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# The PyMca X-Ray Fluorescence Toolkit
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__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__doc__ = """
A 1D plugin is a module that can be added to the PyMca 1D window in order to
perform user defined operations of the plotted 1D data.
Plugins can be automatically installed provided they are in the appropriate place:
- In the user home directory (POSIX systems): *${HOME}/.pymca/plugins*
or *${HOME}/PyMca/plugins* (older PyMca installation)
- In *"My Documents\\\\PyMca\\\\plugins"* (Windows)
Plugins inherit the :class:`Plugin1DBase` class and implement the methods:
- :meth:`Plugin1DBase.getMethods`
- :meth:`Plugin1DBase.getMethodToolTip` (optional but convenient)
- :meth:`Plugin1DBase.getMethodPixmap` (optional)
- :meth:`Plugin1DBase.applyMethod`
and modify the static module variable :const:`MENU_TEXT` and the static module function
:func:`getPlugin1DInstance` according to the defined plugin.
Optionally, plugins may also implement :meth:`Plugin1DBase.activeCurveChanged`
to react to data selection in the plot.
These plugins will be compatible with any 1D-plot window that implements the Plot1D
interface. The plot window interface is described in the Plot1DBase class.
The main items are reproduced here and can be directly accessed as plugin methods.
- :meth:`Plugin1DBase.addCurve`
- :meth:`Plugin1DBase.getActiveCurve`
- :meth:`Plugin1DBase.getAllCurves`
- :meth:`Plugin1DBase.getGraphXLimits`
- :meth:`Plugin1DBase.getGraphYLimits`
- :meth:`Plugin1DBase.getGraphTitle`
- :meth:`Plugin1DBase.getGraphXLabel`
- :meth:`Plugin1DBase.getGraphYLabel`
- :meth:`Plugin1DBase.removeCurve`
- :meth:`Plugin1DBase.setActiveCurve`
- :meth:`Plugin1DBase.setGraphTitle`
- :meth:`Plugin1DBase.setGraphXLimits`
- :meth:`Plugin1DBase.setGraphYLimits`
- :meth:`Plugin1DBase.setGraphXLabel`
- :meth:`Plugin1DBase.setGraphYLabel`
A simple plugin example, normalizing each curve to its maximum and vertically
shifting the curves.
.. code-block:: python
from PyMca5 import Plugin1DBase
class Shifting(Plugin1DBase.Plugin1DBase):
def getMethods(self, plottype=None):
return ["Shift"]
def getMethodToolTip(self, methodName):
if methodName != "Shift":
raise InvalidArgument("Method %s not valid" % methodName)
return "Subtract minimum, normalize to maximum, and shift up by 0.1"
def applyMethod(self, methodName):
if methodName != "Shift":
raise ValueError("Method %s not valid" % methodName)
allCurves = self.getAllCurves()
increment = 0.1
for i in range(len(allCurves)):
x, y, legend, info = allCurves[i][:4]
delta = float(y.max() - y.min())
if delta < 1.0e-15:
delta = 1.0
y = (y - y.min())/delta + i * increment
if i == (len(allCurves) - 1):
replot = True
else:
replot = False
if i == 0:
replace = True
else:
replace = False
self.addCurve(x, y, legend=legend + " %.2f" % (i * increment),
info=info, replace=replace, replot=replot)
MENU_TEXT="Simple Shift Example"
def getPlugin1DInstance(plotWindow, **kw):
ob = Shifting(plotWindow)
return ob
"""
import weakref
try:
from numpy import argsort, nonzero, take
except ImportError:
print("WARNING: numpy not present")
def merge_info_params(info, params):
"""Return a copy of dictionary`info` updated with the content
of dictionary `params`.
If keys don't overlap, this will effectively concatenate info and
params.
:param dict info: Dictionary of custom curve metadata
:param dict params: Dictionary of standard curve metadata (*xlabel,
ylabel, linestyle...*)"""
# TODO. much more keys and values to fix (see McaWindow)
info_params = info.copy()
info_params.update(params)
# xlabel and ylabel default to None in *silx*,
# PyMca plugins expect a string
if info_params.get("xlabel", None) is None:
info_params["xlabel"] = "X"
if info_params.get("ylabel", None) is None:
info_params["ylabel"] = "Y"
return info_params
[docs]class Plugin1DBase(object):
def __init__(self, plotWindow, **kw):
"""
plotWindow is the object instantiating the plugin.
Unless one knows what (s)he is doing, only a proxy should be used.
I pass the actual instance to keep all doors open.
The plot window can be a legacy PyMca plot, in which case
:attr:`_legacy` is set to *True*, or a :class:`PluginsToolButton`
acting as proxy for a *silx* PlotWindow.
"""
self._plotWindow = weakref.proxy(plotWindow)
self._legacy = False
"""
In the transition phase from PyMca plot to silx plot,
the plot window could be a legacy PyMca plot, in which case
:attr:`_legacy` is set to *True*, or a :class:`PluginsToolButton`
acting as proxy for a *silx* PlotWindow (*legacy=False*).
