OpenGL scenegraph updates

 - volumetric rendering
 - isosurfaces, mesh rendering
 - basic transformation and parent/child functionality

examples/GLMeshItem.py

+# -*- coding: utf-8 -*-
+
+##  This example uses the isosurface function to convert a scalar field
+##  (a hydrogen orbital) into a mesh for 3D display.
+
+## Add path to library (just for examples; you do not need this)
+import sys, os
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', '..'))
+
+from pyqtgraph.Qt import QtCore, QtGui
+import pyqtgraph as pg
+import pyqtgraph.opengl as gl
+
+app = QtGui.QApplication([])
+w = gl.GLViewWidget()
+w.show()
+
+g = gl.GLGridItem()
+g.scale(2,2,1)
+w.addItem(g)
+
+import numpy as np
+
+def psi(i, j, k, offset=(25, 25, 50)):
+    x = i-offset[0]
+    y = j-offset[1]
+    z = k-offset[2]
+    th = np.arctan2(z, (x**2+y**2)**0.5)
+    phi = np.arctan2(y, x)
+    r = (x**2 + y**2 + z **2)**0.5
+    a0 = 1
+    #ps = (1./81.) * (2./np.pi)**0.5 * (1./a0)**(3/2) * (6 - r/a0) * (r/a0) * np.exp(-r/(3*a0)) * np.cos(th)
+    ps = (1./81.) * 1./(6.*np.pi)**0.5 * (1./a0)**(3/2) * (r/a0)**2 * np.exp(-r/(3*a0)) * (3 * np.cos(th)**2 - 1)
+    
+    return ps
+    
+    #return ((1./81.) * (1./np.pi)**0.5 * (1./a0)**(3/2) * (r/a0)**2 * (r/a0) * np.exp(-r/(3*a0)) * np.sin(th) * np.cos(th) * np.exp(2 * 1j * phi))**2 
+
+
+print "Generating scalar field.."
+data = np.abs(np.fromfunction(psi, (50,50,100)))
+
+
+#data = np.fromfunction(lambda i,j,k: np.sin(0.2*((i-25)**2+(j-15)**2+k**2)**0.5), (50,50,50)); 
+print "Generating isosurface.."
+faces = pg.isosurface(data, data.max()/4.)
+m = gl.GLMeshItem(faces)
+w.addItem(m)
+m.translate(-25, -25, -50)
+    
+
+    
+#data = np.zeros((5,5,5))
+#data[2,2,1:4] = 1
+#data[2,1:4,2] = 1
+#data[1:4,2,2] = 1
+#tr.translate(-2.5, -2.5, 0)
+#data = np.ones((2,2,2))
+#data[0, 1, 0] = 0
+#faces = pg.isosurface(data, 0.5)
+#m = gl.GLMeshItem(faces)
+#w.addItem(m)
+#m.setTransform(tr)
+
+## Start Qt event loop unless running in interactive mode.
+if sys.flags.interactive != 1:
+    app.exec_()

examples/GLViewWidget.py

@@ -8,12 +8,21 @@ import pyqtgraph.opengl as gl
 
 app = QtGui.QApplication([])
 w = gl.GLViewWidget()
+w.opts['distance'] = 20
 w.show()
 
+ax = gl.GLAxisItem()
+ax.setSize(5,5,5)
+w.addItem(ax)
 
 b = gl.GLBoxItem()
 w.addItem(b)
 
-v = gl.GLVolumeItem()
-w.addItem(v)
+ax2 = gl.GLAxisItem()
+ax2.setParentItem(b)
 
+b.translate(1,1,1)
+
+## Start Qt event loop unless running in interactive mode.
+if sys.flags.interactive != 1:
+    app.exec_()

