ROI tests pass with row-major axis order

pyqtgraph/SRTTransform.py

@@ -3,6 +3,7 @@ from .Qt import QtCore, QtGui
 from .Point import Point
 import numpy as np
 
+
 class SRTTransform(QtGui.QTransform):
     """Transform that can always be represented as a combination of 3 matrices: scale * rotate * translate
     This transform has no shear; angles are always preserved.
@@ -165,6 +166,7 @@ class SRTTransform(QtGui.QTransform):
         
     def matrix(self):
         return np.array([[self.m11(), self.m12(), self.m13()],[self.m21(), self.m22(), self.m23()],[self.m31(), self.m32(), self.m33()]])
+
         
 if __name__ == '__main__':
     from . import widgets

pyqtgraph/graphicsItems/GraphicsItem.py

@@ -37,9 +37,6 @@ class GraphicsItem(object):
         if register:
             GraphicsScene.registerObject(self)  ## workaround for pyqt bug in graphicsscene.items()
                     
-
-                    
-                    
     def getViewWidget(self):
         """
         Return the view widget for this item. 
@@ -95,7 +92,6 @@ class GraphicsItem(object):
     def forgetViewBox(self):
         self._viewBox = None
         
-        
     def deviceTransform(self, viewportTransform=None):
         """
         Return the transform that converts local item coordinates to device coordinates (usually pixels).

pyqtgraph/graphicsItems/ImageItem.py

@@ -279,6 +279,42 @@ class ImageItem(GraphicsObject):
         if gotNewData:
             self.sigImageChanged.emit()
 
+    def dataTransform(self):
+        """Return the transform that maps from this image's input array to its
+        local coordinate system.
+        
+        This transform corrects for the transposition that occurs when image data
+        is interpreted in row-major order.
+        """
+        # Might eventually need to account for downsampling / clipping here
+        tr = QtGui.QTransform()
+        if self.axisOrder == 'row-major':
+            # transpose
+            tr.scale(1, -1)
+            tr.rotate(-90)
+        return tr
+
+    def inverseDataTransform(self):
+        """Return the transform that maps from this image's local coordinate
+        system to its input array.
+        
+        See dataTransform() for more information.
+        """
+        tr = QtGui.QTransform()
+        if self.axisOrder == 'row-major':
+            # transpose
+            tr.scale(1, -1)
+            tr.rotate(-90)
+        return tr
+
+    def mapToData(self, obj):
+        tr = self.inverseDataTransform()
+        return tr.map(obj)
+
+    def mapFromData(self, obj):
+        tr = self.dataTransform()
+        return tr.map(obj)
+
     def quickMinMax(self, targetSize=1e6):
         """
         Estimate the min/max values of the image data by subsampling.

pyqtgraph/graphicsItems/ROI.py

@@ -1017,7 +1017,7 @@ class ROI(GraphicsObject):
         If returnSlice is set to False, the function returns a pair of tuples with the values that would have 
         been used to generate the slice objects. ((ax0Start, ax0Stop), (ax1Start, ax1Stop))
         
-        If the slice can not be computed (usually because the scene/transforms are not properly
+        If the slice cannot be computed (usually because the scene/transforms are not properly
         constructed yet), then the method returns None.
         """
         ## Determine shape of array along ROI axes
@@ -1104,7 +1104,8 @@ class ROI(GraphicsObject):
         
         shape, vectors, origin = self.getAffineSliceParams(data, img, axes, fromBoundingRect=fromBR)
         if not returnMappedCoords:
-            return fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, **kwds)
+            rgn = fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, **kwds)
+            return rgn
         else:
             kwds['returnCoords'] = True
             result, coords = fn.affineSlice(data, shape=shape, vectors=vectors, origin=origin, axes=axes, **kwds)
@@ -1119,29 +1120,34 @@ class ROI(GraphicsObject):
         (shape, vectors, origin) to extract a subset of *data* using this ROI 
         and *img* to specify the subset.
         
+        If *fromBoundingRect* is True, then the ROI's bounding rectangle is used
+        rather than the shape of the ROI.
+        
         See :func:`getArrayRegion <pyqtgraph.ROI.getArrayRegion>` for more information.
         """
         if self.scene() is not img.scene():
             raise Exception("ROI and target item must be members of the same scene.")
         
