neurodatawithoutborders / nwbwidgets Goto Github PK

DataStub with properties:

    filename: '/Users/bichanwu/Desktop/nwb workshop/Steinmetz2019_Cori_2016-12-14.nwb'
        path: '/general/experimenter'
        dims: 1

TypeError                                 Traceback (most recent call last)
~\Anaconda3\lib\site-packages\h5py\_hl\selections.py in select(shape, args, dsid)
     84             try:
---> 85                 int(a)
     86                 if isinstance(a, np.ndarray) and a.shape == (1,):

TypeError: only size-1 arrays can be converted to Python scalars

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
~\Anaconda3\lib\site-packages\nwbwidgets\utils\widgets.py in observer(change)
     30         with out:
     31             clear_output(wait=True)
---> 32             f(**unpack_controls(controls, process_controls))
     33             show_inline_matplotlib_plots()
     34     for k, w in controls.items():

~\Anaconda3\lib\site-packages\nwbwidgets\timeseries.py in plot_grouped_traces(time_series, time_window, order, ax, figsize, group_inds, labels, colors, show_legend, **kwargs)
    304         order = np.arange(time_series.data.shape[1])
    305 
--> 306     mini_data, tt, offsets = _prep_timeseries(time_series, time_window, order)
    307 
    308     if group_inds is not None:

~\Anaconda3\lib\site-packages\nwbwidgets\timeseries.py in _prep_timeseries(time_series, time_window, order)
    285 
    286     unique_sorted_order, inverse_sort = np.unique(order, return_inverse=True)
--> 287     mini_data = time_series.data[t_ind_start:t_ind_stop, unique_sorted_order][:, inverse_sort]
    288 
    289     gap = np.median(np.nanstd(mini_data, axis=0)) * 20

h5py\_objects.pyx in h5py._objects.with_phil.wrapper()

h5py\_objects.pyx in h5py._objects.with_phil.wrapper()

~\Anaconda3\lib\site-packages\h5py\_hl\dataset.py in __getitem__(self, args)
    551 
    552         # Perform the dataspace selection.
--> 553         selection = sel.select(self.shape, args, dsid=self.id)
    554 
    555         if selection.nselect == 0:

~\Anaconda3\lib\site-packages\h5py\_hl\selections.py in select(shape, args, dsid)
     88             except Exception:
     89                 sel = FancySelection(shape)
---> 90                 sel[args]
     91                 return sel
     92 

~\Anaconda3\lib\site-packages\h5py\_hl\selections.py in __getitem__(self, args)
    399         self._id.select_none()
    400         for idx, vector in enumerate(argvector):
--> 401             start, count, step, scalar = _handle_simple(self.shape, vector)
    402             self._id.select_hyperslab(start, count, step, op=h5s.SELECT_OR)
    403 

~\Anaconda3\lib\site-packages\h5py\_hl\selections.py in _handle_simple(shape, args)
    464         else:
    465             try:
--> 466                 x,y,z = _translate_int(int(arg), length)
    467                 s = True
    468             except TypeError:

~\Anaconda3\lib\site-packages\h5py\_hl\selections.py in _translate_int(exp, length)
    484 
    485     if not 0<=exp<length:
--> 486         raise ValueError("Index (%s) out of range (0-%s)" % (exp, length-1))
    487 
    488     return exp, 1, 1

ValueError: Index (2) out of range (0-1)

electrode_table_region = nwbfile.create_electrode_table_region([0,1,2,3], 'all electrodes')
ephys_data = np.random.rand(data_len * 4).reshape((data_len, 4))

/processing/two_photon_imaging/images/max_projection/data

nwb.modules['two_photon_imaging'].data_interfaces['images'].images['max_projection'].data[:]

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\Anaconda3\envs\nwbn_conversion\lib\site-packages\ipywidgets\widgets\widget.py in _handle_msg(self, msg)
    674                 if 'buffer_paths' in data:
    675                     _put_buffers(state, data['buffer_paths'], msg['buffers'])
--> 676                 self.set_state(state)
    677 
    678         # Handle a state request.

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\ipywidgets\widgets\widget.py in set_state(self, sync_data)
    543                     from_json = self.trait_metadata(name, 'from_json',
    544                                                     self._trait_from_json)
--> 545                     self.set_trait(name, from_json(sync_data[name], self))
    546 
    547     def send(self, content, buffers=None):

~\Anaconda3\envs\nwbn_conversion\lib\contextlib.py in __exit__(self, type, value, traceback)
    117         if type is None:
    118             try:
--> 119                 next(self.gen)
    120             except StopIteration:
    121                 return False

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\traitlets\traitlets.py in hold_trait_notifications(self)
   1129                 for changes in cache.values():
   1130                     for change in changes:
-> 1131                         self.notify_change(change)
   1132 
   1133     def _notify_trait(self, name, old_value, new_value):

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\ipywidgets\widgets\widget.py in notify_change(self, change)
    604                 # Send new state to front-end
    605                 self.send_state(key=name)
--> 606         super(Widget, self).notify_change(change)
    607 
    608     def __repr__(self):

