--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/breadcrumbs/src/PlotMatrix.py	Thu Jun 03 18:13:32 2021 +0000
@@ -0,0 +1,96 @@
+"""
+Author: Timothy Tickle
+Description: Plots matrices.
+"""
+
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#####################################################################################
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2012"
+__credits__ = ["Timothy Tickle"]
+__license__ = "MIT"
+__maintainer__ = "Timothy Tickle"
+__email__ = "ttickle@sph.harvard.edu"
+__status__ = "Development"
+
+#External libraries
+import matplotlib.pyplot as plt
+import numpy as np
+from pylab import *
+
+#Plots a matrix
+class PlotMatrix:
+
+  #Given a matrix and labels consistent to the matrix, plot a matrix
+  @staticmethod
+  def funcPlotMatrix(npMatrix, lsXLabels, strOutputFigurePath, strXTitle="X Axis", strYTitle="Y Axis", fFlipYLabels=False):
+    """
+    Given a matrix and labels consistent to the matrix, plot a matrix.
+
+    :param npMatrix: Numpy Array (matrix) to plot.
+    :type: Numpy Array
+    :param lsXLabels: X Labels
+    :type: List of strings
+    :param strOutputFigurePath: File to create the figure file.
+    :type: String
+    :param strXTitle: X Axis label.
+    :type: String
+    :param strYTitle: Y axis label.
+    :type: String
+    :param fFlipYLabels: Flip the Y labels so they are opposite order of x axis.
+    :type: Boolean
+    """
+
+    #Get canvas/figure
+    plt.clf()
+    figConfusionMatrix = plt.figure()
+    objAxis = figConfusionMatrix.add_subplot(111)
+
+    #Get y labels
+    lNewYLabels = list(lsXLabels)
+    if fFlipYLabels:
+        lNewYLabels.reverse()
+
+    #Set x axis and position
+    objAxis.xaxis.set_ticklabels([""]+lsXLabels)
+    objAxis.xaxis.set_ticks_position('top')
+
+    #Set y axis
+    objAxis.yaxis.set_ticklabels([""]+lNewYLabels)
+
+    #Set axis titles
+    ylabel(strYTitle)
+    plt.suptitle(strXTitle)
+
+    #Plot matrix values
+    objPlot = objAxis.imshow(np.array(npMatrix), cmap=get_cmap("Blues"), interpolation='nearest')
+
+    #Plot text values
+    for yIndex, ldRow in enumerate(npMatrix):
+        for xIndex, dValue in enumerate(ldRow):
+            plt.text(xIndex, yIndex, dValue, fontdict = {'size':18,'weight':'bold'} )
+
+    #Add color bar
+    figConfusionMatrix.colorbar(objPlot, ticks=range(int(min(np.array(npMatrix).ravel())),int(max(np.array(npMatrix).ravel()))))
+
+    #Save to a file
+    savefig(strOutputFigurePath)