Technologies: PostGIS, QGIS
I have a vector box named "study_area", and another vector data "floodplain". Now I need to clip the floodplain vector data to produce a floodplain layer that is within in the study area. I am required to use postgis, writing queries for this specific job.
However, I checked the doc, it seems like the st_clip function only works for rasters.
Here is my attempt:
select r.geom as clipped
from study_area as s, usrname."Regulatory_Floodplain" as r
where st_within(r.geom, s.geom) or st_intersects(s.geom, r.geom)
The problem is that it is not entirely in the box:
Any alternatives? Any help will be appreciated, thanks!
You probably want ST_Intersection function, something like
select st_intersection(r.geom, s.geom) as clipped
from study_area as s, usrname."Regulatory_Floodplain" as r
where st_intersects(s.geom, r.geom)
Related
I have troubles extracting a tumor using a RT mask from a dicom image. Due to GDPR I am not allowed to share the dicom images even though they are anonymized. However I am allowed to share the images themself. I want to extract the drawn tumor from the CT images using the draw GTV stored as a RT structure using MATLAB.
Lets say that the file directory where my CT images are stored is called DicomCT and that the RT struct dicom file is called rtStruct.dcm.
I can read and visualize my CT images as follows:
V = dicomreadVolume(“DicomCT”);
V = squeeze(V);
volshow(V)
volume V - 3D CT image
I can load my rt structure using:
Info = dicominfo(“rtStruct.dcm”);
rtContours = dicomContours(Info);
I get the plot giving the different contours.
plotContour(rtContours)
Contours for the GTV of the CT image
I used this link for the information on how to create the mask such that I can apply it to the 3D CT image: https://nl.mathworks.com/help/images/create-and-display-3-d-mask-of-dicom-rt-contour-data.html#d124e5762
The dicom information tells mee the image should be 3mm slices, hence I took 3x3x3 for the referenceInfo.
referenceInfo = imref3d(size(V),3,3,3);
rtMask = createMask(rtContours, 1, referenceInfo)
When I plot my rtMask, I get a grey screen without any trace of the mask. I think that something is wrong with the way that I define the referenceInfo, but I have no idea how to fix it or what is wrong.
volshow(rtMask)
Volume plot of the RT mask
What would be the best way forward?
i was actually having some sort of similar problem to you a couple of days ago. I think you might have two possible problems (none of them your fault).
Your grey screen might be an error rendering that it's not showing because of how the actual volshow() script works. I found it does some things i don't understand with graphics memory and representing numeric type volumes vs logic volumes. I found this the hard way in my job PC where i only have intel HD graphics. Using
iptsetpref('VolumeViewerUseHardware',true)
for logical volumes worked fine for me. You an also test this by trying to replot the mask as double instead of logical by
rtMask = double(rtMask)
volshow(rtMask)
If it's not a rendering error caused by the interactions between your system and volshow() it might be an actual confusion and how the createMask and the actual reference info it needs (created by an actual bad explanation in the tutorial you just linked). Using pixel size info instead of actual axes limits can create partial visualization in segmentation or even missing it bc of scale. This nice person explained more elegantly in this post by using actual geometrical info of the dicom contours as limits.
https://es.mathworks.com/support/search.html/answers/1630195-how-to-convert-dicom-rt-structure-to-binary-mask.html?fq%5B%5D=asset_type_name:answer&fq%5B%5D=category:images/basic-import-and-export&page=1
basically use
plotContour(rtContours);
ax = gca;
referenceInfo = imref3d(size(V),ax.XLim,ax.YLim,ax.ZLim);
rtMask = createMask(rtContours, 1, referenceInfo)
In addition to your code and it might work.
I hope this could be of help to you.
I have a similar case as shown in the below question.
https://gis.stackexchange.com/questions/293695/filling-gaps-between-polygons-using-qgis
That solution uses qgis, but I want to use a postgis function on a table on the geometry column. The solution talks about convex hull but not sure how to use the convex_hull postgis function here. I want to fill the gap by moving/merging the gap to the neighboring polygon.
