I'm trying to analyse TMS-EEG data from Nexstim with FieldTrip Toolbox. I want to make a trial matrix from my raw .nxe data. But how I know which triggers to assign for cfg.trialdef.eventvalue, when cfg is the output variable. I'm trying to mimic the same kind of code as you can find from the tutorial: http://www.fieldtriptoolbox.org/tutorial/tms-eeg
I came up with a solution to the problem. With a command event = ft_read_event('filename.nxe') I got a struct with fields: type, value, sample, duration and offset and this is all I need.
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Creating an array with p_points = vtk.vtkPoints
And then add data to it p_points.InsertNextPoint(value).
There is like 50000 points.
I want to put that point array in a source.
I tried with a programmable one with :
servermanager fetch getPoints that give me the Point Array in it (p_array)
Then with a loop p_array.InsertNextPoint(p_points.GetPoint(index_point))
But with no luck. The points array in the source remain empty.
Thanks
Use a Programmable Source with a script like:
import vtk
pts = vtk.vtkPoints()
for i in xrange(10):
pts.InsertNextPoint(i, i, i)
output.SetPoints(pts)
The output object is pre-defined in the Python environment executed by the Programmable Source and is the output object of the source.
That's working fine but it's quite slow when you have 50000 points (something like 400-500 seconds)
When I am using servermanager.Fetch(ProgrammableSource).GetPoints().InsertNextPoints(x,y,z),
it's updating the array.
I can see it doing a Render(). And a time.sleep().
But at the end of the paraview script execution, the content seems to be blanked.
Am I accessing a temporary set pointer and then it's unset ?
Resolved :
I found a way using a PolylineSource instead of ProgrammableSource.
Thanks for your help Cory
MATLAB's methodsview tool is handy when exploring the API provided by external classes (Java, COM, etc.). Below is an example of how this function works:
myApp = actxserver('Excel.Application');
methodsview(myApp)
I want to keep the information in this window for future reference, by exporting it to a table, a cell array of strings, a .csv or another similar format, preferably without using external tools.
Some things I tried:
This window allows selecting one line at a time and doing "Ctrl+c Ctrl+v" on it, which results in a tab-separated text that looks like this:
Variant GetCustomListContents (handle, int32)
Such a strategy can work when there are only several methods, but not viable for (the usually-encountered) long lists.
I could not find a way to access the table data via the figure handle (w/o using external tools like findjobj or uiinspect), as findall(0,'Type','Figure') "do not see" the methodsview window/figure at all.
My MATLAB version is R2015a.
Fortunately, methodsview.m file is accessible and allows to get some insight on how the function works. Inside is the following comment:
%// Internal use only: option is optional and if present and equal to
%// 'noUI' this function returns methods information without displaying
%// the table. `
After some trial and error, I saw that the following works:
[titles,data] = methodsview(myApp,'noui');
... and returns two arrays of type java.lang.String[][].
From there I found a couple of ways to present the data in a meaningful way:
Table:
dataTable = cell2table(cell(data));
dataTable.Properties.VariableNames = matlab.lang.makeValidName(cell(titles));
Cell array:
dataCell = [cell(titles).'; cell(data)];
Important note: In the table case, the "Return Type" column title gets renamed to ReturnType, since table titles have to be valid MATLAB identifiers, as mentioned in the docs.
I am performing an analysis which involves simulation of over 1000 cases. I extracting lots of data for each case as well (about 70MB). Currently I am saving the results for each case as:
Vessel.TotalForce
Vessel.WindForce
Vessel.CurrentForce
Vessel.WaveForce
Vessel.ConnectionForce
...
Line1.EffectiveTension
Line1.X
Line1.Y
Line2.EfectiveTension
Line2.X
Line2.Y
...
save('CaseNo1.mat')
Now, I need to perform my analysis for CaseNo1.mat to CaseNo1000. Initially I planned to create a Database.mat file by loading all cases in it and then accessing any variable using h5read. This way Matlab doesn't need to load all the data at a time. However, I am concerned now that my database file will be too big.
Is there any way I can read the structured variables from individual case files for example CaseNo1.mat without loading the CaseNo1.mat file in memory.
Matlab examples shows loading just the variables directly from MAT file without loading the whole MAT file. But I am not sure how to read structures data the same way.
x=load('CaseNo1.mat','Line1.X')
says Line1.X not found. But it's there. The command is not correct to access the data. Also tried using h5read, but it says CaseNo1.mat is not an HDF5 file.
Can anyone help with this.
Apart from this, I would also appreciate if there is any suggestion about performing such data intensive analysis.
I was wrong! I'm leaving my old answer for context, though I've edited it to reference this one. I thought I had used matfile() in that way before, but I hadn't. I just did a thorough search and ran a few test cases. You've actually run into a limitation of the way Matlab handles and references structures stored in .mat files. There is, however, a solution. It does involve some refactoring of your original code, but it shouldn't be too egregious.
Vessel_TotalForce
Vessel_WindForce
Vessel_CurrentForce
Vessel_WaveForce
Vessel_ConnectionForce
...
