New upstream version 0.8.0+dfsg

16 files changed, 456 insertions, 57 deletions

diff --git a/silx/gui/plot3d/Plot3DWidget.py b/silx/gui/plot3d/Plot3DWidget.py
index 15e2356..53ff895 100644
--- a/silx/gui/plot3d/Plot3DWidget.py
+++ b/silx/gui/plot3d/Plot3DWidget.py
@@ -28,15 +28,15 @@ from __future__ import absolute_import
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "26/01/2017"
+__date__ = "24/04/2018"
 
 
 import logging
 
 from silx.gui import qt
-from silx.gui.plot.Colors import rgba
+from silx.gui.colors import rgba
 from . import actions
-from .._utils import convertArrayToQImage
+from ..utils._image import convertArrayToQImage
 
 from .. import _glutils as glu
 from .scene import interaction, primitives, transform
diff --git a/silx/gui/plot3d/SFViewParamTree.py b/silx/gui/plot3d/SFViewParamTree.py
index 314e5a1..bb81465 100644
--- a/silx/gui/plot3d/SFViewParamTree.py
+++ b/silx/gui/plot3d/SFViewParamTree.py
@@ -30,7 +30,7 @@ from __future__ import absolute_import
 
 __authors__ = ["D. N."]
 __license__ = "MIT"
-__date__ = "02/10/2017"
+__date__ = "24/04/2018"
 
 import logging
 import sys
@@ -40,7 +40,7 @@ import numpy
 
 from silx.gui import qt
 from silx.gui.icons import getQIcon
-from silx.gui.plot.Colormap import Colormap
+from silx.gui.colors import Colormap
 from silx.gui.widgets.FloatEdit import FloatEdit
 
 from .ScalarFieldView import Isosurface
@@ -1024,13 +1024,13 @@ class IsoSurfaceAddRemoveWidget(qt.QWidget):
         layout.setContentsMargins(0, 0, 0, 0)
         layout.setSpacing(0)
 
-        addBtn = qt.QToolButton()
+        addBtn = qt.QToolButton(self)
         addBtn.setText('+')
         addBtn.setToolButtonStyle(qt.Qt.ToolButtonTextOnly)
         layout.addWidget(addBtn)
         addBtn.clicked.connect(self.__addClicked)
 
-        removeBtn = qt.QToolButton()
+        removeBtn = qt.QToolButton(self)
         removeBtn.setText('-')
         removeBtn.setToolButtonStyle(qt.Qt.ToolButtonTextOnly)
         layout.addWidget(removeBtn)
diff --git a/silx/gui/plot3d/ScalarFieldView.py b/silx/gui/plot3d/ScalarFieldView.py
index a41999b..e5e680c 100644
--- a/silx/gui/plot3d/ScalarFieldView.py
+++ b/silx/gui/plot3d/ScalarFieldView.py
@@ -32,7 +32,7 @@ from __future__ import absolute_import
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "10/01/2017"
+__date__ = "14/06/2018"
 
 import re
 import logging
@@ -42,8 +42,8 @@ from collections import deque
 import numpy
 
 from silx.gui import qt, icons
-from silx.gui.plot.Colors import rgba
-from silx.gui.plot.Colormap import Colormap
+from silx.gui.colors import rgba
+from silx.gui.colors import Colormap
 
 from silx.math.marchingcubes import MarchingCubes
 from silx.math.combo import min_max
@@ -643,7 +643,7 @@ class CutPlane(qt.QObject):
         """Returns the colormap set by :meth:`setColormap`.
 
         :return: The colormap
-        :rtype: ~silx.gui.plot.Colormap.Colormap
+        :rtype: ~silx.gui.colors.Colormap
         """
         return self._colormap
 
@@ -660,7 +660,7 @@ class CutPlane(qt.QObject):
         :param name: Name of the colormap in
             'gray', 'reversed gray', 'temperature', 'red', 'green', 'blue'.
             Or Colormap object.
-        :type name: str or ~silx.gui.plot.Colormap.Colormap
+        :type name: str or ~silx.gui.colors.Colormap
         :param str norm: Colormap mapping: 'linear' or 'log'.
         :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
diff --git a/silx/gui/plot3d/SceneWidget.py b/silx/gui/plot3d/SceneWidget.py
index 4e75515..f005dec 100644
--- a/silx/gui/plot3d/SceneWidget.py
+++ b/silx/gui/plot3d/SceneWidget.py
@@ -28,14 +28,14 @@ from __future__ import absolute_import
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "26/10/2017"
+__date__ = "24/04/2018"
 
