Using pyiron, I want to calculate the mean square displacement of the ions in my system. How do I see the total displacement (i.e. not folded back by periodic boundary conditions) without dumping very frequently and checking when an atom passes over the boundary and gets wrapped?
Try to compare job['output/generic/unwrapped_positions'][-1] and job.structure.positions+job.output.total_displacements[-1]. If they deliver the same values, it's definitely fine both ways. If not, you can post the relevant lines in your notebook here.
I'd like to add a few comments to Jan's answer:
While job['output/generic/unwrapped_positions'] returns the unwrapped positions parsed from the output files, job.output.total_displacements returns the displacement of atoms calculated from each pair of consecutive snapshots. So if an atom moves more than half the box length in any direction, job.output.total_displacements will give wrong coordinates. Therefore, job['output/generic/unwrapped_positions'] is generally more trustworthy, but it is not available in all the codes (since some codes simply do not provide an output for unwrapped positions).
Moreover, if an interactive job is used, it is possible that job.structure.positions does not return the initial positions, i.e. job.structure.positions+job.output.total_displacements won't be initial positions + displacements.
So, in short, my answer to your question would be rather "Use job['output/generic/unwrapped_positions'] and if it's not available, use job.structure.positions+job.output.total_displacements but be aware of potential problems you might be running into."
I have got a SSAS cube, that has a KPI which has a Value as a percentage. I also have a Goal which is also the target percentage to keep the Value below.
I create the KPI fine, but when I import it into the dashboard designer and set the scoring pattern and indicator ( I used tick, exlamation mark, cross - which gives 2 thresholds). It always shows the tick even though its way over the goal.
I have set it to be that decreasing is better and the banding method is "Band by stated score", but it always shows on the scorecard as being On Target.
This is the threshold I currently have.
Is it something to do with having the goal as a percentage? Can anyone explain how Dashboard Designer thresholds work with percentages please??
Update : Seemed to get it to work by setting the thresholds against the actual values in stead.
The percentage works in terms of decimal.
0 = 0%
0.5 = 50%
1 = 100%
In your scenario, you can use -0.01, 0.8, 1, 1.01
Thanks,
Merin
I eventually found the answer to this for anyone who wants to know still.
I did indeed need the "Band by stated score" banding method, the thing I was missing was where does the score come from? This is not immediately obvious but it is in the "Specify the worst value" section when editing the banding settings.
This needs to be set correctly against the threshold values.
I am trying to detect objects in image on an iphone app.
I am using the cvMatchTemplate function, I manage to see some patterns returned by the cvMatchTemplate function (I chose CV_TM_CCOEFF_NORMED).
Positive Results (result image is 163x371):
http://encryptedpixel.files.wordpress.com/2011/07/photo-13-7-11-11-52-19-am.jpeg
cvMinMaxLoc returns: min (102,244) max(11,210)
The min point is making some sense here, the position of the dark spot is really 102,244 in the result image of 163x371
Negative Results:
cvMinMaxLoc returns: min (114,370) max(0,0)
This is not making sense, there is totally no results, why is there still a min point at 114,370?
I need to know how to analyze these results programatically so that I can say "Hey I found the object!" in objectiveC for iPhone app?
Thanks!
cvMinMaxLoc will always return the position of the minimum and maximum values of their input. It only "doesn't make sense" in your particular application. You should check the value at the returned position for the minimum and do something like threshold it to see if that's a probable match for your template. A template match will yield a very low or a very high value, depending on the method you chose.
I'm attempting to gauge the percentage difference between two images.
Having done a lot of reading I seem to have a number of options but I'm not sure what the best method to follow for:
Ease of coding
Performance.
The methods I've seen are:
Non language specific - academic Image comparison - fast algorithm and Mac specific direct pixel access http://www.markj.net/iphone-uiimage-pixel-color/
Does anyone have any advice about what solutions make most sense for the above two cases and have code samples to show how to apply them?
I've had success calculating the difference between two images using the histogram technique mentioned here. redmoskito's answer in the SO question you linked to was actually my inspiration!
The following is an overview of the algorithm I used:
Convert the images to grayscale—compare one channel instead of three.
Divide each image into an n * n grid of "subimages". Then, for subimage pair:
Calculate their colour composition histograms.
Calculate the absolute difference between the two histograms.
The maximum difference found between two subimages is a measure of the two images' difference. Other metrics could also be used (e.g. the average difference betwen subimages).
As tskuzzy noted in his answer, if your ultimate goal is a binary "yes, these two images are (roughly) the same" or "no, they're not", you need some meaningful threshold value. You could produce such a value by passing images into the algorithm and tweaking the threshold based on its output and how similar you think the images are. A form of machine learning, I suppose.
I recently wrote a blog post on this very topic, albeit as part of a larger goal. I also created a simple iPhone app to demonstrate the algorithm. You can find the source on GitHub; perhaps it will help?
It is really difficult to suggest something when you don't tell us more about the images or the variations. Are they shapes? Are they the different objects and you want to know what class of objects? Are they the same object and you want to distinguish the object instance? Are they faces? Are they fingerprints? Are the objects in the same pose? Under the same illumination?
When you say performance, what exactly do you mean? How large are the images? All in all it really depends. With what you've said if it is only ease of coding and performance I would suggest to just find the absolute value of the difference of pixels. That is super easy to code and about as fast as it gets, but really unlikely to work for anything other than the most synthetic examples.
That being said I would like to point you to: DHOG, GLOH, SURF and SIFT.
You can use fairly basic subtraction technique that the lads above suggested. #carlosdc has hit the nail on the head with regard to the type of image this basic technique can be used for. I have attached an example so you can see the results for yourself.
