def display_html(vals): ''' Convert objects into three AXON forms for output in IPython notebook. :param vals: List of objects or ordered dict. :returns: IPython TabbedView widget. ''' from IPython.html.widgets import Tab, HTML # Compact form p1 = dumps(vals, crossref=1) # Formatted form without braces p2 = dumps(vals, pretty=1, crossref=1) # Formatted form with braces p3 = dumps(vals, pretty=1, braces=1, crossref=1) wg = Tab((HTML("<pre>%s</pre>" % p1), HTML("<pre>%s</pre>" % p2), HTML("<pre>%s</pre>" % p3))) wg.set_title(0, "Compact") wg.set_title(1, "Formatted") wg.set_title(2, "Formatted with {}") wg.selected_index = 1 return wg
def status_printer(_, total=None, desc=None, ncols=None, img=None): """ Manage the printing of an IPython/Jupyter Notebook progress bar widget. """ # Fallback to text bar if there's no total # DEPRECATED: replaced with an 'info' style bar # if not total: # return super(mytqdm, mytqdm).status_printer(file) # fp = file # Prepare IPython progress bar try: if total: pbar = IntProgress(min=0, max=total) else: # No total? Show info style bar with no progress tqdm status pbar = IntProgress(min=0, max=1) pbar.value = 1 pbar.bar_style = 'info' except NameError: # #187 #451 #558 raise ImportError( "IntProgress not found. Please update jupyter and ipywidgets." " See https://ipywidgets.readthedocs.io/en/stable" "/user_install.html") if desc: pbar.description = desc if IPYW >= 7: pbar.style.description_width = 'initial' # Prepare status text ptext = HTML() timg = HTML() if img: timg.value = "<br>%s<br>" % img # Only way to place text to the right of the bar is to use a container container = VBox([HBox(children=[pbar, ptext]), timg]) # Prepare layout if ncols is not None: # use default style of ipywidgets # ncols could be 100, "100px", "100%" ncols = str(ncols) # ipywidgets only accepts string try: if int(ncols) > 0: # isnumeric and positive ncols += 'px' except ValueError: pass pbar.layout.flex = '2' container.layout.width = ncols container.layout.display = 'inline-flex' container.layout.flex_flow = 'row wrap' display(container) return container
def __init__(self,start,end): self.pbar = IntProgress(orientation='horizontal',min=start, max=end) self.ptext = HTML() # Only way to place text to the right of the bar is to use a container container = HBox(children=[self.pbar, self.ptext]) display(container)
def status_printer(_, total=None, desc=None, ncols=None): """ Manage the printing of an IPython/Jupyter Notebook progress bar widget. """ # Fallback to text bar if there's no total # DEPRECATED: replaced with an 'info' style bar # if not total: # return super(tqdm_notebook, tqdm_notebook).status_printer(file) # fp = file # Prepare IPython progress bar if IProgress is None: # #187 #451 #558 #872 raise ImportError( "IProgress not found. Please update jupyter and ipywidgets." " See https://ipywidgets.readthedocs.io/en/stable" "/user_install.html") if total: pbar = IProgress(min=0, max=total) else: # No total? Show info style bar with no progress tqdm status pbar = IProgress(min=0, max=1) pbar.value = 1 pbar.bar_style = 'info' if ncols is None: pbar.layout.width = "20px" ltext = HTML() rtext = HTML() if desc: ltext.value = desc container = HBox(children=[ltext, pbar, rtext]) # Prepare layout if ncols is not None: # use default style of ipywidgets # ncols could be 100, "100px", "100%" ncols = str(ncols) # ipywidgets only accepts string try: if int(ncols) > 0: # isnumeric and positive ncols += 'px' except ValueError: pass pbar.layout.flex = '2' container.layout.width = ncols container.layout.display = 'inline-flex' container.layout.flex_flow = 'row wrap' display(container) return container
def status_printer(_, total=None, desc=None, ncols=None): """ Manage the printing of an IPython/Jupyter Notebook progress bar widget. """ # Fallback to text bar if there's no total # DEPRECATED: replaced with an 'info' style bar # if not total: # return super(tqdm_notebook, tqdm_notebook).status_printer(file) # fp = file # Prepare IPython progress bar try: if total: pbar = IntProgress(min=0, max=total) else: # No total? Show info style bar with no progress tqdm status pbar = IntProgress(min=0, max=1) pbar.value = 1 pbar.bar_style = 'info' except NameError: # #187 #451 #558 raise ImportError( "IntProgress not found. Please update jupyter and ipywidgets." " See https://ipywidgets.readthedocs.io/en/stable" "/user_install.html") if desc: pbar.description = desc if IPYW >= 7: pbar.style.description_width = 'initial' # Prepare status text ptext = HTML() # Only way to place text to the right of the bar is to use a container container = HBox(children=[pbar, ptext]) # Prepare layout if ncols is not None: # use default style of ipywidgets # ncols could be 100, "100px", "100%" ncols = str(ncols) # ipywidgets only accepts string try: if int(ncols) > 0: # isnumeric and positive ncols += 'px' except ValueError: pass pbar.layout.flex = '2' container.layout.width = ncols container.layout.display = 'inline-flex' container.layout.flex_flow = 'row wrap' display(container) def print_status(s='', close=False, bar_style=None, desc=None): # Note: contrary to native tqdm, s='' does NOT clear bar # goal is to keep all infos if error happens so user knows # at which iteration the loop failed. # Clear previous output (really necessary?) # clear_output(wait=1) # Get current iteration value from format_meter string if total: # n = None if s: npos = s.find(r'/|/') # cause we use bar_format=r'{n}|...' # Check that n can be found in s (else n > total) if npos >= 0: n = float(s[:npos]) # get n from string s = s[npos + 3:] # remove from string # Update bar with current n value if n is not None: pbar.value = n # Print stats if s: # never clear the bar (signal: s='') s = s.replace('||', '') # remove inesthetical pipes s = escape(s) # html escape special characters (like '?') ptext.value = s # Change bar style if bar_style: # Hack-ish way to avoid the danger bar_style being overriden by # success because the bar gets closed after the error... if not (pbar.bar_style == 'danger' and bar_style == 'success'): pbar.bar_style = bar_style # Special signal to close the bar if close and pbar.bar_style != 'danger': # hide only if no error try: container.close() except AttributeError: container.visible = False # Update description if desc: pbar.description = desc if IPYW >= 7: pbar.style.description_width = 'initial' return print_status
def status_printer(_, total=None, desc=None): """ Manage the printing of an IPython/Jupyter Notebook progress bar widget. """ # Fallback to text bar if there's no total # DEPRECATED: replaced with an 'info' style bar # if not total: # return super(tqdm_notebook, tqdm_notebook).status_printer(file) # fp = file # Prepare IPython progress bar if total: pbar = IntProgress(min=0, max=total) else: # No total? Show info style bar with no progress tqdm status pbar = IntProgress(min=0, max=1) pbar.value = 1 pbar.bar_style = 'info' if desc: pbar.description = desc # Prepare status text ptext = HTML() # Only way to place text to the right of the bar is to use a container container = HBox(children=[pbar, ptext]) display(container) def print_status(s='', close=False, bar_style=None): # Note: contrary to native tqdm, s='' does NOT clear bar # goal is to keep all infos if error happens so user knows # at which iteration the loop failed. # Clear previous output (really necessary?) # clear_output(wait=1) # Get current iteration value from format_meter string if total: n = None if s: npos = s.find(r'/|/') # cause we use bar_format=r'{n}|...' # Check that n can be found in s (else n > total) if npos >= 0: n = int(s[:npos]) # get n from string s = s[npos + 3:] # remove from string # Update bar with current n value if n is not None: pbar.value = n # Print stats if s: # never clear the bar (signal: s='') s = s.replace('||', '') # remove inesthetical pipes s = escape(s) # html escape special characters (like '?') ptext.value = s # Change bar style if bar_style: # Hack-ish way to avoid the danger bar_style being overriden by # success because the bar gets closed after the error... if not (pbar.bar_style == 'danger' and bar_style == 'success'): pbar.bar_style = bar_style # Special signal to close the bar if close and pbar.bar_style != 'danger': # hide only if no error container.visible = False return print_status
def status_printer(self, _, total=None, desc=None, ncols=None): """ Manage the printing of an IPython/Jupyter Notebook progress bar widget. """ # Fallback to text bar if there's no total # DEPRECATED: replaced with an 'info' style bar # if not total: # return super(tqdm_notebook_EX, tqdm_notebook).status_printer(file) # fp = file # Prepare IPython progress bar if total: pbar = IntProgress(min=0, max=total) else: # No total? Show info style bar with no progress tqdm status pbar = IntProgress(min=0, max=1) pbar.value = 1 pbar.bar_style = 'info' if desc: pbar.description = desc # Prepare status text ptext = HTML() # Only way to place text to the right of the bar is to use a container container = HBox(children=[pbar, ptext]) if self.vbox: self.vbox.children = self.vbox.children + (container, ) else: display(container) # Prepare layout if ncols is not None: # use default style of ipywidgets # ncols could be 100, "100px", "100%" ncols = str(ncols) # ipywidgets only accepts string if ncols[-1].isnumeric(): # if last value is digit, assume the value is digit ncols += 'px' pbar.layout.flex = '2' container.layout.width = ncols container.layout.display = 'inline-flex' container.layout.flex_flow = 'row wrap' def print_status(s='', close=False, bar_style=None, desc=None): # Note: contrary to native tqdm, s='' does NOT clear bar # goal is to keep all infos if error happens so user knows # at which iteration the loop failed. # Clear previous output (really necessary?) # clear_output(wait=1) # Get current iteration value from format_meter string if total: # n = None if s: npos = s.find(r'/|/') # cause we use bar_format=r'{n}|…' # Check that n can be found in s (else n > total) if npos >= 0: n = int(s[:npos]) # get n from string s = s[npos + 3:] # remove from string # Update bar with current n value if n is not None: pbar.value = n # Print stats if s: # never clear the bar (signal: s='') s = s.replace('||', '') # remove inesthetical pipes s = escape(s) # html escape special characters (like '?') ptext.value = s # Change bar style if bar_style: # Hack-ish way to avoid the danger bar_style being overriden by # success because the bar gets closed after the error… if not (pbar.bar_style == 'danger' and bar_style == 'success'): pbar.bar_style = bar_style # Special signal to close the bar if close and pbar.bar_style != 'danger': # hide only if no error try: container.close() except AttributeError: container.visible = False if self.vbox: self.vbox.children = tuple(ch for ch in self.vbox.children if ch is not container) # Update description if desc: pbar.description = desc return print_status
def __init__(self, model, opt, maxiters, verbose=False, current_iteration=0, ipython_notebook=True, clear_after_finish=False): self.verbose = verbose if self.verbose: self.model = model self.iteration = current_iteration self.p_iter = self.iteration self.maxiters = maxiters self.len_maxiters = len(str(maxiters)) self.opt_name = opt.opt_name self.model.add_observer(self, self.print_status) self.status = 'running' self.clear = clear_after_finish self.update() try: from IPython.display import display from IPython.html.widgets import IntProgress, HTML, Box, VBox, HBox, FlexBox self.text = HTML(width='100%') self.progress = IntProgress(min=0, max=maxiters) #self.progresstext = Text(width='100%', disabled=True, value='0/{}'.format(maxiters)) self.model_show = HTML() self.ipython_notebook = ipython_notebook except: # Not in Ipython notebook self.ipython_notebook = False if self.ipython_notebook: left_col = VBox(children=[self.progress, self.text], padding=2, width='40%') right_col = Box(children=[self.model_show], padding=2, width='60%') self.hor_align = FlexBox(children=[left_col, right_col], width='100%', orientation='horizontal') display(self.hor_align) try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) right_col.set_css({ 'padding': '2px', }) self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') left_col.add_class("box-flex1") right_col.add_class('box-flex0') except: pass #self.text.add_class('box-flex2') #self.progress.add_class('box-flex1') else: self.exps = exponents(self.fnow, self.current_gradient) print('Running {} Code:'.format(self.opt_name)) print(' {3:7s} {0:{mi}s} {1:11s} {2:11s}'.format( "i", "f", "|g|", "runtime", mi=self.len_maxiters))
class VerboseOptimization(object): def __init__(self, model, opt, maxiters, verbose=False, current_iteration=0, ipython_notebook=True, clear_after_finish=False): self.verbose = verbose if self.verbose: self.model = model self.iteration = current_iteration self.p_iter = self.iteration self.maxiters = maxiters self.len_maxiters = len(str(maxiters)) self.opt_name = opt.opt_name self.model.add_observer(self, self.print_status) self.status = 'running' self.clear = clear_after_finish self.update() try: from IPython.display import display from IPython.html.widgets import IntProgress, HTML, Box, VBox, HBox, FlexBox self.text = HTML(width='100%') self.progress = IntProgress(min=0, max=maxiters) #self.progresstext = Text(width='100%', disabled=True, value='0/{}'.format(maxiters)) self.model_show = HTML() self.ipython_notebook = ipython_notebook except: # Not in Ipython notebook self.ipython_notebook = False if self.ipython_notebook: left_col = VBox(children=[self.progress, self.text], padding=2, width='40%') right_col = Box(children=[self.model_show], padding=2, width='60%') self.hor_align = FlexBox(children=[left_col, right_col], width='100%', orientation='horizontal') display(self.hor_align) try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) right_col.set_css({ 'padding': '2px', }) self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') left_col.add_class("box-flex1") right_col.add_class('box-flex0') except: pass #self.text.add_class('box-flex2') #self.progress.add_class('box-flex1') else: self.exps = exponents(self.fnow, self.current_gradient) print('Running {} Code:'.format(self.opt_name)) print(' {3:7s} {0:{mi}s} {1:11s} {2:11s}'.format( "i", "f", "|g|", "runtime", mi=self.len_maxiters)) def __enter__(self): self.start = time.time() self._time = self.start return self def print_out(self, seconds): if seconds < 60: ms = (seconds % 1) * 100 self.timestring = "{s:0>2d}s{ms:0>2d}".format(s=int(seconds), ms=int(ms)) else: m, s = divmod(seconds, 60) if m > 59: h, m = divmod(m, 60) if h > 23: d, h = divmod(h, 24) self.timestring = '{d:0>2d}d{h:0>2d}h{m:0>2d}'.format( m=int(m), h=int(h), d=int(d)) else: self.timestring = '{h:0>2d}h{m:0>2d}m{s:0>2d}'.format( m=int(m), s=int(s), h=int(h)) else: ms = (seconds % 1) * 100 self.timestring = '{m:0>2d}m{s:0>2d}s{ms:0>2d}'.format( m=int(m), s=int(s), ms=int(ms)) if self.ipython_notebook: names_vals = [ ['optimizer', "{:s}".format(self.opt_name)], ['runtime', "{:>s}".format(self.timestring)], [ 'evaluation', "{:>0{l}}".format(self.iteration, l=self.len_maxiters) ], ['objective', "{: > 12.3E}".format(self.fnow)], [ '||gradient||', "{: >+12.3E}".format(float(self.current_gradient)) ], ['status', "{:s}".format(self.status)], ] #message = "Lik:{:5.3E} Grad:{:5.3E} Lik:{:5.3E} Len:{!s}".format(float(m.log_likelihood()), np.einsum('i,i->', grads, grads), float(m.likelihood.variance), " ".join(["{:3.2E}".format(l) for l in m.kern.lengthscale.values])) html_begin = """<style type="text/css"> .tg-opt {font-family:"Courier New", Courier, monospace !important;padding:2px 3px;word-break:normal;border-collapse:collapse;border-spacing:0;border-color:#DCDCDC;margin:0px auto;width:100%;} .tg-opt td{font-family:"Courier New", Courier, monospace !important;font-weight:bold;color:#444;background-color:#F7FDFA;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt th{font-family:"Courier New", Courier, monospace !important;font-weight:normal;color:#fff;background-color:#26ADE4;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt .tg-left{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:left;} .tg-opt .tg-right{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:right;} </style> <table class="tg-opt">""" html_end = "</table>" html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.value = (self.iteration + 1) #self.progresstext.value = '0/{}'.format((self.iteration+1)) self.model_show.value = self.model._repr_html_() else: n_exps = exponents(self.fnow, self.current_gradient) if self.iteration - self.p_iter >= 20 * np.random.rand(): a = self.iteration >= self.p_iter * 2.78 b = np.any(n_exps < self.exps) if a or b: self.p_iter = self.iteration print('') if b: self.exps = n_exps print('\r', end=' ') print( '{3:} {0:>0{mi}g} {1:> 12e} {2:> 12e}'.format( self.iteration, float(self.fnow), float(self.current_gradient), "{:>8s}".format(self.timestring), mi=self.len_maxiters), end=' ' ) # print 'Iteration:', iteration, ' Objective:', fnow, ' Scale:', beta, '\r', sys.stdout.flush() def print_status(self, me, which=None): self.update() t = time.time() seconds = t - self.start #sys.stdout.write(" "*len(self.message)) if t - self._time > .3 or seconds < .3: self.print_out(seconds) self._time = t self.iteration += 1 def update(self): self.fnow = self.model.objective_function() if self.model.obj_grads is not None: grad = self.model.obj_grads self.current_gradient = np.dot(grad, grad) else: self.current_gradient = np.nan def finish(self, opt): self.status = opt.status if self.verbose and self.ipython_notebook: if 'conv' in self.status.lower(): self.progress.bar_style = 'success' elif self.iteration >= self.maxiters: self.progress.bar_style = 'warning' else: self.progress.bar_style = 'danger' def __exit__(self, type, value, traceback): if self.verbose: self.stop = time.time() self.model.remove_observer(self) self.print_out(self.stop - self.start) if not self.ipython_notebook: print() print('Runtime: {}'.format("{:>9s}".format(self.timestring))) print('Optimization status: {0}'.format(self.status)) print() elif self.clear: self.hor_align.close()
