silx.gui.plot3d: Added HeightMapData and HeightMapRGBA items

doc/source/modules/gui/plot3d/items.rst

@@ -112,6 +112,29 @@ The following classes allows to configure :class:`ScalarField3D` visualization:
              getParameters, setParameters,
              getDisplayValuesBelowMin, setDisplayValuesBelowMin
 
+Height map
+----------
+
+.. currentmodule:: silx.gui.plot3d.items.image
+
+:class:`HeightMapData`
+++++++++++++++++++++++
+
+:class:`HeightMapData` inherits from :class:`.DataItem3D` and also provides its API.
+
+.. autoclass:: HeightMapData
+   :members: getData, setData,
+             getColormappedData, setColormappedData
+
+:class:`HeightMapRGBA`
+++++++++++++++++++++++
+
+:class:`HeightMapRGBA` inherits from :class:`.DataItem3D` and also provides its API.
+
+.. autoclass:: HeightMapRGBA
+   :members: getData, setData,
+             getColorData, setColorData
+
 Clipping plane
 --------------
 

silx/gui/plot3d/items/__init__.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2017-2019 European Synchrotron Radiation Facility
+# Copyright (c) 2017-2021 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
@@ -37,7 +37,7 @@
 from .mixins import (ColormapMixIn, ComplexMixIn, InterpolationMixIn,  # noqa
                      PlaneMixIn, SymbolMixIn)  # noqa
 from .clipplane import ClipPlane  # noqa
-from .image import ImageData, ImageRgba  # noqa
+from .image import ImageData, ImageRgba, HeightMapData, HeightMapRGBA  # noqa
 from .mesh import Mesh, ColormapMesh, Box, Cylinder, Hexagon  # noqa
 from .scatter import Scatter2D, Scatter3D  # noqa
 from .volume import ComplexField3D, ScalarField3D  # noqa

