def button_open(entry):
d = gtk.FileChooserDialog(title='Open Hidden Markov Model',
action=gtk.FILE_CHOOSER_ACTION_OPEN,
buttons=(gtk.STOCK_CANCEL, \
gtk.RESPONSE_CANCEL, \
gtk.STOCK_OPEN, \
gtk.RESPONSE_OK),
parent=self)
d.set_select_multiple(False)
d.set_default_response(gtk.RESPONSE_OK)
filter = gtk.FileFilter()
filter.set_name('Hidden Markov Model')
#filter.add_mime_type('text/*')
for ext1 in ('.txt', '.hmm'):
for ext2 in ('', '.gz', '.bz2'):
filter.add_pattern('*' + ext1 + ext2)
d.add_filter(filter)
filter = gtk.FileFilter()
filter.set_name('All files')
filter.add_mime_type('*/*')
filter.add_pattern('*')
d.add_filter(filter)
response = d.run()
if response != gtk.RESPONSE_OK:
d.destroy()
return
file_name = d.get_filename()
self.hmm = HiddenMarkovModel.load(open(file_name, 'rb'))
d.destroy()
def button_new(entry): d = NewHMMDialog(title='Create new Hidden Markov Model', buttons=(gtk.STOCK_CANCEL, \ gtk.RESPONSE_CANCEL, \ gtk.STOCK_OK, \ gtk.RESPONSE_OK), parent=self) response = d.run() if response == gtk.RESPONSE_OK: self.state_list = d.state_list self.emission_list = d.emission_list d.destroy() else: d.destroy() return #generate default values for tables states_iter = self.state_list.get_iter_root() states = [] while states_iter: states.append(self.state_list.get(states_iter, 0)[0]) states_iter = self.state_list.iter_next(states_iter) emissions_iter = self.emission_list.get_iter_root() observations = [] while emissions_iter: observations.append(self.emission_list.get(emissions_iter, 0)[0]) emissions_iter = self.emission_list.iter_next(emissions_iter) N = len(states) M = len(observations) emissions = [x[:] for x in [[0] * M] * N] for i in xrange(N): emissions[i][i%M] = 1 self.hmm = HiddenMarkovModel(states=states, observations=observations, transitions=[x[:] for x in [[1.0/N]*N]*N], emissions=emissions, initial=[1] + [0]*(N-1))
class HMMWindow(MainWindow):
__gsignals__ = {
'hmm_changed': (gobject.SIGNAL_RUN_FIRST, None, (HiddenMarkovModel,))
}
def __init_menu__(self):
self.menu_bar = gtk.MenuBar()
self.vbox_main.pack_start(self.menu_bar, False, False, 0)
def menu(title, parent=None):
if not parent:
parent = self.menu_bar
def decorator(callback):
menu = gtk.Menu()
menu_item = gtk.MenuItem(title)
menu_item.set_submenu(menu)
parent.append(menu_item)
return menu
return decorator
def button(menu, title):
def decorator(callback):
b = gtk.MenuItem(title)
b.connect('activate', callback)
menu.append(b)
return b
return decorator
# Model menu:
@menu('Model')
def menu_model():
pass
@button(menu_model, 'New …')
def button_new(entry):
d = NewHMMDialog(title='Create new Hidden Markov Model',
buttons=(gtk.STOCK_CANCEL, \
gtk.RESPONSE_CANCEL, \
gtk.STOCK_OK, \
gtk.RESPONSE_OK),
parent=self)
response = d.run()
if response == gtk.RESPONSE_OK:
self.state_list = d.state_list
self.emission_list = d.emission_list
d.destroy()
else:
d.destroy()
return
#generate default values for tables
states_iter = self.state_list.get_iter_root()
states = []
while states_iter:
states.append(self.state_list.get(states_iter, 0)[0])
states_iter = self.state_list.iter_next(states_iter)
emissions_iter = self.emission_list.get_iter_root()
observations = []
while emissions_iter:
observations.append(self.emission_list.get(emissions_iter, 0)[0])
emissions_iter = self.emission_list.iter_next(emissions_iter)
N = len(states)
M = len(observations)
emissions = [x[:] for x in [[0] * M] * N]
for i in xrange(N):
emissions[i][i%M] = 1
self.hmm = HiddenMarkovModel(states=states,
observations=observations,
transitions=[x[:] for x in [[1.0/N]*N]*N],
emissions=emissions,
initial=[1] + [0]*(N-1))
@button(menu_model, 'Open …')
def button_open(entry):
d = gtk.FileChooserDialog(title='Open Hidden Markov Model',
action=gtk.FILE_CHOOSER_ACTION_OPEN,
buttons=(gtk.STOCK_CANCEL, \
