I have 2 medical image datasets for a given patient, each acquired at the same time, each with a different modality. The frame of reference or coordinate space is different for each dataset (and I don't know the origins). One dataset has smaller physical dimensions than the other, the voxel sizes, as well as the number of frames are also different. I want to resample and register the images, does it matter which I do first?
It's better if you resize the images first. This is because image registration algorithms will try to find a transformation that optimizes the match of the images. If you know the proper size of the images, it will be easier for the algorithms to find such transformation.
Related
There was a gif on the internet where someone used some sort of CAD and drew multiple vector pictures in it. On the first frame they zoom-in on a tiny dot, revealing there a whole new different vector picture just on a different scale, and then they proceed to zoom-in further on another tiny dot, revealing another detailed picture, repeating several times. here is the link to the gif
Or another similar example: imagine you have a time-series with a granularity of a millisecond per sample and you zoom out to reveal years-worth of data.
My questions are: how such a fine-detailed data, in the end, gets rendered, when a huge amount of data ends up getting aliased into a single pixel.
Do you have to go through the whole dataset to render that pixel (i.e. in case of time-series: go through million records to just average them out into 1 line or in case of CAD render whole vector picture and blur it into tiny dot), or there are certain level-of-detail optimizations that can be applied so that you don't have to do this?
If so, how do they work and where one can learn about it?
This is a very well known problem in games development. In the following I am assuming you are using a scene graph, a node-based tree of objects.
Typical solutions involve a mix of these techniques:
Level Of Detail (LOD): multiple resolutions of the same model, which are shown or hidden so that only one is "visible" at any time. When to hide and show is usually determined by the distance between camera and object, but you could also include the scale of the object as a factor. Modern 3d/CAD software will sometimes offer you automatic "simplification" of models, which can be used as the low res LOD models.
At the lowest level, you could even just use the object's bounding
box. Checking whether a bounding box is in view is only around 1-7 point checks depending on how you check. And you can utilise object parenting for transitive bounding boxes.
Clipping: if a polygon is not rendered in the view port at all, no need to render it. In the GIF you posted, when the camera zooms in on a new scene, what is left from the larger model is a single polygon in the background.
Re-scaling of world coordinates: as you zoom in, the coordinates for vertices become sub-zero floating point numbers. Given you want all coordinates as precise as possible and given modern CPUs can only handle floats with 64 bits precision (and often use only 32 for better performance), it's a good idea to reset the scaling of the visible objects. What I mean by that is that as your camera zooms in to say 1/1000 of the previous view, you can scale up the bigger objects by a factor of 1000, and at the same time adjust the camera position and focal length. Any newly attached small model would use its original scale, thus preserving its precision.
This transition would be invisible to the viewer, but allows you to stay within well-defined 3d coordinates while being able to zoom in infinitely.
On a higher level: As you zoom into something and the camera gets closer to an object, it appears as if the world grows bigger relative to the view. While normally the camera space is moving and the world gets multiplied by the camera's matrix, the same effect can be achieved by changing the world coordinates instead of the camera.
First, you can use caching. With tiles, like it's done in cartography. You'll still need to go over all the points, but after that you'll be able zoom-in/zoom-out quite rapidly.
But if you don't have extra memory for cache (not so much actually, much less than the data itself), or don't have time to go over all the points you can use probabilistic approach.
It can be as simple as peeking only every other point (or every 10th point or whatever suits you). It yields decent results for some data. Again in cartography it works quite well for shorelines, but not so well for houses or administrative boarders - anything with a lot of straight lines.
Or you can take a more hardcore probabilistic approach: randomly peek some points, and if, for example, there're 100 data points that hit pixel one and only 50 hit pixel two, then you can more or less safely assume that if you'll continue to peek points still pixel one will be twice as likely to be hit that pixel two. So you can just give up and draw pixel one with a twice more heavy color.
