royerlab / napari-dexp Goto Github PK
View Code? Open in Web Editor NEWLicense: BSD 3-Clause "New" or "Revised" License
napari-dexp's People
Contributors
Watchers
napari-dexp's Issues
bump release?
Hey, all. Was running tests on all plugins recently and found this one could not be imported after install, due to a missing napari requirement. I was coming here to suggest that you add napari to your install_requires, since this plugin explicitly imports things from napari. But I see that you've already done that. If main is stable, would be good to cut a new release. thanks!
save selected layers in napari writes wrong format in case napari-dexp is installed
Hi @JoOkuma ,
I observed for some time that when I was attempting to save a labels layer in napari as "test_annotation.tif" to disc, it created a folder called "test_annotation.tif" and stored zarr inside. When I tried to debug this, the following error suggests that napari-dexp is doing this:
|-> Creating Zarr storage: 'C:\structure\data\test_annotation.tif' with read/write mode: 'w-' and store type: 'None'
IndexError Traceback (most recent call last)
[...]
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\implementation.py in __call__(self=<HookImplementation plugin='napari-dexp' spec='napari_write_labels'>, *args=(r'C:\structure\data\test_annotation.tif', <class 'numpy.ndarray'>
Would it be possible to not write anything in case a file ending such as ".tif" is provided here? another writer plugin would then take over (I guess).
Thanks!
Best,
Robert
Here comes the full error log:
|-> Creating Zarr storage: 'C:\structure\data\test_annotation.tif' with read/write mode: 'w-' and store type: 'None'
|-> Opening as Directory store
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
[... skipping hidden 1 frame]
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\implementation.py in __call__(self=<HookImplementation plugin='napari-dexp' spec='napari_write_labels'>, *args=(r'C:\structure\data\test_annotation.tif', <class 'numpy.ndarray'> (512, 512) int32, {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}))
65 def __call__(self, *args):
---> 66 return self.function(*args)
self.function = <function napari_write_labels at 0x0000015E85A8E430>
args = ('C:\\structure\\data\\test_annotation.tif', <class 'numpy.ndarray'> (512, 512) int32, {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}})
67
~\miniconda3\envs\bio1\lib\site-packages\napari_dexp\_writer.py in napari_write_labels(path=r'C:\structure\data\test_annotation.tif', data=<class 'numpy.ndarray'> (512, 512) int32, meta={'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...})
50 def napari_write_labels(path: str, data: Any, meta: Dict) -> str:
---> 51 return writer(path, [(data, meta, 'labels')])
global writer = <function writer at 0x0000015E85A8E310>
path = 'C:\\structure\\data\\test_annotation.tif'
data = <class 'numpy.ndarray'> (512, 512) int32
meta = {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}}
52
~\miniconda3\envs\bio1\lib\site-packages\napari_dexp\_writer.py in writer(path=r'C:\structure\data\test_annotation.tif', layers_data=[(<class 'numpy.ndarray'> (512, 512) int32, {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}, 'labels')])
34 for data, meta, ltype in layers_data:
---> 35 dataset.add_channel(meta['name'],
dataset.add_channel = <bound method ZDataset.add_channel of <dexp.datasets.zarr_dataset.ZDataset object at 0x0000015E9FAE6D60>>
meta = {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}}
global shape = undefined
data.shape = (512, 512)
global dtype = undefined
global np.uint16 = <class 'numpy.uint16'>
ltype = 'labels'
global np.uint32 = <class 'numpy.uint32'>
36 shape=data.shape,
~\miniconda3\envs\bio1\lib\site-packages\dexp\datasets\zarr_dataset.py in add_channel(self=<dexp.datasets.zarr_dataset.ZDataset object>, name='Labels', shape=(512, 512), dtype=<class 'numpy.uint32'>, chunks=None, enable_projections=True, codec='zstd', clevel=3)
339 if chunks is None:
--> 340 chunks = self._default_chunks(shape, dtype)
chunks = None
self._default_chunks = <function ZDataset._default_chunks at 0x0000015E85A85670>
shape = (512, 512)
dtype = <class 'numpy.uint32'>
341
~\miniconda3\envs\bio1\lib\site-packages\dexp\datasets\zarr_dataset.py in _default_chunks(shape=(512, 512), dtype=dtype('uint32'), max_size=2147483647)
166 height = shape[-2]
--> 167 depth = min(max_size // (dtype.itemsize * width * height), shape[-3])
depth = undefined
global min = undefined
max_size = 2147483647
dtype.itemsize = 4
width = 512
height = 512
shape = (512, 512)
168 chunk = (1, depth, height, width)
IndexError: tuple index out of range
The above exception was the direct cause of the following exception:
PluginCallError Traceback (most recent call last)
