Mimic THREEJS loading/parsing approach for DICOM.

Ideally it create a "ImageHelper" (contains geometries + textures + stackHelpers)

Terminology:
Geometry: -
Texture: -
Helper: Geometry + Texture. It is a ThreeJS Object that can be visualized.

Needs to support old and new (XML) VTK formats.

http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf

• one array for color
• one array for opacity

The texture has a limited resolution (currently 256 values) which ends up degrading the data visualization.

In the shaders, AMI only handles unsigned data.

rotate should get the rotation angle as input

this rotation angle should be the angle relative to the current rotation (or relative to the default orientation?)

We should minify the js bundle after running through browserify

https://github.com/scijs/nrrd-js

could be useful for SPL folks
https://github.com/stity/spl-brain-atlas

Must follow @pieper implementation as closely as possible.
(https://github.com/pieper/CommonGL/blob/master/ShaderComputation/ShaderComputation.py)

Underline goal is to extract common (python/JS) GLSL functions and get started with CommonGL.

Sometimes it is painfully slow to scroll between slices in lesson 04 or examples label maps or image compare.

Just rebuilding AMI fixes it sometimes...

Whenever I use a serie to make a 2D representation, following the example, I get almost half the serie that works, then the other half is just noise (like on old tvs).

Here's the view for the images that don't compute

I don't know where it comes from, as it works on the OSIRIX desktop viewer.

It's the same on the example where I load dicom files with those series.
Is there something I'm missing ?

Thanks.

README is outdated, it should reflect current implementation, logic and goals.

It takes 30+ seconds to browserify/babelify/glslify the core - it is way to much

it will also help cleanup the lesson 02, where 2 series are being loaded but it is hard to know which file belong to which series without it.

Showcase how one can connect 2 separated renderers. Useful for remote collaborators.

People should be able to install it with bower.

Use the simple XTK nii parser to get started then maybe get going with Papaya.
https://github.com/xtk/X/blob/master/io/parserNII.js

Create a THREEJS like slice geometry to slice a cube easily.

It takes forever to run npm install.

http://fnndsc.github.io/ami/#geometries_slice

The slice is not well positioned, there is an offset in a direction.

To be investigated and fixed ASAP.

Right now, we are using tweaked THREEJS controls.

We should create medical imaging specific controls.

• for 2D orthographic camera:
  -> scroll: go through slices
• for 3D perspective camera:
  -> scroll: zoom

Allow to hook up special behavior, in XTK like way.

32 bits are stored in RGBA:
https://github.com/FNNDSC/ami/blob/master/src/shaders/glsl/shaders.unpack.glsl

There should be a way to specify if we want to unpack it as integers (as it currently does), or as a float.
https://en.wikipedia.org/wiki/Single-precision_floating-point_format#Converting_from_decimal_representation_to_binary32_format

Raw parser working, needs to be formatted/integrated in VJS and a demo!

Load/parser:
https://github.com/FNNDSC/vjs/blob/master/src/loaders/loaders.trk.js

Demo:
https://github.com/FNNDSC/vjs/blob/master/deprecated/examples/trk_loader/trk_loader.js

See MedXT and Cornerstone

https://www.medxt.com/viewer?s=27462

http://chafey.github.io/cornerstoneDemo/

https://github.com/FNNDSC/ami/blob/master/src/cameras/cameras.orthographic.js

camera.rotate(); // clockwise
camera.rotate(-1); // counter clock-wise

in cameras.ortho

  rotate( clockwise=1) {
    this.center();

    // Pi/2 rotation if camera is positions at the front of the volume
    // else -Pi/2 rotation
    let invertClock = 1;
    if(this.position.distanceTo(this._back) < this.position.distanceTo(this._front)){
      invertClock = -1;
    }

    // Rotate the up vector around the "zCosine"
    let rotation = new THREE.Matrix4().makeRotationAxis(
      this._zCosine, 
      clockwise * invertClock * Math.PI/2);
    this.up.applyMatrix4(rotation);

    this._updateMatrices();
  }

Binary demo dataset from Andreii

Data should be hosted in a proper location and the github repo should only contain source code.

Minimal/(very)small datasets are acceptable for testings.

create a shader texture which will display target data over an object if location matches.

Right now, Nifti parser doesn't read data orientation information.

0 - not filter
1 - trilinear interpolation "filter"
...

Add a method to get well formatted data to display thumbnails easily.

People shouldn't have to write the load sequences in general.

https://github.com/FNNDSC/ami-loader/blob/master/ami-loader.html

Create a simple dicom view element.
Input: data = [image1, image2, image3, etc.]

A THREEJS dev should be confortable with using VJS. Follow same conventions and logic.

VJS allows us to create/update Frame, Stack and Image geometries.
Same for textures.

Might also need helpers such as "ArrowHelper", etc.

Store here larger files not to make git source code too big

Test for both Chrome Version 48, 64-bit and Safari.
The fiddle example could not display anything. Please take a look.

I used the Three.js obj exporter https://github.com/mrdoob/three.js/blob/master/examples/js/exporters/OBJExporter.js

and this code to download the file `

var exporter = new THREE.OBJExporter();
var result = exporter.parse(scene);

var link = document.createElement('a');
document.body.appendChild(link); 
save( new Blob( [ result], { type: 'text/plain' } ), 'model.obj' );

function save( blob, filename ) {

    link.href = URL.createObjectURL( blob );
    link.download = filename || 'data.json';
    link.click();

    // URL.revokeObjectURL( url ); breaks Firefox...

}`

and i get a black box

Using dicomParsers, like in the wado loader:

examples/viewers_dicom2D/index.html three.min.js:631 THREE.WebGLRenderer 75 models.stack.js:235 do not know how to order the frames... – Hemanth Anakapalle 10 hours ago

three.min.js:704 THREE.WebGLProgram: shader error: 0 gl.VALIDATE_STATUS false gl.getProgramInfoLog C:\fakepath(167,37-79): error X4002: indefinite logarithm Warning: D3D shader compilation failed with default flags. (ps_3_0) Retrying with avoid flow control C:\fakepath(167,37-79): error X4002: indefinite logarithm Warning: D3D shader compilation failed with avoid flow control flags. (ps_3_0) Retrying with prefer flow control C:\fakepath(167,37-79): error X4002: indefinite logarithm – Hemanth Anakapalle 10 hours ago

Warning: D3D shader compilation failed with prefer flow control flags. (ps_3_0) Failed to create D3D shaders. – Hemanth Anakapalle 10 hours ago

WebGL: INVALID_OPERATION: useProgram: program not valid three.min.js:671 WebGL: INVALID_OPERATION: drawArrays: no valid shader program in use 254three.min.js:600 WebGL: INVALID_OPERATION: useProgram: program not valid three.min.js:600 WebGL: too many errors, no more errors will be reported to the console for this context. – Hemanth Anakapalle 10 hours ago

I am seeing all these errors over browser console. I am trying this over windows, Is it fine ? –

sitemaps, robots.txt, canonical url, etc.

we should only load 1 series.

As a result, the stack displayed is not always the one presented in the thumbnail.

Is it possible to define what each mouse input do ?
For instance, I want to change the index via mouse wheel, change ww/wc via left click instead of having them in stack helpers.
I cannot find it in any example.

EDIT: I guess I spoke too fast.

Store all LUTs in a map for easy access/add/remove.