Use clip_array or clip_scalar instead of np.clip

Significant performance issues have been identified with np.clip
and thus clip_array was created to speed up the operation.  In addition
clip_scalar was created to clip a scalar value between two other values
this commit replaces many uses of np.clip from operating on scalars to
using clip_scalar instead

examples/GLScatterPlotItem.py

@@ -8,6 +8,7 @@ Demonstrates use of GLScatterPlotItem with rapidly-updating plots.
 import initExample
 
 import pyqtgraph as pg
+from pyqtgraph import functions as fn
 from pyqtgraph.Qt import QtCore, QtGui
 import pyqtgraph.opengl as gl
 import numpy as np
@@ -84,10 +85,10 @@ def update():
     global phase, sp2, d2
     s = -np.cos(d2*2+phase)
     color = np.empty((len(d2),4), dtype=np.float32)
-    color[:,3] = np.clip(s * 0.1, 0, 1)
+    color[:,3] = fn.clip_array(s * 0.1, 0., 1.)
-    color[:,0] = np.clip(s * 3.0, 0, 1)
+    color[:,0] = fn.clip_array(s * 3.0, 0., 1.)
-    color[:,1] = np.clip(s * 1.0, 0, 1)
+    color[:,1] = fn.clip_array(s * 1.0, 0., 1.)
-    color[:,2] = np.clip(s ** 3, 0, 1)
+    color[:,2] = fn.clip_array(s ** 3, 0., 1.)
     sp2.setData(color=color)
     phase -= 0.1
     

examples/GLVolumeItem.py

@@ -11,7 +11,7 @@ import numpy as np
 import pyqtgraph as pg
 from pyqtgraph.Qt import QtCore, QtGui
 import pyqtgraph.opengl as gl
-from pyqtgraph.functions import clip_array
+from pyqtgraph import functions as fn
 
 app = pg.mkQApp("GLVolumeItem Example")
 w = gl.GLViewWidget()
@@ -40,8 +40,8 @@ def psi(i, j, k, offset=(50,50,100)):
 
 
 data = np.fromfunction(psi, (100,100,200))
-positive = np.log(clip_array(data, 0, data.max())**2)
+positive = np.log(fn.clip_array(data, np.finfo(data.dtype).eps, data.max())**2)
-negative = np.log(clip_array(-data, 0, -data.min())**2)
+negative = np.log(fn.clip_array(-data, -np.finfo(data.dtype).eps, -data.min())**2)
 
 d2 = np.empty(data.shape + (4,), dtype=np.ubyte)
 d2[..., 0] = positive * (255./positive.max())

pyqtgraph/Point.py

@@ -6,14 +6,9 @@ Distributed under MIT/X11 license. See license.txt for more information.
 """
 
 from .Qt import QtCore
+from . import functions as fn
 from math import sin, acos, atan2, inf, pi, hypot
 
-def clip(x, mn, mx):
-    if x > mx:
-        return mx
-    if x < mn:
-        return mn
-    return x
 
 class Point(QtCore.QPointF):
     """Extension of QPointF which adds a few missing methods."""
@@ -112,7 +107,7 @@ class Point(QtCore.QPointF):
         if n1 == 0. or n2 == 0.:
             return None
         ## Probably this should be done with arctan2 instead..
-        ang = acos(clip(self.dot(a) / (n1 * n2), -1.0, 1.0)) ### in radians
+        ang = acos(fn.clip_scalar(self.dot(a) / (n1 * n2), -1.0, 1.0)) ### in radians
         c = self.cross(a)
         if c > 0:
             ang *= -1.

pyqtgraph/Vector.py

@@ -4,8 +4,9 @@ Vector.py -  Extension of QVector3D which adds a few missing methods.
 Copyright 2010  Luke Campagnola
 Distributed under MIT/X11 license. See license.txt for more information.
 """
-
+from math import acos
 from .Qt import QtGui, QtCore, QT_LIB
+from . import functions as fn
 import numpy as np
 
 class Vector(QtGui.QVector3D):
@@ -88,7 +89,7 @@ class Vector(QtGui.QVector3D):
         if n1 == 0. or n2 == 0.:
             return None
         ## Probably this should be done with arctan2 instead..
-        ang = np.arccos(np.clip(QtGui.QVector3D.dotProduct(self, a) / (n1 * n2), -1.0, 1.0)) ### in radians
+        ang = acos(fn.clip_scalar(QtGui.QVector3D.dotProduct(self, a) / (n1 * n2), -1.0, 1.0)) ### in radians
 #        c = self.crossProduct(a)
 #        if c > 0:
 #            ang *= -1.

