Traditional log10 mode for PlotDataItem (by adding "mapped data" stage) (#1992)

* make PlotDataItem aware of mapped data

* inf suppression, metadata storage and refactor of data structures

* cleanup, test, and documentation pass

* re-added prepareForPaint, added PlotDataset to sphinx index

* strip more print statements

* indicate (internal) PlotDataset documentation as orphaned to avoid sphinx error

* Do not export PlotDataset

* replacement example

* example comments

examples/logAxis.py

@@ -1,38 +1,44 @@
 # -*- coding: utf-8 -*-
 """
-Test programmatically setting log transformation modes.
+Demonstrate programmatic setting of log transformation modes.
 """
 import initExample ## Add path to library (just for examples; you do not need this)
 
 import numpy as np
-from pyqtgraph.Qt import QtGui, QtCore
 import pyqtgraph as pg
 
-
 app = pg.mkQApp("Log Axis Example")
 
 w = pg.GraphicsLayoutWidget(show=True)
-w.setWindowTitle('pyqtgraph example: logAxis')
-p1 = w.addPlot(0,0, title="X Semilog")
+w.resize(800,800)
+w.setWindowTitle('pyqtgraph example: Log Axis, or How to Recognise Different Types of Curves from Quite a Long Way Away')
+
+p0 = w.addPlot(0,0, title="Linear")
+p1 = w.addPlot(0,1, title="X Semilog")
 p2 = w.addPlot(1,0, title="Y Semilog")
-p3 = w.addPlot(2,0, title="XY Log")
-p1.showGrid(True, True)
-p2.showGrid(True, True)
-p3.showGrid(True, True)
+p3 = w.addPlot(1,1, title="XY Log")
+# configure logarithmic axis scaling:
 p1.setLogMode(True, False)
 p2.setLogMode(False, True)
 p3.setLogMode(True, True)
+
+# 1000 points from 0.1 to 10, chosen to give a compatible range of values across curves:
+x = np.logspace(-1, 1, 1000) 
+plotdata = ( # legend entry, color, and plotted equation:
+    ('1 / 3x'    , '#ff9d47', 1./(3*x) ),
+    ('sqrt x'    , '#b3cf00', 1/np.sqrt(x) ),
+    ('exp. decay', '#00a0b5', 5 * np.exp(-x/1) ), 
+    ('-log x'    , '#a54dff', - np.log10(x) )
+)
+p0.addLegend(offset=(-20,20)) # include legend only in top left plot
+for p in (p0, p1, p2, p3):    # draw identical numerical data in all four plots
+    p.showGrid(True, True)    # turn on grid for all four plots
+    p.showAxes(True, size=(40,None)) # show a full frame, and reserve identical room for y labels
+    for name, color, y in plotdata:  # draw all four curves as defined in plotdata
+        pen = pg.mkPen(color, width=2)
+        p.plot( x,y, pen=pen, name=name )
+
 w.show()
 
-y = np.random.normal(size=1000)
-x = np.linspace(0, 1, 1000)
-p1.plot(x, y)
-p2.plot(x, y)
-p3.plot(x, y)
-
-
-
-#p.getAxis('bottom').setLogMode(True)
-
 if __name__ == '__main__':
     pg.exec()

pyqtgraph/functions.py

@@ -1123,7 +1123,10 @@ def transformCoordinates(tr, coords, transpose=False):
     m = m[:, :-1]
     
     ## map coordinates and return
-    mapped = (m*coords).sum(axis=1)  ## apply scale/rotate
+    # nan or inf points will not plot, but should not generate warnings
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", RuntimeWarning)
+        mapped = (m*coords).sum(axis=1)  ## apply scale/rotate
     mapped += translate
     
     if transpose:
@@ -2042,7 +2045,7 @@ def arrayToQPath(x, y, connect='all', finiteCheck=True):
         only values with 1 will connect to the previous point.  Def
     finiteCheck : bool, default Ture
         When false, the check for finite values will be skipped, which can
-        improve performance. If finite values are present in `x` or `y`,
+        improve performance. If nonfinite values are present in `x` or `y`,
         an empty QPainterPath will be generated.
     
     Returns

pyqtgraph/graphicsItems/ViewBox/ViewBox.py

@@ -1468,6 +1468,10 @@ class ViewBox(GraphicsWidget):
 
         bounds = QtCore.QRectF(range[0][0], range[1][0], range[0][1]-range[0][0], range[1][1]-range[1][0])
         return bounds
+        
+    def update(self, *args, **kwargs):
+        self.prepareForPaint()
+        GraphicsWidget.update(self, *args, **kwargs)
 
     def updateViewRange(self, forceX=False, forceY=False):
         ## Update viewRange to match targetRange as closely as possible, given

tests/graphicsItems/test_PlotDataItem.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 import numpy as np
+import warnings
 import pyqtgraph as pg
 from pyqtgraph.Qt import QtGui
 
@@ -71,6 +72,31 @@ def test_setData():
     pdi.setData([],[])
     assert pdi.xData is None
     assert pdi.yData is None
+    
+def test_nonfinite():
+    def _assert_equal_arrays(a1, a2):
+        assert a1.shape == a2.shape
+        for ( xtest, xgood ) in zip( a1, a2 ):
+            assert( (xtest == xgood) or (np.isnan(xtest) and np.isnan(xgood) ) ) 
+        
+    x = np.array([-np.inf, 0.0, 1.0,  2.0  , np.nan,   4.0 , np.inf])
+    y = np.array([    1.0, 0.0,-1.0, np.inf,   2.0 , np.nan,   0.0 ])
+    pdi = pg.PlotDataItem(x, y)
+    dataset = pdi.getDisplayDataset()
+    _assert_equal_arrays( dataset.x, x )
+    _assert_equal_arrays( dataset.y, y )
+   
+    with warnings.catch_warnings(): 
+        warnings.simplefilter("ignore")
+        x_log = np.log10(x)
+        y_log = np.log10(y)
+    x_log[ ~np.isfinite(x_log) ] = np.nan
+    y_log[ ~np.isfinite(y_log) ] = np.nan
+
+    pdi.setLogMode(True, True)
+    dataset = pdi.getDisplayDataset()
+    _assert_equal_arrays( dataset.x, x_log )
+    _assert_equal_arrays( dataset.y, y_log )
 
 def test_opts():
     # test that curve and scatter plot properties get updated from PlotDataItem methods