joton/reliontomotools

Complementary tools for Relion tomo

reliontomotools's Issues

the tomogram is flipped in Z direction using the converted STAR file from WARP XML files

Hi,
Thanks for the reliontomotools.
I meet with some problems, and can you help me?

I converted the XML files from WARP into the RELION4 STAR files.
commmand: warptomo2relion -i '../WARP/tilt/TS_005.xml' -s '../WARP/tilt/imod/005/TS_005.mrc' -d 1500 -o test_warp_relion --width 4092 --height 5760
After that, the tomograms were generated by the command "relion_tomo_reconstruct_tomogram" for manual inspection.

However, I found that the generated tomograms are Z-flipped compared with the tomograms generated by WARP.
Why are tomograms different generated by RELION4 and WARP? Any idea?

By the way, firstly, I did stack alignment in IMOD, and then import .xf files from imod into the WARP.
When the tilt series were imported from IMOD, the parameter "Don't invert angles" was not ticked in WARP.

Thanks!

list out of range

Hi,

I have been trying to convert my warp files using reliontomotools and I keep having the following error:

Traceback` (most recent call last):
File "/groups/zottigx/.conda/envs/reliontomotools/bin/warptomo2relion", line 8, in
sys.exit(warpTomo2RelionProgram())
File "/groups/zottigx/.conda/envs/reliontomotools/lib/python3.9/site-packages/reliontomotools/warptomo2relion.py", line 527, in warpTomo2RelionProgram
xmlNums = np.array([int(re.findall(f'{tnTmpl}\d+', name)[0][p:])
File "/groups/zottigx/.conda/envs/reliontomotools/lib/python3.9/site-packages/reliontomotools/warptomo2relion.py", line 527, in
xmlNums = np.array([int(re.findall(f'{tnTmpl}\d+', name)[0][p:])
IndexError: list index out of range

*It seems that there is some empty list
*I have tried different inputs and syntax but I can't figure out what is wrong

The command line I am using is

warptomo2relion -i 'frames/TS.mrc.xml' -s 'frames/imod/TS.mrc/TS.mrc.st' -d 1800 -o warp_converted

Should the -i point to the stack or the frames .xml file? I have tried both none worked.

Can the -o be un mrc.st file? Again I have tried both (.mrc and .mrc.st) none worked.

Thank you!

np.float deprecated since version 1.20

Hi!
We ran into an issue with your scripts. The default setup.py install numpy version > 1.20, which produces an error with your scripts as the usage of np.float is deprecated since numpy 1.20. Perhaps you could specify the numpy version in your setup.py with 'numpy<1.20'. (Or update the usage of np.float.)

reliontomotools/setup.py

Line 33 in bfa4382

install_requires=['numpy', 'pandas', 'xmltodict', 'docopt',

Best,
Marten