Also consider how much data you can and want to put in a pixel. If you'll draw a pixel in black and white, then there're only 256 variants of color. And you don't need to be more precise. Or if you're going to draw a pixel in full color then you still need to ask yourself: will anyone notice the difference between something like rgb(123,12,54) and rgb(123,11,54)?
I am new to the field of medical imaging - and trying to solve this (potentially basic problem). For a machine learning purpose, I am trying to standardize and normalize a library of DICOM images, to ensure that all images have the same rotation and are at the same scale (e.g. in mm). I have been playing around with the Mango viewer, and understand that one can create transformation matrices that might be helpful in this regard. I have however the following basic questions:
I would have thought that a scaling of the image would have changed the pixel spacing in the image header. Does this tag not provide the distance between pixels, and should this not change as a result of scaling?
What is the easiest way to standardize a library of images (ideally in python)? Is it possible and should one extract a mean pixel spacing across all images, and then scaling all images to match that mean? or is there a smarter way to ensure consistency in scaling and rotation?
Many thanks in advance, W
Does this tag not provide the distance between pixels, and should this
not change as a result of scaling?
Think of the image voxels as fixed units of space, which are sampling your image. When you apply your transform, you are translating/rotating/scaling your image around within these fixed units of space. That is, the size and shape of the voxels doesn't change. They just sample different parts of your image.
You can resample your image by making your voxels bigger or smaller or changing their shape (pixel spacing), but this can be independent of the transform you are applying to the image.
What is the easiest way to standardize a library of images (ideally in
python)?
One option is FSL-FLIRT, although it only accepts data in NIFTI format, so you'd have to convert your DICOMs to NIFTI. There is also this Python interface to FSL.
Is it possible and should one extract a mean pixel spacing across all
images, and then scaling all images to match that mean? or is there a
smarter way to ensure consistency in scaling and rotation?
I think you'd just to have pick a reference image to register all your other images too. There's no right answer: picking the highest resolution image/voxel dimensions or an average or some resampling into some other set of dimensions all sound reasonable.
I am trying to enlarge a point cloud data set. Suppose I have a point cloud data set consisting of 100 points & I want to enlarge it to say 5 times. Actually I am studying some specific structure which is very small, so I want to zoom in & do some computations. I want something like imresize() in Matlab.
Is there any function to do this? What does resize() function do in PCL? Any idea about how can I do it?
Why would you need this? Points are just numbers, regardless whether they are 1 or 100, until all of them are on the same scale and in the same coordinate system. Their size on the screen is just a visual representation, you can zoom in and out as you wish.
You want them to be a thousandth of their original value (eg. millimeters -> meters change)? Divide them by 1000.
You want them spread out in a 5 times larger space in that particular coordinate system? Multiply their coordinates with 5. But even so, their visual representations will look exactly the same on the screen. The data remains basically the same, they will not be resized per se, they numeric representation will change a bit. It is the simplest affine transform, just a single multiplication.
You want to have finer or coarser resolution of your numeric representation? Or have different range? Change your data type accordingly.
That is, if you deal with a single set.
If you deal with different sets, say, recorded with different kinds of sensors and the numeric representations differ a bit (there are angles between the coordinate systems, mm vs cm scale, etc.) you just have to find the transformation from one coordinate system to the other one and apply it to the first one.
Since you want to increase the number of points while preserving shape/structure of the cloud, I think you want to do something like 'upsampling'.
Here is another SO question on this.
The PCL offers a class for bilateral upsampling.
And as always google gives you a lot of hints on this topic.
Beside (what Ziker mentioned) increasing allocated memory (that's not what you want, right?) or zooming in in visualization you could just rescale your point cloud.
This can be done by multiplying each points dimensions with a constant factor or using an affine transformation. So you can e.g switch from mm to m.
