scenerygraphics/sciview

sciview is a tool for visualization and interaction with ND image and mesh data

sciview's Issues

Add a welcome.md

To alert about changes on the update site

SciView update site wants to downgrade imglib2-* in my Fiji

Hi,

running update Fiji today I spotted that SciView update site was attempting to downgrade some imglib2 stuff... only caught my attention because I would expect imglib2/coreFiji update site to update the imglib2 stuff. See attached screen shot:

Isn't there an issue that SciView is coping more by mistake?

Vlado

PS: Thanks for SciView!

SelectCommand shoots rays, but does not hit objects in scene

@skalarproduktraum, select does shoot spheres when debugRaycast is indicated, but it doesnt hit objects that are already in the scene. It does return the debug spheres along the ray, just not preexisting objects.

https://github.com/scenerygraphics/SciView/blob/f38fc410f4784b0d177dcb8191f6132fb95195d8/src/main/java/sc/iview/SciView.java#L286

Trying to export a STL file throws a NullPointerException

No matter how you create a view with a mesh (add your own programmatically, run SciView>Add Box...), trying to export an STL file causes a NullPointerException at https://github.com/scenerygraphics/SciView/blob/master/src/main/java/sc/iview/io/ExportSTL.java#L30 because there are no viewers in DefaultSciViewService.

Steps to reproduce

1. Run ImageJ
2. Run SciView >Add>Box
3. Run SciView>Export>STL_

Environment

• Win 8.1 64-bit
• JRE 1.8.0_152
• Vulkan renderer (JVM -Dscenery.Renderer=VulkanRenderer)
• Lenovo G50-70

Bounding box with units

Add the ability to enclose objects with bounding boxes that have tick marks indicating units.

Use imagej-mesh for reading/writing meshes

https://github.com/imagej/imagej-plugins-io-mesh

Introduce SciView Object?

Would it be worth it to make a SciView Object/Element/Node type? It would inherit from a Scenery Node, but be able to generate its own IJ2 dialogs for creation/adding, editing, and deleting based on its state and the state of the scenegraph. It could also be used for default implementations of SciJava Event handling, and other SciJava and ImageJ integration.

Recording movies

The scene can currently be animated via rotation. However, the screenshot mechanism leaves much to be desired for creating a proper movie that captures every frame.

Ellipsoid shapes/meshes

We are going to need to be able to render ellipsoid shapes

Interfacing with imglib2-roi

The ability to convert between meshes and ROIs

Scale bar

Scale bar for indicating the unit length (let's do this better than the old 3D viewer)

IJ classpath?

This was needed somewhere (if it actually gives the desired results):

https://imagej.nih.gov/ij/developer/api/ij/IJ.html#getClassLoader--

Distance measurement tool

We need a tool for easily measuring distances in 3D

GoL3D as an animation

What about treating the iteration of the GoL demo as an animation?

Use AnimationService

Mesh IO via scijava's IOPLugin

Use the scijava-common IOPlugin for MeshIO

https://github.com/scijava/scijava-common/blob/master/src/main/java/org/scijava/io/IOPlugin.java

SciView window close event may not register with SciViewService

Save session/history/events

Save the history of interactions with ThreeDViewer

Orthogonal Views

Orthogonal views was another way of viewing an image in 3D. This might be easily achieved via textures and Scenery's Plane Node.

Highlighting with point groups

The original 3D viewer allowed for the highlighting of regions with point groups: http://132.187.25.13/ij3d/?category=Documentation&page=devdoc/HighlightPoints

Change animation properties

Add the ability to change the axis, and angle of rotation

Perhaps add pathing/waypointing?

Commands dont go to the right place if there are multiple ThreeDViewer's open

Open 2 3DVs, close the most recent one, then try to run a command from menu

Only upload releases to ij update site

Application of imagej-ops to meshes and in-scene elements

This is partially depending on a picker to select objects, which can subsequently be modified by the application of relevant ops.

Use LUTs instead of scenery colormaps

I believe that LUTs can be transferred to scenery by converting the LUT into a GenericTexture, then using material.textures.put("normal","fromBuffer:[transferTextureName]") with transferTextureName as the name of the GenericTexture.

Debug messages are printed to `System.out`

Debug messages should be printed using LogService.debug(String) instead of System.out.println(String) so that they can be hidden.

wireframe render of mesh

Multi-channel/RGB volumes

At least a slider to switch between channels if not displaying multi-channel images

Skeleton graphs

Can we set something up to convert the result of a thin op into a skeleton graph?

This is done by AnalyzeSkeleton.

@rimadoma

Maybe this isn't a SciView feature, but we care about this a bit because we started solving for skeletons using a purely graph-based approach.

Resize bug

When I resize in SciView I get a tiling effect:

Overload icon

The idea is in here:

https://github.com/ClearVolume/ClearVolume/blob/master/src/java/clearvolume/utils/ClearVolumeJFrame.java

Menu bar independent of ImageJ

Curtis had some suggestions on how to make sure it also works within ImageJ, but first let's just get it working in standalone.

Support for live acquisition of volumes

Allow volumes to be updated after being loaded.

