Closed CodyCBakerPhD closed 1 day ago
Failed to view the CCF tab of 'electrodes'
import h5py import fsspec from fsspec.implementations.cached import CachingFileSystem from pynwb import NWBHDF5IO s3_url = "https://dandiarchive.s3.amazonaws.com/blobs/631/af9/631af947-1de8-4e36-83b5-8c763d9d18f5" # Brain Wide Map cfs = CachingFileSystem( fs=fsspec.filesystem("http"), cache_storage="/home/jovyan/fsspec_cache", # Local folder for the cache ) file_system = cfs.open(s3_url, "rb") file = h5py.File(file_system) io = NWBHDF5IO(file=file, load_namespaces=True) nwbfile = io.read() nwb2widget(nwbfile) --> navigate to 'electrodes' --> navigate to 'CCF'
TraitError Traceback (most recent call last) File /opt/conda/lib/python3.10/site-packages/ipywidgets/widgets/widget.py:766, in Widget._handle_msg(self, msg) 764 if 'buffer_paths' in data: 765 _put_buffers(state, data['buffer_paths'], msg['buffers']) --> 766 self.set_state(state) 768 # Handle a state request. 769 elif method == 'request_state': File /opt/conda/lib/python3.10/site-packages/ipywidgets/widgets/widget.py:643, in Widget.set_state(self, sync_data) 638 self._send(msg, buffers=echo_buffers) 640 # The order of these context managers is important. Properties must 641 # be locked when the hold_trait_notification context manager is 642 # released and notifications are fired. --> 643 with self._lock_property(**sync_data), self.hold_trait_notifications(): 644 for name in sync_data: 645 if name in self.keys: File /opt/conda/lib/python3.10/contextlib.py:142, in _GeneratorContextManager.__exit__(self, typ, value, traceback) 140 if typ is None: 141 try: --> 142 next(self.gen) 143 except StopIteration: 144 return False File /opt/conda/lib/python3.10/site-packages/traitlets/traitlets.py:1502, in HasTraits.hold_trait_notifications(self) 1500 for changes in cache.values(): 1501 for change in changes: -> 1502 self.notify_change(change) File /opt/conda/lib/python3.10/site-packages/ipywidgets/widgets/widget.py:694, in Widget.notify_change(self, change) 691 if name in self.keys and self._should_send_property(name, getattr(self, name)): 692 # Send new state to front-end 693 self.send_state(key=name) --> 694 super().notify_change(change) File /opt/conda/lib/python3.10/site-packages/traitlets/traitlets.py:1517, in HasTraits.notify_change(self, change) 1515 def notify_change(self, change): 1516 """Notify observers of a change event""" -> 1517 return self._notify_observers(change) File /opt/conda/lib/python3.10/site-packages/traitlets/traitlets.py:1564, in HasTraits._notify_observers(self, event) 1561 elif isinstance(c, EventHandler) and c.name is not None: 1562 c = getattr(self, c.name) -> 1564 c(event) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:130, in lazy_tabs.<locals>.on_selected_index(change) 128 def on_selected_index(change): 129 if isinstance(change.owner.children[change.new], widgets.HTML): --> 130 children[change.new] = vis2widget(tabs_spec[change.new][1](node)) 131 change.owner.children = children File /opt/conda/lib/python3.10/site-packages/nwbwidgets/utils/dependencies.py:66, in check_widget_dependencies.<locals>.wrap.<locals>.wrapped_func(*args, **kwargs) 64 missing = [name for name, dependency in dependencies.items() if not dependency] 65 if not missing: ---> 66 return func(*args, **kwargs) 67 else: 68 txt = "This widget requires the following extra dependencies: {}" File /opt/conda/lib/python3.10/site-packages/nwbwidgets/ecephys.py:109, in show_ccf(electrodes_table, **kwargs) 106 input_kwargs.update(markers=markers) 108 input_kwargs.update(kwargs) --> 109 return ccfwidget.CCFWidget(**input_kwargs) File /opt/conda/lib/python3.10/site-packages/ccfwidget/widget_ccf.py:122, in CCFWidget.__init__(self, tree, swc_morphologies, markers, marker_sizes, marker_opacities, marker_colors, selected_allen_ids, selected_acronyms, rotate, **kwargs) 118 camera = np.array([[ 1.3441567e+03, -2.1723846e+04, 1.7496496e+04], 119 [ 6.5500000e+03, 3.9750000e+03, 5.6750000e+03], 120 [ 3.6606243e-01, -4.4908229e-01, -8.1506038e-01]], dtype=np.float32) 121 size_limit_3d = [256,256,256] --> 122 self.itk_viewer = view(image=self._image, 123 label_image=self._label_image, 124 opacity_gaussians=opacity_gaussians, 125 label_image_blend=0.65, 126 point_sets=markers.copy(), 127 camera=camera, 128 ui_collapsed=True, 129 shadow=False, 130 size_limit_3d=size_limit_3d, 131 background=(0.85,)*3, 132 units="μm", 133 gradient_opacity=0.1) 134 # Todo: initialization should work 135 self.itk_viewer.opacity_gaussians = opacity_gaussians File /opt/conda/lib/python3.10/site-packages/itkwidgets/widget_viewer.py:1090, in