avcarr2/fcwtnet

C# interface for the fCWT C++ code published in this paper: https://www.nature.com/articles/s43588-021-00183-z. fCWT github repo: https://github.com/fastlib/fCWT

fcwtnet's Issues

CWT Line 12

CWT generates an array with 0's in every other position likely stemming from FixOutputArray.

Frequencies does not display correctly

Describe the bug
Y-axis frequencies are not displayed correctly on the scalogram.

To Reproduce
Steps to reproduce the behavior:

1. Create a scalogram from a transient.
2. Observe the y-axis is in Hertz.

Expected behavior
Frequencies of protein ions should be in the range of 200 to 600 kHz.

Screenshots

Migrate from Oxyplot to Plotly.NET

Benefits of Plotly:

• More flexible.
• Zoomable plots
• 3D plots are available

Fix Colors in Heat Map

At some point, the heat map color scheme needs to be updated for aesthetic purposes.

Inadequate unit test "TestSplitRealAndImaginary"

The unit test for TestSplitRealAndImaginary doesn't test that the splitting is working. It uses the already split array to check that the array splitting is working.

Set up gaussian smoothing to use an asymmetrical kernel

The CWT of a typical MS transient can be very asymmetric in the sense that the number of points on the time axis can exceed the number of points in the frequency axis by multiple orders of magnitude. Currently our gaussian smoothing class only uses symmetrical 2D gaussian kernels to smooth data which may lead to insufficient smoothing in one axis and too much smoothing in another.

Adding the option to use an asymmetrical gaussian would allow us to smooth data in a manner consistent with the actual dimensions of our CWT data. This is especially important for finding maxima in plots where there may be time axis oscillation in the in the regions where a peak is meant to be identified. An example of this is shown in the attached files. The first contains the CWT of a transient corresponding to a complex mass spectrum and the second shows high frequency oscillations in many of the peaks appearing in this transient.
complexTransient_modulus.pdf
zoomed_Band2complexTransient_modulus.pdf

Modify GetComponent Method to reflect new CWTOutput object

FCWTNET/FCWTAPI/CWTObject.cs

Line 89 in f4dfb68

private double[,] GetComponent(CWTComponent comp, double[,] originalArray)

Fix broken unit test

• TestPhaseCalculaton() (also this is misspelled)
• TestModulusCalculation()

PlottingUtils Update

Currently, there a Generate(typeofplot) method and then a GenerateCWT(typeofplot). So if you want to change one thing about a plot, you have to change several methods. Make one plot method per type of plot and use optional parameters and overloading to make methods that handle different subtypes of the same plot.

• Example with heatmap.
• Example with XYPlot

Potential issues with wavelet center frequency parameter (C0).

The wavelet center frequency parameter (C0) appears to be behaving in an unexpected way in which varying this parameter does not move the location of frequency bands in the resulting CWT of a given signal. This is a problem because when calculating frequencies through f = C0 / a, a single pure cosine wave's detected frequency will vary depending on what C0 is. Examples of this are given below for C0 = 10, 25 and 50 for a single cosine wave. Varying C0 appears to only affect the width of the resulting ridge.
cosTestCWTHeatmapc0-50.pdf
cosTestCWTHeatmapc0-25.pdf
cosTestCWTHeatmapc0-10.pdf
.

Move modulus and phase calcluation into CWTExtensions

FCWTNET/FCWTAPI/CWTObject.cs

Line 142 in f4dfb68

public double[,] ModulusCalculation()

Does input data need to be saved in CWTObject?

• FCWTNET/FCWTAPI/CWTObject.cs

  Line 20 in f4dfb68

  public double[] InputData { get; }

Probably not necessary to save the input data since it'll likely be loaded from a file.

Deprecated methods?

• FCWTNET/FCWTAPI/CWTObject.cs

  Line 64 in f4dfb68

  public void SplitRealAndImaginary(CWTComponent comp, out double[,]? realCwt, out double[,]? imagCwt)

• FCWTNET/FCWTAPI/CWTObject.cs

  Line 89 in f4dfb68

  private double[,] GetComponent(CWTComponent comp, double[,] originalArray)

• FCWTNET/FCWTAPI/CWTObject.cs

  Line 115 in f4dfb68

  private void GetBothComponents(double[,] originalArray, out double[,] real,