[pyqtgraph] PolyLineROI data is not updating correctly when changing (moving/adding) handles

[Michael Graupner]

Hello,

I have been working on the ImageView class since I wanted to be able to add
multiple PolyLineROIs to the view and display the roiCurves alltogether in
the view below. These two features work well.

However, when I change the handles of an individual roi, or add an handle,
the roiCurve does diplay false values. Something must be in the getArrayRegion
function or around. I am not quite sure where to start looking and would
appreciate any hint.

The behavior can be tested by running roiAnalysis.py here :
https://github.com/mgraupe/pyqtgraph

Thanks a lot in advance.

Cheers,
Michael

[Luke Campagnola]

Hi Michael!
I think I understand the problem, but let's make sure we are talking about
the same behavior. This is what I did:

1. run roiAnalysis.py from your develop branch
2. `imv.addROI([0, 0])` from command line
3. Drag a handle; values in ROI plot change even if the average value
within the ROI should have been unchanged

The reason for this behavior is that getArrayRegion returns an array of the
_rectangular_ region around the ROI, with anything outside the ROI set to
0. If you take the mean over this array, then all those 0s get mixed into
the mean. A really simple option here is to add the ability to specify a
default value other than 0. You could then call getArrayRegion with
default=nan and use np.nanmean to get the correct value.


Luke

Post by Michael Graupner
Hello,
I have been working on the ImageView class since I wanted to be able to
add multiple PolyLineROIs to the view and display the roiCurves alltogether
in the view below. These two features work well.
However, when I change the handles of an individual roi, or add an handle,
the roiCurve does diplay false values. Something must be in the getArrayRegion
function or around. I am not quite sure where to start looking and would
appreciate any hint.
https://github.com/mgraupe/pyqtgraph
Thanks a lot in advance.
Cheers,
Michael
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[Michael Graupner]

Hi Luke,

thanks a lot for your help. You were exactly right. It was the '0'
averaging which screwed up the roi plot. Implementing a change of the
zero's in the mask in ROI.py to nan and using nanmean fixed the problem.

Thanks.

Cheers,
Michael

Post by Luke Campagnola
Hi Michael!
I think I understand the problem, but let's make sure we are talking about
1. run roiAnalysis.py from your develop branch
2. `imv.addROI([0, 0])` from command line
3. Drag a handle; values in ROI plot change even if the average value
within the ROI should have been unchanged
The reason for this behavior is that getArrayRegion returns an array of
the _rectangular_ region around the ROI, with anything outside the ROI set
to 0. If you take the mean over this array, then all those 0s get mixed
into the mean. A really simple option here is to add the ability to specify
a default value other than 0. You could then call getArrayRegion with
default=nan and use np.nanmean to get the correct value.
Luke
On Fri, Sep 7, 2018 at 12:42 PM Michael Graupner <

Post by Michael Graupner
Hello,
I have been working on the ImageView class since I wanted to be able to
add multiple PolyLineROIs to the view and display the roiCurves alltogether
in the view below. These two features work well.
However, when I change the handles of an individual roi, or add an
handle, the roiCurve does diplay false values. Something must be in the getArrayRegion
function or around. I am not quite sure where to start looking and would
appreciate any hint.
https://github.com/mgraupe/pyqtgraph
Thanks a lot in advance.
Cheers,
Michael
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