def make_checkboxes(pt):
c = Container(labels=False)
dt = [
("cameras", DeviceType.CameraDevice),
("shutters", DeviceType.ShutterDevice),
("stages", DeviceType.StageDevice),
("wheels, turrets, etc.", DeviceType.StateDevice),
("other devices", OTHER_DEVICES),
]
for label, dtype in dt:
@magicgui(auto_call=True, dt={"bind": dtype}, vis={"label": label})
def toggle(vis: bool = True, dt=None):
pt.set_dtype_visibility(dt, visible=vis)
toggle.name = label[:2]
c.append(toggle)
@magicgui(auto_call=True, show={"label": "Show read-only"})
def show_ro(show: bool = True):
pt.show_read_only = show
c.append(show_ro)
return c
def to_container(self, **kwargs) -> Container:
"""Return a ``magicgui.widgets.Container`` for this MagicSignature."""
from magicgui.widgets import Container
return Container(
widgets=list(self.widgets(kwargs.get("app")).values()),
**kwargs,
)
def create_gui_nms_slider(self, shape_layer):
from magicgui.widgets import FloatSlider, Container, Label
from torchvision.ops import nms
slider = FloatSlider(min=0.0, max=1.0, step=0.01, name='NMS')
slider_label = Label(name='IoU_threshold')
container = Container(widgets=[slider, slider_label])
def change_boxes(event, shape_layer=shape_layer):
# remove all shapes from layer
self.select_all_shapes(shape_layer)
shape_layer.remove_selected()
# create mask and new information
boxes = torch.tensor([
make_bbox_napari(box, reverse=True)
for box in shape_layer.metadata['boxes']
])
scores = torch.tensor(shape_layer.metadata['scores'])
if boxes.size()[0] > 0:
mask = nms(boxes, scores, slider.value) # torch.tensor
mask = (np.array(mask), )
new_boxes = np.asarray(shape_layer.metadata['boxes'])[mask]
new_labels = shape_layer.metadata['labels'][mask]
new_scores = shape_layer.metadata['scores'][mask]
# set the current properties as workaround
shape_layer.current_properties['labels'] = new_labels
shape_layer.current_properties['scores'] = new_scores
# add shapes to layer
if new_boxes.size > 0:
shape_layer.add(list(new_boxes))
# set the properties
shape_layer.properties['labels'] = new_labels
shape_layer.properties['scores'] = new_scores
# set temporary information
shape_layer.metadata['boxes_nms'] = list(new_boxes)
shape_layer.metadata['labels_nms'] = new_labels
shape_layer.metadata['scores_nms'] = new_scores
# change label
slider_label.value = str(slider.value)
slider.changed.connect(change_boxes)
# invoke nms
container.NMS.value = 1.0
# event triggered when the name of the shape layer changes
self.shape_layer.events.name.connect(change_boxes)
return container
def __init__(self, mmcore=None, parent=None):
super().__init__(parent)
self.pt = PropTable(mmcore)
self.le = LineEdit(label="Filter:")
self.le.native.setPlaceholderText("Filter...")
self.le.changed.connect(self._on_le_change)
right = Container(widgets=[self.le, self.pt], labels=False)
self.cb = make_checkboxes(self.pt)
self.cb.native.layout().addStretch()
self.cb.native.layout().setSpacing(0)
self.pt.show()
self.cb.show()
self._container = Container(
layout="horizontal", widgets=[self.cb, right], labels=False
)
self._container.margins = 0, 0, 0, 0
self.setLayout(QHBoxLayout())
self.setContentsMargins(0, 0, 0, 0)
self.layout().addWidget(self._container.native)
def create_label_menu(shapes_layer, label_feature, labels):
"""Create a label menu widget that can be added to the napari viewer dock
Parameters
----------
shapes_layer : napari.layers.Shapes
a napari shapes layer
label_feature : str
the name of the shapes feature to use the displayed text
labels : List[str]
list of the possible text labels values.
