diff options
Diffstat (limited to 'src/silx/gui/plot/stats/stats.py')
| -rw-r--r-- | src/silx/gui/plot/stats/stats.py | 242 |
1 files changed, 132 insertions, 110 deletions
diff --git a/src/silx/gui/plot/stats/stats.py b/src/silx/gui/plot/stats/stats.py index d266d5c..d575e3f 100644 --- a/src/silx/gui/plot/stats/stats.py +++ b/src/silx/gui/plot/stats/stats.py @@ -1,6 +1,6 @@ # /*########################################################################## # -# Copyright (c) 2017-2022 European Synchrotron Radiation Facility +# Copyright (c) 2017-2023 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 @@ -31,7 +31,6 @@ __license__ = "MIT" __date__ = "06/06/2018" -from collections import OrderedDict from functools import lru_cache import logging @@ -44,12 +43,11 @@ from ..items.roi import RegionOfInterest from ....math.combo import min_max from silx.utils.proxy import docstring -from ....utils.deprecation import deprecated logger = logging.getLogger(__name__) -class Stats(OrderedDict): +class Stats(dict): """Class to define a set of statistic relative to a dataset (image, curve...). @@ -60,15 +58,17 @@ class Stats(OrderedDict): :param List statslist: List of the :class:`Stat` object to be computed. """ + def __init__(self, statslist=None): - OrderedDict.__init__(self) + super().__init__() _statslist = statslist if not None else [] if statslist is not None: for stat in _statslist: self.add(stat) - def calculate(self, item, plot, onlimits, roi, data_changed=False, - roi_changed=False): + def calculate( + self, item, plot, onlimits, roi, data_changed=False, roi_changed=False + ): """ Call all :class:`Stat` object registered and return the result of the computation. @@ -87,27 +87,26 @@ class Stats(OrderedDict): of the calculation as value """ res = {} - context = self._getContext(item=item, plot=plot, onlimits=onlimits, - roi=roi) + context = self._getContext(item=item, plot=plot, onlimits=onlimits, roi=roi) 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)) + logger.debug( + "kind %s not managed by statistic %s" % (context.kind, stat.name) + ) res[statName] = None else: if roi_changed is True: context.clear_mask() if data_changed is True or roi_changed is True: # if data changed or mask changed - context.clipData(item=item, plot=plot, onlimits=onlimits, - roi=roi) + context.clipData(item=item, plot=plot, onlimits=onlimits, roi=roi) # init roi and data res[statName] = stat.calculate(context) return res def __setitem__(self, key, value): assert isinstance(value, StatBase) - OrderedDict.__setitem__(self, key, value) + super().__setitem__(key, value) def add(self, stat): """Add a :class:`Stat` to the set @@ -134,14 +133,11 @@ class Stats(OrderedDict): from ...plot3d import items as items3d # Lazy import if isinstance(item, (items3d.Scatter2D, items3d.Scatter3D)): - context = _plot3DScatterContext(item, plot, onlimits, - roi=roi) - elif isinstance(item, - (items3d.ImageData, items3d.ScalarField3D)): - context = _plot3DArrayContext(item, plot, onlimits, - roi=roi) + context = _plot3DScatterContext(item, plot, onlimits, roi=roi) + elif isinstance(item, (items3d.ImageData, items3d.ScalarField3D)): + context = _plot3DArrayContext(item, plot, onlimits, roi=roi) if context is None: - raise ValueError('Item type not managed') + raise ValueError("Item type not managed") return context @@ -164,6 +160,7 @@ class _StatsContext(object): For now, incompatible with `onlimits` calculation :type roi: Union[None,:class:`_RegionOfInterestBase`] """ + def __init__(self, item, kind, plot, onlimits, roi): assert item assert plot @@ -234,13 +231,6 @@ class _StatsContext(object): """ raise NotImplementedError("Base class") - @deprecated(reason="context are now stored and keep during stats life." - "So this function will be called only once", - replacement="clipData", since_version="0.13.0") - def createContext(self, item, plot, onlimits, roi): - return self.clipData(item=item, plot=plot, onlimits=onlimits, - roi=roi) - def isStructuredData(self): """Returns True if data as an array-like structure. @@ -271,15 +261,18 @@ class _StatsContext(object): def _checkContextInputs(self, item, plot, onlimits, roi): if roi is not None and onlimits is True: - raise ValueError('Stats context is unable to manage both a ROI' - 'and the `onlimits` option') + raise ValueError( + "Stats context is unable to manage both a ROI" + "and the `onlimits` option" + ) class _ScatterCurveHistoMixInContext(_StatsContext): def __init__(self, kind, item, plot, onlimits, roi): self.clear_mask() - _StatsContext.