def __init__(self, model, opt, maxiters, verbose=False, current_iteration=0, ipython_notebook=True, clear_after_finish=False): self.verbose = verbose if self.verbose: self.model = model self.iteration = current_iteration self.p_iter = self.iteration self.maxiters = maxiters self.len_maxiters = len(str(maxiters)) self.opt_name = opt.opt_name self.model.add_observer(self, self.print_status) self.status = 'running' self.clear = clear_after_finish self.update() try: from IPython.display import display from IPython.html.widgets import IntProgress, HTML, Box, VBox, HBox, FlexBox self.text = HTML(width='100%') self.progress = IntProgress(min=0, max=maxiters) #self.progresstext = Text(width='100%', disabled=True, value='0/{}'.format(maxiters)) self.model_show = HTML() self.ipython_notebook = ipython_notebook except: # Not in Ipython notebook self.ipython_notebook = False if self.ipython_notebook: left_col = VBox(children=[self.progress, self.text], padding=2, width='40%') right_col = Box(children=[self.model_show], padding=2, width='60%') self.hor_align = FlexBox(children = [left_col, right_col], width='100%', orientation='horizontal') display(self.hor_align) try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) right_col.set_css({ 'padding': '2px', }) self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') left_col.add_class("box-flex1") right_col.add_class('box-flex0') except: pass #self.text.add_class('box-flex2') #self.progress.add_class('box-flex1') else: self.exps = exponents(self.fnow, self.current_gradient) print('Running {} Code:'.format(self.opt_name)) print(' {3:7s} {0:{mi}s} {1:11s} {2:11s}'.format("i", "f", "|g|", "runtime", mi=self.len_maxiters))
class VerboseOptimization(object): def __init__(self, model, opt, maxiters, verbose=False, current_iteration=0, ipython_notebook=True, clear_after_finish=False): self.verbose = verbose if self.verbose: self.model = model self.iteration = current_iteration self.p_iter = self.iteration self.maxiters = maxiters self.len_maxiters = len(str(maxiters)) self.opt_name = opt.opt_name self.model.add_observer(self, self.print_status) self.status = 'running' self.clear = clear_after_finish self.update() try: from IPython.display import display from IPython.html.widgets import IntProgress, HTML, Box, VBox, HBox, FlexBox self.text = HTML(width='100%') self.progress = IntProgress(min=0, max=maxiters) #self.progresstext = Text(width='100%', disabled=True, value='0/{}'.format(maxiters)) self.model_show = HTML() self.ipython_notebook = ipython_notebook except: # Not in Ipython notebook self.ipython_notebook = False if self.ipython_notebook: left_col = VBox(children=[self.progress, self.text], padding=2, width='40%') right_col = Box(children=[self.model_show], padding=2, width='60%') self.hor_align = FlexBox(children = [left_col, right_col], width='100%', orientation='horizontal') display(self.hor_align) try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) right_col.set_css({ 'padding': '2px', }) self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') left_col.add_class("box-flex1") right_col.add_class('box-flex0') except: pass #self.text.add_class('box-flex2') #self.progress.add_class('box-flex1') else: self.exps = exponents(self.fnow, self.current_gradient) print('Running {} Code:'.format(self.opt_name)) print(' {3:7s} {0:{mi}s} {1:11s} {2:11s}'.format("i", "f", "|g|", "runtime", mi=self.len_maxiters)) def __enter__(self): self.start = time.time() self._time = self.start return self def print_out(self, seconds): if seconds<60: ms = (seconds%1)*100 self.timestring = "{s:0>2d}s{ms:0>2d}".format(s=int(seconds), ms=int(ms)) else: m, s = divmod(seconds, 60) if m>59: h, m = divmod(m, 60) if h>23: d, h = divmod(h, 24) self.timestring = '{d:0>2d}d{h:0>2d}h{m:0>2d}'.format(m=int(m), h=int(h), d=int(d)) else: self.timestring = '{h:0>2d}h{m:0>2d}m{s:0>2d}'.format(m=int(m), s=int(s), h=int(h)) else: ms = (seconds%1)*100 self.timestring = '{m:0>2d}m{s:0>2d}s{ms:0>2d}'.format(m=int(m), s=int(s), ms=int(ms)) if self.ipython_notebook: names_vals = [['optimizer', "{:s}".format(self.opt_name)], ['runtime', "{:>s}".format(self.timestring)], ['evaluation', "{:>0{l}}".format(self.iteration, l=self.len_maxiters)], ['objective', "{: > 12.3E}".format(self.fnow)], ['||gradient||', "{: >+12.3E}".format(float(self.current_gradient))], ['status', "{:s}".format(self.status)], ] #message = "Lik:{:5.3E} Grad:{:5.3E} Lik:{:5.3E} Len:{!s}".format(float(m.log_likelihood()), np.einsum('i,i->', grads, grads), float(m.likelihood.variance), " ".join(["{:3.2E}".format(l) for l in m.kern.lengthscale.values])) html_begin = """<style type="text/css"> .tg-opt {font-family:"Courier New", Courier, monospace !important;padding:2px 3px;word-break:normal;border-collapse:collapse;border-spacing:0;border-color:#DCDCDC;margin:0px auto;width:100%;} .tg-opt td{font-family:"Courier New", Courier, monospace !important;font-weight:bold;color:#444;background-color:#F7FDFA;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt th{font-family:"Courier New", Courier, monospace !important;font-weight:normal;color:#fff;background-color:#26ADE4;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt .tg-left{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:left;} .tg-opt .tg-right{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:right;} </style> <table