# coding: utf-8 # /*########################################################################## # # Copyright (c) 2017-2018 European Synchrotron Radiation Facility # # 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 module provides the :class:`Scatter` item of the :class:`Plot`. """ __authors__ = ["H. Payno"] __license__ = "MIT" __date__ = "06/06/2018" import numpy from silx.gui.plot.items.curve import Curve as CurveItem from silx.gui.plot.items.image import ImageBase as ImageItem from silx.gui.plot.items.scatter import Scatter as ScatterItem from silx.gui.plot.items.histogram import Histogram as HistogramItem from silx.math.combo import min_max from collections import OrderedDict import logging logger = logging.getLogger(__name__) class Stats(OrderedDict): """Class to define a set of statistic relative to a dataset (image, curve...). The goal of this class is to avoid multiple recalculation of some basic operations such as filtering data area where the statistics has to be apply. Min and max are also stored because they can be used several time. :param List statslist: List of the :class:`Stat` object to be computed. """ def __init__(self, statslist=None): OrderedDict.__init__(self) _statslist = statslist if not None else [] if statslist is not None: for stat in _statslist: self.add(stat) def calculate(self, item, plot, onlimits): """ Call all :class:`Stat` object registred and return the result of the computation. :param item: the item for which we want statistics :param plot: plot containing the item :param bool onlimits: True if we want to apply statistic only on visible data. :return dict: dictionary with :class:`Stat` name as ket and result of the calculation as value """ res = {} if isinstance(item, CurveItem): context = _CurveContext(item, plot, onlimits) elif isinstance(item, ImageItem): context = _ImageContext(item, plot, onlimits) elif isinstance(item, ScatterItem): context = _ScatterContext(item, plot, onlimits) elif isinstance(item, HistogramItem): context = _HistogramContext(item, plot, onlimits) else: raise ValueError('Item type not managed') for statName, stat in list(self.items()): if context.kind not in stat.compatibleKinds: logger.debug('kind %s not managed by statistic %s' % (context.kind, stat.name)) res[statName] = None else: res[statName] = stat.calculate(context) return res def __setitem__(self, key, value): assert isinstance(value, StatBase) OrderedDict.__setitem__(self, key, value) def add(self, stat): self.__setitem__(key=stat.name, value=stat) class _StatsContext(object): """ The context is designed to be a simple buffer and avoid repetition of calculations that can appear during stats evaluation. .. warning:: this class gives access to the data to be used for computation . It deal with filtering data visible by the user on plot. The filtering is a simple data sub-sampling. No interpolation is made to fit data to boundaries. :param item: the item for which we want to compute the context :param str kind: the kind of the item :param plot: the plot containing the item :param bool onlimits: True if we want to apply statistic only on visible data. """ def __init__(self, item, kind, plot, onlimits): assert item assert plot assert type(onlimits) is bool self.kind = kind self.min = None self.max = None self.data = None self.values = None self.createContext(item, plot, onlimits) def createContext(self, item, plot, onlimits): raise NotImplementedError("Base class") class _CurveContext(_StatsContext): """ StatsContext for :class:`Curve` :param item: the item for which we want to compute the context :param plot: the plot containing the item :param bool onlimits: True if we want to apply statistic only on visible data. """ def __init__(self, item, plot, onlimits): _StatsContext.__init__(self, kind='curve', item=item, plot=plot, onlimits=onlimits) def createContext(self, item, plot, onlimits): xData, yData = item.getData(copy=True)[0:2] if onlimits: minX, maxX = plot.getXAxis().getLimits() yData = yData[(minX <= xData) & (xData <= maxX)] xData = xData[(minX <= xData) & (xData <= maxX)] self.xData = xData self.yData = yData if len(yData) > 0: self.min, self.max = min_max(yData) else: self.min, self.max = None, None self.data = (xData, yData) self.values = yData class _HistogramContext(_StatsContext): """ StatsContext for :class:`Curve` :param item: the item for which we want to compute the context :param plot: the plot containing the item :param bool onlimits: True if we want to apply statistic only on visible data. """ def __init__(self, item, plot, onlimits): _StatsContext.