Preparing training data
Closed this issue · 2 comments
ojasvijain commented
Hi,
I wanted some clarification on creating the training data. my current format is as follows:
raw/
particles.txt
images/
a.mrc
b.mrc
c.mrc
my particles.txt (tab separated) file looks like:
image_name x_coord y_coord
a.mrc 345 123
b.mrc 234 344
c.mrc 566 987
I am running my train as follows:
topaz train --train-images <path>/raw/images/ \
--train-targets <path>/raw/particles.txt \
--save-prefix=saved_models/model \
-o saved_models/model_tranining.txt \
-n 400 --num-workers=8 --no-pretrained --image-ext .mrc
I am getting the following error:
WARNING: 5846 micrographs listed in the coordinates file are missing from the training images. Image names are listed below.
# Loaded 5846 training micrographs with 0 labeled particles
ERROR: no training particles specified. Check that micrograph names in the particles file match those in the micrographs file/directory.
Traceback (most recent call last):
File "/vast/projects/miti2324/envs/topaz_env/bin/topaz", line 33, in <module>
sys.exit(load_entry_point('topaz-em==0.2.5', 'console_scripts', 'topaz')())
File "/vast/projects/miti2324/envs/topaz_env/lib/python3.6/site-packages/topaz/main.py", line 148, in main
args.func(args)
File "/vast/projects/miti2324/envs/topaz_env/lib/python3.6/site-packages/topaz/commands/train.py", line 641, in main
image_ext=args.image_ext
File "/vast/projects/miti2324/envs/topaz_env/lib/python3.6/site-packages/topaz/commands/train.py", line 272, in load_data
raise Exception('No training particles.')
Exception: No training particles.
Can you tell me if what I'm doing is correct?
DarnellGranberry commented
Can you create a version of particles.txt where the filenames don't contain the extension and give that a try? Also, it won't cause issues with the training, but your output file has a typo.
ojasvijain commented
It ran! Thanks a lot :)
& also, silly typo in the output file - but it still worked