Designing 3D Source Detector Geometry in AtlasViewer - BUNPC/AtlasViewer GitHub Wiki

In AtlasViewer, a probe can be edited or designed from the scratch.
To edit a probe which was already designed, open AtlasViewer in the folder that contains the probe.
To design a new probe, open AtlasViewer in an empty folder.
Then in AtlasViewer, go to Tools > Probe > Create/Edit. Create/Edit panel will replace Image Display panel. Tools available in this panel will be used to create/edit a probe.

Adding Optodes

To add an optode, select Add optode radio button on Create/Edit Probe panel. Also select Optode Type (dropdown menu), Grommet Type (dropdown menu), and Grommet Rot (edit box). Then left click on head surface at an approximate location where you want to add an optode. Below image shows Create/Edit Probe panel for adding Source Type optode, #NIRX2 grommet type, and 20-degree grommet rotation.

This will add a source optode and add spring connections with other optodes that are between 0 and 30mm. This [0 30] can be edited by editing Spring List Dist.
This will also add measurement lists between 0 and 30mm. This [0 30] can edited by editing Measurement List Dist.
Adding source type optode will add measurement list with detector optodes and vice versa.
Edit Spring List Dist before adding an optode.

Above images are after adding one source optode and six detector optodes. Center image shows automatic measurement list and right image shows automatic spring list. This measurement and spring list can be edited.
In general, we want to maintain certain distance between sources and detectors. But while adding optodes by clicking on the head surface, but it is difficult select a point exactly at some distance from other optodes.
So, to move optodes to desired locations we edit spring distance between optodes and register probe to surface.

To edit measurement/spring list for an optode, select Edit Optode radio button on the Create/Edit Probe panel
Then left click near an optode for which you want to edit this lists. This will display Edit Optode panel like below.

In Edit Optode panel, we can toggle between Spring List and Meas List radio buttons.
Distance column in the table is editable, so we can edit distance the distance between the optodes to desired distance.
Table in the image is only showing measurement list for current selected optode.
Select All Optodes check box to see all measurement/sping list.
It is useful to see all measurement/sping list when the probe is small but once probe has large measurement/sping list then visualizing for selected optode is useful.

Above image is displaying spring connections between all optodes. There are some unnecessary spring connections between some optodes (ex. Between 6 and 5, 6 and 2, 7 and 2 etc) and need to maintain 17mm distance between neighboring optodes for this probe.
To delete spring/measurement connection between two optodes select Edit Mode check box.
Left click near first optode, the GUI will display spring/measurement list for the selected optode. Then right click near the optode for which spring/measurement connection needs to be deleted/added.
This will remove if there is already connection between optodes otherwise it will cerate a connection between optodes.

This image after removing unnecessary optodes and editing the distance between optodes to 17mm.
If the spring color is black, then optodes are close to specified distance otherwise they are not. Insert color coding system here*
We are almost ready to register probe to surface to move optodes to desired locations.
we need to assign at least 2 optodes to anchor points to avoid ambiguity in registration.

To assign an anchor point to an optode select Edit Optode radio button and left click near the optode for which anchor points needs to be assigned.
After selecting the optode, enter Anchor point label in the Anchor point edit box. This will assign anchor point to the optode.
In this probe, we assign source 1 to Cz refpoint as we want to fix source1 to Cz. Other two anchor points assigned to 2 dummy nodes that added at CPz and FCz.

Here optode 8 and 9 are dummy optodes. Also, a spring connection added between optode 8 and 2, optode 3 and 9 to align 8, 2,1,3, and 9 close to straight line.

To remove an optode, select Remove Optode radio button on Create/Edit Probe panel. /images/ProbeDesign3D/removeAnOptode.PNG
Then left click with in 10 mm of the optode which you want to remove. If there are multiple optodes with 10mm then it will select nearest optode to the left-click location. A pop-up question dialog will appear to confirm if you really want to delete the selected optode. This pop-up window will display will give you information about which optode is going to be deleted. /images/ProbeDesign3D/removeAnOptodeConfirmation.PNG
This will remove the Source optode number 20, and all spring and measurement connections associated with the optode.
If there are no optodes with in 10mm of the selected location, then nothing happens.

This can be done using Lamdas edit box in Create/Edit Probe /images/ProbeDesign3D/editWavelenghts.PNG
Editing Lambdas edit box will update measurement list. It will create/delete measurement list for each wavelength

Spring List Dist and Measuement List Dist can be edited using below edit boxes /images/ProbeDesign3D/springMeasListEditbox.PNG
Editing Spring List Dist will affect next adding optodes. It doesn’t affect previously added spring list.
Editing Measurement List Dist will give two options. /images/ProbeDesign3D/editMeaslistMessage1.PNG
If you choose No, it will affect only new optodes.
If you choose Yes, it will create new measurement list between sources and detectors within the distance specified in Measurement List Dist Edit box. Before doing that it will give below options.
It will give option to add measurement list that already not present within the specified distance. If you choose to add new measurement list it will add this new measurement list and also adds spring list for this new measurement list that are with in specified distance in Spring List Dist edit box. /images/ProbeDesign3D/editMeaslistMessage2.PNG
It will give option to delete measurement list that already present but outside the specified distance. Deleting this measurement list will not affect spring list. /images/ProbeDesign3D/editMeaslistMessage3.PNG

After making changes to the probe use Register Probe to Surface button to register probe to the surface. This will automatically save the probe.
If probe is not registered and saved, then Click “Register Probe to surface to save the probe” message will be displayed on top right corner of the GUI as shown below.