.data0.xmin))
self.ymax = max(numpy.fabs(self.data0.ymax),
numpy.fabs(self.data0.ymin))
self.radius = numpy.sqrt(numpy.power(self.qmax, 2) + numpy.power(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.data0)
dxl = circ.dxl if hasattr(circ, "dxl") else None
dxw = circ.dxw if hasattr(circ, "dxw") else 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 = new_plot.title = "Circ avg " + self.data0.name
new_plot.source = self.data0.source
new_plot.interactive = True
new_plot.detector = self.data0.detector
# Define axes if not done yet.
new_plot.xaxis("\\rm{Q}", "A^{-1}")
if hasattr(self.data0, "scale") and \
self.data0.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.data0.name
new_plot.id = "Circ avg " + self.data0.name
new_plot.is_data = True
return new_plot
[docs] def onCircularAverage(self):
"""
Perform circular averaging on Data2D
"""
new_plot = self.circularAverage()
item = self._item
if self._item.parent() is not None:
item = self._item.parent()
GuiUtils.updateModelItemWithPlot(item, new_plot, new_plot.id)
self.manager.communicator.plotUpdateSignal.emit([new_plot])
self.manager.communicator.forcePlotDisplaySignal.emit([item, new_plot])
[docs] def updateCircularAverage(self):
"""
Update circular averaging plot on Data2D change
"""
if not hasattr(self, '_item'): return
item = self._item
if self._item.parent() is not None:
item = self._item.parent()
# Get all plots for current item
plots = GuiUtils.plotsFromModel("", item)
if plots is None: return
ca_caption = '2daverage' + self.data0.name
# See if current item plots contain 2D average plot
has_plot = False
for plot in plots:
if plot.group_id is None: continue
if ca_caption in plot.group_id: has_plot = True
# return prematurely if no circular average plot found
if not has_plot: return
# Create a new plot
new_plot = self.circularAverage()
# Overwrite existing plot
GuiUtils.updateModelItemWithPlot(item, new_plot, new_plot.id)
# Show the new plot, if already visible
self.manager.communicator.plotUpdateSignal.emit([new_plot])
[docs] def setSlicer(self, slicer, reset=True):
"""
Clear the previous slicer and create a new one.
slicer: slicer class to create
"""
# Clear current slicer
if self.slicer is not None:
self.slicer.clear()
# Create a new slicer
self.slicer_z += 1
self.slicer = slicer(self, self.ax, item=self._item, zorder=self.slicer_z)
self.ax.set_ylim(self.data0.ymin, self.data0.ymax)
self.ax.set_xlim(self.data0.xmin, self.data0.xmax)
# Draw slicer
self.figure.canvas.draw()
self.slicer.update()
# Reset the model on the Edit slicer parameters widget
self.param_model = self.slicer.model()
if self.slicer_widget and reset:
self.slicer_widget.setModel(self.param_model)
[docs] def onSectorView(self):
"""
Perform sector averaging on Q and draw sector slicer
"""
self.setSlicer(slicer=SectorInteractor)
[docs] def onAnnulusView(self):
"""
Perform sector averaging on Phi and draw annulus slicer
"""
self.setSlicer(slicer=AnnulusInteractor)
[docs] def onBoxSum(self):
"""
Perform 2D Data averaging Qx and Qy.
Display box slicer details.
"""
self.onClearSlicer()
self.slicer_z += 1
self.slicer = BoxSumCalculator(self, self.ax, zorder=self.slicer_z)
self.ax.set_ylim(self.data0.ymin, self.data0.ymax)
self.ax.set_xlim(self.data0.xmin, self.data0.xmax)
self.figure.canvas.draw()
self.slicer.update()
def boxWidgetClosed():
# Need to disconnect the signal!!
self.boxwidget.closeWidgetSignal.disconnect()
# reset box on "Edit Slicer Parameters" window close
self.manager.parent.workspace().removeSubWindow(self.boxwidget_subwindow)
self.boxwidget = None
# Get the BoxSumCalculator model.
self.box_sum_model = self.slicer.model()
# Pass the BoxSumCalculator model to the BoxSum widget
self.boxwidget = BoxSum(self, model=self.box_sum_model)
# Add the plot to the workspace
self.boxwidget_subwindow = self.manager.parent.workspace().addSubWindow(self.boxwidget)
self.boxwidget.closeWidgetSignal.connect(boxWidgetClosed)
self.boxwidget.show()
[docs] def onBoxAveragingX(self):
"""
Perform 2D data averaging on Qx
Create a new slicer.
"""
self.setSlicer(slicer=BoxInteractorX)
[docs] def onBoxAveragingY(self):
"""
Perform 2D data averaging on Qy
Create a new slicer .
