Open horsto opened 1 week ago
evamaxfield
commented
1 week ago Hey! Sorry about this. I am trying my best to keep things up-to-date but I don't have a lot of time these days.
The major piece of work is actually both an upgrade to how we interact with napari and the image loading library. The branch: switch-to-bioio should be working, at least it was last time I was working on it ~2 months ago.
I don't know when I will have an update but I am trying.
horsto
commented
1 week ago Hey, thanks for your reply and don't worry. I did try the switch-to-bioio branch right now and this errors occurs upon opening a .czi (Zeiss) file. This more just to give you feedback - I don't currently rely on this plugin for anything. But count me in as tester when you continue working on it in the future.
WARNING:napari_bioio.core:BioIO: Unsupported file format.
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1323, in ViewerModel._open_or_raise_error(self=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...use_drag_gen={}, _mouse_wheel_gen={}, _keymap={}), paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], kwargs={}, layer_type=None, stack=False)
1322 try:
-> 1323 added = self._add_layers_with_plugins(
self = Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, style=<CursorStyle.STANDARD: 'standard'>, size=1.0), dims=Dims(ndim=2, ndisplay=2, order=(0, 1), axis_labels=('0', '1'), rollable=(True, True), range=(RangeTuple(start=0.0, stop=2.0, step=1.0), RangeTuple(start=0.0, stop=2.0, step=1.0)), margin_left=(0.0, 0.0), margin_right=(0.0, 0.0), point=(0.0, 0.0), last_used=0), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], help='', status='Hold <Alt> key to open plugin selection. Hold <Shift> to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x17ef1c430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, _keymap={})
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
kwargs = {}
stack = False
plugin = 'napari-bioio'
layer_type = None
1324 paths,
1325 kwargs=kwargs,
1326 stack=stack,
1327 plugin=plugin,
1328 layer_type=layer_type,
1329 )
1330 # plugin failed
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1413, in ViewerModel._add_layers_with_plugins(self=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...use_drag_gen={}, _mouse_wheel_gen={}, _keymap={}), paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], stack=False, kwargs={}, plugin='napari-bioio', layer_type=None)
1412 assert len(paths) == 1
-> 1413 layer_data, hookimpl = read_data_with_plugins(
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
stack = False
plugin = 'napari-bioio'
1414 paths, plugin=plugin, stack=stack
1415 )
1417 if layer_data is None:
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/io.py:78, in read_data_with_plugins(paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], plugin='napari-bioio', stack=False)
76 hookimpl: Optional[HookImplementation]
---> 78 res = _npe2.read(paths, plugin, stack=stack)
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
plugin = 'napari-bioio'
stack = False
_npe2 = <module 'napari.plugins._npe2' from '/Users/horst/miniconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/_npe2.py'>
79 if res is not None:
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/plugins/_npe2.py:57, in read(paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], plugin='napari-bioio', stack=False)
56 try:
---> 57 layer_data, reader = io_utils.read_get_reader(
io_utils = <module 'npe2.io_utils' from '/Users/horst/miniconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py'>
plugin = 'napari-bioio'
npe1_path = '/Users/horst/Downloads/Eve data/sample1/central.czi'
58 npe1_path, plugin_name=plugin
59 )
60 except ValueError as e:
61 # plugin wasn't passed and no reader was found
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py:66, in read_get_reader(path='/Users/horst/Downloads/Eve data/sample1/central.czi', plugin_name='napari-bioio', stack=None)
65 new_path, new_stack = v1_to_v2(path)
---> 66 return _read(
new_path = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
new_stack = False
plugin_name = 'napari-bioio'
67 new_path, plugin_name=plugin_name, return_reader=True, stack=new_stack
68 )
69 else:
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/npe2/io_utils.py:176, in _read(paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], stack=False, plugin_name='napari-bioio', return_reader=True, _pm=<npe2._plugin_manager.PluginManager object>)
175 if plugin_name:
--> 176 raise ValueError(
plugin_name = 'napari-bioio'
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
177 f"Reader {plugin_name!r} was selected to open "
178 + f"{paths!r}, but returned no data."
179 )
180 raise ValueError(f"No readers returned data for {paths!r}")
ValueError: Reader 'napari-bioio' was selected to open ['/Users/horst/Downloads/Eve data/sample1/central.czi'], but returned no data.