gtk.RESPONSE_CANCEL, \
gtk.STOCK_OPEN, \
gtk.RESPONSE_OK),
parent=self)
d.set_select_multiple(False)
d.set_default_response(gtk.RESPONSE_OK)
filter = gtk.FileFilter()
filter.set_name('Hidden Markov Model')
#filter.add_mime_type('text/*')
for ext1 in ('.txt', '.hmm'):
for ext2 in ('', '.gz', '.bz2'):
filter.add_pattern('*' + ext1 + ext2)
d.add_filter(filter)
filter = gtk.FileFilter()
filter.set_name('All files')
filter.add_mime_type('*/*')
filter.add_pattern('*')
d.add_filter(filter)
response = d.run()
if response != gtk.RESPONSE_OK:
d.destroy()
return
file_name = d.get_filename()
self.hmm = HiddenMarkovModel.load(open(file_name, 'rb'))
d.destroy()
@button(menu_model, 'Save')
def button_save(entry):
pass
@button(menu_model, 'Save as …')
def button_save_as(entry):
d = gtk.FileChooserDialog(title=None,
action=gtk.FILE_CHOOSER_ACTION_SAVE,
buttons=(gtk.STOCK_CANCEL, \
gtk.RESPONSE_CANCEL, \
gtk.STOCK_SAVE, \
gtk.RESPONSE_OK),
parent=self)
d.set_select_multiple(False)
d.set_default_response(gtk.RESPONSE_OK)
response = d.run()
if response != gtk.RESPONSE_OK:
d.destroy()
return
file_name = d.get_filename()
self.hmm.dump(fp=open(file_name, 'wb'), indent=2)
d.destroy()
menu_model.append(gtk.SeparatorMenuItem())
@button(menu_model, 'Close')
def button_save_as(entry):
self.destroy(self, entry)
# Settings menu:
@menu('Settings')
def menu_settings():
pass
@button(menu_settings, None)
def button_use_matlab(entry):
algorithm.use_next_backend()
self.button_use_matlab.set_label("Use backend %s (currently %s)" % algorithm.get_cur_backend()[::-1])
self.button_use_matlab = button_use_matlab
self.button_use_matlab.set_label("Use backend %s (currently %s)" % algorithm.get_cur_backend()[::-1])
# Operations menu:
@menu('Operations')
def menu_operations():
pass
def button_with_seq(title):
def decorator(callback):
def calc(file_name, seq):
tlv = { 'status_id': self.statusbar.push(0, "Calculating %s" % title) }
def status_cb(status):
if type(status) is float:
self.statusbar.set_fraction(status)
new_status_id = self.statusbar.push(0, "Calculating %s: %s" %
(title, "%.2f%%" % (status*100) if type(status) is float else status))
self.statusbar.remove_message(0, tlv['status_id'])
tlv['status_id'] = new_status_id
callback(file_name, seq, status_cb)
self.statusbar.remove_message(0, tlv['status_id'])
self.statusbar.set_fraction(0)
def action(entry):
result = load_sequence(self, self.hmm.observations)
if result:
thread.start_new_thread(calc, result)
return button(menu_operations, title)(action)
return decorator
@button_with_seq('Probability of an Observed Sequence')
def menu_operations_prob_of_obs_seq(file_name, sequence, status_cb):
result = backend.prob_of_observed_seq(self.hmm, sequence, status_cb)
dialog = gtk.MessageDialog(
parent = self,
buttons = gtk.BUTTONS_OK,
message_format = "Probability of this sequence: %s" % (result),
)
dialog.format_secondary_text("Input Sequence: %s" % abspath(file_name.split("/")[-1]))
dialog.connect('response', lambda dialog, response: dialog.destroy())
dialog.run()
@button_with_seq('Viterbi')
def menu_operations_viterbi(file_name, sequence, status_cb):
(result,f_name) = backend.viterbi(self.hmm, sequence, status_cb)
dialog = gtk.MessageDialog(
parent = self,
buttons = gtk.BUTTONS_OK,
message_format = "Wrote file: %s" % abspath(f_name),
)
dialog.format_secondary_text("Input Sequence: %s\n\nSample of Result (first 10 states): %s" %
(abspath(file_name.split("/")[-1]), str(result).strip('[').strip(']')))
dialog.connect('response', lambda dialog, response: dialog.destroy())
dialog.run()
@button_with_seq('Baum-Welch')
def button_baum_welch_from_seq_file(file_name, sequence, status_cb):
backend.baum_welch(self.hmm, sequence, status_cb)
self.emit('hmm_changed', self._hmm)
# TODO: some dialog
# Help menu:
@menu('Help')
def menu_help():