pyqtgraph/canvas/CanvasItem.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 import numpy as np
 from ..Qt import QtGui, QtCore, QtSvg, QT_LIB
+from .. import functions as fn
 from ..graphicsItems.ROI import ROI
 from .. import SRTTransform, ItemGroup
 import importlib
@@ -240,7 +241,7 @@ class CanvasItem(QtCore.QObject):
         self._graphicsItem.setOpacity(alpha)
         
     def setAlpha(self, alpha):
-        self.alphaSlider.setValue(int(np.clip(alpha * 1023, 0, 1023)))
+        self.alphaSlider.setValue(int(fn.clip_scalar(alpha * 1023, 0, 1023)))
         
     def alpha(self):
         return self.alphaSlider.value() / 1023.

pyqtgraph/graphicsItems/CurvePoint.py

@@ -63,7 +63,7 @@ class CurvePoint(GraphicsObject):
             pos = self.property('position')
             if 'QVariant' in repr(pos):   ## need to support 2 APIs  :(
                 pos = pos.toDouble()[0]
-            index = (len(x)-1) * np.clip(pos, 0.0, 1.0)
+            index = (len(x)-1) * clip_scalar(pos, 0.0, 1.0)
             
         if index != int(index):  ## interpolate floating-point values
             i1 = int(index)

pyqtgraph/graphicsItems/GridItem.py

@@ -147,7 +147,7 @@ class GridItem(UIGraphicsItem):
                     continue
 
                 ppl = dim[ax] / nl[ax]
-                c = np.clip(5 * (ppl-3), 0., 50.).astype(int)
+                c = int(fn.clip_scalar(5 * (ppl-3), 0, 50))
 
                 linePen = self.opts['pen']
                 lineColor = self.opts['pen'].color()

pyqtgraph/graphicsItems/InfiniteLine.py

@@ -593,7 +593,7 @@ class InfLineLabel(TextItem):
                 return
 
             rel = self._posToRel(ev.pos())
-            self.orthoPos = np.clip(self._startPosition + rel - self._cursorOffset, 0, 1)
+            self.orthoPos = fn.clip_scalar(self._startPosition + rel - self._cursorOffset, 0., 1.)
             self.updatePosition()
             if ev.isFinish():
                 self._moving = False

pyqtgraph/graphicsItems/PlotItem/PlotItem.py

@@ -372,7 +372,7 @@ class PlotItem(GraphicsWidget):
         if y is not None:
             self.ctrl.yGridCheck.setChecked(y)
         if alpha is not None:
-            v = np.clip(alpha, 0, 1)*self.ctrl.gridAlphaSlider.maximum()
+            v = fn.clip_scalar(alpha, 0., 1.)*self.ctrl.gridAlphaSlider.maximum()
             self.ctrl.gridAlphaSlider.setValue(v)
         
     def close(self):

pyqtgraph/graphicsItems/ScatterPlotItem.py

@@ -1073,7 +1073,7 @@ class ScatterPlotItem(GraphicsObject):
             # Map points using painter's world transform so they are drawn with pixel-valued sizes
             pts = np.vstack([self.data['x'], self.data['y']])
             pts = fn.transformCoordinates(p.transform(), pts)
-            pts = np.clip(pts, -2 ** 30, 2 ** 30)  # prevent Qt segmentation fault.
+            pts = fn.clip_array(pts, -2 ** 30, 2 ** 30)  # prevent Qt segmentation fault.
             p.resetTransform()
 
             if self.opts['useCache'] and self._exportOpts is False:

pyqtgraph/graphicsItems/ViewBox/ViewBox.py

@@ -666,7 +666,7 @@ class ViewBox(GraphicsWidget):
     def suggestPadding(self, axis):
         l = self.width() if axis==0 else self.height()
         if l > 0:
-            padding = np.clip(1./(l**0.5), 0.02, 0.1)
+            padding = fn.clip_scalar(1./(l**0.5), 0.02, 0.1)
         else:
             padding = 0.02
         return padding

pyqtgraph/imageview/ImageView.py

@@ -17,6 +17,7 @@ from math import log10
 import numpy as np
 
 from ..Qt import QtCore, QtGui, QT_LIB
+from .. import functions as fn
 import importlib
 ui_template = importlib.import_module(
     f'.ImageViewTemplate_{QT_LIB.lower()}', package=__package__)
@@ -513,7 +514,7 @@ class ImageView(QtGui.QWidget):
         
