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URL_STATE.md 6.41 KiB

URL State

Interactive Atlas Viewer could be run with already selected state. It is possible to create or save application URL so, that it will contain specific data which will usefull to run application with already defined state. In URL, this specific data, is saved as URL query parameters.

URL query parameters in Interactive Atlas Viewer

URL query parameters are variables which are located after URL and separated from the URL with "?" mark. URL query parameter variable contains variable name and value. Url query parameters are divided by "&" symbol. it is not possible to use whitespaces in the URL query. In Interactive Atlas Viewer, URL query parameters are used to save or create an application state. There are 6 main parameters which are used to save the application state. They are: navigation, niftiLayers, parcellationSelected, pluginState, regionsSelected and templateSelected.

Example of already filled URL looks like this:

  
https://dev-next-interactive-viewer.apps-dev.hbp.eu/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre+Bundle+Atlas+-+Long+Bundle&navigation=0_0_0_1__0.11092895269393921_0.8756000399589539_-0.44895267486572266_-0.13950254023075104__2500000__1430285_13076858_4495181__204326.41684726204&regionsSelected=31_51_32

4 parameters are mentioned inside the example URL:

  • templateSelected
  • parcellationSelected
  • navigation
  • regionsSelected

Template Selected - parameter

Template Selected parameter, is used to or select the template with using URL. From the given example we can see the parameter:

templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric

In parameter value, whitespaces should be replaced with "+" symbol. So, actually, the selected template name is:

MNI 152 ICBM 2009c Nonlinear Asymmetric

To select a template from URL it is not required to have any other parameter. "Parcellation Selected" and "Navigation" parameters will be automatically added by default values. So, before the application automatically adds parameters, the URL will look like this:

https://dev-next-interactive-viewer.apps-dev.hbp.eu/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric

Parcellation Selected - parameter

Given parameter is used to select parcellation on the template. As in template selection parameter value, whitespaces are changed with "+" symbol. To use Parcellation parameter, selection template should be in URL parameters too. Navigation parameter will be automatically added by default values. So, before the application automatically adds parameters, the URL will look like this:

https://dev-next-interactive-viewer.apps-dev.hbp.eu/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=Fibre+Bundle+Atlas+-+Long+Bundle

From this example selected parcellation name is

Fibre Bundle Atlas - Long Bundle

Navigation - parameter

Navigation parameter is to determine orientation, position and zoom of 2d and 3d parts of the selected template. It does not depend on selected parcellation, but it depends on the selected template.
Navigation parameter itself includes 5 fields - orientation, perspectiveOrientation, perspectiveZoom, position and zoom. They are sorted appropriate and divided by "__" symbol.
This is the navigation parameters part from the example

navigation=0_0_0_1__0.11092895269393921_0.8756000399589539_-0.44895267486572266_-0.13950254023075104__2500000__1430285_13076858_4495181__204326.41684726204

orientation - the field is used to determine an orientation of the 2D part in atlas viewer. The field contains with 4 numbers, divided by "" symbol. 3 of these numbers should have value "0" and one should have value "1". Value 1 will determine the orientation of the 2D image. In the example orientation is a first element - "0_0_0_1".
perspectiveOrientation - the field is used to determine an orientation of the 3D part in atlas viewer. The field contains with 4 numbers, divided by "" symbol. In the example perspective orientation is the second element

0.11092895269393921_0.8756000399589539_-0.44895267486572266_-0.13950254023075104"

perspectiveZoom - the field is used to determine zoom in 3D pard in atlas viewer. It is the single number and is the third element - "2500000"
position - the field is used to determine the position of the dot where the camera is oriented in both 2D and 3D parts of atlas viewer. Field contains with 3 numbers, divided by "_" symbol - "1430285_13076858_4495181".
zoom - the field is used to determine zoom in 2D pard in atlas viewer. It is the single number and is the last element - "204326.41684726204"

Regions Selected - parameter

Every region of selected parcellation has its own integer number as id. To select the region from URL, with templateSelected and parcellationSelected parameters, URL should contain the regionSelected parameter. In this parameter. In the given example, we can see the region parameter part.

regionsSelected=31_51_32

in parameter, different regions are divided with "_" symbol. It meant that in the given example, there are 3 selected parameters - 31, 51 and 32.
The region belongs to parcellation, so user can not add regionsSelected without templateSelected and parcellationSelected parameters. Navigation parameter will be automatically added by default values.

Nifti Layers - parameter

Nifti Layers parameter adds to the application URL, when the user selects the nifti layer of selected regions. The value of this parameter is text. Especially, it is a link where the nifti file is located.
Example

https://dev-next-interactive-viewer.apps-dev.hbp.eu/?niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FJuBrain%2Fv2.2c%2FPMaps%2FIPL_PF.nii&templateSelected=MNI+Colin+27&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas

You see, that value of parameter "niftiLayers" is

https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FJuBrain%2Fv2.2c%2FPMaps%2FIPL_PF.nii

This is the encoded text for URL where %3A is for ":" and %2F is for "/". So, nifti file's URL is

https://Fneuroglancer.humanbrainproject.org/Fprecomputed/JuBrain/v2.2c/PMaps/IPL_PF.nii

Contributing

Feel free to raise an issue in this repo and/or file a PR.