I've got a micrograph showing a number of grains that have a rather clear boundary. I've used OpenCV-Python to detect these boundaries (with a Canny filter), and I think it was rather successful in its attempt, see figure. I would like to identify and mark the individual regions bounded by the detected edges, and then get the area (number of pixels) contained those regions. My apologies if the question was asked (and answered) before, but I could not find any satisfying answers yet.
Thanks in advance
Original image
Original image overlain by the detected edges
If the grain makes no difference in the color (maybe on the raw data rather than a compressed format), you may wanna use the Becke line to distinguish inside and outside. The borders of your grain appear dark on the inside and white on the outside. But this depends also on the focus of the microscope. See here.
In the case that your grains do not enclose totally a background spot you can use a point in polygon approach.
Related
I have the following JPG image. If I want to find the edges where the white page meets the black background. So I can rotate the contents a few degrees clockwise. My aim is to straighten the text for using with Tesseract OCR conversion. I don't see the need to rotate the text blocks as I have seen in similar examples.
In the docs Canny Edge Detection the third arg 200 eg edges = cv.Canny(img,100,200) is maxVal and said to be 'sure to be edges'. Is there anyway to determine these (max/min) values ahead of any trial & error approach?
I have used code examples which utilize the Python cv2 module. But the edge detection is set up for simpler applications.
Is there any approach I can use to take the text out of the equation. For example: only detecting edge lines greater than a specified length?
Any suggestions would be appreciated.
Below is an example of edge detection (above image same min/max values) The outer edge of the page is clearly defined. The image is high contrast b/w. It has even lighting. I can't see a need for the use of an adaptive threshold. Simple global is working. Its just at what ratio to use it.
I don't have the answer to this yet. But to add. I now have the contours of the above doc.
I used find contours tutorial with some customization of the file loading. Note: removing words gives a thinner/cleaner outline.
Consider Otsu.
Its chief virtue is that it is adaptive to local
illumination within the image.
In your case, blank margins might be the saving grace.
Consider working on a series of 2x reduced resolution images,
where new pixel is min() (or even max()!) of original four pixels.
These reduced images might help you to focus on the features
that matter for your use case.
The usual way to deskew scanned text is to binarize and
then keep changing theta until "sum of pixels across raster"
is zero, or small. In particular, with few descenders
and decent inter-line spacing, we will see "lots" of pixels
on each line of text and "near zero" between text lines,
when theta matches the original printing orientation.
Which lets us recover (1.) pixels per line, and (2.) inter-line spacing, assuming we've found a near-optimal theta.
In your particular case, focusing on the ... leader dots
seems a promising approach to finding the globally optimal
deskew correction angle. Discarding large rectangles of
pixels in the left and right regions of the image could
actually reduce noise and enhance the accuracy of
such an approach.
I always wanted to have a device that, from a live camera feed, could detect an object, create a 3D model of it, and then identify it. It would work a lot like the Scanner tool from Subnautica. Imagine my surprise when I found OpenCV, a free-to-use computer vision tool for Python!
My first step is to get the computer to recognize that there is an object at the center of the camera feed. To do this, I found a Canny() function that could detect edges and display them as white lines in a black image, which should make a complete outline of the object in the center. I also used the floodFill() function to fill in the black zone between the white lines with gray, which would show that the computer recognizes that there is an object there. My attempt is in the following image.
The red dot is the center of the live video.
The issue is that the edge lines can have holes in them due to a blur between two colors, which can range from individual pixels to entire missing lines. As a result, the gray gets out and doesn't highlight me as the only object, and instead highlights the entire wall as well. Is there a way to fill those missing pixels in or is there a better way of doing this?
Welcome to SO and the exiting world of machine vision !
What you are describing is a very classical problem in the field, and not a trivial one at all. It depends heavily on the shape and appearance of what you define as the object of interest and the overall structure, homogeneity and color of the background. Remember, the computer has no concept of what an "object" is, the only thing it 'knows' is a matrix of numbers.
In your example, you might start out with selecting the background area by color (or hue, look up HSV). Everything else is your object. This is what classical greenscreening techniques do, and it only works with (a) a homogenous background, which does not share a color with your object and (b) a single or multiple not overlapping objects.
The problem with your edge based approach is that you won't get a closed edge safely, and deciding where the inside and outside of the object is might get tricky.
Advanced ways to do this would get you into Neural Network territory, but maybe try to get the basics down first.
Here are two links to tutorials on converting color spaces and extracting contours:
https://docs.opencv.org/4.x/df/d9d/tutorial_py_colorspaces.html
https://docs.opencv.org/3.4/d4/d73/tutorial_py_contours_begin.html
If you got that figured out, look into stereo vision or 3D imaging in general, and that subnautica scanner might just become reality some day ;)
Good luck !
I'd like to ask if there's a better or faster alternative way to get the largest rectangle inside an almost rectangular contour.
The rectangle should be aligned to both x and y axis and should be completely inside the rectangular contour. That means it would not contain any external white pixels, yet occupy the largest area in the contour.
Test image is here:
I've tried these two but I'm looking if there's a faster and neater way to go around this.
I also tried going through the points of a contour and getting the minimum and maximum points like in here but of course, it just shows similar results to what cv2.boundingRect already does.
Maybe this is a bit of lateral thinking, but looking at your examples and spec when not fill out white pikels contiguouys with the outside bounding box instead. (Like a 'paint pot' brush in Paint-type application).
