ivctrack GUI

ivctrack/AniFrame.py

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+# -*- coding: utf-8 -*-
+'''This file implements a frame allowing to verify the tracking through an animation (which can be saved).
+'''
+__author__ = ' De Almeida Luis <ldealmei@ulb.ac.be>'
+
+#------generic imports------
+from Tkinter import *
+import tkFileDialog
+
+#------specific imports------
+import matplotlib
+matplotlib.use('Tkagg')
+from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
+import matplotlib.pyplot as plt
+import matplotlib.cm as cm
+import matplotlib.animation as anim
+
+#------ivctrack toolbox imports------
+from reader import ZipSource,Reader
+from hdf5_read import get_hdf5_data
+
+class AniFrame(Frame):
+    """Frame displaying the results of the tracking as a video, and allowing to save it. Will NOT work if FFmpeg is not installed."""
+
+    def __init__(self,win,zip_filename):
+        Frame.__init__(self,win)
+
+        self.feat=[]
+        self.data = []
+
+        #----------------------------------------------------GUI IMPLEMENTATION-----------------------------------------
+
+        self.file_var=StringVar()
+        self.file_var.set('HDF5 File: ')
+        self.file_lbl=Label(self,textvariable=self.file_var)
+        self.file_lbl.grid(row=0,column=2,columnspan=2)
+
+        self.file_browse_button=Button(self,text='Browse',command=self.ask_open_and_load_file)
+        self.file_browse_button.grid(row=0,column=4)
+
+        self.soma_var=BooleanVar()
+        self.soma_check=Checkbutton(self,text='Soma',variable=self.soma_var)
+        self.soma_check.grid(column=0,row=1,columnspan=2)
+
+        self.halo_var=BooleanVar()
+        self.halo_check=Checkbutton(self,text='Halo',variable=self.halo_var)
+        self.halo_check.grid(column=0,row=2,columnspan=2)
+
+        self.trajectory_var=BooleanVar()
+        self.trajectory_check=Checkbutton(self,text='Trajectory',variable=self.trajectory_var)
+        self.trajectory_check.grid(column=0,row=3,columnspan=2)
+
+        self.play_button = Button(master=self, text='Preview',command=lambda:(self.play()))
+
+        self.save_button=Button(self,text='Save as..',command=lambda :(self.save()))
+
+        self.dpi_lbl=Label(self,text='Resolution (DPI)')
+        self.var_dpi=IntVar()
+        self.var_dpi.set(200)
+        self.dpi_entry=Entry(self,textvariable=self.var_dpi)
+
+        #-----Configuration of the tracking canvas------        
+        self.f=plt.figure()
+        self.a=self.f.add_subplot(111)
+
+        self.frame_text=self.a.text(10,20,'')
+
+        self.canvas = FigureCanvasTkAgg(self.f, master=self)
+        self.canvas.show()
+        self.canvas.get_tk_widget().grid(row=1,column=2,rowspan=3,columnspan=3)
+
+        #------------------------------------------------------END-------------------------------------------------------------
+
+
+        #------import of the zip file & update of the canvas------
+        self.datazip_filename = zip_filename
+
+        self.reader = Reader(ZipSource(self.datazip_filename))
+        self.bg=self.reader.getframe()
+
+        self.im = self.a.imshow(self.bg,cmap=cm.gray)
+
+        self.a.set_xlim(0,len(self.bg[0,:]))
+        self.a.set_ylim(len(self.bg[:,0]),0)
+
+        #------MP4 writer------
+        self.writer=anim.writers['ffmpeg']
+        self.writer=self.writer(fps=5)
+
+
+    def ask_open_and_load_file(self):
+        self.file_opt={}
+        self.file_opt['filetypes'] =  [('HDF5 file','.hdf5')]
+        self.file_opt['defaultextension'] ='.hdf5'
+        self.file_opt['title'] = 'Select a HDF5 file'
+
+        self.hdf5_filename=tkFileDialog.askopenfilename(**self.file_opt)
+        self.file_var.set('HDF5 File: {}'.format(self.hdf5_filename))
+
+        self.feat,self.data=get_hdf5_data(self.hdf5_filename,fields=['center','halo','soma'])
+        self.halo=[]
+        self.soma=[]
+        self.trajectory=[]
+
+        for k in range(len(self.data)):
+            self.halo.append(self.a.plot([],[],'o'))
+            self.soma.append(self.a.plot([],[]))
+            self.trajectory.append(self.a.plot([],[]))
+
+        self.play_button.grid(row=4,column=1)
+        self.save_button.grid(row=4,column=0)
+        self.dpi_lbl.grid(column=2,row=4)
+        self.dpi_entry.grid(column=3,row=4)
+
+
+    def play(self):
+
+        self.cell_ani = anim.FuncAnimation(fig=self.f, func=self.update_img,init_func=self.init_im,frames=self.reader.N(),blit=False)
+        self.canvas.show()
+        self.play_button.grid_forget()
+
+    def save(self):
+        """Exports the animation to a MP4 file.
