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Running apple.py -s 50 mrc_dir
, where mrc_dir
contains the 001.mrc
micrograph from Micrographs/Micrographs_part1
in EMPIAR 10028, it seems to get stuck somewhere. The output is
================================================================================================== Parameter Report =================================================================================================
particle_size 50
query_image_size 32
max_particle_size 100
min_particle_size 12
minimum_overlap_amount 5
tau1 1875
tau2 18750
container_size 450
proc 1
output_dir star_dir/star_dirmstar_dirnstar_dirtstar_dir/star_dirhstar_dirostar_dirmstar_direstar_dir/star_dirjstar_dirastar_dirnstar_dirdstar_direstar_dirnstar_dir/star_dirpstar_dirrstar_dirostar_dirjstar_direstar_dircstar_dirtstar_dirsstar_dir/star_dirAstar_dirPstar_dirPstar_dirLstar_dirEstar_dirpstar_diristar_dircstar_dirkstar_direstar_dirrstar_dir-star_dirpstar_dirystar_dirtstar_dirhstar_dirostar_dirnstar_dir/star_dirmstar_dirrstar_dircstar_dir_star_dirdstar_diristar_dirrstar_dir
================================================================================================== Progress Report ==================================================================================================
converting 1 mrc files..
Processing 001.mrc..
and it doesn't seem to go any further. Interestingly, the star_dir
folder is created with a rather peculiar structure:
ccblin035:APPLEpicker-python$ find star_dir/
star_dir/
star_dir/star_dirmstar_dirnstar_dirtstar_dir
star_dir/star_dirmstar_dirnstar_dirtstar_dir/star_dirhstar_dirostar_dirmstar_direstar_dir
star_dir/star_dirmstar_dirnstar_dirtstar_dir/star_dirhstar_dirostar_dirmstar_direstar_dir/star_dirjstar_dirastar_dirnstar_dirdstar_direstar_dirnstar_dir
star_dir/star_dirmstar_dirnstar_dirtstar_dir/star_dirhstar_dirostar_dirmstar_direstar_dir/star_dirjstar_dirastar_dirnstar_dirdstar_direstar_dirnstar_dir/star_dirpstar_dirrstar_dirostar_dirjstar_direstar_dircstar_dirtstar_dirsstar_dir
star_dir/star_dirmstar_dirnstar_dirtstar_dir/star_dirhstar_dirostar_dirmstar_direstar_dir/star_dirjstar_dirastar_dirnstar_dirdstar_direstar_dirnstar_dir/star_dirpstar_dirrstar_dirostar_dirjstar_direstar_dircstar_dirtstar_dirsstar_dir/star_dirAstar_dirPstar_dirPstar_dirLstar_dirEstar_dirpstar_diristar_dircstar_dirkstar_direstar_dirrstar_dir-star_dirpstar_dirystar_dirtstar_dirhstar_dirostar_dirnstar_dir
star_dir/star_dirmstar_dirnstar_dirtstar_dir/star_dirhstar_dirostar_dirmstar_direstar_dir/star_dirjstar_dirastar_dirnstar_dirdstar_direstar_dirnstar_dir/star_dirpstar_dirrstar_dirostar_dirjstar_direstar_dircstar_dirtstar_dirsstar_dir/star_dirAstar_dirPstar_dirPstar_dirLstar_dirEstar_dirpstar_diristar_dircstar_dirkstar_direstar_dirrstar_dir-star_dirpstar_dirystar_dirtstar_dirhstar_dirostar_dirnstar_dir/star_dirmstar_dirrstar_dircstar_dir_star_dirdstar_diristar_dirrstar_dir
Perhaps, this is unrelated, however.
There seems to be some setuptools
requirement that is not satisfied. How do we fix this?
Hello, I’m trying to understand better how the tau1 and tau2 parameters in the APPLE particle picker work - I can see from the paper they’re defined as “the percentage of training images that we believe do contain a particle” and “the percentage of training images that we believe may contain a particle,” respectively, but I’m not fully understanding that description. Also, in the config.ini files, these parameters are set as integers above 100 (as in, not percent values) - what are your guidelines for setting these tau parameters for a dataset? I would appreciate any help.
If you give a directory that doesn't contain any MRC files, apple.py
crashes with
converting 0 mrc files..
Traceback (most recent call last):
File "apple.py", line 281, in <module>
apple.pick_particles()
File "apple.py", line 171, in pick_particles
Apple.process_micrograph(data, filenames[0])
IndexError: list index out of range
It would be better if it just terminate instead (perhaps after warning that no MRC files were found).
Hello,
Whenever I am passing my .MRC file , its giving me an error. Can you please tell me the solution.
converting 1 mrc files..
Processing Jul21_18_01_08.mrc..
C:\Users\Sanat Mohrir\AppData\Local\conda\conda\envs\tfg\lib\site-packages\mrcfile\mrcinterpreter.py:203: RuntimeWarning: Map ID string not found - not an MRC file, or file is corrupt
warnings.warn(msg, RuntimeWarning)
C:\Users\Sanat Mohrir\Documents\GitHub\APPLEpicker-python\apple\helper.py:279: RuntimeWarning: invalid value encountered in sqrt
std_all = np.sqrt(var_all)
Hi
After following the instruction to install the package, I executed the first command (python run.py -h) and I got the following error msg.
take_along_axis = npcompat.take_along_axis
AttributeError: module 'dask.array.numpy_compat' has no attribute 'take_along_axis'
It seems like the version incompatibility issue but I get different issues down the road if match the numpy, scipy, and scikit-learn accordingly.
Would it be possible if you can take a look at the issue and possibly provide your working environment's full package versions so that I can create an appropriate virtual environment for this software?
Thank you.
best,
heejong
Firstly, whenever I run the code it identifies my MRC file and it does some processing for some 14-15 minutes and it creates the 'star_dir' folder and after this nearly 15 minutes time, it's giving me the following error. And that folder 'star_dir' stays empty. No '.star' file is created. Can anyone please help me? Thanks in advance !!!
converting 1 mrc files..
Processing micrograph.mrc..
Traceback (most recent call last):
File "run.py", line 49, in
apple.pick_particles()
File "C:\Users\Sanat Mohrir\Documents\GitHub\APPLEpicker-python\apple\apple.py", line 170, in pick_particles
Apple.process_micrograph(data, filenames[0])
File "C:\Users\Sanat Mohrir\Documents\GitHub\APPLEpicker-python\apple\apple.py", line 245, in process_micrograph
centers = picker.extract_particles(segmentation)
File "C:\Users\Sanat Mohrir\Documents\GitHub\APPLEpicker-python\apple\picking.py", line 285, in extract_particles
with open(applepick_path, "w") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\Sanat Mohrir\Documents\GitHub\APPLEpicker-python\star_dir\mrc\micrograph_applepick.star'
I asked @ayeltg and @janden How to increase the accuracy in picking the particles and authors told me to use the config file to customize the tau2 parameter. I have tried it but it is not picking all the parameters correctly can you please help me with the right approach. I have motion corrected .mrc images of particles and after calibration I am getting this output:
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