The above exception was the direct cause of the following exception:
ReaderPluginError Traceback (most recent call last)
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:981, in QtViewer._qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['/Users/horst/Downloads/Eve data/sample1/central.czi'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={})
980 try:
--> 981 self.viewer.open(
self = <napari._qt.qt_viewer.QtViewer object at 0x311c4b2e0>
self.viewer = Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, style=<CursorStyle.STANDARD: 'standard'>, size=1.0), dims=Dims(ndim=2, ndisplay=2, order=(0, 1), axis_labels=('0', '1'), rollable=(True, True), range=(RangeTuple(start=0.0, stop=2.0, step=1.0), RangeTuple(start=0.0, stop=2.0, step=1.0)), margin_left=(0.0, 0.0), margin_right=(0.0, 0.0), point=(0.0, 0.0), last_used=0), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], help='', status='Hold <Alt> key to open plugin selection. Hold <Shift> to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x17ef1c430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, _keymap={})
filenames = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
stack = False
plugin = None
layer_type = None
kwargs = {}
982 filenames,
983 stack=stack,
984 plugin=plugin,
985 layer_type=layer_type,
986 **kwargs,
987 )
988 except ReaderPluginError as e:
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1223, in ViewerModel.open(self=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...use_drag_gen={}, _mouse_wheel_gen={}, _keymap={}), path=['/Users/horst/Downloads/Eve data/sample1/central.czi'], stack=False, plugin=None, layer_type=None, **kwargs={})
1221 # no plugin choice was made
1222 else:
-> 1223 layers = self._open_or_raise_error(
layers = <module 'napari.layers' from '/Users/horst/miniconda3/envs/napari/lib/python3.10/site-packages/napari/layers/__init__.py'>
self = Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, style=<CursorStyle.STANDARD: 'standard'>, size=1.0), dims=Dims(ndim=2, ndisplay=2, order=(0, 1), axis_labels=('0', '1'), rollable=(True, True), range=(RangeTuple(start=0.0, stop=2.0, step=1.0), RangeTuple(start=0.0, stop=2.0, step=1.0)), margin_left=(0.0, 0.0), margin_right=(0.0, 0.0), point=(0.0, 0.0), last_used=0), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], help='', status='Hold <Alt> key to open plugin selection. Hold <Shift> to open files as stack.', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x17ef1c430>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, _keymap={})
_path = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
_stack = False
kwargs = {}
layer_type = None
1224 _path, kwargs, layer_type, _stack
1225 )
1226 added.extend(layers)
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/components/viewer_model.py:1332, in ViewerModel._open_or_raise_error(self=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...use_drag_gen={}, _mouse_wheel_gen={}, _keymap={}), paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], kwargs={}, layer_type=None, stack=False)
1331 except Exception as e:
-> 1332 raise ReaderPluginError(
trans = <napari.utils.translations.TranslationBundle object at 0x169c03250>
plugin = 'napari-bioio'
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
1333 trans._(
1334 'Tried opening with {plugin}, but failed.',
1335 deferred=True,
1336 plugin=plugin,
1337 ),
1338 plugin,
1339 paths,
1340 ) from e
1341 # multiple plugins
1342 else:
ReaderPluginError: Tried opening with napari-bioio, but failed.
The above exception was the direct cause of the following exception:
ReaderPluginError Traceback (most recent call last)
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:1146, in QtViewer.dropEvent(self=<napari._qt.qt_viewer.QtViewer object>, event=<PyQt5.QtGui.QDropEvent object>)
1138 shift_down = (
1139 QGuiApplication.keyboardModifiers()
1140 & Qt.KeyboardModifier.ShiftModifier
1141 )
1142 alt_down = (
1143 QGuiApplication.keyboardModifiers()
1144 & Qt.KeyboardModifier.AltModifier
1145 )
-> 1146 self._open_from_list_of_urls_data(
self = <napari._qt.qt_viewer.QtViewer object at 0x311c4b2e0>
event = <PyQt5.QtGui.QDropEvent object at 0x3136f24d0>
shift_down = <PyQt5.QtCore.Qt.KeyboardModifiers object at 0x31368d310>
alt_down = <PyQt5.QtCore.Qt.KeyboardModifiers object at 0x31368d460>
1147 event.mimeData().urls(),
1148 stack=bool(shift_down),
1149 choose_plugin=bool(alt_down),
1150 )
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:1163, in QtViewer._open_from_list_of_urls_data(self=<napari._qt.qt_viewer.QtViewer object>, urls_list=[PyQt5.QtCore.QUrl('file:///Users/horst/Downloads/Eve data/sample1/central.czi')], stack=False, choose_plugin=False)
1160 else:
1161 filenames.append(url.toString())
-> 1163 self._qt_open(
self = <napari._qt.qt_viewer.QtViewer object at 0x311c4b2e0>
filenames = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
stack = False
choose_plugin = False
1164 filenames,
1165 stack=stack,
1166 choose_plugin=choose_plugin,
1167 )
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:989, in QtViewer._qt_open(self=<napari._qt.qt_viewer.QtViewer object>, filenames=['/Users/horst/Downloads/Eve data/sample1/central.czi'], stack=False, choose_plugin=False, plugin=None, layer_type=None, **kwargs={})
981 self.viewer.open(
982 filenames,
983 stack=stack,
(...)