Returns
-------
label_widget : magicgui.widgets.Container
the container widget with the label combobox
"""
# Create the label selection menu
label_menu = ComboBox(label='text label', choices=labels)
label_widget = Container(widgets=[label_menu])
def update_label_menu():
"""This is a callback function that updates the label menu when
the default features of the Shapes layer change
"""
new_label = str(shapes_layer.feature_defaults[label_feature][0])
if new_label != label_menu.value:
label_menu.value = new_label
shapes_layer.events.feature_defaults.connect(update_label_menu)
def set_selected_features_to_default():
"""This is a callback that updates the feature values of the currently
selected shapes. This is a side-effect of the deprecated current_properties
setter, but does not occur when modifying feature_defaults."""
indices = list(shapes_layer.selected_data)
default_value = shapes_layer.feature_defaults[label_feature][0]
shapes_layer.features[label_feature][indices] = default_value
shapes_layer.events.features()
shapes_layer.events.feature_defaults.connect(
set_selected_features_to_default)
shapes_layer.events.features.connect(shapes_layer.refresh_text)
def label_changed(value: str):
"""This is a callback that update the default features on the Shapes layer
when the label menu selection changes
"""
shapes_layer.feature_defaults[label_feature] = value
shapes_layer.events.feature_defaults()
label_menu.changed.connect(label_changed)
return label_widget
def __init__(self, mmcore=None, parent=None):
super().__init__(parent)
self.setLayout(QVBoxLayout())
self.setContentsMargins(0, 0, 0, 0)
self._container = Container(
widgets=[
get_editor_widget(prop, mmcore)
for prop in iter_dev_props(mmcore)
if LIGHT_LIST.search(prop.name) and prop.has_range
],
labels=True,
)
self.layout().addWidget(self._container.native)
def create_gui_score_slider(self, shape_layer):
from magicgui.widgets import FloatSlider, Container, Label
slider = FloatSlider(min=0.0,
max=1.0,
step=0.05,
name='Score',
value=0.0)
slider_label = Label(name='Score_threshold', value=0.0)
container = Container(widgets=[slider, slider_label])
def change_boxes(event, shape_layer=shape_layer):
# remove all shapes from layer
self.select_all_shapes(shape_layer)
shape_layer.remove_selected()
# create mask and new information
mask = np.where(shape_layer.metadata['scores'] > slider.value)
new_boxes = np.asarray(shape_layer.metadata['boxes'])[mask]
new_labels = shape_layer.metadata['labels'][mask]
new_scores = shape_layer.metadata['scores'][mask]
# set the current properties as workaround
shape_layer.current_properties['labels'] = new_labels
shape_layer.current_properties['scores'] = new_scores
# add shapes to layer
if new_boxes.size > 0:
shape_layer.add(list(new_boxes))
# set the properties
shape_layer.properties['labels'] = new_labels
shape_layer.properties['scores'] = new_scores
# change label
slider_label.value = str(slider.value)
slider.changed.connect(change_boxes)
# invoke scoring
container.Score.value = 0.0
# event triggered when the name of the shape layer changes
self.shape_layer.events.name.connect(change_boxes)
return container
def create_label_menu(shapes_layer, label_property, labels):
"""Create a label menu widget that can be added to the napari viewer dock
Parameters
----------
shapes_layer : napari.layers.Shapes
a napari shapes layer
label_property : str
the name of the shapes property to use the displayed text
labels : List[str]
list of the possible text labels values.
Returns
-------
label_widget : magicgui.widgets.Container
the container widget with the label combobox
"""
# Create the label selection menu
label_menu = ComboBox(label='text label', choices=labels)
label_widget = Container(widgets=[label_menu])
def update_label_menu(event):
"""This is a callback function that updates the label menu when
the current properties of the Shapes layer change
"""
new_label = str(shapes_layer.current_properties[label_property][0])
if new_label != label_menu.value:
label_menu.value = new_label
shapes_layer.events.current_properties.connect(update_label_menu)
def label_changed(event):
"""This is a callback that update the current properties on the Shapes layer
when the label menu selection changes
"""
selected_label = event.value
current_properties = shapes_layer.current_properties
current_properties[label_property] = np.asarray([selected_label])
shapes_layer.current_properties = current_properties
label_menu.changed.connect(label_changed)
return label_widget
def create_gui_text_properties(self, shape_layer):
TextColor = Combobox(
choices=shape_layer._colors, name="text color", value="white"
)
TextSize = Slider(min=1, max=50, name="text size", value=1)
container = Container(widgets=[TextColor, TextSize])
def change_text_color(event):
# This changes the text color
shape_layer.text.color = str(TextColor.value)
def change_text_size(event):
# This changes the text size
shape_layer.text.size = int(TextSize.value)
TextColor.changed.connect(change_text_color)
TextSize.changed.connect(change_text_size)
return container
def create_label_menu(points_layer, labels):
"""Create a label menu widget that can be added to the napari viewer dock
Parameters:
-----------
points_layer : napari.layers.Points
a napari points layer
labels : List[str]
list of the labels for each keypoint to be annotated (e.g., the body parts to be labeled).
