vtkMarchingCubes export nifti surfaces to wavefront OBJ - vtk

I want to run vtkMarchingCubes on a nifti label set. Regions of voxels, for which I want to produce surfaces all share the same value. I have two problems. First, I seem to be setting up the algorithm incorrectly because the resulting vtkPolyData apparently has no vertices. Secondly, it is not clear to me from the vtkOBJExporter documentation how to export the vtkPolyData as a wavefront .OBJ file. If anyone sees any issues with the code below or can tell me how to export the vtkPolyData as an OBJ, I would be grateful.
//Read The Nifti Label File
string input_path = "/MyPath/labels.nii";
nifti_image *im = nifti_image_read(input_path.c_str(),true);
cout<<im->nx<<","<<im->ny<<","<<im->nz<<endl; //Confirms Read Works
// Set up vtk image data
vtkImageImport* importer = vtkImageImport::New();
importer->SetImportVoidPointer((void*)im->data);
importer->SetDataScalarTypeToFloat();
importer->SetDataExtent(0, im->nx-1, 0, im->ny-1, 0, im->nz-1);
importer->SetWholeExtent(0, im->nx-1, 0, im->ny-1, 0, im->nz-1);
vtkImageData* point_cloud = importer->GetOutput();
point_cloud->SetScalarTypeToFloat();
point_cloud->SetExtent(0, im->nx-1, 0, im->ny-1, 0, im->nz-1);
point_cloud->SetSpacing(im->dx, im->dy, im->dz);
//Apply Threshold To Cut Out Other Data
//Is this needed or will Marching Cubes properly identify the region
vtkImageThreshold* threshold = vtkImageThreshold::New();
threshold->ThresholdBetween(label_number,label_number);
threshold->SetInValue(255);
threshold->SetOutValue(0);
threshold->SetInput(point_cloud);
//Apply the Marching Cubes algorithm
vtkMarchingCubes* marching_cubes = vtkMarchingCubes::New();
marching_cubes->SetValue(0, 127.0f);
marching_cubes->SetInput(threshold->GetOutput()); //(vtkDataObject*)point_cloud);
vtkPolyData* surface = marching_cubes->GetOutput();
marching_cubes->Update();
//See That Marching Cubes Worked
cout<<"# Vertices: "<< surface->GetNumberOfVerts()<<endl;
cout<<"# Cells: "<< surface->GetNumberOfCells()<<endl;
//Export (How is this done properly?)
vtkOBJExporter* exporter = vtkOBJExporter::New();
exporter->SetInput(vtkRenderWindow *renWin); //I don't want a render window, I want at file
exporter->SetFilePrefix("/MyPath/surface");
exporter->Write();

You can use this class https://github.com/daviddoria/vtkOBJWriter to write the obj file in the way you would expect (like every other VTK writer). Unfortunately the vtkOBJExporter wants to also write additional information that I never have.

Related

How do I carry over identical texture mapping when exporting to DAE?

I am able to open a 3DS file in MeshLab and when I export to Collada DAE format the textures are visible but they are not being projected onto the mesh in the same way as the preview in MeshLab. For example, the front/back faces of a cube would have the proper texture (suppose it's a polka dot) but the top and bottom have a striped look. How can I apply a single texture and have it appear as intended on all faces, like the imported model before I convert it?
This problem is a result of the end software being used to view the DAE file. It's not a problem with MeshLab.
For example, if loading the file into Away3D be sure to handle the texture materials using the TextureMaterial class instead of the simpler SinglePassMaterialBase such as what you might find in their example code. Here is what I use now, and it displays texture properly:
var material:TextureMaterial = cast(asset, TextureMaterial);
material.ambientColor = 0xffffff;
material.lightPicker = _lightPicker;
material.shadowMethod = new FilteredShadowMapMethod(_light);
material.lightPicker = _lightPicker;
material.gloss = 30;
material.specular = 1;
material.ambient = 1;
material.repeat = true;