But now we don't expect to see PyMca plots any longer.
"""
# PyMcaGraph.Plot has a PLUGINS_DIR class attribute,
# PluginsToolButton does not
if hasattr(plotWindow, "PLUGINS_DIR"):
self._legacy = True
# Window related functions
def windowTitle(self):
name = self._plotWindow.windowTitle()
return name
# fixme: should we support **kw?
[docs] def addCurve(self, x, y, legend=None, info=None,
replace=False, replot=True, **kw):
"""
Add the 1D curve given by x an y to the graph.
:param x: The data corresponding to the x axis
:type x: list or numpy.ndarray
:param y: The data corresponding to the y axis
:type y: list or numpy.ndarray
:param legend: The legend to be associated to the curve
:type legend: string or None
:param info: Dictionary of information associated to the curve
:type info: dict or None
:param replace: Flag to indicate if already existing curves are to be deleted
:type replace: boolean default False
:param replot: Flag to indicate plot is to be immediately updated
:type replot: boolean default True
:param kw: Additional keywords recognized by the plot window.
Beware that the keywords recognized by *silx* and *PyMca*
plot windows may differ.
"""
if self._legacy:
return self._plotWindow.addCurve(x, y, legend=legend, info=info,
replace=replace, replot=replot, **kw)
else:
# fill = info.get("plot_fill", False) if info is not None else False
# fill = kw.get("fill", fill)
# linewidth = kw.get("linewidth", None)
return self._plotWindow.addCurve(x, y, legend=legend, info=info,
replace=replace, resetzoom=replot,
# fill=fill, linewidth=linewidth, # Fixme: are these needed?
**kw)
[docs] def getActiveCurve(self, just_legend=False):
"""
:param just_legend: Flag to specify the type of output required
:type just_legend: boolean
:return: legend of the active curve or list ``[x, y, legend, info]``
:rtype: string or list
Function to access the graph currently active curve.
It returns None in case of not having an active curve.
Default output has the form::
xvalues, yvalues, legend, dict
where dict is a dictionary containing curve info.
For the time being, only the plot labels associated to the
curve are warranted to be present under the keys xlabel, ylabel.
If just_legend is True:
The legend of the active curve (or None) is returned.
"""
curve = self._plotWindow.getActiveCurve(just_legend=just_legend)
# silx specific: when there is only one curve, get it, even if not active
# (PyMca's getActiveCurve already does this)
if curve is None and not self._legacy:
if len(self.getAllCurves(just_legend=True)) == 1:
curve = self._plotWindow.getCurve()
if self._legacy or just_legend or curve is None:
return curve
# silx PlotWindow
x, y, legend, info, params = curve
return x, y, legend, merge_info_params(info, params)
[docs] def getAllCurves(self, just_legend=False):
"""
:param just_legend: Flag to specify the type of output required
:type just_legend: boolean
:return: legend of the curves or list ``[[x, y, legend, info], ...]``
:rtype: list of strings or list of curves
It returns an empty list in case of not having any curve.
If just_legend is *False*, it returns a list of the form::
[[xvalues0, yvalues0, legend0, dict0],
[xvalues1, yvalues1, legend1, dict1],
[...],
[xvaluesn, yvaluesn, legendn, dictn]]
If just_legend is *True*, it returns a list of the form::
[legend0, legend1, ..., legendn]
"""
all_curves = []
for curve in self._plotWindow.getAllCurves(just_legend=just_legend):
if just_legend or self._legacy:
all_curves.append(curve)
else:
x, y, legend, info, params = curve
all_curves.append([x, y, legend, merge_info_params(info, params)])
return all_curves
def getCurve(self, legend):
curve = self._plotWindow.getCurve(legend)
if self._legacy or curve is None:
return curve
# silx PlotWindow
x, y, legend, info, params = curve
return x, y, legend, merge_info_params(info, params)
[docs] def getMonotonicCurves(self):
"""
Convenience method that calls :meth:`getAllCurves` and makes sure that all of
the X values are strictly increasing.
It returns a list of the form::
[[xvalues0, yvalues0, legend0, dict0],
[xvalues1, yvalues1, legend1, dict1],
[...],
[xvaluesn, yvaluesn, legendn, dictn]]
"""
allCurves = []
for curve in self.getAllCurves():
x, y, legend, info = curve[0:4]
# Sort
idx = argsort(x, kind='mergesort')
xproc = take(x, idx)
yproc = take(y, idx)
# Ravel, Increase
xproc = xproc.ravel()
idx = nonzero((xproc[1:] > xproc[:-1]))[0]
xproc = take(xproc, idx)
yproc = take(yproc, idx)
allCurves.append([xproc, yproc, legend, info])
return allCurves
[docs] def getGraphXLimits(self):
"""
Get the graph X limits.
