Filechooser UI should now have smaller buttons; Added enzyme activity zones & legend; added legend for data lines; default view renders a graph; graph now updates properly after clearing data and after selecting a reference profile

main.kv

@@ -12,6 +12,7 @@
             text: 'Continuing will clear the graph and turn off logging to file.'
         BoxLayout:
             orientation: 'horizontal'
+            size_hint_y: 0.1
             Button:
                 id: cancel_button
                 text: 'Cancel'
@@ -70,11 +71,10 @@
             text: 'Select a reference temperature profile (csv)'
             size_hint_y: 0.1
         FileChooserListView:
-            size_hint_y: 0.8
             id: filechooser
             filters: ['*.csv']
         BoxLayout:
-            size_hiny_y: 0.1
+            size_hint_y: 0.1
             orientation: 'horizontal'
             Button:
                 text: 'Cancel'

main.py

@@ -8,7 +8,7 @@ from kivy.core.image.img_pygame import ImageLoaderPygame
 import kivy.graphics.texture
 from kivy.graphics.texture import Texture
 from kivy.logger import Logger
-from kivy.properties import DictProperty, ListProperty, NumericProperty, ObjectProperty, StringProperty
+from kivy.properties import BooleanProperty, DictProperty, ListProperty, NumericProperty, ObjectProperty, StringProperty
 from kivy.uix.boxlayout import BoxLayout
 from kivy.uix.button import Button
 from kivy.uix.dropdown import DropDown
@@ -23,6 +23,8 @@ import kivy.lang
 import matplotlib
 matplotlib.use('Agg')
 import matplotlib.image
+import matplotlib.lines
+import matplotlib.patches
 import matplotlib.pyplot
 import numpy
 import os
@@ -366,6 +368,21 @@ class PlotWidget(Image):
     image_output_file = StringProperty('')
     raw_data_output_file = StringProperty('')
     reference_profile_file = StringProperty('')
+    # @TODO Include a way to change these properties.
+    show_betaglucan = BooleanProperty(True)
+    show_protease = BooleanProperty(True)
+    show_betaamylase = BooleanProperty(True)
+    show_alphaamylase = BooleanProperty(True)
+
+    # Common data that we should only instantiate once
+    # Source : http://www.howtobrew.com/section3/chapter14-1.html
+    # accessed on march 21, 2015
+    # x_vertices = ((x, y), width, height, color, legend_string)
+    betaglucan_vertices = ((0, 35), 12000, 10, '#57ff14', 'Betaglucanase')
+    protease_vertices = ((0,45), 12000, 10, '#f3ff14', 'Protease / Peptidase')
+    betaamylase_vertices = ((0,55), 12000, 10.6, '#ffc014', 'Beta Amylase')
+    alphaamylase_vertices = ((0, 67.7), 12000, 4.5, '#ff6614', 'Alpha Amylase')
+
 
     def __init__(self, **kwargs):
         super(PlotWidget, self).__init__(**kwargs)
@@ -381,6 +398,34 @@ class PlotWidget(Image):
         self.image_data = None
         self._image_raw_data = None
         self.reference_profile = None
+        self.do_update()
+
+
+    def update_patches(self, tmax = None):
+        items = [
+            (self.show_betaglucan, self.betaglucan_vertices),
+            (self.show_protease, self.protease_vertices),
+            (self.show_betaamylase, self.betaamylase_vertices),
+            (self.show_alphaamylase, self.alphaamylase_vertices)
+        ]
+        legend_handles = []
+        legend_strings = []
+        for show, config in items:
+            color = '0.5' # default color.
+            if show:
+                origin, width, height, color, name = config
+                if tmax is not None:
+                    width = tmax
+                p = self.plot_axes.add_patch(
+                    matplotlib.patches.Rectangle(origin, width, height,
+                                                 fc = color, visible = True,
+                                                 fill = True)
+                    #matplotlib.patches.Polygon(vertices, facecolor = color)
+                )
+                legend_handles.append(p)
+                legend_strings.append(name)
+        self.figure.legend(legend_handles, legend_strings, 'upper left',
+                           title = 'Enzyme Activity Zones')
 
