Added functions.transformCoordinates() for mapping numpy arrays of coordinates...

Added functions.transformCoordinates() for mapping numpy arrays of coordinates from QTransform and QMatrix4x4

Minor updates:
- fixed SRTTransform3D.matrix()
- ViewBox fix: updateAutoRange leaves unused axes completely unchanged
- documentation updates

SRTTransform3D.py

@@ -201,11 +201,11 @@ class SRTTransform3D(QtGui.QMatrix4x4):
         
     def matrix(self, nd=3):
         if nd == 3:
-            return np.array(self.copyDataTo())
+            return np.array(self.copyDataTo()).reshape(4,4)
         elif nd == 2:
-            m = np.array(self.copyDataTo())
+            m = np.array(self.copyDataTo()).reshape(4,4)
             m[2] = m[3]
-            m[:,2] = n[:,3]
+            m[:,2] = m[:,3]
             return m[:3,:3]
         else:
             raise Exception("Argument 'nd' must be 2 or 3")

functions.py

@@ -461,9 +461,75 @@ def affineSlice(data, shape, origin, vectors, axes, order=1, returnCoords=False,
 def transformToArray(tr):
     """
     Given a QTransform, return a 3x3 numpy array.
-    """
-    return np.array([[tr.m11(), tr.m12(), tr.m13()],[tr.m21(), tr.m22(), tr.m23()],[tr.m31(), tr.m32(), tr.m33()]])
+    Given a QMatrix4x4, return a 4x4 numpy array.
+    
+    Example: map an array of x,y coordinates through a transform::
+    
+        ## coordinates to map are (1,5), (2,6), (3,7), and (4,8)
+        coords = np.array([[1,2,3,4], [5,6,7,8], [1,1,1,1]])  # the extra '1' coordinate is needed for translation to work
         
+        ## Make an example transform
+        tr = QtGui.QTransform()
+        tr.translate(3,4)
+        tr.scale(2, 0.1)
+        
+        ## convert to array
+        m = pg.transformToArray()[:2]  # ignore the perspective portion of the transformation
+        
+        ## map coordinates through transform
+        mapped = np.dot(m, coords)
+    """
+    #return np.array([[tr.m11(), tr.m12(), tr.m13()],[tr.m21(), tr.m22(), tr.m23()],[tr.m31(), tr.m32(), tr.m33()]])
+    ## The order of elements given by the method names m11..m33 is misleading--
+    ## It is most common for x,y translation to occupy the positions 1,3 and 2,3 in
+    ## a transformation matrix. However, with QTransform these values appear at m31 and m32.
+    ## So the correct interpretation is transposed:
+    if isinstance(tr, QtGui.QTransform):
+        return np.array([[tr.m11(), tr.m21(), tr.m31()], [tr.m12(), tr.m22(), tr.m32()], [tr.m13(), tr.m23(), tr.m33()]])
+    elif isinstance(tr, QtGui.QMatrix4x4):
+        return np.array(tr.copyDataTo()).reshape(4,4)
+    else:
+        raise Exception("Transform argument must be either QTransform or QMatrix4x4.")
+
+def transformCoordinates(tr, coords):
+    """
+    Map a set of 2D or 3D coordinates through a QTransform or QMatrix4x4.
+    The shape of coords must be (2,...) or (3,...)
+    The mapping will _ignore_ any perspective transformations.
+    """
+    nd = coords.shape[0]
+    m = transformToArray(tr)    
+    m = m[:m.shape[0]-1]  # remove perspective
+    
+    ## If coords are 3D and tr is 2D, assume no change for Z axis
+    if m.shape == (2,3) and nd == 3:
+        m2 = np.zeros((3,4))
+        m2[:2, :2] = m[:2,:2]
+        m2[:2, 3] = m[:2,2]
+        m2[2,2] = 1
+        m = m2
+    
+    ## if coords are 2D and tr is 3D, ignore Z axis
+    if m.shape == (3,4) and nd == 2:
+        m2 = np.empty((2,3))
+        m2[:,:2] = m[:2,:2]
+        m2[:,2] = m[:2,3]
+        m = m2
+    
+    ## reshape tr and coords to prepare for multiplication
+    m = m.reshape(m.shape + (1,)*(coords.ndim-1))
+    coords = coords[np.newaxis, ...]
+    
+    # separate scale/rotate and translation    
+    translate = m[:,-1]  
+    m = m[:, :-1]
+    
+    ## map coordinates and return
+    mapped = (m*coords).sum(axis=0)  ## apply scale/rotate
+    mapped += translate
+    return mapped
+    
+    
 def solve3DTransform(points1, points2):
     """
     Find a 3D transformation matrix that maps points1 onto points2

