diff options
Diffstat (limited to 'src/silx/gui/plot3d/items/scatter.py')
| -rw-r--r-- | src/silx/gui/plot3d/items/scatter.py | 224 |
1 files changed, 116 insertions, 108 deletions
diff --git a/src/silx/gui/plot3d/items/scatter.py b/src/silx/gui/plot3d/items/scatter.py index c93db88..b8f2f39 100644 --- a/src/silx/gui/plot3d/items/scatter.py +++ b/src/silx/gui/plot3d/items/scatter.py @@ -1,6 +1,6 @@ # /*########################################################################## # -# Copyright (c) 2017-2020 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 @@ -28,16 +28,13 @@ __authors__ = ["T. Vincent"] __license__ = "MIT" __date__ = "15/11/2017" -try: - from collections import abc -except ImportError: # Python2 support - import collections as abc +from collections import abc import logging +import sys import numpy +from matplotlib.tri import Triangulation -from ....utils.deprecation import deprecated from ... import _glutils as glu -from ...plot._utils.delaunay import delaunay from ..scene import function, primitives, utils from ...plot.items import ScatterVisualizationMixIn @@ -65,7 +62,8 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): noData = numpy.zeros((0, 1), dtype=numpy.float32) symbol, size = self._getSceneSymbol() self._scatter = primitives.Points( - x=noData, y=noData, z=noData, value=noData, size=size) + x=noData, y=noData, z=noData, value=noData, size=size + ) self._scatter.marker = symbol self._getScenePrimitive().children.append(self._scatter) @@ -77,7 +75,7 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): if event in (ItemChangedType.SYMBOL, ItemChangedType.SYMBOL_SIZE): symbol, size = self._getSceneSymbol() self._scatter.marker = symbol - self._scatter.setAttribute('size', size, copy=True) + self._scatter.setAttribute("size", size, copy=True) super(Scatter3D, self)._updated(event) @@ -92,10 +90,10 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): True (default) to copy the data, False to use provided data (do not modify!) """ - self._scatter.setAttribute('x', x, copy=copy) - self._scatter.setAttribute('y', y, copy=copy) - self._scatter.setAttribute('z', z, copy=copy) - self._scatter.setAttribute('value', value, copy=copy) + self._scatter.setAttribute("x", x, copy=copy) + self._scatter.setAttribute("y", y, copy=copy) + self._scatter.setAttribute("z", z, copy=copy) + self._scatter.setAttribute("value", value, copy=copy) self._setColormappedData(self.getValueData(copy=False), copy=False) self._updated(ItemChangedType.DATA) @@ -107,10 +105,12 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): False to return internal data (do not modify!) :return: (x, y, z, value) """ - return (self.getXData(copy), - self.getYData(copy), - self.getZData(copy), - self.getValueData(copy)) + return ( + self.getXData(copy), + self.getYData(copy), + self.getZData(copy), + self.getValueData(copy), + ) def getXData(self, copy=True): """Returns X data coordinates. @@ -120,7 +120,7 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): :return: X coordinates :rtype: numpy.ndarray """ - return self._scatter.getAttribute('x', copy=copy).reshape(-1) + return self._scatter.getAttribute("x", copy=copy).reshape(-1) def getYData(self, copy=True): """Returns Y data coordinates. @@ -130,7 +130,7 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): :return: Y coordinates :rtype: numpy.ndarray """ - return self._scatter.getAttribute('y', copy=copy).reshape(-1) + return self._scatter.getAttribute("y", copy=copy).reshape(-1) def getZData(self, copy=True): """Returns Z data coordinates. @@ -140,7 +140,7 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): :return: Z coordinates :rtype: numpy.ndarray """ - return self._scatter.getAttribute('z', copy=copy).reshape(-1) + return self._scatter.getAttribute("z", copy=copy).reshape(-1) def getValueData(self, copy=True): """Returns data values. @@ -150,14 +150,9 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): :return: data values :rtype: numpy.ndarray """ - return