napari LayerGroup discussion

an_example.py

import numpy as np
import skimage.data

from napari.layers import *


def small_layergroup():
    tree = Layergroup(name='small-tree')

    branch = Layergroup(name='branch')
    tree.append(branch)

    twig = Layergroup(name='twig')
    twig.append(Image(skimage.data.chelsea(), name='chelsea'))
    branch.append(twig)
    
    branch.append(Image(skimage.data.camera(), name='camera'))
    branch.append(Points(np.random.random((10, 3)) * 200, name='points'))  # 10 points in 3D, range scaled to 200 pixels
    
    tree.append(Image(skimage.data.astronaut(), name='astronaut'))
    
    return tree


def big_layergroup():
    data = skimage.data.camera()

    tree = Layergroup(name='tree')
    branch1 = Layergroup(name='branch1')
    branch2 = Layergroup(name='branch2')
    branch3 = Layergroup(name='branch3')
    branch2.append(Image(skimage.data.camera(), name='image1_on_branch2_on_branch1'))
    branch2.append(Image(skimage.data.chelsea(), name='image2_on_branch2_on_branch1'))
    branch3.append(Image(skimage.data.astronaut(), name='image1_on_branch3_on_branch1'))
    branch1.append(branch2)
    branch1.append(branch3)
    branch1.append(Image(skimage.data.camera(), name='image1_on_branch1'))
    
    branch4 = Layergroup(name='branch4')
    branch4.append(Image(skimage.data.camera(), name='image1_on_branch4'))
    branch4.append(Image(skimage.data.chelsea(), name='image2_on_branch4'))

    branch5 = Layergroup(name='branch5')
    branch5.append(Image(skimage.data.astronaut(), name='image1_on_branch5'))

    tree.append(branch1)
    tree.append(branch4)
    tree.append(branch5)
    tree.append(Image(skimage.data.camera(), name='single_img'))

    return tree


ltree = small_layergroup()
lg = big_layergroup()

error_msg_emittergroup.txt

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-19-ee15db06cedf> in <module>
----> 1 viewer.add_layer(lg)

c:\users\genevieve\documents\github\napari\napari\components\add_layers_mixin.py in add_layer(self, layer)
     45         layer.dims.events.order.connect(self._on_layers_change)
     46         layer.dims.events.range.connect(self._on_layers_change)
---> 47         self.layers.append(layer)
     48         self._update_layers(layers=[layer])
     49

c:\users\genevieve\documents\github\napari\napari\components\layergroup.py in append(self, item)
     85     def append(self, item):
     86         item._parent = self
---> 87         return self._children.append(item)
     88
     89     def _get_extent(self, *args, **kwargs):

c:\users\genevieve\documents\github\napari\napari\utils\list\_model.py in append(self, obj)
     58     def append(self, obj):
     59         TypedList.append(self, obj)
---> 60         self.events.added(item=obj, index=len(self) - 1)
     61
     62     def pop(self, key):

c:\users\genevieve\documents\github\napari\napari\utils\event.py in __call__(self, *args, **kwargs)
    506                     continue
    507
--> 508                 self._invoke_callback(cb, event)
    509                 if event.blocked:
    510                     break

c:\users\genevieve\documents\github\napari\napari\utils\event.py in _invoke_callback(self, cb, event)
    523             cb(event)
    524         except Exception:
--> 525             _handle_exception(
    526                 self.ignore_callback_errors,
    527                 self.print_callback_errors,

c:\users\genevieve\documents\github\napari\napari\utils\event.py in _invoke_callback(self, cb, event)
    521     def _invoke_callback(self, cb, event):
    522         try:
--> 523             cb(event)
    524         except Exception:
    525             _handle_exception(

c:\users\genevieve\documents\github\napari\napari\_qt\qt_controls.py in _add(self, event)
     65         """
     66         layer = event.item
---> 67         controls = create_qt_controls(layer)
     68         self.addWidget(controls)
     69         self.widgets[layer] = controls

