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IDProjectCategoryView StatusLast Update
0003452Slicer4Core: Usabilitypublic2018-05-29 23:51
ReporterfedorovAssigned Tojcfr 
PrioritynormalSeveritymajorReproducibilityalways
Status assignedResolutionopen 
Product VersionSlicer 4.3.0 
Target VersionbacklogFixed in Version 
Summary0003452: Unable to use Volume module Threshold widget in a meaningful way
Description

For the attached dataset, I need to hide the values that are 0, and I want to see everything else (threshold out everything 0).

Can someone instruct me step by step how I can do this? I am unable to accomplish this simple task with Volumes modulemanual Threshold feature.

TagsNo tags attached.

Relationships

related to 0002952 acknowledgedjcfr Popup slider range in Volumes GUI is not initialized correctly 

Activities

2013-10-17 09:24

 

BC5Visit2_Ktrans_masked.nrrd (52,922 bytes)

2013-10-17 09:24

 

pieper

pieper

2013-10-17 10:50

administrator   ~0010190

Reminder sent to: finetjul

@Julien - is there an easy fix for this?

fedorov

fedorov

2013-10-17 11:52

developer   ~0010191

to make sure there is no ambiguity, here's the code that accomplishes what I tried unsuccessfully to do via the Volumes threshold widget:

v = slicer.util.getNode(name)
d = v.GetDisplayNode()
d.SetApplyThreshold(1)
d.SetThreshold(0.000001,10)

finetjul

finetjul

2013-10-17 12:44

administrator   ~0010192

Here is what I do on Windows 7:

  • Open Slicer 4.3.0
  • Load Bc5Visit2...nrrd
  • Select ColdToHotRainbow as Lookup Table
  • Select Manual Min/Max
  • Move the W/L right handle down to 0.016
  • Select Manual threshold
  • In the threshold popup, move the right handle to 10
  • In the threshold double slider, move the right handle to 10
  • In the threshold left spinbox, click to the right of the '0' digit and type '.' then 6 times '0' and finally '1'
    -> I end up having a threshold of [0.000001, 10]

I would admit:

  • the popup sliders are no longer useful (now that we can control the number of digits) and can be too much in the way
  • there is a bug when typing the 2nd '0', the value becomes -0.01
fedorov

fedorov

2013-10-17 13:25

developer   ~0010193

Julien: I confirm I can follow your steps and it does work on Mac.

However, the steps are a mystery to me starting from "- Move the W/L right handle down to 0.016". In Slicer3, I was able to just type in the actual values for window and level - I didn't need to read the manual or ask how to do that.

FYI, it is not just me who has problems understanding this GUI: I asked both Ron and Steve how to accomplish the task, and they did not have an answer.

finetjul

finetjul

2013-10-17 14:26

administrator   ~0010194

Andrei, I am not saying the Volumes module is intuitive, I agree it is not.
But to improve it, we need to know what exactly is not working.
I don't understand what you mean behind the mystery of "- Move the W/L right handle down to 0.016". The W/L is slightly different than the Threshold, so before we focus on the W/L, do you have something not working (bug) or un-intuitive you want to report about the Threshold ?

Concerning the W/L, there are different issues you reported:

  • a) it is un-intuitive to have to move the right handle to down to 0.016 in order to change the color mapping in the slice view
  • b) typing 0.016 in the Max spinbox when the W/L slider is in "Manual Min/Max" mode is not working
  • c) typing 0.001 in the L spinbox when the W/L slider is in "Manual W/L" mode is not working

For a) I am not sure what can be changed. feel free to suggest something else.
For b) and c), it is working for me, please detail a workflow where it is not.

Again, I know there are lots of issues with the W/L and Threshold.
But I would like to know which one is the one bothering you in particular in order to prioritize the resolution. (We could be removing the popups but maybe the real issue is in the automatic decimals of the spinbox (and there, there are lots of corner cases, so again, we need to identify which behavior do we want).

fedorov

fedorov

2013-10-18 06:03

developer   ~0010195

Julien, the reason I mentioned the mystery of W/L is because you list it in the steps to set Threshold, and I was not sure if it is needed or not. I understand now you probably did it just to have a meaningful visualization.

What is confusing to me is that the values for Threshold (and same for W/L) are constrained by the popup widget, which is not visible. My intuition is that if GUI says "Threshold", I should be able to enter the numbers for threshold, and apply them. Specific suggestions for the GUI:

1) add 2 simple spin boxes that allow to set the numeric values for W/L and Threshold bounds (2 each), perhaps include regular double slider widget - this is how we had it in Slicer3 I think
2) move the current widgets into Advanced tab collapsed by default

What do you think?

lassoan

lassoan

2017-06-09 23:49

developer   ~0014711

It is indeed an annoying issue but there are workarounds and overall it does not seem to actually block any particular project.

lassoan

lassoan

2018-05-29 23:51

developer   ~0015792

Retargeting stale issues to backlog.

Issue History

Date Modified Username Field Change
2013-10-17 09:24 fedorov New Issue
2013-10-17 09:24 fedorov Status new => assigned
2013-10-17 09:24 fedorov Assigned To => pieper
2013-10-17 09:24 fedorov File Added: BC5Visit2_Ktrans_masked.nrrd
2013-10-17 09:24 fedorov File Added: Screenshot at Oct 17 13-24-48.png
2013-10-17 09:26 fedorov Assigned To pieper => finetjul
2013-10-17 10:12 finetjul Assigned To finetjul => jcfr
2013-10-17 10:50 pieper Note Added: 0010190
2013-10-17 11:52 fedorov Note Added: 0010191
2013-10-17 12:44 finetjul Note Added: 0010192
2013-10-17 13:25 fedorov Note Added: 0010193
2013-10-17 14:26 finetjul Note Added: 0010194
2013-10-18 06:03 fedorov Note Added: 0010195
2013-10-18 09:33 finetjul Relationship added related to 0002952
2017-06-09 23:49 lassoan Severity block => major
2017-06-09 23:49 lassoan Note Added: 0014711
2018-05-29 23:51 lassoan Target Version => backlog
2018-05-29 23:51 lassoan Note Added: 0015792