__init__(self, item=item, kind=kind, - plot=plot, onlimits=onlimits, roi=roi) + _StatsContext.__init__( + self, item=item, kind=kind, plot=plot, onlimits=onlimits, roi=roi + ) def _set_mask_validity(self, onlimits, from_, to_): self._onlimits = onlimits @@ -292,8 +285,7 @@ class _ScatterCurveHistoMixInContext(_StatsContext): self._to_ = None def is_mask_valid(self, onlimits, from_, to_): - return (onlimits == self.onlimits and from_ == self._from_ and - to_ == self._to_) + return onlimits == self.onlimits and from_ == self._from_ and to_ == self._to_ class _CurveContext(_ScatterCurveHistoMixInContext): @@ -308,15 +300,15 @@ class _CurveContext(_ScatterCurveHistoMixInContext): For now, incompatible with `onlinits` calculation :type roi: Union[None, :class:`ROI`] """ + def __init__(self, item, plot, onlimits, roi): - _ScatterCurveHistoMixInContext.__init__(self, kind='curve', item=item, - plot=plot, onlimits=onlimits, - roi=roi) + _ScatterCurveHistoMixInContext.__init__( + self, kind="curve", item=item, plot=plot, onlimits=onlimits, roi=roi + ) @docstring(_StatsContext) def clipData(self, item, plot, onlimits, roi): - self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, - roi=roi) + self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, roi=roi) self.roi = roi self.onlimits = onlimits xData, yData = item.getData(copy=True)[0:2] @@ -353,10 +345,11 @@ class _CurveContext(_ScatterCurveHistoMixInContext): self.axes = (xData,) def _checkContextInputs(self, item, plot, onlimits, roi): - _StatsContext._checkContextInputs(self, item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext._checkContextInputs( + self, item=item, plot=plot, onlimits=onlimits, roi=roi + ) if roi is not None and not isinstance(roi, ROI): - raise TypeError('curve `context` can ony manage 1D roi') + raise TypeError("curve `context` can ony manage 1D roi") class _HistogramContext(_ScatterCurveHistoMixInContext): @@ -371,15 +364,15 @@ class _HistogramContext(_ScatterCurveHistoMixInContext): For now, incompatible with `onlinits` calculation :type roi: Union[None, :class:`ROI`] """ + def __init__(self, item, plot, onlimits, roi): - _ScatterCurveHistoMixInContext.__init__(self, kind='histogram', - item=item, plot=plot, - onlimits=onlimits, roi=roi) + _ScatterCurveHistoMixInContext.__init__( + self, kind="histogram", item=item, plot=plot, onlimits=onlimits, roi=roi + ) @docstring(_StatsContext) def clipData(self, item, plot, onlimits, roi): - self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, - roi=roi) + self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, roi=roi) yData, edges = item.getData(copy=True)[0:2] xData = item._revertComputeEdges(x=edges, histogramType=item.getAlignment()) @@ -392,13 +385,16 @@ class _HistogramContext(_ScatterCurveHistoMixInContext): mask = mask == 0 self._set_mask_validity(onlimits=onlimits, from_=minX, to_=maxX) elif roi: - if self.is_mask_valid(onlimits=onlimits, from_=roi._fromdata, to_=roi._todata): + if self.is_mask_valid( + onlimits=onlimits, from_=roi._fromdata, to_=roi._todata + ): mask = self.mask else: mask = (roi._fromdata <= xData) & (xData <= roi._todata) mask = mask == 0 - self._set_mask_validity(onlimits=onlimits, from_=roi._fromdata, - to_=roi._todata) + self._set_mask_validity( + onlimits=onlimits, from_=roi._fromdata, to_=roi._todata + ) else: mask = numpy.zeros_like(yData) mask = mask.astype(numpy.uint32) @@ -414,11 +410,12 @@ class _HistogramContext(_ScatterCurveHistoMixInContext): self.axes = (self.xData,) def _checkContextInputs(self, item, plot, onlimits, roi): - _StatsContext._checkContextInputs(self, item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext._checkContextInputs( + self, item=item, plot=plot, onlimits=onlimits, roi=roi + ) if roi is not None and not isinstance(roi, ROI): - raise TypeError('curve `context` can ony manage 1D roi') + raise TypeError("curve `context` can ony manage 1D roi") class _ScatterContext(_ScatterCurveHistoMixInContext): @@ -434,15 +431,15 @@ class _ScatterContext(_ScatterCurveHistoMixInContext): For now, incompatible with `onlinits` calculation :type roi: Union[None, :class:`ROI`] """ + def __init__(self, item, plot, onlimits, roi): - _ScatterCurveHistoMixInContext.__init__(self, kind='scatter', - item=item, plot=plot, - onlimits=onlimits, roi=roi) + _ScatterCurveHistoMixInContext.__init__( + self, kind="scatter", item=item, plot=plot, onlimits=onlimits, roi=roi + ) @docstring(_ScatterCurveHistoMixInContext) def clipData(self, item, plot, onlimits, roi): - self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, - roi=roi) + self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, roi=roi) valueData = item.getValueData(copy=True) xData = item.getXData(copy=True) yData = item.getYData(copy=True) @@ -461,8 +458,9 @@ class _ScatterContext(_ScatterCurveHistoMixInContext): yData = yData[(minY <= yData) & (yData <= maxY)] if roi: - if self.is_mask_valid(onlimits=onlimits, from_=roi.getFrom(), - to_=roi.getTo()): + if self.is_mask_valid( + onlimits=onlimits, from_=roi.getFrom(), to_=roi.getTo() + ): mask = self.mask else: mask = (xData < roi.getFrom()) | (xData > roi.getTo()) @@ -480,11 +478,12 @@ class _ScatterContext(_ScatterCurveHistoMixInContext): self.min, self.max = None, None def _checkContextInputs(self, item, plot, onlimits, roi): - _StatsContext._checkContextInputs(self, item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext._checkContextInputs( + self, item=item, plot=plot, onlimits=onlimits, roi=roi + ) if roi is not None and not isinstance(roi, ROI): - raise TypeError('curve `context` can ony manage 1D roi') + raise TypeError("curve `context` can ony manage 1D roi") class _ImageContext(_StatsContext): @@ -511,13 +510,14 @@ class _ImageContext(_StatsContext): For now, incompatible with `onlinits` calculation :type roi: Union[None, :class:`ROI`] """ + def __init__(self, item, plot, onlimits, roi): self.clear_mask() - _StatsContext.__init__(self, kind='image', item=item, - plot=plot, onlimits=onlimits, roi=roi) + _StatsContext.__init__( + self, kind="image", item=item, plot=plot, onlimits=onlimits, roi=roi + ) - def _set_mask_validity(self, xmin: float, xmax: float, ymin: float, ymax - : float): + def _set_mask_validity(self, xmin: float, xmax: float, ymin: float, ymax: float): self._mask_x_min = xmin self._mask_x_max = xmax self._mask_y_min = ymin @@ -530,13 +530,16 @@ class _ImageContext(_StatsContext): self._mask_y_max = None def is_mask_valid(self, xmin, xmax, ymin, ymax): - return (xmin == self._mask_x_min and xmax == self._mask_x_max and - ymin == self._mask_y_min and ymax == self._mask_y_max) + return ( + xmin == self._mask_x_min + and xmax == self._mask_x_max + and ymin == self._mask_y_min + and ymax == self._mask_y_max + ) @docstring(_StatsContext) def clipData(self, item, plot, onlimits, roi): - self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, - roi=roi) + self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, roi=roi) self.origin = item.getOrigin() self.scale = item.getScale() @@ -560,8 +563,9 @@ class _ImageContext(_StatsContext): if XMaxBound <= XMinBound or YMaxBound <= YMinBound: self.data = None else: - self.data = self.data[YMinBound:YMaxBound + 1, - XMinBound:XMaxBound + 1] + self.data = self.data[ + YMinBound : YMaxBound + 1, XMinBound : XMaxBound + 1 + ] mask = numpy.zeros_like(self.data) elif roi: minX, maxX = 0, self.data.shape[1] @@ -572,8 +576,9 @@ class _ImageContext(_StatsContext): XMaxBound = min(maxX, self.data.shape[1]) YMaxBound = min(maxY, self.data.shape[0]) - if self.is_mask_valid(xmin=XMinBound, xmax=XMaxBound, - ymin=YMinBound, ymax=YMaxBound): + if self.is_mask_valid( + xmin=XMinBound, xmax=XMaxBound, ymin=YMinBound, ymax=YMaxBound + ): mask = self.mask else: for x in range(XMinBound, XMaxBound): @@ -581,8 +586,9 @@ class _ImageContext(_StatsContext): _x = (x * self.scale[0]) + self.origin[0] _y = (y * self.scale[1]) + self.origin[1] mask[y, x] = not roi.contains((_x, _y)) - self._set_mask_validity(xmin=XMinBound, xmax=XMaxBound, - ymin=YMinBound, ymax=YMaxBound) + self._set_mask_validity( + xmin=XMinBound, xmax=XMaxBound, ymin=YMinBound, ymax=YMaxBound + ) self.values = numpy.ma.array(self.data, mask=mask) if self.values.compressed().size > 0: self.min, self.max = min_max(self.values.compressed()) @@ -590,15 +596,18 @@ class _ImageContext(_StatsContext): self.min, self.max = None, None if self.values is not None: - self.axes = (self.origin[1] + self.scale[1] * numpy.arange(self.data.shape[0]), - self.origin[0] + self.scale[0] * numpy.arange(self.data.shape[1])) + self.axes = ( + self.origin[1] + self.scale[1] * numpy.arange(self.data.shape[0]), + self.origin[0] + self.scale[0] * numpy.arange(self.data.shape[1]), + ) def _checkContextInputs(self, item, plot, onlimits, roi): - _StatsContext._checkContextInputs(self, item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext._checkContextInputs( + self, item=item, plot=plot, onlimits=onlimits, roi=roi + ) if roi is not None and not isinstance(roi, RegionOfInterest): - raise TypeError('curve `context` can ony manage 2D roi') + raise TypeError("curve `context` can ony manage 2D roi") class _plot3DScatterContext(_StatsContext): @@ -615,14 +624,15 @@ class _plot3DScatterContext(_StatsContext): For now, incompatible with `onlinits` calculation :type roi: Union[None, :class:`ROI`] """ + def __init__(self, item, plot, onlimits, roi): - _StatsContext.__init__(self, kind='scatter', item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext.__init__( + self, kind="scatter", item=item, plot=plot, onlimits=onlimits, roi=roi + ) @docstring(_StatsContext) def clipData(self, item, plot, onlimits, roi): - self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, - roi=roi) + self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, roi=roi) if onlimits: raise RuntimeError("Unsupported plot %s" % str(plot)) values = item.getValueData(copy=False) @@ -646,11 +656,12 @@ class _plot3DScatterContext(_StatsContext): self.min, self.max = None, None def _checkContextInputs(self, item, plot, onlimits, roi): - _StatsContext._checkContextInputs(self, item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext._checkContextInputs( + self, item=item, plot=plot, onlimits=onlimits, roi=roi + ) if roi is not None and not isinstance(roi, RegionOfInterest): - raise TypeError('curve `context` can ony manage 2D roi') + raise TypeError("curve `context` can ony manage 2D roi") class _plot3DArrayContext(_StatsContext): @@ -667,14 +678,15 @@ class _plot3DArrayContext(_StatsContext): For now, incompatible with `onlinits` calculation :type roi: Union[None, :class:`ROI`] """ + def __init__(self, item, plot, onlimits, roi): - _StatsContext.__init__(self, kind='image', item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext.__init__( + self, kind="image", item=item, plot=plot, onlimits=onlimits, roi=roi + ) @docstring(_StatsContext) def clipData(self, item, plot, onlimits, roi): - self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, - roi=roi) + self._checkContextInputs(item=item, plot=plot, onlimits=onlimits, roi=roi) if onlimits: raise RuntimeError("Unsupported plot %s" % str(plot)) @@ -696,14 +708,15 @@ class _plot3DArrayContext(_StatsContext): self.min, self.max = None, None def _checkContextInputs(self, item, plot, onlimits, roi): - _StatsContext._checkContextInputs(self, item=item, plot=plot, - onlimits=onlimits, roi=roi) + _StatsContext._checkContextInputs( + self, item=item, plot=plot, onlimits=onlimits, roi=roi + ) if roi is not None and not isinstance(roi, RegionOfInterest): - raise TypeError('curve `context` can ony manage 2D roi') + raise TypeError("curve `context` can ony manage 2D roi") -BASIC_COMPATIBLE_KINDS = 'curve', 'image', 'scatter', 'histogram' +BASIC_COMPATIBLE_KINDS = "curve", "image", "scatter", "histogram" class StatBase(object): @@ -714,6 +727,7 @@ class StatBase(object): :param List[str] compatibleKinds: The kind of items (curve, scatter...) for which the statistic apply. """ + def __init__(self, name, compatibleKinds=BASIC_COMPATIBLE_KINDS, description=None): self.name = name self.compatibleKinds = compatibleKinds @@ -726,7 +740,7 @@ class StatBase(object): :param _StatsContext context: :return dict: key is stat name, statistic computed is the dict value """ - raise NotImplementedError('Base class') + raise NotImplementedError("Base class") def getToolTip(self, kind): """ @@ -749,6 +763,7 @@ class Stat(StatBase): :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 @@ -759,16 +774,18 @@ class Stat(StatBase): if context.kind in self.compatibleKinds: return self._fct(context.values) else: - raise ValueError('Kind %s not managed by %s' - '' % (context.kind, self.name)) + raise ValueError( + "Kind %s not managed by %s" "" % (context.kind, self.name) + ) else: return None class StatMin(StatBase): """Compute the minimal value on data""" + def __init__(self): - StatBase.__init__(self, name='min') + StatBase.__init__(self, name="min") @docstring(StatBase) def calculate(self, context): @@ -777,8 +794,9 @@ class StatMin(StatBase): class StatMax(StatBase): """Compute the maximal value on data""" + def __init__(self): - StatBase.__init__(self, name='max') + StatBase.__init__(self, name="max") @docstring(StatBase) def calculate(self, context): @@ -787,8 +805,9 @@ class StatMax(StatBase): class StatDelta(StatBase): """Compute the delta between minimal and maximal on data""" + def __init__(self): - StatBase.__init__(self, name='delta') + StatBase.__init__(self, name="delta") @docstring(StatBase) def calculate(self, context): @@ -822,8 +841,9 @@ class _StatCoord(StatBase): class StatCoordMin(_StatCoord): """Compute the coordinates of the first minimum value of the data""" + def __init__(self): - _StatCoord.__init__(self, name='coords min') + _StatCoord.__init__(self, name="coords min") @docstring(StatBase) def calculate(self, context): @@ -840,8 +860,9 @@ class StatCoordMin(_StatCoord): class StatCoordMax(_StatCoord): """Compute the coordinates of the first maximum value of the data""" + def __init__(self): - _StatCoord.__init__(self, name='coords max') + _StatCoord.__init__(self, name="coords max") @docstring(StatBase) def calculate(self, context): @@ -860,8 +881,9 @@ class StatCoordMax(_StatCoord): class StatCOM(StatBase): """Compute data center of mass""" + def __init__(self): - StatBase.__init__(self, name='COM', description='Center of mass') + StatBase.__init__(self, name="COM", description="Center of mass") @docstring(StatBase) def calculate(self, context): @@ -870,7 +892,7 @@ class StatCOM(StatBase): values = numpy.ma.array(context.values, mask=context.mask, dtype=numpy.float64) sum_ = numpy.sum(values) - if sum_ == 0. or numpy.ma.is_masked(sum_): + if sum_ == 0.0 or numpy.ma.is_masked(sum_): return (numpy.nan,) * len(context.axes) if context.isStructuredData(): @@ -878,11 +900,11 @@ class StatCOM(StatBase): for index, axis in enumerate(context.axes): axes = tuple([i for i in range(len(context.axes)) if i != index]) centerofmass.append( - numpy.sum(axis * numpy.sum(values, axis=axes)) / sum_) + numpy.sum(axis * numpy.sum(values, axis=axes)) / sum_ + ) return tuple(reversed(centerofmass)) else: - return tuple( - numpy.sum(axis * values) / sum_ for axis in context.axes) + return tuple(numpy.sum(axis * values) / sum_ for axis in context.axes) @docstring(StatBase) def getToolTip(self, kind): |