d3.js geo - rendering svg path

I'd like to create choropleth map of Czech Republic. Inspired by this article http://bl.ocks.org/mbostock/4060606, I have created this
http://jsfiddle.net/1duds8tz/2/
var width = 960;
var height = 500;
var svg = d3.select("body").append("svg").attr("width", width).attr("height", height);
var offset = [width / 2, height / 2];
var projection = d3.geo.mercator().scale(6000).center([15.474, 49.822]).translate(offset);
var path = d3.geo.path().projection(projection);
queue().defer(d3.json, "..map.geojson").await(ready);
function ready(error, reg) {
var group = svg.selectAll("g").data(reg.features).enter().append("g");
group.append("path").attr("d", path).attr("fill", "none").attr("stroke", "#222");
}
When I tried to fill svg path with some color, I ended on this
http://jsfiddle.net/1duds8tz/3/
group.append("path").attr("d", path).attr("fill", "red").attr("stroke", "#222");
There are odd values in path d attribute.
My GeoJSON data must be somehow faulty but I can't figure what is wrong.
Everything looks right here: https://gist.github.com/anonymous/4e51227dd83be8c2311d
Your geoJSON is corrupted and as a result your polygons are being drawn as the interiors of an infinitely bounded polygon. That's why when you attempt to give a fill to the path, it goes beyond the extent of the screen but still displays the border just fine. I tried to reverse the winding order of your coordinates array, and that seemed to fix all of them except for "Brno-venkov", which might be the source of your problems (especially given its administrative shape).
I'd suggest going back to where you created the original GeoJSON and try to re-export it with simplification. If you want to reverse the coordinates on your GeoJSON to correct the winding order, that's pretty simple:
geodata = d3.selectAll("path").data();
for (x in geodata) {geodata[x].geometry.coordinates[0] = geodata[x].geometry.coordinates[0].reverse()}
But this won't fix the problem polygon, nor will not reversing its coordinates.
In case you are familiar with svg manipulation you can try geojson2svg. This allows you manipulate svg in standard way but you have to code a little more. In case your application requires d3 for many other purpose then d3 is best solution.
I've got exactly the same problem with Mapzen's .geojson files.
.reverse()-ing isn't good enough, if you can't make sure all your data has the same winding order.
I solved it with this one:
https://www.npmjs.com/package/geojson-rewind
You'll need to have npm & require available
Install it, and save it to your project
npm i -g geojson-rewind
Import it, to make it useable
var rewind = require('geojson-rewind');
Use it on the data, in this case:
req = rewind(req);
Tip: If you are working with static data, you can do this only once on the console, and you're good to go.

OpenGL glColorPointer renders black

Here is the breakdown: I load a model from an obj file and store into buffers as follows :vbo for vertexes, ibo for indexes , vao for state and num_indices an int with total indices number. To get the model color I exported a separate off file and extracted color information per vertex and I have an array with 4 values for each vertex so the size of the array is vertexno*4. My draw function looks like this.
glUniformMatrix4fv(location_model_matrix,1,false,glm::value_ptr(model_matrix));
glUniformMatrix4fv(location_view_matrix,1,false,glm::value_ptr(view_matrix));
glUniformMatrix4fv(location_projection_matrix,1,false,glm::value_ptr(projection_matrix));
//glUniform4f(location_object_color,1,1,1,1);
glBindVertexArray(mesh_vao);
glEnableClientState( GL_COLOR_ARRAY );
glEnableClientState( GL_VERTEX_ARRAY );
glColorPointer( 4, GL_FLOAT, 0, colors );
glDrawElements(GL_TRIANGLES,mesh_num_indices,GL_UNSIGNED_INT,0);
And the model renders black. I also have some cubes drawn in the draw function which I color using glUniform4f(location_object_color,rgba) and if I uncomment then the loaded mesh will take the same color as the last drawn cube.
In my constructor I have something like this:
glClearColor(0.5,0.5,0.5,1);
glClearDepth(1);
glEnable(GL_DEPTH_TEST);
gl_program_shader = lab::loadShader("shadere\\shader_vertex.glsl", "shadere\\shader_fragment.glsl");
location_model_matrix = glGetUniformLocation(gl_program_shader, "model_matrix");
location_view_matrix = glGetUniformLocation(gl_program_shader, "view_matrix");
location_projection_matrix = glGetUniformLocation(gl_program_shader, "projection_matrix");
location_object_color = glGetUniformLocation(gl_program_shader, "object_color");
If need be I can provide my shader_vertex and shader_fragment , I considered it to be a problem but im not so sure so if anyone knows why my model isn't being colored please throw a hand.

