[WIP] Added KZ spectrum smoothing and tests #631
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
acesnik
approved these changes
May 19, 2022
nbollis
approved these changes
May 19, 2022
Alexander-Sol
approved these changes
May 19, 2022
trishorts
requested changes
Jun 14, 2022
| double[] smoothedIntArray = KZ1D(YArray, window, iterations); | ||
| if(smoothedIntArray.Length < YArray.Length) | ||
| { | ||
| throw new ArgumentException("output length is unequal to input length"); |
There was a problem hiding this comment.
let's change this to an mzlib exception with a message. add a unit test for that exception to make sure it happens and to make sure the message is correct. this gets passed to metamorpheus and are really helpful
| /// Algorithm employed is the Kolmogorov-Zurbenko algorithm originally written in C for R: | ||
| /// https://github.com/cran/kza/blob/master/src/kz.c | ||
| /// </summary> | ||
| public double[,] SmoothSpectrumKZ(int window, int iterations) |
There was a problem hiding this comment.
let's use an informative name for window and have variable explanations for window and iterations before the method with recommendations.
| /// </summary> | ||
| /// <param name="x"></param><summary>double array (double[]) of the intensity values.</summary> | ||
| /// <param name="window"></param><summary>The window size over which to perform the filtering.</summary> | ||
| /// <param name="iterations"></param><summary>The number of smoothering iterations to perform.</summary> |
| /// <summary> | ||
| /// Computes the moving average for a given window. Used in conjuction with the KZ1D method. | ||
| /// </summary> | ||
| /// <param name="v"></param><summary>The source data array.</summary> |
There was a problem hiding this comment.
let's use more informative variable names here for v and w at least
| } | ||
| if (z == 0) | ||
| { | ||
| return double.NaN; |
There was a problem hiding this comment.
please cover this with a unit test
avcarr2
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
My new deconvolution algorithm idea relies on high quality smoothing of the data. I implemented the Kolmogorov-Zurbenko filter, directly porting to C# most of the C code written originally for R found here: https://github.com/cran/kza/blob/master/src/kz.c.
This is a re-do of my previous commit that included some changes that I didn't want to include in this pull request.