c:\structure\code\napari\napari\_qt\qt_main_window.py in <lambda>()
573 save_selected_layers.setStatusTip(trans._('Save selected layers'))
574 save_selected_layers.triggered.connect(
--> 575 lambda: self.qt_viewer._save_layers_dialog(selected=True)
global self.qt_viewer._save_layers_dialog = undefined
global selected = undefined
576 )
577
c:\structure\code\napari\napari\_qt\qt_viewer.py in _save_layers_dialog(self=<napari._qt.qt_viewer.QtViewer object>, selected=True)
523 if filename:
524 with warnings.catch_warnings(record=True) as wa:
--> 525 saved = self.viewer.layers.save(filename, selected=selected)
saved = undefined
self.viewer.layers.save = <bound method LayerList.save of [<Labels layer 'Labels' at 0x15e9de21250>]>
filename = 'C:/structure/data/test_annotation.tif'
selected = True
526 error_messages = "\n".join(
527 [str(x.message.args[0]) for x in wa]
c:\structure\code\napari\napari\components\layerlist.py in save(self=[<Labels layer 'Labels' at 0x15e9de21250>], path='C:/structure/data/test_annotation.tif', selected=True, plugin=None)
328 return []
329
--> 330 return save_layers(path, layers, plugin=plugin)
save_layers = <function save_layers at 0x0000015E9FB201F0>
path = 'C:/structure/data/test_annotation.tif'
layers = [<Labels layer 'Labels' at 0x15e9de21250>]
plugin = None
331
332 def _selection_context(self) -> dict:
c:\structure\code\napari\napari\plugins\io.py in save_layers(path='C:/structure/data/test_annotation.tif', layers=[<Labels layer 'Labels'>], plugin=None)
207 )
208 elif len(layers) == 1:
--> 209 _written = _write_single_layer_with_plugins(
_written = undefined
global _write_single_layer_with_plugins = <function _write_single_layer_with_plugins at 0x0000015E9FB20820>
path = 'C:/structure/data/test_annotation.tif'
layers = [<Labels layer 'Labels' at 0x15e9de21250>]
global plugin_name = undefined
plugin = None
210 path, layers[0], plugin_name=plugin
211 )
c:\structure\code\napari\napari\plugins\io.py in _write_single_layer_with_plugins(path='C:/structure/data/test_annotation.tif', layer=<Labels layer 'Labels'>, plugin_name=None)
405
406 # Call the hook_caller
--> 407 return hook_caller(
hook_caller = <HookCaller napari_write_labels>
global _plugin = undefined
plugin_name = None
path = 'C:/structure/data/test_annotation.tif'
global abspath_or_url = <function abspath_or_url at 0x0000015EEF5139D0>
global data = undefined
layer.data = <class 'numpy.ndarray'> (512, 512) int32
global meta = undefined
layer._get_state = <bound method Labels._get_state of <Labels layer 'Labels' at 0x15e9de21250>>
408 _plugin=plugin_name,
409 path=abspath_or_url(path),
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\hooks.py in __call__(self=<HookCaller napari_write_labels>, _plugin=None, _skip_impls=[], *args=(), **kwargs={'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}, 'path': r'C:\structure\data\test_annotation.tif'})
518 return self._call_plugin(_plugin, **kwargs)
519
--> 520 result = self.call_with_result_obj(_skip_impls=_skip_impls, **kwargs)
result = undefined
self.call_with_result_obj = <bound method HookCaller.call_with_result_obj of <HookCaller napari_write_labels>>
_skip_impls = []
kwargs = {'path': 'C:\\structure\\data\\test_annotation.tif', 'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}}}
521 return result.result
522
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\hooks.py in call_with_result_obj(self=<HookCaller napari_write_labels>, _skip_impls=[], **kwargs={'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}, 'path': r'C:\structure\data\test_annotation.tif'})
459 self._check_call_kwargs(kwargs)
460 impls = [imp for imp in self.get_hookimpls() if imp not in _skip_impls]
--> 461 return self._hookexec(self, impls, kwargs)
self._hookexec = <bound method PluginManager._hookexec of <napari.plugins._plugin_manager.NapariPluginManager object at 0x0000015EF5FEC4F0>>
self = <HookCaller napari_write_labels>
impls = [<HookImplementation plugin='svg' spec='napari_write_labels' trylast>, <HookImplementation plugin='builtins' spec='napari_write_labels' trylast>, <HookImplementation plugin='napari-dexp' spec='napari_write_labels'>]
kwargs = {'path': 'C:\\structure\\data\\test_annotation.tif', 'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}}}
462
463 def __call__(
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\manager.py in _hookexec(self=<napari.plugins._plugin_manager.NapariPluginManager object>, caller=<HookCaller napari_write_labels>, methods=[<HookImplementation plugin='svg' spec='napari_write_labels' trylast>, <HookImplementation plugin='builtins' spec='napari_write_labels' trylast>, <HookImplementation plugin='napari-dexp' spec='napari_write_labels'>], kwargs={'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}, 'path': r'C:\structure\data\test_annotation.tif'})