Extruding multiple polygons with multiple holes and texturing the combined shape

This question is related to this question. The answer shows very nice way to extrude polygons that have holes (see the excellent live example). The main learning of the answer was that paths in three.js (r58) cannot have more than one moveTo command and it have to be in the start of the path, which means that path have to be broken by moveTos, so that moveTo start always a new path.
Extruding in three.js means that 2D paths are converted to 3D shapes using possible beveling. It is suitable for extruding texts to make 3D letters and words, but can be used also to extrude custom paths.
Now there arises two questions:
how is it possible to handle polygons that have multiple hole-polygons and multiple non-hole-polygons?
how is it possible to add a texture to generated shape as a whole?
I made an example of this as SVG in http://jsbin.com/oqomuj/1/edit:
The image is produced using this path:
<path d="
M57.11,271.77 L57.11,218.33 L41.99,218.63 L105.49,165.77 L138.41,193.18 L138.41,172.2 L152.53,172.2 L152.53,204.93 L168.99,218.63 L153.21,218.63 L153.21,271.77Z
M74.14,264.13 L105.49,264.13 L105.49,232.8 L74.14,232.8Z
M115.35,250.7 L135.96,250.7 L135.96,232.61 L115.35,232.61Z
M56.11,145.77 L56.11,92.33 L40.99,92.63 L104.49,39.77 L137.41,67.18 L137.41,46.2 L151.53,46.2 L151.53,78.93 L152.53,79.76 L155.55,77.23 L159.5,74.52 L168.65,69.81 L176.46,66.93 L188.04,64.16 L200.63,62.7 L213.65,62.7 L226.05,64.09 L234.83,66.06 L245.65,69.73 L252.87,73.27 L259.12,77.34 L262.63,80.33 L265.6,83.47 L268.01,86.76 L269.83,90.17 L271.08,93.68 L271.76,99.08 L271.04,104.64 L269.75,108.2 L267.87,111.63 L265.42,114.91 L262.44,118.01 L258.95,120.92 L255.02,123.63 L245.86,128.34 L238.06,131.22 L226.48,133.99 L213.88,135.44 L200.63,135.44 L188.04,133.99 L176.46,131.22 L168.65,128.34 L159.5,123.63 L155.55,120.92 L152.21,118.12 L152.21,145.77Z
M73.14,138.13 L104.49,138.13 L104.49,106.8 L73.14,106.8Z
M114.35,124.7 L134.96,124.7 L134.96,106.61 L114.35,106.61Z
M207.26,117.33 L210.57,117.26 L216.87,116.53 L222.66,115.15 L227.8,113.18 L233.11,110 L236.34,106.99 L238.51,103.64 L239.42,100.48 L239.42,97.67 L238.51,94.51 L236.34,91.16 L233.11,88.15 L227.8,84.97 L222.66,83 L216.87,81.62 L210.57,80.89 L203.94,80.89 L197.65,81.62 L191.86,83 L186.71,84.97 L181.41,88.15 L178.18,91.16 L176.01,94.51 L175.1,97.67 L175.1,100.48 L176.01,103.64 L178.18,106.99 L181.41,110 L186.71,113.18 L191.86,115.15 L197.65,116.53 L203.94,117.26Z
"></path>
and this path converted to individual arrays of vertices:
var lower_house_material = [{x:57.11,y:271.77},{x:57.11,y:218.33},{x:41.99,y:218.63},{x:105.49,y:165.77},{x:138.42,y:193.18},{x:138.42,y:172.2},{x:152.53,y:172.2},{x:152.53,y:204.93},{x:168.99,y:218.63},{x:153.21,y:218.63},{x:153.21,y:271.77}];
var lower_house_hole_1 = [{x:74.14,y:264.13},{x:105.49,y:264.13},{x:105.49,y:232.8},{x:74.14,y:232.8}];
var lower_house_hole_2 = [{x:115.35,y:250.7},{x:135.96,y:250.7},{x:135.96,y:232.61},{x:115.35,y:232.61}];
var upper_house_material = [{x:56.11,y:145.77},{x:56.11,y:92.33},{x:40.99,y:92.63},{x:104.49,y:39.77},{x:137.42,y:67.18},{x:137.42,y:46.2},{x:151.53,y:46.2},{x:151.53,y:78.93},{x:152.53,y:79.76},{x:155.55,y:77.23},{x:159.5,y:74.52},{x:168.65,y:69.81},{x:176.46,y:66.93},{x:188.04,y:64.16},{x:200.63,y:62.7},{x:213.65,y:62.7},{x:226.05,y:64.1},{x:234.83,y:66.06},{x:245.65,y:69.73},{x:252.87,y:73.27},{x:259.12,y:77.35},{x:262.63,y:80.33},{x:265.6,y:83.47},{x:268.01,y:86.76},{x:269.84,y:90.17},{x:271.08,y:93.68},{x:271.76,y:99.08},{x:271.04,y:104.64},{x:269.75,y:108.2},{x:267.87,y:111.63},{x:265.42,y:114.91},{x:262.44,y:118.01},{x:258.96,y:120.92},{x:255.02,y:123.63},{x:245.86,y:128.34},{x:238.06,y:131.22},{x:226.48,y:133.99},{x:213.88,y:135.45},{x:200.63,y:135.45},{x:188.04,y:133.99},{x:176.46,y:131.22},{x:168.65,y:128.34},{x:159.5,y:123.63},{x:155.55,y:120.92},{x:152.21,y:118.12},{x:152.21,y:145.77}];
var upper_house_hole_1 = [{x:73.14,y:138.13},{x:104.49,y:138.13},{x:104.49,y:106.8},{x:73.14,y:106.8}];
var upper_house_hole_2 = [{x:114.35,y:124.7},{x:134.96,y:124.7},{x:134.96,y:106.61},{x:114.35,y:106.61}];