Line1_EffectiveTension
Line1_X
Line1_Y
Line2_EfectiveTension
Line2_X
Line2_Y
...
save('CaseNo1.mat')
Then to access, just use matfile (or load) as you were before. Like so:
Vessel_WaveForce = load('CaseNo1.mat'', 'Vessel_WaveForce')
It's important to note that this restriction doesn't appear to be caused by anything you've chosen to do in your program, but rather is imposed by the way Matlab interacts with it's native storage files when they contain structures.
EDIT: This answer works, but doesn't actually solve the problem posed in OP's question. I thought I had used matfile to generate a handle that I could access, but I was wrong. See my other answer for details.
You could use matfile, like so:
myMatFileHandle = matfile('caseNo1.mat');
thisVessel = myMatFileHandle.vessel;
Also, from the little bit I can see, you seem to be on the right track for high-volume analysis. Just remember to use sparse when applicable, and generally avoid conditionals inside of loops if possible.
Good luck!
The objective of storing data in structured format is:
To be organized
Easy scripting post processor where looping through data under one data set it required.
To store structured dataset containing integer, floating and string variables in MAT file and to be able to read just the required variable using h5read command was sought. Matlab load command is not able to read variable beyond first level from stored data in a MAT file. The h5write couldn't write string variables. Hence needed a work around to solve this problem.
To do this I have used following method:
filename = 'myMatFile';
Vessel.TotalForce = %store some data
Vessel.WindForce = %store some data
Vessel.CurrentForce = %store some data
Vessel.WaveForce = %store some data
Vessel.ConnectionForce = %store some data
...
Lin1.LineType = 'Wire'
Line1.ArcLength_0.EffectiveTension = %store some data
Line1.ArcLength_50.EffectiveTension= %store some data
Line1.ArcLength_100.EffectiveTension= %store some data
Lin2.LineType = 'Chain'
Line2.ArcLength_0.EffectiveTension= %store some data
Line2.ArcLength_50.EffectiveTension= %store some data
Line2.ArcLength_100.EffectiveTension= %store some data
save([filename '_temp.mat']);
PointToMat=matfile([filename '.mat'],'Writable',true);
PointToMat.(char(filename)) = load([filename '_temp.mat']);
delete([filename '_temp.mat']);
Now to read from the MAT file created, we can use h5read as usual. To extract the EffectiveTension for Line1, ArcLength_0:
EffectiveTension = h5read([filename '.mat'],['/' filename '/Line1/ArcLength_0/EffectiveTension']);
For string variables, h5read returns decimal values corresponding to each character. To obtain the actual string I used:
name = char(h5read([filename '.mat'],['/' filename '/Line1/LineType']));
Tried this method on my data set which is about 200MB and I could process them pretty fast. Hope this would help someone someday.
Short answer:
Having saved the data into a MAT file with the '-v7.3' option, use something like h5read(filename, '/Line2/X') to read just one structure field. You can even read an array partially, for example:
s.a = 1:100;
save('test.mat', '-v7.3', 's');
clear
h5read('test.mat', '/s/a', [1 10], [1 5], [1 3])
returns each third element of the 1:100 array, starting with the 10th element and returning 5 values:
10 13 16 19 22
Long answer:
See answer by #Amitava for the more elaborate code and topic coverage.
I'm working on automated model building. In some cases I have do convert a bus into another bus (the structure is the same, but there can be variants in the names). It works for a static model where I can change the datatype of the inputs and outputs, but I didn't find any way to do this from the command line or directly in an embedded MATLAB function.
Does anybody know a way to do this?
mfb = find(sfroot, '-isa', 'Stateflow.EMChart', 'Name', 'test');
out = get(mfb, 'Outputs');
out.set('DataType', ['Bus: ' component_source.test]);
I've been looking throught the documentation, but can't seem to find the bit I want.
I have a for loop and I would like to be able to view every value in the for loop.
for example here is a part of my code:
for d = 1 : nb
%for loop performs blade by blade averaging and produces a column vector
for cc = navg : length(atbmat);
atb2 = (sum(atbmat((cc-(navg-1):cc),d)))/navg;
atbvec2(:,cc) = atb2;
end
%assigns column vector 'atbvec2' to the correct column of the matrix 'atbmat2'
atbmat2(d,1:length(atbvec2)) = atbvec2;
end
I would like to view every value of atb2. I'm a python user(new to MATLAB) and would normally use a simple print statement to find this.
I'm sure there is a way to do it, but I can't quite find how.
Thankyou in advance.
you can use disp in Matlab to print to the screen but you might want to use sprintf first to format it nicely. However for debugging you're better off using a break point and then inspect the variable in the workspace browser graphically. To me, this is one of Matlab's best features.
Have a look at the "Examine Values" section of this article
The simplest way to view it everywhere is to change this line:
atb2 = (sum(atbmat((cc-(navg-1):cc),d)))/navg;
Into this, without semicolon:
atb2 = (sum(atbmat((cc-(navg-1):cc),d)))/navg
That being said, given the nature of your calculation, you could get the information you need as well by simply storing every value of abt2 and observing them afterwards. This may be done in atbmat2 already?
If you want to look at each value at the time it happens, consider setting a breakpoint or conditional breakpoint after the line where abt2 is assigned.