 import numpy
 import weakref
 
 from silx.third_party import enum
 from .. import qt
-from ..plot.Colors import rgba
+from ..colors import rgba
 
 from .Plot3DWidget import Plot3DWidget
 from . import items
@@ -567,7 +567,7 @@ class SceneWidget(Plot3DWidget):
 
     def clearItems(self):
         """Remove all item from :class:`SceneWidget`."""
-        return self.getSceneGroup().clear()
+        return self.getSceneGroup().clearItems()
 
     # Colors
 
diff --git a/silx/gui/plot3d/SceneWindow.py b/silx/gui/plot3d/SceneWindow.py
index 5121a17..56fb21f 100644
--- a/silx/gui/plot3d/SceneWindow.py
+++ b/silx/gui/plot3d/SceneWindow.py
@@ -163,6 +163,13 @@ class SceneWindow(qt.QMainWindow):
         """
         return self._sceneWidget
 
+    def getGroupResetWidget(self):
+        """Returns the :class:`GroupPropertiesWidget` of this window.
+
+        :rtype: GroupPropertiesWidget
+        """
+        return self._sceneGroupResetWidget
+
     def getParamTreeView(self):
         """Returns the :class:`ParamTreeView` of this window.
 
@@ -173,20 +180,20 @@ class SceneWindow(qt.QMainWindow):
     def getInteractiveModeToolBar(self):
         """Returns the interactive mode toolbar.
 
-        :rtype: InteractiveModeToolBar
+        :rtype: ~silx.gui.plot3d.tools.InteractiveModeToolBar
         """
         return self._interactiveModeToolBar
 
     def getViewpointToolBar(self):
         """Returns the viewpoint toolbar.
 
-        :rtype: ViewpointToolBar
+        :rtype: ~silx.gui.plot3d.tools.ViewpointToolBar
         """
         return self._viewpointToolBar
 
     def getOutputToolBar(self):
         """Returns the output toolbar.
 
-        :rtype: OutputToolBar
+        :rtype: ~silx.gui.plot3d.tools.OutputToolBar
         """
         return self._outputToolBar
diff --git a/silx/gui/plot3d/_model/items.py b/silx/gui/plot3d/_model/items.py
index 7009ea1..02485fe 100644
--- a/silx/gui/plot3d/_model/items.py
+++ b/silx/gui/plot3d/_model/items.py
@@ -30,18 +30,19 @@ from __future__ import absolute_import, division
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "11/01/2018"
+__date__ = "24/04/2018"
 
 
 import functools
+import logging
 import weakref
 
 import numpy
 
 from silx.third_party import six
 
-from ..._utils import convertArrayToQImage
-from ...plot.Colormap import preferredColormaps
+from ...utils._image import convertArrayToQImage
+from ...colors import preferredColormaps
 from ... import qt, icons
 from .. import items
 from ..items.volume import Isosurface, CutPlane
@@ -50,6 +51,9 @@ from ..items.volume import Isosurface, CutPlane
 from .core import AngleDegreeRow, BaseRow, ColorProxyRow, ProxyRow, StaticRow
 
 
+_logger = logging.getLogger(__name__)
+
+
 class _DirectionalLightProxy(qt.QObject):
     """Proxy to handle directional light with angles rather than vector.
     """
@@ -472,7 +476,11 @@ class DataItem3DTransformRow(StaticRow):
         """
         item = self.item()
         if item is not None:
-            item.setScale(scale.x(), scale.y(), scale.z())
+            sx, sy, sz = scale.x(), scale.y(), scale.z()
+            if sx == 0. or sy == 0. or sz == 0.:
+                _logger.warning('Cannot set scale to 0: ignored')
+            else:
+                item.setScale(scale.x(), scale.y(), scale.z())
 
 
 class GroupItemRow(Item3DRow):
@@ -519,7 +527,7 @@ class GroupItemRow(Item3DRow):
 
