Comments (9)
I will certainly up vote. However, in lieu of this feature it would be great for collaboration and reproduction purposes to share the code that you can as markdown/text. I will use the notebook you shared. thanks!
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great to hear that, here we go!
from ipyniivue_experimental import AnyNiivue, SliceType
# based on https://niivue.github.io/niivue/features/additive.voxels.html
volumes = [
{ "path": "../images/mni152.nii.gz" },
{
"path": "../images/narps-4965_9U7M-hypo1_unthresh.nii.gz",
"colormap": "red",
"cal_min": 2,
"cal_max": 4,
},
{
"path": "../images/narps-4735_50GV-hypo1_unthresh.nii.gz",
"colormap": "green",
"cal_min": 2,
"cal_max": 4,
},
]
nv = AnyNiivue()
nv.load_volumes(volumes)
nv
nv.volumes[0].colorbarVisible = False
nv.volumes[1].cal_min = 1
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I don't see
volume.visible
used anywhere in the codebase, or a way to set the visibility of an existing volume in the viewer. In fact, setting"visible": false
in the JS Viewer doesn't seem to do anything?
@manzt , right. visible
as used with NVImage
is a relic that should be removed in a future version of niivue. However, visible
is used in drawMesh3D
.
So, perhaps it is best to omit visible
from ipyniivue
volumes. We hide images by setting their opacity
to zero.
What do you think?
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![image](https://private-user-images.githubusercontent.com/44469195/306701686-9a74ce2b-3fa7-405f-8788-ea094a95aed0.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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._cXPRH378U7d8imyyD_NIJmmxH0GOWNLYPR14PEJ9wg)
from ipyniivue.
Please try to avoid pasting large images without code. It makes it very hard to reproduce. Would be great to have the code snippet you shared, and just an image of the expected notebook output.
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I know, I really wish there was a feature to drag and drop notebooks directly into issues!
Feel free to upvote this discussion for that -> https://github.com/orgs/community/discussions/50144
here's the notebook, just committed it to the main branch
https://github.com/niivue/ipyniivue-experimental/blob/main/demo/additive_voxels.ipynb
from ipyniivue.
I don't see volume.visible
used anywhere in the codebase, or a way to set the visibility of an existing volume in the viewer. In fact, setting "visible": false
in the JS Viewer doesn't seem to do anything?
from ipyniivue.
I found it used like this in basic.multiplanar.html
var volumeList1 = [
{
url: "../images/mni152.nii.gz",
colormap: "gray",
visible: false,
opacity: 1
},
{
url: "../images/hippo.nii.gz",
colormap: "red",
visible: true,
opacity: 1
}
];
and I found it here
https://niivue.github.io/niivue/features/mesh.layers.html
![image](https://private-user-images.githubusercontent.com/44469195/306729609-2f4f3a67-46c2-46f7-b341-aea12fef84d5.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.m1RzuMeae62tUBmnyYyDZuGaL-9vxpg560fppyZXOGY)
var checkbox1 = document.getElementById("meshCheckbox1");
checkbox1.onclick = function () {
nv1.setMeshProperty(nv1.meshes[0].id, 'visible', checkbox1.checked);
console.log(`visible=${nv1.meshes[0].visible}`);
}
from ipyniivue.
great that min and max is working now!
What do you think would be a good next example to implement?
I think that staying with Volumes and going for
https://niivue.github.io/niivue/features/colormaps.html
would be a good choice.
import * as niivue from "../dist/index.js";
var slider = document.getElementById("gammaSlider");
slider.oninput = function () {
nv1.setGamma(this.value * 0.01);
};
invertCheck.onchange = function () {
nv1.volumes[0].colormapInvert = this.checked;
nv1.updateGLVolume();
}
selectCheck.onchange = function () {
if (this.checked)
nv1.setSelectionBoxColor([0, 1, 0, 0.7]);
else
nv1.setSelectionBoxColor([1, 1, 1, 0.5]);
}
crossCheck.onchange = function () {
if (this.checked)
nv1.setCrosshairColor([0, 1, 0, 1]);
else
nv1.setCrosshairColor([1, 0, 0, 1]);
}
wideCheck.onchange = function () {
if (this.checked)
nv1.setCrosshairWidth(3);
else
nv1.setCrosshairWidth(1);
}
document.getElementById("custom").addEventListener("click", doCustom);
function doCustom() {
var val = document.getElementById("scriptText").value;
val += ';let key = "Custom"; nv1.addColormap(key, cmap); nv1.volumes[0].colormap = key;nv1.updateGLVolume();';
val && eval(val);
}
document.getElementById("saveBmp").addEventListener("click", doSaveBmp);
function doSaveBmp() {
nv1.saveScene("ScreenShot.png");
}
var volumeList1 = [
{
url: "../images/mni152.nii.gz",
colormap: "gray",
opacity: 1,
visible: true,
},
];
var nv1 = new niivue.Niivue({backColor: [0.3, 0.3, 0.3, 1]});
nv1.attachTo("gl1");
nv1.loadVolumes(volumeList1);
nv1.opts.multiplanarForceRender = true;
nv1.opts.isColorbar = true;
let cmaps = nv1.colormaps();
let cmapEl = document.getElementById("colormaps");
for (let i = 0; i < cmaps.length; i++) {
let btn = document.createElement("button");
btn.innerHTML = cmaps[i];
btn.onclick = function () {
nv1.setColormap(nv1.volumes[0].id, cmaps[i]);
};
cmapEl.appendChild(btn);
}
I think the two new functions here are nv1.saveScene and nv1.volumes[0].colormapInvert
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Related Issues (20)
- a
- Graph features
- Add custom colormaps
- devDependency requirement on @jupyterlab/builder@^4.0.0
- load_meshes HOT 1
- Building documentation HOT 8
- Review code of NiiVue Jupyter notebook integration in IPyNiiVue HOT 4
- load_meshes does not add the mesh to self.meshes in MacOS and Linux HOT 5
- Restarting the kernel fails to destroy the NiiVue object
- jupyterlab 4 support HOT 4
- ENH: Integration with MNE-Python
- Possible to add overlays and/or possibly saving the whole scene as .html file to harddrive?
- Prototype of ipyniivue using anywidget HOT 7
- Project admin, milestones, and roadmap
- Priorities HOT 6
- Better camel/snake scale conversion HOT 10
- Exposing `nv.saveScene` on the python side HOT 1
- Deleting big files HOT 2
- Larger NIfTI images cause Jupyter Notebook to crash
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