# Copyright 2019 United Kingdom Research and Innovation
# Copyright 2019 The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Authors:
# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
# Kyle Pidgeon (UKRI-STFC)
try:
from ipywidgets import interactive_output
import ipywidgets as widgets
except ImportError as ie:
raise ImportError("please conda/pip install ipywidgets") from ie
import matplotlib.pyplot as plt
from matplotlib import gridspec
import numpy
from IPython.display import HTML, display
import random
from cil.utilities.display import set_origin
def display_slice(container, clim, direction, title, cmap, size, axis_labels, origin):
def get_slice_3D(x, minmax, roi_hdir, roi_vdir, equal_aspect):
if direction == 0:
img = container[x]
x_label = axis_labels[2]
y_label = axis_labels[1]
elif direction == 1:
img = container[:,x,:]
x_label = axis_labels[2]
y_label = axis_labels[0]
elif direction == 2:
img = container[:,:,x]
x_label = axis_labels[1]
y_label = axis_labels[0]
if size is None:
fig = plt.figure()
else:
fig = plt.figure(figsize=size)
dtitle = ''
if isinstance(title, (list, tuple)):
dtitle = title[x]
else:
dtitle = title
gs = gridspec.GridSpec(1, 2, figure=fig, width_ratios=(1,.05), height_ratios=(1,))
# image
ax = fig.add_subplot(gs[0, 0])
img, data_origin, _ = set_origin(img, origin)
aspect = 'equal'
if not equal_aspect:
aspect = (roi_hdir[1] - roi_hdir[0]) / (roi_vdir[1] - roi_vdir[0])
if 'right' in origin:
roi_hdir = roi_hdir[1], roi_hdir[0]
if 'upper' in origin:
roi_vdir = roi_vdir[1], roi_vdir[0]
aximg = ax.imshow(img, cmap=cmap, origin=data_origin, aspect=aspect)
cmin = clim[0] + (minmax[0] / 100)*(clim[1]-clim[0])
cmax = clim[0] + (minmax[1] / 100)*(clim[1]-clim[0])
aximg.set_clim((cmin, cmax))
ax.set_xlim(*roi_hdir)
ax.set_ylim(*roi_vdir)
ax.set_xlabel(x_label)
ax.set_ylabel(y_label)
ax.set_title(f'{dtitle} {x}')
# colorbar
ax = fig.add_subplot(gs[0, 1])
plt.colorbar(aximg, cax=ax)
plt.tight_layout()
plt.show(fig)
return get_slice_3D
[docs]def islicer(data, direction=0, title=None, slice_number=None, cmap='gray',
minmax=None, size=None, axis_labels=None, origin='lower-left',
play_interval=500):
"""
Creates an interactive slider that slices a 3D volume along an axis.
Parameters
----------
data : DataContainer or numpy.ndarray
A 3-dimensional dataset from which 2-dimensional slices will be
shown
direction : int
Axis to slice on. Can be 0,1,2 or the axis label, default 0
title : str, list of str or tuple of str, default=''
Title for the display
slice_number : int, optional
Start slice number (default is None, which results in the center
slice being shown initially)
cmap : str or matplotlib.colors.Colormap, default='gray'
Set the colour map
minmax : tuple
Colorbar (min, max) values, default None (uses the min, max of
values in `data`)
size : int or tuple, optional
Specify the figure size in inches. If `int` this specifies the
width, and scales the height in order to keep the standard
`matplotlib` aspect ratio, default None (use the default matplotlib
figure size)
axis_labels : list of str, optional
The axis labels to use for each of the 3 dimensions in the data
(default is None, resulting in labels extracted from the data, or
['X','Y','Z'] if no labels are present)
origin : {'lower-left', 'upper-left', 'lower-right', 'upper-right'}
Sets the display origin
play_interval : int, default=500
The interval of time (in ms) a slice is selected for when iterating
through a set of them
Returns
-------
box : ipywidgets.Box
The top-level widget container.
"""
if axis_labels is None:
if hasattr(data, "dimension_labels"):
axis_labels = [*data.dimension_labels]
else:
axis_labels = ['X', 'Y', 'Z']
if isinstance (data, numpy.ndarray):
container = data
elif hasattr(data, "__getitem__"):
container = data
elif hasattr(data, "as_array"):
container = data.as_array()
if not isinstance (direction, int):
if direction in data.dimension_labels:
direction = data.get_dimension_axis(direction)
if slice_number is None:
slice_number = int(data.shape[direction]/2)
if title is None:
title = "Direction {}: Slice".format(axis_labels[direction])
style = {'slider_width': '80%'}
layout = widgets.Layout(width='200px')
slice_slider = widgets.IntSlider(
min=0,
max=data.shape[direction]-1,
step=1,
value=slice_number,
continuous_update=True,
layout=layout,
style=style,
)
slice_selector_full = widgets.VBox([widgets.Label('Slice index (direction {})'.format(axis_labels[direction])), slice_slider])
play_slices = widgets.Play(
min=0,
max=data.shape[direction]-1,
step=1,
interval=play_interval,
value=slice_number,
disabled=False,
)
widgets.jslink((play_slices, 'value'), (slice_slider, 'value'))
amax = container.max()
amin = container.min()
if minmax is None:
minmax = (amin, amax)
if isinstance (size, (int, float)):
default_ratio = 6./8.