157 The result object produced by the multicall loop.
158 """
--> 159 return self._inner_hookexec(caller, methods, kwargs)
self._inner_hookexec = <function PluginManager.__init__.<locals>.<lambda> at 0x0000015EF5E08040>
caller = <HookCaller napari_write_labels>
methods = [<HookImplementation plugin='svg' spec='napari_write_labels' trylast>, <HookImplementation plugin='builtins' spec='napari_write_labels' trylast>, <HookImplementation plugin='napari-dexp' spec='napari_write_labels'>]
kwargs = {'path': 'C:\\structure\\data\\test_annotation.tif', 'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}}}
160
161 def iter_available(
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\manager.py in <lambda>(c=<HookCaller napari_write_labels>, m=[<HookImplementation plugin='svg' spec='napari_write_labels' trylast>, <HookImplementation plugin='builtins' spec='napari_write_labels' trylast>, <HookImplementation plugin='napari-dexp' spec='napari_write_labels'>], k={'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}, 'path': r'C:\structure\data\test_annotation.tif'})
118 self.trace = _tracing.TagTracer().get("pluginmanage")
119 self.hook = _HookRelay(self)
--> 120 self._inner_hookexec: HookExecFunc = lambda c, m, k: c.multicall(
global self._inner_hookexec = undefined
global HookExecFunc = typing.Callable[[ForwardRef('HookCaller'), typing.List[napari_plugin_engine.implementation.HookImplementation], dict], napari_plugin_engine.callers.HookResult]
c = <HookCaller napari_write_labels>
m = [<HookImplementation plugin='svg' spec='napari_write_labels' trylast>, <HookImplementation plugin='builtins' spec='napari_write_labels' trylast>, <HookImplementation plugin='napari-dexp' spec='napari_write_labels'>]
k = {'path': 'C:\\structure\\data\\test_annotation.tif', 'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'name': 'Labels', 'metadata': {}, 'scale': [1.0, 1.0], 'translate': [0.0, 0.0], 'rotate': [[1.0, 0.0], [0.0, 1.0]], 'shear': [0.0], 'opacity': 0.7, 'blending': 'translucent', 'visible': True, 'multiscale': False, 'num_colors': 50, 'properties': {}, 'rendering': 'iso_categorical', 'plane': {'position': (0.0, 0.0, 0.0), 'normal': (1.0, 0.0, 0.0), 'thickness': 10.0, 'enabled': False}, 'seed': 0.5, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}}}
c.multicall = <function _multicall at 0x0000015EF5983D30>
global firstresult = undefined
c.is_firstresult = True
121 m, k, firstresult=c.is_firstresult
122 )
~\miniconda3\envs\bio1\lib\site-packages\napari_plugin_engine\callers.py in _multicall(hook_impls=[<HookImplementation plugin='svg' spec='napari_write_labels' trylast>, <HookImplementation plugin='builtins' spec='napari_write_labels' trylast>, <HookImplementation plugin='napari-dexp' spec='napari_write_labels'>], caller_kwargs={'data': <class 'numpy.ndarray'> (512, 512) int32, 'meta': {'blending': 'translucent', 'color': {0: <class 'numpy.ndarray'> (4,) float32, None: <class 'numpy.ndarray'> (4,) float32}, 'data': <class 'numpy.ndarray'> (512, 512) int32, 'metadata': {}, 'multiscale': False, 'name': 'Labels', 'num_colors': 50, 'opacity': 0.7, 'plane': {'enabled': False, 'normal': (1.0, 0.0, 0.0), 'position': (0.0, 0.0, 0.0), 'thickness': 10.0}, 'properties': {}, ...}, 'path': r'C:\structure\data\test_annotation.tif'}, firstresult=True)
209 finally:
210 if firstresult and errors:
--> 211 raise errors[-1]
errors = [PluginCallError("Error in plugin 'napari-dexp', hook 'napari_write_labels': tuple index out of range")]
212
213 outcome = HookResult(
PluginCallError: Error in plugin 'napari-dexp', hook 'napari_write_labels': tuple index out of range
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.