class="tg-opt">""" html_end = "</table>" html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.value = (self.iteration+1) #self.progresstext.value = '0/{}'.format((self.iteration+1)) self.model_show.value = self.model._repr_html_() else: n_exps = exponents(self.fnow, self.current_gradient) if self.iteration - self.p_iter >= 20 * np.random.rand(): a = self.iteration >= self.p_iter * 2.78 b = np.any(n_exps < self.exps) if a or b: self.p_iter = self.iteration print('') if b: self.exps = n_exps print('\r', end=' ') print('{3:} {0:>0{mi}g} {1:> 12e} {2:> 12e}'.format(self.iteration, float(self.fnow), float(self.current_gradient), "{:>8s}".format(self.timestring), mi=self.len_maxiters), end=' ') # print 'Iteration:', iteration, ' Objective:', fnow, ' Scale:', beta, '\r', sys.stdout.flush() def print_status(self, me, which=None): self.update() t = time.time() seconds = t-self.start #sys.stdout.write(" "*len(self.message)) if t-self._time > .3 or seconds < .3: self.print_out(seconds) self._time = t self.iteration += 1 def update(self): self.fnow = self.model.objective_function() if self.model.obj_grads is not None: grad = self.model.obj_grads self.current_gradient = np.dot(grad, grad) else: self.current_gradient = np.nan def finish(self, opt): self.status = opt.status if self.verbose and self.ipython_notebook: if 'conv' in self.status.lower(): self.progress.bar_style = 'success' elif self.iteration >= self.maxiters: self.progress.bar_style = 'warning' else: self.progress.bar_style = 'danger' def __exit__(self, type, value, traceback): if self.verbose: self.stop = time.time() self.model.remove_observer(self) self.print_out(self.stop - self.start) if not self.ipython_notebook: print() print('Runtime: {}'.format("{:>9s}".format(self.timestring))) print('Optimization status: {0}'.format(self.status)) print() elif self.clear: self.hor_align.close()
def optimize(self, method='HS', maxiter=500, ftol=1e-6, gtol=1e-6, step_length=1., callback=None, verbose=True): """ Optimize the model. The strategy is to run conjugate natural gradients on the variational parameters, interleaved with gradient based optimization of any non-variational parameters. self.hyperparam_interval dictates how often this happens. Arguments --------- :method: ['FR', 'PR','HS','steepest'] -- conjugate gradient method :maxiter: int :ftol: float :gtol: float :step_length: float """ assert method in ['FR', 'PR','HS','steepest'], 'invalid conjugate gradient method specified.' ## For GPy style notebook verbosity if verbose: try: from IPython.display import display from IPython.html.widgets import IntProgress, HTML, Box, VBox, HBox, FlexBox self.text = HTML(width='100%') self.progress = IntProgress(min=0, max=maxiter) self.progress.bar_style = 'info' self.status = 'Running' html_begin = """<style type="text/css"> .tg-opt {font-family:"Courier New", Courier, monospace !important;padding:2px 3px;word-break:normal;border-collapse:collapse;border-spacing:0;border-color:#DCDCDC;margin:0px auto;width:100%;} .tg-opt td{font-family:"Courier New", Courier, monospace !important;font-weight:bold;color:#444;background-color:#F7FDFA;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt th{font-family:"Courier New", Courier, monospace !important;font-weight:normal;color:#fff;background-color:#26ADE4;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt .tg-left{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:left;} .tg-opt .tg-right{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:right;} </style> <table class="tg-opt">""" html_end = "</table>" self.ipython_notebook = True except: # Not in Ipython notebook self.ipython_notebook = False else: self.ipython_notebook = False if self.ipython_notebook: left_col = VBox(children=[self.progress, self.text], padding=2, width='100%') self.hor_align = FlexBox(children = [left_col], width='100%', orientation='horizontal') display(self.hor_align) try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') left_col.add_class("box-flex1") except: pass self.start = time.time() self._time = self.start ## --- iteration = 0 bound_old = self.bound() searchDir_old = 0. iteration_failed = False while True: if callback is not None: callback() grad,natgrad = self.vb_grad_natgrad() grad,natgrad = -grad,-natgrad squareNorm = np.dot(natgrad,grad) # used to monitor convergence #find search direction if (method=='steepest') or not iteration: beta = 0 elif (method=='PR'): beta = np.dot((natgrad-natgrad_old),grad)/squareNorm_old elif (method=='FR'): beta = squareNorm/squareNorm_old elif (method=='HS'): beta = np.dot((natgrad-natgrad_old),grad)/np.dot((natgrad-natgrad_old),grad_old) if np.isnan(beta) or (beta < 0.): beta = 0. searchDir = -natgrad + beta*searchDir_old # Try a conjugate step phi_old = self.get_vb_param().copy() try: self.set_vb_param(phi_old + step_length*searchDir) bound = self.bound() except LinAlgError: self.set_vb_param(phi_old) bound = bound_old-1 iteration += 1 # Make sure there's an increase in the bound, else revert to steepest, which is guaranteed to increase the bound. # (It's the same as VBEM.) if bound < bound_old: searchDir = -natgrad try: self.set_vb_param(phi_old + step_length*searchDir) bound = self.bound() except LinAlgError: import warnings warnings.warn("Caught LinalgError in setting variational parameters, trying to continue with old parameter settings", LinAlgWarning) self.set_vb_param(phi_old) bound = self.bound() iteration_failed = False iteration += 1 if verbose: if self.ipython_notebook: t = time.time() seconds = t-self.start self.status = 'Running' self.progress.bar_style = 'info' names_vals = [['conjugate gradient method', "{:s}".format(method)], ['runtime', "{:.1f}s".format(seconds)], ['evaluation', "{}".format(iteration)], ['objective', "{:12.5f}".format(-bound)], ['||gradient||', "{:12.5f}".format(float(squareNorm))], ['beta', "{:12.5f}".format(beta)], ['status', "{:s}".format(self.status)], ] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.progress.value = iteration self.text.value = html_begin + html_body + html_end else: print('\riteration '+str(iteration)+' bound='+str(bound) + ' grad='+str(squareNorm) + ', beta='+str(beta)) sys.stdout.flush() # Converged yet? try the parameters if so if np.abs(bound-bound_old) <= ftol: if verbose: if self.ipython_notebook: self.status = 'vb converged (ftol)' names_vals[-1] = ['status', "{:s}".format(self.status)] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.bar_style = 'success' else: print('vb converged (ftol)') if self.optimize_parameters() < 1e-1: break if squareNorm <= gtol: if verbose: if self.ipython_notebook: self.status = 'vb converged (gtol)' names_vals[-1] = ['status', "{:s}".format(self.status)] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.bar_style = 'success' else: print('vb converged (gtol)') if self.optimize_parameters() < 1e-1: break if iteration >= maxiter: if verbose: if self.ipython_notebook: self.status = 'maxiter exceeded' names_vals[-1] = ['status', "{:s}".format(self.status)] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.bar_style = 'warning' else: print('maxiter exceeded') break #store essentials of previous iteration natgrad_old = natgrad.copy() # copy: better safe than sorry. grad_old = grad.copy() searchDir_old = searchDir.copy() squareNorm_old = squareNorm # hyper param_optimisation if ((iteration >1) and not (iteration%self.hyperparam_interval)) or iteration_failed: self.optimize_parameters() bound_old = bound # Clean up temporary fields after optimization if self.ipython_notebook: del self.text del self.progress del self.hor_align
def optimize(self, method='HS', maxiter=500, ftol=1e-6, gtol=1e-6, step_length=1., callback=None, verbose=True): """ Optimize the model. The strategy is to run conjugate natural gradients on the variational parameters, interleaved with gradient based optimization of any non-variational parameters. self.hyperparam_interval dictates how often this happens. Arguments --------- :method: ['FR', 'PR','HS','steepest'] -- conjugate gradient method :maxiter: int :ftol: float :gtol: float :step_length: float """ assert method in ['FR', 'PR', 'HS', 'steepest' ], 'invalid conjugate gradient method specified.' ## For GPy style notebook verbosity if verbose: try: from IPython.display import display from IPython.html.widgets import IntProgress, HTML, Box, VBox, HBox, FlexBox self.text = HTML(width='100%') self.progress = IntProgress(min=0, max=maxiter) self.progress.bar_style = 'info' self.status = 'Running' html_begin = """<style type="text/css"> .tg-opt {font-family:"Courier New", Courier, monospace !important;padding:2px 3px;word-break:normal;border-collapse:collapse;border-spacing:0;border-color:#DCDCDC;margin:0px auto;width:100%;} .tg-opt td{font-family:"Courier New", Courier, monospace !important;font-weight:bold;color:#444;background-color:#F7FDFA;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt th{font-family:"Courier New", Courier, monospace !important;font-weight:normal;color:#fff;background-color:#26ADE4;border-style:solid;border-width:1px;overflow:hidden;word-break:normal;border-color:#DCDCDC;} .tg-opt .tg-left{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:left;} .tg-opt .tg-right{font-family:"Courier New", Courier, monospace !important;font-weight:normal;text-align:right;} </style> <table class="tg-opt">""" html_end = "</table>" self.ipython_notebook = True except: # Not in Ipython notebook