silx/gui/plot3d/items/image.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2017-2020 European Synchrotron Radiation Facility
+# Copyright (c) 2017-2021 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
@@ -174,3 +174,252 @@ def getData(self, copy=True):
         :return: The image data
         """
         return self._image.getData(copy=copy)
+
+
+class _HeightMap(DataItem3D):
+    """Base class for 2D data array displayed as a height field.
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        DataItem3D.__init__(self, parent=parent)
+        self.__data = numpy.zeros((0, 0), dtype=numpy.float32)
+
+    def _pickFull(self, context, threshold=0., sort='depth'):
+        """Perform picking in this item at given widget position.
+
+        :param PickContext context: Current picking context
+        :param float threshold: Picking threshold in pixel.
+            Perform picking in a square of size threshold x threshold.
+        :param str sort: How returned indices are sorted:
+
+            - 'index' (default): sort by the value of the indices
+            - 'depth':  Sort by the depth of the points from the current
+              camera point of view.
+        :return: Object holding the results or None
+        :rtype: Union[None,PickingResult]
+        """
+        assert sort in ('index', 'depth')
+
+        rayNdc = context.getPickingSegment(frame='ndc')
+        if rayNdc is None:  # No picking outside viewport
+            return None
+
+        # TODO no colormapped or color data
+        # Project data to NDC
+        heightData = self.getData(copy=False)
+        if heightData.size == 0:
+            return  # Nothing displayed
+
+        height, width = heightData.shape
+        z = numpy.ravel(heightData)
+        y, x = numpy.mgrid[0:height, 0:width]
+        dataPoints = numpy.transpose((numpy.ravel(x),
+                                      numpy.ravel(y),
+                                      z,
+                                      numpy.ones_like(z)))
+
+        primitive = self._getScenePrimitive()
+
+        pointsNdc = primitive.objectToNDCTransform.transformPoints(
+            dataPoints, perspectiveDivide=True)
+
+        # Perform picking
+        distancesNdc = numpy.abs(pointsNdc[:, :2] - rayNdc[0, :2])
+        # TODO issue with symbol size: using pixel instead of points
+        threshold += 1.  # symbol size
+        thresholdNdc = 2. * 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]
+
+        if sort == 'depth':
+            # Sort picked points from front to back
+            picked = picked[numpy.argsort(pointsNdc[picked, 2])]
+
+        if picked.size > 0:
+            # Convert indices from 1D to 2D
+            return PickingResult(self,
+                                 positions=dataPoints[picked, :3],
+                                 indices=(picked // height, picked % height),
+                                 fetchdata=self.getData)
+        else:
+            return None
+
+    def setData(self, data, copy: bool=True):
+        """Set the height field data.
+
+        :param data:
+        :param copy: True (default) to copy the data,
+            False to use as is (do not modify!).
+        """
+        data = numpy.array(data, copy=copy)
+        assert data.ndim == 2
+
+        self.__data = data
+        self._updated(ItemChangedType.DATA)
+
+    def getData(self, copy: bool=True) -> numpy.ndarray:
+        """Get the height field 2D data.
+
+        :param bool copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        """
+        return numpy.array(self.__data, copy=copy)
+
+
+class HeightMapData(_HeightMap, ColormapMixIn):
+    """Description of a 2D height field associated to a colormapped dataset.
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        _HeightMap.__init__(self, parent=parent)
+        ColormapMixIn.__init__(self)
+
+        self.__data = numpy.zeros((0, 0), dtype=numpy.float32)
+
+    def _updated(self, event=None):
+        if event == ItemChangedType.DATA:
+            self.__updateScene()
+        super()._updated(event=event)
+
+    def __updateScene(self):
+        """Update display primitive to use"""
+        self._getScenePrimitive().children = []  # Remove previous primitives
+        ColormapMixIn._setSceneColormap(self, None)
+
+        if not self.isVisible():
+            return  # Update when visible
+
+        data = self.getColormappedData(copy=False)
+        heightData = self.getData(copy=False)
+
+        if data.size == 0 or heightData.size == 0:
+            return  # Nothing to display
+
+        # Display as a set of points
+        height, width = heightData.shape
+        # Generates coordinates
+        y, x = numpy.mgrid[0:height, 0:width]
+
+        if data.shape != heightData.shape:  # data and height size miss-match
+            # Colormapped data is interpolated (nearest-neighbour) to match the height field
+            data = data[numpy.floor(y * data.shape[0] / height).astype(numpy.int),
+                        numpy.floor(x * data.shape[1] / height).astype(numpy.int)]
+
+        x = numpy.ravel(x)
+        y = numpy.ravel(y)
+
+        primitive = primitives.Points(
+            x=x,
+            y=y,
+            z=numpy.ravel(heightData),
+            value=numpy.ravel(data),
+            size=1)
+        primitive.marker = 's'
+        ColormapMixIn._setSceneColormap(self, primitive.colormap)
+        self._getScenePrimitive().children = [primitive]
+
+    def setColormappedData(self, data, copy: bool=True):
+        """Set the 2D data used to compute colors.
+
+        :param data: 2D array of data
+        :param copy: True (default) to copy the data,
+            False to use as is (do not modify!).
+        """
+        data = numpy.array(data, copy=copy)
+        assert data.ndim == 2
+
+        self.__data = data
+        self._updated(ItemChangedType.DATA)
+
+    def getColormappedData(self, copy: bool=True) -> numpy.ndarray:
+        """Returns the 2D data used to compute colors.
+
+        :param copy:
+            True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        """
+        return numpy.array(self.__data, copy=copy)
+
+
+class HeightMapRGBA(_HeightMap):
+    """Description of a 2D height field associated to a RGB(A) image.
+
+    :param parent: The View widget this item belongs to.
+    """
+
+    def __init__(self, parent=None):
+        _HeightMap.__init__(self, parent=parent)
+
+        self.__rgba = numpy.zeros((0, 0, 3), dtype=numpy.float32)
+
+    def _updated(self, event=None):
+        if event == ItemChangedType.DATA:
+            self.__updateScene()
+        super()._updated(event=event)
+
+    def __updateScene(self):
+        """Update display primitive to use"""
+        self._getScenePrimitive().children = []  # Remove previous primitives
+
+        if not self.isVisible():
+            return  # Update when visible
+
+        rgba = self.getColorData(copy=False)
+        heightData = self.getData(copy=False)
+        if rgba.size == 0 or heightData.size == 0:
+            return  # Nothing to display
+
+        # Display as a set of points
+        height, width = heightData.shape
+        # Generates coordinates
+        y, x = numpy.mgrid[0:height, 0:width]
+
+        if rgba.shape[:2] != heightData.shape:  # image and height size miss-match
+            # RGBA data is interpolated (nearest-neighbour) to match the height field
+            rgba = rgba[numpy.floor(y * rgba.shape[0] / height).astype(numpy.int),
+                        numpy.floor(x * rgba.shape[1] / height).astype(numpy.int)]
+
+        x = numpy.ravel(x)
+        y = numpy.ravel(y)
+
+        primitive = primitives.ColorPoints(
+            x=x,
+            y=y,
+            z=numpy.ravel(heightData),
+            color=rgba.reshape(-1, rgba.shape[-1]),
+            size=1)
+        primitive.marker = 's'
+        self._getScenePrimitive().children = [primitive]
+
+    def setColorData(self, data, copy: bool=True):
+        """Set the RGB(A) image to use.
+
+        Supported array format: float32 in [0, 1], uint8.
+
+        :param data:
+            The RGBA image data as an array of shape (H, W, Channels)
+        :param copy: True (default) to copy the data,
+            False to use as is (do not modify!).
+        """
+        data = numpy.array(data, copy=copy)
+        assert data.ndim == 3
+        assert data.shape[-1] in (3, 4)
+        # TODO check type
+
+        self.__rgba = data
+        self._updated(ItemChangedType.DATA)
+
+    def getColorData(self, copy: bool=True) -> numpy.ndarray:
+        """Get the RGB(A) image data.
+
+        :param copy: True (default) to get a copy,
+            False to get internal representation (do not modify!).
+        """
+        return numpy.array(self.__rgba, copy=copy)