self._scatter.getAttribute('value', copy=copy).reshape(-1) + return self._scatter.getAttribute("value", copy=copy).reshape(-1) - @deprecated(reason="Consistency with PlotWidget items", - replacement="getValueData", since_version="0.10.0") - def getValues(self, copy=True): - return self.getValueData(copy) - - def _pickFull(self, context, threshold=0., sort='depth'): + def _pickFull(self, context, threshold=0.0, sort="depth"): """Perform picking in this item at given widget position. :param PickContext context: Current picking context @@ -171,9 +166,9 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): :return: Object holding the results or None :rtype: Union[None,PickingResult] """ - assert sort in ('index', 'depth') + assert sort in ("index", "depth") - rayNdc = context.getPickingSegment(frame='ndc') + rayNdc = context.getPickingSegment(frame="ndc") if rayNdc is None: # No picking outside viewport return None @@ -184,49 +179,57 @@ class Scatter3D(DataItem3D, ColormapMixIn, SymbolMixIn): primitive = self._getScenePrimitive() - dataPoints = numpy.transpose((xData, - self.getYData(copy=False), - self.getZData(copy=False), - numpy.ones_like(xData))) + dataPoints = numpy.transpose( + ( + xData, + self.getYData(copy=False), + self.getZData(copy=False), + numpy.ones_like(xData), + ) + ) pointsNdc = primitive.objectToNDCTransform.transformPoints( - dataPoints, perspectiveDivide=True) + dataPoints, perspectiveDivide=True + ) # Perform picking distancesNdc = numpy.abs(pointsNdc[:, :2] - rayNdc[0, :2]) # TODO issue with symbol size: using pixel instead of points threshold += self.getSymbolSize() - thresholdNdc = 2. * threshold / numpy.array(primitive.viewport.size) - picked = numpy.where(numpy.logical_and( + thresholdNdc = 2.0 * threshold / numpy.array(primitive.viewport.size) + picked = numpy.where( + numpy.logical_and( numpy.all(distancesNdc < thresholdNdc, axis=1), - numpy.logical_and(rayNdc[0, 2] <= pointsNdc[:, 2], - pointsNdc[:, 2] <= rayNdc[1, 2])))[0] + numpy.logical_and( + rayNdc[0, 2] <= pointsNdc[:, 2], pointsNdc[:, 2] <= rayNdc[1, 2] + ), + ) + )[0] - if sort == 'depth': + if sort == "depth": # Sort picked points from front to back picked = picked[numpy.argsort(pointsNdc[picked, 2])] if picked.size > 0: - return PickingResult(self, - positions=dataPoints[picked, :3], - indices=picked, - fetchdata=self.getValueData) + return PickingResult( + self, + positions=dataPoints[picked, :3], + indices=picked, + fetchdata=self.getValueData, + ) else: return None -class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, - ScatterVisualizationMixIn): +class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, ScatterVisualizationMixIn): """2D scatter data with settable visualization mode. :param parent: The View widget this item belongs to. """ _VISUALIZATION_PROPERTIES = { - ScatterVisualizationMixIn.Visualization.POINTS: - ('symbol', 'symbolSize'), - ScatterVisualizationMixIn.Visualization.LINES: - ('lineWidth',), + ScatterVisualizationMixIn.Visualization.POINTS: ("symbol", "symbolSize"), + ScatterVisualizationMixIn.Visualization.LINES: ("lineWidth",), ScatterVisualizationMixIn.Visualization.SOLID: (), } """Dict {visualization mode: property names used in this mode}""" @@ -241,7 +244,7 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, ScatterVisualizationMixIn.__init__(self) self._heightMap = False - self._lineWidth = 1. + self._lineWidth = 1.0 self._x = numpy.zeros((0,), dtype=numpy.float32) self._y = numpy.zeros((0,), dtype=numpy.float32) @@ -260,7 +263,7 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, for child in self._getScenePrimitive().children: if isinstance(child, primitives.Points): child.marker = symbol - child.setAttribute('size', size, copy=True) + child.setAttribute("size", size, copy=True) elif event is ItemChangedType.VISIBLE: # TODO smart update?, need dirty flags @@ -281,7 +284,7 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, By default, it is the current visualization mode. :return: """ - assert name in ('lineWidth', 