The first shows a image from a simulation at some time t. A second image was subtracted away from the first which was taken some (simulation) time later t + dt. The subtracted image (in black and white for clarity) then shows how the simulation has changed in that time. This was done as described above and is very powerful and easy to code.
Hope this aids you in some way
This is some old nasty FORTRAN, but should give you the basic approach. It is not that difficult at all. Due to the fact that I am doing it on a two colour pallette you would do this operation for R, G and B. That is compute the intensities or values in each cell/pixal, store them in some array. Do the same for the other image, and subtract one array from the other, this will leave you with some coulorfull subtraction image. My advice would be to do as the lads suggest above, compute the magnitude of the sum of the R, G and B componants so you just get one value. Write that to array, do the same for the other image, then subtract. Then create a new range for either R, G or B and map the resulting subtracted array to this, the will enable a much clearer picture as a result.
* =============================================================
SUBROUTINE SUBTRACT(FNAME1,FNAME2,IOS)
* This routine writes a model to files
* =============================================================
* Common :
INCLUDE 'CONST.CMN'
INCLUDE 'IO.CMN'
INCLUDE 'SYNCH.CMN'
INCLUDE 'PGP.CMN'
* Input :
CHARACTER fname1*(sznam),fname2*(sznam)
* Output :
integer IOS
* Variables:
logical glue
character fullname*(szlin)
character dir*(szlin),ftype*(3)
integer i,j,nxy1,nxy2
real si1(2*maxc,2*maxc),si2(2*maxc,2*maxc)
* =================================================================
IOS = 1
nomap=.true.
ftype='map'
dir='./pictures'
! reading first image
if(.not.glue(dir,fname2,ftype,fullname))then
write(*,31) fullname
return
endif
OPEN(unit2,status='old',name=fullname,form='unformatted',err=10,iostat=ios)
read(unit2,err=11)nxy2
read(unit2,err=11)rad,dxy
do i=1,nxy2
do j=1,nxy2
read(unit2,err=11)si2(i,j)
enddo
enddo
CLOSE(unit2)
! reading second image
if(.not.glue(dir,fname1,ftype,fullname))then
write(*,31) fullname
return
endif
OPEN(unit2,status='old',name=fullname,form='unformatted',err=10,iostat=ios)
read(unit2,err=11)nxy1
read(unit2,err=11)rad,dxy
do i=1,nxy1
do j=1,nxy1
read(unit2,err=11)si1(i,j)
enddo
enddo
CLOSE(unit2)
! substracting images
if(nxy1.eq.nxy2)then
nxy=nxy1
do i=1,nxy1
do j=1,nxy1
si(i,j)=si2(i,j)-si1(i,j)
enddo
enddo
else
print *,'SUBSTRACT: Different sizes of image arrays'
IOS=0
return
endif
* normal finishing
IOS=0
nomap=.false.
return
* exceptional finishing
10 write (*,30) fullname
return
11 write (*,32) fullname
return
30 format('Cannot open file ',72A)
31 format('Improper filename ',72A)
32 format('Error reading from file ',72A)
end
! =============================================================
Hope this is of some use. All the best.
Out of the methods described in your first link, the histogram comparison method is by far the simplest to code and the fastest. However key point matching will provide far more accurate results since you want to know a precise number describing the difference between two images.
To implement the histogram method, I would do the following:
Compute the red, green, and blue histograms of each image
Add up the differences between each bucket
If the difference is above a certain threshold, then the percentage is 0%
Otherwise the colors found in the images are similar. So then do a pixel by pixel comparison and convert the difference into a percentage.
I don't know any precise algorithms for finding the key points of an image. However once you find them for each image you can do a pixel by pixel comparison for each of the key points.
The only effect AudioUnit on iOS is the "iTunes EQ", which only lets you use EQ pre-sets. I would like to use a customized eq in my audio graph
I came across this question on the subject and saw an answer suggesting using this DSP code in the render callback. This looks promising and people seem to be using this effectively on various platforms. However, my implementation has a ton of noise even with a flat eq.
Here's my 20 line integration into the "MixerHostAudio" class of Apple's "MixerHost" example application (all in one commit):
https://github.com/tassock/mixerhost/commit/4b8b87028bfffe352ed67609f747858059a3e89b
Any ideas on how I could get this working? Any other strategies for integrating an EQ?
Edit: Here's an example of the distortion I'm experiencing (with the eq flat):
http://www.youtube.com/watch?v=W_6JaNUvUjA
In the code in EQ3Band.c, the filter coefficients are used without being initialized. The init_3band_state method initialize just the gains and frequencies, but the coefficients themselves - es->f1p0 etc. are not initialized, and therefore contain some garbage values. That might be the reason for the bad output.
This code seems wrong in more then one way.
A digital filter is normally represented by the filter coefficients, which are constant, the filter inner state history (since in most cases the output depends on history) and the filter topology, which is the arithmetic used to calculate the output given the input and the filter (coeffs + state history). In most cases, and of course when filtering audio data, you expect to get 0's at the output if you feed 0's to the input.
The problems in the code you linked to:
The filter coefficients are changed in each call to the processing method:
es->f1p0 += (es->lf * (sample - es->f1p0)) + vsa;
The input sample is usually multiplied by the filter coefficients, not added to them. It doesn't make any physical sense - the sample and the filter coeffs don't even have the same physical units.
If you feed in 0's, you do not get 0's at the output, just some values which do not make any sense.
I suggest you look for another code - the other option is debugging it, and it would be harder.
In addition, you'd benefit from reading about digital filters:
http://en.wikipedia.org/wiki/Digital_filter
https://ccrma.stanford.edu/~jos/filters/