Open aloboa opened 5 months ago
I have tried to display (drag and drop) zarr files:
from a saved project but always get: KeyError: 'metadata' Traceback:
KeyError: 'metadata'
--------------------------------------------------------------------------- MultipleReaderError Traceback (most recent call last) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/_qt/qt_viewer.py in _qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={}) 965 try: --> 966 self.viewer.open( self.viewer.open = <bound method ViewerModel.open of Viewer(camera=Camera(center=(0.0, 255.5, 255.5), zoom=1.595703125, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(101.0, 543.14749082007336, 501.78641370869042), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 204.0, 1.0), (0.0, 512.0, 1.0), (0.0, 512.0, 1.0)), current_step=(101, 255, 255), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'corrected' at 0x7caf2852aaf0>], help='use <2> for transform', status={'layer_base': 'corrected.zarr', 'source_type': 'plugin', 'plugin': 'napari Sediment', 'coordinates': ' [101 543 502]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<bound method SedimentWidget._shift_move_callback of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_drag_callbacks=[], mouse_double_click_callbacks=[<bound method SedimentWidget._add_analysis_roi of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_wheel_callbacks=[<function dims_scroll at 0x7caf6e9a9430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'A': <bound method ConvPaintWidget.hide_annotation of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>, 'R': <bound method ConvPaintWidget.hide_prediction of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>})> filenames = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] stack = False plugin = None layer_type = None kwargs = {} 967 filenames, ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/components/viewer_model.py in open(self=Viewer(camera=Camera(center=(0.0, 255.5, 255.5),...vPaintSpectralWidget object at 0x7caf38230b80>>}), path=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, plugin=None, layer_type=None, **kwargs={}) 1104 else: -> 1105 layers = self._open_or_raise_error( layers = undefined self._open_or_raise_error = <bound method ViewerModel._open_or_raise_error of Viewer(camera=Camera(center=(0.0, 255.5, 255.5), zoom=1.595703125, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(101.0, 543.14749082007336, 501.78641370869042), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 204.0, 1.0), (0.0, 512.0, 1.0), (0.0, 512.0, 1.0)), current_step=(101, 255, 255), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'corrected' at 0x7caf2852aaf0>], help='use <2> for transform', status={'layer_base': 'corrected.zarr', 'source_type': 'plugin', 'plugin': 'napari Sediment', 'coordinates': ' [101 543 502]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<bound method SedimentWidget._shift_move_callback of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_drag_callbacks=[], mouse_double_click_callbacks=[<bound method SedimentWidget._add_analysis_roi of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_wheel_callbacks=[<function dims_scroll at 0x7caf6e9a9430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'A': <bound method ConvPaintWidget.hide_annotation of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>, 'R': <bound method ConvPaintWidget.hide_prediction of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>})> _path = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] kwargs = {} layer_type = None _stack = False 1106 _path, kwargs, layer_type, _stack ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/components/viewer_model.py in _open_or_raise_error(self=Viewer(camera=Camera(center=(0.0, 255.5, 255.5),...vPaintSpectralWidget object at 0x7caf38230b80>>}), paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], kwargs={}, layer_type=None, stack=False) 1224 else: -> 1225 raise MultipleReaderError( global MultipleReaderError = <class 'napari.errors.reader_errors.MultipleReaderError'> global trans._ = <bound method TranslationBundle._ of <napari.utils.translations.TranslationBundle object at 0x7cafce6a5100>> path_message = '/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr' global plugins = undefined readers = {'napari-sediment': 'napari Sediment', 'napari': 'napari builtins'} global deferred = undefined global list = undefined readers.keys = <built-in method keys of dict object at 0x7caf64de8300> paths = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] 1226 trans._( MultipleReaderError: Multiple plugins found capable of reading /media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr. Select plugin from {'napari-sediment': 'napari Sediment', 'napari': 'napari builtins'} and pass to reading function e.g. `viewer.open(..., plugin=...)