+        """
+        self.file_opt={}
+        self.file_opt['filetypes'] =  [('MP4 files','.mp4')]
+        self.file_opt['defaultextension'] ='.mp4'
+        self.file_opt['title'] = 'Save sequence as..'
+
+        soma=self.soma_var.get()
+        halo=self.halo_var.get()
+        trajectory=self.trajectory_var.get()
+
+        self.mp4_filename=tkFileDialog.asksaveasfilename(**self.file_opt)
+
+        with self.writer.saving(self.f,self.mp4_filename,self.var_dpi.get()):
+            self.reader.rewind()
+            for i in range(self.reader.N()):
+                print "Grabing frame ",i
+
+                self.bg=self.reader.getframe()
+                self.im.set_data(self.bg)
+                try:
+                    self.reader.next()
+                except IndexError:
+                    pass
+                if halo:
+                    self.plot_halo(i)
+                if soma:
+                    self.plot_soma(i)
+                if trajectory:
+                    self.plot_trajectory(i)
+
+                self.frame_text.set_text(i)
+
+                self.writer.grab_frame()
+        print "Video correctly saved as ", self.mp4_filename
+
+
+    def update_img(self,frame):
+
+        self.reader.moveto(frame)
+        self.bg=self.reader.getframe()
+
+        self.im.set_data(self.bg)
+
+        if self.halo_var.get():
+            self.plot_halo(frame)
+        elif not self.halo_var.get():
+            for k in range(len(self.data)):
+                self.halo[k][0].set_data([],[])
+
+        if self.soma_var.get():
+            self.plot_soma(frame)
+        elif not self.soma_var.get():
+            for k in range(len(self.data)):
+                self.soma[k][0].set_data([],[])
+
+        if self.trajectory_var.get():
+            self.plot_trajectory(frame)
+        elif not self.trajectory_var.get():
+            for k in range(len(self.data)):
+                self.trajectory[k][0].set_data([],[])
+
+        self.frame_text.set_text(frame)
+
+    def init_im(self):
+        pass
+
+    def plot_halo(self,i):
+        k=0
+        for d in self.data:
+            t=d['halo']
+            x=t[i,:,0]
+            y=t[i,:,1]
+            self.halo[k][0].set_data(x,y)
+            k+=1
+
+    def plot_soma(self,i):
+        k=0
+        for d in self.data:
+            t=d['soma']
+            x=t[i,:,0]
+            y=t[i,:,1]
+            self.soma[k][0].set_data(x,y)
+            k+=1
+
+    def plot_trajectory(self,i):
+        k=0
+        for d in self.data:
+            t=d['center']
+            x=t[0:i,0]
+            y=t[0:i,1]
+            self.trajectory[k][0].set_data(x,y)
+            k+=1

ivctrack/MainWindow.py

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+# -*- coding: utf-8 -*-
+'''This file implements the menu frame of the GUI for the ivctrack module
+'''
+__author__ = ' De Almeida Luis <ldealmei@ulb.ac.be>'
+
+#------generic imports------
+from Tkinter import *
+import tkFileDialog
+
+#-------local imports------
+from TrackingFrame import TrackingFrame
+from PlotFrame import PlotFrame
+from AniFrame import AniFrame
+from MeasFrameV3 import MeasFrameV3
+
+
+
+class MainFrame(Frame):
+
+    """Main menu frame : The user can either start a new tracking or view results from previous trackings
+        The .zip file which contains the image sequences is linked to the menu window and can only be modified from there"""
+    def __init__(self,win):
+        Frame.__init__(self,win,width=700,height=700)
+        self.pack()
+
+        self.track_frame=None
+        self.plot_frame=None
+        self.meas_frame=None
+        self.ani_frame=None
+
+        self.menu_buttons=[]
+
+        self.datazip_filename=""
+
+        self.file_opt={}
+        self.file_opt['filetypes'] =  [('ZIP file','.zip')]
+        self.file_opt['defaultextension'] ='.zip'
+        self.file_opt['title'] = 'Select a zipped sequence file'
+
+
+        #----------------------------------------------------GUI IMPLEMENTATION-----------------------------------------
+
