diff options
Diffstat (limited to 'src/silx/gui/plot3d/ScalarFieldView.py')
| -rw-r--r-- | src/silx/gui/plot3d/ScalarFieldView.py | 353 |
1 files changed, 180 insertions, 173 deletions
diff --git a/src/silx/gui/plot3d/ScalarFieldView.py b/src/silx/gui/plot3d/ScalarFieldView.py index 0633221..e1d34fd 100644 --- a/src/silx/gui/plot3d/ScalarFieldView.py +++ b/src/silx/gui/plot3d/ScalarFieldView.py @@ -76,9 +76,9 @@ class Isosurface(qt.QObject): def __init__(self, parent): super(Isosurface, self).__init__(parent=parent) - self._level = float('nan') + self._level = float("nan") self._autoLevelFunction = None - self._color = rgba('#FFD700FF') + self._color = rgba("#FFD700FF") self._data = None self._group = scene.Group() @@ -91,7 +91,7 @@ class Isosurface(qt.QObject): if data is None: self._data = None else: - self._data = numpy.array(data, copy=copy, order='C') + self._data = numpy.array(data, copy=copy, order="C") self._update() @@ -167,7 +167,7 @@ class Isosurface(qt.QObject): if color != self._color: self._color = color if len(self._group.children) != 0: - self._group.children[0].setAttribute('color', self._color) + self._group.children[0].setAttribute("color", self._color) self.sigColorChanged.emit() def _update(self): @@ -176,7 +176,7 @@ class Isosurface(qt.QObject): if self._data is None: if self.isAutoLevel(): - self._level = float('nan') + self._level = float("nan") else: if self.isAutoLevel(): @@ -191,12 +191,12 @@ class Isosurface(qt.QObject): "Error while executing iso level function %s.%s", module, name, - exc_info=True) - level = float('nan') + exc_info=True, + ) + level = float("nan") else: - _logger.info( - 'Computed iso-level in %f s.', time.time() - st) + _logger.info("Computed iso-level in %f s.", time.time() - st) if level != self._level: self._level = level @@ -206,19 +206,19 @@ class Isosurface(qt.QObject): return st = time.time() - vertices, normals, indices = MarchingCubes( - self._data, - isolevel=self._level) - _logger.info('Computed iso-surface in %f s.', time.time() - st) + vertices, normals, indices = MarchingCubes(self._data, isolevel=self._level) + _logger.info("Computed iso-surface in %f s.", time.time() - st) if len(vertices) == 0: return else: - mesh = primitives.Mesh3D(vertices, - colors=self._color, - normals=normals, - mode='triangles', - indices=indices) + mesh = primitives.Mesh3D( + vertices, + colors=self._color, + normals=normals, + mode="triangles", + indices=indices, + ) self._group.children = [mesh] @@ -233,9 +233,9 @@ class SelectedRegion(object): :param scale: Scale from array to data coordinates (sx, sy, sz) """ - def __init__(self, arrayRange, dataBBox, - translation=(0., 0., 0.), - scale=(1., 1., 1.)): + def __init__( + self, arrayRange, dataBBox, translation=(0.0, 0.0, 0.0), scale=(1.0, 1.0, 1.0) + ): self._arrayRange = numpy.array(arrayRange, copy=True, dtype=numpy.int64) assert self._arrayRange.shape == (3, 2) assert numpy.all(self._arrayRange[:, 1] >= self._arrayRange[:, 0]) @@ -261,9 +261,11 @@ class SelectedRegion(object): :return: A numpy array with (zslice, yslice, zslice) :rtype: numpy.ndarray """ - return (slice(*self._arrayRange[0]), - slice(*self._arrayRange[1]), - slice(*self._arrayRange[2])) + return ( + slice(*self._arrayRange[0]), + slice(*self._arrayRange[1]), + slice(*self._arrayRange[2]), + ) def getDataRange(self): """Range in the data coordinates of the selection: 3x2 array of float @@ -348,12 +350,13 @@ class CutPlane(qt.QObject): # Plane with texture on the data bounding box self._dataPlane = cutplane.CutPlane(normal=(0, 1, 0)) self._dataPlane.strokeVisible = False - self._dataPlane.alpha = 1. + self._dataPlane.alpha = 1.0 self._dataPlane.visible = self._visible self._dataPlane.plane.addListener(self._planePositionChanged) self._colormap = Colormap( - name='gray', normalization='linear', vmin=None, vmax=None) + name="gray", normalization="linear", vmin=None, vmax=None + ) self.getColormap().sigChanged.connect(self._colormapChanged) self._updateSceneColormap() @@ -369,8 +372,8 @@ class CutPlane(qt.QObject): bounds = self._planeStroke.parent.bounds(dataBounds=True) if bounds is not None: self._planeStroke.plane.point = numpy.clip( - self._planeStroke.plane.point, - a_min=bounds[0], a_max=bounds[1]) + self._planeStroke.plane.point, a_min=bounds[0], a_max=bounds[1] + ) @staticmethod def _syncPlanes(master, slave): @@ -379,14 +382,12 @@ class CutPlane(qt.QObject): :param PlaneInGroup master: Reference PlaneInGroup :param PlaneInGroup slave: PlaneInGroup to align """ - masterToSlave = transform.StaticTransformList([ - slave.objectToSceneTransform.inverse(), - master.objectToSceneTransform]) - - point = masterToSlave.transformPoint( - master.plane.point) - normal = masterToSlave.transformNormal( - master.plane.normal) + masterToSlave = transform.StaticTransformList( + [slave.objectToSceneTransform.inverse(), master.objectToSceneTransform] + ) + + point = masterToSlave.transformPoint(master.plane.point) + normal = masterToSlave.transformNormal(master.plane.normal) slave.plane.setPlane(point, normal) def _sfViewDataChanged(self): @@ -407,8 +408,7 @@ class CutPlane(qt.QObject): def _sfViewTransformChanged(self): """Handle transform changed in the ScalarFieldView""" self._keepPlaneInBBox() - self._syncPlanes(master=self._planeStroke, - slave=self._dataPlane) + self._syncPlanes(master=self._planeStroke, slave=self._dataPlane) self.sigPlaneChanged.emit() def _planeChanged(self, source, *args, **kwargs): @@ -423,14 +423,11 @@ class CutPlane(qt.QObject): if self.__syncPlane: self.__syncPlane = False if source is self._planeStroke.plane: - self._syncPlanes(master=self._planeStroke, - slave=self._dataPlane) + self._syncPlanes(master=self._planeStroke, slave=self._dataPlane) elif source is self._dataPlane.plane: - self._syncPlanes(master=self._dataPlane, - slave=self._planeStroke) + self._syncPlanes(master=self._dataPlane, slave=self._planeStroke) else: - _logger.error('Received an unknown object %s', - str(source)) + _logger.error("Received an unknown object %s", str(source)) if self._planeStroke.visible or self._dataPlane.visible: self.sigPlaneChanged.emit() @@ -447,7 +444,7 @@ class CutPlane(qt.QObject): """Returns whether the cut plane is defined or not (bool)""" return self._planeStroke.isValid - def _plane(self, coordinates='array'): + def _plane(self, coordinates="array"): """Returns the scene plane to set. :param str coordinates: The coordinate system to use: @@ -455,15 +452,14 @@ class CutPlane(qt.QObject): :rtype: Plane :raise ValueError: If coordinates is not correct """ - if coordinates == 'scene': + if coordinates == "scene": return self._planeStroke.plane - elif coordinates == 'array': + elif coordinates == "array": return self._dataPlane.plane else: - raise ValueError( - 'Unsupported coordinates: %s' % str(coordinates)) + raise ValueError("Unsupported coordinates: %s" % str(coordinates)) - def getNormal(self, coordinates='array'): + def getNormal(self, coordinates="array"): """Returns the normal of the plane (as a unit vector) :param str coordinates: The coordinate system to use: @@ -474,7 +470,7 @@ class CutPlane(qt.QObject): """ return self._plane(coordinates).normal - def setNormal(self, normal, coordinates='array'): + def setNormal(self, normal, coordinates="array"): """Set the normal of the plane. :param normal: 3-tuple of float: nx, ny, nz @@ -484,7 +480,7 @@ class CutPlane(qt.QObject): """ self._plane(coordinates).normal = normal - def getPoint(self, coordinates='array'): + def getPoint(self, coordinates="array"): """Returns a point on the plane. :param str coordinates: The coordinate system to use: @@ -495,7 +491,7 @@ class CutPlane(qt.QObject): """ return self._plane(coordinates).point - def setPoint(self, point, constraint=True, coordinates='array'): + def setPoint(self, point, constraint=True, coordinates="array"): """Set a point contained in the plane. Warning: The plane might not intersect the bounding box of the data. @@ -511,7 +507,7 @@ class CutPlane(qt.QObject): if constraint: self._keepPlaneInBBox() - def getParameters(self, coordinates='array'): + def getParameters(self, coordinates="array"): """Returns the plane equation parameters: a*x + b*y + c*z + d = 0 :param str coordinates: The coordinate system to use: @@ -522,7 +518,7 @@ class CutPlane(qt.QObject): """ return self._plane(coordinates).parameters - def setParameters(self, parameters, constraint=True, coordinates='array'): + def setParameters(self, parameters, constraint=True, coordinates="array"): """Set the plane equation parameters: a*x + b*y + c*z + d = 0 Warning: The plane might not intersect the bounding box of the data. @@ -644,11 +640,7 @@ class CutPlane(qt.QObject): """ return self._colormap - def setColormap(self, - name='gray', - norm=None, - vmin=None, - vmax=None): + def setColormap(self, name="gray", norm=None, vmin=None, vmax=None): """Set the colormap to use. By either providing a :class:`Colormap` object or @@ -662,8 +654,9 @@ class CutPlane(qt.QObject): :param float vmin: The minimum value of the range or None for autoscale :param float vmax: The maximum value of the range or None for autoscale """ - _logger.debug('setColormap %s %s (%s, %s)', - name, str(norm), str(vmin), str(vmax)) + _logger.debug( + "setColormap %s %s (%s, %s)", name, str(norm), str(vmin), str(vmax) + ) self._colormap.sigChanged.disconnect(self._colormapChanged) @@ -672,9 +665,10 @@ class CutPlane(qt.QObject): self._colormap = name else: if norm is None: - norm = 'linear' + norm = "linear" self._colormap = Colormap( - name=name, normalization=norm, vmin=vmin, vmax=vmax) + name=name, normalization=norm, vmin=vmin, vmax=vmax + ) self._colormap.sigChanged.connect(self._colormapChanged) self._colormapChanged() @@ -718,12 +712,12 @@ class _CutPlaneImage(object): self._isValid = False self._data = numpy.zeros((0, 0), dtype=numpy.float32) self._index = 0 - self._xLabel = '' - self._yLabel = '' - self._normalLabel = '' - self._scale = float('nan'), float('nan') - self._translation = float('nan'), float('nan') - self._position = float('nan') + self._xLabel = "" + self._yLabel = "" + self._normalLabel = "" + self._scale = float("nan"), float("nan") + self._translation = float("nan"), float("nan") + self._position = float("nan") sfView = cutPlane.parent() if not sfView or not