IVAS Feedback/3.0

From Northwestern University Center for Atom-Probe Tomography
Revision as of 19:16, 29 December 2006 by Karnesky (talk | contribs) (→‎Bugs: replies)
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This feedback will be sent to Imago based on demand. Feedback presented at the training meeting has been moved to IVAS Feedback/3.0/training.

Please sign your comments with four tildes (~~~~).

When reporting bugs:

  • Note the machine or machines the the error happened on
  • Steps to reproduce issue
  • Note how often you've been able to reproduce the problem
  • Include a screenshot if it would be useful.
  • If a crash or lock-up:
    • Any other applications running?
    • Data on network or local drive?
    • Save all the files in C:\Documents and Settings\<USERNAME>\Application Data\ivas-3.0\dev\var\log to P:\software\IVAS errors\ under a new directory with a short description of your bug
    • Also put any data files we might use to help reproduce the crash or lookup in this directory.
    • Also put screenshot in this directory.

Bugs

  • When using the clipping control for a large( z > 1000 nm) dataset, I kept getting "not a valid number" when I tried to manually type in values for the z range. This is even though they were positive integers that were less than the end z value... When using the slider bar I didn't get any error message. Also, if I removed the comma from the fields, I didn't get the error message. This took place on Cain. Mulholla 14:01, 20 November 2006 (CST)
    • Sounds like a legitimate issue. We are receiving more requests to add commas to large numbers. I would assume this wouldn’t trouble you as long as the text parsing handled commas w/o error.
      • Yup.
  • If I have the Display Ranges window open and I create interfaces, run a proxigram, or run the envelope method I am not always able to close the Display Ranges window.
    • We have encountered this issue, the “Display Ranges” window just won’t die. The user can close it but once they come back to the associated 3D display it comes right back
  • On multiple datsets, I cannot change the polygon filter level. I create interfaces, right click on the interface group in the analysis window, and do launch interface analysis. When I then try to change the polygon filter, I get "Unexpected exception" This occurred on multiple datasets on multiple machines(cain and eve). I placed one dataset and the exact error message in P:\software\IVAS errors\3 Mulholla 16:40, 6 December 2006 (CST)
    • Please provide range file/parameters --Rick 11:18, 29 December 2006 (CST)
    • I can address the polygon filter bug; I'll leave it to Tom to address

the other points.

    • Next time you create interfaces, left click on the interface group node in the Analyses tab. At the bottom of the Analyses tab you'll see the properties of the interface group node. One of the editable properties is the Filter Level (polygons). This filter level is the same as the polygon filter level that you see when you launch the interface analysis panel. The problem you are running into is that the polygon filter level in the interface analysis panel cannot be lower than the Filter Level (polygons) in the properties section of the Analyses tab.
    • When you need to create interfaces and you want to work in the interface analysis tab, first lower the Filter Level (polygons) to the point that you can see all of the interfaces you are interested in. Then launch the interface analysis panel and you will be able to set the polygon filter level to any number as long as it is greater than or equal to the Filter Level (polygons).
      • And thanks to Dave. If that is Mike's problem, I guess we had also talked about it before.

Feature Requests

Export of Statistical Information

Also, I had a note written down that NU wants to be able to export the statistical information from interfaces. The interface group entry in the analyses panel allows the center, roughness, # of polygons, surface area and volume of all interfaces not currently filtered out to be exported to a csv. Is that sufficient for what the group needs or is there more required? --David Reinhard

Eventually: the total number of enclosed atoms and the composition would be useful.
Also: it should be exportable from wherever some of this information is displayed (so both the interface panel if that is kept & the analysis tree).

API/Scripting and Batch Processing Enhancements

  • An API would be nice
    • It would be nice, but David doesn't know when we'll get one. It doesn't sound like plans to add one have been canceled.
    • Regarding the API. As you might have noticed IVAS has changed quite a bit since 2.3. While the GUI shouldn't see drastic change in the future, the underlying implementation of certain functionality will still be subject to some drastic changes. We are still at a point where we can't publish an API and be certain we are able to maintain it from release to release. Also, we don't have any internal customers who would utilize this feature so it's been very hard for the development team to determine what the proper scope should be. If you could give me an prioritized list of what you would want access to it might help us to start targeting stability in the various APIs we implement and use. Note that I can't commit to delivering anything, but it's never too early to start.

Specific wants for API

Please re-order by your priority!

Documentation!
  • Even minimal documentation (auto-generated javadoc or doxygen would be fine to start with) on all classes which could be accessed from jython would be immensely useful
  • This could be fairly easily expanded so that we'd know what was "stable" and what may be changed
  • For stable and commonly used methods, more helpful/detailed (human-generated) comments would be the nest step
  • Finally, some particularly useful methods may benefit from examples
Precipitate properties
  • A stable way to access the ellipsoid methods used in precip.py
ROIs
  • A method to get a list of all ROIs and a mehod to return properties on an individual RO (to sort/select them by area/volume/roughness)
  • A method to generate a proxigram on a given ROI
  • A method to export the proxigram to CSV
  • A method to export a POS for a given ROI
3D window interaction
  • A method to insert text in the 3D analysis window
  • A method to draw basic shapes (the cube/cylinder/spheres (without locked aspect ratios))in the 3D analysis window

Questions

Why, when I right-click on 'Mass Spectrum Analysis' and 'Display Bulk Composition' does the total number of ion counts (if I sum up all the individual ion type counts) not equal the 'Spectrum Ranged Ion Count' in the 'Mass Spectrum Analysis' 'Properties' panel?

I am looking at this right now for a straightforward analysis - no complex ions, unknown ion types, or other funny business. The sum of the individual ion counts is ~3.0M, while the 'Spectrum Ranged Ion Count' shows ~2.6M. Why??!!?? --Jason

Are you seeing the bug we reported (which was confirmed):
When the range of an element is changed in the mass spectrum window and the update button on the bottom right is clicked, the Spectrum Ranged Ion Count under properties of Mass Spectrum Analysis is not updated. One has to additionally right click on Mass Spectrum Analysis and then select Update Mass Spectrum. --Rick 10:52, 29 December 2006 (CST)
that's it ... duh. --Jason
  • Status of 64-bit? --Rick 11:19, 29 December 2006 (CST)