var upper_house_hole_3 = [{x:207.26,y:117.33},{x:210.57,y:117.26},{x:216.87,y:116.53},{x:222.66,y:115.15},{x:227.8,y:113.18},{x:233.11,y:110},{x:236.34,y:106.99},{x:238.51,y:103.64},{x:239.42,y:100.48},{x:239.42,y:97.67},{x:238.51,y:94.51},{x:236.34,y:91.16},{x:233.11,y:88.15},{x:227.8,y:84.97},{x:222.66,y:83},{x:216.87,y:81.62},{x:210.57,y:80.89},{x:203.94,y:80.89},{x:197.65,y:81.62},{x:191.86,y:83},{x:186.71,y:84.97},{x:181.41,y:88.15},{x:178.18,y:91.16},{x:176.01,y:94.51},{x:175.1,y:97.67},{x:175.1,y:100.48},{x:176.01,y:103.64},{x:178.18,y:106.99},{x:181.41,y:110},{x:186.71,y:113.18},{x:191.86,y:115.15},{x:197.65,y:116.53},{x:203.94,y:117.26}];
The question is, how this like structure can be converted to 3D object in three.js so that it can be extruded using THREE.ExtrudeGeometry( shape, extrusionSettings ) and after that textured as a whole?
I can examine the path data to know what hole belongs to what polygon and handle all as separate shapes, but because I want to use one texture image across all the shapes, I think the preferred way is to handle all material-polygons as one shape, and hole-polygons as other shape and use something like:
var shape = [lower_house_material, upper_house_material];
shape.holes = [lower_house_hole_1, lower_house_hole_2, upper_house_hole_1, upper_house_hole_2, upper_house_hole_3];
var 3d_geometry = THREE.ExtrudeGeometry( shape, extrusionSettings );
So the 3d_geometry should be at the end one mesh to which I can append a texture this way:
var textureFront = new THREE.ImageUtils.loadTexture( 'textureFront.png');
var textureSide = new THREE.ImageUtils.loadTexture( 'textureSide.png');
var materialFront = new THREE.MeshBasicMaterial( { map: textureFront } );
var materialSide = new THREE.MeshBasicMaterial( { map: textureSide } );
var materialArray = [ materialFront, materialSide ];
var faceMaterial = new THREE.MeshFaceMaterial(materialArray);
var final_mesh = new THREE.Mesh(3d_geometry, faceMaterial );
And one of the textures could be something like this (256x256px):
And texture applied:
And because the mesh is extruded, there is also 3D thickness on the above, but you got the idea of texturing.
I know that y-coordinates have to be flipped but it is a trivial task and not the point of my question, but if three.js has ready-made function for clipping y, it would be helpful.
I have spent hours to examine the three.js source code, examples and documentation, but because the most frequent word there is "todo", it cannot help much. And I'm very newbie to three.js, I would think that this may be trivial task for some experienced three.js user.
UPDATE: And just to make sure, the hole polygons are always well-behaved, which means that hole polygons are always fully inside material-polygons and there are no duplicate vertices or self-intersections either in material-polygons or hole-polygons and all material-polygons have CW winding order and holes CCW.
UPDATE: Merging geometries was not a solution for texturing the whole extruded polygon set by one texture: http://jsfiddle.net/C5dga. The texture is repeated on all individual shapes, so merging geometries in this case has no real meaning. The solution could be possibly found on merging shapes before they are extruded, but not found solution for this yet.
You can merge geometries as in the following snippet, resulting in just a single mesh. From your prior questions, you already know how to texture a single geometry.
var geometry1 = new THREE.ExtrudeGeometry( shape1, extrusionSettings );
var geometry2 = new THREE.ExtrudeGeometry( shape2, extrusionSettings );
geometry1.merge( geometry2 );
. . .
var mesh = new THREE.Mesh( geometry1, material );
scene.add( mesh );
Fiddle: http://jsfiddle.net/pHn2B/88/
Fiddle: http://jsfiddle.net/C5dga/13/ (with texture)
EDIT: As an alternative to creating separate geometries and using the merge utility, you can create a single geometry using the following pattern, instead:
var geometry1 = new THREE.ExtrudeGeometry( [ shape1, shape2 ], extrusionSettings );
EDIT: updated to three.js r.70