cutPlane.isValid(): @@ -735,10 +729,10 @@ class _CutPlaneImage(object): _logger.info("No data available") return - normal = cutPlane.getNormal(coordinates='array') - point = cutPlane.getPoint(coordinates='array') + normal = cutPlane.getNormal(coordinates="array") + point = cutPlane.getPoint(coordinates="array") - if numpy.linalg.norm(numpy.cross(normal, (1., 0., 0.))) < 0.0017: + if numpy.linalg.norm(numpy.cross(normal, (1.0, 0.0, 0.0))) < 0.0017: if not 0 <= point[0] <= data.shape[2]: _logger.info("Plane outside dataset") return @@ -746,7 +740,7 @@ class _CutPlaneImage(object): slice_ = data[:, :, index] xAxisIndex, yAxisIndex, normalAxisIndex = 1, 2, 0 # y, z, x - elif numpy.linalg.norm(numpy.cross(normal, (0., 1., 0.))) < 0.0017: + elif numpy.linalg.norm(numpy.cross(normal, (0.0, 1.0, 0.0))) < 0.0017: if not 0 <= point[1] <= data.shape[1]: _logger.info("Plane outside dataset") return @@ -754,7 +748,7 @@ class _CutPlaneImage(object): slice_ = numpy.transpose(data[:, index, :]) xAxisIndex, yAxisIndex, normalAxisIndex = 2, 0, 1 # z, x, y - elif numpy.linalg.norm(numpy.cross(normal, (0., 0., 1.))) < 0.0017: + elif numpy.linalg.norm(numpy.cross(normal, (0.0, 0.0, 1.0))) < 0.0017: if not 0 <= point[2] <= data.shape[0]: _logger.info("Plane outside dataset") return @@ -762,8 +756,9 @@ class _CutPlaneImage(object): slice_ = data[index, :, :] xAxisIndex, yAxisIndex, normalAxisIndex = 0, 1, 2 # x, y, z else: - _logger.warning('Unsupported normal: (%f, %f, %f)', - normal[0], normal[1], normal[2]) + _logger.warning( + "Unsupported normal: (%f, %f, %f)", normal[0], normal[1], normal[2] + ) return # Store cut plane image info @@ -774,8 +769,11 @@ class _CutPlaneImage(object): # Only store extra information when no transform matrix is set # Otherwise this information can be meaningless - if numpy.all(numpy.equal(sfView.getTransformMatrix(), - numpy.identity(3, dtype=numpy.float32))): + if numpy.all( + numpy.equal( + sfView.getTransformMatrix(), numpy.identity(3, dtype=numpy.float32) + ) + ): labels = sfView.getAxesLabels() self._xLabel = labels[xAxisIndex] self._yLabel = labels[yAxisIndex] @@ -787,8 +785,9 @@ class _CutPlaneImage(object): translation = sfView.getTranslation() self._translation = translation[xAxisIndex], translation[yAxisIndex] - self._position = float(index * scale[normalAxisIndex] + - translation[normalAxisIndex]) + self._position = float( + index * scale[normalAxisIndex] + translation[normalAxisIndex] + ) def isValid(self): """Returns True if the cut plane image is defined (bool)""" @@ -860,7 +859,8 @@ class ScalarFieldView(Plot3DWindow): def __init__(self, parent=None): super(ScalarFieldView, self).__init__(parent) self._colormap = Colormap( - name='gray', normalization='linear', vmin=None, vmax=None) + name="gray", normalization="linear", vmin=None, vmax=None + ) self._selectedRange = None # Store iso-surfaces @@ -869,35 +869,37 @@ class ScalarFieldView(Plot3DWindow): # Transformations self._dataScale = transform.Scale() self._dataTranslate = transform.Translate() - self._dataTransform = transform.Matrix() # default to identity + self._dataTransform = transform.Matrix() # default to identity - self._foregroundColor = 1., 1., 1., 1. - self._highlightColor = 0.7, 0.7, 0., 1. + self._foregroundColor = 1.0, 1.0, 1.0, 1.0 + self._highlightColor = 0.7, 0.7, 0.0, 1.0 self._data = None self._dataRange = None self._group = primitives.BoundedGroup() self._group.transforms = [ - self._dataTranslate, self._dataTransform, self._dataScale] + self._dataTranslate, + self._dataTransform, + self._dataScale, + ] self._bbox = axes.LabelledAxes() self._bbox.children = [self._group] - self._outerScale = transform.Scale(1., 1., 1.) + self._outerScale = transform.Scale(1.0, 1.0, 1.0) self._bbox.transforms = [self._outerScale] self.getPlot3DWidget().viewport.scene.children.append(self._bbox) self._selectionBox = primitives.Box() self._selectionBox.strokeSmooth = False - self._selectionBox.strokeWidth = 1. + self._selectionBox.strokeWidth = 1.0 # self._selectionBox.fillColor = 1., 1., 1., 0.3 # self._selectionBox.fillCulling = 'back' self._selectionBox.visible = False self._group.children.append(self._selectionBox) self._cutPlane = CutPlane(sfView=self) - self._cutPlane.sigVisibilityChanged.connect( - self._planeVisibilityChanged) + self._cutPlane.sigVisibilityChanged.connect(self._planeVisibilityChanged) planeStroke, dataPlane = self._cutPlane._get3DPrimitives() self._bbox.children.append(planeStroke) self._group.children.append(dataPlane) @@ -905,13 +907,16 @@ class ScalarFieldView(Plot3DWindow): self._isogroup = primitives.GroupDepthOffset() self._isogroup.transforms = [ # Convert from z, y, x from marching cubes to x, y, z - transform.Matrix(( - (0., 0., 1., 0.), - (0., 1., 0., 0.), - (1., 0., 0., 0.), - (0., 0., 0., 1.))), + transform.Matrix( + ( + (0.0, 0.0, 1.0, 0.0), + (0.0, 1.0, 0.0, 0.0), + (1.0, 0.0, 0.0, 0.0), + (0.0, 0.0, 0.0, 1.0), + ) + ), # Offset to match cutting plane coords - transform.Translate(0.5, 0.5, 0.5) + transform.Translate(0.5, 0.5, 0.5), ] self._group.children.append(self._isogroup) @@ -931,7 +936,7 @@ class ScalarFieldView(Plot3DWindow): stream = qt.QDataStream(ioDevice) - stream.writeString('<ScalarFieldView>') + stream.writeString("<ScalarFieldView>") isoSurfaces = self.getIsosurfaces() @@ -940,7 +945,7 @@ class ScalarFieldView(Plot3DWindow): # TODO : delegate the serialization to the serialized items # isosurfaces if nIsoSurfaces: - tagIn = '<IsoSurfaces nIso={0}>'.format(nIsoSurfaces) + tagIn = "<IsoSurfaces nIso={0}>".format(nIsoSurfaces) stream.writeString(tagIn) for surface in isoSurfaces: @@ -951,16 +956,16 @@ class ScalarFieldView(Plot3DWindow): stream.writeDouble(level) stream.writeBool(visible) - stream.writeString('</IsoSurfaces>') + stream.writeString("</IsoSurfaces>") - stream.writeString('<Style>') + stream.writeString("<Style>") background = self.getBackgroundColor() foreground = self.getForegroundColor() highlight = self.getHighlightColor() stream << background << foreground << highlight - stream.writeString('</Style>') + stream.writeString("</Style>") - stream.writeString('</ScalarFieldView>') + stream.writeString("</ScalarFieldView>") def loadConfig(self, ioDevice): """ @@ -972,14 +977,13 @@ class ScalarFieldView(Plot3DWindow): tagStack = deque() - tagInRegex = re.compile('<(?P<itemId>[^ /]*) *' - '(?P<args>.*)>') + tagInRegex = re.compile("<(?P<itemId>[^ /]*) *" "(?P<args>.