I'm new to ParaView and completely lost with all the different data formats. All I want to do is display an elevation grid which is produced by a program. I store the elevation grid in a two dimensional array of floats which is indexed by x and y coordinates and stores the z coordinate. In other words elevationGrid[x][y] stores the height above the point (x, y).
Which file format should I use for this and how is it defined? It would be ideal if someone could give an example file for, say, a 3x3 grid.
A first approach with a 5x5 grid and equation z = x^2+y^2, using a very simple input format. This is a general approach, not especially dedicated to structured grid.
The following has been done with Paraview 3.14.1.
1) Save your data in csv format, i.e. :
"x","y","z"
-0.5,-0.5,0.5
-0.30000001,-0.5,0.34000001
-0.1,-0.5,0.26
[...]
0.1,0.5,0.26
0.30000001,0.5,0.34000001
0.5,0.5,0.5
2) Open in Paraview your csv file
Fill the required import options.
3) Convert your table to geometrical points
Apply Filters > Alphabetical > Table to points
You will be asked to give each variables for each coordinates.
4) Display 3D view to see your points
Create a new visualization view (add a new tab) and choose "3D View".
Activate your TableToPoints filter clicking on the little eye near its name in the pipeline.
If evething is okay, at this point you will see your scatter plot.
5) Last step: create a surface
Apply Filters > Alphabetical > Delaunay 2D
And using default options, one finally obtains:
EDIT:
I remember the name of the dedicated function to create elevation map... It is the Wrap by scalar function. You can combine it with some above steps to get more easily what you want. I could give you an example if necessary.
Related
I can make 2D dimensional netcdf maps of some quantity. I open it in panoply and there is color map of that quantity. But I cannot visualize some boolean value.
Can I somehow mark particular grid points with some symbol on the map (it can be diamond, square, triangle... whatever), is there a way how to do it in Fortran90? I accept also python related help.
Again: I mean there would be color map (from real values) (which I can do) and at the same time some values will have e. g. triangle on it.
If I understand the question correctly, then you can easily do that with Python and using some plotting library (e.g Matplotlib). With Fortran it is extremely tricky as it does not natively support plotting in my mind.
Basically with Python you just have to :
read the wanted variables (coordinates and the field itself)
make the map of the field i.e make the plot
find the locations you want to highlight and just add those locations to the plot
If there is a given 2d array of an image, where threshold has been done and now is in binary information.
Is there any particular way to process this image to that I get multiple blob's coordinates on the image?
I can't use openCV because this process needs to run simultaneously on 10+ simulated robots on a custom simulator in C.
I need the blobs xy coordinates, but first I need to find those multiple blobs first.
Simplest criteria of pixel group size should be enough. But I don't have any clue how to start the coding.
PS: Single blob should be no problem. Problem is multiple blobs.
Just a head start ?
Have a look at QuickBlob which is a small, standalone C library that sounds perfectly suited for your needs.
QuickBlob comes with a small command-line tool (csv-blobs) that outputs the position and size of each blob found within the input image:
./csv-blobs white image.png
X,Y,size,color
28.37,10.90,41,white
51.64,10.36,42,white
...
Here's an example (output image is produced thanks to the show-blobs.py tiny Python utility that comes with QuickBlob):
You can go through the binary image labeling the connected parts with an algorithm like the following:
Create a 2D array of ints, labelArray, that will hold the labels of the connected regions and initiate it to all zeros.
Iterate over each binary pixel, p, row by row
A. If p is true and the corresponding value for this position in the labelArray is 0 (unlabeled), assign it to a new label and do a breadth-first search that will add all surrounding binary pixels that are also true to that same label.
The only issue now is if you have multiple blobs that are touching each other. Because you know the size of the blobs, you should be able to figure out how many blobs are in a given connected region. This is the tricky part. You can try doing a k-means clustering at this point. You can also try other methods like using binary dilation.
I know that I am very late to the party, but I am just adding this for the benefipeople who are researching this problem.
Here is a nice description that might fit your needs.
http://www.mcs.csueastbay.edu/~grewe/CS6825/Mat/BinaryImageProcessing/BlobDetection.htm
Hi have about 5000 2d images from multiple CT-scans and need to get them sorted. The dataset is directly imported from a GE workstation.
Right now the images are in bunches of about 10 sorted images at a time in some random order.
How could we get these images sorted? If you would suggest dicominfo please tell us exactly which parameter to go after.
Thank you!
How the DICOM CT images should be sorted is ultimately dependent on the usage context, but as a rule of thumb I would recommend that you first group the images based on (patient), study and series using these tags:
(0010,0020) Patient ID
(0020,000D) Study Instance UID
(0020,000E) Series Instance UID
To sort the images within one series, you could use the Instance Number (0020,0013), although there is no guarantee that this value is set since it is a type 2 attribute.
Another alternative is to use the Image Position (Patient) (0020,0032), which is mandatory in CT images. You would need to check the Image Orientation (Patient) (0020,0037) to decide how to sort on position. Often CT image orientation is (1,0,0), (0,1,0), and then the Z (third) component of the image position can be used as the basis for sorting.