'symbol', 'symbolSize') + assert name in ("lineWidth", "symbol", "symbolSize") if visualization is None: visualization = self.getVisualization() assert visualization in self.supportedVisualizations() @@ -322,11 +325,11 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, :param float width: Width in pixels """ width = float(width) - assert width >= 1. + assert width >= 1.0 if width != self._lineWidth: self._lineWidth = width for child in self._getScenePrimitive().children: - if hasattr(child, 'lineWidth'): + if hasattr(child, "lineWidth"): child.lineWidth = width self._updated(ItemChangedType.LINE_WIDTH) @@ -342,15 +345,14 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, True (default) to make a copy of the data, False to avoid copy if possible (do not modify the arrays). """ - x = numpy.array( - x, copy=copy, dtype=numpy.float32, order='C').reshape(-1) - y = numpy.array( - y, copy=copy, dtype=numpy.float32, order='C').reshape(-1) + x = numpy.array(x, copy=copy, dtype=numpy.float32, order="C").reshape(-1) + y = numpy.array(y, copy=copy, dtype=numpy.float32, order="C").reshape(-1) assert len(x) == len(y) if isinstance(value, abc.Iterable): value = numpy.array( - value, copy=copy, dtype=numpy.float32, order='C').reshape(-1) + value, copy=copy, dtype=numpy.float32, order="C" + ).reshape(-1) assert len(value) == len(x) else: # Single scalar value = numpy.array((float(value),), dtype=numpy.float32) @@ -376,9 +378,11 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, False to return internal data (do not modify!) :return: (x, y, value) """ - return (self.getXData(copy=copy), - self.getYData(copy=copy), - self.getValueData(copy=copy)) + return ( + self.getXData(copy=copy), + self.getYData(copy=copy), + self.getValueData(copy=copy), + ) def getXData(self, copy=True): """Returns X data coordinates. @@ -410,12 +414,7 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, """ return numpy.array(self._value, copy=copy) - @deprecated(reason="Consistency with PlotWidget items", - replacement="getValueData", since_version="0.10.0") - def getValues(self, copy=True): - return self.getValueData(copy) - - def _pickPoints(self, context, points, threshold=1., sort='depth'): + def _pickPoints(self, context, points, threshold=1.0, sort="depth"): """Perform picking while in 'points' visualization mode :param PickContext context: Current picking context @@ -429,34 +428,41 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, :return: Object holding the results or None :rtype: Union[None,PickingResult] """ - assert sort in ('index', 'depth') + assert sort in ("index", "depth") - rayNdc = context.getPickingSegment(frame='ndc') + rayNdc = context.getPickingSegment(frame="ndc") if rayNdc is None: # No picking outside viewport return None # Project data to NDC primitive = self._getScenePrimitive() pointsNdc = primitive.objectToNDCTransform.transformPoints( - points, perspectiveDivide=True) + points, perspectiveDivide=True + ) # Perform picking distancesNdc = numpy.abs(pointsNdc[:, :2] - rayNdc[0, :2]) thresholdNdc = threshold / numpy.array(primitive.viewport.size) - picked = numpy.where(numpy.logical_and( - numpy.all(distancesNdc < thresholdNdc, axis=1), - numpy.logical_and(rayNdc[0, 2] <= pointsNdc[:, 2], - pointsNdc[:, 2] <= rayNdc[1, 2])))[0] + picked = numpy.where( + numpy.logical_and( + numpy.all(distancesNdc < thresholdNdc, axis=1), + numpy.logical_and( + rayNdc[0, 2] <= pointsNdc[:, 2], pointsNdc[:, 2] <= rayNdc[1, 2] + ), + ) + )[0] - if sort == 'depth': + if sort == "depth": # Sort picked points from front to back picked = picked[numpy.argsort(pointsNdc[picked, 2])] if picked.size > 0: - return PickingResult(self, - positions=points[picked, :3], - indices=picked, - fetchdata=self.getValueData) + return PickingResult( + self, + positions=points[picked, :3], + indices=picked, + fetchdata=self.getValueData, + ) else: return None @@ -477,7 +483,8 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, trianglesIndices = self._cachedTrianglesIndices.reshape(-1, 