+        self.track_button=Button(self,text='Start Tracking',command=lambda : self.track())
+        self.track_button.pack(fill='both')
+        self.menu_buttons.append(self.track_button)
+
+        self.plot_button=Button(self,text='Plot Results',command=lambda : self.plot())
+        self.plot_button.pack(fill='both')
+        self.menu_buttons.append(self.plot_button)
+
+        self.meas_button=Button(self,text='Measurements',command=lambda : self.measurements())
+        self.meas_button.pack(fill='both')
+        self.menu_buttons.append(self.meas_button)
+
+        self.ani_button=Button(self,text='Player',command=lambda : self.play())
+        self.ani_button.pack(fill='both')
+        self.menu_buttons.append(self.ani_button)
+
+        self.zip_var=StringVar()
+        self.change_zip_button=Button(self,textvariable=self.zip_var,command= lambda : self.change_zip())
+        self.menu_buttons.append(self.change_zip_button)
+
+        self.quit_button=Button(self,text='Quit',command=win.quit)
+        self.quit_button.pack(fill='both')
+        self.menu_buttons.append(self.quit_button)
+
+        self.back_button=Button(self,text='Back',command = lambda : self.back())
+
+        #------------------------------------------------------END-------------------------------------------------------------
+
+
+    def back(self):
+        """Return to the menu window.  """
+        try :
+            self.track_frame.pack_forget()
+            self.track_frame=None
+        except:
+            pass
+        try :
+            self.plot_frame.pack_forget()
+            self.plot_frame=None
+        except:
+            pass
+        try :
+            self.meas_frame.pack_forget()
+            self.meas_frame=None
+        except:
+            pass
+        try:
+            self.ani_frame.pack_forget()
+            self.ani_frame=None
+        except:
+            pass
+
+        self.back_button.pack_forget()
+        for button in self.menu_buttons:
+            button.pack(fill='both')
+
+    def track(self):
+        """Method that transits from the menu to the tracking frame """
+        if self.datazip_filename=="":
+            self.change_zip()
+
+        self.track_frame=TrackingFrame(win,self.datazip_filename)
+
+        self.track_frame.pack()
+
+        for button in self.menu_buttons:
+            button.pack_forget()
+
+        self.back_button.pack(side='bottom')
+
+    def plot(self):
+        """Method that transits from the menu to the plotting frame """
+
+        if self.datazip_filename=="":
+            self.change_zip()
+
+        self.plot_frame=PlotFrame(win,self.datazip_filename)
+
+        self.plot_frame.pack()
+
+        for button in self.menu_buttons:
+            button.pack_forget()
+
+        self.back_button.pack(side='bottom')
+
+    def measurements(self):
+        """Method that transits from the menu to the frame that displays multiple measures"""
+
+        if self.datazip_filename=="":
+            self.change_zip()
+        self.meas_frame=MeasFrameV3(win,self.datazip_filename)
+
+        self.meas_frame.pack()
+
+        for button in self.menu_buttons:
+            button.pack_forget()
+
+        self.back_button.pack(side='bottom')
+
+    def play(self):
+        """Method that transits from the menu to the frame that plays the tracking and allows to save it to .mp4"""
+        if self.datazip_filename=="":
+            self.change_zip()
+
+        self.ani_frame=AniFrame(win,self.datazip_filename)
+
+        self.ani_frame.pack()
+
+        for button in self.menu_buttons:
+            button.pack_forget()
+
+        self.back_button.pack(side='bottom')
+
+    def change_zip(self):
+        """Method that allows the user to change the current sequence ZIP file """
+        self.datazip_filename=tkFileDialog.askopenfilename(**self.file_opt)
+        try:
+            self.zip_var.set("Change Zip File ({})".format(self.datazip_filename.rsplit('/')[-1]))
+        except AttributeError:
+            pass
+
+
+if __name__== '__main__':
+
+    win=Tk()
+    win.wm_title('IVCTrack GUI')
+    root=MainFrame(win)
+    root.mainloop()