IVAS Feedback/3.0/training

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This set of feedback was sent to Imago on Nov 8, following the Nov 7 IVAS 3.0 software training (NU). All feedback was discussed. Those that were available in writing before the meeting have additional comments underneath, even if it is to just say they were noted at the meeting. Comments in gray have been addressed to our satisfaction.

Please find our updated feedback on IVAS 3.0 (with some expected action items) below.

Much of the feedback is straight-forward, but I'd like to draw everyone's attention to the very first feature request (to bring back POS analysis), as we were told that it runs counter to a business decision. We use and need this feature to analyze data collected on the LEAP prior to the concept of "analysis folders" and to share data easily between users. We also need it to use some LEAP data that we've analyzed outside of IVAS. We are aware of work-arounds, but they are tedious and losing features in a high-value (and high-price) product without prior consultation is not acceptable. I hope that, in the future, we are asked before such valuable features are removed (as Jason asked about whether we needed the data lock features back in May).

Thanks again to David for the useful meeting!

Feature Requests


  • Bring back POS analysis
    • It was apparently a marketing decision to remove it. We must lobby to have this vital feature restored!
      • Please try [Ctrl]-[Shift]-P. This is not a published feature and is intended for use with our collaborators. Unfortunately Dave Reinhard was not aware of this.
        • Many thanks for the keyboard shortcut! Are there any other useful "secret cheat codes?"
    • What would the POS analysis be used for? I'm not sure if that's a feature that I typically use or not and I haven't used 3.0 much yet. Thanks for the cheat code though.
      • POS analysis allows you to do a "quick analysis" using only a POS file and a range file. It is the only real way to open data analyzed by versions of IVAS that didn't have the concept of "projects" (or data collected on the 3dap/analyzed by Apex or artificially created data). Giving someone a POS and a range file (as opposed to a whole project folder) is also a useful way to easily share a dataset.

Better Organization of Related Functions

  • Make some related functionalities and information accessible in easy-to-find windows
  • add total numbers and errors to bulk composition feature - Dieter Nov 2
    • Noted
    • Add errors to precip analysis script
      • (Tom said he'd do this)
  • Decrease number of clicks needed to do common tasks (e.g. turn ions on/off)
    • Note the context menu to bring up the ion list.
      • Some of this could be alleviated by adding more palettes such as this to the toolbar.
  • where is the equivalent of the old "Details" tab that showed the total atoms by species (with percentages), the box dimensions, the approximate atomic density, etc.
    • The old “Details” tab has been broken up. When you left-click on the “Mass Spectrum Analysis” in the “Analyses” panel you will see a list of properties for at the bottom of the Analyses panel. In the list of properties you can see some things that used to be in the “Details” tab such as the number of hits in the spectrum, the number of ranged hits, etc. You can right click on the “Mass Spectrum Analysis” and select “Display Bulk Composition” to bring up a floating window which displays the counts and % of each ion. The box dimensions can be found in the properties section of the “Analyses” panel when you left-click on the “Top-Level ROI”. I don’t believe the approximate atomic density is displayed anymore.
      • It might be useful to have a script which would display this together. An additional feature request would be to have the approximate min and max tip radii present in analysis (I believe it has been available only in the reconstruction).
        • It would be great to have the basic info for an analysis combined in one single property window that can be accessed easily. I consider "basic info" to include: box dimensions, number of ranged atoms and percentages for each element, color code, and totals ranged and entire mass spectrum. This information next to the 3D reconstruction not only gives you the basics but it is also greatly useful for a quick check if something has gone awry during reconstruction and mass ranging. Adding to this basic property window the capability to switch on and off visibility of individual and all elements would make it an extremely efficient tool. Perhaps also export numerical data of this window to text-format (CSV?) with the colors in (R,G,B) values added - Dieter Nov 2
          • Noted

Other Interface Improvements

  • User-customizable toolbars/preferences
    • User-customizable isosurface interface polygon filter (on/off by default and default threshold)
  • I look at mass spectra using a log scale 99% of the time. Is there a way to customize mass spectrum display to default in log mode? Dieter 19:01, 2 November 2006 (CST)
    • Not yet. There should be.
  • bring back image capture for mass spectrum - Dieter Nov 2
    • Not intentionally removed. It should come back. Image capture should be added to nearly any sub-window.
  • bring back or name clearly numbers of total ranged ions and total ions in spectrum (the latter is in mass spectrum properties but oddly named) - Dieter Nov 2
    • Noted
  • Ability to turn all PPTs off and on in the precip analysis script
    • This can be done as long as you are using a mouse with a scroll wheel. When you have the mouse pointer to the right of the precipitate list (hovering over either the Ion Count list or Axis Lengths list) you can double click the scroll wheel to invert your current selection (so if they are all selected it will turn them all off) and you can double click the left mouse button to turn them all on. Usually double clicking with the right mouse button would turn them all off but in this case a right click brings up an export option. This double clicking methodology also works to the right of the ion lists which are to the right of 1D composition profiles and proxigram profiles.

  • In the mass range property window, it is not clear if the number of atoms displayed equals the actual number of atoms if the number is smaller than the max number displayed. - Dieter Nov 2
    • Yes--The number of displayed atoms will equal the number of atoms in the dataset when it is less than the max number
  • Make it easier to set color, transparency, etc. of multiple objects.
    • Shift+click or Ctrl-click will allow this.

Background Subtraction

  • Allow user-definable backgrounds
    • how about a spline through counts in 'background-mass-ranges' created in exact the same way as one makes 'regular' mass windows? - Dieter Nov 2
  • "Local" backgrounds in the region of a peak
    • an example for "local" background: the background can be defined for a specific region or peak by a noise-range to the left and to the right of that region or peak. - Dieter Nov 2
  • Make this work across more than just the histogram (allow it to remove atoms from a reconstruction, perhaps based on whether it is inside or outside of a feature)

  • It was acknowledged that this could be improved, but the specific improvements which will be made & the priority are unknown.

