osprai/trunk/vu_module.py

"""
vu: Viewer module for SPRI data in a ba class.
This uses the old Tk GUI toolkit.
Christopher Lausted, Institute for Systems Biology, 
OSPRAI developers
Last modified on 100416 (yymmdd)

Example:
#import vu_module as vu
#io_module as io
#ba1 = io.readsprit("spritdata.txt")
#vu.dotgraph(ba1, "Title")
#vu.linegraph(ba1, "Title")
#vu.dualgraph(ba1, ba2, "Title")
#vu.scatterplot(ba1, t1, t2, t3, t4, title)
"""
__version__ = "100416"


## Import libraries
import ba_class as ba               ## Our Biosensor Array class.
import numpy as np
from datetime import date
import Tkinter as Tk
import tkSimpleDialog as dialog
import matplotlib as mpl
mpl.use('TkAgg')
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
from matplotlib.figure import Figure


def linegraph(baLine, title=""):
    """Graph data of baLine using lines."""
    global root, fig, ax, canvas  ## Tk/mpl globals.
    global ba0, ba1, ba2   ## Ref to ba for roilist, dotgraph, linegraph
    global gTitle          ## Title for graph.
    ba0, ba1, ba2 = baLine, 0, baLine
    gTitle = title
    createSensorgramTkWindow()
    show()
    root.mainloop()
    return
    ## End of linegraph().
    
def dotgraph(baDot, title=""):
    """Graph data of baDot using dots."""
    global root, fig, ax, canvas  ## Tk/mpl globals..
    global ba0, ba1, ba2   ## Ref to ba for roilist, dotgraph, linegraph
    global gTitle          ## Title for graph.
    ba0, ba1, ba2 = baDot, baDot, 0
    gTitle = title
    createSensorgramTkWindow()
    show()
    root.mainloop()
    return
    ## End of dotgraph().
    
def dualgraph(baDot, baLine, title=""):
    """Graph data using dots and lines."""
    global root, fig, ax, canvas  ## Tk/mpl globals.
    global ba0, ba1, ba2   ## Ref to ba for roilist, dotgraph, linegraph
    global gTitle          ## Title for graph.
    ba0, ba1, ba2 = baDot, baDot, baLine
    gTitle = title
    createSensorgramTkWindow()
    show()
    root.mainloop()
    return
    ## End of dualgraph().

def show():
    """Graph data of ba using Tk window."""
    global root, fig, ax, canvas
    global ba1, ba2
    global gTitle
    
    ## Prepare graph labels.
    ax.clear()
    if (gTitle==""): gTitle='SPR Data plotted %s' % date.today().isoformat()
    ax.set_title(gTitle)
    ax.set_xlabel('Time (s)')
    ax.set_ylabel('SPR Response')
    ax.grid(True)
    
    ## Plot traces of real data.
    if (ba1 != 0):
        ## Dotted traces.
        marker = ['r,', 'g,', 'b,', 'c,', 'm,', 'y,'] + ['k,'] * 100
        for i,j in enumerate(roiList()):
            txt = str(j) + ':' + ba1.roi[j].name
            t = ba1.roi[j].time
            y = ba1.roi[j].value
            ax.plot(t, y, marker[i], label=txt)
    if (ba2 != 0):
        ## Line traces.
        marker = ['r', 'g', 'b', 'c', 'm', 'y'] + ['k'] * 100
        for i,j in enumerate(roiList()):
            txt = str(j) + ':' + ba2.roi[j].name
            t = ba2.roi[j].time
            y = ba2.roi[j].value
            ax.plot(t, y, marker[i], label=txt)
    
    ## Format legend.
    leg = ax.legend(loc='upper right')
    for t in leg.get_texts(): t.set_fontsize('x-small')
    #for t in leg.get_lines(): t.set_linestyle('None')
    #labels = [line.get_label() for line in ax.lines]
    #fig.legend(ax.lines, labels, 'right')
    
    canvas.draw()
    return
    ## End of show().
    