`. During handling of the above exception, another exception occurred: KeyError Traceback (most recent call last) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/_qt/qt_viewer.py in dropEvent(self=<napari._qt.qt_viewer.QtViewer object>, event=<PyQt5.QtGui.QDropEvent object>) 1329 filenames.append(url.toString()) 1330 -> 1331 self._qt_open( self._qt_open = <bound method QtViewer._qt_open of <napari._qt.qt_viewer.QtViewer object at 0x7caf675a5c10>> filenames = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] global stack = undefined global bool = undefined shift_down = <PyQt5.QtCore.Qt.KeyboardModifiers object at 0x7caf285220b0> global choose_plugin = undefined alt_down = <PyQt5.QtCore.Qt.KeyboardModifiers object at 0x7caf28522660> 1332 filenames, 1333 stack=bool(shift_down), ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/_qt/qt_viewer.py in _qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={}) 982 ) 983 except MultipleReaderError: --> 984 handle_gui_reading(filenames, self, stack, **kwargs) global handle_gui_reading = <function handle_gui_reading at 0x7caf6d8afd30> filenames = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] self = <napari._qt.qt_viewer.QtViewer object at 0x7caf675a5c10> stack = False kwargs = {} 985 986 def _toggle_chunk_outlines(self): ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/_qt/dialogs/qt_reader_dialog.py in handle_gui_reading(paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], qt_viewer=<napari._qt.qt_viewer.QtViewer object>, stack=False, plugin_name=None, error=None, plugin_override=False, **kwargs={}) 199 display_name, persist = readerDialog.get_user_choices() 200 if display_name: --> 201 open_with_dialog_choices( global open_with_dialog_choices = <function open_with_dialog_choices at 0x7caf6d8e0310> display_name = 'napari Sediment' persist = False readerDialog._extension = '/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr' readers = {'napari-sediment': 'napari Sediment', 'napari': 'napari builtins'} paths = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] stack = False qt_viewer = <napari._qt.qt_viewer.QtViewer object at 0x7caf675a5c10> kwargs = {} 202 display_name, 203 persist, ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/_qt/dialogs/qt_reader_dialog.py in open_with_dialog_choices(display_name='napari Sediment', persist=False, extension='/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr', readers={'napari': 'napari builtins', 'napari-sediment': 'napari Sediment'}, paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, qt_viewer=<napari._qt.qt_viewer.QtViewer object>, **kwargs={}) 292 ][0] 293 # may throw error, but we let it this time --> 294 qt_viewer.viewer.open(paths, stack=stack, plugin=plugin_name, **kwargs) qt_viewer.viewer.open = <bound method ViewerModel.open of Viewer(camera=Camera(center=(0.0, 255.5, 255.5), zoom=1.595703125, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(101.0, 543.14749082007336, 501.78641370869042), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 204.0, 1.0), (0.0, 512.0, 1.0), (0.0, 512.0, 1.0)), current_step=(101, 255, 255), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'corrected' at 0x7caf2852aaf0>], help='use <2> for transform', status={'layer_base': 'corrected.zarr', 'source_type': 'plugin', 'plugin': 'napari Sediment', 'coordinates': ' [101 543 502]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<bound method SedimentWidget._shift_move_callback of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_drag_callbacks=[], mouse_double_click_callbacks=[<bound method SedimentWidget._add_analysis_roi of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_wheel_callbacks=[<function dims_scroll at 0x7caf6e9a9430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'A': <bound method ConvPaintWidget.hide_annotation of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>, 'R': <bound method ConvPaintWidget.hide_prediction of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>})> paths = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] stack = False global plugin = undefined plugin_name = 'napari-sediment' kwargs = {} 295 296 if persist: ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/components/viewer_model.py in open(self=Viewer(camera=Camera(center=(0.0, 255.5, 255.5),...vPaintSpectralWidget object at 0x7caf38230b80>>}), path=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, plugin='napari-sediment', layer_type=None, **kwargs={}) 1093 if plugin: 1094 added.extend( -> 1095 self._add_layers_with_plugins( self._add_layers_with_plugins = <bound method ViewerModel._add_layers_with_plugins of Viewer(camera=Camera(center=(0.0, 255.5, 255.5), zoom=1.595703125, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(101.0, 543.14749082007336, 501.78641370869042), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 204.0, 1.0), (0.0, 512.0, 1.0), (0.0, 512.0, 1.0)), current_step=(101, 255, 255), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'corrected' at 0x7caf2852aaf0>], help='use <2> for transform', status={'layer_base': 'corrected.zarr', 'source_type': 'plugin', 'plugin': 'napari Sediment', 'coordinates': ' [101 543 502]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[<bound method SedimentWidget._shift_move_callback of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_drag_callbacks=[], mouse_double_click_callbacks=[<bound method SedimentWidget._add_analysis_roi of <napari_sediment.sediment_widget.SedimentWidget object at 0x7caf38374a60>>], mouse_wheel_callbacks=[<function dims_scroll at 0x7caf6e9a9430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'A': <bound method ConvPaintWidget.hide_annotation of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>, 'R': <bound method