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#/*##########################################################################
# Copyright (C) 2004-2018 V.A. Sole, European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# 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.
#
#############################################################################*/
import numpy
from PyMca5.PyMcaCore.Plugin2DBase import Plugin2DBase
from PyMca5.PyMcaGui import PyMcaQt as qt
from silx.gui.plot import Plot2D
from silx.math.medianfilter import medfilt2d
class Medfilt2DPlugin(Plugin2DBase):
def __init__(self, plotWindow):
Plugin2DBase.__init__(self, plotWindow)
self.methods = {
"Median filter": [self._medfilt2D,
"Open a plot showing a filtered image",
None]
}
self.widget = None
def getMethods(self, plottype=None):
"""
:return: A list with the NAMES associated to the callable methods
that are applicable to the specified type plot. The list can be empty.
:rtype: list[string]
"""
return list(self.methods.keys())
def _getMethod(self, name):
method = self.methods.get(name)
if method is None:
raise NameError("method %s not found" % name)
return method
def getMethodToolTip(self, name):
"""
Returns the help associated to the particular method name or None.
:param name: The method for which a tooltip is asked
:rtype: string
"""
return self._getMethod(name)[1]
def getMethodPixmap(self, name):
"""
:param name: The method for which a pixmap is asked
:rtype: QPixmap or None
"""
return self._getMethod(name)[2]
def applyMethod(self, name):
"""
The plugin is asked to apply the method associated to name.
"""
return self._getMethod(name)[0]()
def _medfilt2D(self):
if self.widget is None:
self.widget = Plot2DMedFilt()
self.widget.show()
active_image = self._plotWindow.getActiveImage()
if active_image is None:
return
data = active_image.getData()
if data.ndim > 2:
raise NotImplementedError("Median filter not implemented for RGB images")
self.widget.setColormap(active_image.getColormap())
self.widget.setLegend("medfilt2d(%s)" % active_image.getLegend())
self.widget.setRawData(data)
def activeImageChanged(self, prev, new):
if self.widget is None or not self.widget.isVisible() or new is None:
return
self._medfilt2D()
class Plot2DMedFilt(Plot2D):
# TODO: we could allow setting different X- and Y-filter width.
def __init__(self, parent=None):
Plot2D.__init__(self, parent=parent)
self.toolBar().addSeparator()
label = qt.QLabel(self)
label.setText("Median filter width:")
self.spinbox = qt.QSpinBox(self)
self.spinbox.setMinimum(1)
self.spinbox.setValue(1)
self.spinbox.setSingleStep(2)
self.spinbox.valueChanged[int].connect(self._medfiltWidthChanged)
self.spinbox.setEnabled(False)
self.toolBar().addWidget(label)
self.toolBar().addWidget(self.spinbox)
self._data = None
self._legend = None
self._colormap = None
def setLegend(self, legend):
"""
:param str legend:
:return:
"""
self._legend = legend
def setRawData(self, data, legend=None):
"""Set raw image data to be filtered.
:param numpy.ndarray data:
:param str legend:
:return:
"""
if data is None:
self.spinbox.setEnabled(False)
self._data = None
return
if data.ndim != 2:
raise TypeError("Data must be a 2D array")
self._data = data
self.spinbox.setMaximum(max(data.shape))
self.spinbox.setEnabled(True)
self._applyFilter()
def setColormap(self, colormap):
self._colormap = colormap
@property
def medfilt_width(self):
return self.spinbox.value()
def _medfiltWidthChanged(self, width):
self._applyFilter()
def _applyFilter(self):
# medfilt2D requires the data to be C-contiguous with silx <= 0.9
self.addImage(medfilt2d(numpy.ascontiguousarray(self._data),
kernel_size=self.medfilt_width),
colormap=self._colormap,
legend=self._legend)
MENU_TEXT = "2D median filter"
def getPlugin2DInstance(plotWindow, **kw):
"""
"""
ob = Medfilt2DPlugin(plotWindow)
return ob
if __name__ == "__main__":
# python -m PyMca5.PyMcaPlugins.Medfilt2DPlugin
from PyMca5.PyMcaGui.PluginsToolButton import PluginsToolButton
from PyMca5 import PyMcaPlugins
import os
from silx.test.utils import add_relative_noise
from silx.gui.plot import PlotWidget
# build a plot widget with a plugin toolbar button
app = qt.QApplication([])
master_plot = PlotWidget()
toolb = qt.QToolBar(master_plot)
plugins_tb_2d = PluginsToolButton(plot=master_plot,
parent=toolb,
method="getPlugin2DInstance")
plugins_tb_2d.getPlugins(
method="getPlugin2DInstance",
directoryList=[os.path.dirname(PyMcaPlugins.__file__)])
toolb.addWidget(plugins_tb_2d)
master_plot.addToolBar(toolb)
master_plot.show()
# add a noisy image
a, b = numpy.meshgrid(numpy.linspace(-10, 10, 500),
numpy.linspace(-10, 5, 400),
indexing="ij")
myimg = numpy.asarray(numpy.sin(a * b) / (a * b),
dtype='float32')
myimg = add_relative_noise(myimg,
max_noise=10.) # %
master_plot.addImage(myimg)
app.exec()
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