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
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c7264ded31
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4
main.kv
4
main.kv
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@ -12,6 +12,7 @@
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text: 'Continuing will clear the graph and turn off logging to file.'
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BoxLayout:
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orientation: 'horizontal'
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size_hint_y: 0.1
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Button:
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id: cancel_button
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text: 'Cancel'
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@ -70,11 +71,10 @@
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text: 'Select a reference temperature profile (csv)'
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size_hint_y: 0.1
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FileChooserListView:
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size_hint_y: 0.8
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id: filechooser
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filters: ['*.csv']
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BoxLayout:
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size_hiny_y: 0.1
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size_hint_y: 0.1
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orientation: 'horizontal'
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Button:
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text: 'Cancel'
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94
main.py
94
main.py
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@ -8,7 +8,7 @@ from kivy.core.image.img_pygame import ImageLoaderPygame
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import kivy.graphics.texture
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from kivy.graphics.texture import Texture
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from kivy.logger import Logger
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from kivy.properties import DictProperty, ListProperty, NumericProperty, ObjectProperty, StringProperty
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from kivy.properties import BooleanProperty, DictProperty, ListProperty, NumericProperty, ObjectProperty, StringProperty
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from kivy.uix.boxlayout import BoxLayout
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from kivy.uix.button import Button
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from kivy.uix.dropdown import DropDown
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@ -23,6 +23,8 @@ import kivy.lang
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import matplotlib
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matplotlib.use('Agg')
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import matplotlib.image
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import matplotlib.lines
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import matplotlib.patches
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import matplotlib.pyplot
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import numpy
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import os
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@ -366,6 +368,21 @@ class PlotWidget(Image):
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image_output_file = StringProperty('')
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raw_data_output_file = StringProperty('')
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reference_profile_file = StringProperty('')
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# @TODO Include a way to change these properties.
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show_betaglucan = BooleanProperty(True)
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show_protease = BooleanProperty(True)
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show_betaamylase = BooleanProperty(True)
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show_alphaamylase = BooleanProperty(True)
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# Common data that we should only instantiate once
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# Source : http://www.howtobrew.com/section3/chapter14-1.html
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# accessed on march 21, 2015
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# x_vertices = ((x, y), width, height, color, legend_string)
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betaglucan_vertices = ((0, 35), 12000, 10, '#57ff14', 'Betaglucanase')
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protease_vertices = ((0,45), 12000, 10, '#f3ff14', 'Protease / Peptidase')
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betaamylase_vertices = ((0,55), 12000, 10.6, '#ffc014', 'Beta Amylase')
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alphaamylase_vertices = ((0, 67.7), 12000, 4.5, '#ff6614', 'Alpha Amylase')
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def __init__(self, **kwargs):
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super(PlotWidget, self).__init__(**kwargs)
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@ -381,6 +398,34 @@ class PlotWidget(Image):
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self.image_data = None
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self._image_raw_data = None
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self.reference_profile = None
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self.do_update()
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def update_patches(self, tmax = None):
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items = [
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(self.show_betaglucan, self.betaglucan_vertices),
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(self.show_protease, self.protease_vertices),
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(self.show_betaamylase, self.betaamylase_vertices),
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(self.show_alphaamylase, self.alphaamylase_vertices)
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]
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legend_handles = []
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legend_strings = []
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for show, config in items:
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color = '0.5' # default color.
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if show:
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origin, width, height, color, name = config
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if tmax is not None:
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width = tmax
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p = self.plot_axes.add_patch(
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matplotlib.patches.Rectangle(origin, width, height,
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fc = color, visible = True,
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fill = True)
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#matplotlib.patches.Polygon(vertices, facecolor = color)
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)
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legend_handles.append(p)
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legend_strings.append(name)
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self.figure.legend(legend_handles, legend_strings, 'upper left',
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title = 'Enzyme Activity Zones')
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def clear_data(self):
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@ -390,6 +435,7 @@ class PlotWidget(Image):
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self.texture = None
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self.image_output_file = ''
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self.raw_data_output_file = ''
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self.do_update()
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def do_update(self):
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@ -417,30 +463,44 @@ class PlotWidget(Image):
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def to_image_data(self):
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if not self.data.any():
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return
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#Logger.debug('self.data: ' + str(self.data))
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#Logger.debug('self.data shape: ' + str(self.data.shape))
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# Add in polygons for hilightning particular temperature ranges of interest.
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plot_args = []
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t = None
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time_max = 60
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temp_max = 80
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handles = []
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if self.data.any():
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data = numpy.copy(self.data)
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data = data.transpose()
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#Logger.debug('transpoed data: ' + str(data))
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#Logger.debug('transposed data shape: ' + str(data.shape))
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t, temperature = numpy.split(data, 2, axis = 0)
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reference_data = None
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if t[0][-1] > time_max:
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time_max = t[0][-1]
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if numpy.nanmax(temperature[0]) > temp_max:
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temp_max = numpy.nanmax(temperature[0])
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plot_args.extend((t[0], temperature[0], 'b'))
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handles.append('Recorded Temperature Profile')
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if self.reference_profile is not None and self.reference_profile.any():
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reference_data = numpy.copy(self.reference_profile)
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reference_data = reference_data.transpose()
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t2, reference_temperature = numpy.split(reference_data, 2, axis = 0)
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# Add t[0] to all reference points to make it fit on the current graph
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if t:
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t2 = numpy.add(t2, t[0][0])
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#Logger.debug('PlotWidget: reference profile t: ' + str(t2))
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#Logger.debug('PlotWidget: reference profile temp: ' + str(reference_temperature))
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#Logger.debug('PlotWidget: time: ' + str(t[0]))
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#Logger.debug('PlotWidget: temperature: ' + str(temperature[0]))
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if reference_data is not None and reference_data.any():
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self.plot_axes.plot(t[0], temperature[0], 'b', t2[0], reference_temperature[0], 'r')
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else:
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self.plot_axes.plot(t[0], temperature[0], 'b')
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if t2[0][-1] > time_max:
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time_max = t2[0][-1]
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if numpy.nanmax(reference_temperature[0]) > temp_max:
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temp_max = numpy.nanmax(reference_temperature[0])
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plot_args.extend((t2[0], reference_temperature[0], 'r'))
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handles.append('Reference Temperature Profile')
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lines = self.plot_axes.plot(*plot_args)
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# Patches must be changed after the axes are plotted.
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self.update_patches(time_max)
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self.plot_axes.legend(lines, handles, 'upper right', title = 'Temperature Profiles')
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if not lines:
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# Set a default in case no data is plotted. This may allow patches to show,
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# and it will look a little nicer before recording starts.
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self.plot_axes.set_xlim(0, time_max)
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self.plot_axes.set_ylim(0, temp_max)
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image_data = StringIO.StringIO()
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self.figure.savefig(image_data, format = 'png')
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image_data.seek(0)
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@ -487,6 +547,7 @@ class PlotWidget(Image):
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def on_reference_profile_file(self, *args, **kwargs):
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Logger.debug('PlotWidget: on_reference_profile_file ' + str(self.reference_profile_file))
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self.load_reference_profile()
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self.do_update()
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def load_reference_profile(self):
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@ -496,6 +557,7 @@ class PlotWidget(Image):
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delimiter=',')
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Logger.debug('PlotWidget: reference_profile: ' + str(self.reference_profile))
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class YesNoModalView(Popup):
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def process(self, result, *args, **kwargs):
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