         # Find item
         for row in self.children():
-            if row.item() is item:
+            if isinstance(row, Item3DRow) and row.item() is item:
                 self.removeRow(row)
                 break  # Got it
         else:
@@ -764,7 +772,7 @@ class ColormapRow(_ColormapBaseProxyRow):
 
     def _getName(self):
         """Proxy for :meth:`Colormap.getName`"""
-        if self._colormap is not None:
+        if self._colormap is not None and self._colormap.getName() is not None:
             return self._colormap.getName().title()
         else:
             return ''
diff --git a/silx/gui/plot3d/actions/io.py b/silx/gui/plot3d/actions/io.py
index 5126000..f30abeb 100644
--- a/silx/gui/plot3d/actions/io.py
+++ b/silx/gui/plot3d/actions/io.py
@@ -39,12 +39,11 @@ import os
 
 import numpy
 
-from silx.gui import qt
-from silx.gui.plot.actions.io import PrintAction as _PrintAction
+from silx.gui import qt, printer
 from silx.gui.icons import getQIcon
 from .Plot3DAction import Plot3DAction
 from ..utils import mng
-from ..._utils import convertQImageToArray
+from ...utils._image import convertQImageToArray
 
 
 _logger = logging.getLogger(__name__)
@@ -157,11 +156,7 @@ class PrintAction(Plot3DAction):
 
         :rtype: QPrinter
         """
-        # TODO This is a hack to sync with silx plot PrintAction
-        # This needs to be centralized
-        if _PrintAction._printer is None:
-            _PrintAction._printer = qt.QPrinter()
-        return _PrintAction._printer
+        return printer.getDefaultPrinter()
 
     def _triggered(self, checked=False):
         plot3d = self.getPlot3DWidget()
diff --git a/silx/gui/plot3d/items/__init__.py b/silx/gui/plot3d/items/__init__.py
index b50ea5a..b2a9dab 100644
--- a/silx/gui/plot3d/items/__init__.py
+++ b/silx/gui/plot3d/items/__init__.py
@@ -38,6 +38,6 @@ from .mixins import (ColormapMixIn, InterpolationMixIn,  # noqa
                      PlaneMixIn, SymbolMixIn)  # noqa
 from .clipplane import ClipPlane  # noqa
 from .image import ImageData, ImageRgba  # noqa
-from .mesh import Mesh  # noqa
+from .mesh import Mesh, Box, Cylinder, Hexagon  # noqa
 from .scatter import Scatter2D, Scatter3D  # noqa
 from .volume import ScalarField3D  # noqa
diff --git a/silx/gui/plot3d/items/mesh.py b/silx/gui/plot3d/items/mesh.py
index 8535728..12a3941 100644
--- a/silx/gui/plot3d/items/mesh.py
+++ b/silx/gui/plot3d/items/mesh.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2017 European Synchrotron Radiation Facility
+# 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
@@ -35,6 +35,7 @@ import numpy
 
 from ..scene import primitives
 from .core import DataItem3D, ItemChangedType
+from ..scene.transform import Rotate
 
