I am importing data from a .mat file and then extracting certain signals from it and I call this data, data. data is a 1x1 struct with 1 field, FT_est_X, where X is the the particular run that I collected the samples from. Here is the code snippet of how I do that.
data = load('site_data_all_2.mat');
t = data.FT_est_2.time;
% estimated data
Fx = data.FT_est_2.signals(1).values;
Fy = data.FT_est_2.signals(2).values;
Fz = data.FT_est_2.signals(3).values;
Mx = data.FT_est_2.signals(4).values;
My = data.FT_est_2.signals(5).values;
Mz = data.FT_est_2.signals(6).values;
So, you can see that this data was collected from run 2. Now, let's say I want to load in a file named site_data_all_3.mat (run 3), what happens is that all the data below %estimated data changes its name--everything stays the same, except the 2 becomes a 3 (e.g. Fx would be Fx = data.FT_est_3.signals(1).values;. Currently, I have to manually enter in the 3 for each variable; can anyone tell me how I can only change the file name and it will automatically change the variable names for me? Essentially, I just want it to be Fx = data.name_of_struct_field.signals(1).values.
Thank you!
You could construct the string some programmatic way (maybe with an iteration variable), but here's the simple answer of defining the fieldname as a string and simply using it. At the next iteration, update the fieldname variable and repeat.
fieldname = 'FT_est_2';
Fx = data.(fieldname).signals(1).values;
Related
I'm new to MATLAB, and I can't manage to make my function work in order to save my data into a .mat file.
The input:
A structure, with 5 fields:
data: 3D matrix of 19x1000x143
labels: 1x143 matrix with 1 or -1 in it
subject_number: an integer
sampling_rate: an integer, 500 Hz
channel_names: 1x19 matrix with text in it
name: a string for the name of the file
clean: a matrix 1x143 with 1 or 0 in it.
The idea is to save only the clean data, marked as 1 in the clean matrix.
If clean(i) is equal to 1:
save data(:,:,i) and labels(:,i)
This is the code I've tried to implement in the saving.m file:
function saving(EEG_struct, clean, name)
subject_number = EEG_struct.subject_number;
fs = EEG_struct.sampling_rate;
chan_names = EEG_struct.channel_names;
nb_epoch = size(EEG_struct.data, 3);
for j=1:nb_epoch
if clean(j) == 1
% Keep the epoch and label
data = cat(3, data, EEG_struct.data(:,:,j));
labels = cat(2, labels, EEG_struct.labels(:,j));
end
end
save(name, data, labels, subject_number, fs, chan_names)
As you can see, I would like to save the data as a structure with the same shape as the EEG_struct input.
Moreover, I would like to use a parfor instead of a for, but it raised me an error I didn't quite get:
An UndefinedFunction error was thrown on the workers for 'data'. This might be because the file containing 'data' is not accessible on the workers. Use addAttachedFiles(pool, files) to specify the required files to be attached. See the documentation for 'parallel.Pool/addAttachedFiles' for more details. Caused by: Undefined function or variable 'data'.
Thanks for the help !
You can use your clean variable as a logical index and parse out your data and labels at once. So there is no need for a loop.
Also the save command needs the "names" of the vars to save not the variables themselves. So I just put ' ' around each one.
function saving(EEG_struct, clean, name)
subject_number = EEG_struct.subject_number;
fs = EEG_struct.sampling_rate;
chan_names = EEG_struct.channel_names;
nb_epoch = size(EEG_struct.data, 3);
%No need for a loop at all
data = EEG_struct.data(:,:,logical(clean));
labels = EEG_struct.labels(logical(clean)); %This is a 1xN so I removed the extra colon operator
save(name, 'data', 'labels', 'subject_number', 'fs', 'chan_names');
EDIT:
Per you comment if you want to just leave everything in the structure. I gave you 2 options for how to save it.
function saving(EEG_struct, clean, name)
%Crop out ~clead data
EEG_struct.data = EEG_struct.data(:,:,logical(clean));
EEG_struct.labels = EEG_struct.labels(logical(clean)); %This is a 1xN so I removed the extra colon operator
% Option 1
save(name, 'EEG_struct');
% Option2
save(name, '-struct', 'EEG_struct');
Option 1 will directly save the struct to the MAT file. So if you were to load the data back like this:
test = load(name);
test =
EEG_struct: [1x1 struct]
You would get your structure placed inside another structure ... which might not be ideal or require an extra line to de-nest it. On the other hand just loading the MAT file with no outputs load(name) would put EEG_struct into your current workspace. But if in a function then it sort of springs into existence without every being declared which makes code a bit harder to follow.
