I am trying to measure an angle using the Markups tool. In the markups list, I have a series of three 3D points anchoring the angle but no output for the actual angle (in degrees). Where is the angle measurement saved?
Slicer version 4.11.10-2019-08-22
Markups measurements (length, angle, area, etc.) are still work in progress. Currently angle is only displayed in 3D view but not saved anywhere. We plan to add a measurement section to Markups module GUI where all measurements for the selected markup would be displayed. We could also show selected measurements in a tree (similarly to the Data module, but with an extra column added for displaying one or a few values).
How many angles would you measure in a scene? How many cases do you plan to measure? How do you plan to use the angle values? Copy each value to Excel? Or go through a number of cases with CaseIterator extension to add a few angle markups to each case; then extract all the angle values using a Python script?
Actionly, you can compurter the angle by simple geomatric math with 3 points(RAS).
Hi @lassoan, our group is also interested in saving a list of angle measurements. It would be great to be able to do this from the Markups module. Is there a plan for when this may be available? If it will be a while we may look into a temporary solution.
Thanks for your advice.
I plan to replace the node selector combobox in Markups module with a subject hierarchy tree view (filtered to only show markups nodes). The tree view can show some measurement results (1-2 values) in a column. This is what I have now (everything works except measurement values are not yet written to the extra column, I just typed those there manually):
Do you think this would work for you?
How would you use the measurement results? Copy to clipboard (so that it can be pasted into Excel) Saved to the scene file? Saved to a table node? Exported to some json/xml/csv file (not managed by the scene)?
Andras this looks great. Is it available to try in the preview version so that we can give feedback after testing a bit? Eg, is the “New Folder” option equivalent of compiling in all individual measurements in a single place?
We don’t use the scene files a lot, and especially not for storing results. Being able to export them to a csv file is necessary (either to a table export first, or directly saving them). Can we reload a measurement table to recreate them in the scene? Or is strictly values (not the points that will be saved)
I just added the folder to show that you can organize your data in subject hierarchy folders (same as in Data module). You can use the folders any way you want. @cpinter works on allowing folders to override display properties of all nodes within it (e.g., you can temporarily show/hide or override color of all markup nodes within a folder).
Is there a good approach/format that you would be confident to recommend?
Exporting measurements to a table node would not be difficult. There could be an “export” section in markups module GUI to create a table node from selected measurements from all selected markups.
Tables would be regular table nodes, so you could load them again into the scene. However, maintaining two-way links robustly between some original data (e.g., point sets) and measurements on them would require UUIDs and cross-references. Instead of reinventing the wheel, it could make sense to use DICOM for this.
Is there a version I can give it a try? Some of your questions are better answered after testing a few things.
I work in this branch: https://github.com/lassoan/Slicer/tree/markups-module-node-selector-tree. You can build it to try it on your computer (or I can create a Windows install package if you cannot easily build Slicer).
I planned to spend a bit more time, maybe 1-2 days with testing and tuning before I commit it to the master branch.
We (or at least I) currently have a certificate issue with our corporate proxy that limits our ability to do stuff that requires https, including cloning repos. If you don’t mind sending me a windows install package that will be great, or I can wait a couple days for you to commit to the master and hope by that time certificate issue is resolved.
I’ve committed the markups module GUI to the master branch. It should be available in tomorrow’s Preview Release.