Removed the basicStatistics directory/contents because nothing there was being used except corestats, which I moved to utility

Removed box plot code from Plot.py since we no longer use it either

2 files changed, 100 insertions, 133 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d60e2bb2..3a8b8dd5 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -36,11 +36,10 @@ from numarray import linear_algebra as la
 from numarray import ones, array, dot, swapaxes
 
 import reaper
-# sys.path.append("..") Never in a running webserver
-from basicStatistics import corestats
 
 import svg
 import webqtlUtil
+import corestats
 from base import webqtlConfig
 
 import utility.logger
@@ -315,137 +314,6 @@ def find_outliers(vals):
     logger.debug(pf(locals()))
     return upper_bound, lower_bound
 
-
-def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"):
-    xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
-    plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
-    plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
-    iValues = []
-    for item in data:
-        for item2 in item[1]:
-            try:
-                iValues.append(item2[1])
-            except:
-                iValues.append(item2)
-
-    #draw frame
-    max_Y = max(iValues)
-    min_Y = min(iValues)
-    scaleY = detScale(min_Y, max_Y)
-    Yll = scaleY[0]
-    Yur = scaleY[1]
-    nStep = scaleY[2]
-    stepY = (Yur - Yll)/nStep
-    stepYPixel = plotHeight/(nStep)
-    canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset)
-
-    ##draw Y Scale
-    YYY = Yll
-    YCoord = plotHeight + yTopOffset
-    scaleFont=pid.Font(ttf="cour",size=11,bold=1)
-    for i in range(nStep+1):
-        strY = cformat(d=YYY, rank=0)
-        YCoord = max(YCoord, yTopOffset)
-        canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord)
-        canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont)
-        YYY += stepY
-        YCoord -= stepYPixel
-
-    ##draw X Scale
-    stepX = plotWidth/len(data)
-    XCoord = xLeftOffset + 0.5*stepX
-    YCoord = plotHeight + yTopOffset
-    scaleFont = pid.Font(ttf="tahoma",size=12,bold=0)
-    labelFont = pid.Font(ttf="tahoma",size=13,bold=0)
-    for item in data:
-        itemname, itemvalue = item
-        canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black)
-        canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\
-        YCoord +20,font=labelFont)
-
-        nValue = len(itemvalue)
-        catValue = []
-        for item2 in itemvalue:
-            try:
-                tstrain, tvalue = item2
-            except:
-                tvalue = item2
-            if nValue <= 4:
-                canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5)
-            else:
-                catValue.append(tvalue)
-        if catValue != []:
-            catMean = gmean(catValue)
-            catMedian = gmedian(catValue)
-            lowHinge = gpercentile(catValue, 25)
-            upHinge = gpercentile(catValue, 75)
-            Hstep = 1.5*(upHinge - lowHinge)
-
-            outlier = []
-            extrem = []
-
-            upperAdj = None
-            for item in catValue:
-                if item >= upHinge + 2*Hstep:
-                    extrem.append(item)
-                elif item >= upHinge + Hstep:
-                    outlier.append(item)
-                elif item > upHinge and  item < upHinge + Hstep:
-                    if upperAdj == None or item > upperAdj:
-                        upperAdj = item
-                else:
-                    pass
-            lowerAdj = None
-            for item in catValue:
-                if item <= lowHinge - 2*Hstep:
-                    extrem.append(item)
-                elif item <= lowHinge - Hstep:
-                    outlier.append(item)
-                if item < lowHinge and  item > lowHinge - Hstep:
-                    if lowerAdj == None or item < lowerAdj:
-                        lowerAdj = item
-                    else:
-                        pass
-            canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-                    XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll))
-            canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \
-                    XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll))
-            if upperAdj != None:
-                canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \
-                XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-                canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \
-                XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll))
-            if lowerAdj != None:
-                canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \
-                XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-                canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \
-                XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll))
-
-            outlierFont = pid.Font(ttf="cour",size=12,bold=0)
-            if outlier != []:
-                for item in outlier:
-                    yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-                    #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-                    canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange)
-            if extrem != []:
-                for item in extrem:
-                    yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll)
-                    #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3)
-                    canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red)
-
-            canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \
-                    color=pid.blue,size=3)
-            #print(catMean, catMedian, cat25per, cat75per)
-            pass
-
-        XCoord += stepX
-
-    labelFont=pid.Font(ttf="verdana",size=18,bold=0)
-    canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \
-    YCoord +40, font=labelFont)
-    canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\
-     font=labelFont, angle =90)
-
 def plotSecurity(canvas, text="12345"):
     if not text:
         return
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
new file mode 100644
index 00000000..c48183ed
--- /dev/null
+++ b/wqflask/utility/corestats.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+#  corestats.py (COREy STATS)
+#  Copyright (c) 2006-2007, Corey Goldberg (corey@goldb.org)
+#
+#    statistical calculation class
+#    for processing numeric sequences
+#
+#  license: GNU LGPL
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2.1 of the License, or (at your option) any later version.
+
+import sys
+
+#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+class Stats:
+
+    def __init__(self, sequence):
+        # sequence of numbers we will process
+        # convert all items to floats for numerical processing
+        self.sequence = [float(item) for item in sequence]
+
+
+    def sum(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return sum(self.sequence)
+
+
+    def count(self):
+        return len(self.sequence)
+
+
+    def min(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return min(self.sequence)
+
+
+    def max(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return max(self.sequence)
+
+
+    def avg(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            return sum(self.sequence) / len(self.sequence)
+
+
+    def median(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            self.sequence.sort()
+            return self.sequence[len(self.sequence) // 2]
+
+
+    def stdev(self):
+        if len(self.sequence) < 1:
+            return None
+        else:
+            avg = self.avg()
+            sdsq = sum([(i - avg) ** 2 for i in self.sequence])
+            stdev = (sdsq / (len(self.sequence) - 1)) ** .5
+            return stdev
+
+
+    def percentile(self, percentile):
+        if len(self.sequence) < 1:
+            value = None
+        elif (percentile >= 100):
+            sys.stderr.write('ERROR: percentile must be < 100.  you supplied: %s\n'% percentile)
+            value = None
+        else:
+            element_idx = int(len(self.sequence) * (percentile / 100.0))
+            self.sequence.sort()
+            value = self.sequence[element_idx]
+        return value
+
+
+# Sample script using this class:
+# -------------------------------------------
+#    #!/usr/bin/env python
+#    import corestats
+#
+#    sequence = [1, 2.5, 7, 13.4, 8.0]
+#    stats = corestats.Stats(sequence)
+#    print stats.avg()
+#    print stats.percentile(90)
+# -------------------------------------------
\ No newline at end of file