def btnNext():  
    ## Show next six traces on the graph.
    global ba0
    lo = max(roiList()) + 1
    if (lo == len(ba0.roi)): return
    lo = max(lo,0)
    hi = lo + 6
    hi = min(hi, len(ba0.roi))
    ba0.set_plot_list(range(lo, hi))
    show()
    return
    
def btnPrev():
    ## Show the previous six traces on the graph.
    global ba0
    lo = min(roiList()) - 6
    lo = max(lo,0)
    hi = lo + 6
    hi = min(hi, len(ba0.roi))
    ba0.set_plot_list(range(lo, hi))
    show()
    return

def btnTraces():
    ## Ask for list of traces to show on graph.
    global ba0
    txt = "Which ROIs would you like to see? (e.g. 19,20,21)"
    txt = dialog.askstring(title="Input",prompt=txt)
    txt = txt + ","  ## Be sure eval() produces a list.
    ba0.set_plot_list(eval(txt))
    show()
    return


def roiList():
    ## List of first six plottable ROIs.
    global ba0
    #x = [i for i in range(len(ba.roi)) if ba0.roi[i].plottable]
    x = [i.index for i in ba0.roi if i.plottable]
    return x[:6]


def createSensorgramTkWindow():
    """
    Create a Tk window for the Matplotlib graph.
    This window has three buttons which will allow the user to 
    """
    global root, fig, ax, canvas
    root = Tk.Tk()
    root.wm_title("TK matplotlib Osprai Sensorgram")
    ## Prepare a matplotlib Figure/Axes.
    fig = Figure(figsize=(6,4), dpi=100)
    ax = fig.add_subplot(111)
    ax.hold(True)  # Hold data until ax.clear().
    #ax.set_position([0.1, 0.1, 0.6, 0.8])  # Fraction of frame [left,bot,w,h]
    ## Define tk.DrawingArea
    canvas = FigureCanvasTkAgg(fig, master=root)
    #canvas.show()
    canvas.get_tk_widget().pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
    ## Add a pylab-style toolbar.
    toolbar = NavigationToolbar2TkAgg( canvas, root )
    toolbar.update()
    canvas._tkcanvas.pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
    ## Add buttons.
    button1 = Tk.Button(master=root, text='Next6', command=btnNext)
    button1.pack(side=Tk.RIGHT)
    button2 = Tk.Button(master=root, text='Choose..', command=btnTraces)
    button2.pack(side=Tk.RIGHT)
    button3 = Tk.Button(master=root, text='Prev6', command=btnPrev)
    button3.pack(side=Tk.RIGHT)
    return
    ## End of createSensorgramTkWindow().
    
    
##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##  ##


def scatterplot(ba0, t1, t2, t3, t4, title):
    """
    Plot binding changes between (t4-t3) versus (t2-t1).
    Also print the results to the standard output.
    """
     ## Create a Tk window for the ccatterplot graph.
     ## Variables root, fig, ax, canvas are local here, not global.
    root = Tk.Tk()
    root.wm_title("TK matplotlib Osprai Sensorgram")
    ## Prepare a matplotlib Figure/Axes.
    fig = Figure(figsize=(6,4), dpi=100)
    ax = fig.add_subplot(111)
    ax.hold(True)  # Hold data until ax.clear().
    ## Define tk.DrawingArea
    canvas = FigureCanvasTkAgg(fig, master=root)
    canvas.get_tk_widget().pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
    ## Add a pylab-style toolbar.
    toolbar = NavigationToolbar2TkAgg( canvas, root )
    toolbar.update()
    canvas._tkcanvas.pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
    
    ## Prepare graph labels.
    ax.clear()
    if (title==""): title='Scatterplot of %s' % date.today().isoformat()
    ax.set_title(title)
    ax.set_xlabel('Binding12')
    ax.set_ylabel('Binding34')
    ax.grid(True)
    
    ## Get array of values at each of the four time points.
    y1 = np.array([np.average(iroi.time2val(t1-15, t1+15)) for iroi in ba0.roi])
    y2 = np.array([np.average(iroi.time2val(t2-15, t2+15)) for iroi in ba0.roi])
    y3 = np.array([np.average(iroi.time2val(t3-15, t3+15)) for iroi in ba0.roi])
    y4 = np.array([np.average(iroi.time2val(t4-15, t4+15)) for iroi in ba0.roi])
    dx, dy = (y2-y1), (y4-y3)
    
    ## Print to stdout
    print "Name", "Binding12", "Binding34"
    for i in range(len(dx)): print ba0.roi[i].name, dx[i], dy[i]
    
    ## Plot
    ax.plot(dx, dy, 'bo')  ## Blue circles with 'bo'.
    canvas.draw()
    root.mainloop()
    return
    ## End of scatterplot()