986 **kwargs,
987 )
988 except ReaderPluginError as e:
--> 989 handle_gui_reading(
filenames = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
self = <napari._qt.qt_viewer.QtViewer object at 0x311c4b2e0>
stack = False
layer_type = None
kwargs = {}
990 filenames,
991 self,
992 stack,
993 e.reader_plugin,
994 e,
995 layer_type=layer_type,
996 **kwargs,
997 )
998 except MultipleReaderError:
999 handle_gui_reading(filenames, self, stack, **kwargs)
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/dialogs/qt_reader_dialog.py:190, in handle_gui_reading(paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], qt_viewer=<napari._qt.qt_viewer.QtViewer object>, stack=False, plugin_name='napari-bioio', error=ReaderPluginError('Tried opening with napari-bioio, but failed.'), plugin_override=False, **kwargs={'layer_type': None})
163 """Present reader dialog to choose reader and open paths based on result.
164
165 This function is called whenever ViewerModel._open_or_get_error returns
(...)
187 Dictates whether checkbox to remember choice is unchecked by default
188 """
189 _path = paths[0]
--> 190 readers = prepare_remaining_readers(paths, plugin_name, error)
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
plugin_name = 'napari-bioio'
error = ReaderPluginError('Tried opening with napari-bioio, but failed.')
191 error_message = str(error) if error else ''
192 readerDialog = QtReaderDialog(
193 parent=qt_viewer,
194 pth=_path,
(...)
197 persist_checked=plugin_override,
198 )
File ~/miniconda3/envs/napari/lib/python3.10/site-packages/napari/_qt/dialogs/qt_reader_dialog.py:245, in prepare_remaining_readers(paths=['/Users/horst/Downloads/Eve data/sample1/central.czi'], plugin_name='napari-bioio', error=ReaderPluginError('Tried opening with napari-bioio, but failed.'))
243 # if there's no other readers left, raise the exception
244 if not readers and error:
--> 245 raise ReaderPluginError(
trans = <napari.utils.translations.TranslationBundle object at 0x169c03250>
paths[0] = '/Users/horst/Downloads/Eve data/sample1/central.czi'
paths = ['/Users/horst/Downloads/Eve data/sample1/central.czi']
len(paths) > 1 = False
len(paths) = 1
plugin_name = 'napari-bioio'
error = ReaderPluginError('Tried opening with napari-bioio, but failed.')
246 trans._(
247 'Tried to read {path_message} with plugin {plugin}, because it was associated with that file extension/because it is the only plugin capable of reading that path, but it gave an error. Try associating a different plugin or installing a different plugin for this kind of file.',
248 path_message=(
249 f'[{paths[0]}, ...]' if len(paths) > 1 else paths[0]
250 ),
251 plugin=plugin_name,
252 ),
253 plugin_name,
254 paths,
255 ) from error
257 return readers
ReaderPluginError: Tried to read /Users/horst/Downloads/Eve data/sample1/central.czi with plugin napari-bioio, because it was associated with that file extension/because it is the only plugin capable of reading that path, but it gave an error. Try associating a different plugin or installing a different plugin for this kind of file.Perfect! An error that makes sense!
This is because as a part of the switch to bioio, we are now able to split apart different readers instead of them all being bundled together causing bad legal problems for us.
You should (hopefully) be able to solve this error by running pip install bioio-czi in your terminal. This installs CZI support https://github.com/bioio-devs/bioio-czi
horsto
commented
1 week ago Oh beautiful, that did work! Thanks! And its fast and seems to be stable. Cool.
evamaxfield
commented
1 week ago Woohoo! Thanks for being a tester!
Going to re-open this so others who have the same issue and try these same steps.
Also, for others coming to this issue, here are the reasons for our moving to bioio: https://bioio-devs.github.io/bioio/MIGRATION.html#why-use-bioio-rather-than-aicsimageio
psobolewskiPhD
commented
6 days ago I was going to check on this but hadn't gotten a chance yet. Sorry! Excited for the new hotness!
Description
Fresh install of Napari and
napari-aicsimageio. Opening Tif or CZI files results in proper opening, but the application closes upon "playing" with the image / time sliders. Every single time. This happens after about 2-3 seconds when scrubbing through the data. No warning is generated.Environment
napari: 0.5.3 Platform: macOS-14.6.1-arm64-arm-64bit System: MacOS 14.6.1 Python: 3.9.18 (main, Sep 11 2023, 08:25:10) [Clang 14.0.6 ] Qt: 6.6.1 PyQt6: NumPy: 1.24.4 SciPy: 1.9.1 Dask: 2024.8.0 VisPy: 0.14.3 magicgui: 0.9.1 superqt: 0.6.7 in-n-out: 0.2.1 app-model: 0.2.8 npe2: 0.7.7