def initPsiMatrix(self,master):
"""initializes Matrix containing psi values
should do the following:
1. display matrix of Edits? MatrixWidget
2. load data and display it
3. colorcode
"""
self.matrixTL = tk.Toplevel(master)
self.psi_matrix = SimpleTable(self.matrixTL)
self.psi_matrix.grid(sticky="nsew")
self.psi_matrix.fill(self.d.sList,self.d.pairwise_stats['psi'])
self.psi_matrix.fill_labels(self.d.sList)
class PooGUI(tk.Frame):
"""the main frame with the GUI, contains three sections and a menu bar
- the main section is the plotting area using matplotlib
- in the top right are sliders,
- bottom right is a list of samples
we have the following objects:
-sList: a list of all samples
-hList: a list of all hyperbolas
-data: the raw SNP data (mbsData obj?)
-coords: data structure with coordinates
-psi: np.array[s1,s2] : psi
-v: constant multiplier of hyperbolas
-xlim, ylim: plotting limits
"""
#---------------------------------------------------------------------
# drawing stuff for points, should eventually be moved to an
# appropriate plotting class,psi, data
#---------------------------------------------------------------------
def dummyElements(self):
#vars I need
self.activeCanvas
self.canvas['H'] #replace with self.canvas[]...
self.canvas['Psi']
self.sample_frame
self.origin_frame
self.slider_frame
self.bgi
self.matrixTL
self.psimatrix
#vars in config
self.lwd #should be in either plot...
self.threshold
#vars in Data
self.v
self.clusters
self.psi
self.data
self.psi_sum
self.oList
self.hList #??
self.sList #???
#vars I don't need
#maybees
def __init__(self, master=None):
"""the main constructor of the frame. As it is quite big,
i split it up into subfunctions for the various ui parts.
Might be worth to instead use children classes instead.
The main app window will have a status bar at the bottom with
progress messages and stuff. The main window will be
the square matplotlib canvas on the right and a narrowish bar
with samples, sliders, etc on the right
"""
tk.Frame.__init__(self, master, relief=tk.SUNKEN)
self.master = master
self.d = Data(self)
self.c = Config(O)
self.canvas = dict()
self.d.sList = []
self.d.oList = []
self.init_canvas_hyperbolas()
self.init_canvas_pwp(active=True)
self.init_sample_frame()
#self.init_statusbar()
self.init_slider_frame()
self.init_menubar()
#enable expansion
tk.Grid.rowconfigure(self,1,weight=10)
tk.Grid.rowconfigure(self,2,weight=1)
tk.Grid.columnconfigure(self,1,weight=1)
tk.Grid.columnconfigure(self,2,weight=1)
tk.Grid.columnconfigure(self,0,weight=2)
def initPsiMatrix(self,master):
"""initializes Matrix containing psi values
should do the following:
1. display matrix of Edits? MatrixWidget
2. load data and display it
3. colorcode
"""
self.matrixTL = tk.Toplevel(master)
self.psi_matrix = SimpleTable(self.matrixTL)
self.psi_matrix.grid(sticky="nsew")
self.psi_matrix.fill(self.d.sList,self.d.pairwise_stats['psi'])
self.psi_matrix.fill_labels(self.d.sList)
def init_menubar(self):
"""
this function loads and populates the menubar, and will register its events
"""
self.menubar = tk.Menu(self)
menu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="File", menu=menu)
menu.add_command(label="Load SNP",command=self.loadSNP)
menu.add_command(label="Load Coords", command=self.loadCoords)
menu.add_command(label="Load Background Image", command=self.loadBGI)
menu.add_command(label="Save plot", command=self.save_plot)
menu.add_command(label="Quit", command=self.quit)
menu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Edit", menu=menu)
menu.add_command(label="Set Reference Coordinates")
menu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="View", menu=menu)
menu.add_command(label="Hyperbolas",
command=self.showHyperbolaCanvas)
menu.add_command(label="Pairwise Psi",
command=self.showPsiCanvas)
menu = tk.Menu(self.menubar, tearoff=0)
self.menubar.add_cascade(label="Run", menu=menu)
menu.add_command(label="Find Origin All", command=self.optimizeAll)
menu.add_command(label="Find Origin Visible")
try:
self.master.config(menu=self.menubar)
except AttributeError:
# master is a toplevel window (Python 1.4/Tkinter 1.63)
self.master.tk.call(master, "config", "-menu", self.menubar)
def init_canvas_hyperbolas(self, active=False):
"""
this function creates the matplotlib canvas that will be used
to draw stuff
master: parent frame
active: is this displayed on startup?