Returns:
--------
label_menu : QComboBox
the label menu qt widget
"""
# Create the label selection menu
label_menu = ComboBox(label='feature_label', choices=labels)
label_widget = Container(widgets=[label_menu])
def update_label_menu(event):
"""Update the label menu when the point selection changes"""
new_label = str(points_layer.current_properties['label'][0])
if new_label != label_menu.value:
label_menu.value = new_label
points_layer.events.current_properties.connect(update_label_menu)
def label_changed(event):
"""Update the Points layer when the label menu selection changes"""
selected_label = event.value
current_properties = points_layer.current_properties
current_properties['label'] = np.asarray([selected_label])
points_layer.current_properties = current_properties
label_menu.changed.connect(label_changed)
return label_widget
"""Demonstrates decorating a method.
Once the class is instantiated, `instance.method_name` will return a FunctionGui
in which the instance will always be provided as the first argument (i.e. "self") when
the FunctionGui or method is called.
"""
from magicgui import event_loop, magicgui
from magicgui.widgets import Container
class MyObject:
def __init__(self, name):
self.name = name
self.counter = 0.0
@magicgui(auto_call=True)
def method(self, sigma: float = 0):
print(
f"instance: {self.name}, counter: {self.counter}, sigma: {sigma}")
self.counter = self.counter + sigma
return self.name
with event_loop():
a = MyObject("a")
b = MyObject("b")
container = Container(widgets=[a.method, b.method])
container.show()
assert a.method() == "a"
assert b.method() == "b"
def track_explorer(R, keep_only=False):
"""
Track explorer app. Written using magicgui (Thanks @tlambert03!)
Allows one to easily browse through tracks, plot the data and see the corresponding movies. Can also be used for curation and quality control.
Parameters:
keep_only : [False] Bool - If true, only tracks that are in PosLbl.track_to_use will be loaded in a given position. This can be used to filter unwanted tracks before examining for quality with the explorer.
"""
from typing import List
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
from magicgui import magicgui
from magicgui.widgets import Checkbox, PushButton, Container
from oyLabImaging.Processing.imvisutils import get_or_create_viewer
from scipy import stats
from napari import run
from natsort import natsorted
cmaps = ['cyan', 'magenta', 'yellow', 'red', 'green', 'blue']
viewer = get_or_create_viewer()
matplotlib.use('Agg')
mpl_fig = plt.figure()
ax = mpl_fig.add_subplot(111)
fc = FigureCanvasQTAgg(mpl_fig)
#attr_list = ['area', 'convex_area','centroid','perimeter','eccentricity','solidity','inertia_tensor_eigvals', 'orientation'] #todo: derive list from F regioprops
position = list(natsorted(R.PosLbls.keys()))[0]
PosLbl0 = R.PosLbls[position]
attr_list = [
f for f in list(PosLbl0.framelabels[0].regionprops)
if not f.startswith(('mean', 'median', 'max', 'min', '90th',
'slice'))
]
attr_cmap = plt.cm.get_cmap('tab20b', len(attr_list)).colors
@magicgui(
auto_call=True,
position={
"choices": natsorted([str(a) for a in R.PosLbls.keys()])
},
track_id={
"choices":
range(R.PosLbls[sorted([str(a) for a in R.PosLbls.keys()
])[0]].get_track(0).numtracks)
},
channels={
"widget_type": "Select",
"choices": list(R.channels)
},
features={
"widget_type": "Select",
"choices": attr_list
},
)
def widget(position: List[str], track_id: int, channels: List[str],
features: List[str]):
# preserving these parameters for things that the graphing function
# needs... so that anytime this is called we have to graph.
...
