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neuniversity / ALY6140

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Confused about binary files... #10

Open richardshiii opened 5 years ago

richardshiii commented 5 years ago

Hi all, I am working on the .abf file in assignment, and found some useful codes to generate graphs that look similar to frequency distributions. However, I still don't quite understand how binary files work, and I am stuck on coming up with ideas to manipulate those files. Any suggestions?

Coding from online sources: import pyabf abf = pyabf.ABF("16o03002.abf") abf.setSweep(3) print(abf.sweepY) print(abf.sweepC) print(abf.sweepX)

Jin-pengSong commented 5 years ago

Hi, I also see that code you posted. How can you install pyABF?

richardshiii commented 5 years ago

You can install pyABF package by typing "pip install pyabf" in your terminal. ALso, here is an useful link for pyABF is: https://pypi.org/project/pyabf/, you can read through the tutorial in order to understand more about the meanings of each command.

aanranran commented 5 years ago

Hi Richard,

I have the same question with you before and just got solved. If you type

abf = pyabf.ABF("16o03002.abf")

This means you have import your abf file as abf. And then you can type

print(abf)

This code will show you clearly about the details of your abf fiile as following:

ABF file (16o03002.abf) with 2 channels, 6 sweeps, and a total length of 0.10 min.

Then you can define the meaning of abf.setSweep(3),which means you are setting NO.3 sweeps. Moreover, abf.sweepX means sweep times (seconds), and abf.sweepY means sweep data (ADC). Together with a new package, matplotlib, they can become a plot line as X-axis and Y-axis.

Hope my answer can solve your questions above!

shahtrupt commented 5 years ago

Thank you for the post and the information. It was indeed helpful. richardshiii Thanks for sharing https://pypi.org/project/pyabf/. It has some information about plotting.

kn1510 commented 5 years ago

I am encountering similar issue with binary files. Link shared by Richard is real helpful. Thanks for this help!