Develop Reference

Move ax.text a bit away from data point

I am trying to create a type of map that plots a route between points.
As such I have something that looks like the image below:
And as you can see, the bll label is very close to the data point. I would like it to be a bit further away, so you can actually see the dot.
Also, the text is just a regular ax.text plot with x and y values.
My problem is, that yes, I could just add some kind of percentage value or something. However, depending on the coordinate and x-value, this will not be the same depending on you being very far left, where x => 0, or far right where x => max value of the plot. Then you could argue I could just add 10 or 20 units, but in my case I produce different maps depending on different routes. So this means that the x-axis values are not the same. Sometimes the map is big, and sometimes it's small. So using the same value in all maps will make bll text move either very much or very little depending on size.
Also, if I am ever to zoom on the map, this would adjust the text as well if I were to use some kind of value extension, since the distance between the data point AND the text will also increase relative to the size of the zoom, like this figure:
Can this be solved in a somewhat simple manner ?
Best regards

Comparing fluorescence intensity of finger print residue after 5 contacts

I have an image as follows that shows the residue of fluorescent powder left on a surface after 5 sequential contacts. Is it possible to quantify the a difference in the amount of residue between contacts?
I have looked at Fiji/ImageJ and selected each finger print at a time to get the mean grey value but I don't see much difference to be honest. Any help or thoughts would be very much appreciated. Happy to think about python or matlab.

In order for the quantification of the intensities to be useful, I would imagine you would need to assume your image was evenly lit and that any fluorescence you see isn't a result of oversaturation. That being said, in principle, you could contour the given fingerprint, duplicate it to a new image, and then measure the stack histogram after adjusting the threshold such that regions darker than your fingerprint powder are set to black. Perhaps the change in distribution will illustrate the change that occurs, if any.
Edit:
First: merge the RGB channels by adding them to one another using the channel calculator function. Your signal is the result of multiple colors, so splitting it does not make sense to me here.
The steps would then be:
Duplicate your given print to a new window.
Use "Adjust Threshold" to set a threshold of 0-n, where n is the highest intensity that doesn't include your fingerprint.
Run the command "Edit/Selection/Create Selection."
Run the command "Edit/Clear."
Press "ctrl+H" to measure the histogram of the pixels, and then "List" to get the actual values.
Repeat for each print and plot on the same chart.
When you are already obtaining the actual histogram values, and not just the range from the particle analyzer, then I'm not sure there's much else that I can personally suggest.

python : shift values along a curve

I am trying to figure out a way to do this sort of thing.
I would be happy to hear any suggestions on this type of interpolation.
I have 2 fixed values A and H, and n extra random values in between.
In my example they are on a path, although I would be happy also if I could figure out how to solve it for a straight line.
Passing a global variable to my script I would like to displace these in between points in such a way that they are changed to gradually increasing/decreasing their distance between themselves and the two extremes accordingly (incrementally as shown on the image).

Separating Meshes with vtkPolyDataConnectivityFilter

I am having a hard time using vtk, especially the vtkPolyDataConnectivityFilter. I feed in the output of a Marching Cubes algorithm that created a surface from a 3d point cloud.
However, when i try to set
filt = vtk.vtkConnectivityFilter()
filt.SetInputData(surface_data) # get the data from the MC alg.
filt.SetExtractionModeToLargestRegion()
filt.ColorRegionsOn()
filt.Update()
filt.GetNumberOfExtractedRegions() # will 53 instead of 1
it gives me weird results. I cannot use the extraction modes for specific regions or seed a single point, since i don't know them in advance.
I need to separate the points of the largest mesh from the smaller ones and keep only the large mesh.
When i render the whole output it shows me the right extracted region. However, the different regions are still contained in the dataset and there is no way to separate it.
What am i doing wrong?
Best J

I had the same problem where I had to segment an STL file converted to vtkpolydata.
If you look at the example https://www.vtk.org/Wiki/VTK/Examples/Cxx/PolyData/PolyDataConnectivityFilter_SpecifiedRegion , you will find they use the member function SetExtractionModeToSpecifiedRegions().
Replace you code with the following:
filt.SetInputData(surface_data)
filt.SetExtractionModeToSpecifiedRegions()
filt.AddSpecifiedRegion(0) #Manually increment from 0 up to filt.GetNumberOfExtractedRegions()
filt.Update()
You will need to render and view the specified region to figure out the index of the segmented region your actually interested in.

2D-Histogram With A Third Data Set In Python

I have a specific problem that maybe can help me with. I have, currently, 3 arrays of data and I want to make a 2D histogram of the first two while using the third array as values that get summed up in each particular bin. I also want to include a color bar that shows the scale of different colors you see in the histogram.
As a start I looked into using matplotlib.pyplot.hexbin to do this and it seems to work fine but I don't want to have hexagons as the shape of my bins. Is somebody able to point me to some resources on how to do this?