self.ipython_notebook = False else: self.ipython_notebook = False if self.ipython_notebook: left_col = VBox(children=[self.progress, self.text], padding=2, width='100%') self.hor_align = FlexBox(children=[left_col], width='100%', orientation='horizontal') display(self.hor_align) try: self.text.set_css('width', '100%') left_col.set_css({ 'padding': '2px', 'width': "100%", }) self.hor_align.set_css({ 'width': "100%", }) self.hor_align.remove_class('vbox') self.hor_align.add_class('hbox') left_col.add_class("box-flex1") except: pass self.start = time.time() self._time = self.start ## --- iteration = 0 bound_old = self.bound() searchDir_old = 0. iteration_failed = False while True: if callback is not None: callback() grad, natgrad = self.vb_grad_natgrad() grad, natgrad = -grad, -natgrad squareNorm = np.dot(natgrad, grad) # used to monitor convergence #find search direction if (method == 'steepest') or not iteration: beta = 0 elif (method == 'PR'): beta = np.dot((natgrad - natgrad_old), grad) / squareNorm_old elif (method == 'FR'): beta = squareNorm / squareNorm_old elif (method == 'HS'): beta = np.dot((natgrad - natgrad_old), grad) / np.dot( (natgrad - natgrad_old), grad_old) if np.isnan(beta) or (beta < 0.): beta = 0. searchDir = -natgrad + beta * searchDir_old # Try a conjugate step phi_old = self.get_vb_param().copy() try: self.set_vb_param(phi_old + step_length * searchDir) bound = self.bound() except LinAlgError: self.set_vb_param(phi_old) bound = bound_old - 1 iteration += 1 # Make sure there's an increase in the bound, else revert to steepest, which is guaranteed to increase the bound. # (It's the same as VBEM.) if bound < bound_old: searchDir = -natgrad try: self.set_vb_param(phi_old + step_length * searchDir) bound = self.bound() except LinAlgError: import warnings warnings.warn( "Caught LinalgError in setting variational parameters, trying to continue with old parameter settings", LinAlgWarning) self.set_vb_param(phi_old) bound = self.bound() iteration_failed = False iteration += 1 if verbose: if self.ipython_notebook: t = time.time() seconds = t - self.start self.status = 'Running' self.progress.bar_style = 'info' names_vals = [ ['conjugate gradient method', "{:s}".format(method)], ['runtime', "{:.1f}s".format(seconds)], ['evaluation', "{}".format(iteration)], ['objective', "{:12.5f}".format(-bound)], ['||gradient||', "{:12.5f}".format(float(squareNorm))], ['beta', "{:12.5f}".format(beta)], ['status', "{:s}".format(self.status)], ] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format(name) html_body += "<td class='tg-right'>{}</td>".format(val) html_body += "</tr>" self.progress.value = iteration self.text.value = html_begin + html_body + html_end else: print('\riteration ' + str(iteration) + ' bound=' + str(bound) + ' grad=' + str(squareNorm) + ', beta=' + str(beta)) sys.stdout.flush() # Converged yet? try the parameters if so if np.abs(bound - bound_old) <= ftol: if verbose: if self.ipython_notebook: self.status = 'vb converged (ftol)' names_vals[-1] = ['status', "{:s}".format(self.status)] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format( name) html_body += "<td class='tg-right'>{}</td>".format( val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.bar_style = 'success' else: print('vb converged (ftol)') if self.optimize_parameters() < 1e-1: break if squareNorm <= gtol: if verbose: if self.ipython_notebook: self.status = 'vb converged (gtol)' names_vals[-1] = ['status', "{:s}".format(self.status)] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format( name) html_body += "<td class='tg-right'>{}</td>".format( val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.bar_style = 'success' else: print('vb converged (gtol)') if self.optimize_parameters() < 1e-1: break if iteration >= maxiter: if verbose: if self.ipython_notebook: self.status = 'maxiter exceeded' names_vals[-1] = ['status', "{:s}".format(self.status)] html_body = "" for name, val in names_vals: html_body += "<tr>" html_body += "<td class='tg-left'>{}</td>".format( name) html_body += "<td class='tg-right'>{}</td>".format( val) html_body += "</tr>" self.text.value = html_begin + html_body + html_end self.progress.bar_style = 'warning' else: print('maxiter exceeded') break #store essentials of previous iteration natgrad_old = natgrad.copy() # copy: better safe than sorry. grad_old = grad.copy() searchDir_old = searchDir.copy() squareNorm_old = squareNorm # hyper param_optimisation if ((iteration > 1) and not (iteration % self.hyperparam_interval) ) or iteration_failed: self.optimize_parameters() bound_old = bound # Clean up temporary fields after optimization if self.ipython_notebook: del self.text del self.progress del self.hor_align