 
     def clear_data(self):
@@ -390,6 +435,7 @@ class PlotWidget(Image):
         self.texture = None
         self.image_output_file = ''
         self.raw_data_output_file = ''
+        self.do_update()
 
 
     def do_update(self):
@@ -417,30 +463,44 @@ class PlotWidget(Image):
 
 
     def to_image_data(self):
-        if not self.data.any():
+        # Add in polygons for hilightning particular temperature ranges of interest.
-            return
+        plot_args = []
-        #Logger.debug('self.data: ' + str(self.data))
+        t = None
-        #Logger.debug('self.data shape: ' + str(self.data.shape))
+        time_max = 60
-        data = numpy.copy(self.data)
+        temp_max = 80
-        data = data.transpose()
+        handles = []
-        #Logger.debug('transpoed data: ' + str(data))
+        if self.data.any():
-        #Logger.debug('transposed data shape: ' + str(data.shape))
+            data = numpy.copy(self.data)
-        t, temperature = numpy.split(data, 2, axis = 0)
+            data = data.transpose()
-        reference_data = None
+            t, temperature = numpy.split(data, 2, axis = 0)
+            if t[0][-1] > time_max:
+                time_max = t[0][-1]
+            if numpy.nanmax(temperature[0]) > temp_max:
+                temp_max = numpy.nanmax(temperature[0])
+            plot_args.extend((t[0], temperature[0], 'b'))
+            handles.append('Recorded Temperature Profile')
         if self.reference_profile is not None and self.reference_profile.any():
             reference_data = numpy.copy(self.reference_profile)
             reference_data = reference_data.transpose()
             t2, reference_temperature = numpy.split(reference_data, 2, axis = 0)
             # Add t[0] to all reference points to make it fit on the current graph
-            t2 = numpy.add(t2, t[0][0])
+            if t:
-            #Logger.debug('PlotWidget: reference profile t: ' + str(t2))
+                t2 = numpy.add(t2, t[0][0])
-            #Logger.debug('PlotWidget: reference profile temp: ' + str(reference_temperature))
+            if t2[0][-1] > time_max:
-        #Logger.debug('PlotWidget: time: ' + str(t[0]))
+                time_max = t2[0][-1]
-        #Logger.debug('PlotWidget: temperature: ' + str(temperature[0]))
+            if numpy.nanmax(reference_temperature[0]) > temp_max:
-        if reference_data is not None and reference_data.any():
+                temp_max = numpy.nanmax(reference_temperature[0])
-            self.plot_axes.plot(t[0], temperature[0], 'b', t2[0], reference_temperature[0], 'r')
+            plot_args.extend((t2[0], reference_temperature[0], 'r'))
-        else:
+            handles.append('Reference Temperature Profile')
-            self.plot_axes.plot(t[0], temperature[0], 'b')
+        lines = self.plot_axes.plot(*plot_args)
+        # Patches must be changed after the axes are plotted.
+        self.update_patches(time_max)
+        self.plot_axes.legend(lines, handles, 'upper right', title = 'Temperature Profiles')
+        if not lines:
+            # Set a default in case no data is plotted. This may allow patches to show,
+            # and it will look a little nicer before recording starts.
+            self.plot_axes.set_xlim(0, time_max)
+            self.plot_axes.set_ylim(0, temp_max)
         image_data = StringIO.StringIO()
         self.figure.savefig(image_data, format = 'png')
         image_data.seek(0)
@@ -487,6 +547,7 @@ class PlotWidget(Image):
     def on_reference_profile_file(self, *args, **kwargs):
         Logger.debug('PlotWidget: on_reference_profile_file ' + str(self.reference_profile_file))
         self.load_reference_profile()
+        self.do_update()
 
 
     def load_reference_profile(self):
@@ -496,6 +557,7 @@ class PlotWidget(Image):
                                                delimiter=',')
         Logger.debug('PlotWidget: reference_profile: ' + str(self.reference_profile))
 
+
 class YesNoModalView(Popup):
 
     def process(self, result, *args, **kwargs):