 
 class Mesh(DataItem3D):
@@ -143,3 +144,396 @@ class Mesh(DataItem3D):
         :rtype: str
         """
         return self._mesh.drawMode
+
+
+class _CylindricalVolume(DataItem3D):
+    """Class that represents a volume with a rotational symmetry along z
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        DataItem3D.__init__(self, parent=parent)
+        self._mesh = None
+
+    def _setData(self, position, radius, height, angles, color, flatFaces,
+                 rotation):
+        """Set volume geometry data.
+
+        :param numpy.ndarray position:
+            Center position (x, y, z) of each volume as (N, 3) array.
+        :param float radius: External radius ot the volume.
+        :param float height: Height of the volume(s).
+        :param numpy.ndarray angles: Angles of the edges.
+        :param numpy.array color: RGB color of the volume(s).
+        :param bool flatFaces:
+            If the volume as flat faces or not. Used for normals calculation.
+        """
+
+        self._getScenePrimitive().children = []  # Remove any previous mesh
+
+        if position is None or len(position) == 0:
+            self._mesh = 0
+        else:
+            volume = numpy.empty(shape=(len(angles) - 1, 12, 3),
+                                 dtype=numpy.float32)
+            normal = numpy.empty(shape=(len(angles) - 1, 12, 3),
+                                 dtype=numpy.float32)
+
+            for i in range(0, len(angles) - 1):
+                """
+                       c6
+                       /\
+                      /  \
+                     /    \
+                  c4|------|c5
+                    | \    |
+                    |  \   |
+                    |   \  |
+                    |    \ |
+                  c2|------|c3
+                     \    /
+                      \  /
+                       \/
+                       c1     
+                """
+                c1 = numpy.array([0, 0, -height/2])
+                c1 = rotation.transformPoint(c1)
+                c2 = numpy.array([radius * numpy.cos(angles[i]),
+                                  radius * numpy.sin(angles[i]),
+                                  -height/2])
+                c2 = rotation.transformPoint(c2)
+                c3 = numpy.array([radius * numpy.cos(angles[i+1]),
+                                  radius * numpy.sin(angles[i+1]),
+                                  -height/2])
+                c3 = rotation.transformPoint(c3)
+                c4 = numpy.array([radius * numpy.cos(angles[i]),
+                                  radius * numpy.sin(angles[i]),
+                                  height/2])
+                c4 = rotation.transformPoint(c4)
+                c5 = numpy.array([radius * numpy.cos(angles[i+1]),
+                                  radius * numpy.sin(angles[i+1]),
+                                  height/2])
+                c5 = rotation.transformPoint(c5)
+                c6 = numpy.array([0, 0, height/2])
+                c6 = rotation.transformPoint(c6)
+
+                volume[i] = numpy.array([c1, c3, c2,
+                                         c2, c3, c4,
+                                         c3, c5, c4,
+                                         c4, c5, c6])
+                if flatFaces:
+                    normal[i] = numpy.array([numpy.cross(c3-c1, c2-c1),  # c1
+                                             numpy.cross(c2-c3, c1-c3),  # c3
+                                             numpy.cross(c1-c2, c3-c2),  # c2
+                                             numpy.cross(c3-c2, c4-c2),  # c2
+                                             numpy.cross(c4-c3, c2-c3),  # c3
+                                             numpy.cross(c2-c4, c3-c4),  # c4
+                                             numpy.cross(c5-c3, c4-c3),  # c3
+                                             numpy.cross(c4-c5, c3-c5),  # c5
+                                             numpy.cross(c3-c4, c5-c4),  # c4
+                                             numpy.cross(c5-c4, c6-c4),  # c4
+                                             numpy.cross(c6-c5, c5-c5),  # c5
+                                             numpy.cross(c4-c6, c5-c6)])  # c6
+                else:
+                    normal[i] = numpy.array([numpy.cross(c3-c1, c2-c1),
+                                             numpy.cross(c2-c3, c1-c3),
+                                             numpy.cross(c1-c2, c3-c2),
+                                             c2-c1, c3-c1, c4-c6,  # c2 c2 c4
+                                             c3-c1, c5-c6, c4-c6,  # c3 c5 c4
+                                             numpy.cross(c5-c4, c6-c4),
+                                             numpy.cross(c6-c5, c5-c5),
+                                             numpy.cross(c4-c6, c5-c6)])
+
+            # Multiplication according to the number of positions