     def setCurrentIndex(self, ind):
         """Set the currently displayed frame index."""
-        index = np.clip(ind, 0, self.getProcessedImage().shape[self.axes['t']]-1)
+        index = fn.clip_scalar(ind, 0, self.getProcessedImage().shape[self.axes['t']]-1)
         self.ignorePlaying = True
         # Implicitly call timeLineChanged
         self.timeLine.setValue(self.tVals[index])

pyqtgraph/opengl/GLViewWidget.py

@@ -344,7 +344,7 @@ class GLViewWidget(QtWidgets.QOpenGLWidget):
             self.opts['rotation'] = q
         else: # default euler rotation method
             self.opts['azimuth'] += azim
-            self.opts['elevation'] = np.clip(self.opts['elevation'] + elev, -90, 90)
+            self.opts['elevation'] = fn.clip_scalar(self.opts['elevation'] + elev, -90., 90.)
         self.update()
         
     def pan(self, dx, dy, dz, relative='global'):

pyqtgraph/opengl/items/GLScatterPlotItem.py

@@ -3,7 +3,7 @@ from OpenGL.GL import *
 from OpenGL.arrays import vbo
 from .. GLGraphicsItem import GLGraphicsItem
 from .. import shaders
-from ...functions import clip_array
+from ... import functions as fn
 from ...Qt import QtGui
 import numpy as np
 
@@ -62,12 +62,12 @@ class GLScatterPlotItem(GLGraphicsItem):
         
         ## Generate texture for rendering points
         w = 64
-        def fn(x,y):
+        def genTexture(x,y):
             r = np.hypot((x-(w-1)/2.), (y-(w-1)/2.))
-            return 255 * (w/2. - clip_array(r, w/2.-1.0, w/2.))
+            return 255 * (w / 2 - fn.clip_array(r, w / 2 - 1, w / 2))
         pData = np.empty((w, w, 4))
         pData[:] = 255
-        pData[:,:,3] = np.fromfunction(fn, pData.shape[:2])
+        pData[:,:,3] = np.fromfunction(genTexture, pData.shape[:2])
         pData = pData.astype(np.ubyte)
         
         if getattr(self, "pointTexture", None) is None:

pyqtgraph/parametertree/SystemSolver.py

@@ -2,6 +2,7 @@ from collections import OrderedDict
 import numpy as np
 import copy
 from math import log2
+from .. import functions as fn
 
 
 class SystemSolver(object):
@@ -391,7 +392,7 @@ if __name__ == '__main__':
                 sh = self.shutter   # this raises RuntimeError if shutter has not
                                    # been specified
                 ap = 4.0 * (sh / (1./60.)) * (iso / 100.) * (2 ** exp) * (2 ** light)
-                ap = np.clip(ap, 2.0, 16.0)
+                ap = fn.clip_scalar(ap, 2.0, 16.0)
             except RuntimeError:
                 # program mode; we can select a suitable shutter
                 # value at the same time.

pyqtgraph/widgets/ColorMapWidget.py

@@ -161,7 +161,7 @@ class ColorMapParameter(ptree.types.GroupParameter):
             elif op == 'Set':
                 colors[mask] = colors2[mask]            
                 
-        colors = np.clip(colors, 0, 1)
+        colors = fn.clip_array(colors, 0., 1.)
         if mode == 'byte':
             colors = (colors * 255).astype(np.ubyte)
         
@@ -210,7 +210,7 @@ class RangeColorMapItem(ptree.types.SimpleParameter):
     def map(self, data):
         data = data[self.fieldName]
         
-        scaled = np.clip((data-self['Min']) / (self['Max']-self['Min']), 0, 1)
+        scaled = fn.clip_array((data-self['Min']) / (self['Max']-self['Min']), 0, 1)
         cmap = self.value()
         colors = cmap.map(scaled, mode='float')
         

pyqtgraph/widgets/GraphicsView.py

@@ -378,7 +378,7 @@ class GraphicsView(QtGui.QGraphicsView):
             return
         
         if ev.buttons() == QtCore.Qt.RightButton:
-            delta = Point(np.clip(delta[0], -50, 50), np.clip(-delta[1], -50, 50))
+            delta = Point(fn.clip_scalar(delta[0], -50, 50), fn.clip_scalar(-delta[1], -50, 50))
             scale = 1.01 ** delta
             self.scale(scale[0], scale[1], center=self.mapToScene(self.mousePressPos))
             self.sigDeviceRangeChanged.emit(self, self.range)