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#/*##########################################################################
# Copyright (C) 2004-2022 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
"""
This plugin opens a widget to view a stack as a scatter plot, by using
positioner data as X and Y coordinates.
"""
__author__ = "V.A. Sole - ESRF"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import logging
import numpy
from contextlib import contextmanager
# import order may matter for qt binding selection
from PyMca5.PyMcaGui import PyMcaQt as qt
from silx.gui import qt as silx_qt
from PyMca5 import StackPluginBase
from silx.gui.plot.ScatterView import ScatterView
from silx.gui.widgets.BoxLayoutDockWidget import BoxLayoutDockWidget
from silx.gui.colors import Colormap
_logger = logging.getLogger(__name__)
# _logger.setLevel(logging.DEBUG)
# Probe OpenGL availability and widget
isGLAvailable = False
try:
import OpenGL
except ImportError:
_logger.debug("pyopengl not installed")
else:
# sanity check from silx.gui._glutils.OpenGLWidget
if not hasattr(silx_qt, 'QOpenGLWidget') and\
(not silx_qt.HAS_OPENGL or
silx_qt.QApplication.instance() and not silx_qt.QGLFormat.hasOpenGL()):
_logger.debug("qt has a QOpenGLWidget: %s", hasattr(silx_qt, 'QOpenGLWidget'))
_logger.debug("qt.HAS_OPENGL: %s", silx_qt.HAS_OPENGL)
_logger.debug("silx_qt.QGLFormat.hasOpenGL(): %s",
silx_qt.QApplication.instance() and not silx_qt.QGLFormat.hasOpenGL())
else:
isGLAvailable = True
_logger.debug("GL availability: %s", isGLAvailable)
class AxesPositionersSelector(qt.QWidget):
sigSelectionChanged = qt.pyqtSignal(object, object)
def __init__(self, parent=None):
qt.QWidget.__init__(self, parent)
hlayout = qt.QHBoxLayout()
self.setLayout(hlayout)
self._initializing = True
xlabel = qt.QLabel("X:", parent=parent)
self.xPositioner = qt.QComboBox(parent)
self.xPositioner.currentIndexChanged.connect(self._emitSelectionChanged)
ylabel = qt.QLabel("Y:", parent=parent)
self.yPositioner = qt.QComboBox(parent)
self.yPositioner.currentIndexChanged.connect(self._emitSelectionChanged)
self._initializing = False
hlayout.addWidget(xlabel)
hlayout.addWidget(self.xPositioner)
hlayout.addWidget(ylabel)
hlayout.addWidget(self.yPositioner)
self._nPoints = None
"""If set to an integer, only motors with this number of data points
can be added."""
self._initComboBoxes()
def _initComboBoxes(self):
self.xPositioner.clear()
self.xPositioner.insertItem(0, "None")
self.yPositioner.clear()
self.yPositioner.insertItem(0, "None")
def _emitSelectionChanged(self, idx):
if not self._initializing:
self.sigSelectionChanged.emit(*self.getSelectedPositioners())
def setNumPoints(self, n):
self._nPoints = n
def unsetNumPoints(self):
self._nPoints = None
def fillPositioners(self, positioners):
"""
:param dict positioners: Dictionary of positioners
The key is the motor name, the value are the motor's position data
"""
currentX, currentY = self.getSelectedPositioners()
self._initializing = True
self._initComboBoxes()
i = 0
for motorName, motorValues in positioners.items():
if not numpy.isscalar(motorValues) and self._nPoints is not None and self._nPoints != motorValues.size:
# checks consistency of number of data points (but accepts scalars)
continue
else:
i += 1
self.xPositioner.insertItem(i, motorName)
self.yPositioner.insertItem(i, motorName)
if currentX in positioners and currentY in positioners:
self.xPositioner.setCurrentIndex(self.xPositioner.findText(currentX))
self.yPositioner.setCurrentIndex(self.yPositioner.findText(currentY))
self._initializing = False
def getSelectedPositioners(self):
"""
:return: 2-tuple of selected positioner names (or None)
