They published code to model RGC on/off cell distributions. Seemed useful to incorporate in our TODO list.

Nicolas and I are starting to make our way through the hm version of the color threshold code.

First issue. It crashes because it can't find routine coneAdapt. This appears to be in folder frontend/isetbio dev. Presumably putting that folder on our path will fix the problem.

But I think we need a convention as to what should go on the path. Currently, I put everything in isetbio on my path, on the view that it is a toolbox. But I put nothing in frontend on my path, on the view that it is a project.

If we are going to put part of frontend on the path, I will add code that does that dynamically for scripts in frontend.

Or, perhaps, development of routines for isetbio should happen in the isetbio repository.

Thoughts?

I either just did or will soon create a dev branch for frontend -- I don't think we should be developing on a branch called HJ. The dev branch was just forked from the HJ branch, however.

I think the idea is that we will issue pull requests for changes to go into the dev branch, and periodically update the master branch from the dev branch.

We need some standards and conventions for checking code in, as well as some agreement about what goes into toolboxes (that go onto the Matlab path, either statically or added dynamically) and what sits in stand-alone project directories, etc.

I may need to understand "pull requests" to have a well-formed view about this.

I really like to see history comments inside the source code for routines. I may be in the minority on this, but I would like to discuss it.

Should we try systematically to have Contents.m files in toolbox directories?

In simulations/colorContours, there is a lot of redundancy. For example:

a) At the top level there is colorContours.m, which is some version of a script I wrote. This is also in dhb/colorCountours.m

b) But the top level isn't just code I wrote. coneSamples.m was created by Haomiao and may or may not play nicely with colorContours.m

c) There is a copy of StockmanSharpeNomogram.m in this directory, which shadows the master copy that is in Psychtoolbox. I don't think we want to do that. We should just assume that the PTB is on the path. Having copies of PTB routines is the road to madness, unless we decide we want to systematically suck them into isetbio from PTB as needed. But that would then need to happen regularly to keep things up to date.

d) I am not sure what the role of the stuff in subdir hh is. There is a routine AbsorbtancetoAbsorbance. An updated copy of this now lives in the PTB, and some time ago this was renamed to AbsorptanceToAbsorbance to demonstrate that we know how to spell. Does this whole directory have a purpose now? What is it?

e) Both dhb and hj have code for computing color contours. We would like to get down to just one set of nicely validated code. What is the path from here to there?

The deed is done: frontend -> computationaleyebrain. Let's hope not too much breaks.

Hi,
I just did some subtree merge from wandell/frontend repository (branch Haomiao) to here. By subtree merge, all history and log of old frontend repository should be there. Currently, the repository code structure is like:

data/ - store some useful data file
external tools/   - includes external toolbox or functions (ellipse fitting, etc.)
isetbio dev/ - includes some under development functions or trials for isetbio, possibly, we should remove this one and move all its content to isetbio dev branch
scripts/ - helpful scripts, we might add some comments to make them something like tutorials
simulations - all kinds of simulations here
tutorials - contains well-commented tutorials
validation - validation scripts

If you have any suggestions for the code structures here, please let me know.
To do the subtree merge, the following command is used:

$ git remote add -f frontend https://github.com/wandell/frontend.git
$ git merge -s ours --no-commit frontend/Haomiao
$ git read-tree --prefix=/ -u frontend/Haomiao
$ git pull -s subtree frontend Haomiao
$ git commit -m "Merge from wandell/frontend branch Haomiao to isetbio/frontend"
$ git push

A helpful reference page for subtree merging can be found here

I'm planning move wandell/frontend master branch into simulations/colorContour/dhb later today (I'm not sure if this is the right thing to do). If you get any good suggestions on, let me know.

Best Regards,
HJ