pass
@button(menu_help, 'About')
def button_save_as(entry):
dialog = gtk.AboutDialog()
pic = gtk.gdk.pixbuf_new_from_file(join(dirname(abspath(__file__)), 'about-icon.png'))
dialog.set_logo(pic)
dialog.set_name('Telematik Hidden Markov Tool')
dialog.set_version('1.0')
dialog.set_copyright("Copyright © 2012 René Kijewski\nCopyright © 2012 Stefan Friesel\nCopyright © 2012 Simon Putzke\nCopyright © 2012 Daniel Snider")
dialog.set_comments("A tool for analyses of hidden Markov models\n\nSummer Semester 2012, Prof. Dr. Katinka Wolter")
dialog.set_website("http://kijewski.github.com/swp-telematik-2012-hidden-markov/")
dialog.set_website_label("Development Website")
dialog.run()
dialog.destroy()
def _display_widget_do_hmm_changed(self, hmm):
self.notebook.display_widget.set_hmm(hmm)
def __init_xdot__(self):
self.notebook.display_widget = HMMDisplayWidget()
self.notebook.append_page(self.notebook.display_widget, gtk.Label("graphical"))
def on_url_clicked(widget, kind, index, event):
dialog = gtk.MessageDialog(
parent = self,
buttons = gtk.BUTTONS_OK,
message_format="You clicked on the %d. %s" % (index+1, kind)
)
dialog.connect('response', lambda dialog, response: dialog.destroy())
dialog.run()
return True
self.notebook.display_widget.connect('hmm_clicked', on_url_clicked)
self.connect_object('hmm_changed', HMMWindow._display_widget_do_hmm_changed, self)
def __init_status_bar__(self):
self.statusbar = StatusProgressBar()
self.statusbar.push(0, 'Telehmmatic started …')
self.vbox_main.pack_end(self.statusbar, False, True, 0)
def on_initial_values_updated(self, table):
assert(row == 0)
try:
initial = [float(table[0][i]) for i in xrange(len(self.hmm.initial))]
s = sum(initial)
self.hmm.initial = [x/s for x in initial]
finally:
self.emit('hmm_changed', self._hmm)
def on_emission_values_updated(self, table):
try:
emissions = [[float(table[state, emission]) for emission in xrange(len(self.hmm.observations))] for state in xrange(len(self.hmm.states))]
s = [sum(emissions[state]) for state in xrange(len(self.hmm.states))]
self.hmm.emissions = [[emissions[state][emission]/s[state] for emission in xrange(len(self.hmm.observations))] for state in xrange(len(self.hmm.states))]
finally:
self.emit('hmm_changed', self._hmm)
def on_transition_values_updated(self, table):
try:
transitions = [[float(table[current, next]) for next in xrange(len(self.hmm.states))] for current in xrange(len(self.hmm.states))]
s = [sum(transitions[current]) for current in xrange(len(self.hmm.states))]
self.hmm.transitions = [[transitions[current][next]/s[current] for next in xrange(len(self.hmm.states))] for current in xrange(len(self.hmm.states))]
finally:
self.emit('hmm_changed', self._hmm)
def _init_notebook(self):
self.notebook = gtk.Notebook()
self.__init_xdot__()
transition_tab = TransitionTab(self)
self.connect('hmm_changed', transition_tab.on_hmm_changed)
self.notebook.append_page(transition_tab, gtk.Label('transitions'))
emission_tab = EmissionTab(self)
self.connect('hmm_changed', emission_tab.on_hmm_changed)
self.notebook.append_page(emission_tab, gtk.Label('emissions'))
initial_tab = InitialTab(self)
self.connect('hmm_changed', initial_tab.on_hmm_changed)
self.notebook.append_page(initial_tab, gtk.Label('initial'))
self.vbox_main.pack_start(self.notebook)
def __init__(self):
super(HMMWindow, self).__init__('Telehmmatic')
self.__init_menu__()
self.__init_status_bar__()
self._init_notebook()
#on startup, load a simple example hmm for testing and illustration
self.hmm = load_default_hmm()
self.show_all()
@property
def hmm(self):
return self._hmm
@hmm.setter
def hmm(self, hmm):
self._hmm = hmm
self.emit('hmm_changed', self._hmm)
def load_default_hmm(): return HiddenMarkovModel.load(open(join(dirname(abspath(__file__)), pardir, pardir, 'default_model.hmm'), 'rb'))
