working with Matplotlib I have produced some resistivity cross sections of the soil, obtaining pictures like this:
Now I would like to display all those sections in 3D so as to visualise better the spatial distribution of resistivity in the field (i.e. a so-called fence diagram). I would also like to plot the 2D map of the site where those measurements were carried out at the base of my plot (say on the XY plane).
As far as I have seen this is not feasible (or at least not convenient) with Matplotlib in 3D hence I decided to switch to Mayavi.
My questions are:
is it feasible georeferenced rasters and then properly place them on the correct (vertical) planes (not necessarily parallel to the cartesian ones) with Mayavi? Does imshow() serves this purpose?
is it better to recreate the contours in Mayavi at the proper locations? If this is the case I did not find a function to create contours from unstructured data (the input images were created with tricontour/tricontourf in Matplotlib). I do not think interpolating over a structured grid in scipy would do, given the non convex domain.
Ok, answering my own question:
mesh = mlab.triangular_mesh
surf = mlab.pipeline.surface(mesh)
seems to do the job.
To be consistent with the previous work, the triangulation, duly masked, can be directly imported from Matplotlib.
Related
The shape and positions of all the polygons are known beforehand. The polygons are not overlapping and will be of different colors and shapes, and there could be quite many of them. The polygons are defined in floating point based coordinates and will be painted on top of a JPEG photo as annotation.
How could I create the resulting image file as fast as possible after I get to know which color I should give each polygon?
If it would save time I would like to perform as much as possible of the computations beforehand. All information regarding geometry and positions of the polygons are known in advance. The JPEG photo is also known in advance. The only information not known beforehand is the color of each polygon.
The JPEG photo has a size of 250x250 pixels, so that would also be the image size of the resulting rasterised image.
The computations will be done on a Linux computer with a standard graphics card, so OpenGL might be a viable option. I know there are also rasterisation libraries like Cairo that could be used to paint polygons. What I wonder is if I could take advantage of the fact that I know so much of the input in advance and use that to speed up the computation. The only thing missing is the color of each polygon.
Preferably I would like to find a solution that would only precompute things in the form of data files. In other words as soon as the polygon colors are known, the algorithm would load the other information from datafiles (JPEG file, polygon geometry file and/or possibly precomputed datafiles). Of course it would be faster to start the computation out with a "warm" state ready in the GPU/CPU/RAM but I'd like to avoid that. The choice of programming language is not so import, but could for instance be C++.
To give some more background information: The JavaScript library OpenSeadragon that is running in a web browser requests image tiles from a web server. The idea is that measurement points (i.e. the polygons) could be plotted on-the-fly on to pregenerated Zooming Images (DZI format) by the web server. So for one image tile the algorithm would only need to be run one time. The aim is low latency.
For my bachelor thesis I need to analyse images taken in the ocean to count and measure the size of water particles.
my problem:
besides the wanted water particles, the images show hexagonal patches all over the image in:
- different sizes
- not regular shape
- different greyscale values
(Example image below!)
It is clear that these patches will falsify my image analysis concerning the size and number of particles.
For this reason this patches need to be detected and deleted somehow.
Since it will be just a little part of the work in my thesis, I don't want to spend much time in it and already tried classic ways like: (imageJ)
playing with the threshold (resulting in also deleting wanted water particles)
analyse image including the hexagonal patches and later sort out the biggest areas (the hexagonal patches have quite the biggest areas, but you will still have a lot of haxagons)
playing with filters: using gaussian filter on a duplicated image and subtract the copy from the original deletes many patches (in reducing the greyscale value) but also deletes little wanted water particles and so again falsifies the result
a more complicated and time consuming solution would be to use a implemented library in for example matlab or opencv to detect points, that describe the shapes.
but so far I could not find any code that fits my task.
Does anyone of you have created such a code I could use for my task or any other idea?
You can see a lot of hexagonal patches in different depths also.
the little spots with an greater pixel value are the wanted particles!
Image processing is quite an involved area so there are no hard and fast rules.
But if it was me I would 'Mask' the image. This involves either defining what you want to keep or remove as a pixel 'Mask'. You then scan the mask over the image recursively and compare the mask to the image portion selected. You then select or remove the section (depending on your method) if it meets your criterion.
One such example of a criteria would be the spatial and grey-scale error weighted against a likelihood function (eg Chi-squared, square mean error etc.) or a Normal distribution that you define the uncertainty..
Some food for thought
Maybe you can try with the Hough transform:
https://en.wikipedia.org/wiki/Hough_transform
Matlab have an built-in function, hough, wich implements this, but only works for lines. Maybe you can start from that and change it to recognize hexagons.