view(image, label_image, label_image_names, label_image_weights, label_image_blend, cmap, lut, select_roi, interpolation, gradient_opacity, opacity_gaussians, channels, slicing_planes, shadow, blend_mode, point_sets, point_set_colors, point_set_opacities, point_set_representations, point_set_sizes, geometries, geometry_colors, geometry_opacities, ui_collapsed, rotate, annotations, axes, mode, **kwargs) 1087 if image is None and len(images): # only one image is rendered 1088 image = images[0] -> 1090 viewer = Viewer(image=image, 1091 label_image=label_image, 1092 label_image_names=label_image_names, 1093 label_image_blend=label_image_blend, 1094 label_image_weights=label_image_weights, 1095 cmap=cmap, 1096 lut=lut, 1097 select_roi=select_roi, 1098 interpolation=interpolation, 1099 gradient_opacity=gradient_opacity, 1100 opacity_gaussians=opacity_gaussians, 1101 slicing_planes=slicing_planes, 1102 shadow=shadow, blend_mode=blend_mode, 1103 point_sets=point_sets, 1104 point_set_colors=point_set_colors, 1105 point_set_opacities=point_set_opacities, 1106 point_set_representations=point_set_representations, 1107 point_set_sizes=point_set_sizes, 1108 geometries=geometries, geometry_colors=geometry_colors, 1109 geometry_opacities=geometry_opacities, 1110 rotate=rotate, ui_collapsed=ui_collapsed, 1111 annotations=annotations, axes=axes, mode=mode, 1112 **kwargs) 1113 return viewer File /opt/conda/lib/python3.10/site-packages/itkwidgets/widget_viewer.py:369, in Viewer.__init__(self, **kwargs) 365 if have_label_image: 366 # Interpolation is not currently supported with label maps 367 kwargs['interpolation'] = False --> 369 super(Viewer, self).__init__(**kwargs) 371 if not self.image and not self.label_image: 372 return File /opt/conda/lib/python3.10/site-packages/ipywidgets/widgets/widget.py:502, in Widget.__init__(self, **kwargs) 500 """Public constructor""" 501 self._model_id = kwargs.pop('model_id', None) --> 502 super().__init__(**kwargs) 504 Widget._call_widget_constructed(self) 505 self.open() File /opt/conda/lib/python3.10/site-packages/traitlets/traitlets.py:1362, in HasTraits.__init__(self, *args, **kwargs) 1360 for key in changed: 1361 value = self._traits[key]._cross_validate(self, getattr(self, key)) -> 1362 self.set_trait(key, value) 1363 changes[key]['new'] = value 1364 self._cross_validation_lock = False File /opt/conda/lib/python3.10/site-packages/traitlets/traitlets.py:1742, in HasTraits.set_trait(self, name, value) 1740 raise TraitError(f"Class {cls.__name__} does not have a trait named {name}") 1741 else: -> 1742 getattr(cls, name).set(self, value) File /opt/conda/lib/python3.10/site-packages/traittypes/traittypes.py:108, in Array.set(self, obj, value) 107 def set(self, obj, value): --> 108 new_value = self._validate(obj, value) 109 old_value = obj._trait_values.get(self.name, self.default_value) 110 obj._trait_values[self.name] = new_value File /opt/conda/lib/python3.10/site-packages/traitlets/traitlets.py:738, in TraitType._validate(self, obj, value) 736 return value 737 if hasattr(self, "validate"): --> 738 value = self.validate(obj, value) 739 if obj._cross_validation_lock is False: 740 value = self._cross_validate(obj, value) File /opt/conda/lib/python3.10/site-packages/ipydatawidgets/ndarray/traits.py:25, in NDArray.validate(self, obj, value) 24 def validate(self, obj, value): ---> 25 value = super(NDArray, self).validate(obj, value) 26 if value is None or value is Undefined: 27 return value File /opt/conda/lib/python3.10/site-packages/traittypes/traittypes.py:105, in Array.validate(self, obj, value) 103 except (ValueError, TypeError) as e: 104 raise TraitError(e) --> 105 return super(Array, self).validate(obj, value) File /opt/conda/lib/python3.10/site-packages/traittypes/traittypes.py:76, in SciType.validate(self, obj, value) 74 try: 75 for validator in self.validators: ---> 76 value = validator(self, value) 77 return value 78 except (ValueError, TypeError) as e: File /opt/conda/lib/python3.10/site-packages/ipydatawidgets/ndarray/traits.py:40, in shape_constraints.<locals>.validator(trait, value) 38 return value 39 if len(value.shape) != len(args): ---> 40 raise TraitError('%s shape expected to have %s components, but got %s components' % ( 41 trait.name, len(args), value.shape)) 42 for i, constraint in enumerate(args): 43 if constraint is not None: TraitError: label_image_weights shape expected to have 1 components, but got () components
Linux
3.10
No response
What happened?
Failed to view the CCF tab of 'electrodes'
Steps to Reproduce
Traceback
Operating System
Linux
Python Version
3.10
Package Versions
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