# do your graphing here
PosLbl = R.PosLbls[position]
t0 = PosLbl.get_track(track_id)
ax.cla()
ax.set_xlabel('Timepoint')
ax.set_ylabel('kAU')
ch_choices = widget.channels.choices
for ch in channels:
ax.plot(t0.T,
stats.zscore(t0.mean(ch)),
color=cmaps[ch_choices.index(ch)])
f_choices = widget.features.choices
for ch in features:
feat_to_plot = eval("t0.prop('" + ch + "')")
if np.ndim(feat_to_plot) == 1:
ax.plot(t0.T,
stats.zscore(feat_to_plot, nan_policy='omit'),
'--',
color=attr_cmap[f_choices.index(ch)],
alpha=0.33)
else:
mini_cmap = plt.cm.get_cmap('jet',
np.shape(feat_to_plot)[1])
for dim in np.arange(np.shape(feat_to_plot)[1]):
ax.plot(t0.T,
stats.zscore(feat_to_plot[:, dim],
nan_policy='omit'),
'--',
color=mini_cmap(dim),
alpha=0.33)
#ax.plot(t0.T, feat_to_plot[:,dim],'--', color=mini_cmap(dim), alpha=0.25)
ax.legend(channels + features)
fc.draw()
@widget.position.changed.connect
def _on_position_changed():
PosLbl = R.PosLbls[widget.position.value]
try:
PosLbl.track_to_use
except:
PosLbl.track_to_use = []
viewer.layers.clear()
#update track_id choices - bug in choices:
if keep_only:
J = PosLbl.track_to_use
else:
J = range(PosLbl.get_track(0).numtracks)
widget.track_id.choices = []
widget.track_id.choices = J
#update keep_btn value
#keep_btn.value= widget.track_id.value in PosLbl.track_to_use
@widget.track_id.changed.connect
def _on_track_changed(new_track: int):
PosLbl = R.PosLbls[widget.position.value]
viewer.layers.clear()
keep_btn.value = widget.track_id.value in PosLbl.track_to_use
#print("you cahnged to ", new_track)
movie_btn = PushButton(text="Movie")
widget.insert(1, movie_btn)
@movie_btn.clicked.connect
def _on_movie_clicked():
PosLbl = R.PosLbls[widget.position.value]
channels = widget.channels.get_value()
track_id = widget.track_id.get_value()
t0 = PosLbl.get_track(track_id)
viewer.layers.clear()
ch_choices = widget.channels.choices
t0.show_movie(
Channel=channels,
cmaps=[cmaps[ch_choices.index(ch)] for ch in channels])
btn = PushButton(text="NEXT")
widget.insert(-1, btn)
@btn.clicked.connect
def _on_next_clicked():
choices = widget.track_id.choices
current_index = choices.index(widget.track_id.value)
widget.track_id.value = choices[(current_index + 1) %
(len(choices))]
PosLbl = R.PosLbls[widget.position.value]
try:
PosLbl.track_to_use
except:
PosLbl.track_to_use = []
keep_btn = Checkbox(text="Keep")
keep_btn.value = widget.track_id.value in PosLbl.track_to_use
widget.append(keep_btn)
@keep_btn.clicked.connect
def _on_keep_btn_clicked(value: bool):
#print("keep is now", value)
PosLbl = R.PosLbls[widget.position.value]
if value == True:
if widget.track_id.value not in PosLbl.track_to_use:
PosLbl.track_to_use.append(widget.track_id.value)
if value == False:
if widget.track_id.value in PosLbl.track_to_use:
PosLbl.track_to_use.remove(widget.track_id.value)
R.PosLbls[widget.position.value] = PosLbl
# widget.native
# ... points to the underlying backend widget
container = Container(layout='horizontal')
# magicgui container expect magicgui objects
# but we can access and modify the underlying QLayout
# https://doc.qt.io/qt-5/qlayout.html#addWidget
layout = container.native.layout()
layout.addWidget(fc)
layout.addWidget(widget.native) # adding native, because we're in Qt
#container.show(run=True)
# OR
viewer.window.add_dock_widget(container)
#run()
matplotlib.use('Qt5Agg')
