From e740cb4b4931f0e068c6524b97957e5c082323e0 Mon Sep 17 00:00:00 2001
From: Luke Campagnola <luke.campagnola@gmail.com>
Date: Tue, 3 May 2016 09:13:25 -0700
Subject: [PATCH] updated examples to use normal axis order, fixed a few ROI
 bugs

---
 examples/ROIExamples.py        |  6 ++++++
 examples/imageAnalysis.py      |  6 +++---
 pyqtgraph/graphicsItems/ROI.py | 24 +++++++++++++-----------
 3 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/examples/ROIExamples.py b/examples/ROIExamples.py
index 55c671ad..e52590f6 100644
--- a/examples/ROIExamples.py
+++ b/examples/ROIExamples.py
@@ -11,6 +11,7 @@ import pyqtgraph as pg
 from pyqtgraph.Qt import QtCore, QtGui
 import numpy as np
 
+pg.setConfigOptions(imageAxisOrder='normal')
 
 ## Create image to display
 arr = np.ones((100, 100), dtype=float)
@@ -24,6 +25,11 @@ arr[:, 50] = 10
 arr += np.sin(np.linspace(0, 20, 100)).reshape(1, 100)
 arr += np.random.normal(size=(100,100))
 
+# add an arrow for asymmetry
+arr[10, :50] = 10
+arr[9:12, 44:48] = 10
+arr[8:13, 44:46] = 10
+
 
 ## create GUI
 app = QtGui.QApplication([])
diff --git a/examples/imageAnalysis.py b/examples/imageAnalysis.py
index be64815e..18e96e97 100644
--- a/examples/imageAnalysis.py
+++ b/examples/imageAnalysis.py
@@ -58,10 +58,10 @@ win.show()
 
 
 # Generate image data
-data = np.random.normal(size=(100, 200))
+data = np.random.normal(size=(200, 100))
 data[20:80, 20:80] += 2.
 data = pg.gaussianFilter(data, (3, 3))
-data += np.random.normal(size=(100, 200)) * 0.1
+data += np.random.normal(size=(200, 100)) * 0.1
 img.setImage(data)
 hist.setLevels(data.min(), data.max())
 
@@ -80,7 +80,7 @@ p1.autoRange()
 def updatePlot():
     global img, roi, data, p2
     selected = roi.getArrayRegion(data, img)
-    p2.plot(selected.mean(axis=1), clear=True)
+    p2.plot(selected.mean(axis=0), clear=True)
 
 roi.sigRegionChanged.connect(updatePlot)
 updatePlot()
diff --git a/pyqtgraph/graphicsItems/ROI.py b/pyqtgraph/graphicsItems/ROI.py
index d5f41af4..267773fd 100644
--- a/pyqtgraph/graphicsItems/ROI.py
+++ b/pyqtgraph/graphicsItems/ROI.py
@@ -1020,11 +1020,8 @@ class ROI(GraphicsObject):
         If the slice can not be computed (usually because the scene/transforms are not properly
         constructed yet), then the method returns None.
         """
-        #print "getArraySlice"
-        
         ## Determine shape of array along ROI axes
         dShape = (data.shape[axes[0]], data.shape[axes[1]])
-        #print "  dshape", dShape
         
         ## Determine transform that maps ROI bounding box to image coordinates
         try:
@@ -1033,25 +1030,28 @@ class ROI(GraphicsObject):
             return None
             
         ## Modify transform to scale from image coords to data coords
-        #m = QtGui.QTransform()
-        tr.scale(float(dShape[0]) / img.width(), float(dShape[1]) / img.height())
-        #tr = tr * m
+        axisOrder = getConfigOption('imageAxisOrder')
+        if axisOrder == 'normal':
+            tr.scale(float(dShape[1]) / img.width(), float(dShape[0]) / img.height())
+        else:
+            tr.scale(float(dShape[0]) / img.width(), float(dShape[1]) / img.height())
         
         ## Transform ROI bounds into data bounds
         dataBounds = tr.mapRect(self.boundingRect())
-        #print "  boundingRect:", self.boundingRect()
-        #print "  dataBounds:", dataBounds
         
         ## Intersect transformed ROI bounds with data bounds
-        intBounds = dataBounds.intersected(QtCore.QRectF(0, 0, dShape[0], dShape[1]))
-        #print "  intBounds:", intBounds
+        if axisOrder == 'normal':
+            intBounds = dataBounds.intersected(QtCore.QRectF(0, 0, dShape[1], dShape[0]))
+        else:
+            intBounds = dataBounds.intersected(QtCore.QRectF(0, 0, dShape[0], dShape[1]))
         
         ## Determine index values to use when referencing the array. 
         bounds = (
             (int(min(intBounds.left(), intBounds.right())), int(1+max(intBounds.left(), intBounds.right()))),
             (int(min(intBounds.bottom(), intBounds.top())), int(1+max(intBounds.bottom(), intBounds.top())))
         )
-        #print "  bounds:", bounds
+        if axisOrder == 'normal':
+            bounds = bounds[::-1]
         
         if returnSlice:
             ## Create slice objects
@@ -1650,6 +1650,8 @@ class MultiRectROI(QtGui.QGraphicsObject):
             
         ## make sure orthogonal axis is the same size
         ## (sometimes fp errors cause differences)
+        if getConfigOption('imageAxisOrder') == 'normal':
+            axes = axes[::-1]
         ms = min([r.shape[axes[1]] for r in rgns])
         sl = [slice(None)] * rgns[0].ndim
         sl[axes[1]] = slice(0,ms)