I started with the vol3d function from MATLAB file exchange for the 3D display part but its slowing down the entire application.
I am working on a MATLAB based GUI. Need to display a volume of size 512X512X512, single precision. The display has 4 different views of the volume. 3 standard orthogonal views and the 4th view is the 3D rendered isometric view.
With vol3D, The display is looking fine but its causing the GUI little lagging and slow. If I remove the vol3d function, the GUI works fine, faster.
I am new in the field of 3D volume rendering. What are the alternatives to this volume rendering in MATLAB. Is there any way to call some C-subroutine using mex, do the calculation in C and display in MATLAB. I have a good GPU(GeForce gtx titan x, 12 gb) but I am afraid I am not utilizing it well for the volume rendering thing.
Any suggestions are welcome.
thanx for reading :)
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I'm trying to figure out a good way to programmatically generate contours describing a 2D surface, from a 3D STEP model. Application is generating NC code for a laser-cutting program from a 3D model.
Note: it's easy enough to do this in a wide variety of CAD systems. I am writing software that needs to do it automatically.
For example, this (a STEP model):
Needs to become this (a vector file, like an SVG or a DXF):
Perhaps the most obvious way of tackling the problem is to parse the STEP model and run some kind of algorithm to detect planes and select the largest as the cut surface, then generate the contour. Not a simple task!
I've also considered using a pre-existing SDK to render the model using an orthographic camera, capture a high-res image, and then operating on it to generate the appropriate contours. This method would work, but it will be CPU-heavy, and its accuracy will be limited to the pixel resolution of the rendered image - not ideal.
This is perhaps a long shot, but does anyone have thoughts about this? Cheers!
I would use a CAD library to load the STEP file (not a CAD API), look for the planar face with the higher number of edge curves in the face loop and transpose them on the XY plane. Afterward, finding 2D geometry min/max for centering etc. would be pretty easy.
Depending on the programming language you are using I would search for "CAD control" or "CAD component" on Google combining it with "STEP import".
I am trying to register two volumetric images from brain (PET and CT or even PET and MR). Each of these volumetric images contains different numbers of 2D images (slices).
For example, CT has 150 slices and PET has 100 slices. I was thinking of using an interpolation method to calculate and reduce the number of CT slices to 100. Is this a correct approach? Does anyone know of any resources that could be helpful for me? like a pseudo code, or steps that I should go through for registering two volumetric images.
Thank you :)
If you know the spacing information for the 150 CT slices and the 100 PET slices, you can look into MATLAB's interp1 function for interpolating along one axis to rescale the images to the same number of pixels. From here it might be possible to use MATLAB's imregister to perform registration.
If you are looking to learn how registration works under the hood (transforming between pixel and physical coordinates, transforming/resampling images, etc.), one resource I can direct you to is the ITK Software Guide pdf.
In particular, try reading Book 1 Section 4.1.4 (page 41 of the pdf) on image representation, and Book 2 Section 3.9 (page 532 of the pdf) on transforms.
In general, the problem of transforming and interpolating with 3D images in registration can be pretty cumbersome to write code for. You need to ask yourself about the spacing and orientation of pixels, how to transform and interpolate images so that their grids overlap, and you also need to decide what to do with pixels in your grid that lie outside the image boundary when evaluating the similarity metric.
While it's up to you to do what you think is best, I suggest you use existing registration programs if they are capable of doing what you want:
MATLAB's imregister (I have never used it so I can't comment on it)
simpleITK for Python
the ITK for C++ has a learning curve but gives full control over the registration process
elastix is a command line program that uses a text file of parameters to perform registration.
3D slicer has a graphical user interface for simple linear registration
I use matlab to render a complex mesh (using trimesh, material, camlight, view...) and need not display it to the user, just to get the rendered image. This is discussed in another question.
Using any of the suggested solutions (save-as image, saving into a video object, and using undocumented hardcopy) is very slow (~1sec), especially compared to rendering the plot itself, including painting on the screen takes less than 0.5sec.
I believe it is caused by hardcopy method not to utilize the GPU, while rendering the original plot for display do use the GPU; using GPU-Z monitor software I see the GPU working during ploting but not during hardcopy.
The figure use 'opengl' as renderer, but hardcopy, which is the underlying implementation of all the suggested methods, don't seem to respect this...
Any suggestion on how to configure it to use the GPU?
EDITED: following this thread I've moved to use the following, but GPU usage is still a flatliner.
cdata=hardcopy(f, '-Dopengl', '-r0')
Being used to Matlab and its great capabilities of drawing vector graphics, I am looking for something similar in OpenCV. OpenCV drawing functions seem to raster the lines or points at pixel level. Currently, I am dumping the data into text, copy-paste to Matlab and doing all the plots. I also thought about using Matlab engine to pass it the parameters and running plots, but it seems to be too much mess for simple debug operation.
I want to be able to do the following:
Zoom in, out of the image
Draw a line/point which is re-rastered each time I do zoom, like in Matlab.
Currently, I found image watch plugin to take care of zooming, but it does not help with the second part.
Any idea?
OpenCV has a lot of capabilities to process an image but only minimal ones for displaying the result. It has nothing that can display vector graphics like Matlab. When I need to see polygons on image (or just polygons) I am dumping them to file and using third party viewer (usually Giv viewer).
I have two images of yeast plates:
Permissive:
Xgal:
The to images should be in the same spot and roughly the same size. I am trying to use one of the images to generate a grid and then apply that grid to the other image. The grid is made by looking at the colonies on permissive plate, the plate should have 1536 colonies on it. The problem is that the camera that was used to take the images moves a bit up and down and the images can also be shifted slightly due to the other plate not being in exactly the same place.
This then means that when I use the permissive plate to generate the grid on the xgal plate the grid shifts. Does anyone know a way in which I can compensate for this? I am using perl with the gd module. Any advice would be greatly appreciated. Thank you
I've done this in other languages in relation to motion analysis. You can mathematically determine the shift in position between two images using cross correlation.
Fortunately, you may not need to actually do the maths :) You could use something like ImageMagick, which provides a lot of image processing functions for you, and is perl scriptable. Independently scripts already exists for tasks very much like yours -- see.
If you have only a few pairs of images and, as in the examples, they are very different in appearance then an alternative method to Tim Barrass' would be
Open the first image in gimp, find the co-ordinates of a landmark feature
Open the second image in gimp, find the co-ordinates of the same landmark
Calculate the offset
Shift the second image using ImageMagick's convert command with the affine option. Set the parameters sx=sy=1.0, rx=ry=0.0, tx= negative horizontal offset, ty= negative vertical offset