Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno

1 files changed, 80 insertions, 47 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index cce8435d..61f408d2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,32 +24,35 @@
 #
 # Last updated by GeneNetwork Core Team 2010/10/20
 
-from __future__ import print_function
-
-import piddle as pid
-from pprint import pformat as pf
+from PIL import ImageColor
+from PIL import ImageDraw
+from PIL import ImageFont
 
 from math import *
-import random
-import sys, os
-from numarray import linear_algebra as la
-from numarray import ones, array, dot, swapaxes
-
-import reaper
 
-import webqtlUtil
-import corestats
+import utility.corestats as corestats
 from base import webqtlConfig
-
+from utility.pillow_utils import draw_rotated_text
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
+# ---- Define common colours ---- #
+BLUE = ImageColor.getrgb("blue")
+BLACK = ImageColor.getrgb("black")
+# ---- END: Define common colours ---- #
+
+# ---- FONT FILES ---- #
+VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf"
+COUR_FILE = "./wqflask/static/fonts/courbd.ttf"
+TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf"
+# ---- END: FONT FILES ---- #
+
 def cformat(d, rank=0):
     'custom string format'
     strD = "%2.6f" % d
 
     if rank == 0:
-        while strD[-1] in ('0','.'):
+        while strD[-1] in ('0', '.'):
             if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
                 break
             elif strD[-1] == '.':
@@ -77,7 +80,7 @@ def frange(start, end=None, inc=1.0):
     # Need to adjust the count. AFAICT, it always comes up one short.
         count += 1
     L = [start] * count
-    for i in xrange(1, count):
+    for i in range(1, count):
         L[i] = start + i * inc
     return L
 
@@ -88,7 +91,7 @@ def find_outliers(vals):
     >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537])
     (11.252500000000001, 0.5364999999999993)
 
-    >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
+    >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
     (32.0, -8.0)
 
     If there are no vals, returns None for the upper and lower bounds,
@@ -116,7 +119,8 @@ def find_outliers(vals):
 
 # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
 # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
-def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+    im_drawer = ImageDraw.Draw(canvas)
     xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
 
     plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -152,7 +156,7 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
        j = int((item-xLow)/step)
        Count[j] += 1
 
-    yLow, yTop, stepY=detScale(0,max(Count))
+    yLow, yTop, stepY=detScale(0, max(Count))
 
     #draw data
     xScale = plotWidth/(xTop-xLow)
@@ -163,67 +167,91 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
        if count:
            xc = (dataXY[i]-xLow)*xScale+xLeftOffset
            yc =-(count-yLow)*yScale+yTopOffset+plotHeight
-           canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
+           im_drawer.rectangle(
+               xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)),
+               outline=barColor, fill=barColor)
 
     #draw drawing region
-    canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+    im_drawer.rectangle(
+        xy=((xLeftOffset, yTopOffset), (xLeftOffset+plotWidth, yTopOffset+plotHeight))
+    )
 
     #draw scale
-    scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+    scaleFont=ImageFont.truetype(font=COUR_FILE, size=11)
     x=xLow
     for i in range(int(stepX)+1):
        xc=xLeftOffset+(x-xLow)*xScale
-       canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
+       im_drawer.line(
+           xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)),
+           fill=axesColor)
        strX = cformat(d=x, rank=0)
-       canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
+       im_drawer.text(
+           text=strX,
+           xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2,
+               yTopOffset+plotHeight+14), font=scaleFont)
        x+= (xTop - xLow)/stepX
 
     y=yLow
     for i in range(int(stepY)+1):
        yc=yTopOffset+plotHeight-(y-yLow)*yScale
-       canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+       im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor)
        strY = "%d" %y
-       canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+       im_drawer.text(
+           text=strY,
+           xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5),
+           font=scaleFont)
        y+= (yTop - yLow)/stepY
 
     #draw label
-    labelFont=pid.Font(ttf="tahoma",size=17,bold=0)
+    labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17)
     if XLabel:
-       canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
-               yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
+       im_drawer.text(
+           text=XLabel,
+           xy=(xLeftOffset+(
+               plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0,
+               yTopOffset+plotHeight+yBottomOffset-10),
+           font=labelFont, fill=labelColor)
 
     if YLabel:
-       canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
-               font=labelFont,color=labelColor,angle=90)
-
-    labelFont=pid.Font(ttf="verdana",size=16,bold=0)
+        draw_rotated_text(canvas, text=YLabel,
+                          xy=(19,
+                              yTopOffset+plotHeight-(
+                                  plotHeight-im_drawer.textsize(
+                                      YLabel, font=labelFont)[0])/2.0),
+                          font=labelFont, fill=labelColor, angle=90)
+
+    labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16)
     if title:
-       canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
-               20,font=labelFont,color=labelColor)
+       im_drawer.text(
+           text=title,
+           xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
+               title, font=labelFont)[0])/2.0,
+               20),
+           font=labelFont, fill=labelColor)
 
 # This function determines the scale of the plot
-def detScaleOld(min,max):
+def detScaleOld(min, max):
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         if a < c*5.0:
             c/=2.0
         #print a,b,c
         low=c*floor(min/c)
         high=c*ceil(max/c)
-        return [low,high,round((high-low)/c)]
+        return [low, high, round((high-low)/c)]
 
 def detScale(min=0,max=0):
 
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         if max != 0:
@@ -235,7 +263,7 @@ def detScale(min=0,max=0):
                 min -= 0.1*a
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         low=c*floor(min/c)
         high=c*ceil(max/c)
         n = round((high-low)/c)
@@ -253,7 +281,7 @@ def detScale(min=0,max=0):
             high=c*ceil(max/c)
             n = round((high-low)/c)
 
-        return [low,high,n]
+        return [low, high, n]
 
 def bluefunc(x):
     return 1.0 / (1.0 + exp(-10*(x-0.6)))
@@ -262,21 +290,26 @@ def redfunc(x):
     return 1.0 / (1.0 + exp(10*(x-0.5)))
 
 def greenfunc(x):
-    return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
+    return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3)
 
 def colorSpectrum(n=100):
     multiple = 10
     if n == 1:
-        return [pid.Color(1,0,0)]
+        return [ImageColor.getrgb("rgb(100%,0%,0%)")]
     elif n == 2:
-        return [pid.Color(1,0,0),pid.Color(0,0,1)]
+        return [ImageColor.getrgb("100%,0%,0%)"),
+                ImageColor.getrgb("rgb(0%,0%,100%)")]
     elif n == 3:
-        return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
+        return [ImageColor.getrgb("rgb(100%,0%,0%)"),
+                ImageColor.getrgb("rgb(0%,100%,0%)"),
+                ImageColor.getrgb("rgb(0%,0%,100%)")]
     N = n*multiple
     out = [None]*N;
     for i in range(N):
         x = float(i)/N
-        out[i] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
+        out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format(
+            *[int(i*100) for i in (
+                redfunc(x), greenfunc(x), bluefunc(x))]))
     out2 = [out[0]]
     step = N/float(n-1)
     j = 0
@@ -292,4 +325,4 @@ def _test():
 
 
 if __name__=="__main__":
-    _test()
\ No newline at end of file
+    _test()