Error in Pyramid mean shift filtering of image of certain dimensions?

I'm trying to run the mean shift segmentation using pyramids as explained in the Learning OpenCV book on some images. Both source and destination images are 8-bit, three-channel color images of the same width and height as mentioned.
However correct output is obtained only on a 1600x1200 or 1024x768 images. Other images of sizes 625x391 and 644x438 are causing a runtime error
"Sizes of input arguments do not match in function cvPyrUp()"
My code is this:
IplImage *filtered = cvCreateImage(cvGetSize(img),img->depth,img->nChannels);
cvPyrMeanShiftFiltering( img, filtered, 20, 40, 1);
The program uses the parameters as given in the sample. I've tried decreasing values thinking it to be an image dimensions problem, but no luck.
By resizing image dimensions to 644x392 and 640x320 the mean-shift is running properly. I've read that "pyramid segmentation requires images that are N-times divisible by 2, where N is the number of pyramid layers to be computed" but how is that applicable here?
Any suggestions please.
Well you have anything wring except that when you apply cvPyrMeanShiftFiltering
you should do it like this:
//A suggestion to avoid the runtime error
IplImage *filtered = cvCreateImage(cvGetSize(img),img->depth,img->nChannels);
cvCopy(img,filtered,NULL);
//Values only you should know
int level = kLevel;
int spatial_radius = kSpatial_Radius;
int color_radius = = kColor_Radius;
//Here comes the thing
filtered->width &= -(1<<level);
filtered->height &= -(1<<level);
//Now you are free to do your thing
cvPyrMeanSihftFiltering(filtered, filtered,spatial_radius,color_radius,level);
The thing is that this kind of pyramidal filter modifies som things acording the level you use. Try this and tell me later if worked.
Hope i can help.

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