As long as you have a column to group them by (e.g., "postal_code"), you can do:
SELECT
st_convexhull(st_collect(geom_column))
FROM
my_geom_table
GROUP BY
grouping_column -- e.g., "postal_code"
I'm trying to display liquid crystal directors using ParaView. The director is a spin-2 field that should look like a headless vector, centred in the middle, like the cylinders in this picture:
https://pbs.twimg.com/media/C8fj1bWXoAEFy5R.png
I know how to make an arrow filter, like this other picture, but it's not what I want:
https://summerofhpc.prace-ri.eu/wp-content/uploads/2013/07/arrows.png
I can't find the filter that will do what I need. Could you please tell me if I need to create a custom filter or if there's a quicker way to obtain this result within ParaView?
My data are expressed as 3D vectors within a VTU (unstructured grid) file.
Thanks in advance and sorry for the newbie question!
I'm currently working on an alignment script which aligns two images very well. Usually, I get a data set which contains over 50 images of cells. I normally calculate a transformation matrix (T) based on fluorescent beads. However, this T-matrix gave rise to polarization in unpolarized cells, indicating that the transformation is not optimal. Therefore I switched to another script, which calculates a T-matrix based on cells and not beads. This new T-matrix aligns almost perfectly for a fraction of the cells, but there is always a portion of the images which aligns not so good.
I would like to continue with the alignment on cells, because this script works much better than the alignment on beads. In order to have optimal T-matrix for each image, I would like to calculate unique T-matrices for each image couple. I'm not very skilled in Matlab so the solution I could think of did not work.
Below you can find the current script. It functions by creating variables of the images I want to align and assign them to im1 and im2 in the script:
function [T] = alim(im1, im2, Tstart)
%ALIM Determines the transformation between the cameras.
im3=im2;
if (nargin>2)
im2=imwarp(im2, Tstart,'OutputView',imref2d(size(im1)));
end
optimizer = registration.optimizer.RegularStepGradientDescent;
optimizer.MaximumIterations=500;
metric = registration.metric.MattesMutualInformation;
T = imregtform(im2, im1, 'affine', optimizer, metric);
if (nargin>2)
T.T=Tstart.T*T.T;
end
figure;
imshowpair(im1,imwarp(im3,T,'OutputView',imref2d(size(im1))));
end
I tried to incorporate a loop which imports all images from the folder sequentially and assign these to im1 and im2. However, the problems that arises is that the type of data changes from uint16 into cell, which can't be used for this type of transformation. One defines in the script the location of the folders 'CAM1' and 'CAM2' and the number of images in these folders ('imnum')
for i:imnum
x{i}=imread(strcat(link,'CAM1\',num2str(i),'.tif'));
y{i}=imread(strcat(link,'CAM2\',num2str(i),'.tif'));
I would like to have your view on this problem and hopefully you can make some suggestions on how I can import the images in a folder in one go and keep the data type uint16. I'm always open for suggestions so if you have other ideas on how to solve my problem, I would love it if you shared them with me. If anything is unclear, please contact me with questions!
With kind regards,
Reinier
x is a cell array, where each element x{i} is a uint16 array. Cell arrays can hold any other datatype, including more cell arrays, and are a great way to wrap collections of objects, especially when their sizes and/or types may differ.
In your case, just call your function like this:
T = alim(x{i}, y{i}, tstart);
Or, even better, put the output matrix into a similar cell:
T{i} = alim(x{i}, y{i}, tstart);
I am working with MATLAB for a school project. The assignment is to import a matrix file supplied to me, and display it as a new figure using image. Right now, I can make an image with
m1 = load('matrix1.csv'); image(m1)
But the image is rotated to the right. How do I rotate it so the image is presented horizontally rather than vertically?
Your issue is likely arising from the fact that there are different ways of storing data (row-major vs. column-major). In this case, your .csv file clearly is not in the format you are expecting. The easiest thing to do is to simply transpose the matrix containing your data:
m1 = m1';
image(m1);
If there is something crazier going on and this flips it the wrong way (I don't think this should be the case, but you never know), you can try the rotate command: http://www.mathworks.com/help/matlab/ref/rot90.html