silx/gui/plot3d/test/testSceneWindow.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2019 European Synchrotron Radiation Facility
+# Copyright (c) 2019-2021 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
@@ -37,7 +37,7 @@
 from silx.gui import qt
 
 from silx.gui.plot3d.SceneWindow import SceneWindow
-
+from silx.gui.plot3d.items import HeightMapData, HeightMapRGBA
 
 class TestSceneWindow(TestCaseQt, ParametricTestCase):
     """Tests SceneWidget picking feature"""
@@ -114,6 +114,42 @@ def testAdd(self):
         sceneWidget.resetZoom('front')
         self.qapp.processEvents()
 
+    def testHeightMap(self):
+        """Test height map items"""
+        sceneWidget = self.window.getSceneWidget()
+
+        height = numpy.arange(10000).reshape(100, 100) /100.
+
+        for shape in ((100, 100), (4, 5), (150, 20), (110, 110)):
+            with self.subTest(shape=shape):
+                items = []
+
+                # Colormapped data height map
+                data = numpy.arange(numpy.prod(shape)).astype(numpy.float32).reshape(shape)
+
+                heightmap = HeightMapData()
+                heightmap.setData(height)
+                heightmap.setColormappedData(data)
+                heightmap.getColormap().setName('viridis')
+                items.append(heightmap)
+                sceneWidget.addItem(heightmap)
+
+                # RGBA height map
+                colors = numpy.zeros(shape + (3,), dtype=numpy.float32)
+                colors[:, :, 1] = numpy.random.random(shape)
+
+                heightmap = HeightMapRGBA()
+                heightmap.setData(height)
+                heightmap.setColorData(colors)
+                heightmap.setTranslation(100., 0., 0.)
+                items.append(heightmap)
+                sceneWidget.addItem(heightmap)
+
+                self.assertEqual(sceneWidget.getItems(), tuple(items))
+                sceneWidget.resetZoom('front')
+                self.qapp.processEvents()
+                sceneWidget.clearItems()
+
     def testChangeContent(self):
         """Test add/remove/clear items"""
         sceneWidget = self.window.getSceneWidget()

silx/gui/plot3d/tools/PositionInfoWidget.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2018-2019 European Synchrotron Radiation Facility
+# Copyright (c) 2018-2021 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
@@ -144,6 +144,8 @@ def clear(self):
                         items.Scatter2D,
                         items.ImageData,
                         items.ImageRgba,
+                        items.HeightMapData,
+                        items.HeightMapRGBA,
                         items.Mesh,
                         items.Box,
                         items.Cylinder,