I have been working a self project in image processing and robotics where instead robot as usual detecting colors and picking out the object, it tries to detect the holes(resembling different polygons) on the board. For a better understanding of the setup here is an image:
As you can see I have to detect these holes, find out their shapes and then use the robot to fit the object into the holes. I am using a kinect depth camera to get the depth image. The pic is shown below:
I was lost in thought of how to detect the holes with the camera, initially using masking to remove the background portion and some of the foreground portion based on the depth measurement,but this did not work out as, at different orientations of the camera the holes would merge with the board... something like inranging (it fully becomes white). Then I came across adaptiveThreshold function
adaptiveThreshold(depth1,depth3,255,ADAPTIVE_THRESH_GAUSSIAN_C,THRESH_BINARY,7,-1.0);
With noise removal using erode, dilate, and gaussian blur; which detected the holes in a better manner as shown in the picture below. Then I used the cvCanny edge detector to get the edges but so far it has not been good as shown in the picture below.After this I tried out various feature detectors from SIFT, SURF, ORB, GoodFeaturesToTrack and found out that ORB gave the best times and the features detected. After this I tried to get the relative camera pose of a query image by finding its keypoints and matching those keypoints for good matches to be given to the findHomography function. The results are as shown below as in the diagram:
In the end i want to get the relative camera pose between the two images and move the robot to that position using the rotational and translational vectors got from the solvePnP function.
So is there any other method by which I could improve the quality of the
holes detected for the keypoints detection and matching?
I had also tried contour detection and approxPolyDP but the approximated shapes are not really good:
I have tried tweaking the input parameters for the threshold and canny functions but
this is the best I can get
Also ,is my approach to get the camera pose correct?
UPDATE : No matter what I tried I could not get good repeatable features to map. Then I read online that a depth image is cheap in resolution and its only used for stuff like masking and getting the distances. So , it hit me that the features are not proper because of the low resolution image with its messy edges. So I thought of detecting features on a RGB image and using the depth image to get only the distances of those features. The quality of features I got were literally off the charts.It even detected the screws on the board!! Here are the keypoints detected using GoodFeaturesToTrack keypoint detection..
I met an another hurdle while getting the distancewith the distances of the points not coming out properly. I searched for possible causes and it occured to me after quite a while that there was a offset in the RGB and depth images because of the offset between the cameras.You can see this from the first two images. I then searched the net on how to compensate this offset but could not find a working solution.
If anyone one of you could help me in compensate the offset,it would be great!
UPDATE: I could not make good use of the goodFeaturesToTrack function. The function gives the corners in Point2f type .If you want to compute the descriptors we need the keypoints and converting Point2f to Keypoint with the code snippet below leads to the loss of scale and rotational invariance.
for( size_t i = 0; i < corners1.size(); i++ )
{
keypoints_1.push_back(KeyPoint(corners1[i], 1.f));
}
The hideous result from the feature matching is shown below .
I have to start on different feature matchings now.I'll post further updates. It would be really helpful if anyone could help in removing the offset problem.
Compensating the difference between image output and the world coordinates:
You should use good old camera calibration approach for calibrating the camera response and possibly generating a correction matrix for the camera output (in order to convert them into real scales).
It's not that complicated once you have printed out a checkerboard template and capture various shots. (For this application you don't need to worry about rotation invariance. Just calibrate the world view with the image array.)
You can find more information here: http://www.vision.caltech.edu/bouguetj/calib_doc/htmls/own_calib.html
--
Now since I can't seem to comment on the question, I'd like to ask if your specific application requires the machine to "find out" the shape of the hole on the fly. If there are finite amount of hole shapes, you may then model them mathematically and look for the pixels that support the predefined models on the B/W edge image.
Such as (x)^2+(y)^2-r^2=0 for a circle with radius r, whereas x and y are the pixel coordinates.
That being said, I believe more clarification is needed regarding the requirements of the application (shape detection).
If you're going to detect specific shapes such as the ones in your provided image, then you're better off using a classifer. Delve into Haar classifiers, or better still, look into Bag of Words.
Using BoW, you'll need to train a bunch of datasets, consisting of positive and negative samples. Positive samples will contain N unique samples of each shape you want to detect. It's better if N would be > 10, best if >100 and highly variant and unique, for good robust classifier training.
Negative samples would (obviously), contain stuff that do not represent your shapes in any way. It's just for checking the accuracy of the classifier.
Also, once you have your classifier trained, you could distribute your classifier data (say, suppose you use SVM).
