nsherry4 / peakaboo Goto Github PK

The session files saved to disk (and presumably passed when opening a subplot) don't include the visibility of the fittings.

Shrinking the map window should shrink the map when the zoom is set to 1, but it just adds scroll-bars

Using output/input streams is a holdover from trying to support applets.

Currently, the maximum number of interpolation iterations is limited by total map size as a matter of performance. This can lead to very small maps having very high levels of interpolation allowed, which doesn't really make sense. Interpolation should be limited to 2 or 3 levels regardless of map size.

Currently, users can set a max energy to scale their data properly, but if the scan does not start at 0 energy, it can skew the results, especially when points of interest are in different parts of a spectrum

After some complex series of steps which I have not been able to identify, the ratio view in the mapping window will fail to draw (or draw in white) one side of the ratio data.

Workaround: Close the map window and remap. Failing that, save your session, close Peakaboo, reopen it and reload your data and your session.

Re-plotting sub region shows element list which is linked to original plot's element list. If you toggle the visibility of an element fit in one, it impacts the other.

In the section "Details of Peak Fitting", there is a citation which does not have a match in the bibliography.

Should Peakaboo remember preferences like log/linear, axes, etc between sessions?

Fitting functions should accept energy values rather than channel values in order to make them more reliable.

Since SavedSettings has been reworked, the UndoController can be simplified to store saved settings as a string instead of a byte array.

DataSource/Sink plugins should use Path instead of File for read(). This will make it easier to point a DataSource/Sink plugin at files inside a Zip file, for example.

Trying to select an interpolated region to re-plot it doesn't make any sense, because the actual scan data isn't that granular.

Interpolation and selections should be mutually exclusive.

Mapping with 0 fittings selected doesn't make sense, but it's allowed, and throws an exception when you do it.

Because any new SubsetDataSource needs to recalculate the mean/max scans and other values, it can take a long time to load a large subset of a large data set.

The UI should show the "Calculating Values" progress meter that it shows as part of opening data for the first time.

Different XRF data from different equipment is going to have differently properties, including different peak shapes, widths, etc. The user should be able to calibrate peak width and fitting function.

Should peak height be reported in units of counts, or be scaled to the relative intensity of the strongest line in the TransitionSeries?

https://github.com/tschoonj/xraylib

Currently, plot/map images are saved at whatever size the window is at. This can make it hard to produce maps the same size on two different computers/monitors. When exporting images, the size should be confirmed with the user.

Maybe the default can be the current size, but we should probably also provide some other sensible defaults to choose from, along with manual entry.

When selecting a fitting in the plot window, it's portion of the fit should be highlighted so the user can see where exactly it is without having to toggle visibility on/off

The remove/clear icons should be enabled, but they are not.

The energy calibration currently looks for the best "rough" fit, then uses the slower "quality" algorithm to refine the result. Instead, the rough algorithm should be used to rule out, say, 99% of possibilities, leaving the rest for the quality algorithm to verify and then refine.

Composite and Overlay map log view check boxes both control the same log view parameter in the model, but they don't update their value when the other alters the model.

A subplot generated using a bounding box ought to be able to provide data dimensions, but when the subplot is remapped, the map doesn't show those dimensions.

Documentation needs to be updated with new screenshots, and with information on new features.

Because the dimensions of the data change, the index values used to store the bad scans are no longer accurate, and now mark the wrong scan as bad, or cause index out of bounds exceptions

for that reason, 'bad scan' data is intentionally discarded in Peakaboo 3 when creating a subplot view

This could be addressed by recalculating the index values, or by storing the 'bad scan' data as a boolean list in the DataSource object so that CopiedDataSource could do the index adjustments for it, as well

Using peak locations rather than full fitting may be able to speed this process up. Maybe even enough for it to still be useful after #5

Making map selections for Ratio maps should select a range of ratios.

Loading a session should only show .peakaboo file extensions, but it shows everything

Some filters, like the FFT low-pass filter, need to operate on spectra with a length which is a power of 2. Having a check for each filter if it can handle non-standard lengths will prevent this sort of problem.

Settings like escape peak type, fwhmBase, etc are being kept in sync manually by defining the presets twice.

It looks like with Java 9 (and at least my impl of Java 8), setting the application title via the Toolkit's awtAppClassName field is no longer allowed, and generates deprecation warnings. This means that (on linux, at least) the application name is not set, and appears blank.

This is poor form, and we should find a better way to do this.

Observed in dataset w/ ~160keV calibration