Merge pull request #273 from campagnola/numpy-fix

Corrections for numpy API changes

pyqtgraph/functions.py

@@ -6,8 +6,18 @@ Distributed under MIT/X11 license. See license.txt for more infomation.
 """
 
 from __future__ import division
+import warnings
+import numpy as np
+import decimal, re
+import ctypes
+import sys, struct
 from .python2_3 import asUnicode, basestring
 from .Qt import QtGui, QtCore, USE_PYSIDE
+from . import getConfigOption, setConfigOptions
+from . import debug
+
+
+
 Colors = {
     'b': QtGui.QColor(0,0,255,255),
     'g': QtGui.QColor(0,255,0,255),
@@ -27,14 +37,6 @@ SI_PREFIXES_ASCII = 'yzafpnum kMGTPEZY'
 
 
 
-from .Qt import QtGui, QtCore, USE_PYSIDE
-from . import getConfigOption, setConfigOptions
-import numpy as np
-import decimal, re
-import ctypes
-import sys, struct
-
-from . import debug
 
 def siScale(x, minVal=1e-25, allowUnicode=True):
     """
@@ -378,7 +380,8 @@ def eq(a, b):
         return True
         
     try:
-        e = a==b
+        with warnings.catch_warnings(module=np):  # ignore numpy futurewarning (numpy v. 1.10)
+            e = a==b
     except ValueError:
         return False
     except AttributeError: 
@@ -1374,22 +1377,17 @@ def arrayToQPath(x, y, connect='all'):
     arr[1:-1]['y'] = y
 
     # decide which points are connected by lines
-    if connect == 'pairs':
-        connect = np.empty((n/2,2), dtype=np.int32)
-        if connect.size != n:
-            raise Exception("x,y array lengths must be multiple of 2 to use connect='pairs'")
-        connect[:,0] = 1
-        connect[:,1] = 0
-        connect = connect.flatten()
-    if connect == 'finite':
-        connect = np.isfinite(x) & np.isfinite(y)
-        arr[1:-1]['c'] = connect
-    if connect == 'all':
+    if eq(connect, 'all'):
         arr[1:-1]['c'] = 1
+    elif eq(connect, 'pairs'):
+        arr[1:-1]['c'][::2] = 1
+        arr[1:-1]['c'][1::2] = 0
+    elif eq(connect, 'finite'):
+        arr[1:-1]['c'] = np.isfinite(x) & np.isfinite(y)
     elif isinstance(connect, np.ndarray):
         arr[1:-1]['c'] = connect
     else:
-        raise Exception('connect argument must be "all", "pairs", or array')
+        raise Exception('connect argument must be "all", "pairs", "finite", or array')
 
     #profiler('fill array')
     # write last 0
@@ -1580,7 +1578,7 @@ def isocurve(data, level, connected=False, extendToEdge=False, path=False):
             #vertIndex = i - 2*j*i + 3*j + 4*k  ## this is just to match Bourk's vertex numbering scheme
             vertIndex = i+2*j
             #print i,j,k," : ", fields[i,j,k], 2**vertIndex
-            index += fields[i,j] * 2**vertIndex
+            np.add(index, fields[i,j] * 2**vertIndex, out=index, casting='unsafe')
             #print index
     #print index
     
@@ -2096,7 +2094,7 @@ def isosurface(data, level):
             for k in [0,1]:
                 fields[i,j,k] = mask[slices[i], slices[j], slices[k]]
                 vertIndex = i - 2*j*i + 3*j + 4*k  ## this is just to match Bourk's vertex numbering scheme
-                index += fields[i,j,k] * 2**vertIndex
+                np.add(index, fields[i,j,k] * 2**vertIndex, out=index, casting='unsafe')
     
     ### Generate table of edges that have been cut
     cutEdges = np.zeros([x+1 for x in index.shape]+[3], dtype=np.uint32)
@@ -2165,7 +2163,7 @@ def isosurface(data, level):
         ### expensive:
         verts = faceShiftTables[i][cellInds]
         #profiler()
-        verts[...,:3] += cells[:,np.newaxis,np.newaxis,:]  ## we now have indexes into cutEdges
+        np.add(verts[...,:3], cells[:,np.newaxis,np.newaxis,:], out=verts[...,:3], casting='unsafe')  ## we now have indexes into cutEdges
         verts = verts.reshape((verts.shape[0]*i,)+verts.shape[2:])
         #profiler()
         

pyqtgraph/graphicsItems/ScatterPlotItem.py

@@ -145,7 +145,7 @@ class SymbolAtlas(object):
                 arr = fn.imageToArray(img, copy=False, transpose=False)
             else:
                 (y,x,h,w) = sourceRect.getRect()
-                arr = self.atlasData[x:x+w, y:y+w]
+                arr = self.atlasData[int(x):int(x+w), int(y):int(y+w)]
             rendered[key] = arr
             w = arr.shape[0]
             avgWidth += w
@@ -180,10 +180,10 @@ class SymbolAtlas(object):
             self.atlasRows[-1][2] = x
         height = y + rowheight
 
-        self.atlasData = np.zeros((width, height, 4), dtype=np.ubyte)
+        self.atlasData = np.zeros((int(width), int(height), 4), dtype=np.ubyte)
         for key in symbols:
             y, x, h, w = self.symbolMap[key].getRect()
-            self.atlasData[x:x+w, y:y+h] = rendered[key]
+            self.atlasData[int(x):int(x+w), int(y):int(y+h)] = rendered[key]
         self.atlas = None
         self.atlasValid = True
         self.max_width = maxWidth