E.g. (red pixels being the ones you would turn black from white):
You could probably even limit the process to the outer N pixels.
============================
So how might one implement this? It is essentially a version of the "flood fill" algorithm used in pixel graphics programmes, except that you start not from a single seed pixel but checking every point on the edge of the outside bounding rectangle. You start filling in and build a stack of points you need to come back to because you can't necessarily follow every area at once and may need to go back on your self.
You can look that algorithm up, but a 'pure' version will be very stack-heavy if you push every point you can't follow right now, particularly starting with the whole boundary of the shape.
I haven't implemented it this way, but my first thought would be a scan from a boundary inwards, taking a whole line of pixels at a time and mark all the 'white' pixels with a new 3rd colour, then on the next row you fill all the white pixels touching the previously marked pixels and so on. (doesn't matter whether you mark the changed pixels as a 3rd colour, a mask, or alpha-channel or whatever - but you must be able to tell newly filled in pixels from the old black ones.
As you go, you need to check for any 'stranded' areas where you need to work backwards to fill in white areas that are not directly connected to the outside:
Start filling from the edge...
Watch out for stranded areas - if you find one, scan backwards to fill before going to where you were before, to carry one (you may need to recurse if you stranded area turns back on itself again, though in your particular application this shouldn't be a huge issue, unlike some graphics applications)
And continue, not forgetting to fill in from the other edges if required (see note below) until you come to a row with no further pixels to fill and no more back-filling to do. Then restart at the far side of the image as you need to start a backward pass from the far side to catch anything else on that side.
For a practical implementation there is some thinking to do. Your examples will have a lot of filling at the edge but not much by way of complex internal shapes to follow, which keeps things simple. But you need to work from all 4 sides to do it efficiently - perhaps working in as a series of concentric rectangles rather than one side at a time. More complexity working through the design but massively more efficient in this example.
Food for thought anyhow.
I have an image containing cells. I can't provide it, but it is similar to the image used as an example here: http://blogs.mathworks.com/steve/2006/06/02/cell-segmentation/ but without the characteristic nuclei.
I have done some processing and am now left with a pretty good segmentation, but some cells are close to each other and I need to split them. Most of them consist of more or less overlapping ellipses.
I am certain that a few iterations of simple erosion will split almost all of those regions. But some of the other cells are so small, they will disappear before the others split. Therefore I need an algorithm that erodes the image, allowing region splitting, but does not delete the last pixel of a region.
I want to use watershed afterwards to segment the cells.
I guess I could implement this on my own by searching for cennected regions and then tracking that I don't lose any or something like that, but the implementation seems messy even in my head and I think there must be an easier way. So my question is basically, what's the name of this so I can google an implementation? Or if there is no off-the-shelf solution, what's an elegant way of implementing this without dozens of iterations and for loops etc.
(Language is python)
It's a classical problem, and if the overlap between cells is too important, let's say 40% or more, then there is not a good solution.
However, if the overlap is not important, here is the solution:
You start from the segmentation you have, let's call it S
You computer the ultimate eroded UE(S). It will give you the center of each cell. It will give you something like the red points on this image. In this image, they use a distance map, an ultimate eroded will be more stable. If there are still many red points per cell, then a dilation of the UE(S) will fix your problem like this example.
You invert Inv(S) or compute the voronoi diagram Voi(S) in order to have a marker in the background.
Watershed on the gradient image of S, using the UE(S) as inner marker (perfect because you have one point by cell) and Inv(S) or Voi(S) as background/outer marker.
You will get something like this example.
How to go from the image on the left to the image on the right programmatically using Python (and maybe some tools, like OpenCV)?
I made this one by hand using an online tool for clipping. I am completely noob in image processing (especially in practice). I was thinking to apply some edge or contour detection to create a mask, which I will apply later on the original image to paint everything else (except the region of interest) black. But I failed miserably.
The goal is to preprocess a dataset of very similar images, in order to train a CNN binary classifier. I tried to train it by just cropping the image close to the region of interest, but the noise is so high that the CNN learned absolutely nothing.
Can someone help me do this preprocessing?
I used OpenCV's implementation of watershed algorithm to solve your problem. You can find out how to use it if you read this great tutorial, so I will not explain this into a lot of detail.
I selected four points (markers). One is located on the region that you want to extract, one is outside and the other two are within lower/upper part of the interior that does not interest you. I then created an empty integer array (the so-called marker image) and filled it with zeros. Then I assigned unique values to pixels at marker positions.
The image below shows the marker positions and marker values, drawn on the original image:
I could also select more markers within the same area (for example several markers that belong to the area you want to extract) but in that case they should all have the same values (in this case 255).
Then I used watershed. The first input is the image that you provided and the second input is the marker image (zero everywhere except at marker positions). The algorithm stores the result in the marker image; the region that interests you is marked with the value of the region marker (in this case 255):
I set all pixels that did not have the 255 value to zero. I dilated the obtained image three times with 3x3 kernel. Then I used the dilated image as a mask for the original image (i set all pixels outside the mask to zero) and this is the result i got:
You will probably need some kind of method that will find markers automatically. The difficulty of this task depends heavily on the set of the input images. In some cases, the method can be really straightforward and simple (as in the tutorial linked above) but sometimes this can be a tough nut to crack. But I can't recommend anything because I don't know how your images look like in general (you only provided one). :)