On Noahs Laptop chisurf does not start when using the snap distribution. There is an error (likely missing libary) with the snap package.

See error message below

'''
Traceback (most recent call last):
File "mfm_gui.py", line 27, in
import mfm
File "/snap/chisurf/7/mfm/init.py", line 226, in
from . import fitting
File "/snap/chisurf/7/mfm/fitting/init.py", line 3, in
import models
File "/snap/chisurf/7/mfm/fitting/models/init.py", line 16, in
from mfm import plots
File "/snap/chisurf/7/mfm/plots/init.py", line 4, in
from .MolView import *
File "/snap/chisurf/7/mfm/plots/MolView.py", line 6, in
from OpenGL.GL import *
File "/snap/chisurf/7/python/lib/python2.7/site-packages/OpenGL/GL/init.py", line 4, in
from OpenGL.GL.VERSION.GL_1_1 import *
File "/snap/chisurf/7/python/lib/python2.7/site-packages/OpenGL/GL/VERSION/GL_1_1.py", line 14, in
from OpenGL.raw.GL.VERSION.GL_1_1 import *
File "/snap/chisurf/7/python/lib/python2.7/site-packages/OpenGL/raw/GL/VERSION/GL_1_1.py", line 7, in
from OpenGL.raw.GL import _errors
File "/snap/chisurf/7/python/lib/python2.7/site-packages/OpenGL/raw/GL/_errors.py", line 4, in
_error_checker = _ErrorChecker( _p, _p.GL.glGetError )
AttributeError: 'NoneType' object has no attribute 'glGetError'
'''

Describe the bug
Selecting FRET:FD Fit does not open a Fit window

To Reproduce
Steps to reproduce the behavior:

1. Load a dataset into ChiSurf
2. Select model: 'FRET: FD (Discrete)
3. Press add fit
4. Nothing happens

Expected behavior
A fit window appears, enabling D0 calibrated lifetime fits

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: [win10 x64
• Version 17.03.24

Additional context
Using the Record Movie feature, this command was executed:

cs.add_fit(model_name='FRET: FD (Discrete)', dataset_idx=[1])

Describe the bug
Upon using parameter scan for lifetime fractions (xl1, xl2, ..), the fit does not execute the scan but reports nonsense values.

Edit: the issue appears for lifetime fits and gauss fits.

Screenshots
lifetime fit:

Gauss fit:

Desktop (please complete the following information):
windows, cs 17.03.24

I have experienced that when one fits vv and vh decays with purpose of getting depolarization times and their amplitudes, one can get very good fit of vv and vh decays, but when these model vv and vh decays are combined into anisotropy, it does not necessarily fit into raw anisotropy decay.
After first fit iteration, user has to export model decays, combine them into anisotropy, and see how it fits into actual anisotropy decay. I experienced that often it misfits in the maximum (where r0 and g-factor contribute the most). Then, additional interation is needed to try to improve the fit. Again-export model decays, combine them, check how it fits.
It would be great if there would be a feature that combines vv and vh model decays, and overlays it with raw anisotropy, as additional fit quality check.

A class decorated by mfm.decorator.register has no direct access to its docstring.

This is an unwanted behavior.

The GUI elements are currently not covered in the unitests run by Travis-CI

Ideally the GUI elements are testes also in Travis.

See:
https://electronjs.org/docs/tutorial/testing-on-headless-ci
https://docs.travis-ci.com/user/gui-and-headless-browsers/

When exporting the data, writing frequency is not uniform: often it happens that initially writes data with dt step, and then few points with 2*dt step, and then goes back to dt writing frequency, and so on. This happens randomly in the data array, and is difficulty for post-processing of the saved data- such as combining VV and VH models into anisotropy etc.

Hi Thomas,

the latest Mac release of ChiSurf is quite old, and I would like to use the newest version natively on Mac.

Here is what I did:

1. Clone the repository.
2. Make a new conda environment from the environment.yml file.
3. Activate this environment.
4. Run python setup.py install
5. Run chisurf from terminal.

Here is the error I get.

(chisurf) Anders@Anders-MBP chisurf % chisurf
Traceback (most recent call last):
  File "/Users/Anders/opt/anaconda3/envs/chisurf/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2458, in resolve
    return functools.reduce(getattr, self.attrs, module)
AttributeError: module 'chisurf.gui' has no attribute 'gui'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/Anders/opt/anaconda3/envs/chisurf/bin/chisurf", line 11, in <module>
    load_entry_point('chisurf==19.9.22', 'gui_scripts', 'chisurf')()
  File "/Users/Anders/opt/anaconda3/envs/chisurf/lib/python3.7/site-packages/pkg_resources/__init__.py", line 490, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Users/Anders/opt/anaconda3/envs/chisurf/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2859, in load_entry_point
    return ep.load()
  File "/Users/Anders/opt/anaconda3/envs/chisurf/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2450, in load
    return self.resolve()
  File "/Users/Anders/opt/anaconda3/envs/chisurf/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2460, in resolve
    raise ImportError(str(exc))
ImportError: module 'chisurf.gui' has no attribute 'gui'

Not sure what is going wrong. I also tried running chisurf from code (base.py), but I get import errors.