"""
self.canvas['H'] = HyperbolaCanvas(self, self.c,
self.d.sList,
self.d, width=300, height=300)
self.canvas['H'].grid(column=0,row=0,rowspan=3,sticky="ewns")
if not active:
self.canvas['H'].hide()
else:
self.activeCanvas = self.canvas['H']
def init_canvas_pwp(self, active=False):
"""
this function creates the matplotlib canvas that will be used
to draw stuff
master: parent frame
active: is this displayed on startup?
"""
self.canvas['Psi'] = PWPCanvas(self, self.c, self.d.sList,
self.d, width=300, height=300)
self.canvas['Psi'].grid(column=0,row=0,rowspan=3,sticky="ewns")
if not active:
self.canvas['Psi'].hide()
else:
self.activeCanvas = self.canvas['Psi']
def init_statusbar(self):
"""function that creates a status bar at the bottom of the window"""
self.sb = StatusBar(self)
self.sb.grid(row=3,column=0,columnspan=2, sticky="ew")
def init_slider_frame(self):
self.slider_frame = SliderFrame(self,self, v=self.d.get_v())
self.slider_frame.grid(column=1, row=0, sticky="")
def init_sample_frame(self):
self.sample_frame = SampleFrame(self, width=200, height=100)
self.origin_frame = OriginFrame(self, width=200, height=100)
for i in range(4):
self.add_sample( SampleUI(master=self.sample_frame,
data=self.d, config=self.c,
cluster=None, text="SS%d"%i) )
self.d.sList[i].grid(column=0,row=i)
self.sample_frame.grid(column=1, row=1, sticky="ns")
self.origin_frame.grid(column=1, row=2, sticky="ns")
#--------------------------------------------------
def reset_sample_list(self):
#reset everything:
for sampleUI in self.d.sList:
sampleUI.destroy()
self.d.sList = []
self.canvas['H'].samples = []
self.canvas['Psi'].samples = []
def add_sample(self, s):
self.d.sList.append(s)
self.canvas['H'].samples.append(s)
self.canvas['Psi'].samples.append(s)
def changeV(self,ele,val):
"""
function that updates hyperbola when v is changed
"""
#see if the value is actually a float, if not, return
self.d.set_v( float( val.get() ))
#update, whole thing, there might be a more efficient way to do this
self.canvas['H'].update_()
if self.activeCanvas == self.canvas['H']:
self.activeCanvas.redraw()
def changeLwd(self,val):
"""
function that updates hyperbola when v is changed
"""
print "Changing lwd" , val.get()
#see if the value is actually a float, if not, return
self.c.psi_lwd = float( val.get() )
#redraw, whole thing, there might be a more efficient way to do this
self.canvas['Psi'].update_()
if self.activeCanvas ==self.canvas['Psi']:
self.activeCanvas.redraw()
def changeThreshold(self,val):
"""
function that updates hyperbola when v is changed
"""
print "Changing threshold" , val.get()
#see if the value is actually a float, if not, return
self.c.psi_threshold = float( val.get() )
#update, whole thing, there might be a more efficient way to do this
self.canvas['Psi'].update_()
if self.activeCanvas ==self.canvas['Psi']:
self.activeCanvas.redraw()
#---------------------------------------------------------------------
# optimizing, should move to data
#---------------------------------------------------------------------
def optimizeAll(self):
ev,msev, pv,dv = [],[],[],[]
activeStat = self.d.get_active_stat
for cluster_id in self.d.clusters:
cluster = self.d.clusters[cluster_id]
n_pops = cluster.n_pops
if n_pops <= 3:
print "Warning, Cluster too small"
data = np.empty((n_pops * (n_pops -1 ) /2, 5 ))
row = 0
for i, s1 in enumerate(cluster.pops):
for j0, s2 in enumerate(cluster.pops[i+1:]):
j = i+j0 + 1
data[row] = s1.get_x(), s1.get_y(), \
s2.get_x(), s2.get_y(), \
self.d.get_active_stat(s1.pop, s2.pop)
row += 1
e,mse,p,d = optimize.tdoa3(data,x0=O["opt_start"])
print e[0]
ev.append(e[0])
msev.append(mse)
pv.append(p)
dv.append(d)
self.d.set_v( e[0][0] )
self.slider_frame.v_scale.set( e[0][0] )
self.canvas['H'].update_()
if self.activeCanvas == self.canvas['H']:
self.activeCanvas.redraw()
if cluster.origin is None:
opt = \
InferredOrigin(master=self.origin_frame,x=e[0][1],y=e[0][2],
text="Origin "+cluster.name)
opt.set_color("red")
cluster.origin = opt
else:
opt = cluster.origin
opt.tX.set("%2.2f"%(e[0][1]))
opt.tY.set("%2.2f"%(e[0][2]))
opt.set_x(e[0][1])
opt.set_y(e[0][2])
opt.update_()
print "UPDATED ORIGN"