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\traitlets\traitlets.py in notify_change(self, change)
   1174                 c = getattr(self, c.name)
   1175 
-> 1176             c(change)
   1177 
   1178     def _add_notifiers(self, handler, name, type):

c:\users\luiz\documents\github\nwb-jupyter-widgets\nwbwidgets\base.py in on_selected_index(change)
    116         if change.new is not None and isinstance(change.owner.children[change.new], widgets.HTML):
    117             children[change.new] = nwb2widget(list(d.values())[change.new], neurodata_vis_spec=neurodata_vis_spec,
--> 118                                               **pass_kwargs)
    119             change.owner.children = children
    120 

c:\users\luiz\documents\github\nwb-jupyter-widgets\nwbwidgets\base.py in nwb2widget(node, neurodata_vis_spec, **pass_kwargs)
    162             spec = neurodata_vis_spec[ndtype]
    163             if isinstance(spec, dict):
--> 164                 return lazy_tabs(spec, node)
    165             elif callable(spec):
    166                 return vis2widget(spec(node, neurodata_vis_spec=neurodata_vis_spec, **pass_kwargs))

c:\users\luiz\documents\github\nwb-jupyter-widgets\nwbwidgets\base.py in lazy_tabs(in_dict, node)
    142     tabs_spec = list(in_dict.items())
    143 
--> 144     children = [tabs_spec[0][1](node)] + [widgets.HTML('Rendering...')
    145                                           for _ in range(len(tabs_spec) - 1)]
    146     tab = widgets.Tab(children=children)

c:\users\luiz\documents\github\nwb-jupyter-widgets\nwbwidgets\behavior.py in show_spatial_series_over_time(node, **kwargs)
     37     if ndims == 1:
     38         fig, ax = plt.subplots()
---> 39         ax.plot(tt, data, **kwargs)
     40         ax.set_xlabel('t (sec)')
     41         if unit:

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\matplotlib\axes\_axes.py in plot(self, scalex, scaley, data, *args, **kwargs)
   1664         """
   1665         kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D._alias_map)
-> 1666         lines = [*self._get_lines(*args, data=data, **kwargs)]
   1667         for line in lines:
   1668             self.add_line(line)

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\matplotlib\axes\_base.py in __call__(self, *args, **kwargs)
    223                 this += args[0],
    224                 args = args[1:]
--> 225             yield from self._plot_args(this, kwargs)
    226 
    227     def get_next_color(self):

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\matplotlib\axes\_base.py in _plot_args(self, tup, kwargs)
    389             x, y = index_of(tup[-1])
    390 
--> 391         x, y = self._xy_from_xy(x, y)
    392 
    393         if self.command == 'plot':

~\Anaconda3\envs\nwbn_conversion\lib\site-packages\matplotlib\axes\_base.py in _xy_from_xy(self, x, y)
    268         if x.shape[0] != y.shape[0]:
    269             raise ValueError("x and y must have same first dimension, but "
--> 270                              "have shapes {} and {}".format(x.shape, y.shape))
    271         if x.ndim > 2 or y.ndim > 2:
    272             raise ValueError("x and y can be no greater than 2-D, but have "

ValueError: x and y must have same first dimension, but have shapes (81863,) and (81862,)

/stimulus/templates/Natural_Images_Lum_Matched_set_training_2017.07.14/data

nwb.stimulus['Natural_Images_Lum_Matched_set_training_2017.07.14'].data[:]

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
<ipython-input-1-33af5fa05d5c> in <module>
      1 from pynwb import NWBFile, NWBHDF5IO
----> 2 from nwbwidgets import nwb2widget
      3 
      4 import scipy.io
      5 import numpy as np

~\Anaconda3\envs\convert_to_nwb\lib\site-packages\nwbwidgets\__init__.py in <module>
----> 1 from .view import nwb2widget

~\Anaconda3\envs\convert_to_nwb\lib\site-packages\nwbwidgets\view.py in <module>
      3 import pynwb
      4 from collections import OrderedDict
----> 5 from nwbwidgets import behavior, misc, base, ecephys, image, ophys
      6 from matplotlib.pyplot import Figure
      7 from pynwb.base import ProcessingModule

~\Anaconda3\envs\convert_to_nwb\lib\site-packages\nwbwidgets\ophys.py in <module>
      4 from pynwb.base import NWBDataInterface
      5 from collections import OrderedDict
----> 6 from .utils.cmaps import linear_transfer_function
      7 
      8 

ModuleNotFoundError: No module named 'nwbwidgets.utils'

Python Executable: Conda
Python Version: 3.7
Operating System: Windows
HDMF Version: pynwb 1.3.0

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~/miniconda3/envs/py37/lib/python3.7/site-packages/ipywidgets/widgets/widget.py in _handle_msg(self, msg)
    667                 if 'buffer_paths' in data:
    668                     _put_buffers(state, data['buffer_paths'], msg['buffers'])
--> 669                 self.set_state(state)
    670 
    671         # Handle a state request.