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.
  • The ability to keep locally made enhancements on an upgrade would be nice.
    • This should be doable.
  • In the short term: please modify precip.py to dump the 3d transformation matrices to a text file. We use this in our inter-precipitate distance analysis, but must modify precip.py with each new version of IVAS.
    • This should be doable. In general, ALL tables should be exportable.
      • It’s on the list.
  • Groups of ROIs should be able to be handled both as:
    • A collection (e.g. We want to create ONE mass spectrum for the whole set and already can perform a proxigram for the whole set)
    • Individuals to batch process (e.g. we want to perform a proxigram for EACH ROI and already can create mass spectra for each one).


  • What happened to online help?
    • David doesn't know, but the fact that the documentation hasn't been updated for 3.0 yet may have something to do with it.
  • Can we receive an updated PDF of the full documentation.
    • Yes--when it is actually written.

VRML Export

  • Allow export without the switch statements, to make files which are smaller & more compatible
  • Allow the support of the VRML sphere object, rather than a polygon, to decrease filesize
  • Noted


  • RDF
  • Some way to draw a line & get out a measured length
  • Ability to differentiate top/bottom of interface
  • Plotting enhancements
    • Ability to rotate and reposition axes and labels in 3d window for legibility
    • Ability to specify axes font/label and size
    • Ability to specify thickness of lines in plots and bounding box in 3d window


  • What is the best way to report, track, and prioritize feedback? Is this collection on NUCAPT's wiki still tracked by Imago? Could Imago provide some feedback mechanism so that NUCAPT can track and influence prioritization and progress? What log files should be sent when bugs are encountered?
    • A useful feature request may be to provide some feedback agent that would send the needed log files & allow the user to enter details to send to Imago. Please note that it is critically important that all NUCAPT users (not just the user who sent it) have the ability to look at that feedback too!

  • What is the "spectrum underflow?"
    • Spectrum underflow is the number of ions with m/q below the minimum spectrum m/q value. This should usually be 0, but may change if 1) a POS file was generated outside of IVAS and contains m/q values < 0 or 2) the minimum spectrum value is > 0 (possible in IVAS, but not exposed in the UI).
  • Right clicking on a ROI and selecting "create mass spectrum analysis" produces a very different result from exporting the ROI and then opening that to view the mass spectrum analysis. Why is this?
    • This could have been a user error
    • Or it could have been inside/outside issue
  • How does the volume calculation handle surfaces with holes? (Don't know if this was asked--we've gotten this answer before & I include it for completeness)
    • Undefined. I wouldn’t put much faith in volume for incomplete with missing polygons.


  • Not shipping with RAK's improvements to envelope.exe (which can mean aborts for "too many clusters")
    • David will look into why.
      • Tom said he did not get it.
        • Sent again --Rick 13:00, 16 November 2006 (CST)
  • DATA LOSS Re-reconstructing has sometimes led to lockups. After forcing IVAS to close & restarting it, previous reconstructions in the project folder were gone.
    • Could be related to trying to start saving a reconstruction when a save is already in progress.
      • But "save reconstruction" was pressed once.
        • Noted
  • If one opens a saved analysis state (.py script) from an earlier version of IVAS and tries to Display Bulk Composition IVAS gives a java.lang.NullPointerException error. If the analysis state is opened and saved as a new analysis state in IVAS 3.0 then Display Bulk Composition works.
    • Known issue & you've provided the work around :-)
      • We'll inventory how critical it is that old scripts be converted into something more usable.
  • 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.
    • Noted and reproduced. Should be fixed.
    • Related: Sometimes changing # of atoms displayed in tree doesn't work or takes a while to update
    • Also, some isosurface updates aren't committed
      • Couldn't reproduce. Is this last one related to the OK/Accept button "weirdness" on the isosurface propertes in the alphas for 3.0?
  • When exporting clipped pos file, the generated file shows layers. Especially happens when the original file has "isosurface" present.
    • Yang will send examples
  • Creating a project from a POS has led to rescaling and/or clipping of that POS.
    • Noted
  • Occasional java error (to be sent by Yang) when modifying ranges during reconstruction[This happens mainly like: open IVAS, finish first reconstruction, close the tab, open the second reconstruction(may or may not be from the same RHIT file), and modify the ranges, java error happens].
    • This sounds like it may be a known issue
  • Cylinder ROI's sometimes start jumping around while being dragged.
  • Another known issue that should have some priority: dual monitor bug.
    • Java3D bug--issue opened upstream, which Imago must "wait out."
  • IVAS sometimes locks up while the dataset is being rotated around. It simply gets stuck sometimes while one is rapidly turning it around; this has happened even after the 3d grid is complete.
    • Noted. Couldn't immediately reproduce.
  • Polygon filter on analysis panel doesn't work (still works in tree)
    • This whole panel might be removed.
      • I spent some time with this and found a workaround. The polygon filter on the analysis panel will work as long as you do not set it lower than the lowest setting you have entered into the polygon filter of the interface group node in the analyses panel. So when you create interfaces you can set the polygon filter of the interface group down to 0 and it will automatically reset itself to be equal to the smallest interface. You can then change it back to a higher setting or leave it there. You can then launch the analysis panel and the polygon filter should work fine. One other note about the analysis panel, do not display the interfaces in wireframe in both the analysis panel and the main 3D display; if you do you will get an error, but you can click ok and just change the display type to surface or points. I did not get any error when I had both displays in points mode or surface mode.