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Diffstat (limited to 'silx/gui/plot3d/items/volume.py')
| -rw-r--r-- | silx/gui/plot3d/items/volume.py | 798 |
1 files changed, 0 insertions, 798 deletions
diff --git a/silx/gui/plot3d/items/volume.py b/silx/gui/plot3d/items/volume.py deleted file mode 100644 index ae91e82..0000000 --- a/silx/gui/plot3d/items/volume.py +++ /dev/null @@ -1,798 +0,0 @@ -# coding: utf-8 -# /*########################################################################## -# -# Copyright (c) 2017-2019 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 3D array item class and its sub-items. -""" - -from __future__ import absolute_import - -__authors__ = ["T. Vincent"] -__license__ = "MIT" -__date__ = "24/04/2018" - -import logging -import time -import numpy - -from silx.math.combo import min_max -from silx.math.marchingcubes import MarchingCubes - -from ....utils.proxy import docstring -from ... import _glutils as glu -from ... import qt -from ...colors import rgba - -from ..scene import cutplane, primitives, transform, utils - -from .core import BaseNodeItem, Item3D, ItemChangedType, Item3DChangedType -from .mixins import ColormapMixIn, ComplexMixIn, InterpolationMixIn, PlaneMixIn -from ._pick import PickingResult - - -_logger = logging.getLogger(__name__) - - -class CutPlane(Item3D, ColormapMixIn, InterpolationMixIn, PlaneMixIn): - """Class representing a cutting plane in a :class:`ScalarField3D` item. - - :param parent: 3D Data set in which the cut plane is applied. - """ - - def __init__(self, parent): - plane = cutplane.CutPlane(normal=(0, 1, 0)) - - Item3D.__init__(self, parent=None) - ColormapMixIn.__init__(self) - InterpolationMixIn.__init__(self) - PlaneMixIn.__init__(self, plane=plane) - - self._dataRange = None - self._data = None - - self._getScenePrimitive().children = [plane] - - # Connect scene primitive to mix-in class - ColormapMixIn._setSceneColormap(self, plane.colormap) - InterpolationMixIn._setPrimitive(self, plane) - - self.setParent(parent) - - def _updateData(self, data, range_): - """Update used dataset - - No copy is made. - - :param Union[numpy.ndarray[float],None] data: The dataset - :param Union[List[float],None] range_: - (min, min positive, max) values - """ - self._data = None if data is None else numpy.array(data, copy=False) - self._getPlane().setData(self._data, copy=False) - - # Store data range info as 3-tuple of values - self._dataRange = range_ - self._setRangeFromData( - None if self._dataRange is None else numpy.array(self._dataRange)) - - self._updated(ItemChangedType.DATA) - - def _syncDataWithParent(self): - """Synchronize this instance data with that of its parent""" - parent = self.parent() - if parent is None: - data, range_ = None, None - else: - data = parent.getData(copy=False) - range_ = parent.getDataRange() - self._updateData(data, range_) - - def _parentChanged(self, event): - """Handle data change in the parent this plane belongs to""" - if event == ItemChangedType.DATA: - self._syncDataWithParent() - - def setParent(self, parent): - oldParent = self.parent() - if isinstance(oldParent, Item3D): - oldParent.sigItemChanged.disconnect(self._parentChanged) - - super(CutPlane, self).setParent(parent) - - if isinstance(parent, Item3D): - parent.sigItemChanged.connect(self._parentChanged) - - self._syncDataWithParent() - - # Colormap - - def getDisplayValuesBelowMin(self): - """Return whether values <= colormap min are displayed or not. - - :rtype: bool - """ - return self._getPlane().colormap.displayValuesBelowMin - - def setDisplayValuesBelowMin(self, display): - """Set whether to display values <= colormap min. - - :param bool display: True to show values below min, - False to discard them - """ - display = bool(display) - if display != self.getDisplayValuesBelowMin(): - self._getPlane().colormap.displayValuesBelowMin = display - self._updated(ItemChangedType.ALPHA) - - def getDataRange(self): - """Return the range of the data as a 3-tuple of values. - - positive min is NaN if no data is positive. - - :return: (min, positive min, max) or None. - :rtype: Union[List[float],None] - """ - return None if self._dataRange is None else tuple(self._dataRange) - - def getData(self, copy=True): - """Return 3D dataset. - - :param bool copy: - True (default) to get a copy, - False to get the internal data (DO NOT modify!) - :return: The data set (or None if not set) - """ - if self._data is None: - return None - else: - return numpy.array(self._data, copy=copy) - - def _pickFull(self, context): - """Perform picking in this item at given widget position. - - :param PickContext context: Current picking context - :return: Object holding the results or None - :rtype: Union[None,PickingResult] - """ - rayObject = context.getPickingSegment(frame=self._getScenePrimitive()) - if rayObject is None: - return None - - points = utils.segmentPlaneIntersect( - rayObject[0, :3], - rayObject[1, :3], - planeNorm=self.getNormal(), - planePt=self.getPoint()) - - if len(points) == 1: # Single intersection - if numpy.any(points[0] < 0.): - return None # Outside volume - z, y, x = int(points[0][2]), int(points[0][1]), int(points[0][0]) - - data = self.getData(copy=False) - if data is None: - return None # No dataset - - depth, height, width = data.shape - if z < depth and y < height and x < width: - return PickingResult(self, - positions=[points[0]], - indices=([z], [y], [x])) - else: - return None # Outside image - else: # Either no intersection or segment and image are coplanar - return None - - -class Isosurface(Item3D): - """Class representing an iso-surface in a :class:`ScalarField3D` item. - - :param parent: The DataItem3D this iso-surface belongs to - """ - - def __init__(self, parent): - Item3D.__init__(self, parent=None) - self._data = None - self._level = float('nan') - self._autoLevelFunction = None - self._color = rgba('#FFD700FF') - self.setParent(parent) - - def _syncDataWithParent(self): - """Synchronize this instance data with that of its parent""" - parent = self.parent() - if parent is None: - self._data = None - else: - self._data = parent.getData(copy=False) - self._updateScenePrimitive() - - def _parentChanged(self, event): - """Handle data change in the parent this isosurface belongs to""" - if event == ItemChangedType.DATA: - self._syncDataWithParent() - - def setParent(self, parent): - oldParent = self.parent() - if isinstance(oldParent, Item3D): - oldParent.sigItemChanged.disconnect(self._parentChanged) - - super(Isosurface, self).setParent(parent) - - if isinstance(parent, Item3D): - parent.sigItemChanged.connect(self._parentChanged) - - self._syncDataWithParent() - - def getData(self, copy=True): - """Return 3D dataset. - - :param bool copy: - True (default) to get a copy, - False to get the internal data (DO NOT modify!) - :return: The data set (or None if not set) - """ - if self._data is None: - return None - else: - return numpy.array(self._data, copy=copy) - - def getLevel(self): - """Return the level of this iso-surface (float)""" - return self._level - - def setLevel(self, level): - """Set the value at which to build the iso-surface. - - Setting this value reset auto-level function - - :param float level: The value at which to build the iso-surface - """ - self._autoLevelFunction = None - level = float(level) - if level != self._level: - self._level = level - self._updateScenePrimitive() - self._updated(Item3DChangedType.ISO_LEVEL) - - def isAutoLevel(self): - """True if iso-level is rebuild for each data set.""" - return self.getAutoLevelFunction() is not None - - def getAutoLevelFunction(self): - """Return the function computing the iso-level (callable or None)""" - return self._autoLevelFunction - - def setAutoLevelFunction(self, autoLevel): - """Set the function used to compute the iso-level. - - WARNING: The function might get called in a thread. - - :param callable autoLevel: - A function taking a 3D numpy.ndarray of float32 and returning - a float used as iso-level. - Example: numpy.mean(data) + numpy.std(data) - """ - assert callable(autoLevel) - self._autoLevelFunction = autoLevel - self._updateScenePrimitive() - - def getColor(self): - """Return the color of this iso-surface (QColor)""" - return qt.QColor.fromRgbF(*self._color) - - def setColor(self, color): - """Set the color of the iso-surface - - :param color: RGBA color of the isosurface - :type color: QColor, str or array-like of 4 float in [0., 1.] - """ - color = rgba(color) - if color != self._color: - self._color = color - primitive = self._getScenePrimitive() - if len(primitive.children) != 0: - primitive.children[0].setAttribute('color', self._color) - self._updated(ItemChangedType.COLOR) - - def _updateScenePrimitive(self): - """Update underlying mesh""" - self._getScenePrimitive().children = [] - - data = self.getData(copy=False) - - if data is None: - if self.isAutoLevel(): - self._level = float('nan') - - else: - if self.isAutoLevel(): - st = time.time() - try: - level = float(self.getAutoLevelFunction()(data)) - - except Exception: - module_ = self.getAutoLevelFunction().