+            vertices = numpy.tile(volume.reshape(-1, 3), (len(position), 1))\
+                .reshape((-1, 3))
+            normals = numpy.tile(normal.reshape(-1, 3), (len(position), 1))\
+                .reshape((-1, 3))
+
+            # Translations
+            numpy.add(vertices, numpy.tile(position, (1, (len(angles)-1) * 12))
+                      .reshape((-1, 3)), out=vertices)
+
+            # Colors
+            if numpy.ndim(color) == 2:
+                color = numpy.tile(color, (1, 12 * (len(angles) - 1)))\
+                    .reshape(-1, 3)
+
+            self._mesh = primitives.Mesh3D(
+                vertices, color, normals, mode='triangles', copy=False)
+            self._getScenePrimitive().children.append(self._mesh)
+
+        self.sigItemChanged.emit(ItemChangedType.DATA)
+
+
+class Box(_CylindricalVolume):
+    """Description of a box.
+
+    Can be used to draw one box or many similar boxes.
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        super(Box, self).__init__(parent)
+        self.position = None
+        self.size = None
+        self.color = None
+        self.rotation = None
+        self.setData()
+
+    def setData(self, size=(1, 1, 1), color=(1, 1, 1),
+                position=(0, 0, 0), rotation=(0, (0, 0, 0))):
+        """
+        Set Box geometry data.
+
+        :param numpy.array size: Size (dx, dy, dz) of the box(es).
+        :param numpy.array color: RGB color of the box(es).
+        :param numpy.ndarray position:
+            Center position (x, y, z) of each box as a (N, 3) array.
+        :param tuple(float, array) rotation:
+                Angle (in degrees) and axis of rotation.
+                If (0, (0, 0, 0)) (default), the hexagonal faces are on
+                xy plane and a side face is aligned with x axis.
+        """
+        self.position = numpy.atleast_2d(numpy.array(position, copy=True))
+        self.size = numpy.array(size, copy=True)
+        self.color = numpy.array(color, copy=True)
+        self.rotation = Rotate(rotation[0],
+                               rotation[1][0], rotation[1][1], rotation[1][2])
+
+        assert (numpy.ndim(self.color) == 1 or
+                len(self.color) == len(self.position))
+
+        diagonal = numpy.sqrt(self.size[0]**2 + self.size[1]**2)
+        alpha = 2 * numpy.arcsin(self.size[1] / diagonal)
+        beta = 2 * numpy.arcsin(self.size[0] / diagonal)
+        angles = numpy.array([0,
+                              alpha,
+                              alpha + beta,
+                              alpha + beta + alpha,
+                              2 * numpy.pi])
+        numpy.subtract(angles, 0.5 * alpha, out=angles)
+        self._setData(self.position,
+                      numpy.sqrt(self.size[0]**2 + self.size[1]**2)/2,
+                      self.size[2],
+                      angles,
+                      self.color,
+                      True,
+                      self.rotation)
+
+    def getPosition(self, copy=True):
+        """Get box(es) position(s).
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        :return: Position of the box(es) as a (N, 3) array.
+        :rtype: numpy.ndarray
+        """
+        return numpy.array(self.position, copy=copy)
+
+    def getSize(self):
+        """Get box(es) size.
+
+        :return: Size (dx, dy, dz) of the box(es).
+        :rtype: numpy.ndarray
+        """
+        return numpy.array(self.size, copy=True)
+
+    def getColor(self, copy=True):
+        """Get box(es) color.
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        :return: RGB color of the box(es).
+        :rtype: numpy.ndarray
+        """
+        return numpy.array(self.color, copy=copy)
+
+
+class Cylinder(_CylindricalVolume):
+    """Description of a cylinder.
+
+    Can be used to draw one cylinder or many similar cylinders.
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        super(Cylinder, self).__init__(parent)
+        self.position = None
+        self.radius = None
+        self.height = None
+        self.color = None
+        self.nbFaces = 0
+        self.rotation = None
+        self.setData()
+
+    def setData(self, radius=1, height=1, color=(1, 1, 1), nbFaces=20,
+                position=(0, 0, 0), rotation=(0, (0, 0, 0))):
+        """
+        Set the cylinder geometry data
+
+        :param float radius: Radius of the cylinder(s).
+        :param float height: Height of the cylinder(s).
+        :param numpy.array color: RGB color of the cylinder(s).
+        :param int nbFaces:
+            Number of faces for cylinder approximation (default 20).
+        :param numpy.ndarray position:
+            Center position (x, y, z) of each cylinder as a (N, 3) array.
+        :param tuple(float, array) rotation:
+                Angle (in degrees) and axis of rotation.
+                If (0, (0, 0, 0)) (default), the hexagonal faces are on