"""
selected = [None, None]
if self.xPositioner.currentText() != "None":
selected[0] = self.xPositioner.currentText()
if self.yPositioner.currentText() != "None":
selected[1] = self.yPositioner.currentText()
return selected
class MaskScatterViewWidget(qt.QMainWindow):
def __init__(self, parent=None, backend="mpl"):
qt.QMainWindow.__init__(self, parent)
self._scatterView = ScatterView(parent=self, backend=backend)
self._scatterView.setColormap(Colormap("temperature"))
self._scatterView.getScatterItem().setSymbol("s")
self._axesSelector = AxesPositionersSelector(parent=self._scatterView)
self._axesSelector.sigSelectionChanged.connect(self._setAxesData)
self.setCentralWidget(self._scatterView)
_axesSelectorDock = BoxLayoutDockWidget()
_axesSelectorDock.setWindowTitle('Axes selection')
_axesSelectorDock.setWidget(self._axesSelector)
self.addDockWidget(qt.Qt.BottomDockWidgetArea, _axesSelectorDock)
self._positioners = {}
self._xdata = None
self._ydata = None
self._stackImage = None
def getMaskToolsWidget(self):
return self._scatterView.getMaskToolsWidget()
def resetZoom(self):
return self._scatterView.resetZoom()
def fillPositioners(self, positioners):
self._positioners = positioners
self._axesSelector.fillPositioners(positioners)
def setNumPoints(self, n):
self._axesSelector.setNumPoints(n)
def _setAxesData(self, xPositioner, yPositioner):
"""
:param str xPositioner: motor name, or None
:param str yPositioner: motor name, or None
:return:
"""
if xPositioner not in [None, ""]:
assert xPositioner in self._positioners
self._xdata = self._positioners[xPositioner]
else:
self._xdata = None
if yPositioner not in [None, ""]:
assert yPositioner in self._positioners
self._ydata = self._positioners[yPositioner]
else:
self._ydata = None
if self._stackImage is not None:
self.setData()
if not self._scatterView.getMaskToolsWidget().isVisible():
# synchronization inactive, force mask redrawing
mask = self._scatterView.getMaskToolsWidget().getSelectionMask()
if mask is not None:
self._scatterView.getMaskToolsWidget().setSelectionMask(mask)
self._scatterView.resetZoom()
def setData(self, stackImage=None):
first_time = self._stackImage is None
if first_time:
assert stackImage is not None
if stackImage is None:
# use previous data
stackImage = self._stackImage
else:
# update stored data
self._stackImage = stackImage
nrows, ncols = stackImage.shape
# flatten image
stackValues = stackImage.reshape((-1,))
# get regular grid coordinates as a 1D array
if self._xdata is None or self._ydata is None:
defaultX, defaultY = numpy.meshgrid(numpy.arange(ncols),
numpy.arange(nrows))
defaultX.shape = stackValues.shape
defaultY.shape = stackValues.shape
xdata = self._xdata if self._xdata is not None else defaultX
ydata = self._ydata if self._ydata is not None else defaultY
if numpy.isscalar(xdata):
xdata = xdata * numpy.ones_like(stackValues)
_logger.debug("converting scalar to constant 1D array for x")
elif len(xdata.shape) > 1:
_logger.debug("flattening %s array", str(xdata.shape))
xdata = xdata.reshape((-1,))
if numpy.isscalar(ydata):
ydata = ydata * numpy.ones_like(stackValues)
_logger.debug("converting scalar to constant 1D array for y")
elif len(ydata.shape) > 1:
_logger.debug("flattening %s array", str(ydata.shape))
ydata = ydata.reshape((-1,))
self._scatterView.setData(xdata, ydata, stackValues,
copy=False)
if first_time:
self._scatterView.resetZoom()
class MaskScatterViewPlugin(StackPluginBase.StackPluginBase):
"""
Widget to handle a stack as a scatter plot, by using
positioner data as X and Y coordinates.
The position data can be loaded via the load positioners plugin
if not detected automatically.
