List of valid top-level scripts in this repo?

[MichaelCurrie]

Is there a complete list of actually vetted, runnable top-level scripts in the SegWormMatlabClasses repo?

e.g. What’s the “main” command I can run to get the features generated from an .avi file, or to calculate the features from a normalized worm file, etc?

[JimHokanson]

I updated the readme since it was obviously very out of date.

It includes links to functions that show you how to do most of the things the repo can do. This includes, for example, calculating features from a normalized worm.

I'm not sure exactly what you mean by getting the features generated from an .avi file, but my guess is that I don't have code to do that :)

Feel free to update the readme.

Jim

[MichaelCurrie]

OK got it.

So I cannot do video to normalized worm (unfinished at seg_worm.parseWormFromVideo)

I can do normalized worm to features via seg_worm.testing.features.t_001__mrcCodeVsNewCode

I can do features to stats via seg_worm.testing.stats.t001_oldVsNewStats

However now I'm getting the error: Undefined function or variable '[gausswin](http://www.mathworks.com/help/signal/ref/gausswin.html?refresh=true)'. Looks like I need to buy the [Signal Processing Toolbox]() :S :)

[MichaelCurrie]

OK I bought the toolbox, and my new error is:

[WARNING getMyBasePath.m:50 ] The function 'getMyBasePath' is being deprecated in favor of 'sl.stack.getMyBasePath'. Please change your code Reason This function has been moved to the stack package Undefined variable "sl" or class "sl.struct.getSubField".

Error in seg_worm.stats/movement_specs/getData (line 65) data = sl.struct.getSubField(feature_obj,obj.feature_field);

Error in seg_worm.features/compareToOldFeatures (line 48) x = cur_spec.getData(old_worm);

So drilling through the code I see that line 65 of +seg_worm\+stats\movement_specs.m references an sl.struct.getSubField, but this does not exist in the matlab_standard_library repo.

[JimHokanson]

My bad. I've added it to the standard library repo.

Jim

[MichaelCurrie]

Nearly works! The comparison runs now, but at the end (or perhaps partway through) I've got an error saying that sl.struct.dealArray doesn't exist in matlab_standard_library.

[MichaelCurrie]

OK you added that function now to matlab_standard_library, and now I'm getting the following when I run seg_worm.testing.features.t_001__mrcCodeVsNewCode. Is this the same as what you get when you run it?

[JimHokanson]

I failed to accurately classify a bug in the old code, which made the motion comparison fail. I updated the code to handle this properly.

[MichaelCurrie]

Looks like that did the trick! Everything is equal or is close. Thanks.