__init__(self, kind='histogram', item=item, plot=plot, onlimits=onlimits) def createContext(self, item, plot, onlimits): xData, edges = item.getData(copy=True)[0:2] yData = item._revertComputeEdges(x=edges, histogramType=item.getAlignment()) if onlimits: minX, maxX = plot.getXAxis().getLimits() yData = yData[(minX <= xData) & (xData <= maxX)] xData = xData[(minX <= xData) & (xData <= maxX)] self.xData = xData self.yData = yData if len(yData) > 0: self.min, self.max = min_max(yData) else: self.min, self.max = None, None self.data = (xData, yData) self.values = yData class _ScatterContext(_StatsContext): """ StatsContext for :class:`Scatter` :param item: the item for which we want to compute the context :param plot: the plot containing the item :param bool onlimits: True if we want to apply statistic only on visible data. """ def __init__(self, item, plot, onlimits): _StatsContext.__init__(self, kind='scatter', item=item, plot=plot, onlimits=onlimits) def createContext(self, item, plot, onlimits): xData, yData, valueData, xerror, yerror = item.getData(copy=True) assert plot if onlimits: minX, maxX = plot.getXAxis().getLimits() minY, maxY = plot.getYAxis().getLimits() # filter on X axis valueData = valueData[(minX <= xData) & (xData <= maxX)] yData = yData[(minX <= xData) & (xData <= maxX)] xData = xData[(minX <= xData) & (xData <= maxX)] # filter on Y axis valueData = valueData[(minY <= yData) & (yData <= maxY)] xData = xData[(minY <= yData) & (yData <= maxY)] yData = yData[(minY <= yData) & (yData <= maxY)] if len(valueData) > 0: self.min, self.max = min_max(valueData) else: self.min, self.max = None, None self.data = (xData, yData, valueData) self.values = valueData class _ImageContext(_StatsContext): """ StatsContext for :class:`ImageBase` :param item: the item for which we want to compute the context :param plot: the plot containing the item :param bool onlimits: True if we want to apply statistic only on visible data. """ def __init__(self, item, plot, onlimits): _StatsContext.__init__(self, kind='image', item=item, plot=plot, onlimits=onlimits) def createContext(self, item, plot, onlimits): self.origin = item.getOrigin() self.scale = item.getScale() self.data = item.getData() if onlimits: minX, maxX = plot.getXAxis().getLimits() minY, maxY = plot.getYAxis().getLimits() XMinBound = int((minX - self.origin[0]) / self.scale[0]) YMinBound = int((minY - self.origin[1]) / self.scale[1]) XMaxBound = int((maxX - self.origin[0]) / self.scale[0]) YMaxBound = int((maxY - self.origin[1]) / self.scale[1]) XMinBound = max(XMinBound, 0) YMinBound = max(YMinBound, 0) if XMaxBound <= XMinBound or YMaxBound <= YMinBound: return self.noDataSelected() data = item.getData() self.data = data[YMinBound:YMaxBound + 1, XMinBound:XMaxBound + 1] else: self.data = item.getData() if self.data.size > 0: self.min, self.max = min_max(self.data) else: self.min, self.max = None, None self.values = self.data BASIC_COMPATIBLE_KINDS = { 'curve': CurveItem, 'image': ImageItem, 'scatter': ScatterItem, 'histogram': HistogramItem, } class StatBase(object): """ Base class for defining a statistic. :param str name: the name of the statistic. Must be unique. :param compatibleKinds: the kind of items (curve, scatter...) for which the statistic apply. :rtype: List or tuple """ def __init__(self, name, compatibleKinds=BASIC_COMPATIBLE_KINDS, description=None): self.name = name self.compatibleKinds = compatibleKinds self.description = description def calculate(self, context): """ compute the statistic for the given :class:`StatsContext` :param context: :return dict: key is stat name, statistic computed is the dict value """ raise NotImplementedError('Base class') def getToolTip(self, kind): """ If necessary add a tooltip for a stat kind :param str kinf: the kind of item the statistic is compute for. :return: tooltip or None if no tooltip """ return None class Stat(StatBase): """ Create a StatBase class based on a function pointer. :param str name: name of the statistic. Used as id :param fct: function which should have as unique mandatory parameter the data. Should be able to adapt to all `kinds` defined as compatible :param tuple kinds: the compatible item kinds of the function (curve, image...) """ def __init__(self, name, fct, kinds=BASIC_COMPATIBLE_KINDS): StatBase.