Option 2 uses the '-struct' option which breaks out each field automatically into separate vars in the MAT file. So loading like this:
EEG_struct = load(name);
Will put all the fields back together again. To me at least this looks cleaner when done within a function but is probably just my preference
So comment out which ever you prefer. Also, not I did not include clean in the save. You could either append it to the MAT or add it to your structure.
To get a structure the same as EEG_struct but with only the data/labels corresponding with the clean variable, you can simply make a copy of the existing structure and remove the rows where clean=0
function saving(EEG_struct, clean, name)
newstruct = EEG_struct;
newstruct.data(:,:,logical(~clean)) = '';
newstruct.labels(logical(~clean)) = '';
save(name,'newstruct');
I have an excel file and I need to read it based on string values in the 4th column. I have written the following but it does not work properly:
[num,txt,raw] = xlsread('Coordinates','Centerville');
zn={};
ctr=0;
for i = 3:size(raw,1)
tf = strcmp(char(raw{i,4}),char(raw{i-1,4}));
if tf == 0
ctr = ctr+1;
end
zn{ctr}=raw{i,4};
end
data=zeros(1,10); % 10 corresponds to the number of columns I want to read (herein, columns 'J' to 'S')
ctr=0;
for j = 1:length(zn)
for i=3:size(raw,1)
tf=strcmp(char(raw{i,4}),char(zn{j}));
if tf==1
ctr=ctr+1;
data(ctr,:,j)=num(i-2,10:19);
end
end
end
It gives me a "15129x10x22 double" thing and when I try to open it I get the message "Cannot display summaries of variables with more than 524288 elements". It might be obvious but what I am trying to get as the output is 'N = length(zn)' number of matrices which represent the data for different strings in the 4th column (so I probably need a struct; I just don't know how to make it work). Any ideas on how I could fix this? Thanks!
Did not test it, but this should help you get going:
EDIT: corrected wrong indexing into raw vector. Also, depending on the format you might want to restrict also the rows of the raw matrix. From your question, I assume something like selector = raw(3:end,4); and data = raw(3:end,10:19); should be correct.
[~,~,raw] = xlsread('Coordinates','Centerville');
selector = raw(:,4);
data = raw(:,10:19);
[selector,~,grpidx] = unique(selector);
nGrp = numel(selector);
out = cell(nGrp,1);
for i=1:nGrp
idx = grpidx==i;
out{i} = cell2mat(data(idx,:));
end
out is the output variable. The key here is the variable grpidx that is an output of the unique function and allows you to trace back the unique values to their position in the original vector. Note that unique as I used it may change the order of the string values. If that is an issue for you, use the setOrderparameter of the unique function and set it to 'stable'
I have a long list of variables in my workspace.
First, I'm finding the potential variables I could be interested in using the who function. Next, I'd like to loop through this list to find the size of each variable, however who outputs only the name of the variables as a string.
How could I use this list to refer to the values of the variables, rather than just the name?
Thank you,
list = who('*time*')
list =
'time'
'time_1'
'time_2'
for i = 1:size(list,1);
len(i,1) = length(list(i))
end
len =
1
1
1
If you want details about the variables, you can use whos instead which will return a struct that contains (among other things) the dimensions (size) and storage size (bytes).
As far as getting the value, you could use eval but this is not recommended and you should instead consider using cell arrays or structs with dynamic field names rather than dynamic variable names.
S = whos('*time*');
for k = 1:numel(S)
disp(S(k).name)
disp(S(k).bytes)
disp(S(k).size)
% The number of elements
len(k) = prod(S(k).size);
% You CAN get the value this way (not recommended)
value = eval(S(k).name);
end
#Suever nicely explained the straightforward way to get this information. As I noted in a comment, I suggest that you take a step back, and don't generate those dynamically named variables to begin with.
You can access structs dynamically, without having to resort to the slow and unsafe eval:
timestruc.field = time;
timestruc.('field1') = time_1;
fname = 'field2';
timestruc.(fname) = time_2;
The above three assignments are all valid for a struct, and so you can address the fields of a single data struct by generating the field strings dynamically. The only constraint is that field names have to be valid variable names, so the first character of the field has to be a letter.
