Source code for mermaid.viewers

Implements various viewers to display 3D data
from __future__ import print_function

from builtins import str
from builtins import range
from builtins import object
from abc import ABCMeta, abstractmethod

import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from future.utils import with_metaclass

def _create_some_test_data():
    a = np.sin(np.linspace(0, np.pi, 20))
    b = np.sin(np.linspace(0, np.pi*5, 20))
    data = np.outer(a, b)[..., np.newaxis] * a
    return data

def _print_debug(str, flag=False):
    if flag:

[docs]class FigureEventHandler(object): """Class to implement general event handling for matplotlib figures. In particular this class allows for easy event handling within different subplots. """ def __init__(self, fig): """ Constructor :param fig: figure handle """ self.fig = fig """figure handle""" self._remove_keymap_conflicts({'j', 'k'}) """conflicts with keys that should be removed""" self.ax_events = dict() """dictionary that keeps track of all the events""" self.ax_events['button_press_event']=[] self.ax_events['button_release_event']=[] self.ax_events['key_press_event']=[] self.ax_events['key_release_event']=[] self.supported_events = ['button_press_event','button_release_event', 'key_press_event','key_release_event'] """events that are currently supported by the figure event handler""" self.sync_d = dict() """dictionary to hold information about synchronization of subplots (for synchronized slicing)""" self.connect()
[docs] def reset_synchronize(self): """ Removes all the subplot synchronizations """ self.sync_d.clear()
[docs] def synchronize(self,axes): """ Sets synchornization information (i.e., which axes need to be synchronized) :param axes: list of axes """ for e in axes: self.sync_d[e]=axes
def _is_supported_event(self, eventname): if self.supported_events.count(eventname)>0: return True else: return False def _remove_keymap_conflicts(self, new_keys_set): for prop in plt.rcParams: if prop.startswith('keymap.'): keys = plt.rcParams[prop] remove_list = set(keys) & new_keys_set for key in remove_list: keys.remove(key)
[docs] def connect(self): """ Connect to all the events """ 'connect to all the events we need' self.cidbuttonpress = self.fig.canvas.mpl_connect( 'button_press_event', self._on_mouse_press) self.cidbuttonrelease = self.fig.canvas.mpl_connect( 'button_release_event', self._on_mouse_release) self.cidkeypress = self.fig.canvas.mpl_connect( 'key_press_event', self._on_key_press) self.cidkeyrelease = self.fig.canvas.mpl_connect( 'key_release_event', self._on_key_release)
[docs] def disconnect(self): """ Disconnect from all events """ 'disconnect all the stored connection ids' self.fig.canvas.mpl_disconnect(self._on_mouse_press) self.fig.canvas.mpl_disconnect(self._on_mouse_release) self.fig.canvas.mpl_disconnect(self._on_key_press) self.fig.canvas.mpl_disconnect(self._on_key_release)
def _event_is_registered(self, eventname, ax): if eventname in self.ax_events: registeredEvents = self.ax_events[eventname] for e in registeredEvents: if e[0] is ax: return True return False
[docs] def add_axes_event(self, eventname, ax, eventfcn, getsyncfcn=None,setsyncfcn=None): """ Associates events with a particular axis :param eventname: event name: 'button_press_event', not yet supported: 'button_release_event', 'key_press_event', 'key_release_event' :param ax: axis handle :param eventfcn: function that should be called :param getsyncfcn: function that returns synchronization information :param setsyncfcn: function that takes synchronization information """ if self._is_supported_event(eventname): _print_debug('Registering an event') if not self._event_is_registered(eventname, ax): self.ax_events[eventname].append((ax,eventfcn,getsyncfcn,setsyncfcn)) else: print('Event ' + eventname + ' is not supported and cannot be registered')