-        origin = self.mapToItem(img, QtCore.QPointF(0, 0))
+        origin = img.mapToData(self.mapToItem(img, QtCore.QPointF(0, 0)))
         
         ## vx and vy point in the directions of the slice axes, but must be scaled properly
-        vx = self.mapToItem(img, QtCore.QPointF(1, 0)) - origin
+        vx = img.mapToData(self.mapToItem(img, QtCore.QPointF(1, 0))) - origin
-        vy = self.mapToItem(img, QtCore.QPointF(0, 1)) - origin
+        vy = img.mapToData(self.mapToItem(img, QtCore.QPointF(0, 1))) - origin
         
         lvx = np.sqrt(vx.x()**2 + vx.y()**2)
         lvy = np.sqrt(vy.x()**2 + vy.y()**2)
-        pxLen = img.width() / float(data.shape[axes[0]])
+        #pxLen = img.width() / float(data.shape[axes[0]])
-        #img.width is number of pixels, not width of item.
+        ##img.width is number of pixels, not width of item.
-        #need pxWidth and pxHeight instead of pxLen ?
+        ##need pxWidth and pxHeight instead of pxLen ?
-        sx =  pxLen / lvx
+        #sx =  pxLen / lvx
-        sy =  pxLen / lvy
+        #sy =  pxLen / lvy
+        sx = 1.0 / lvx
+        sy = 1.0 / lvy
         
         vectors = ((vx.x()*sx, vx.y()*sx), (vy.x()*sy, vy.y()*sy))
         if fromBoundingRect is True:
             shape = self.boundingRect().width(), self.boundingRect().height()
-            origin = self.mapToItem(img, self.boundingRect().topLeft())
+            origin = img.mapToData(self.mapToItem(img, self.boundingRect().topLeft()))
             origin = (origin.x(), origin.y())
         else:
             shape = self.state['size']
@@ -1150,10 +1156,10 @@ class ROI(GraphicsObject):
         shape = [abs(shape[0]/sx), abs(shape[1]/sy)]
         
         if getConfigOption('imageAxisOrder') == 'row-major':
-            vectors = [vectors[1][::-1], vectors[0][::-1]]
+            # transpose output
+            vectors = vectors[::-1]
             shape = shape[::-1]
-            origin = origin[::-1]
+
-        
         return shape, vectors, origin
 
     def renderShapeMask(self, width, height):

pyqtgraph/graphicsItems/tests/test_ROI.py

@@ -8,7 +8,7 @@ from pyqtgraph.tests import assertImageApproved, mouseMove, mouseDrag, mouseClic
 app = pg.mkQApp()
 
 
-def test_getArrayRegion():
+def test_getArrayRegion(transpose=False):
     pr = pg.PolyLineROI([[0, 0], [27, 0], [0, 28]], closed=True)
     pr.setPos(1, 1)
     rois = [
@@ -23,13 +23,19 @@ def test_getArrayRegion():
         
         origMode = pg.getConfigOption('imageAxisOrder')
         try:
-            pg.setConfigOptions(imageAxisOrder='col-major')
+            if transpose:
-            check_getArrayRegion(roi, 'roi/'+name, testResize)
+                pg.setConfigOptions(imageAxisOrder='row-major')
-            pg.setConfigOptions(imageAxisOrder='row-major')
+                check_getArrayRegion(roi, 'roi/'+name, testResize, transpose=True)
-            check_getArrayRegion(roi, 'roi/'+name, testResize, transpose=True)
+            else:
+                pg.setConfigOptions(imageAxisOrder='col-major')
+                check_getArrayRegion(roi, 'roi/'+name, testResize)
         finally:
             pg.setConfigOptions(imageAxisOrder=origMode)
     
+
+def test_getArrayRegion_axisorder():
+    test_getArrayRegion(transpose=True)
+
     
 def check_getArrayRegion(roi, name, testResize=True, transpose=False):
     initState = roi.getState()
@@ -55,8 +61,8 @@ def check_getArrayRegion(roi, name, testResize=True, transpose=False):
     vb2.setPos(6, 203)
     vb2.resize(188, 191)
     
-    img1 = TransposedImageItem(border='w', transpose=transpose)
+    img1 = pg.ImageItem(border='w')
-    img2 = TransposedImageItem(border='w', transpose=transpose)
+    img2 = pg.ImageItem(border='w')
 
     vb1.addItem(img1)
     vb2.addItem(img2)
@@ -68,6 +74,9 @@ def check_getArrayRegion(roi, name, testResize=True, transpose=False):
     data[:, :, 2, :] += 10
     data[:, :, :, 3] += 10
     
+    if transpose:
+        data = data.transpose(0, 2, 1, 3)
+    
     img1.setImage(data[0, ..., 0])
     vb1.setAspectLocked()
     vb1.enableAutoRange(True, True)
@@ -75,6 +84,12 @@ def check_getArrayRegion(roi, name, testResize=True, transpose=False):
     roi.setZValue(10)
     vb1.addItem(roi)
 
+    if isinstance(roi, pg.RectROI):
+        if transpose:
+            assert roi.getAffineSliceParams(data, img1, axes=(1, 2)) == ([28.0, 27.0], ((1.0, 0.0), (0.0, 1.0)), (1.0, 1.0))
+        else:
+            assert roi.getAffineSliceParams(data, img1, axes=(1, 2)) == ([27.0, 28.0], ((1.0, 0.0), (0.0, 1.0)), (1.0, 1.0))
+
     rgn = roi.getArrayRegion(data, img1, axes=(1, 2))
     #assert np.all((rgn == data[:, 1:-2, 1:-2, :]) | (rgn == 0))
     img2.setImage(rgn[0, ..., 0])