size = ( size , size * default_ratio )
min_max = widgets.IntRangeSlider(
value=[0, 100],
min=0,
max=100,
step=5,
disabled=False,
continuous_update=True,
orientation='horizontal',
readout=True,
layout=layout,
style=style,
)
min_max_full = widgets.VBox([widgets.Label('Display window percent'), min_max])
dirs_remaining = [i for i in range(3) if i != direction]
h_dir, v_dir = dirs_remaining[1], dirs_remaining[0]
h_dir_size = container.shape[h_dir]
v_dir_size = container.shape[v_dir]
roi_select_hdir = widgets.IntRangeSlider(
value=[0, h_dir_size-1],
min=0,
max=h_dir_size-1,
step=1,
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='d',
layout=layout,
style=style,
)
roi_select_hdir_full = widgets.VBox([widgets.Label(f'Range: {axis_labels[h_dir]}'), roi_select_hdir])
roi_select_vdir = widgets.IntRangeSlider(
value=[0, v_dir_size-1],
min=0,
max=v_dir_size-1,
step=1,
disabled=False,
continuous_update=False,
orientation='horizontal',
readout=True,
readout_format='d',
layout=layout,
style=style,
)
roi_select_vdir_full = widgets.VBox([widgets.Label(f'Range: {axis_labels[v_dir]}'), roi_select_vdir])
equal_aspect = widgets.Checkbox(
value=True,
description='Pixel aspect ratio = 1',
disabled=False,
indent=False,
layout=widgets.Layout(width='auto'),
)
box_layout = widgets.Layout(
display='flex',
flex_flow='column',
align_items='flex-start',
justify_content='center',
)
selectors = widgets.Box([
play_slices,
slice_selector_full,
min_max_full,
roi_select_hdir_full,
roi_select_vdir_full,
equal_aspect],
layout=box_layout)
out = interactive_output(
display_slice(
container,
minmax,
direction,
title=title,
cmap=cmap,
size=size,
axis_labels=axis_labels,
origin=origin),
{'x': slice_slider,
'minmax': min_max,
'roi_hdir': roi_select_hdir,
'roi_vdir': roi_select_vdir,
'equal_aspect': equal_aspect})
box = widgets.HBox(children=[out, selectors],
layout=widgets.Layout(
display='flex',
justify_content='center'))
return box
[docs]def link_islicer(*args):
'''Links islicer's slice-selection widgets
Parameters
----------
*args : tuple of ipywidgets.Box
The widget containers returned from `islicer`, from which the slice
selection sliders will be extracted and linked.
'''
slice_sliders = [arg.children[-1].children[1].children[1] for arg in args]
play_widgets = [arg.children[-1].children[0] for arg in args][1:]
for p in play_widgets:
p.layout.visibility = 'hidden'
linked = [(widg, 'value') for widg in slice_sliders]
# link pair-wise
pairs = [(linked[i+1],linked[i]) for i in range(len(linked)-1)]
for pair in pairs:
widgets.link(*pair)
display(*args)
# https://stackoverflow.com/questions/31517194/how-to-hide-one-specific-cell-input-or-output-in-ipython-notebook/52664156
def hide_toggle(for_next=False):
this_cell = """$('div.cell.code_cell.rendered.selected')"""
next_cell = this_cell + '.next()'
toggle_text = 'Toggle show/hide' # text shown on toggle link
target_cell = this_cell # target cell to control with toggle
js_hide_current = '' # bit of JS to permanently hide code in current cell (only when toggling next cell)
if for_next:
target_cell = next_cell
toggle_text += ' next cell'
js_hide_current = this_cell + '.find("div.input").hide();'
js_f_name = 'code_toggle_{}'.format(str(random.randint(1,2**64)))
html = """
<script>
function {f_name}() {{
{cell_selector}.find('div.input').toggle();
}}
{js_hide_current}
</script>
<a href="javascript:{f_name}()">{toggle_text}</a>
""".format(
f_name=js_f_name,
cell_selector=target_cell,
js_hide_current=js_hide_current,
toggle_text=toggle_text
)
return HTML(html)