~/miniconda3/envs/py37/lib/python3.7/site-packages/ipywidgets/widgets/widget.py in set_state(self, sync_data)
    537                     from_json = self.trait_metadata(name, 'from_json',
    538                                                     self._trait_from_json)
--> 539                     self.set_trait(name, from_json(sync_data[name], self))
    540 
    541     def send(self, content, buffers=None):

~/miniconda3/envs/py37/lib/python3.7/contextlib.py in __exit__(self, type, value, traceback)
    117         if type is None:
    118             try:
--> 119                 next(self.gen)
    120             except StopIteration:
    121                 return False

~/miniconda3/envs/py37/lib/python3.7/site-packages/traitlets/traitlets.py in hold_trait_notifications(self)
   1129                 for changes in cache.values():
   1130                     for change in changes:
-> 1131                         self.notify_change(change)
   1132 
   1133     def _notify_trait(self, name, old_value, new_value):

~/miniconda3/envs/py37/lib/python3.7/site-packages/ipywidgets/widgets/widget.py in notify_change(self, change)
    598                 # Send new state to front-end
    599                 self.send_state(key=name)
--> 600         super(Widget, self).notify_change(change)
    601 
    602     def __repr__(self):

~/miniconda3/envs/py37/lib/python3.7/site-packages/traitlets/traitlets.py in notify_change(self, change)
   1174                 c = getattr(self, c.name)
   1175 
-> 1176             c(change)
   1177 
   1178     def _add_notifiers(self, handler, name, type):

~/Desktop/nwb_janelia/nwb_jupyter/nwb-jupyter-widgets/nwbwidgets/view.py in on_selected_index(change)
     25     def on_selected_index(change):
     26         if change.new is not None and isinstance(change.owner.children[change.new], widgets.HTML):
---> 27             children[change.new] = nwb2widget(list(d.values())[change.new], neurodata_vis_spec=neurodata_vis_spec)
     28             change.owner.children = children
     29 

~/Desktop/nwb_janelia/nwb_jupyter/nwb-jupyter-widgets/nwbwidgets/view.py in nwb2widget(node, neurodata_vis_spec)
     90                 return tab
     91             elif callable(spec):
---> 92                 return vis2widget(spec(node, neurodata_vis_spec=neurodata_vis_spec))
     93     out1 = widgets.Output()
     94     with out1:

~/Desktop/nwb_janelia/nwb_jupyter/nwb-jupyter-widgets/nwbwidgets/base.py in show_timeseries(node, **kwargs)
     15     fig, ax = plt.subplots()
     16     if node.timestamps:
---> 17         ax.plot(node.timestamps, node.data)
     18     else:
     19         ax.plot(np.arange(len(node.data)) / node.rate + node.starting_time, node.data)

~/miniconda3/envs/py37/lib/python3.7/site-packages/matplotlib/__init__.py in inner(ax, data, *args, **kwargs)
   1808                         "the Matplotlib list!)" % (label_namer, func.__name__),
   1809                         RuntimeWarning, stacklevel=2)
-> 1810             return func(ax, *args, **kwargs)
   1811 
   1812         inner.__doc__ = _add_data_doc(inner.__doc__,

~/miniconda3/envs/py37/lib/python3.7/site-packages/matplotlib/axes/_axes.py in plot(self, scalex, scaley, *args, **kwargs)
   1609         kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D._alias_map)
   1610 
-> 1611         for line in self._get_lines(*args, **kwargs):
   1612             self.add_line(line)
   1613             lines.append(line)

~/miniconda3/envs/py37/lib/python3.7/site-packages/matplotlib/axes/_base.py in _grab_next_args(self, *args, **kwargs)
    391                 this += args[0],
    392                 args = args[1:]
--> 393             yield from self._plot_args(this, kwargs)
    394 
    395 

~/miniconda3/envs/py37/lib/python3.7/site-packages/matplotlib/axes/_base.py in _plot_args(self, tup, kwargs)
    351         # downstream.
    352         if any(v is None for v in tup):
--> 353             raise ValueError("x, y, and format string must not be None")
    354 
    355         kw = {}

ValueError: x, y, and format string must not be None

conda create -n nwbtest python=3.7
python setup.py develop

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/conda/envs/nwb/lib/python3.7/site-packages/nwbwidgets/__init__.py", line 1, in <module>
    from .view import nwb2widget
  File "/opt/conda/envs/nwb/lib/python3.7/site-packages/nwbwidgets/view.py", line 6, in <module>
    from nwbwidgets import behavior, misc, base, ecephys, image, ophys
  File "/opt/conda/envs/nwb/lib/python3.7/site-packages/nwbwidgets/base.py", line 8, in <module>
    from pynwb.core import DynamicTable, NWBBaseType
ImportError: cannot import name 'NWBBaseType' from 'pynwb.core' (/opt/conda/envs/nwb/lib/python3.7/site-packages/pynwb/core.py)