*)>") - tagOutRegex = re.compile('</(?P<itemId>[^ ]*)>') + tagOutRegex = re.compile("</(?P<itemId>[^ ]*)>") - tagRootInRegex = re.compile('<ScalarFieldView>') + tagRootInRegex = re.compile("<ScalarFieldView>") - isoSurfaceArgsRegex = re.compile('nIso=(?P<nIso>[0-9]*)') + isoSurfaceArgsRegex = re.compile("nIso=(?P<nIso>[0-9]*)") stream = qt.QDataStream(ioDevice) @@ -988,26 +992,27 @@ class ScalarFieldView(Plot3DWindow): if tagMatch is None: # TODO : explicit error - raise ValueError('Unknown data.') + raise ValueError("Unknown data.") - itemId = 'ScalarFieldView' + itemId = "ScalarFieldView" tagStack.append(itemId) while True: - tag = stream.readString() tagMatch = tagOutRegex.match(tag) if tagMatch: - closeId = tagMatch.groupdict()['itemId'] + closeId = tagMatch.groupdict()["itemId"] if closeId != itemId: # TODO : explicit error - raise ValueError('Unexpected closing tag {0} ' - '(expected {1})' - ''.format(closeId, itemId)) + raise ValueError( + "Unexpected closing tag {0} " + "(expected {1})" + "".format(closeId, itemId) + ) - if itemId == 'ScalarFieldView': + if itemId == "ScalarFieldView": # reached end break else: @@ -1019,23 +1024,24 @@ class ScalarFieldView(Plot3DWindow): if tagMatch is None: # TODO : explicit error - raise ValueError('Unknown data.') + raise ValueError("Unknown data.") tagStack.append(itemId) matchDict = tagMatch.groupdict() - itemId = matchDict['itemId'] + itemId = matchDict["itemId"] # TODO : delegate the deserialization to the serialized items - if itemId == 'IsoSurfaces': - argsMatch = isoSurfaceArgsRegex.match(matchDict['args']) + if itemId == "IsoSurfaces": + argsMatch = isoSurfaceArgsRegex.match(matchDict["args"]) if not argsMatch: # TODO : explicit error - raise ValueError('Failed to parse args "{0}".' - ''.format(matchDict['args'])) + raise ValueError( + 'Failed to parse args "{0}".' "".format(matchDict["args"]) + ) argsDict = argsMatch.groupdict() - nIso = int(argsDict['nIso']) + nIso = int(argsDict["nIso"]) if nIso: for surface in self.getIsosurfaces(): self.removeIsosurface(surface) @@ -1046,7 +1052,7 @@ class ScalarFieldView(Plot3DWindow): visible = stream.readBool() surface = self.addIsosurface(level, color=color) surface.setVisible(visible) - elif itemId == 'Style': + elif itemId == "Style": background = qt.QColor() foreground = qt.QColor() highlight = qt.QColor() @@ -1055,22 +1061,23 @@ class ScalarFieldView(Plot3DWindow): self.setForegroundColor(foreground) self.setHighlightColor(highlight) else: - raise ValueError('Unknown entry tag {0}.' - ''.format(itemId)) + raise ValueError("Unknown entry tag {0}." "".format(itemId)) def _initPanPlaneAction(self): """Creates and init the pan plane action""" self._panPlaneAction = qt.QAction(self) - self._panPlaneAction.setIcon(icons.getQIcon('3d-plane-pan')) - self._panPlaneAction.setText('Pan plane') + self._panPlaneAction.setIcon(icons.getQIcon("3d-plane-pan")) + self._panPlaneAction.setText("Pan plane") self._panPlaneAction.setCheckable(True) self._panPlaneAction.setToolTip( - 'Pan the cutting plane. Press <b>Ctrl</b> to rotate the scene.') + "Pan the cutting plane. Press <b>Ctrl</b> to rotate the scene." + ) self._panPlaneAction.setEnabled(False) self._panPlaneAction.triggered[bool].connect(self._planeActionTriggered) self.getPlot3DWidget().sigInteractiveModeChanged.connect( - self._interactiveModeChanged) + self._interactiveModeChanged + ) toolbar = self.findChild(InteractiveModeToolBar) if toolbar is not None: @@ -1078,10 +1085,10 @@ class ScalarFieldView(Plot3DWindow): def _planeActionTriggered(self, checked=False): self._panPlaneAction.setChecked(True) - self.setInteractiveMode('plane') + self.setInteractiveMode("plane") def _interactiveModeChanged(self): - self._panPlaneAction.setChecked(self.getInteractiveMode() == 'plane') + self._panPlaneAction.setChecked(self.getInteractiveMode() == "plane") self._updateColors() def _planeVisibilityChanged(self, visible): @@ -1089,9 +1096,9 @@ class ScalarFieldView(Plot3DWindow): if visible != self._panPlaneAction.isEnabled(): self._panPlaneAction.setEnabled(visible) if visible: - self.setInteractiveMode('plane') + self.setInteractiveMode("plane") elif self._panPlaneAction.isChecked(): - self.setInteractiveMode('rotate') + self.setInteractiveMode("rotate") def setInteractiveMode(self, mode): """Choose the current interaction. @@ -1102,23 +1109,24 @@ class ScalarFieldView(Plot3DWindow): return sceneScale = self.getPlot3DWidget().viewport.scene.transforms[0] - if mode == 'plane': + if mode == "plane": mode = interaction.PanPlaneZoomOnWheelControl( self.getPlot3DWidget().viewport, self._cutPlane._get3DPrimitives()[0], - mode='position', + mode="position", orbitAroundCenter=False, - scaleTransform=sceneScale) + scaleTransform=sceneScale, + ) self.getPlot3DWidget().setInteractiveMode(mode) self._updateColors() def getInteractiveMode(self): - """Returns the current interaction mode, see :meth:`setInteractiveMode` - """ - if isinstance(self.getPlot3DWidget().eventHandler, - interaction.PanPlaneZoomOnWheelControl): - return 'plane' + """Returns the current interaction mode, see :meth:`setInteractiveMode`""" + if isinstance( + self.getPlot3DWidget().eventHandler, interaction.PanPlaneZoomOnWheelControl + ): + return "plane" else: return self.getPlot3DWidget().getInteractiveMode() @@ -1143,7 +1151,7 @@ class ScalarFieldView(Plot3DWindow): self.centerScene() else: - data = numpy.array(data, copy=copy, dtype=numpy.float32, order='C') + data = numpy.array(data, copy=copy, dtype=numpy.float32, order="C") assert data.ndim == 3 assert min(data.shape) >= 2 @@ -1160,7 +1168,7 @@ class ScalarFieldView(Plot3DWindow): if dataRange is not None: min_positive = dataRange.min_positive if min_positive is None: - min_positive = float('nan') + min_positive = float("nan") dataRange = dataRange.minimum, min_positive, dataRange.maximum self._dataRange = dataRange @@ -1203,7 +1211,7 @@ class ScalarFieldView(Plot3DWindow): # Transformations - def setOuterScale(self, sx=1., sy=1., sz=1.): + def setOuterScale(self, sx=1.0, sy=1.0, sz=1.0): """Set the scale to apply to the whole scene including the axes. This is useful when axis lengths in data space are really different. @@ -1222,7 +1230,7 @@ class ScalarFieldView(Plot3DWindow): """ return self._outerScale.scale - def setScale(self, sx=1., sy=1., sz=1.): + def setScale(self, sx=1.0, sy=1.0, sz=1.0): """Set the scale of the 3D scalar field (i.e., size of a voxel). :param float sx: Scale factor along the X axis @@ -1236,11 +1244,10 @@ class ScalarFieldView(Plot3DWindow): self.centerScene() # Reset viewpoint def getScale(self): - """Returns the scales provided by :meth:`setScale` as a numpy.ndarray. - """ + """Returns the scales provided by :meth:`setScale` as a numpy.ndarray.""" return self._dataScale.scale - def setTranslation(self, x=0., y=0., z=0.): + def setTranslation(self, x=0.0, y=0.0, z=0.0): """Set the translation of the origin of the data array in data coordinates. :param float x: Offset of the data origin on the X axis @@ -1254,8 +1261,7 @@ class ScalarFieldView(Plot3DWindow): self.centerScene() # Reset viewpoint def getTranslation(self): - """Returns the offset set by :meth:`setTranslation` as a numpy.ndarray. - """ + """Returns the offset set by :meth:`setTranslation` as a numpy.ndarray.""" return self._dataTranslate.translation