__module__ - name = self.getAutoLevelFunction().__name__ - _logger.error( - "Error while executing iso level function %s.%s", - module_, - name, - exc_info=True) - level = float('nan') - - else: - _logger.info( - 'Computed iso-level in %f s.', time.time() - st) - - if level != self._level: - self._level = level - self._updated(Item3DChangedType.ISO_LEVEL) - - if not numpy.isfinite(self._level): - return - - st = time.time() - vertices, normals, indices = MarchingCubes( - 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) - self._getScenePrimitive().children = [mesh] - - def _pickFull(self, context): - """Perform picking in this item at given widget position. - - :param PickContext context: Current picking context - :return: Object holding the results or None - :rtype: Union[None,PickingResult] - """ - rayObject = context.getPickingSegment(frame=self._getScenePrimitive()) - if rayObject is None: - return None - rayObject = rayObject[:, :3] - - data = self.getData(copy=False) - bins = utils.segmentVolumeIntersect( - rayObject, numpy.array(data.shape) - 1) - if bins is None: - return None - - # gather bin data - offsets = [(i, j, k) for i in (0, 1) for j in (0, 1) for k in (0, 1)] - indices = bins[:, numpy.newaxis, :] + offsets - binsData = data[indices[:, :, 0], indices[:, :, 1], indices[:, :, 2]] - # binsData.shape = nbins, 8 - # TODO up-to this point everything can be done once for all isosurfaces - - # check bin candidates - level = self.getLevel() - mask = numpy.logical_and(numpy.nanmin(binsData, axis=1) <= level, - level <= numpy.nanmax(binsData, axis=1)) - bins = bins[mask] - binsData = binsData[mask] - - if len(bins) == 0: - return None # No bin candidate - - # do picking on candidates - intersections = [] - depths = [] - for currentBin, data in zip(bins, binsData): - mc = MarchingCubes(data.reshape(2, 2, 2), isolevel=level) - points = mc.get_vertices() + currentBin - triangles = points[mc.get_indices()] - t = glu.segmentTrianglesIntersection(rayObject, triangles)[1] - t = numpy.unique(t) # Duplicates happen on triangle edges - if len(t) != 0: - # Compute intersection points and get closest data point - points = t.reshape(-1, 1) * (rayObject[1] - rayObject[0]) + rayObject[0] - # Get closest data points by rounding to int - intersections.extend(points) - depths.extend(t) - - if len(intersections) == 0: - return None # No intersected triangles - - intersections = numpy.array(intersections)[numpy.argsort(depths)] - indices = numpy.transpose(numpy.round(intersections).astype(numpy.int)) - return PickingResult(self, positions=intersections, indices=indices) - - -class ScalarField3D(BaseNodeItem): - """3D scalar field on a regular grid. - - :param parent: The View widget this item belongs to. - """ - - _CutPlane = CutPlane - """CutPlane class associated to this class""" - - _Isosurface = Isosurface - """Isosurface classe associated to this class""" - - def __init__(self, parent=None): - BaseNodeItem.__init__(self, parent=parent) - - # Gives this item the shape of the data, no matter - # of the isosurface/cut plane size - self._boundedGroup = primitives.BoundedGroup() - - # Store iso-surfaces - self._isosurfaces = [] - - self._data = None - self._dataRange = None - - self._cutPlane = self._CutPlane(parent=self) - self._cutPlane.setVisible(False) - - 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.))), - # Offset to match cutting plane coords - transform.Translate(0.5, 0.5, 0.5) - ] - - self._getScenePrimitive().children = [ - self._boundedGroup, - self._cutPlane._getScenePrimitive(), - self._isogroup] - - @staticmethod - def _computeRangeFromData(data): - """Compute range info (min, min positive, max) from data - - :param Union[numpy.ndarray,None] data: - :return: Union[List[float],None] - """ - if data is None: - return None - - dataRange = min_max(data, min_positive=True, finite=True) - if dataRange.minimum is None: # Only non-finite data - return None - - if dataRange is