"""
def __init__(self, stackWindow, **kw):
StackPluginBase.StackPluginBase.__init__(self, stackWindow, **kw)
tooltip = "Stack as a scatter plot, using positioners as axes"
self.methodDict = {'Show (mpl)': [self._showWidgetMpl,
tooltip + " (matplotlib backend)",
None]}
self.__methodKeys = ['Show (mpl)']
self._createdBackends = []
if isGLAvailable:
self.methodDict['Show (gl)'] = [self._showWidgetGL,
tooltip + " (OpenGL backend)",
None]
self.__methodKeys.append('Show (gl)')
self._scatterViews = {"gl": None,
"mpl": None}
def _buildWidget(self, backend):
scatterView = MaskScatterViewWidget(parent=None, backend=backend)
self._scatterViews[backend] = scatterView
self._createdBackends.append(backend)
self._setData(backend)
callback = self._scatterMaskChangedGl if backend == "gl" else self._scatterMaskChangedMpl
scatterView.getMaskToolsWidget().sigMaskChanged.connect(
callback)
nPoints = self._getNumStackPoints()
scatterView.setNumPoints(nPoints)
positioners = self._getStackPositioners()
scatterView.fillPositioners(positioners)
# try to figure out if there are good X and Y candidates
X = None
Y = None
for key in positioners:
if key.lower() == "x":
if len(positioners[key]) == nPoints:
X = key
elif key.lower() == "y":
if len(positioners[key]) == nPoints:
Y = key
if X:
scatterView._axesSelector.xPositioner.setCurrentText(X)
if Y:
scatterView._axesSelector.yPositioner.setCurrentText(Y)
def _showWidgetMpl(self):
self._showWidget(backend="mpl")
def _showWidgetGL(self):
self._showWidget(backend="gl")
def _showWidget(self, backend):
if self._scatterViews[backend] is None:
self._buildWidget(backend=backend)
# Show
self._scatterViews[backend].show()
self._scatterViews[backend].raise_()
# Draw mask, if any
self.selectionMaskUpdated()
@contextmanager
def _scatterMaskDisconnected(self, backend):
# This context manager allows to call self.setStackSelectionMask
# without entering an infinite loop, by temporarily disconnecting
# callbacks from our mask signals.
# Disconnect
callback = self._scatterMaskChangedGl if backend == "gl" else self._scatterMaskChangedMpl
self._scatterViews[backend].getMaskToolsWidget().sigMaskChanged.disconnect(
callback)
try:
yield
finally:
# Reconnect
callback = self._scatterMaskChangedGl if backend == "gl" else self._scatterMaskChangedMpl
self._scatterViews[backend].getMaskToolsWidget().sigMaskChanged.connect(
callback)
def _setData(self, backend):
stack_images, stack_names = self.getStackROIImagesAndNames()
self._scatterViews[backend].setData(stack_images[0])
self._scatterViews[backend].resetZoom()
def _isScatterViewVisible(self, backend):
if self._scatterViews[backend] is None:
return False
if self._scatterViews[backend].isHidden():
return False
return True
def _scatterMaskChangedGl(self):
self._scatterMaskChanged("gl")
def _scatterMaskChangedMpl(self):
self._scatterMaskChanged("mpl")
def _scatterMaskChanged(self, backend):
scattermask = self._scatterViews[backend].getMaskToolsWidget().getSelectionMask()
if scattermask is not None:
shape = self.getStackOriginalImage().shape
mask = scattermask.reshape(shape)
else:
mask = scattermask
with self._scatterMaskDisconnected(backend):
self.setStackSelectionMask(mask)
def _getNumStackPoints(self):
stack_images, stack_names = self.getStackROIImagesAndNames()
return stack_images[0].size
def _getStackPositioners(self):
info = self.getStackInfo()
return info.get("positioners", {})
def stackUpdated(self):
for backend in self._createdBackends:
if not self._isScatterViewVisible(backend):
return
self._setData(backend)
self._scatterViews[backend].setNumPoints(self._getNumStackPoints())
self._scatterViews[backend].fillPositioners(self._getStackPositioners())
def selectionMaskUpdated(self):
for backend in self._createdBackends:
if not self._isScatterViewVisible(backend):
return
mask = self.getStackSelectionMask()
if mask is not None:
scatterMask = mask.reshape((-1,))
else:
scatterMask = None
self._scatterViews[backend].getMaskToolsWidget().setSelectionMask(scatterMask)
def stackClosed(self):
for sv in self._scatterViews.values():
if sv is not None:
sv.close()
def stackROIImageListUpdated(self):
self.stackUpdated()
# Methods implemented by the plugin
def getMethods(self):
return self.__methodKeys
def getMethodToolTip(self, name):
return self.methodDict[name][1]
def getMethodPixmap(self, name):
return self.methodDict[name][2]
def applyMethod(self, name):
return self.methodDict[name][0]()
MENU_TEXT = "Mask Scatter View"
def getStackPluginInstance(stackWindow, **kw):
ob = MaskScatterViewPlugin(stackWindow)
return ob
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