Deconvolution error

[Reza Khayat]

Hi,

I'm getting the following error when trying the deconvolution step of the tutorial. 

======================BELOW THIS LINE==================

Traceback (most recent call last):
  File "/home/rkhayat/Applications/IsoNet/bin/isonet.py", line 159, in deconv
    deconv_one(it.rlnMicrographName,deconv_tomo_name,defocus=it.rlnDefocus/10000.0, pixel_size=it.rlnPixelSize,snrfalloff=it.rlnSnrFalloff, deconvstrength=it.rlnDeconvStrength,highpassnyquist=highpassnyquist,chunk_size=chunk_size,overlap_rate=overlap_rate,ncpu=ncpu)
  File "/home/rkhayat/Applications/IsoNet/util/deconvolution.py", line 196, in deconv_one
    tom_deconv_tomo(tomo,out_tomo,pixel_size,defocus,snrfalloff,deconvstrength,highpassnyquist,phaseflipped=False, phaseshift=0,ncpu=ncpu)
  File "/home/rkhayat/Applications/IsoNet/util/deconvolution.py", line 58, in tom_deconv_tomo
    ctf = tom_ctf1d(angpix*1e-10, 300e3, 2.7e-3, -defocus*1e-6, 0.07, phaseshift / 180 * np.pi, 0);
  File "/home/rkhayat/Applications/IsoNet/util/deconvolution.py", line 18, in tom_ctf1d
    points = points.astype(np.float)
  File "/home/rkhayat/Applications/IsoNet/isonet_env/lib/python3.8/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float'

=======================ABOVE THIS LINE=============================

Any help would be appreciated.

[YUNTAO LIU]

Hi Rena,

This might caused by newest numpy does not support np.float.

This bug is fixed in the recently for IsoNet on GitHub. You can git clone and replace your older version. 

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Reza Khayat]

Hi Yunfao,

Cloning git did not fix the problem -perhaps I did this incorrectly. The version I downloaded is July8 2022. Downgrading numpy (pip install "numpy<1.24.0") did fix the problem, so thanks for pointing me in the correct direction. Programs works with no issues for the HIV data set. Time to try my data :-)

Best wishes,

Reza

On Thursday, June 22, 2023 at 2:54:53 PM UTC-4 yun...@g.ucla.edu wrote:

Hi Rena,

This might caused by newest numpy does not support np.float.

This bug is fixed in the recently for IsoNet on GitHub. You can git clone and replace your older version. 

On Thursday, June 22, 2023, Reza Khayat <khaya...@gmail.com> wrote:

Hi,

I'm getting the following error when trying the deconvolution step of the tutorial. 

======================BELOW THIS LINE==================

Traceback (most recent call last):
  File "/home/rkhayat/Applications/IsoNet/bin/isonet.py", line 159, in deconv
    deconv_one(it.rlnMicrographName,deconv_tomo_name,defocus=it.rlnDefocus/10000.0, pixel_size=it.rlnPixelSize,snrfalloff=it.rlnSnrFalloff, deconvstrength=it.rlnDeconvStrength,highpassnyquist=highpassnyquist,chunk_size=chunk_size,overlap_rate=overlap_rate,ncpu=ncpu)
  File "/home/rkhayat/Applications/IsoNet/util/deconvolution.py", line 196, in deconv_one
    tom_deconv_tomo(tomo,out_tomo,pixel_size,defocus,snrfalloff,deconvstrength,highpassnyquist,phaseflipped=False, phaseshift=0,ncpu=ncpu)
  File "/home/rkhayat/Applications/IsoNet/util/deconvolution.py", line 58, in tom_deconv_tomo
    ctf = tom_ctf1d(angpix*1e-10, 300e3, 2.7e-3, -defocus*1e-6, 0.07, phaseshift / 180 * np.pi, 0);
  File "/home/rkhayat/Applications/IsoNet/util/deconvolution.py", line 18, in tom_ctf1d
    points = points.astype(np.float)
  File "/home/rkhayat/Applications/IsoNet/isonet_env/lib/python3.8/site-packages/numpy/__init__.py", line 284, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float'

=======================ABOVE THIS LINE=============================

Any help would be appreciated.

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