DeStripe error with ome-zarr #8
Description
I converted my tiff to ome.zarr/ome-ngff using the NGFFconverter and used napari-ome-zarr plugin, .
I can open the zarr file in napari and navigate it but when I start DeStripe I get the error below
Best regards,
Romain
Start DeStripe...
---------------------------------------------------------------------------
UnsupportedFileFormatError Traceback (most recent call last)
File /opt/conda/envs/leonardo/lib/python3.9/site-packages/lsfm_destripe_napari/_widget.py:451, in DestripeWidget. process(self=<lsfm_destripe_napari._widget.DestripeWidget object>)
437 return
438 model = DeStripe(
439 resample_ratio=params["resample_ratio"],
440 guided_upsample_kernel=params["guided_upsample_kernel"],
(...)
449 backend=params["backend"],
450 )
--> 451 output_image = model.train(
model = <lsfm_destripe.core.DeStripe object at 0x79b6a070eb80>
params = {'mask': None, 'input_image': <MultiScaleData at 0x79b8e9116700. 5 levels, '>u2', shapes: ((5, 2 40, 2304, 2304), (5, 240, 1152, 1152), (5, 240, 576, 576), (5, 240, 288, 288), (5, 240, 144, 144))>, 'resample_ra tio': 3, 'guided_upsample_kernel': 49, 'hessian_kernel_sigma': 1.0, 'lambda_masking_mse': 1.0, 'lambda_tv': 1.0, 'lambda_hessian': 1.0, 'inc': 16, 'n_epochs': 300, 'wedge_degree': 29, 'n_neighbors': 16, 'backend': 'jax', 'is_v ertical': True, 'angle_offset': [0.0], 'non_positive': False}
params["is_vertical"] = True
params["input_image"] = <MultiScaleData at 0x79b8e9116700. 5 levels, '>u2', shapes: ((5, 240, 2304, 2304) , (5, 240, 1152, 1152), (5, 240, 576, 576), (5, 240, 288, 288), (5, 240, 144, 144))>
params["mask"] = None
params["angle_offset"] = [0.0]
params["non_positive"] = False
452 is_vertical=params["is_vertical"],
453 x=params["input_image"],
454 mask=params["mask"],
455 angle_offset=params["angle_offset"],
456 display=False,
457 non_positive=params["non_positive"],
458 display_angle_orientation=False,
459 )
460 self.viewer.add_image(
461 output_image,
462 name="destriped image",
463 )
File /opt/conda/envs/leonardo/lib/python3.9/site-packages/lsfm_destripe/core.py:433, in DeStripe.train(self=<lsfm_destripe.core.DeStripe object>, is_vertical=True, x=<MultiScaleData at 0x79b8e9116700. 5 levels, '>u...6, 576), (5, 240, 288, 288), (5, 240, 144, 144))>, mask=None, fusion_mask=None, display=False, display_angle_orientation=False, non_positive=False, **kwargs={'angle_offset': [0.0]})
431 print("Start DeStripe...\n")
432 flag_compose = False
--> 433 X_handle = AICSImage(x)
x = <MultiScaleData at 0x79b8e9116700. 5 levels, '>u2', shapes: ((5, 240, 2304, 2304), (5, 240, 1152, 1152), (5, 240, 576, 576), (5, 240, 288, 288), (5, 240, 144, 144))>
AICSImage = <class 'aicsimageio.aics_image.AICSImage'>
434 X = X_handle.get_image_dask_data("ZYX", T=0, C=0)[:, None, ...]
435 else:
File /opt/conda/envs/leonardo/lib/python3.9/site-packages/aicsimageio/aics_image.py:277, in AICSImage.__init__(self=<class 'aicsimageio.aics_image.AICSImage'> instance, image=<MultiScaleData at 0x79b8e9116700. 5 levels, '>u...6, 576), (5, 240, 288, 288), (5, 240, 144, 144))>, reader=None, reconstruct_mosaic=True, fs_kwargs={}, **kwargs={})
267 def __init__(
268 self,
269 image: types.ImageLike,
(...)
273 **kwargs: Any,
274 ):
275 if reader is None:
276 # Determine reader class and create dask delayed array
--> 277 ReaderClass = self.determine_reader(image, fs_kwargs=fs_kwargs, **kwargs)
Exception trying to inspect frame. No more locals available.
278 else:
279 # Init reader
280 ReaderClass = reader
File /opt/conda/envs/leonardo/lib/python3.9/site-packages/aicsimageio/aics_image.py:257, in AICSImage.determine_reader(image=<MultiScaleData at 0x79b8e9116700. 5 levels, '>u...6, 576), (5, 240, 288, 288), (5, 240, 144, 144))>, fs_kwargs={}, **kwargs={})
255 # If we haven't hit anything yet, we likely don't support this file / object
256 image_type = str(type(image))
--> 257 raise exceptions.UnsupportedFileFormatError(
exceptions = <module 'aicsimageio.exceptions' from '/opt/conda/envs/leonardo/lib/python3.9/site-packages/aicsimageio/exceptions.py'>
image_type = "<class 'napari.layers._multiscale_data.MultiScaleData'>"
258 "AICSImage",
259 image_type,
260 msg_extra=(
261 "You may need to install an extra format dependency. "
262 "See all known format extensions and their extra install "
263 "name with `aicsimageio.formats.FORMAT_IMPLEMENTATIONS`."
264 ),
265 )
UnsupportedFileFormatError: AICSImage does not support the image: '<class 'napari.layers._multiscale_data.MultiScaleData'>'. You may need to install an extra format dependency. See all known format extensions and their extra install name with `aicsimageio.formats.FORMAT_IMPLEMENTATIONS`.