def setTransformMatrix(self, matrix3x3): @@ -1346,9 +1352,7 @@ class ScalarFieldView(Plot3DWindow): :return: object describing the labels """ - return self._Labels((self._bbox.xlabel, - self._bbox.ylabel, - self._bbox.zlabel)) + return self._Labels((self._bbox.xlabel, self._bbox.ylabel, self._bbox.zlabel)) # Colors @@ -1356,7 +1360,7 @@ class ScalarFieldView(Plot3DWindow): """Update item depending on foreground/highlight color""" self._bbox.tickColor = self._foregroundColor self._selectionBox.strokeColor = self._foregroundColor - if self.getInteractiveMode() == 'plane': + if self.getInteractiveMode() == "plane": self._cutPlane.setStrokeColor(self._highlightColor) self._bbox.color = self._foregroundColor else: @@ -1435,18 +1439,17 @@ class ScalarFieldView(Plot3DWindow): elif None in (xrange_, yrange, zrange): # One of the range is None and no data available - raise RuntimeError( - 'Data is not set, cannot get default range from it.') + raise RuntimeError("Data is not set, cannot get default range from it.") # Clip selected region to data shape and make sure min <= max - selectedRange = numpy.array(( - (max(0, min(*zrange)), - min(self._data.shape[0], max(*zrange))), - (max(0, min(*yrange)), - min(self._data.shape[1], max(*yrange))), - (max(0, min(*xrange_)), - min(self._data.shape[2], max(*xrange_))), - ), dtype=numpy.int64) + selectedRange = numpy.array( + ( + (max(0, min(*zrange)), min(self._data.shape[0], max(*zrange))), + (max(0, min(*yrange)), min(self._data.shape[1], max(*yrange))), + (max(0, min(*xrange_)), min(self._data.shape[2], max(*xrange_))), + ), + dtype=numpy.int64, + ) # numpy.equal supports None if not numpy.all(numpy.equal(selectedRange, self._selectedRange)): @@ -1460,7 +1463,8 @@ class ScalarFieldView(Plot3DWindow): scales = self._selectedRange[:, 1] - self._selectedRange[:, 0] self._selectionBox.size = scales[::-1] self._selectionBox.transforms = [ - transform.Translate(*self._selectedRange[::-1, 0])] + transform.Translate(*self._selectedRange[::-1, 0]) + ] self.sigSelectedRegionChanged.emit(self.getSelectedRegion()) @@ -1470,10 +1474,14 @@ class ScalarFieldView(Plot3DWindow): return None else: dataBBox = self._group.transforms.transformBounds( - self._selectedRange[::-1].T).T - return SelectedRegion(self._selectedRange, dataBBox, - translation=self.getTranslation(), - scale=self.getScale()) + self._selectedRange[::-1].T + ).T + return SelectedRegion( + self._selectedRange, + dataBBox, + translation=self.getTranslation(), + scale=self.getScale(), + ) # Handle iso-surfaces @@ -1528,8 +1536,8 @@ class ScalarFieldView(Plot3DWindow): :param isosurface: The isosurface object to remove""" if isosurface not in self.getIsosurfaces(): _logger.warning( - "Try to remove isosurface that is not in the list: %s", - str(isosurface)) + "Try to remove isosurface that is not in the list: %s", str(isosurface) + ) else: isosurface.sigLevelChanged.disconnect(self._updateIsosurfaces) self._isosurfaces.remove(isosurface) @@ -1544,6 +1552,5 @@ class ScalarFieldView(Plot3DWindow): def _updateIsosurfaces(self, level=None): """Handle updates of iso-surfaces level and add/remove""" # Sorting using minus, this supposes data 'object' to be max values - sortedIso = sorted(self.getIsosurfaces(), - key=lambda iso: - iso.getLevel()) + sortedIso = sorted(self.getIsosurfaces(), key=lambda iso: -iso.getLevel()) self._isogroup.children = [iso._get3DPrimitive() for iso in sortedIso] |