Port BigDataViewer's Overlay Orientation/position indicator

BDV's indicator of scene orientation runs on top of the 2D Graphics obtained from a JPanel, so this also involves the JPanel wrapping of ThreeDViewer

Visual discrepancy when using scenery's fitInto in conjunction with ops

This isn't an issue, but I wanted to document this somewhere.

If you do something like:

msh.fitInto( 15.0f, true );

Then call an op like convex hull on msh

The convex hull will not look like a convex hull. This is because fitInto only alters the rendering, not the underlying mesh.

Want: labeled mesh data

See IJ forum post: http://forum.imagej.net/t/problem-with-bioformats-plugin/4854/3

Clean Pom

Especially repositories

Complex surface area measurements

Measuring surface areas by accounting for multiple elements of the scene. In a way this is kind of like image calculator but with meshes.

Reference forum post: http://forum.imagej.net/t/surface-area-measurements-in-bonej/5420/2

Manipulating objects in scene

Manipulation of objects, such as rotation, translation, would be nice.

Enable bounding box display for selected objects

Scenery support via https://github.com/scenerygraphics/scenery/blob/master/src/main/kotlin/graphics/scenery/BoundingGrid.kt

Issues with scenery 0.2.4-SNAPSHOT

I am confirming (bonej-org/BoneJ2#86) the OpenGL black screen with the 0.2.4-SNAPSHOT of scenery when running basic tests from SciView.

The Vulkan failure to compile also exists (with enforcer on).

When the enforcer is skipped, Vulkan renders (no black screen like in OpenGL). However, when toggling to VR this error comes up: scenerygraphics/scenery#135

Transparency for meshes

Transparency for mesh rendering existed in the previous 3D Viewer. This requires a little more effort for the Scenery-based renderer due to shaders.

Displaying 4D data

Displaying data that changes over time, see http://132.187.25.13/ij3d/?category=Documentation&page=devdoc/4DViewer

Volume rendering

This is a bigger question involving Scenery and ClearVolume.

Bugs in 0.1.0

• Tried to run convex hull on Robert's shell mesh (in main/resources) and got:

java.lang.IndexOutOfBoundsException
	at java.nio.Buffer.checkIndex(Buffer.java:540)
	at java.nio.DirectFloatBufferU.get(DirectFloatBufferU.java:253)
	at graphics.scenery.HasGeometry$DefaultImpls.recalculateNormals(HasGeometry.kt:825)
	at graphics.scenery.Mesh.recalculateNormals(Mesh.kt:14)
	at sc.iview.process.MeshConverter.toScenery(MeshConverter.java:85)
	at sc.iview.SciView.addMesh(SciView.java:724)
	at sc.iview.ops.ConvexHull.run(ConvexHull.java:66)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)

• When voxelizing a mesh, 2 images are shown instead of 1.

• When loading the shell mesh, then voxelizing it, and reimporting as isosurface, I got:

java.lang.ClassCastException: net.imglib2.type.numeric.integer.UnsignedByteType cannot be cast to net.imglib2.type.logic.BitType
	at net.imglib2.type.logic.BitType.compareTo(BitType.java:55)
	at net.imagej.ops.threshold.apply.ApplyThresholdComparable.compute(ApplyThresholdComparable.java:56)
	at net.imagej.ops.threshold.apply.ApplyThresholdComparable.compute(ApplyThresholdComparable.java:46)
	at net.imagej.ops.special.computer.BinaryComputerOp.compute(BinaryComputerOp.java:93)
	at net.imagej.ops.map.MapIterableToIterable.compute(MapIterableToIterable.java:58)
	at net.imagej.ops.map.MapIterableToIterable.compute(MapIterableToIterable.java:47)
	at net.imagej.ops.threshold.apply.ApplyConstantThreshold.compute(ApplyConstantThreshold.java:73)
	at net.imagej.ops.threshold.apply.ApplyConstantThreshold.compute(ApplyConstantThreshold.java:50)
	at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:52)
	at net.imagej.ops.threshold.AbstractApplyThresholdIterable.compute(AbstractApplyThresholdIterable.java:43)
	at net.imagej.ops.special.hybrid.UnaryHybridCF.calculate(UnaryHybridCF.java:61)
	at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:71)
	at net.imagej.ops.special.hybrid.UnaryHybridCF.run(UnaryHybridCF.java:97)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:944)
	at net.imagej.ops.OpEnvironment.run(OpEnvironment.java:156)
	at net.imagej.ops.threshold.ThresholdNamespace.apply(ThresholdNamespace.java:82)
	at sc.iview.io.ImportIsosurface.run(ImportIsosurface.java:67)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:748)

Edit @skalarproduktraum: Changed to task list

Controlling the slice cutoff depth

for slicing through the scene

Compatibility with 3D_Viewer

The 3D viewer in SNT is getting on everybody's nerves, as it now stalls half-way through the most simple operation. Before I look into it (I will spending the next months fixing SNT), I was wondering if we should start using ThreeDViewer. Do you have any advice on this? Are there any plans to make the ThreeDViewer backward compatible with the legacy 3D_Viewer?

Use ImageDisplay framework

Add an updateVolume method

Editing an object's properties

It should be possible to manipulate an object's properties, such as colors, textures, etc..