graphicsItems/ROI.py

@@ -854,9 +854,18 @@ class ROI(GraphicsObject):
         else:
             kwds['returnCoords'] = True
             result, coords = fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, **kwds)
-            tr = fn.transformToArray(img.transform())[:,:2].reshape((3, 2) + (1,)*(coords.ndim-1))
-            coords = coords[np.newaxis, ...]
-            mapped = (tr*coords).sum(axis=0)
+            #tr = fn.transformToArray(img.transform())[:2]  ## remove perspective transform values
+            
+            ### separate translation from scale/rotate
+            #translate = tr[:,2]
+            #tr = tr[:,:2]
+            #tr = tr.reshape((2,2) + (1,)*(coords.ndim-1))
+            #coords = coords[np.newaxis, ...]
+            
+            ### map coordinates and return
+            #mapped = (tr*coords).sum(axis=0)  ## apply scale/rotate
+            #mapped += translate.reshape((2,1,1))
+            mapped = fn.transformCoordinates(img.transform(), coords)
             return result, mapped
             
             

graphicsItems/ViewBox/ViewBox.py

@@ -538,6 +538,7 @@ class ViewBox(GraphicsWidget):
         if self.state['autoVisibleOnly'][0] is True:
             order = [1,0]
 
+        args = {}
         for ax in order:
             if self.state['autoRange'][ax] is False:
                 continue
@@ -563,6 +564,7 @@ class ViewBox(GraphicsWidget):
                     
                 targetRect[0][0] = childRect.left()
                 targetRect[0][1] = childRect.right()
+                args['xRange'] = targetRect[0]
             else:
                 ## Make corrections to Y range
                 if self.state['autoPan'][1]:
@@ -576,8 +578,11 @@ class ViewBox(GraphicsWidget):
                     
                 targetRect[1][0] = childRect.top()
                 targetRect[1][1] = childRect.bottom()
-            
-        self.setRange(xRange=targetRect[0], yRange=targetRect[1], padding=0, disableAutoRange=False)
+                args['yRange'] = targetRect[1]
+        args['padding'] = 0
+        args['disableAutoRange'] = False
+        #self.setRange(xRange=targetRect[0], yRange=targetRect[1], padding=0, disableAutoRange=False)
+        self.setRange(**args)
         
     def setXLink(self, view):
         """Link this view's X axis to another view. (see LinkView)"""
@@ -1213,7 +1218,8 @@ class ViewBox(GraphicsWidget):
 
     @staticmethod
     def forgetView(vid, name):
-        
+        if ViewBox is None:     ## can happen as python is shutting down
+            return
         ## Called with ID and name of view (the view itself is no longer available)
         for v in ViewBox.AllViews.iterkeys():
             if id(v) == vid:

parametertree/Parameter.py

@@ -614,7 +614,8 @@ class Parameter(QtCore.QObject):
         about to be made to the tree and only one change signal should be
         emitted at the end.
         
-        Example:
+        Example::
+
             with param.treeChangeBlocker():
                 param.addChild(...)
                 param.removeChild(...)
@@ -638,11 +639,14 @@ class Parameter(QtCore.QObject):
     def treeStateChanged(self, param, changes):
         """
         Called when the state of any sub-parameter has changed. 
+        
+        ==========  ================================================================
         Arguments:
-            param: the immediate child whose tree state has changed.
-                   note that the change may have originated from a grandchild.
-            changes: list of tuples describing all changes that have been made
-                     in this event: (param, changeDescr, data)
+        param       The immediate child whose tree state has changed.
+                    note that the change may have originated from a grandchild.
+        changes     List of tuples describing all changes that have been made
+                    in this event: (param, changeDescr, data)
+        ==========  ================================================================
                      
         This function can be extended to react to tree state changes.
         """
@@ -668,4 +672,4 @@ class SignalBlocker:
         self.exitFn()
     
     
-    
\ No newline at end of file
+