__init__(self, name, kinds) self._fct = fct def calculate(self, context): if context.kind in self.compatibleKinds: return self._fct(context.values) else: raise ValueError('Kind %s not managed by %s' '' % (context.kind, self.name)) class StatMin(StatBase): """ Compute the minimal value on data """ def __init__(self): StatBase.__init__(self, name='min') def calculate(self, context): return context.min class StatMax(StatBase): """ Compute the maximal value on data """ def __init__(self): StatBase.__init__(self, name='max') def calculate(self, context): return context.max class StatDelta(StatBase): """ Compute the delta between minimal and maximal on data """ def __init__(self): StatBase.__init__(self, name='delta') def calculate(self, context): return context.max - context.min class StatCoordMin(StatBase): """ Compute the first coordinates of the data minimal value """ def __init__(self): StatBase.__init__(self, name='coords min') def calculate(self, context): if context.kind in ('curve', 'histogram'): return context.xData[numpy.argmin(context.yData)] elif context.kind == 'scatter': xData, yData, valueData = context.data return (xData[numpy.argmin(valueData)], yData[numpy.argmin(valueData)]) elif context.kind == 'image': scaleX, scaleY = context.scale originX, originY = context.origin index1D = numpy.argmin(context.data) ySize = (context.data.shape[1]) x = index1D % context.data.shape[1] y = (index1D - x) / ySize x = x * scaleX + originX y = y * scaleY + originY return (x, y) else: raise ValueError('kind not managed') def getToolTip(self, kind): if kind in ('scatter', 'image'): return '(x, y)' else: return None class StatCoordMax(StatBase): """ Compute the first coordinates of the data minimal value """ def __init__(self): StatBase.__init__(self, name='coords max') def calculate(self, context): if context.kind in ('curve', 'histogram'): return context.xData[numpy.argmax(context.yData)] elif context.kind == 'scatter': xData, yData, valueData = context.data return (xData[numpy.argmax(valueData)], yData[numpy.argmax(valueData)]) elif context.kind == 'image': scaleX, scaleY = context.scale originX, originY = context.origin index1D = numpy.argmax(context.data) ySize = (context.data.shape[1]) x = index1D % context.data.shape[1] y = (index1D - x) / ySize x = x * scaleX + originX y = y * scaleY + originY return (x, y) else: raise ValueError('kind not managed') def getToolTip(self, kind): if kind in ('scatter', 'image'): return '(x, y)' else: return None class StatCOM(StatBase): """ Compute data center of mass """ def __init__(self): StatBase.__init__(self, name='COM', description='Center of mass') def calculate(self, context): if context.kind in ('curve', 'histogram'): xData, yData = context.data deno = numpy.sum(yData).astype(numpy.float32) if deno == 0.: return numpy.nan else: return numpy.sum(xData * yData).astype(numpy.float32) / deno elif context.kind == 'scatter': xData, yData, values = context.data deno = numpy.sum(values).astype(numpy.float32) if deno == 0.: return numpy.nan, numpy.nan else: xcom = numpy.sum(xData * values).astype(numpy.float32) / deno ycom = numpy.sum(yData * values).astype(numpy.float32) / deno return (xcom, ycom) elif context.kind == 'image': yData = numpy.sum(context.data, axis=1) xData = numpy.sum(context.data, axis=0) dataXRange = range(context.data.shape[1]) dataYRange = range(context.data.shape[0]) xScale, yScale = context.scale xOrigin, yOrigin = context.origin denoY = numpy.sum(yData) if denoY == 0.: ycom = numpy.nan else: ycom = numpy.sum(yData * dataYRange) / denoY ycom = ycom * yScale + yOrigin denoX = numpy.sum(xData) if denoX == 0.: xcom = numpy.nan else: xcom = numpy.sum(xData * dataXRange) / denoX xcom = xcom * xScale + xOrigin return (xcom, ycom) else: raise ValueError('kind not managed') def getToolTip(self, kind): if kind in ('scatter', 'image'): return '(x, y)' else: return None