+                xy plane and a side face is aligned with x axis.
+        """
+        self.position = numpy.atleast_2d(numpy.array(position, copy=True))
+        self.radius = float(radius)
+        self.height = float(height)
+        self.color = numpy.array(color, copy=True)
+        self.nbFaces = int(nbFaces)
+        self.rotation = Rotate(rotation[0],
+                               rotation[1][0], rotation[1][1], rotation[1][2])
+
+        assert (numpy.ndim(self.color) == 1 or
+                len(self.color) == len(self.position))
+
+        angles = numpy.linspace(0, 2*numpy.pi, self.nbFaces + 1)
+        self._setData(self.position,
+                      self.radius,
+                      self.height,
+                      angles,
+                      self.color,
+                      False,
+                      self.rotation)
+
+    def getPosition(self, copy=True):
+        """Get cylinder(s) position(s).
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        :return: Position(s) of the cylinder(s) as a (N, 3) array.
+        :rtype: numpy.ndarray
+        """
+        return numpy.array(self.position, copy=copy)
+
+    def getRadius(self):
+        """Get cylinder(s) radius.
+
+        :return: Radius of the cylinder(s).
+        :rtype: float
+        """
+        return self.radius
+
+    def getHeight(self):
+        """Get cylinder(s) height.
+
+        :return: Height of the cylinder(s).
+        :rtype: float
+        """
+        return self.height
+
+    def getColor(self, copy=True):
+        """Get cylinder(s) color.
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        :return: RGB color of the cylinder(s).
+        :rtype: numpy.ndarray
+        """
+        return numpy.array(self.color, copy=copy)
+
+
+class Hexagon(_CylindricalVolume):
+    """Description of a uniform hexagonal prism.
+
+    Can be used to draw one hexagonal prim or many similar hexagonal
+    prisms.
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        super(Hexagon, self).__init__(parent)
+        self.position = None
+        self.radius = 0
+        self.height = 0
+        self.color = None
+        self.rotation = None
+        self.setData()
+
+    def setData(self, radius=1, height=1, color=(1, 1, 1),
+                position=(0, 0, 0), rotation=(0, (0, 0, 0))):
+        """
+        Set the uniform hexagonal prism geometry data
+
+        :param float radius: External radius of the hexagonal prism
+        :param float height: Height of the hexagonal prism
+        :param numpy.array color: RGB color of the prism(s)
+        :param numpy.ndarray position:
+            Center position (x, y, z) of each prism as a (N, 3) array
+        :param tuple(float, array) rotation:
+                Angle (in degrees) and axis of rotation.
+                If (0, (0, 0, 0)) (default), the hexagonal faces are on
+                xy plane and a side face is aligned with x axis.
+        """
+        self.position = numpy.atleast_2d(numpy.array(position, copy=True))
+        self.radius = float(radius)
+        self.height = float(height)
+        self.color = numpy.array(color, copy=True)
+        self.rotation = Rotate(rotation[0], rotation[1][0], rotation[1][1],
+                               rotation[1][2])
+
+        assert (numpy.ndim(self.color) == 1 or
+                len(self.color) == len(self.position))
+
+        angles = numpy.linspace(0, 2*numpy.pi, 7)
+        self._setData(self.position,
+                      self.radius,
+                      self.height,
+                      angles,
+                      self.color,
+                      True,
+                      self.rotation)
+
+    def getPosition(self, copy=True):
+        """Get hexagonal prim(s) position(s).
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+         :return: Position(s) of hexagonal prism(s) as a (N, 3) array.
+         :rtype: numpy.ndarray
+         """
+        return numpy.array(self.position, copy=copy)
+
+    def getRadius(self):
+        """Get hexagonal prism(s) radius.
+
+        :return: Radius of hexagon(s).
+        :rtype: float
+        """
+        return self.radius
+
+    def getHeight(self):
+        """Get hexagonal prism(s) height.
+
+        :return: Height of hexagonal prism(s).
+        :rtype: float
+        """
+        return self.height
+
+    def getColor(self, copy=True):
+        """Get hexagonal prism(s) color.
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        :return: RGB color of the hexagonal prism(s).
+        :rtype: numpy.ndarray
+        """
+        return numpy.array(self.color, copy=copy)
diff --git a/silx/gui/plot3d/items/mixins.py b/silx/gui/plot3d/items/mixins.py
index 41ad3c3..8e96441 100644
--- a/silx/gui/plot3d/items/mixins.py
+++ b/silx/gui/plot3d/items/mixins.py
@@ -27,7 +27,7 @@
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "15/11/2017"
+__date__ = "24/04/2018"
 