[docs] def remove_axes_event(self, eventname, ax): """ Removes an event from an axis :param eventname: event name: 'button_press_event', not yet supported: 'button_release_event', 'key_press_event', 'key_release_event' :param ax: axis handle """ if self._is_supported_event(eventname): _print_debug('Removing an event ... ') if eventname in self.ax_events: registeredEvents = self.ax_events[eventname] for e in registeredEvents: if e[0] is ax: registeredEvents.remove( e ) _print_debug('Removed!') return else: print('Event ' + eventname + ' is not supported and cannot be removed')
def _broadcast(self, broadCastTo, syncInfo, eventName): registeredEvents = self.ax_events[eventName] for e in registeredEvents: for b in broadCastTo: if b is e[0]: # found the axes if e[3] is not None: e[3](syncInfo) # now sync it def _on_mouse_press(self, event): _print_debug('Pressed mouse button') # get current axis if event.inaxes is not None: ax = event.inaxes registeredEvents = self.ax_events['button_press_event'] # get corresponding event function and dispatch it for e in registeredEvents: if e[0] is ax: _print_debug('Dispatching event') e[1](event) if e[0] in self.sync_d and e[2] is not None: _print_debug('Broadcasting') syncInfo = e[2]() self._broadcast(self.sync_d[e[0]], syncInfo, 'button_press_event') # and now draw the canvas self.fig.canvas.draw() def _on_mouse_release(self, event): pass def _on_key_press(self, event): pass def _on_key_release(self, event): pass
[docs]class ImageViewer(with_metaclass(ABCMeta, object)): """ Abstract class for an image viewer. """ def __init__(self, ax, data ): """ Constructor. :param ax: axis :param data: data to show """ = ax = data
[docs] @abstractmethod def show(self): """ Displays the image """ pass
[docs] def display_title(self): """ Displays the title for a figure """ pass
[docs]class ImageViewer3D(with_metaclass(ABCMeta, ImageViewer)): """ Abstract class for a 3D image viewer. """ def __init__(self, ax, data ): super(ImageViewer3D,self).__init__(ax,data)
[docs] @abstractmethod def previous_slice(self): """ display the previous slice """ pass
[docs] @abstractmethod def next_slice(self): """ display the next slice """ pass
[docs] @abstractmethod def set_synchronize(self, index): """ Synchronize to a particular slice :param index: slice index """ pass
[docs] @abstractmethod def get_synchronize(self): """ Get index to which should be synchronized :return: slice index """ pass
[docs] def on_mouse_press(self, event): """ Implements going forward and backward in slices depending based on clicking in the left or the right of an image :param event: event data """ x = event.xdata y = event.ydata xlim = ylim = xrange = abs(xlim[0] - xlim[1]) yrange = abs(ylim[0] - ylim[1]) _print_debug('X = ' + str(x)) _print_debug('Y = ' + str(y)) _print_debug('xlim = ' + str(xlim)) _print_debug('ylim = ' + str(ylim)) if abs(y - ylim[0]) <= yrange: if abs(x - xlim[0]) <= 0.4 * xrange: _print_debug('Previous slice') self.previous_slice() elif abs(x - xlim[1]) <= 0.4 * xrange: _print_debug('Next slice') self.next_slice() self.display_title()
[docs]class ImageViewer3D_Sliced(ImageViewer3D): """ 3D image viewer specialization to 3D sliced viewing """ def __init__(self, ax, data, sliceDim, textStr='Slice', showColorbar=False): """ Constructor :param ax: axis :param data: data to be displayed (3D image volume) :param sliceDim: dimension along which to slice :param textStr: text string that should be displayed :param showColorbar: (bool) should a colorbar be displayed? """ self.sliceDim = sliceDim """dimension to slice""" self.textStr = textStr """title string""" self.index = data.shape[self.sliceDim] // 2 """slice index to display""" self.showColorbar = showColorbar """dispaly colorbar True/False""" super(ImageViewer3D_Sliced,self).__init__(ax,data) def _get_slice_at_dimension(self, index): # slicing a along a given dimension at index, index slc = [slice(None)] * len( slc[self.sliceDim] = slice(index, index+1) return ([slc]).squeeze()
[docs] def previous_slice(self): """ Display previous slice """ plt.cla() self.index = (self.index - 1) %[self.sliceDim] # wrap around using %[0].set_array(self.get_slice_at_dimension(self.index))
[docs] def next_slice(self): """ Display next slice """ plt.cla() self.index = (self.index + 1) %[self.sliceDim][0].set_array(self.get_slice_at_dimension(self.index))
[docs] def set_synchronize(self, index): """ Synchronize slice view to a particular slice :param index: slice index to synchronize to """ plt.cla() self.index = (index) %[self.sliceDim][0].set_array(self.get_slice_at_dimension(self.index)) self.display_title()
[docs] def get_synchronize(self): """ Get current slice index :return: current slice index """ return self.index
[docs] def display_title(self): """ Display figure title """ font = {'size': 10} plt.title( self.textStr + ' = ' + str(self.index) + '/' + str([self.sliceDim]-1),font )
[docs] def show(self): """ Show the current slice """ plt.cla() #print('debugging {}'.format(self.index), 'slice_dim{}'.format(self.sliceDim),'img_shape{}'.format( cim = divider = make_axes_locatable( cax = divider.append_axes('right', size='5%', pad=0.05) plt.gcf().colorbar(cim, cax=cax, orientation='vertical').ax.tick_params(labelsize=3) self.display_title()
[docs]class ImageViewer3D_Sliced_Contour(ImageViewer3D_Sliced): """ Specialization of 3D sliced viewer to also display contours """ def __init__(self, ax, data, phi, sliceDim, textStr='Slice', showColorbar=False): """ Constructor :param ax: axis :param data: data (image array, XxYxZ) :param phi: map (dimxXxYxZ) :param sliceDim: slice dimension :param textStr: title string :param showColorbar: (bool) show colorbar """ self.phi = phi """map""" super(ImageViewer3D_Sliced_Contour,self).__init__(ax,data, sliceDim, textStr, showColorbar)
[docs] def get_phi_slice_at_dimension(self,index): """ Get map (based on which we can draw contours) at a particular slice index :param index: slice index :return: returns the map at this slice index """ # slicing a along a given dimension at index, index slc = [slice(None)] * len(self.phi.shape) slc[self.sliceDim+1] = slice(index, index+1) return (self.phi[slc]).squeeze()
[docs] def show_contours(self): """ display the contours for a particular slice """ phiSliced = self.get_phi_slice_at_dimension(self.index) for d in range(0,self.sliceDim): plt.contour(phiSliced[d,:,:], np.linspace(-1,1,20),colors='r',linestyles='solid') for d in range(self.sliceDim+1,3): plt.contour(phiSliced[d,:,:], np.linspace(-1,1,20),colors='r',linestyles='solid')
[docs] def previous_slice(self): """ display previous slice """ super(ImageViewer3D_Sliced_Contour,self).previous_slice() self.show_contours()
[docs] def next_slice(self): """ display next slice """ super(ImageViewer3D_Sliced_Contour,self).next_slice() self.show_contours()
[docs] def set_synchronize(self, index): """ set slice to a particular index (to synchronize views) :param index: slice index """ super(ImageViewer3D_Sliced_Contour,self).set_synchronize(index) self.show_contours()
[docs] def show(self): """ Show the image with contours overlaid """ super(ImageViewer3D_Sliced_Contour,self).show() self.show_contours()
[docs]def test_viewer(): """ simple test viewer """ data = _create_some_test_data() fig,ax = plt.subplots(1,3) plt.setp(plt.gcf(), 'facecolor', 'white')'bmh') ivx = ImageViewer3D_Sliced( ax[0], data, 0, 'X slice') ivy = ImageViewer3D_Sliced( ax[1], data, 1, 'Y slice') ivz = ImageViewer3D_Sliced( ax[2], data, 2, 'Z slice') feh = FigureEventHandler(fig) feh.add_axes_event('button_press_event', ax[0], ivx.on_mouse_press) feh.add_axes_event('button_press_event', ax[1], ivy.on_mouse_press) feh.add_axes_event('button_press_event', ax[2], ivz.on_mouse_press) feh.synchronize([ax[0], ax[1], ax[2]])