"""
self.setSlicer(slicer=BoxInteractorY)
[docs] def onColorMap(self):
"""
Display the color map dialog and modify the plot's map accordingly
"""
color_map_dialog = ColorMap(self, cmap=self.cmap,
vmin=self.vmin,
vmax=self.vmax,
data=self.data0)
color_map_dialog.apply_signal.connect(self.onApplyMap)
if color_map_dialog.exec_() == QtWidgets.QDialog.Accepted:
self.onApplyMap(color_map_dialog.norm(), color_map_dialog.cmap())
[docs] def onApplyMap(self, v_values, cmap):
"""
Update the chart color map based on data passed from the widget
"""
self.cmap = str(cmap)
self.vmin, self.vmax = v_values
# Redraw the chart with new cmap
self.plot()
[docs] def showPlot(self, data, qx_data, qy_data, xmin, xmax, ymin, ymax,
zmin, zmax, label='data2D', cmap=DEFAULT_CMAP, show_colorbar=True,
update=False):
"""
Render and show the current data
"""
self.qx_data = qx_data
self.qy_data = qy_data
self.xmin = xmin
self.xmax = xmax
self.ymin = ymin
self.ymax = ymax
self.zmin = zmin
self.zmax = zmax
# If we don't have any data, skip.
if data is None:
return
if data.ndim == 0:
return
elif data.ndim == 1:
output = PlotUtilities.build_matrix(data, self.qx_data, self.qy_data)
else:
output = copy.deepcopy(data)
# get the x and y_bin arrays.
x_bins, y_bins = PlotUtilities.get_bins(self.qx_data, self.qy_data)
self.data0.x_bins = x_bins
self.data0.y_bins = y_bins
zmin_temp = self.zmin
# check scale
if self.scale == 'log_{10}':
#with numpy.errstate(all='ignore'):
# output = numpy.log10(output)
#index = numpy.isfinite(output)
#if not index.all():
# cutoff = (numpy.quantile(output[index], 0.05) - numpy.log10(2) if index.any() else 0.)
# output[output < cutoff] = cutoff
# output[~index] = cutoff
try:
if self.zmin <= 0 and len(output[output > 0]) > 0:
zmin_temp = self.zmin
output[output > 0] = numpy.log10(output[output > 0])
elif self.zmin <= 0:
zmin_temp = self.zmin
output[output > 0] = numpy.zeros(len(output))
output[output <= 0] = MIN_Z
else:
zmin_temp = self.zmin
output[output > 0] = numpy.log10(output[output > 0])
except:
#Too many problems in 2D plot with scale
output[output > 0] = numpy.log10(output[output > 0])
pass
vmin, vmax = None, None
self.cmap = cmap
if self.dimension != 3:
#Re-adjust colorbar
self.figure.subplots_adjust(left=0.2, right=.8, bottom=.2)
zmax_temp = self.zmax
if self.vmin is not None:
zmin_temp = self.vmin
zmax_temp = self.vmax
if self.im is not None and update:
self.im.set_data(output)
else:
self.im = self.ax.imshow(output, interpolation='nearest',
origin='lower',
vmin=zmin_temp, vmax=zmax_temp,
cmap=self.cmap,
extent=(self.xmin, self.xmax,
self.ymin, self.ymax))
cbax = self.figure.add_axes([0.88, 0.2, 0.02, 0.7])
# Current labels for axes
self.ax.set_ylabel(self.y_label)
self.ax.set_xlabel(self.x_label)
# Title only for regular charts
if not self.quickplot:
self.ax.set_title(label=self._title)
if cbax is None:
self.ax.set_frame_on(False)
cb = self.figure.colorbar(self.im, shrink=0.8, aspect=20)
else:
cb = self.figure.colorbar(self.im, cax=cbax)
cb.update_bruteforce(self.im)
cb.set_label('$' + self.scale + '$')
self.vmin = cb.vmin
self.vmax = cb.vmax
if show_colorbar is False:
cb.remove()
else:
# clear the previous 2D from memory
self.figure.clear()
self.figure.subplots_adjust(left=0.1, right=.8, bottom=.1)
data_x, data_y = numpy.meshgrid(self.data0.x_bins[0:-1],
self.data0.y_bins[0:-1])
ax = Axes3D(self.figure)
# Disable rotation for large sets.
# TODO: Define "large" for a dataset
SET_TOO_LARGE = 500
if len(data_x) > SET_TOO_LARGE:
ax.disable_mouse_rotation()
self.figure.canvas.resizing = False
im = ax.plot_surface(data_x, data_y, output, rstride=1,
cstride=1, cmap=cmap,
linewidth=0, antialiased=False)
self.ax.set_axis_off()
if self.dimension != 3:
self.figure.canvas.draw_idle()
else:
self.figure.canvas.draw()
[docs] def imageShow(self, img, origin=None):
"""
Show background image
:Param img: [imread(path) from matplotlib.pyplot]
"""
if origin is not None:
im = self.ax.imshow(img, origin=origin)
else:
im = self.ax.imshow(img)
[docs] def replacePlot(self, id, new_plot):
"""
Replace data in current chart.
This effectively refreshes the chart with changes to one of its plots
"""
self.plot(data=new_plot)
[docs] def onMplMouseDown(self, event):
"""
Display x/y/intensity on click
"""
# Check that the LEFT button was pressed
if event.button != 1:
return
if event.inaxes is None:
return
x_click = 0.0
y_click = 0.0
try:
x_click = float(event.xdata) # / size_x
y_click = float(event.ydata) # / size_y
except:
self.position = None
x_str = GuiUtils.formatNumber(x_click)
y_str = GuiUtils.formatNumber(y_click)
coord_str = "x: {}, y: {}".format(x_str, y_str)
self.manager.communicate.statusBarUpdateSignal.emit(coord_str)
[docs]class Plotter2D(QtWidgets.QDialog, Plotter2DWidget):
"""
Plotter widget implementation
"""
[docs] def __init__(self, parent=None, quickplot=False, dimension=2):
QtWidgets.QDialog.__init__(self)
Plotter2DWidget.__init__(self, manager=parent, quickplot=quickplot, dimension=dimension)
icon = QtGui.QIcon()
icon.addPixmap(QtGui.QPixmap(":/res/ball.ico"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
self.setWindowIcon(icon)