c:\users\genevieve\documents\github\napari\napari\_qt\layers\utils.py in create_qt_controls(layer)
     35             Qt controls widget
     36     """
---> 37     controls = layer_to_controls[type(layer)](layer)
     38
     39     return controls

c:\users\genevieve\documents\github\napari\napari\_qt\layers\qt_image_base_layer.py in __init__(self, layer)
     44         super().__init__(layer)
     45
---> 46         self.layer.events.colormap.connect(self._on_colormap_change)
     47         self.layer.events.gamma.connect(self.gamma_slider_update)
     48         self.layer.events.contrast_limits.connect(self._on_clims_change)

AttributeError: 'EmitterGroup' object has no attribute 'colormap'

error_msg_layer2visual.txt

In [26]: viewer.add_layer(lg)
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-26-ee15db06cedf> in <module>
----> 1 viewer.add_layer(lg)

c:\users\genevieve\documents\github\napari\napari\components\add_layers_mixin.py in add_layer(self, layer)
     45         layer.dims.events.order.connect(self._on_layers_change)
     46         layer.dims.events.range.connect(self._on_layers_change)
---> 47         self.layers.append(layer)
     48         self._update_layers(layers=[layer])
     49

c:\users\genevieve\documents\github\napari\napari\components\layergroup.py in append(self, item)
     85     def append(self, item):
     86         item._parent = self
---> 87         return self._children.append(item)
     88
     89     def _get_extent(self, *args, **kwargs):

c:\users\genevieve\documents\github\napari\napari\utils\list\_model.py in append(self, obj)
     58     def append(self, obj):
     59         TypedList.append(self, obj)
---> 60         self.events.added(item=obj, index=len(self) - 1)
     61
     62     def pop(self, key):

c:\users\genevieve\documents\github\napari\napari\utils\event.py in __call__(self, *args, **kwargs)
    506                     continue
    507
--> 508                 self._invoke_callback(cb, event)
    509                 if event.blocked:
    510                     break

c:\users\genevieve\documents\github\napari\napari\utils\event.py in _invoke_callback(self, cb, event)
    523             cb(event)
    524         except Exception:
--> 525             _handle_exception(
    526                 self.ignore_callback_errors,
    527                 self.print_callback_errors,

c:\users\genevieve\documents\github\napari\napari\utils\event.py in _invoke_callback(self, cb, event)
    521     def _invoke_callback(self, cb, event):
    522         try:
--> 523             cb(event)
    524         except Exception:
    525             _handle_exception(

c:\users\genevieve\documents\github\napari\napari\_qt\qt_viewer.py in _add_layer(self, event)
    225         layers = event.source
    226         layer = event.item
--> 227         vispy_layer = create_vispy_visual(layer)
    228         vispy_layer.camera = self.view.camera
    229         vispy_layer.node.parent = self.view.scene

c:\users\genevieve\documents\github\napari\napari\_vispy\utils.py in create_vispy_visual(layer)
     30         Vispy visual node
     31     """
---> 32     visual = layer_to_visual[type(layer)](layer)
     33
     34     return visual

KeyError: <class 'napari.components.layergroup.LayerGroup'>

In [27]: lg
Out[27]:
<LayerGroup 'LayerGroup' at 0x16e52c054f0>
  +--<Image layer 'camera' at 0x16e52c054f0>
  +--<Image layer 'astronaut' at 0x16e52c054f0>

layergroup_discussion_notes.md

A LayerGroup class for napari

Original issue: napari/napari#970 Branch with in-progress work: https://github.com/GenevieveBuckley/napari/tree/layergroup

Juan suggested napari uses the composite design pattern for layergroups: https://en.wikipedia.org/wiki/Composite_pattern There's a nice example of a python implementation of this pattern here: https://refactoring.guru/design-patterns/composite/python/example