:return: Two floats with the X axis limits
"""
return self._plotWindow.getGraphXLimits()
[docs] def getGraphYLimits(self):
"""
Get the graph Y (left) limits.
:return: Two floats with the Y (left) axis limits
"""
return self._plotWindow.getGraphYLimits()
[docs] def getGraphTitle(self):
"""
:return: The graph title
:rtype: string
"""
return self._plotWindow.getGraphTitle()
[docs] def getGraphXLabel(self):
"""
:return: The graph X axis label
:rtype: string
"""
return self._plotWindow.getGraphXLabel()
def getGraphXTitle(self):
print("getGraphXTitle deprecated, use getGraphXLabel")
return self._plotWindow.getGraphXLabel()
[docs] def getGraphYLabel(self):
"""
:return: The graph Y axis label
:rtype: string
"""
return self._plotWindow.getGraphYLabel()
def getGraphYTitle(self):
print("getGraphYTitle deprecated, use getGraphYLabel")
return self._plotWindow.getGraphYLabel()
[docs] def setGraphXLimits(self, xmin, xmax, replot=False):
"""
Set the graph X limits.
:param xmin: minimum value of the axis
:type xmin: float
:param xmax: minimum value of the axis
:type xmax: float
:param replot: Flag to indicate plot is to be immediately updated
:type replot: boolean default False
"""
if self._legacy:
return self._plotWindow.setGraphXLimits(xmin, xmax, replot=replot)
return self._plotWindow.setGraphXLimits(xmin, xmax)
# TODO: support param axis='right'?
[docs] def setGraphYLimits(self, ymin, ymax, replot=False):
"""
Set the graph Y (left) limits.
:param ymin: minimum value of the axis
:type ymin: float
:param ymax: minimum value of the axis
:type ymax: float
:param replot: Flag to indicate plot is to be immediately updated
:type replot: boolean default False
"""
if self._legacy:
return self._plotWindow.setGraphYLimits(ymin, ymax, replot=replot)
return self._plotWindow.setGraphYLimits(ymin, ymax)
[docs] def removeCurve(self, legend, replot=True):
"""
Remove the curve associated to the supplied legend from the graph.
The graph will be updated if replot is true.
:param legend: The legend associated to the curve to be deleted
:type legend: string or None
:param replot: Flag to indicate plot is to be immediately updated
:type replot: boolean default True
"""
if self._legacy:
self._plotWindow.removeCurve(legend, replot=replot)
return self._plotWindow.removeCurve(legend)
[docs] def setActiveCurve(self, legend):
"""
Funtion to request the plot window to set the curve with the specified legend
as the active curve.
:param legend: The legend associated to the curve
:type legend: string
"""
return self._plotWindow.setActiveCurve(legend)
[docs] def setGraphTitle(self, title):
"""
:param title: The title to be set
:type title: string
"""
return self._plotWindow.setGraphTitle(title)
def setGraphXTitle(self, title):
print("setGraphXTitle deprecated, use setGraphXLabel")
self.setGraphXLabel(title)
[docs] def setGraphXLabel(self, title):
"""
:param title: The title to be associated to the X axis
:type title: string
"""
if self._legacy:
return self._plotWindow.setGraphXTitle(title)
return self._plotWindow.setGraphXLabel(title)
def setGraphYTitle(self, title):
print("setGraphYTitle deprecated, use setGraphYLabel")
self.setGraphYLabel(title)
[docs] def setGraphYLabel(self, title):
"""
:param title: The title to be associated to the X axis
:type title: string
"""
if self._legacy:
return self._plotWindow.setGraphYTitle(title)
return self._plotWindow.setGraphYLabel(title)
# Methods to be implemented by the plugin
[docs] def getMethods(self, plottype=None):
"""
:param plottype: string or None for the case the plugin only support
one type of plots. Implemented values "SCAN", "MCA" or 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]
"""
print("getMethods not implemented")
return []
[docs] def getMethodPixmap(self, name):
"""
:param name: The method for which a pixmap is asked
:rtype: QPixmap or None
"""
return None
[docs] def applyMethod(self, name):
"""
The plugin is asked to apply the method associated to name.
"""
print("applyMethod not implemented")
return
[docs] def activeCurveChanged(self, prev, new):
"""A plugin may implement this method which is called
when the active curve changes in the plot.
:param prev: Legend of the previous active curve,
or None if no curve was active.
:param new: Legend of the new active curve,
or None if no curve is currently active.
"""
pass
MENU_TEXT = "Plugin1D Base"
"""This is the name of the plugin, as it appears in the plugins menu."""
[docs]def getPlugin1DInstance(plotWindow, **kw):
"""
This function will be called by the plot window instantiating and calling
the plugins. It passes itself as first argument, but the default implementation
of the base class only keeps a weak reference to prevent circular references.
"""
ob = Plugin1DBase(plotWindow)
return ob