If the series also contains a localizer image, this image would have to be excluded from positional sorting.
I am programming a basic GUI in MATLAB that utilizes the mapping toolbox. The GUI will display a grayscale image and then plot discrete points over the data, all of this over the necessary map projection. It is important that I plot onto map axes (those created by the axesm command) rather than the vanilla cartesian space. I have no problem doing all this from the command line, but I cannot find a way to implement a GUI version and its driving me nuts.
The problem is that I need to specify the map axes as being the child of the parent figure. The normal axes has a property that can be set, doing something like:
axesHandle = axes('Parent', parentHandle, ...);
or
set(axesHandle, 'Parent', parentHandle);
However, there is no equivalent parent property for the map axes created by the axesm function, so I have no way to manipulate the axes within the figure. How can I do this?
Update: If I create a plot within the map axes in an empty figure, get(figureHandle, 'Children') returns the handle of the axesm object (thanks #slayton!), so the map axes object must be implicitly added to the children of the figure by MATLAB.
Should I be concerned that the map axes do not refer back to the parent figure, or should I just let it be? I wonder if this is a classic case of MATLAB forcing me to not comply with the standards the manual tells me to implement.
From reading your question what I think you are trying to do is grab the handle of the axes object. This can be done as the axes is created using either axes or subplot
a = axes();
a = subplot(x,y,z);
% both return an handle to the newly created axes object
Additionally if the axes is created automagically by a function call like plot or image you can get the axes handle that too:
p = plot(1:10); %returns a handle to a line object
a = get(p,'Parent');
i = image(); %returns a handle to an image object
a = get(i, 'Parent');
Finally, neither of those two options is available you can always get the axes handle from its containing figure with:
a = get(figureHandle, 'Children');
Remember though that this will return a vector of axes handles if your figure contains more than one axes.
Finally when it comes time to draw draw your points to the axes that contains your map image you simply need to call:
line(xPoints, yPoints, 'linestyle', 'none', 'marker', '.', 'color', 'r', 'size', 15)
This will draw the vertices of the line using large red dots.
I'm not sure if this answers your question because the code you provided doesn't line up with the question you asked.
The code you provided looks like you are trying to move an axes from one figure to another. You can totally do this!
f = figure('Position', [100 100 100 100]);
a = axes('Parent', f);
pause
f2 = figure('Position', [250 100 100 100]);
set(a,'Parent', f2);
After much trial and error and reading of documentation, I have found that there is no way to explicitly specify the parent of the map axes. Instead, they are implicitly added on top of the current axes. In the instance that no axes exist in the current figure, calling axesm creates an axes object and then places the axesm object inside. When you take this route, you have to grab the axes object handle by calling gca:
mapAxesHandle = axesm(...);
axesHandle = gca(...);
This makes it frustrating to use the mapping toolbox when writing a GUI from scratch, but that's the way Mathworks makes it happen. Thanks to #slayton for useful info. I'd upvote but my reputation is <15 :(
I have to make an application that recognizes inside an black and white image a piece of tetris given by the user. I read the image to analyze into an array.
How can I do something like this using C?
Assuming that you already loaded the images into arrays, what about using regular expressions?
You don't need exact shape matching but approximately, so why not give it a try!
Edit: I downloaded your doc file. You must identify a random pattern among random figures on a 2D array so regex isn't suitable for this problem, lets say that's the bad news. The good news is that your homework is not exactly image processing, and it's much easier.
It's your homework so I won't create the code for you but I can give you directions.
You need a routine that can create a new piece from the original pattern/piece rotated. (note: with piece I mean the 4x4 square - all the cells of it)
You need a routine that checks if a piece matches an area from the 2D image at position x,y - the matching area would have corners (x-2, y-2, x+1, y+1).
You search by checking every image position (x,y) for a match.
Since you must use parallelism you can create 4 threads and assign to each thread a different rotation to search.
You might not want to implement that from scratch (unless required, of course) ... I'd recommend looking for a suitable library. I've heard that OpenCV is good, but never done any work with machine vision myself so I haven't tested it.
Search for connected components (i.e. using depth-first search; you might want to avoid recursion if efficiency is an issue; use your own stack instead). The largest connected component should be your tetris piece. You can then further analyze it (using the shape, the size or some kind of border description)
Looking at the shapes given for tetris pieces in Wikipedia, called "I,J,L,O,S,T,Z", it seems that the ratios of the sides of the bounding box (easy to find given a binary image and C) reveal whether you have I (4:1) or O (1:1); the other shapes are 2:3.
To detect which of the remaining shapes you have (J,L,S,T, or Z), it looks like you could collect the length and position of the shape's edges that fall on the bounding box's edges. Thus, T would show 3 and 1 along the 3-sides, and 1 and 1 along the 2 sides. Keeping track of the positions helps distinguish J from L, S from Z.