Talley's been thinking about how to handle the Qt view side of things, and suggests:

• https://doc.qt.io/qt-5/qabstractitemmodel.html
• https://doc.qt.io/qt-5/qtreeview.html

Tutorial; https://pythonspot.com/pyqt5-treeview/ This is useful: https://doc.qt.io/qtforpython/PySide2/QtCore/QAbstractItemModel.html This is a good tutorial on QTreeView: https://doc.qt.io/qt-5/modelview.html#3-1-treeview

new_for_layergroups.py

# Talley using the __new__ method on the LayerGroup, worked ok as a proof of principle.
# He says "here's a general gist. "
# "I'm definitely not proposing we use something exactly like this, " 
# "but it shows where some of these properties live and how to check for them and/or overwrite them. "
# "Haven't tested this code except to make sure it doesn't error."

class LayerGroupDescriptor:
    def __init__(self, attr_name):
        self.attr_name = attr_name
        self.private_name = '_' + attr_name

    def __get__(self, obj, objtype=None):
        return getattr(obj, obj.private_name)

    def __set__(self, obj, value):
        setattr(obj, self.private_name, value)
        obj._visible = value
        if getattr(obj, '_children', None):
            for child in obj:
                setattr(child, self.attr_name, value)


class LayerGroup(Layer):
    def __new__(cls):
        obj = super().__new__(cls)
        for attr_name in dir(Layer):
            # things like properties and abstractmethods live on the class
            # not on the instance...
            attribute = getattr(LayerGroup, attr_name)
            if isinstance(attribute, property):

                print(attr_name + " is an @property")
                setattr(LayerGroup, attr_name, LayerGroupDescriptor(attr_name))
                # the getter function is at attribute.fget
                # the setter function is at attribute.fset

            # abstract methods live on the Layer class, not on layergroup
            attribute = getattr(Layer, attr_name)
            if getattr(attribute, '__isabstractmethod__', False):
                print(attr_name + " is an abstract method")
        return obj

play_with_visuals

(napari-dev) C:\Users\Genevieve>ipython --gui=qt
Python 3.8.1 (default, Mar  2 2020, 13:06:26) [MSC v.1916 64 bit (AMD64)]
Type 'copyright', 'credits' or 'license' for more information
IPython 7.13.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: %load_ext autoreload

In [2]: %autoreload 2

In [3]: import napari

In [4]: from skimage.data import camera, astronaut

In [5]: import numpy as np

In [6]: data = np.random.random((100,100))

In [7]: from napari.layers import *

In [8]: from napari.components import LayerGroup

In [9]: cam = Image(camera(), name='camera')

In [10]: astro = Image(astronaut(), name='astro')

In [11]: lg = LayerGroup()

In [12]: lg.append(cam)

In [13]: lg.append(astro)

In [14]: lg
Out[14]:
<LayerGroup 'LayerGroup' at 0x1be9e70bd00>
  +--<Image layer 'camera' at 0x1be9e70bd00>
  +--<Image layer 'astro' at 0x1be9e70bd00>

In [15]: viewer = napari.Viewer()

QTree_example.py

# https://stackoverflow.com/questions/27898718/multi-level-qtreeview
import sys

from qtpy.QtGui import QStandardItemModel, QStandardItem
from qtpy.QtWidgets import QApplication, QWidget, QTreeView, QHBoxLayout

import skimage.data

from napari.components.layergroup import LayerGroup
from napari.layers import *


def small_tree():
    tree = LayerGroup(name='small-tree')
    tree.append(Image(skimage.data.camera(), name='camera'))
    tree.append(Image(skimage.data.astronaut(), name='astronaut'))
    return tree


def construct_layergroup_tree():
    data = skimage.data.camera()

    tree = LayerGroup(name='tree')

    branch1 = LayerGroup(name='branch1')
    branch1.append(Image(data, name='image1_on_branch1'))
    branch1.append(Image(data, name='image2_on_branch1'))