If i understand your question correctly
If you have defined your cloud like this
pcl::PointCloud<pcl::PointXYZ>::Ptr cloud (new pcl::PointCloud<pcl::PointXYZ>);
in fact you can do resize
cloud->points.resize (cloud->width * cloud->height);
Note that doing resize does nothing more than allocate more memory for variable thus after resizing original data remain in cloud. So if you want to have empty resized cloud dont forget to add cloud->clear();
If you just want zoom some pcd for visual puposes(i.e you cant see what is shape of cloud because its too small) why dont you use PCL Visualization and zoom by scrolling up/down
I'm not sure this is the right place but here I go:
I have a database of 300 picture in high-resolution. I want to compute the PCA on this database and so far here is what I do: - reshape every image as a single column vector - create a matrix of all my data (500x300) - compute the average column and substract it to my matrix, this gives me X - compute the correlation C = X'X (300x300) - find the eigenvectors V and Eigen Values D of C. - the PCA matrix is given by XV*D^-1/2, where each column is a Principal Component
This is great and gives me correct component.
Now what I'm doing is doing the same PCA on the same database, except that the images have a lower resolution.
Here are my results, low-res on the left and high-res on the right. Has you can see most of them are similar but SOME images are not the same (the ones I circled)
Is there any way to explain this? I need for my algorithm to have the same images, but one set in high-res and the other one in low-res, how can I make this happen?
thanks
It is very possible that the filter you used could have done a thing or two to some of the components. After all, lower resolution images don't contain higher frequencies that, too, contribute to which components you're going to get. If component weights (lambdas) at those images are small, there's also a good possibility of errors.
I'm guessing your component images are sorted by weight. If they are, I would try to use a different pre-downsampling filter and see if it gives different results (essentially obtain lower resolution images by different means). It is possible that the components that come out differently have lots of frequency content in the transition band of that filter. It looks like images circled with red are nearly perfect inversions of each other. Filters can cause such things.
If your images are not sorted by weight, I wouldn't be surprised if the ones you circled have very little weight and that could simply be a computational precision error or something of that sort. In any case, we would probably need a little more information about how you downsample, how you sort the images before displaying them. Also, I wouldn't expect all images to be extremely similar because you're essentially getting rid of quite a few frequency components. I'm pretty sure it wouldn't have anything to do with the fact that you're stretching out images into vectors to compute PCA, but try to stretch them out in a different direction (take columns instead of rows or vice versa) and try that. If it changes the result, then perhaps you might want to try to perform PCA somewhat differently, not sure how.
I have a 3D floating-point matrix, in worst-case scenario the size could be (200000x1000000x100), I want to visualize this matrix using Qt/OpenGL.
Since the number of elements is extremely high, I want to render them in a way that when the camera is far away from the matrix, I just show a number of interesting points that gives an approximation of how the matrix look like. When the camera gets closer, I want to get more details and hence more elements are calculated.
I would like to know if there are techniques that deals with this kind of visualization.
The general idea is called level-of-detail rendering and is a whole science in itself.
For your domain i would recommend two steps:
1) Reduce the number of cells by averaging (arithmetic-mean function) them in cubes of different sizes and caching those cubes (on disk as well as RAM). "Different" means here, that you have the same data in multiple sizes of cubes, e.g. coarse-grained cubes of 10000x10000x10000 and finer cubes of 100x100x100 cells resulting in multiple levels-of-detail. You have to organize these in a hierarchical structure (the larger ones containing multiple smaller ones) and for this i would recommend an Octree:
http://en.wikipedia.org/wiki/Octree
2) The second step is to actually render parts of this Octree:
To do this use the distance of your camera-point to the sub-cubes. Go through the cubes and decide to either enter the sub-cube or render the larger cube by using this distance-function and heuristically chosen or guessed threshold-values.
(2) can be further optimized but this is optional: To optimize this rendering organize the to-be-rendered cube's into layers: The direction of the layers (whether it is in x, y, or z-slices) depends on your camera-viewpoint to which it should be near-perpendicular. Then render each slice into a texture and voila you only have to render a single quad with that texture for each slice, 1000 quads are no problem to render.
Qt has some way of rendering huge number of elements efficiently. Check the examples/demo that is part of QT.