not None: - min_positive = dataRange.min_positive - if min_positive is None: - min_positive = float('nan') - return dataRange.minimum, min_positive, dataRange.maximum - - def setData(self, data, copy=True): - """Set the 3D scalar data represented by this item. - - Dataset order is zyx (i.e., first dimension is z). - - :param data: 3D array - :type data: 3D numpy.ndarray of float32 with shape at least (2, 2, 2) - :param bool copy: - True (default) to make a copy, - False to avoid copy (DO NOT MODIFY data afterwards) - """ - if data is None: - self._data = None - self._boundedGroup.shape = None - - else: - data = numpy.array(data, copy=copy, dtype=numpy.float32, order='C') - assert data.ndim == 3 - assert min(data.shape) >= 2 - - self._data = data - self._boundedGroup.shape = self._data.shape - - self._dataRange = self._computeRangeFromData(self._data) - self._updated(ItemChangedType.DATA) - - def getData(self, copy=True): - """Return 3D dataset. - - :param bool copy: - True (default) to get a copy, - False to get the internal data (DO NOT modify!) - :return: The data set (or None if not set) - """ - if self._data is None: - return None - else: - return numpy.array(self._data, copy=copy) - - def getDataRange(self): - """Return the range of the data as a 3-tuple of values. - - positive min is NaN if no data is positive. - - :return: (min, positive min, max) or None. - """ - return self._dataRange - - # Cut Plane - - def getCutPlanes(self): - """Return an iterable of all :class:`CutPlane` of this item. - - This includes hidden cut planes. - - For now, there is always one cut plane. - """ - return (self._cutPlane,) - - # Handle iso-surfaces - - # TODO rename to sigItemAdded|Removed? - sigIsosurfaceAdded = qt.Signal(object) - """Signal emitted when a new iso-surface is added to the view. - - The newly added iso-surface is provided by this signal - """ - - sigIsosurfaceRemoved = qt.Signal(object) - """Signal emitted when an iso-surface is removed from the view - - The removed iso-surface is provided by this signal. - """ - - def addIsosurface(self, level, color): - """Add an isosurface to this item. - - :param level: - The value at which to build the iso-surface or a callable - (e.g., a function) taking a 3D numpy.ndarray as input and - returning a float. - Example: numpy.mean(data) + numpy.std(data) - :type level: float or callable - :param color: RGBA color of the isosurface - :type color: str or array-like of 4 float in [0., 1.] - :return: isosurface object - :rtype: ~silx.gui.plot3d.items.volume.Isosurface - """ - isosurface = self._Isosurface(parent=self) - isosurface.setColor(color) - if callable(level): - isosurface.setAutoLevelFunction(level) - else: - isosurface.setLevel(level) - isosurface.sigItemChanged.connect(self._isosurfaceItemChanged) - - self._isosurfaces.append(isosurface) - - self._updateIsosurfaces() - - self.sigIsosurfaceAdded.emit(isosurface) - return isosurface - - def getIsosurfaces(self): - """Return an iterable of all :class:`.Isosurface` instance of this item""" - return tuple(self._isosurfaces) - - def removeIsosurface(self, isosurface): - """Remove an iso-surface from this item. - - :param ~silx.gui.plot3d.Plot3DWidget.Isosurface 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)) - else: - isosurface.sigItemChanged.disconnect(self._isosurfaceItemChanged) - self._isosurfaces.remove(isosurface) - self._updateIsosurfaces() - self.sigIsosurfaceRemoved.emit(isosurface) - - def clearIsosurfaces(self): - """Remove all :class:`.Isosurface` instances from this item.""" - for isosurface in self.getIsosurfaces(): - self.removeIsosurface(isosurface) - - def _isosurfaceItemChanged(self, event): - """Handle update of isosurfaces upon level changed""" - if event == Item3DChangedType.ISO_LEVEL: - self._updateIsosurfaces() - - def _updateIsosurfaces(self): - """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 isosurface: - isosurface.getLevel()) - self._isogroup.children = [iso._getScenePrimitive() for iso in sortedIso] - - # BaseNodeItem - - def getItems(self): - """Returns the list of items currently present in this item. - - :rtype: tuple - """ - return self.getCutPlanes() + self.getIsosurfaces() - - -################## -# ComplexField3D # -################## - -class ComplexCutPlane(CutPlane, ComplexMixIn): - """Class representing a cutting plane in a :class:`ComplexField3D` item. - - :param parent: 3D Data set in which the cut plane is applied. - """ - - def __init__(self, parent): - ComplexMixIn.