self.d.oList.append(opt)
opt.grid(in_=self.origin_frame)
self.canvas['H'].panel.add_artist( opt.circH )
self.canvas['H'].update_()
self.canvas['Psi'].panel.add_artist( opt.circP )
#origins shouldn't be movable
#opt.circH.connect()
#opt.circP.connect()
self.activeCanvas.redraw()
return ev, msev, pv, dv
#------------------------------------Hyperbola---------------------------------
# loading files and data
#---------------------------------------------------------------------
def loadSNP(self,f=None):
"""loads SNP and saves them in data"""
if f == None:
f = tkFileDialog.askopenfile(mode='r')
self.d.load_snp( np.loadtxt(f) )
self.canvas['H'].draw_all_hyperbolas()
self.canvas['Psi'].draw_all_pairwise_psi()
self.initPsiMatrix(self.master)
#---------------------------- Sorting stuff ------------------------
# this set of functions handles all the sorting of elements
#--------------------------------------------------
def update_sample_order(self):
"""
when the samples are sorted and have to be reordered, this function
does it
"""
self.d.sList = sorted(self.d.sList)
self.sample_frame.update_sample_order(self.d.sList)
self.psi_matrix.update_sample_order(self.d.sList)
#--------------------------------------------------
def loadCoords(self,f=None):
"""loads Coords, creates the corresponding UI elements
and the circles for plotting
"""
default_cluster = self.d.default_cluster
self.reset_sample_list()
if f is None:
f = tkFileDialog.askopenfile(mode='r',initialfile="coords.txt")
print f
else:
f = open( f )
for i,line in enumerate(f):
p = Population()
p.load_line(line)
self.d.add_pop(p)
sUI = SampleUIWPop(pop=p, master=self.sample_frame,
config = self.c, data=self.d,
cluster=default_cluster)
sUI.grid(column=0,row=i, sticky="ew")
#create plotting circles and register events
self.canvas['H'].panel.add_artist( sUI.circH )
self.canvas['Psi'].panel.add_artist( sUI.circP )
sUI.circH.connect()
sUI.circP.connect()
self.add_sample( sUI )
self.nCoords = len( self.d.sList )
self.activeCanvas.redraw()
def loadPsi(self,f=None):
"""loads Psi directly. Assumes Coordinates are already loaded"""
if f is None:
f = tkFileDialog.askopenfile(mode='r',initialfile="psi.txt")
self.d.add_pw_stat('psi', AntiCommutativePWStat(f=pw_psi))
if self.d.pw_default_stat is None:
self.d.set_pw_default_stat('psi')
psiRaw = np.loadtxt(f, dtype="S100")
for row in psiRaw:
self.d.pairwise_stats['psi'][ row[0], row[1] ] = float(row[2])
psi_sum = psi_sum_cluster(self.d.pairwise_stats['psi'],
self.d.sList)
self.d.add_single_pop_stat('psi_sum',psi_sum)
self.d.sort_stat="psi_sum"
self.initPsiMatrix(self.master)
self.d.update_all_colors()
self.d.update_sample_order()
#self.set_colors()
self.canvas['H'].draw_all_hyperbolas()
self.canvas['Psi'].draw_all_pairwise_psi()
def loadBGI(self, f=None):
"""loads Background image"""
if f is None:
f = tkFileDialog.askopenfile(mode='r')
try:
self.bgi = mpimg.imread(f)
except:
raise ValueError("could not read image file, see"+ \
" matplotlib.image.imread for"+ \
" supported formats")
self.canvas['H'].addBGI(self.bgi)
self.canvas['Psi'].addBGI(self.bgi)
def removeBGI(self):
self.canvas['H'].removeBGI()
self.canvas['Psi'].removeBGI()
self.activeCanvas.redraw()
def save_plot(self, f=None):
if f == None:
f = tkFileDialog.asksaveasfilename(initialfile="plot.pdf")
self.activeCanvas.fig.savefig(f)
#---------------------------------------------------------------------
# various constructors
#---------------------------------------------------------------------
def loadOptions(self):
self.lwd = O['psi_lwd']
self.threshold = O['psi_threshold']
#---------------------------------------------------------------------
# other stuff
#---------------------------------------------------------------------
def quit(self):
"""quits app"""
print "bye"
root.quit()
root.destroy()
def showPsiCanvas(self):
self.canvas['H'].hide()
self.canvas['Psi'].show()
self.activeCanvas = self.canvas['Psi']
for s in self.d.sList:
s.updateCircles()
self.activeCanvas.redraw()
def showHyperbolaCanvas(self):
self.canvas['H'].show()
self.activeCanvas = self.canvas['H']
self.canvas['Psi'].hide()
for s in self.d.sList:
s.updateCircles()
self.activeCanvas.redraw()