What did I do wrong?

A successful builds in the master branch should be uploaded to anaconda cloud as a new conda package

see:
https://gist.github.com/zshaheen/fe76d1507839ed6fbfbccef6b9c13ed9

Hi Thomas,

when specifying a background curve and using the automatic estimation of background and fluorescence photons from the measurement durations, we noticed that we could not get a correct fit. To understand how things are implemented, I looked into the code and noticed that the model decay, before being multiplied by the estimated photon number, is not normalized to an area of 1.
Here are the respective lines in models/tcspc/lifetime.py

        # Calculate background curve from reference measurement
        if isinstance(
                background_curve,
                chisurf.curve.Curve
        ):
            if shift_bg_with_irf:
                background_curve = background_curve << self.convolve.timeshift

            bg_y = np.copy(background_curve.y)
            bg_y /= bg_y.sum()
            bg_y *= self.generic.n_ph_bg

            decay *= self.generic.n_ph_fl
            decay += bg_y

It turns out that the sum of the decay is > 1.

Is this intended behavior? Otherwise, I would suggest to normalize the decay to its sum before multiplying with the photon number, as done for the background pattern.

On macOS Catalina the main windows needs to be defocused and focused. Otherwise the items in the menu bar cannot be clicked. For miniconda PyQt and macOS Catalina this is a known problem (see napari/napari#380)

Is your feature request related to a problem? Please describe.
Mykola mentioned that you can also script ChiSurf, which is a really powerfull feature.
The commands can be deduced from the input in the terminal window. However the text on the terminal window is white on a white background. i.e. not readable unless selected.

Describe the solution you'd like
Make either the text or the background black,.

Describe alternatives you've considered

Additional context

Is your feature request related to a problem? Please describe.
I would like to save-fits from the command line or from a script

Describe the solution you'd like
To know the command which is run when the button File>Save Fit Results>Save Current Fit is pressed

Describe alternatives you've considered
I've tried the command:
cs.current_fit.save(path, name)
But it seems that is must be embedded to create a dir etc.

Additional context
I've visited the google groups page as was suggested on the github welcome page, but I was denied access.

Is your feature request related to a problem? Please describe.
We are currently trying to analyze some TIR-FCS data, and tried to use ChiSurf for that. The problem: For that (and other non-Gaussian MDFs, like Lorentzian) we need the error function erf(x), which is not supported right now.

We already received a partial solution with a new parse.py for the 2017 release which supports the "classical" error function erf(x), which kind of worked. Two problems remain (see attachments), which I assume are connected:

1. The fit does not converge (when I press "Fit", I get NaN in all free parameters).
2. Towards long lag times, the model returns nonsense. I am not 100 % sure why, but my experience using erf(x) and modifications thereof (erfc(x), erfcx(x)) in Origin suggests that it's due to the extreme values returned by the error function, causing overflow/underflow. That's why I would also like a dedicated solver for the scaled complementary error function erfcx(x)=exp(x^2)*(1-erf(x)), which will circumvent the problem if I'm right about my assumption. At least when testing in Origin, it did.

Describe the solution you'd like
Introduction of error function erf(x), complementary error function erfc(x), and scaled complementary error function erfcx(x) into ChiSurf models, and perhaps addition of simple TIR-FCS models (see Hassler et al. BiophysJ 2005 and Hassler et al. Opt Expr 2005) as default models in future release. I can also contribute the latter, once the former is taken care of.

Describe alternatives you've considered

Additional context
Screenshot of model in ChiSurf (parameters manually set, not fitted):

JSON file with model as used in screenshot (sorry in advance if there is a comma error again):
3D_TIR-Gauss_Model_json.txt

Is your feature request related to a problem? Please describe.
For the CD95 project we are doing many TCSPC fits, similar to the TGR5 project. The option to run scripts in Chisurf is already quite helpful. Is it also possible to create a Chisurf instance from a python interpreter and do fitting there? In this way chisurf TCSPC fitting can be embedded in whatever analysis other analysis is undertaken.
We do live-cell data, so we generate a lot of data for which I'd like to automate the analysis.

Describe the solution you'd like

• which dir must be added to $PYTHONPATH
• how to import the chisurf package
• how to initialize a Chisurf instance
  From there the combination command line + cs gui should enable scripting Donor only calibrated Donor Acceptor fits.

Describe alternatives you've considered
I have a few scripts for running batch fits in Chisurf. It works ok, but it's a bit messy and I'd like to automate human clicking as far as routine analysis is concerned. If it works nicely, it can be modularly implemented wherever TCSPC fitting is needed.

Additional context
Chisurf running py2.7 and Jupyter QtConsole 4.2.1 (I couldn't find the software version).
Is pain to be expected from running py2.7 chisurf in 3.7 interpreter?

Many thanks,