ConvPaintWidget.hide_prediction of <napari_sediment.classifier.ConvPaintSpectralWidget object at 0x7caf38230b80>>})> _path = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] kwargs = {} plugin = 'napari-sediment' layer_type = None stack = False _stack = False 1096 _path, 1097 kwargs=kwargs, ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/components/viewer_model.py in _add_layers_with_plugins(self=Viewer(camera=Camera(center=(0.0, 255.5, 255.5),...vPaintSpectralWidget object at 0x7caf38230b80>>}), paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, kwargs={}, plugin='napari-sediment', layer_type=None) 1293 else: 1294 assert len(paths) == 1 -> 1295 layer_data, hookimpl = read_data_with_plugins( layer_data = undefined hookimpl = undefined read_data_with_plugins = <function read_data_with_plugins at 0x7caf449ad4c0> paths = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] plugin = 'napari-sediment' stack = False 1296 paths, plugin=plugin, stack=stack 1297 ) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/plugins/io.py in read_data_with_plugins(paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], plugin='napari-sediment', stack=False) 75 hookimpl: Optional[HookImplementation] 76 ---> 77 res = _npe2.read(paths, plugin, stack=stack) res = undefined global _npe2.read = <function read at 0x7caf6e9709d0> paths = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] plugin = 'napari-sediment' stack = False 78 if res is not None: 79 _ld, hookimpl = res ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari/plugins/_npe2.py in read(paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], plugin='napari-sediment', stack=False) 61 npe1_path = paths[0] 62 try: ---> 63 layer_data, reader = io_utils.read_get_reader( layer_data = undefined reader = undefined global io_utils.read_get_reader = <function read_get_reader at 0x7caf75ef58b0> npe1_path = '/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr' plugin_name = 'napari-sediment' plugin = 'napari-sediment' 64 npe1_path, plugin_name=plugin 65 ) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/npe2/io_utils.py in read_get_reader(path='/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr', plugin_name='napari-sediment', stack=None) 64 # Napari 0.4.15 and older, hopefully we can drop this and make stack mandatory 65 new_path, new_stack = v1_to_v2(path) ---> 66 return _read( global _read = <function _read at 0x7caf75ef5a60> new_path = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] plugin_name = 'napari-sediment' global return_reader = undefined stack = None new_stack = False 67 new_path, plugin_name=plugin_name, return_reader=True, stack=new_stack 68 ) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/npe2/io_utils.py in _read(paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False, plugin_name='napari-sediment', return_reader=True, _pm=<npe2._plugin_manager.PluginManager object>) 170 if read_func is not None: 171 # if the reader function raises an exception here, we don't try to catch it --> 172 if layer_data := read_func(paths, stack=stack): layer_data = undefined read_func = <function reader_function at 0x7caf64e97f70> paths = ['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'] stack = False 173 return (layer_data, rdr) if return_reader else layer_data 174 ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/npe2/manifest/contributions/_readers.py in npe1_compat(paths=['/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'], stack=False) 57 def npe1_compat(paths, *, stack): 58 path = v2_to_v1(paths, stack) ---> 59 return callable_(path) global callable_ = undefined path = '/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr' 60 61 return npe1_compat ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari_sediment/_reader.py in reader_function(path='/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr') 65 #paths = [path] if isinstance(path, str) else path 66 # load all files into array ---> 67 array, metadata = read_spectral(path)# for _path in paths] array = undefined metadata = undefined global read_spectral = <function read_spectral at 0x7caf449ade50> path = '/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr' 68 # stack arrays into single array 69 #data = np.squeeze(np.stack(arrays)) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/napari_sediment/_reader.py in read_spectral(path=PosixPath('/media/alobo/SP PHD U3/CERTEC/20240430_erica2/HSI/IQ_Prefire/297/napari/roi_0/pure.zarr'), bands=None, row_bounds=None, col_bounds=None) 120 elif path.suffix == '.zarr': 121 zarr_image = read_hyper_zarr(path) --> 122 metadata = zarr_image.attrs['metadata'] metadata = undefined zarr_image.attrs = <zarr.attrs.Attributes object at 0x7caf650065b0> 123 if bands is None: 124 bands = np.arange(zarr_image.shape[0]) ~/miniconda3/envs/sediment2/lib/python3.9/site-packages/zarr/attrs.py in __getitem__(self=<zarr.attrs.Attributes object>, item='metadata') 72 73 def __getitem__(self, item): ---> 74 return self.asdict()[item] self.asdict = <bound method Attributes.asdict of <zarr.attrs.Attributes object at 0x7caf650065b0>> item = 'metadata' 75 76 def _write_op(self, f, *args, **kwargs): KeyError: 'metadata'
I have tried to display (drag and drop) zarr files:
from a saved project but always get:
KeyError: 'metadata'Traceback: