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tlambert03 / LLSpy

Lattice light-sheet post-processing utility.
http://llspy.readthedocs.io
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lls gui #42

Closed BCinquin closed 6 months ago

BCinquin commented 9 months ago

Description

Starting the GUI

nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2023 NVIDIA Corporation Built on Fri_Nov__3_17:51:05_Pacific_Daylight_Time_2023 Cuda compilation tools, release 12.3, V12.3.103 Build cuda_12.3.r12.3/compiler.33492891_0

What I Did

After following the instruction to install LLSPY.

(llsenv) C:\Users\Bertrand>lls gui
Traceback (most recent call last):
  File "C:\Users\Bertrand\Anaconda\envs\llsenv\Scripts\lls-script.py", line 6, in <module>
    from llspy.bin.llspy_cli import cli
  File "C:\Users\Bertrand\Anaconda\envs\llsenv\lib\site-packages\llspy\__init__.py", line 21, in <module>
    from .llsdir import LLSdir, preview, process, RegDir
  File "C:\Users\Bertrand\Anaconda\envs\llsenv\lib\site-packages\llspy\llsdir.py", line 22, in <module>
    from . import parse, schema, util
  File "C:\Users\Bertrand\Anaconda\envs\llsenv\lib\site-packages\llspy\schema.py", line 3, in <module>
    from voluptuous import (
  File "C:\Users\Bertrand\Anaconda\envs\llsenv\lib\site-packages\voluptuous\__init__.py", line 3, in <module>
    from voluptuous.schema_builder import *
  File "C:\Users\Bertrand\Anaconda\envs\llsenv\lib\site-packages\voluptuous\schema_builder.py", line 1
    from __future__ import annotations
    ^
SyntaxError: future feature annotations is not defined

Thank you for your help...

tlambert03 commented 9 months ago

hi. At this point, this package is largely in maintenance mode, so while we can probably figure this particular problem out for you, I'd encourage you to start considering alternatives for your workflow. maybe @pr4deepr can comment on whether https://github.com/BioimageAnalysisCoreWEHI/napari_lattice can replace llspy at this point? ... or perhaps also suggest other things to consider?

anyway, to your questions specifically: it looks like whatever version of voluptuous you ended up with has dropped support for python 3.6... so either you need to update your version of python (which, i'm not sure, may break stuff about llspy), or you need to downgrade various packages in your environment to be compatible with python 3.6. The first thing you could try is pip install 'voluptuous<0.13' and see if that works?

pr4deepr commented 9 months ago

Thanks for pinging me @tlambert03. Lot of napari_lattice is inspired by LLSpy and your code, so thanks Talley!

I've included support for deskewing in X and Y in napari_lattice, so it should work. I have tested it on data from the Janelia lattice design successfully. However, it does not read the folder of tiffs or the text file with metadata. You may have to resave it as a tiff stack or load the folder of tiffs in napari. Otherwise, you can enter all the other metadata.

We're in the middle of making some changes; its taking much longer than we thought and has grown bigger! :)

Cheers Pradeep

BCinquin commented 9 months ago

Thank you very much !

Napari_Lattice it is though !

Best regards

Bertrand

Le mer. 6 déc. 2023 à 01:18, Pradeep Rajasekhar @.***> a écrit :

Thanks for pinging me @tlambert03 https://github.com/tlambert03. Lot of napari_lattice is inspired by LLSpy and your code, so thanks Talley!

I've included support for deskewing in X and Y in napari_lattice, so it should work. I have tested it on data from the Janelia lattice design successfully. However, it does not read the folder of tiffs or the text file with metadata. You may have to resave it as a tiff stack or load the folder of tiffs in napari. Otherwise, you can enter all the other metadata.

We're in the middle of making some changes https://github.com/BioimageAnalysisCoreWEHI/napari_lattice/pull/47; its taking much longer than we thought and has grown bigger! :)

Cheers Pradeep

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tlambert03 commented 6 months ago

with #43 ,this package should support all versions of python after 3.7 again. I'll push a new release soonish if you still want to try @BCinquin