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NRRDLoader: Fix spacing issue when loading 16 bit images. #25767

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Merged
merged 7 commits into from
Apr 4, 2023
Merged

NRRDLoader: Fix spacing issue when loading 16 bit images. #25767

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afd6e73
fixed the nrrd images' spacing issue on loading 16 bits images
skycoco Apr 4, 2023
6f67a7b
undo the ijk_to_transition matrix4 changes, continue use set(row-majo…
skycoco Apr 4, 2023
8020091
Update NRRDLoader.js
Mugen87 Apr 4, 2023
077458e
Update Volume.js
Mugen87 Apr 4, 2023
107e3a4
using array instead of vector3 when creating RASDimensions
skycoco Apr 4, 2023
8a2bd55
Merge branch 'mrdoob:dev' into dev_link_2
LinkunGao Apr 4, 2023
880c600
update
skycoco Apr 4, 2023
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10 changes: 8 additions & 2 deletions examples/jsm/loaders/NRRDLoader.js
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Original file line number Diff line number Diff line change
Expand Up @@ -363,6 +363,7 @@ class NRRDLoader extends Loader {

const volume = new Volume();
volume.header = headerObject;
volume.segmentation = this.segmentation;
//
// parse the (unzipped) data to a datastream of the correct type
//
Expand Down Expand Up @@ -445,7 +446,7 @@ class NRRDLoader extends Loader {
}


if ( ! headerObject.vectors || this.segmentation ) {
if ( ! headerObject.vectors ) {

volume.matrix.set(
1, 0, 0, 0,
Expand All @@ -472,7 +473,12 @@ class NRRDLoader extends Loader {

volume.inverseMatrix = new Matrix4();
volume.inverseMatrix.copy( volume.matrix ).invert();
volume.RASDimensions = new Vector3( volume.xLength, volume.yLength, volume.zLength ).applyMatrix4( volume.matrix ).round().toArray().map( Math.abs );

volume.RASDimensions = [
Math.floor( volume.xLength * spacingX ),
Math.floor( volume.yLength * spacingY ),
Math.floor( volume.zLength * spacingZ )
];

// .. and set the default threshold
// only if the threshold was not already set
Expand Down
25 changes: 20 additions & 5 deletions examples/jsm/misc/Volume.js
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Original file line number Diff line number Diff line change
Expand Up @@ -194,10 +194,18 @@ class Volume {
this.sliceList = [];


/**
* @member {boolean} segmentation in segmentation mode, it can load 16-bits nrrds correctly
*/
this.segmentation = false;


/**
* @member {Array} RASDimensions This array holds the dimensions of the volume in the RAS space
*/



}

/**
Expand Down Expand Up @@ -332,13 +340,20 @@ class Volume {

}

firstDirection.applyMatrix4( volume.inverseMatrix ).normalize();

let iLength, jLength;

if( ! this.segmentation ) {

firstDirection.applyMatrix4( volume.inverseMatrix ).normalize();
secondDirection.applyMatrix4( volume.inverseMatrix ).normalize();
axisInIJK.applyMatrix4( volume.inverseMatrix ).normalize();

}
firstDirection.arglet = 'i';
secondDirection.applyMatrix4( volume.inverseMatrix ).normalize();
secondDirection.arglet = 'j';
axisInIJK.applyMatrix4( volume.inverseMatrix ).normalize();
const iLength = Math.floor( Math.abs( firstDirection.dot( dimensions ) ) );
const jLength = Math.floor( Math.abs( secondDirection.dot( dimensions ) ) );
iLength = Math.floor( Math.abs( firstDirection.dot( dimensions ) ) );
jLength = Math.floor( Math.abs( secondDirection.dot( dimensions ) ) );
const planeWidth = Math.abs( iLength * firstSpacing );
const planeHeight = Math.abs( jLength * secondSpacing );

Expand Down