## Print a message to the users so they see this module is loaded.
print "Loaded vu_module.py version ", __version__

################################# End of module #################################
Revision:	16
Committed:	Sun Apr 18 05:34:10 2010 UTC (11 years ago) by clausted
File size:	7919 byte(s)
Log Message:	Fix bug in "Next" button script.
Line	File contents
1	"""
2	vu: Viewer module for SPRI data in a ba class.
3	This uses the old Tk GUI toolkit.
4	Christopher Lausted, Institute for Systems Biology,
5	OSPRAI developers
6	Last modified on 100416 (yymmdd)
7
8	Example:
9	#import vu_module as vu
10	#io_module as io
11	#ba1 = io.readsprit("spritdata.txt")
12	#vu.dotgraph(ba1, "Title")
13	#vu.linegraph(ba1, "Title")
14	#vu.dualgraph(ba1, ba2, "Title")
15	#vu.scatterplot(ba1, t1, t2, t3, t4, title)
16	"""
17	__version__ = "100416"
18
19
20	## Import libraries
21	import ba_class as ba ## Our Biosensor Array class.
22	import numpy as np
23	from datetime import date
24	import Tkinter as Tk
25	import tkSimpleDialog as dialog
26	import matplotlib as mpl
27	mpl.use('TkAgg')
28	from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
29	from matplotlib.figure import Figure
30
31
32	def linegraph(baLine, title=""):
33	"""Graph data of baLine using lines."""
34	global root, fig, ax, canvas ## Tk/mpl globals.
35	global ba0, ba1, ba2 ## Ref to ba for roilist, dotgraph, linegraph
36	global gTitle ## Title for graph.
37	ba0, ba1, ba2 = baLine, 0, baLine
38	gTitle = title
39	createSensorgramTkWindow()
40	show()
41	root.mainloop()
42	return
43	## End of linegraph().
44
45	def dotgraph(baDot, title=""):
46	"""Graph data of baDot using dots."""
47	global root, fig, ax, canvas ## Tk/mpl globals..
48	global ba0, ba1, ba2 ## Ref to ba for roilist, dotgraph, linegraph
49	global gTitle ## Title for graph.
50	ba0, ba1, ba2 = baDot, baDot, 0
51	gTitle = title
52	createSensorgramTkWindow()
53	show()
54	root.mainloop()
55	return
56	## End of dotgraph().
57
58	def dualgraph(baDot, baLine, title=""):
59	"""Graph data using dots and lines."""
60	global root, fig, ax, canvas ## Tk/mpl globals.
61	global ba0, ba1, ba2 ## Ref to ba for roilist, dotgraph, linegraph
62	global gTitle ## Title for graph.
63	ba0, ba1, ba2 = baDot, baDot, baLine
64	gTitle = title
65	createSensorgramTkWindow()
66	show()
67	root.mainloop()
68	return
69	## End of dualgraph().
70
71	def show():
72	"""Graph data of ba using Tk window."""
73	global root, fig, ax, canvas
74	global ba1, ba2
75	global gTitle
76
77	## Prepare graph labels.
78	ax.clear()
79	if (gTitle==""): gTitle='SPR Data plotted %s' % date.today().isoformat()
80	ax.set_title(gTitle)
81	ax.set_xlabel('Time (s)')
82	ax.set_ylabel('SPR Response')
83	ax.grid(True)
84
85	## Plot traces of real data.
86	if (ba1 != 0):
87	## Dotted traces.
88	marker = ['r,', 'g,', 'b,', 'c,', 'm,', 'y,'] + ['k,'] * 100
89	for i,j in enumerate(roiList()):
90	txt = str(j) + ':' + ba1.roi[j].name
91	t = ba1.roi[j].time
92	y = ba1.roi[j].value
93	ax.plot(t, y, marker[i], label=txt)
94	if (ba2 != 0):
95	## Line traces.
96	marker = ['r', 'g', 'b', 'c', 'm', 'y'] + ['k'] * 100
97	for i,j in enumerate(roiList()):
98	txt = str(j) + ':' + ba2.roi[j].name
99	t = ba2.roi[j].time
100	y = ba2.roi[j].value
101	ax.plot(t, y, marker[i], label=txt)
102
103	## Format legend.
104	leg = ax.legend(loc='upper right')
105	for t in leg.get_texts(): t.set_fontsize('x-small')
106	#for t in leg.get_lines(): t.set_linestyle('None')
107	#labels = [line.get_label() for line in ax.lines]
108	#fig.legend(ax.lines, labels, 'right')
109
110	canvas.draw()
111	return
112	## End of show().
113
114	def btnNext():
115	## Show next six traces on the graph.
116	global ba0
117	lo = max(roiList()) + 1
118	if (lo == len(ba0.roi)): return
119	lo = max(lo,0)
120	hi = lo + 6
121	hi = min(hi, len(ba0.roi))
122	ba0.set_plot_list(range(lo, hi))
123	show()
124	return
125
126	def btnPrev():
127	## Show the previous six traces on the graph.
128	global ba0
129	lo = min(roiList()) - 6
