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There seems to be some setuptools requirement that is not satisfied. How do we fix this?

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)

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:

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

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.

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).

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'