Closed bendichter closed 1 year ago
I'm really not sure where the issue is here yet. While trying to run on the DANDI Hub, I am getting a strange h5py error:
--------------------------------------------------------------------------- ValueError 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:94, in dict2accordion.<locals>.on_selected_index(change) 92 def on_selected_index(change): 93 if change.new is not None and isinstance(change.owner.children[change.new], widgets.HTML): ---> 94 children[change.new] = nwb2widget( 95 list(d.values())[change.new], neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs 96 ) 97 change.owner.children = children File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:204, in nwb2widget(node, neurodata_vis_spec, **pass_kwargs) 202 return lazy_tabs(spec, node) 203 elif callable(spec): --> 204 visualization = spec(node, neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs) 205 return vis2widget(visualization) 206 out1 = widgets.Output() File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:236, in processing_module(node, neurodata_vis_spec) 235 def processing_module(node: ProcessingModule, neurodata_vis_spec: dict) -> widgets.Widget: --> 236 return nwb2widget(node.data_interfaces, neurodata_vis_spec=neurodata_vis_spec) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:204, in nwb2widget(node, neurodata_vis_spec, **pass_kwargs) 202 return lazy_tabs(spec, node) 203 elif callable(spec): --> 204 visualization = spec(node, neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs) 205 return vis2widget(visualization) 206 out1 = widgets.Output() File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:83, in dict2accordion(d, neurodata_vis_spec, **pass_kwargs) 81 def dict2accordion(d: dict, neurodata_vis_spec: dict, **pass_kwargs) -> widgets.Widget: 82 if len(d) == 1: ---> 83 return nwb2widget(list(d.values())[0], neurodata_vis_spec=neurodata_vis_spec) 84 children = [widgets.HTML("Rendering...") for _ in d] 85 accordion = widgets.Accordion(children=children, selected_index=None) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:204, in nwb2widget(node, neurodata_vis_spec, **pass_kwargs) 202 return lazy_tabs(spec, node) 203 elif callable(spec): --> 204 visualization = spec(node, neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs) 205 return vis2widget(visualization) 206 out1 = widgets.Output() File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:355, in show_multi_container_interface(node, neurodata_vis_spec) 352 else: 353 cls_conf = node.__clsconf__ --> 355 return dict2accordion( 356 {x["attr"]: getattr(node, x["attr"]) for x in cls_conf}, 357 neurodata_vis_spec=neurodata_vis_spec, 358 ) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:83, in dict2accordion(d, neurodata_vis_spec, **pass_kwargs) 81 def dict2accordion(d: dict, neurodata_vis_spec: dict, **pass_kwargs) -> widgets.Widget: 82 if len(d) == 1: ---> 83 return nwb2widget(list(d.values())[0], neurodata_vis_spec=neurodata_vis_spec) 84 children = [widgets.HTML("Rendering...") for _ in d] 85 accordion = widgets.Accordion(children=children, selected_index=None) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:204, in nwb2widget(node, neurodata_vis_spec, **pass_kwargs) 202 return lazy_tabs(spec, node) 203 elif callable(spec): --> 204 visualization = spec(node, neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs) 205 return vis2widget(visualization) 206 out1 = widgets.Output() File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:83, in dict2accordion(d, neurodata_vis_spec, **pass_kwargs) 81 def dict2accordion(d: dict, neurodata_vis_spec: dict, **pass_kwargs) -> widgets.Widget: 82 if len(d) == 1: ---> 83 return nwb2widget(list(d.values())[0], neurodata_vis_spec=neurodata_vis_spec) 84 children = [widgets.HTML("Rendering...") for _ in d] 85 accordion = widgets.Accordion(children=children, selected_index=None) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/base.py:204, in nwb2widget(node, neurodata_vis_spec, **pass_kwargs) 