130	lo = max(lo,0)
131	hi = lo + 6
132	hi = min(hi, len(ba0.roi))
133	ba0.set_plot_list(range(lo, hi))
134	show()
135	return
136
137	def btnTraces():
138	## Ask for list of traces to show on graph.
139	global ba0
140	txt = "Which ROIs would you like to see? (e.g. 19,20,21)"
141	txt = dialog.askstring(title="Input",prompt=txt)
142	txt = txt + "," ## Be sure eval() produces a list.
143	ba0.set_plot_list(eval(txt))
144	show()
145	return
146
147
148	def roiList():
149	## List of first six plottable ROIs.
150	global ba0
151	#x = [i for i in range(len(ba.roi)) if ba0.roi[i].plottable]
152	x = [i.index for i in ba0.roi if i.plottable]
153	return x[:6]
154
155
156	def createSensorgramTkWindow():
157	"""
158	Create a Tk window for the Matplotlib graph.
159	This window has three buttons which will allow the user to
160	"""
161	global root, fig, ax, canvas
162	root = Tk.Tk()
163	root.wm_title("TK matplotlib Osprai Sensorgram")
164	## Prepare a matplotlib Figure/Axes.
165	fig = Figure(figsize=(6,4), dpi=100)
166	ax = fig.add_subplot(111)
167	ax.hold(True) # Hold data until ax.clear().
168	#ax.set_position([0.1, 0.1, 0.6, 0.8]) # Fraction of frame [left,bot,w,h]
169	## Define tk.DrawingArea
170	canvas = FigureCanvasTkAgg(fig, master=root)
171	#canvas.show()
172	canvas.get_tk_widget().pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
173	## Add a pylab-style toolbar.
174	toolbar = NavigationToolbar2TkAgg( canvas, root )
175	toolbar.update()
176	canvas._tkcanvas.pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
177	## Add buttons.
178	button1 = Tk.Button(master=root, text='Next6', command=btnNext)
179	button1.pack(side=Tk.RIGHT)
180	button2 = Tk.Button(master=root, text='Choose..', command=btnTraces)
181	button2.pack(side=Tk.RIGHT)
182	button3 = Tk.Button(master=root, text='Prev6', command=btnPrev)
183	button3.pack(side=Tk.RIGHT)
184	return
185	## End of createSensorgramTkWindow().
186
187
188	## ## ## ## ## ## ## ## ## ## ## ## ## ## ## ## ## ##
189
190
191	def scatterplot(ba0, t1, t2, t3, t4, title):
192	"""
193	Plot binding changes between (t4-t3) versus (t2-t1).
194	Also print the results to the standard output.
195	"""
196	## Create a Tk window for the ccatterplot graph.
197	## Variables root, fig, ax, canvas are local here, not global.
198	root = Tk.Tk()
199	root.wm_title("TK matplotlib Osprai Sensorgram")
200	## Prepare a matplotlib Figure/Axes.
201	fig = Figure(figsize=(6,4), dpi=100)
202	ax = fig.add_subplot(111)
203	ax.hold(True) # Hold data until ax.clear().
204	## Define tk.DrawingArea
205	canvas = FigureCanvasTkAgg(fig, master=root)
206	canvas.get_tk_widget().pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
207	## Add a pylab-style toolbar.
208	toolbar = NavigationToolbar2TkAgg( canvas, root )
209	toolbar.update()
210	canvas._tkcanvas.pack(side=Tk.TOP, fill=Tk.BOTH, expand=1)
211
212	## Prepare graph labels.
213	ax.clear()
214	if (title==""): title='Scatterplot of %s' % date.today().isoformat()
215	ax.set_title(title)
216	ax.set_xlabel('Binding12')
217	ax.set_ylabel('Binding34')
218	ax.grid(True)
219
220	## Get array of values at each of the four time points.
221	y1 = np.array([np.average(iroi.time2val(t1-15, t1+15)) for iroi in ba0.roi])
222	y2 = np.array([np.average(iroi.time2val(t2-15, t2+15)) for iroi in ba0.roi])
223	y3 = np.array([np.average(iroi.time2val(t3-15, t3+15)) for iroi in ba0.roi])
224	y4 = np.array([np.average(iroi.time2val(t4-15, t4+15)) for iroi in ba0.roi])
225	dx, dy = (y2-y1), (y4-y3)
226
227	## Print to stdout
228	print "Name", "Binding12", "Binding34"
229	for i in range(len(dx)): print ba0.roi[i].name, dx[i], dy[i]
230
231	## Plot
232	ax.plot(dx, dy, 'bo') ## Blue circles with 'bo'.
233	canvas.draw()
234	root.mainloop()
235	return
236	## End of scatterplot()
237
238
239	## Print a message to the users so they see this module is loaded.
240	print "Loaded vu_module.py version ", __version__
241
242	################################# End of module #################################