examples/GLVolumeItem.py

+# -*- coding: utf-8 -*-
+## Add path to library (just for examples; you do not need this)
+import sys, os
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', '..'))
+
+from pyqtgraph.Qt import QtCore, QtGui
+import pyqtgraph.opengl as gl
+
+app = QtGui.QApplication([])
+w = gl.GLViewWidget()
+w.opts['distance'] = 200
+w.show()
+
+
+#b = gl.GLBoxItem()
+#w.addItem(b)
+g = gl.GLGridItem()
+g.scale(10, 10, 1)
+w.addItem(g)
+
+import numpy as np
+## Hydrogen electron probability density
+def psi(i, j, k, offset=(50,50,100)):
+    x = i-offset[0]
+    y = j-offset[1]
+    z = k-offset[2]
+    th = np.arctan2(z, (x**2+y**2)**0.5)
+    phi = np.arctan2(y, x)
+    r = (x**2 + y**2 + z **2)**0.5
+    a0 = 2
+    #ps = (1./81.) * (2./np.pi)**0.5 * (1./a0)**(3/2) * (6 - r/a0) * (r/a0) * np.exp(-r/(3*a0)) * np.cos(th)
+    ps = (1./81.) * 1./(6.*np.pi)**0.5 * (1./a0)**(3/2) * (r/a0)**2 * np.exp(-r/(3*a0)) * (3 * np.cos(th)**2 - 1)
+    
+    return ps
+    
+    #return ((1./81.) * (1./np.pi)**0.5 * (1./a0)**(3/2) * (r/a0)**2 * (r/a0) * np.exp(-r/(3*a0)) * np.sin(th) * np.cos(th) * np.exp(2 * 1j * phi))**2 
+
+
+data = np.fromfunction(psi, (100,100,200))
+positive = np.log(np.clip(data, 0, data.max())**2)
+negative = np.log(np.clip(-data, 0, -data.min())**2)
+
+d2 = np.empty(data.shape + (4,), dtype=np.ubyte)
+d2[..., 0] = positive * (255./positive.max())
+d2[..., 1] = negative * (255./negative.max())
+d2[..., 2] = d2[...,1]
+d2[..., 3] = d2[..., 0]*0.3 + d2[..., 1]*0.3
+d2[..., 3] = (d2[..., 3].astype(float) / 255.) **2 * 255
+    
+v = gl.GLVolumeItem(d2)
+v.translate(-50,-50,-100)
+w.addItem(v)
+
+
+## Start Qt event loop unless running in interactive mode.
+if sys.flags.interactive != 1:
+    app.exec_()

examples/Plotting.py

@@ -67,6 +67,21 @@ y = np.sin(np.linspace(0, 10, 1000)) + np.random.normal(size=1000, scale=0.1)
 p7.plot(y, fillLevel=-0.3, brush=(50,50,200,100))
 
 
+x2 = np.linspace(-100, 100, 1000)
+data2 = np.sin(x2) / x2
+p8 = win.addPlot(title="Region Selection")
+p8.plot(data2, pen=(255,255,255,200))
+lr = pg.LinearRegionItem([400,700])
+lr.setZValue(-10)
+p8.addItem(lr)
+
+p9 = win.addPlot(title="Zoom on selected region")
+p9.plot(data2)
+def update():
+    p9.setXRange(*lr.getRegion())
+lr.sigRegionChanged.connect(update)
+update()
+
 ## Start Qt event loop unless running in interactive mode.
 if sys.flags.interactive != 1:
     app.exec_()

graphicsItems/AxisItem.py

@@ -297,7 +297,18 @@ class AxisItem(GraphicsWidget):
         pw = 10 ** (np.floor(np.log10(dif))-1)
         scaledIntervals = intervals * pw
         scaledTickCounts = dif / scaledIntervals 
-        i1 = np.argwhere(scaledTickCounts < optimalTickCount)[0,0]
+        try:
+            i1 = np.argwhere(scaledTickCounts < optimalTickCount)[0,0]
+        except:
+            print "AxisItem can't determine tick spacing:"
+            print "scaledTickCounts", scaledTickCounts
+            print "optimalTickCount", optimalTickCount
+            print "dif", dif
+            print "scaledIntervals", scaledIntervals
+            print "intervals", intervals
+            print "pw", pw
+            print "pixelSpacing", pixelSpacing
+            i1 = 1
         
         distBetweenIntervals = (optimalTickCount-scaledTickCounts[i1]) / (scaledTickCounts[i1-1]-scaledTickCounts[i1])
         

opengl/GLGraphicsItem.py

@@ -6,6 +6,8 @@ class GLGraphicsItem(QtCore.QObject):
         self.__parent = None
         self.__view = None
         self.__children = set()
+        self.__transform = QtGui.QMatrix4x4()
+        self.__visible = True
         self.setParentItem(parentItem)
         self.setDepthValue(0)
         
@@ -16,6 +18,11 @@ class GLGraphicsItem(QtCore.QObject):
             item.__children.add(self)
         self.__parent = item
         