3) triangles = points[trianglesIndices, :3] selectedIndices, t, barycentric = glu.segmentTrianglesIntersection( - rayObject, triangles) + rayObject, triangles + ) closest = numpy.argmax(barycentric, axis=1) indices = trianglesIndices.reshape(-1, 3)[selectedIndices, closest] @@ -488,10 +495,9 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, # Compute intersection points and get closest data point positions = t.reshape(-1, 1) * (rayObject[1] - rayObject[0]) + rayObject[0] - return PickingResult(self, - positions=positions, - indices=indices, - fetchdata=self.getValueData) + return PickingResult( + self, positions=positions, indices=indices, fetchdata=self.getValueData + ) def _pickFull(self, context): """Perform picking in this item at given widget position. @@ -509,22 +515,20 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, else: zData = numpy.zeros_like(xData) - points = numpy.transpose((xData, - self.getYData(copy=False), - zData, - numpy.ones_like(xData))) + points = numpy.transpose( + (xData, self.getYData(copy=False), zData, numpy.ones_like(xData)) + ) mode = self.getVisualization() if mode is self.Visualization.POINTS: # TODO issue with symbol size: using pixel instead of points # Get "corrected" symbol size _, threshold = self._getSceneSymbol() - return self._pickPoints( - context, points, threshold=max(3., threshold)) + return self._pickPoints(context, points, threshold=max(3.0, threshold)) elif mode is self.Visualization.LINES: # Picking only at point - return self._pickPoints(context, points, threshold=5.) + return self._pickPoints(context, points, threshold=5.0) else: # mode == 'solid' return self._pickSolid(context, points) @@ -543,36 +547,38 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, heightMap = self.isHeightMap() if mode is self.Visualization.POINTS: - z = value if heightMap else 0. + z = value if heightMap else 0.0 symbol, size = self._getSceneSymbol() primitive = primitives.Points( - x=x, y=y, z=z, value=value, - size=size, - colormap=self._getSceneColormap()) + x=x, y=y, z=z, value=value, size=size, colormap=self._getSceneColormap() + ) primitive.marker = symbol else: # TODO run delaunay in a thread # Compute lines/triangles indices if not cached if self._cachedTrianglesIndices is None: - triangulation = delaunay(x, y) - if triangulation is None: + try: + triangulation = Triangulation(x, y) + except (RuntimeError, ValueError): + _logger.debug("Delaunay tesselation failed: %s", sys.exc_info()[1]) return None self._cachedTrianglesIndices = numpy.ravel( - triangulation.simplices.astype(numpy.uint32)) + triangulation.triangles.astype(numpy.uint32) + ) - if (mode is self.Visualization.LINES and - self._cachedLinesIndices is None): + if mode is self.Visualization.LINES and self._cachedLinesIndices is None: # Compute line indices self._cachedLinesIndices = utils.triangleToLineIndices( - self._cachedTrianglesIndices, unicity=True) + self._cachedTrianglesIndices, unicity=True + ) if mode is self.Visualization.LINES: indices = self._cachedLinesIndices - renderMode = 'lines' + renderMode = "lines" else: indices = self._cachedTrianglesIndices - renderMode = 'triangles' + renderMode = "triangles" # TODO supports x, y instead of copy if heightMap: @@ -590,14 +596,15 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, if len(value) > 1: value = value[indices] triangleNormals = utils.trianglesNormal(coordinates) - normal = numpy.empty((len(triangleNormals) * 3, 3), - dtype=numpy.float32) + normal = numpy.empty( + (len(triangleNormals) * 3, 3), dtype=numpy.float32 + ) normal[0::3, :] = triangleNormals normal[1::3, :] = triangleNormals normal[2::3, :] = triangleNormals indices = None else: - normal = (0., 0., 1.) + normal = (0.0, 0.0, 1.0) else: normal = None @@ -607,7 +614,8 @@ class Scatter2D(DataItem3D, ColormapMixIn, SymbolMixIn, normal=normal, colormap=self._getSceneColormap(), indices=indices, - mode=renderMode) + mode=renderMode, + ) primitive.lineWidth = self.getLineWidth() primitive.lineSmooth = False |