202 return lazy_tabs(spec, node) 203 elif callable(spec): --> 204 visualization = spec(node, neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs) 205 return vis2widget(visualization) 206 out1 = widgets.Output() File /opt/conda/lib/python3.10/site-packages/nwbwidgets/timeseries.py:268, in show_timeseries(node, **kwargs) 266 def show_timeseries(node, **kwargs): 267 if len(node.data.shape) == 1: --> 268 return SingleTracePlotlyWidget(node, **kwargs) 269 elif len(node.data.shape) == 2: 270 return BaseGroupedTraceWidget(node, **kwargs) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/timeseries.py:323, in SingleTracePlotlyWidget.__init__(self, timeseries, foreign_time_window_controller, **kwargs) 317 def __init__( 318 self, 319 timeseries: TimeSeries, 320 foreign_time_window_controller: StartAndDurationController = None, 321 **kwargs, 322 ): --> 323 super().__init__( 324 timeseries=timeseries, 325 foreign_time_window_controller=foreign_time_window_controller, 326 **kwargs, 327 ) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/timeseries.py:291, in AbstractTraceWidget.__init__(self, timeseries, foreign_time_window_controller, **kwargs) 288 self.out_fig = None 290 if foreign_time_window_controller is None: --> 291 tmin = get_timeseries_mint(timeseries) 292 tmax = get_timeseries_maxt(timeseries) 293 self.time_window_controller = StartAndDurationController(tmax, tmin) File /opt/conda/lib/python3.10/site-packages/nwbwidgets/utils/timeseries.py:75, in get_timeseries_mint(node) 62 """ 63 Returns the minimum time of any TimeSeries 64 (...) 72 73 """ 74 if node.timestamps is not None: ---> 75 return node.timestamps[0] 76 elif np.isnan(node.starting_time): 77 return 0 File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper() File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper() File /opt/conda/lib/python3.10/site-packages/h5py/_hl/dataset.py:766, in Dataset.__getitem__(self, args, new_dtype) 763 if new_dtype is None: 764 new_dtype = getattr(self._local, 'astype', None) --> 766 if self._fast_read_ok and (new_dtype is None): 767 try: 768 return self._fast_reader.read(args) File /opt/conda/lib/python3.10/site-packages/h5py/_hl/base.py:534, in cached_property.__get__(self, obj, cls) 531 if obj is None: 532 return self --> 534 value = obj.__dict__[self.func.__name__] = self.func(obj) 535 return value File /opt/conda/lib/python3.10/site-packages/h5py/_hl/dataset.py:745, in Dataset._fast_read_ok(self) 741 @cached_property 742 def _fast_read_ok(self): 743 """Is this dataset suitable for simple reading""" 744 return ( --> 745 self._extent_type == h5s.SIMPLE 746 and isinstance(self.id.get_type(), (h5t.TypeIntegerID, h5t.TypeFloatID)) 747 ) File /opt/conda/lib/python3.10/site-packages/h5py/_hl/base.py:534, in cached_property.__get__(self, obj, cls) 531 if obj is None: 532 return self --> 534 value = obj.__dict__[self.func.__name__] = self.func(obj) 535 return value File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper() File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper() File /opt/conda/lib/python3.10/site-packages/h5py/_hl/dataset.py:634, in Dataset._extent_type(self) 630 @cached_property 631 @with_phil 632 def _extent_type(self): 633 """Get extent type for this dataset - SIMPLE, SCALAR or NULL""" --> 634 return self.id.get_space().get_simple_extent_type() File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper() File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper() File h5py/h5d.pyx:347, in h5py.h5d.DatasetID.get_space() ValueError: Invalid dataset identifier (invalid dataset identifier)
No response
Linux
3.10
duplicate of #264
bendichter
commented
1 year ago bendichter
commented
1 year ago
What happened?
I'm really not sure where the issue is here yet. While trying to run on the DANDI Hub, I am getting a strange h5py error:
Steps to Reproduce
No response
Traceback
No response
Operating System
Linux
Python Version
3.10
Package Versions
No response
Code of Conduct