+        if self.__parent is not None and self.view() is not self.__parent.view():
+            if self.view() is not None:
+                self.view().removeItem(self)
+            self.__parent.view().addItem(self)
+        
     def parentItem(self):
         return self.__parent
         
@@ -42,6 +49,69 @@ class GLGraphicsItem(QtCore.QObject):
         """Return the depth value of this item. See setDepthValue for mode information."""
         return self.__depthValue
         
+    def setTransform(self, tr):
+        self.__transform = tr
+        self.update()
+        
+    def applyTransform(self, tr, local):
+        """
+        Multiply this object's transform by *tr*. 
+        If local is True, then *tr* is multiplied on the right of the current transform:
+            newTransform = transform * tr
+        If local is False, then *tr* is instead multiplied on the left:
+            newTransform = tr * transform
+        """
+        if local:
+            self.setTransform(self.transform() * tr)
+        else:
+            self.setTransform(tr * self.transform())
+        
+    def transform(self):
+        return self.__transform
+        
+    def translate(self, dx, dy, dz, local=False):
+        """
+        Translate the object by (*dx*, *dy*, *dz*) in its parent's coordinate system.
+        If *local* is True, then translation takes place in local coordinates.
+        """
+        tr = QtGui.QMatrix4x4()
+        tr.translate(dx, dy, dz)
+        self.applyTransform(tr, local=local)
+        
+    def rotate(self, angle, x, y, z, local=False):
+        """
+        Rotate the object around the axis specified by (x,y,z).
+        *angle* is in degrees.
+        
+        """
+        tr = QtGui.QMatrix4x4()
+        tr.rotate(angle, x, y, z)
+        self.applyTransform(tr, local=local)
+    
+    def scale(self, x, y, z, local=True):
+        """
+        Scale the object by (*dx*, *dy*, *dz*) in its local coordinate system.
+        If *local* is False, then scale takes place in the parent's coordinates.
+        """
+        tr = QtGui.QMatrix4x4()
+        tr.scale(x, y, z)
+        self.applyTransform(tr, local=local)
+    
+    
+    def hide(self):
+        self.setVisible(False)
+        
+    def show(self):
+        self.setVisible(True)
+    
+    def setVisible(self, vis):
+        self.__visible = vis
+        self.update()
+        
+    def visible(self):
+        return self.__visible
+    
+    
     def initializeGL(self):
         """
         Called after an item is added to a GLViewWidget. 
@@ -57,4 +127,15 @@ class GLGraphicsItem(QtCore.QObject):
         but the caller will take care of pushing/popping.
         """
         pass
-        
\ No newline at end of file
+        
+    def update(self):
+        v = self.view()
+        if v is None:
+            return
+        v.updateGL()
+        
+    def mapFromParent(self, point):
+        tr = self.transform()
+        if tr is None:
+            return point
+        return tr.inverted()[0].map(point)
\ No newline at end of file

opengl/GLViewWidget.py

@@ -33,14 +33,15 @@ class GLViewWidget(QtOpenGL.QGLWidget):
         #print "set view", item, self, item.view()
         self.updateGL()
         
+    def removeItem(self, item):
+        self.items.remove(item)
+        item._setView(None)
+        self.updateGL()
+        
+        
     def initializeGL(self):
         glClearColor(0.0, 0.0, 0.0, 0.0)
-        glEnable(GL_DEPTH_TEST)
-
-        glEnable( GL_ALPHA_TEST )
         self.resizeGL(self.width(), self.height())
-        self.generateAxes()
-        #self.generatePoints()
         
     def resizeGL(self, w, h):
         glViewport(0, 0, w, h)
@@ -75,15 +76,7 @@ class GLViewWidget(QtOpenGL.QGLWidget):
     def paintGL(self):
         self.setProjection()
         self.setModelview()
-
         glClear( GL_DEPTH_BUFFER_BIT | GL_COLOR_BUFFER_BIT )
-        glDisable( GL_DEPTH_TEST )
-        #print "draw list:", self.axisList
-        glCallList(self.axisList)  ## draw axes
-        #glCallList(self.pointList)
-        #self.drawPoints()
-        #self.drawAxes()
-        
         self.drawItemTree()
         
