sakoho81 / miplib Goto Github PK

Hi,

Thank you for your earlier comment. i'm having some issue trying to run the 3d fsc. i don't think its the same issue as before with the threshold not crossing.

python gives some warning: RankWarning: Polyfit may be poorly conditioned, otherwise it fails for the spline giving:
"A value in x_new is above the interpolation range."

I really wanted to see if i could do the 1 dataset fsc but it just flat lines. i can do the projections ok with the FRC...any thoughts? maybe some setting i'm not aware of? there are a lot of options that i'm not clear about. thank you for your time.

How do I use the image quality assessment functions? For example : In batch_evaluate_image_quality(path, options) what are the 'options' ?
Also, can I use this method for ranking images of beads?

Hi,
I'm very interested in your open source code, and attempts to reconstruct, but when I changed the input of the example, I met some error below (multiple sets of data were tried, just part of them were wrong ), I tried to change the border of the minimum optimization problem, but useless. I'm confused, what is the problem of this error? data or the interpolation value?

//..
error: ~.conda\envs\miplib\lib\site-packages\scipy\interpolate\interpolate.py in _check_bounds(self, x_new)
689 "range.")
690 if self.bounds_error and above_bounds.any():
--> 691 raise ValueError("A value in x_new is above the interpolation "
692 "range.")
693

ValueError: A value in x_new is above the interpolation range.

Hi Thank you for your generous sharing of the code, they are pretty neat and readable. I am wondering if you could please explain that in the definition of the three-sigma criteria (analysis.py): 3/(sqrt(number of points) + 3 - 1), what does the +3-1 account for in the denominator?

I really appreciate any help you can provide.

Yes it's me again, haha. I appreciate your work very much and I have read your procedures carefully，but I still have some doubts due to my own inadequacies.
1、Unable to open file ops_ext.cp36-win_amd64.pyd，so I can't understand how to use the function div_unit_grad() and the update_estimate_poisson() .What is the meaning of their return value？I can only literally understand what they mean，like calculate divergence and Poisson distribution ？
2、I want to use total variation regularization to constrain the RL deconvolution.Can I just assign a value to tv-lambda?What is the appropriate value for tv-lambda, I'll assign it to him. Running the program often results in errors
3、In your article, after using the background mask to remove the background ,the deconvolution works very well.I've added a paragraph “ rl_auto_background=Ture ”to the args_list ,but it doesn't seem to be working properly.
I hope you can give me some guidance in your busy schedule. Thank you！

Hi,

I liked your article. i was looking for fsc/frc analysis and the work you did to develop deconvolution algorithm based on the psf is pretty neat. I was trying to use it using the library.

1. if you could update the "FRC based frequency domain filtering" notebooks for broken links? example. ffutils and ideal_fft_filter. didn't take me long to debug but was confusing to figure out where you had moved files.

2.Could i ask for some ground rules on the shape/format for data that the code is looking for (only square?) More importantly i'm trying to figure out why i get the following error...only sometimes. I had a stack of 91 images and 90 work but i can't figure out why this one won't. I also tried to upscale an image so 200x200 --> 400x400 and i get the same error. I had a dickens of a time trying to puzzle out how to change args in the arg list. Perhaps there is some size limit? or is it that i'm not correcting some other parameter? i haven't been able to puzzle it out yet. Thank you again. love the code i want to share it with a colleague who might find it useful for x-ray fluorescence microscopy deconvolution.

If i could request a meeting to discuss? [email protected]

best regards,

Aaron

I'm trying to install your library into a fresh conda environment on a Ubuntu system with an Nvidia Titan RTX GPU and ran into a few issues. I replicated these issues on a Windows 10 machine with an Nvidia Titan XP.

1. pyculib is no longer maintained - so you need to pull it from channel numba (or somewhere else)
2. I believe cudatoolkit=7.5 is no longer on the conda channel. Is it safe to update this to the modern toolkit version (e.g. 10.2?) Or does your library require an older version of CUDA? If so, what channel should it be installed from?
3. Once I get the package installed using a modified environment_client.yml to address 1 and 2 above, I am unable to run the examples. This appears to be an issue with changes to Numpy on how boolean operations are handled. If I try to run the One Image Sectioned FSC and 3D Wiener Filtering notebook, I get the follow error for this code:
   %% capture
result = fsc.calculate_one_image_sectioned_fsc(image,args,z_correction=z_correction)

Error (truncated to most important part):
TypeError: numpy boolean subtract, the '-' operator, is deprecated, use the bitwise_xor, the '^' operator, or the logical _xor function instead.

What version of Numpy is the library complied for? After some internet searching, this appears to be a change in Numpy somewhere around version 1.14, but if I try numpy=1.13.3 in the enviroment_client.yml file, I get a version mismatch error when attempting import miplib.ui.cli.miplib_entry_point_options as options.

Thanks.

Some tif images don't include pixel size information in their tags.I have to assign a value to their ‘spacing’ attribute.But that's not accurate and it doesn't work well.I'd be happy if you had a good solution.Thank you！