But here's a quick way out of the trap you got yourself into: save your workspace (well, the relevant part) in a .mat file, and read it back in. You can do this in a way that will give you a struct with fields that are exactly your variable names:
time = 1;
time_1 = 2;
time_2 = rand(4);
save('tmp.mat','time*'); % or just save('tmp.mat')
S = load('tmp.mat');
afterwards S will be a struct, each field will correspond to a variable you saved into 'tmp.mat':
>> S
S =
time: 1
time_1: 2
time_2: [4x4 double]
An example writing variables from workspace to csv files:
clear;
% Writing variables of myfile.mat to csv files
load('myfile.mat');
allvars = who;
for i=1:length(allvars)
varname = strjoin(allvars(i));
evalstr = strcat('csvwrite(', char(39), varname, '.csv', char(39), ', ', varname, ')');
eval(evalstr);
end
I have a large amount of .csv files from my experiments (200+) and previously I have been reading them in seperately and also for later steps in my data handling this is tedious work.
co_15 = csvread('CO_15K.csv',5,0);
co_25 = csvread('CO_25K.csv',5,0);
co2_15 = csvread('CO2_15K.csv',5,0);
co2_80 = csvread('CO2_80K.csv',5,0);
h2o_15 = csvread('H2O_15K.csv',1,0);
etc.....
So I want to make a cell at the beginning of my code looking like this and then a for loop that just reads them automatically.
input = {'co_15' 5;'co_25' 5;...
'co2_15' 5; 'co2_80' 5;...
'h2o_15' 1; 'h2o_140' 1;...
'methanol_15' 5;'methanol_120' 5;'methanol_140' 5;...
'ethanol_15' 5;'ethanol_80' 1;'ethanol_140' 5;...
'co2_ethanol_15' 5 ;'co2_ethanol_80' 5;...
'h2o_ethanol_15' 1 ;'h2o_ethanol_140' 1;...
'methanol_ethanol_15' 5;'methanol_ethanol_120' 5;'methanol_ethanol_140' 5};
for n = 1:size(input,1)
input{n,1} = csvread(strcat(input{n,1},'k.csv'),input{n,2},0);
end
The cell in this code is 19 rows and 2 columns, the rows are all the files and the columns will contain the parameters to handle the data. Now the problem I can't find a solution for is that my first column is a string name and I want that string name to be the name of the variable where csvread writes its data to but the way I set it up now it just overwrites the string in the first column of the cell with the csv data. To be extra clear I want my matlab workspace to have variables with string names in the first column containing the data of my csv files. How do I solve this?
You don't actually want to do this. Even the Mathworks will tell you not to do this. If you are trying to use variable names to keep track of related data like this, there is always a better data structure to hold your data.
One way would be to have a cell array
data = cell(size(input(:,1)));
for n = 1:size(input,1)
data{n} = csvread(strcat(input{n,1},'k.csv'),input{n,2},0);
end
Another good option is to use a struct. You could have a single struct with dynamic field names that correspond to your data.
data = struct();
for n = 1:size(input,1)
data.(input{n,1}) = csvread(strcat(input{n,1},'k.csv'),input{n,2},0);
end
Or actually create an array of structs and hold both the name and the data within the struct.
for n = 1:size(input, 1)
data(n).name = input{n,1};
data(n).data = csvread(strcat(input{n,1},'k.csv'),input{n,2},0);
end
If you absolutly insist on doing this (again, it's is very much not recommended), then you could do it using eval:
for n = 1:size(input, 1)
data = csvread(strcat(input{n,1},'k.csv'),input{n,2},0);
eval([input{n, 1}, '= data;']);
end
I have a loop which runs 100 times. In each iteration there is a string, double and a table assigned, and in the next iteration new values are assigned for them. What I want to do is to accumulate these values and after the loop finishes save the total result as result.mat using the matlab save function. I've tried putting them in cell-array but its not working so far, so if anyone could please advise how this can be done.
This is what I did:
results_cell=(100,3);
.
.
.
results_cell(i,1)=stringA;
results_cell(i,2)=TableA;
results_cell(i,3)=DoubleA;
But it gives this error Coversion to Cell from Table is not possible. So I've tried converting TableA to array of Doubles using table2array but I still get this Coversion to Cell from Double is not possible
I think using a structure would be a good way to store your data, since they are of different types and you can assign it meaningful field names for easy reference.
For example, let's call the structure Results. You can initialize it like so.
Results = struct('StringData',[],'TableData',[],'DoubleData',[])
Since you know its dimensions, you can even do this:
N = 100;
Results(N).StringData = [];
Results(N).TableData = [];
Results(N).DoubleData = [];
This automatically create a 1xN structure with 3 fields.
Then in your loop you can assign each field with its associated data like so:
for k = 1:N
Results(k).StringData = String(k);
Results(k).TableData = Table(k);
Results(k).DoubleData = Double(k);
end
where String(k), Table(k) and Double(k) are just generic names for your actual data.
When you're done with the loop you can access any type of data using a single index and the right field name.
In order to save a .mat file, use something like this:
save SomeFileName.mat Results
Which you can load into the workspace as you would with any .mat file:
Eg:
S = load('SomeFileName.mat')
R = S.Results
Hope that helps!