    branch2 = LayerGroup(name='branch2')
    branch2.append(Image(data, name='image1_on_branch2'))

    branch3 = LayerGroup(name='branch3')
    branch4 = LayerGroup(name='branch4')
    branch5 = LayerGroup(name='branch5')
    branch4.append(Image(data, name='image1_on_branch4_on_branch3'))
    branch4.append(Image(data, name='image2_on_branch4_on_branch3'))
    branch5.append(Image(data, name='image1_on_branch5_on_branch3'))
    branch3.append(branch4)
    branch3.append(branch5)
    branch3.append(Image(data, name='image1_on_branch3'))

    tree.append(branch1)
    tree.append(branch2)
    tree.append(branch3)
    tree.append(Image(data, name='single_img'))

    return tree


class MainFrame(QWidget):
    def __init__(self):
        QWidget.__init__(self)

        tree = construct_layergroup_tree()

        self.tree = QTreeView(self)
        self.tree.setIndentation(20)
        self.tree.setHeaderHidden(True)
        self.tree.setAlternatingRowColors(True)

        layout = QHBoxLayout(self)
        layout.addWidget(self.tree)

        root_model = QStandardItemModel()
        self.tree.setModel(root_model)
        root_item = QStandardItem(tree.name)
        root_model.invisibleRootItem().appendRow(root_item)
        self._populateTree(tree, root_item)
        self.tree.expandAll()

    def _populateTree(self, tree, parent):
        for child in tree:
            child_item = QStandardItem(child.name)
            parent.appendRow(child_item)
            if isinstance(child, LayerGroup):
                self._populateTree(child, child_item)


if __name__ == "__main__":
    app = QApplication(sys.argv)
    main = MainFrame()
    main.show()
    sys.exit(app.exec_())

toy_example.py

import skimage.data

from napari.layers.base.base import LayerGroup
from napari.layers import *


def small_tree():
    tree = LayerGroup(name='small-tree')
    tree.append(Image(skimage.data.camera(), name='camera'))
    tree.append(Image(skimage.data.astronaut(), name='astronaut'))
    return tree


def construct_layergroup_tree():
    data = skimage.data.camera()

    tree = LayerGroup(name='tree')

    branch1 = LayerGroup(name='branch1')
    branch1.append(Image(data, name='image1_on_branch1'))
    branch1.append(Image(data, name='image2_on_branch1'))

    branch2 = LayerGroup(name='branch2')
    branch2.append(Image(data, name='image1_on_branch2'))

    branch3 = LayerGroup(name='branch3')
    branch4 = LayerGroup(name='branch4')
    branch5 = LayerGroup(name='branch5')
    branch4.append(Image(data, name='image1_on_branch4_on_branch3'))
    branch4.append(Image(data, name='image2_on_branch4_on_branch3'))
    branch5.append(Image(data, name='image1_on_branch5_on_branch3'))
    branch3.append(branch4)
    branch3.append(branch5)
    branch3.append(Image(data, name='image1_on_branch3'))
    
    tree.append(branch1)
    tree.append(branch2)
    tree.append(branch3)
    tree.append(Image(data, name='single_img'))

    return tree


def check_visibility(layergroup):
    print("Visible? {} {}".format(layergroup.visible, layergroup.name))
    for child in layergroup:
        if type(child) == LayerGroup:
            check_visibility(child)
        else:
            print("Visible? {} {}".format(child.visible, child.name))


def main():
    tree = construct_layergroup_tree()

    print("A heirarchical layergroup")
    print(tree.__repr__())

    print("\nLet's have a look at the visibility of each layer")
    check_visibility(tree)

    print("\nLet's change part of the layergroup tree")
    tree[0].visible = False
    check_visibility(tree)

    print("\nNow let's change the whole tree at once")
    tree.visible = False
    check_visibility(tree)


if __name__ == "__main__":
    main()