 
 import collections
@@ -38,7 +38,7 @@ from silx.math.combo import min_max
 from ...plot.items.core import ItemMixInBase
 from ...plot.items.core import ColormapMixIn as _ColormapMixIn
 from ...plot.items.core import SymbolMixIn as _SymbolMixIn
-from ...plot.Colors import rgba
+from ...colors import rgba
 
 from ..scene import primitives
 from .core import Item3DChangedType, ItemChangedType
diff --git a/silx/gui/plot3d/items/volume.py b/silx/gui/plot3d/items/volume.py
index a1f40f7..a7b5923 100644
--- a/silx/gui/plot3d/items/volume.py
+++ b/silx/gui/plot3d/items/volume.py
@@ -29,7 +29,7 @@ from __future__ import absolute_import
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "15/11/2017"
+__date__ = "24/04/2018"
 
 import logging
 import time
@@ -39,7 +39,7 @@ from silx.math.combo import min_max
 from silx.math.marchingcubes import MarchingCubes
 
 from ... import qt
-from ...plot.Colors import rgba
+from ...colors import rgba
 
 from ..scene import cutplane, primitives, transform
 
diff --git a/silx/gui/plot3d/scene/primitives.py b/silx/gui/plot3d/scene/primitives.py
index abf7dd4..af00b6d 100644
--- a/silx/gui/plot3d/scene/primitives.py
+++ b/silx/gui/plot3d/scene/primitives.py
@@ -27,7 +27,7 @@ from __future__ import absolute_import, division, unicode_literals
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "25/07/2016"
+__date__ = "24/04/2018"
 
 
 import collections
@@ -38,7 +38,7 @@ import string
 
 import numpy
 
-from silx.gui.plot.Colors import rgba
+from silx.gui.colors import rgba
 
 from ... import _glutils
 from ..._glutils import gl
@@ -1246,12 +1246,12 @@ class _Points(Geometry):
         $clippingCall(vCameraPosition);
 
         float alpha = alphaSymbol(gl_PointCoord, vSize);
-        if (alpha == 0.0) {
-            discard;
-        }
 
         gl_FragColor = $valueToColorCall(vValue);
         gl_FragColor.a *= alpha;
+        if (gl_FragColor.a == 0.0) {
+            discard;
+        }
     }
     """))
 
diff --git a/silx/gui/plot3d/scene/text.py b/silx/gui/plot3d/scene/text.py
index 903fc21..c2983d5 100644
--- a/silx/gui/plot3d/scene/text.py
+++ b/silx/gui/plot3d/scene/text.py
@@ -28,13 +28,13 @@ from __future__ import absolute_import, division, unicode_literals
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "17/10/2016"
+__date__ = "24/04/2018"
 
 
 import logging
 import numpy
 
-from silx.gui.plot.Colors import rgba
+from silx.gui.colors import rgba
 
 from ... import _glutils
 from ..._glutils import gl
diff --git a/silx/gui/plot3d/scene/utils.py b/silx/gui/plot3d/scene/utils.py
index 04abd04..3752289 100644
--- a/silx/gui/plot3d/scene/utils.py
+++ b/silx/gui/plot3d/scene/utils.py
@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2015-2017 European Synchrotron Radiation Facility
+# Copyright (c) 2015-2018 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
@@ -227,12 +227,7 @@ def trianglesNormal(positions):
                           positions[:, 2] - positions[:, 0])
 
     # Normalize normals
-    if numpy.version.version < '1.8.0':
-        # Debian 7 support: numpy.linalg.norm has no axis argument
-        norms = numpy.array(tuple(numpy.linalg.norm(vec) for vec in normals),
-                            dtype=normals.dtype)
-    else:
-        norms = numpy.linalg.norm(normals, axis=1)
+    norms = numpy.linalg.norm(normals, axis=1)
     norms[norms == 0] = 1
 
     return normals / norms.reshape(-1, 1)
diff --git a/silx/gui/plot3d/scene/viewport.py b/silx/gui/plot3d/scene/viewport.py
index 0cacbf0..41aa999 100644
--- a/silx/gui/plot3d/scene/viewport.py
+++ b/silx/gui/plot3d/scene/viewport.py
@@ -33,12 +33,12 @@ from __future__ import absolute_import, division, unicode_literals
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "25/07/2016"
+__date__ = "24/04/2018"
 
 
 import numpy
 
-from silx.gui.plot.Colors import rgba
+from silx.gui.colors import rgba
 
 from ..._glutils import gl
 
diff --git a/silx/gui/plot3d/tools/GroupPropertiesWidget.py b/silx/gui/plot3d/tools/GroupPropertiesWidget.py
index 30e11de..5b0bcdb 100644
--- a/silx/gui/plot3d/tools/GroupPropertiesWidget.py
+++ b/silx/gui/plot3d/tools/GroupPropertiesWidget.py
@@ -28,11 +28,11 @@ from __future__ import absolute_import
 
 __authors__ = ["T. Vincent"]
 __license__ = "MIT"
-__date__ = "11/01/2018"
+__date__ = "24/04/2018"
 
 from ....gui import qt
-from ....gui.plot.Colormap import Colormap
-from ....gui.plot.ColormapDialog import ColormapDialog
+from ....gui.colors import Colormap
+from ....gui.dialog.ColormapDialog import ColormapDialog
 
 from ..items import SymbolMixIn, ColormapMixIn