     def drawItemTree(self, item=None):
@@ -94,14 +87,19 @@ class GLViewWidget(QtOpenGL.QGLWidget):
             items.append(item)
         items.sort(lambda a,b: cmp(a.depthValue(), b.depthValue()))
         for i in items:
+            if not i.visible():
+                continue
             if i is item:
+                i.paint()
+            else:
                 glMatrixMode(GL_MODELVIEW)
                 glPushMatrix()
-                i.paint()
+                tr = i.transform()
+                a = np.array(tr.copyDataTo()).reshape((4,4))
+                glMultMatrixf(a.transpose())
+                self.drawItemTree(i)
                 glMatrixMode(GL_MODELVIEW)
                 glPopMatrix()
-            else:
-                self.drawItemTree(i)
             
         
     def cameraPosition(self):
@@ -118,65 +116,7 @@ class GLViewWidget(QtOpenGL.QGLWidget):
         )
         
         return pos
-        
-        
-
-    def generateAxes(self):
-        self.axisList = glGenLists(1)
-        glNewList(self.axisList, GL_COMPILE)
 
-        #glShadeModel(GL_FLAT)
-        #glFrontFace(GL_CCW)
-        #glEnable( GL_LIGHT_MODEL_TWO_SIDE )
-        glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
-        glEnable( GL_BLEND )
-        glEnable( GL_ALPHA_TEST )
-        #glAlphaFunc( GL_ALWAYS,0.5 )
-        glEnable( GL_POINT_SMOOTH )
-        glDisable( GL_DEPTH_TEST )
-        glBegin( GL_LINES )
-        
-        glColor4f(1, 1, 1, .3)
-        for x in range(-10, 11):
-            glVertex3f(x, -10, 0)
-            glVertex3f(x,  10, 0)
-        for y in range(-10, 11):
-            glVertex3f(-10, y, 0)
-            glVertex3f( 10, y, 0)
-        
-        
-        glColor4f(0, 1, 0, .6)  # z is green
-        glVertex3f(0, 0, 0)
-        glVertex3f(0, 0, 5)
-
-        glColor4f(1, 1, 0, .6)  # y is yellow
-        glVertex3f(0, 0, 0)
-        glVertex3f(0, 5, 0)
-
-        glColor4f(0, 0, 1, .6)  # x is blue
-        glVertex3f(0, 0, 0)
-        glVertex3f(5, 0, 0)
-        glEnd()
-        glEndList()
-        
-    def generatePoints(self):
-        self.pointList = glGenLists(1)
-        glNewList(self.pointList, GL_COMPILE)
-        width = 7
-        alpha = 0.02
-        n = 40
-        glPointSize( width )
-        glBegin(GL_POINTS)
-        for x in range(-n, n+1):
-            r = (n-x)/(2.*n)
-            glColor4f(r, r, r, alpha)
-            for y in range(-n, n+1):
-                for z in range(-n, n+1):
-                    glVertex3f(x, y, z)
-        glEnd()
-        glEndList()
-        
-        
     def mousePressEvent(self, ev):
         self.mousePos = ev.pos()
         

opengl/MeshData.py

+class MeshData(object):
+    """
+    Class for storing 3D mesh data. May contain:
+        - list of vertex locations
+        - list of edges
+        - list of triangles
+        - colors per vertex, edge, or tri
+        - normals per vertex or tri
+    """
+
+    def __init__(self ...):
+
+
+    def generateFaceNormals(self):
+        
+    
+    def generateVertexNormals(self):
+        """
+        Assigns each vertex the average of its connected face normals.
+        If face normals have not been computed yet, then generateFaceNormals will be called.
+        """
+        
+        
+    def reverseNormals(self):
+    
\ No newline at end of file

