Last week, on a CYX image, I was able to get the code below to process the external image:
steinbock="singularity run -B /X/$FOLDER:/data --env STEINBOCK_MASK_DTYPE=uint32 docker://ghcr.io/bodenmillergroup/steinbock:0.16.1
where $FOLDER has been defined previously. then the following code is generates the issue:
$steinbock preprocess external images --img /data/external --imgout /data/images --infoout /data/images/images.csv
Now, when I run the same code on the same image, I receive the following error. I'm not sure if this is a steinbock issue or a singularity issue. Wondering if you could point me in the right direction? Thanks
Traceback (most recent call last):
File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/usr/lib/python3.8/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/app/steinbock/steinbock/main.py", line 5, in
from ._cli import steinbock_cmd_group
File "/app/steinbock/steinbock/_cli/init.py", line 1, in
from ._cli import steinbock_cmd_group
File "/app/steinbock/steinbock/_cli/_cli.py", line 12, in
from .visualization import view_cmd
File "/app/steinbock/steinbock/_cli/visualization.py", line 9, in
from ..visualization import view
File "/app/steinbock/steinbock/visualization.py", line 14, in
) -> Optional[napari.Viewer]:
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/_lazy.py", line 48, in getattr
submod = import_module(
File "/usr/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/viewer.py", line 8, in
from .components.viewer_model import ViewerModel
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/components/init.py", line 18, in
from .dims import Dims
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/components/dims.py", line 12, in
class Dims(EventedModel):
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/utils/events/evented_model.py", line 82, in new
cls = super().new(mcs, name, bases, namespace, **kwargs)
File "pydantic/main.py", line 197, in pydantic.main.ModelMetaclass.new
File "pydantic/fields.py", line 506, in pydantic.fields.ModelField.infer
File "pydantic/fields.py", line 436, in pydantic.fields.ModelField.init
File "pydantic/fields.py", line 552, in pydantic.fields.ModelField.prepare
File "pydantic/fields.py", line 668, in pydantic.fields.ModelField._type_analysis
File "/usr/lib/python3.8/typing.py", line 774, in subclasscheck
return issubclass(cls, self.origin)
TypeError: issubclass() arg 1 must be a class
Hi,
Last week, on a CYX image, I was able to get the code below to process the external image:
steinbock="singularity run -B /X/$FOLDER:/data --env STEINBOCK_MASK_DTYPE=uint32 docker://ghcr.io/bodenmillergroup/steinbock:0.16.1where $FOLDER has been defined previously. then the following code is generates the issue:$steinbock preprocess external images --img /data/external --imgout /data/images --infoout /data/images/images.csvNow, when I run the same code on the same image, I receive the following error. I'm not sure if this is a steinbock issue or a singularity issue. Wondering if you could point me in the right direction? Thanks
Traceback (most recent call last): File "/usr/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "/app/steinbock/steinbock/main.py", line 5, in
from ._cli import steinbock_cmd_group
File "/app/steinbock/steinbock/_cli/init.py", line 1, in
from ._cli import steinbock_cmd_group
File "/app/steinbock/steinbock/_cli/_cli.py", line 12, in
from .visualization import view_cmd
File "/app/steinbock/steinbock/_cli/visualization.py", line 9, in
from ..visualization import view
File "/app/steinbock/steinbock/visualization.py", line 14, in
) -> Optional[napari.Viewer]:
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/_lazy.py", line 48, in getattr
submod = import_module(
File "/usr/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/viewer.py", line 8, in
from .components.viewer_model import ViewerModel
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/components/init.py", line 18, in
from .dims import Dims
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/components/dims.py", line 12, in
class Dims(EventedModel):
File "/opt/steinbock-venv/lib/python3.8/site-packages/napari/utils/events/evented_model.py", line 82, in new
cls = super().new(mcs, name, bases, namespace, **kwargs)
File "pydantic/main.py", line 197, in pydantic.main.ModelMetaclass.new
File "pydantic/fields.py", line 506, in pydantic.fields.ModelField.infer
File "pydantic/fields.py", line 436, in pydantic.fields.ModelField.init
File "pydantic/fields.py", line 552, in pydantic.fields.ModelField.prepare
File "pydantic/fields.py", line 668, in pydantic.fields.ModelField._type_analysis
File "/usr/lib/python3.8/typing.py", line 774, in subclasscheck
return issubclass(cls, self.origin)
TypeError: issubclass() arg 1 must be a class