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egluckthaler / starfish

starfish: a modular toolkit for giant mobile element annotation
GNU Affero General Public License v3.0
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skimage_feature #9

Closed BenAuxier closed 2 months ago

BenAuxier commented 2 months ago

Hi,

Just did a clean install of starfish, but I get an error at the annotate step:

File "/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/bin/starfish", line 7, in <module> from starfish.core.starfish import starfish File "/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/lib/python3.8/site-packages/starfish/__init__.py", line 1, in <module> from . import ( `File "/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/lib/python3.8/site-packages/starfish/image.py", line 1, in

` `from starfish.core.image import ( # noqa: F401` ` File "/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/lib/python3.8/site-packages/starfish/core/image/__init__.py", line 2, in ` ` from ._registration import LearnTransform` ` File "/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/lib/python3.8/site-packages/starfish/core/image/_registration/LearnTransform/__init__.py", line 2, in ` ` from .translation import Translation` ` File "/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/lib/python3.8/site-packages/starfish/core/image/_registration/LearnTransform/translation.py", line 2, in ` ` from skimage.feature import register_translation` `ImportError: cannot import name 'register_translation' from 'skimage.feature' (/mnt/LTR_userdata/auxie001/programs/conda/envs/starfish/lib/python3.8/site-packages/skimage/feature/__init__.py)` From the sci-kit image blog, [here](https://scikit-image.org/docs/stable/release_notes/release_0.19.html#scikit-image-0-19-0-2021-12-03) I think the feature register_translation has been removed as of v0.19.3, and now they suggest using skimage.registration.phase_cross_correlation()
egluckthaler commented 2 months ago

thanks for the heads up Ben. I'm going to look into this. Does the error pop up right away when you execute the command, or does it pop up later?

egluckthaler commented 2 months ago

I cannot replicate the error on a clean conda install of starfish on Linux version 5.14.0-375.el9.x86_64 RedHat. What machine are you using?

BenAuxier commented 2 months ago

Ah, I see I cannot replicate it either. I did include gffread and seqtk in my install, so not totally clean. That might be a cause. Now using a conda environment with only starfish inside doesn't seem to raise any issues.