opengl/items/GLAxisItem.py

+from OpenGL.GL import *
+from .. GLGraphicsItem import GLGraphicsItem
+from pyqtgraph import QtGui
+
+__all__ = ['GLAxisItem']
+
+class GLAxisItem(GLGraphicsItem):
+    def __init__(self, size=None):
+        GLGraphicsItem.__init__(self)
+        if size is None:
+            size = QtGui.QVector3D(1,1,1)
+        self.setSize(size=size)
+    
+    def setSize(self, x=None, y=None, z=None, size=None):
+        """
+        Set the size of the axes (in its local coordinate system; this does not affect the transform)
+        Arguments can be x,y,z or size=QVector3D().
+        """
+        if size is not None:
+            x = size.x()
+            y = size.y()
+            z = size.z()
+        self.__size = [x,y,z]
+        self.update()
+        
+    def size(self):
+        return self.__size[:]
+    
+    
+    def paint(self):
+
+        glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
+        glEnable( GL_BLEND )
+        glEnable( GL_ALPHA_TEST )
+        glEnable( GL_POINT_SMOOTH )
+        #glDisable( GL_DEPTH_TEST )
+        glBegin( GL_LINES )
+        
+        x,y,z = self.size()
+        glColor4f(0, 1, 0, .6)  # z is green
+        glVertex3f(0, 0, 0)
+        glVertex3f(0, 0, z)
+
+        glColor4f(1, 1, 0, .6)  # y is yellow
+        glVertex3f(0, 0, 0)
+        glVertex3f(0, y, 0)
+
+        glColor4f(0, 0, 1, .6)  # x is blue
+        glVertex3f(0, 0, 0)
+        glVertex3f(x, 0, 0)
+        glEnd()

opengl/items/GLBoxItem.py

 from OpenGL.GL import *
 from .. GLGraphicsItem import GLGraphicsItem
+from pyqtgraph.Qt import QtGui
+import pyqtgraph as pg
 
 __all__ = ['GLBoxItem']
 
 class GLBoxItem(GLGraphicsItem):
+    def __init__(self, size=None, color=None):
+        GLGraphicsItem.__init__(self)
+        if size is None:
+            size = QtGui.QVector3D(1,1,1)
+        self.setSize(size=size)
+        if color is None:
+            color = (255,255,255,80)
+        self.setColor(color)
+    
+    def setSize(self, x=None, y=None, z=None, size=None):
+        """
+        Set the size of the box (in its local coordinate system; this does not affect the transform)
+        Arguments can be x,y,z or size=QVector3D().
+        """
+        if size is not None:
+            x = size.x()
+            y = size.y()
+            z = size.z()
+        self.__size = [x,y,z]
+        self.update()
+        
+    def size(self):
+        return self.__size[:]
+    
+    def setColor(self, *args):
+        """Set the color of the box. Arguments are the same as those accepted by functions.mkColor()"""
+        self.__color = pg.Color(*args)
+        
+    def color(self):
+        return self.__color
+    
     def paint(self):
         glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
         glEnable( GL_BLEND )
@@ -13,34 +46,34 @@ class GLBoxItem(GLGraphicsItem):
         glDisable( GL_DEPTH_TEST )
         glBegin( GL_LINES )
         
-        glColor4f(1, 1, 1, .3)
-        w = 10
-        glVertex3f(-w, -w, -w)
-        glVertex3f(-w, -w,  w)
-        glVertex3f( w, -w, -w)
-        glVertex3f( w, -w,  w)
-        glVertex3f(-w,  w, -w)
-        glVertex3f(-w,  w,  w)
-        glVertex3f( w,  w, -w)
-        glVertex3f( w,  w,  w)
+        glColor4f(*self.color().glColor())
+        x,y,z = self.size()
+        glVertex3f(0, 0, 0)
+        glVertex3f(0, 0, z)
+        glVertex3f(x, 0, 0)
+        glVertex3f(x, 0, z)
+        glVertex3f(0, y, 0)
+        glVertex3f(0, y, z)
+        glVertex3f(x, y, 0)
+        glVertex3f(x, y, z)
 
-        glVertex3f(-w, -w, -w)
-        glVertex3f(-w,  w, -w)
-        glVertex3f( w, -w, -w)
-        glVertex3f( w,  w, -w)
-        glVertex3f(-w, -w,  w)
-        glVertex3f(-w,  w,  w)
-        glVertex3f( w, -w,  w)
-        glVertex3f( w,  w,  w)
+        glVertex3f(0, 0, 0)
+        glVertex3f(0, y, 0)
+        glVertex3f(x, 0, 0)
+        glVertex3f(x, y, 0)
+        glVertex3f(0, 0, z)
+        glVertex3f(0, y, z)
+        glVertex3f(x, 0, z)
+        glVertex3f(x, y, z)
         
-        glVertex3f(-w, -w, -w)
-        glVertex3f( w, -w, -w)
-        glVertex3f(-w,  w, -w)
-        glVertex3f( w,  w, -w)
-        glVertex3f(-w, -w,  w)
-        glVertex3f( w, -w,  w)
-        glVertex3f(-w,  w,  w)
-        glVertex3f( w,  w,  w)
+        glVertex3f(0, 0