Here are some links to get you started with Bag of Words:
https://gilscvblog.wordpress.com/2013/08/23/bag-of-words-models-for-visual-categorization/
Sample code:
http://answers.opencv.org/question/43237/pyopencv_from-and-pyopencv_to-for-keypoint-class/
I have a target image to be searched for a curve along its edges and a template image that contains the curve. What I need to achieve is to find the best match of the curve in the template image within the target image, and based on the score, to find out whether there is a match or not. That also includes rotation and resizing of the curve. The target image can be the output of a Canny Edge detector if that makes things easier.
I am considering to use OpenCV (by using Python or Processing/Java or if those have limited access to the required functions then by using C) to make things practical and efficient, however could not find out if I can use any functions (or a combination of them) in OpenCV that are useable for doing this job. I have been reading through the OpenCV documentation and thought at first that Contours could do this job, however all the examples show closed shapes as opposed to my case where I need to match a open curve to a part of an edge.
So is there a way to do this either by using OpenCV or with any known code or algorithm that you would suggest?
Here are some images to illustrate the problem:
My first thought was Generalized Hough Transform. However I don't know any good implementation for that.
I would try SIFT or SURF first on the canny edge image. It usually is used to find 2d areas, not 1d contours, but if you take the minimum bounding box around your contour and use that as the search pattern, it should work.
OpenCV has an implementation for that:
Features2D + Homography to find a known object
A problem may be getting a good edge image, those black shapes in the back could be distracting.
Also see this Stackoverflow answer:
Image Processing: Algorithm Improvement for 'Coca-Cola Can' Recognition
My aim is to detect the vein pattern in leaves which characterize various species of plants
I have already done the following:
Original image:
After Adaptive thresholding:
However the veins aren't that clear and get distorted , Is there any way i could get a better output
EDIT:
I tried color thresholding my results are still unsatisfactory i get the following image
Please help
The fact that its a JPEG image is going to give the "block" artifacts, which in the example you posted causes most square areas around the veins to have lots of noise, so ideally work on an image that's not been through lossy compression. If that's not possible then try filtering the image to remove some of the noise.
The veins you are wanting to extract have a different colour from the background, leaf and shadow so some sort of colour based threshold might be a good idea. There was a recent S.O. question with some code that might help here.
After that some sort of adaptive normalisation would help increase the contrast before you threshold it.
[edit]
Maybe thresholding isn't an intermediate step that you want to do. I made the following by filtering to remove jpeg artifacts, doing some CMYK channel math (more cyan and black) then applying adaptive equalisation. I'm pretty sure you could then go on to produce (subpixel maybe) edge points using image gradients and non-maxima supression, and maybe use the brightness at each point and the properties of the vein structure (mostly joining at a tangent) to join the points into lines.
In the past I made good experiences with the Edge detecting algorithm difference of Gaussian. Which basically works like this:
You blur the image twice with the gaussian blurr algorithm but with differenct blur radii.
Then you calculate the difference between both images.
Pixel with same color beneath each other will creating a same blured color.
Pixel with different colors beneath each other wil reate a gradient which is depending on the blur radius. For bigger radius the gradient will stretch more far. For smaller ones it wont.
So basically this is bandpass filter. If the selected radii are to small a vain vill create 2 "parallel" lines. But since the veins of leaves are small compared with the extends of the Image you mostly find radii, where a vein results in 1 line.
Here I added th processed picture.
Steps I did on this picture:
desaturate (grayscaled)
difference of Gaussian. Here I blured the first Image with a radius of 10px and the second image with a radius of 2px. The result you can see below.
This is only a quickly created result. I would guess that by optimizing the parametes, you can even get better ones.
This sounds like something I did back in college with neural networks. The neural network stuff is a bit hard so I won't go there. Anyways, patterns are perfect candidates for the 2D Fourier transform! Here is a possible scheme:
You have training data and input data
Your data is represented as a the 2D Fourier transform
If your database is large you should run PCA on the transform results to convert a 2D spectrogram to a 1D spectrogram
Compare the hamming distance by testing the spectrum (after PCA) of 1 image with all of the images in your dataset.
You should expect ~70% recognition with such primitive methods as long as the images are of approximately the same rotation. If the images are not of the same rotation.you may have to use SIFT. To get better recognition you will need more intelligent training sets such as a Hidden Markov Model or a neural net. The truth is to getting good results for this kind of problem may be quite a lot of work.
Check out: https://theiszm.wordpress.com/2010/07/20/7-properties-of-the-2d-fourier-transform/