Git Product home page Git Product logo

fretraj-demo's Introduction

fretraj-demo's People

Contributors

fdsteffen avatar

Stargazers

 avatar  avatar

Watchers

 avatar  avatar

fretraj-demo's Issues

unable to reproduce demo results locally

I am trying to recreate the FRETraj-demo results locally without success. I cloned the FRETraj-demo repo and installed FRETraj in a clean python 3.8 environment with conda. I then installed the necessary dependencies as needed.
Here's a text file for the current environment: environment.txt.

I ran the original notebook on Binder (no changes made) and compared the results to my local instance to try to see where things went wrong. At the calculation of the ACVs my local results differ. Running

acv_D = ft.cloud.Volume.from_frames(traj, 'Cy3-20-C5', labels, selected_frames)
acv_A = ft.cloud.Volume.from_frames(traj, 'Cy5-44-P1', labels, selected_frames)

results in the ValueError messages Empty Accessible volume at position 626. Is your attachment point buried? and Empty Accessible volume at position 1395. Is your attachment point buried?.

Any ideas as to how I can resolve this discrepancy?

Example notebook errors out at in [18] on Binder

Hello,

I am trying to run the FRETraj-demo locally and I am running into problems in the execution. So, I am trying to compare the original output on Binder to my output. Running the notebook on Binder, I noticed that the notebook errors out at the very end:

[18]: experiment = ft.burst.Experiment('.', parameters, compute_anisotropy=False)

KeyError                                  Traceback (most recent call last)
<ipython-input-18-bae323b89d31> in <module>
----> 1 experiment = ft.burst.Experiment('.', parameters, compute_anisotropy=False)

/srv/conda/envs/notebook/lib/python3.8/site-packages/fretraj/burst.py in __init__(self, directory, parameters, binwidth, compute_anisotropy, verbose, show_progress)
    538             if show_progress:
    539                 with multiprocessing.Pool() as pool:
--> 540                     if os.environ['_'].split('/')[-1] == 'jupyter':
    541                         self.bursts = list(tqdm.notebook.tqdm(pool.imap(self.calcBurst, burstsizes,
    542                                            chunksize=int(self.parameters['sampling']['nbursts']/50)),

/srv/conda/envs/notebook/lib/python3.8/os.py in __getitem__(self, key)
    673         except KeyError:
    674             # raise KeyError with the original key value
--> 675             raise KeyError(key) from None
    676         return self.decodevalue(value)
    677 

KeyError: '_'

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.