Closed tsbischof closed 1 year ago
@tsbischof Thanks a lot for the effort! The CI pipeline is ages old. Don't worry about it now. I will also test it locally and then eventually migrate to GH Actions.
BTW with reference to your C code in https://github.com/tsbischof/libpicoquant, are you planning to create a libpicoquant Python package (https://pypi.org/project/libpicoquant)? I would gladly add it to the PyCorrFit dependency list (see OP in #84).
@GrantFoley Please just comment here whether we can put your data to the public domain (CC-0) :pray:
I do intend to revisit libpicoquant and add a Python version. I started fleshing it out last week and will upload hopefully over the weekend.
Hi everyone,
Thank you very much for all of your work on this. Yes, you have my permission to make the data samples public.
Grant
I had some follow up questions about the future steps for data analysis. If I take the .cor file that is produced in from the picoharp, are there any additional steps that I need to take before PyCorrFit can read this data? I know these these things take some time to install and develop, but I was just wanting to be prepared. Thank you both again @paulmueller and @tsbischof for your help thus far, and please let me know if I can provide any additional information or help.
@GrantFoley Unfortunately, depending on how you are installing PyCorrFit, you will have to wait for one of those issues: #201 #202 #203, or you install PyCorrFit from the main branch.
But as far as I can tell, the develop branch should allow you to read in and work with the cor files directly, with no further modification
Correct, except that there is now only one main
branch (to keep things simple).
Ok then. How do I install PyCorrFit from the main branch? I installed PyCorrFit using the installation instructions provided on the documentation page (https://pycorrfit.readthedocs.io/en/stable/). I am using the windows version.
The simplest option should be to clone the repository and install using pip:
git clone http://github.com/FCS-analysis/PyCorrFit
cd PyCorrFit
pip install .[GUI]
This assumes you have added Python to your path and have git installed.
Hi Thomas,
This is not working for me. I am using an anaconda environment that has python 3.11 and git installed. However, when I attempt to run pip install .[GUI], it says it is unable to create the process. Do you have any suggestions? Thanks
Grant
I had another question that came up. I was trying to install pycorrfit from the source, as outlined here https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source#windows I have downloaded anaconda distribution and made an environment with Python 3.10.8. I have also downloaded MikTex. I have installed all of the required packages except for wxpython, the reason for that one being it cannot download with a Python version greater than 3.9.x. Aside from this, the most recent error I have come across is an ImportError, which states it cannot import name 'MutableSet' from 'collections'. Do either of you have any suggestions for working around this? Thanks.
Grant
Sorry, I currently cannot (due to my available time) give support in that direction.
To keep the general workflow simple, please create a new issue for anything not related to the cor-reader here.
This branch implements the PicoQuant cor file format, as discussed in #84. It has been tested against Python 3.10 on ubuntu 22.04, with the sample data file provided in #84. I had to update a few of the calls to numpy to specify data sizes (e.g. np.int -> np.int64), but otherwise the changes are just to add the new format.
@GrantFoley Would you give permission for me to make your data samples public? I would add the ptu file to tsbischof/libpicoquant, and the cor file to FCS-analysis/FCSdata. The intent would be to provide these as examples for future development and testing.