__init__(self) - CutPlane.__init__(self, parent=parent) - - def _syncDataWithParent(self): - """Synchronize this instance data with that of its parent""" - parent = self.parent() - if parent is None: - data, range_ = None, None - else: - mode = self.getComplexMode() - data = parent.getData(mode=mode, copy=False) - range_ = parent.getDataRange(mode=mode) - self._updateData(data, range_) - - def _updated(self, event=None): - """Handle update of the cut plane (and take care of mode change - - :param Union[None,ItemChangedType] event: The kind of update - """ - if event == ItemChangedType.COMPLEX_MODE: - self._syncDataWithParent() - super(ComplexCutPlane, self)._updated(event) - - -class ComplexIsosurface(Isosurface): - """Class representing an iso-surface in a :class:`ComplexField3D` item. - - :param parent: The DataItem3D this iso-surface belongs to - """ - - def __init__(self, parent): - super(ComplexIsosurface, self).__init__(parent) - - def _syncDataWithParent(self): - """Synchronize this instance data with that of its parent""" - parent = self.parent() - if parent is None: - self._data = None - else: - self._data = parent.getData( - mode=parent.getComplexMode(), copy=False) - self._updateScenePrimitive() - - def _parentChanged(self, event): - """Handle data change in the parent this isosurface belongs to""" - if event == ItemChangedType.COMPLEX_MODE: - self._syncDataWithParent() - super(ComplexIsosurface, self)._parentChanged(event) - - -class ComplexField3D(ScalarField3D, ComplexMixIn): - """3D complex field on a regular grid. - - :param parent: The View widget this item belongs to. - """ - - _CutPlane = ComplexCutPlane - _Isosurface = ComplexIsosurface - - def __init__(self, parent=None): - self._dataRangeCache = None - - ComplexMixIn.__init__(self) - ScalarField3D.__init__(self, parent=parent) - - @docstring(ComplexMixIn) - def setComplexMode(self, mode): - if mode != self.getComplexMode(): - self.clearIsosurfaces() # Reset isosurfaces - ComplexMixIn.setComplexMode(self, mode) - - def setData(self, data, copy=True): - """Set the 3D complex data represented by this item. - - Dataset order is zyx (i.e., first dimension is z). - - :param data: 3D array - :type data: 3D numpy.ndarray of float32 with shape at least (2, 2, 2) - :param bool copy: - True (default) to make a copy, - False to avoid copy (DO NOT MODIFY data afterwards) - """ - if data is None: - self._data = None - self._dataRangeCache = None - self._boundedGroup.shape = None - - else: - data = numpy.array(data, copy=copy, dtype=numpy.complex64, order='C') - assert data.ndim == 3 - assert min(data.shape) >= 2 - - self._data = data - self._dataRangeCache = {} - self._boundedGroup.shape = self._data.shape - - self._updated(ItemChangedType.DATA) - - def getData(self, copy=True, mode=None): - """Return 3D dataset. - - This method does not cache data converted to a specific mode, - it computes it for each request. - - :param bool copy: - True (default) to get a copy, - False to get the internal data (DO NOT modify!) - :param Union[None,Mode] mode: - The kind of data to retrieve. - If None (the default), it returns the complex data, - else it computes the requested scalar data. - :return: The data set (or None if not set) - :rtype: Union[numpy.ndarray,None] - """ - if mode is None: - return super(ComplexField3D, self).getData(copy=copy) - else: - return self._convertComplexData(self._data, mode) - - def getDataRange(self, mode=None): - """Return the range of the requested data as a 3-tuple of values. - - Positive min is NaN if no data is positive. - - :param Union[None,Mode] mode: - The kind of data for which to get the range information. - If None (the default), it returns the data range for the current mode, - else it returns the data range for the requested mode. - :return: (min, positive min, max) or None. - :rtype: Union[None,List[float]] - """ - if self._dataRangeCache is None: - return None - - if mode is None: - mode = self.getComplexMode() - - if mode not in self._dataRangeCache: - # Compute it and store it in cache - data = self.getData(copy=False, mode=mode) - self._dataRangeCache[mode] = self._computeRangeFromData(data) - - return self._dataRangeCache[mode] |