Matlab function works very slow

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Extrapolating from a .mat file of the vectors x, y, z I have seen that my code is very slow in the operation and I can not understand why, even though I have done a lot of evidence about it.
The .mat file is initially composed of a 1x1 struct to which I access (in the code is: fileAllData{i,1}), a 2x1 cell to which I access (in the code: (attivita{1,j})) and finally the final cell to which I access ({s,1}).

function[x, y, z, s] = getXYZ(pathData, j, i, s)

        fullDataPath = sprintf(...); 

        fileAllData = importdata(fullDataPath);

        m = fileAllData{i,1}.(attivita{1,j}){s,1};



        x = m(1,:)';

        y = m(2,:)';

        z = m(3,:)';

        .....

        s = s+1;



    end





        Main function:

        .....

        for j = 1:K         

            for i = 1:nSubjects 

            s = 1;

                     while s<=trials(j)



                         [x, y, z, s] = getXYZ(pathData, j, i, s);

                      end

            end

        end

        ...

What can be attributed to slowness? I do not know how to access data more efficiently. What can I try?

asked Nov 22 '18 at 14:24

Sara Savio

1416

2

Have you tried profiling this function? You can do that by setting up a script which calls the function, and pressing "Run and Time" in the top bar. That'll tell you which parts of your function are the most time consuming. Run that, then edit the question to contain the result and investigate from there.

– Adriaan
Nov 22 '18 at 14:31

Second the suggestion on profiling, also - how much total data is there? Would it make more sense to read the file once and get the data in memory, then process it?

– paisanco
Nov 22 '18 at 14:32

I solve the problem with the suggestion of Adriaan, thank you very very much

– Sara Savio
Nov 22 '18 at 14:46

Sara, if you solved the problem, please post an answer here, and accept it. Thanks!

– Cris Luengo
Nov 22 '18 at 19:09

I bet your problem is in importdata. I’d suggest reading in the data only once, reading data is expensive.

– Cris Luengo
Nov 22 '18 at 19:10

add a comment |

function[x, y, z, s] = getXYZ(pathData, j, i, s)

        fullDataPath = sprintf(...); 

        fileAllData = importdata(fullDataPath);

        m = fileAllData{i,1}.(attivita{1,j}){s,1};



        x = m(1,:)';

        y = m(2,:)';

        z = m(3,:)';

        .....

        s = s+1;



    end





        Main function:

        .....

        for j = 1:K         

            for i = 1:nSubjects 

            s = 1;

                     while s<=trials(j)



                         [x, y, z, s] = getXYZ(pathData, j, i, s);

                      end

            end

        end

        ...

What can be attributed to slowness? I do not know how to access data more efficiently. What can I try?

asked Nov 22 '18 at 14:24

Sara Savio

1416

2

Have you tried profiling this function? You can do that by setting up a script which calls the function, and pressing "Run and Time" in the top bar. That'll tell you which parts of your function are the most time consuming. Run that, then edit the question to contain the result and investigate from there.

– Adriaan
Nov 22 '18 at 14:31

Second the suggestion on profiling, also - how much total data is there? Would it make more sense to read the file once and get the data in memory, then process it?

– paisanco
Nov 22 '18 at 14:32

I solve the problem with the suggestion of Adriaan, thank you very very much

– Sara Savio
Nov 22 '18 at 14:46

Sara, if you solved the problem, please post an answer here, and accept it. Thanks!

– Cris Luengo
Nov 22 '18 at 19:09

I bet your problem is in importdata. I’d suggest reading in the data only once, reading data is expensive.

– Cris Luengo
Nov 22 '18 at 19:10

add a comment |

function[x, y, z, s] = getXYZ(pathData, j, i, s)

        fullDataPath = sprintf(...); 

        fileAllData = importdata(fullDataPath);

        m = fileAllData{i,1}.(attivita{1,j}){s,1};



        x = m(1,:)';

        y = m(2,:)';

        z = m(3,:)';

        .....

        s = s+1;



    end





        Main function:

        .....

        for j = 1:K         

            for i = 1:nSubjects 

            s = 1;

                     while s<=trials(j)



                         [x, y, z, s] = getXYZ(pathData, j, i, s);

                      end

            end

        end

        ...

What can be attributed to slowness? I do not know how to access data more efficiently. What can I try?

asked Nov 22 '18 at 14:24

Sara Savio

1416

function[x, y, z, s] = getXYZ(pathData, j, i, s)

        fullDataPath = sprintf(...); 

        fileAllData = importdata(fullDataPath);

        m = fileAllData{i,1}.(attivita{1,j}){s,1};



        x = m(1,:)';

        y = m(2,:)';

        z = m(3,:)';

        .....

        s = s+1;



    end





        Main function:

        .....

        for j = 1:K         

            for i = 1:nSubjects 

            s = 1;

                     while s<=trials(j)



                         [x, y, z, s] = getXYZ(pathData, j, i, s);

                      end

            end

        end

        ...

What can be attributed to slowness? I do not know how to access data more efficiently. What can I try?

matlab performance function time

asked Nov 22 '18 at 14:24

Sara Savio

1416

asked Nov 22 '18 at 14:24

Sara Savio

1416

asked Nov 22 '18 at 14:24

Sara Savio

1416

asked Nov 22 '18 at 14:24

Sara Savio

1416

asked Nov 22 '18 at 14:24

Sara Savio

1416

2

Have you tried profiling this function? You can do that by setting up a script which calls the function, and pressing "Run and Time" in the top bar. That'll tell you which parts of your function are the most time consuming. Run that, then edit the question to contain the result and investigate from there.

– Adriaan
Nov 22 '18 at 14:31

Second the suggestion on profiling, also - how much total data is there? Would it make more sense to read the file once and get the data in memory, then process it?

– paisanco
Nov 22 '18 at 14:32

I solve the problem with the suggestion of Adriaan, thank you very very much

– Sara Savio
Nov 22 '18 at 14:46

Sara, if you solved the problem, please post an answer here, and accept it. Thanks!

– Cris Luengo
Nov 22 '18 at 19:09

I bet your problem is in importdata. I’d suggest reading in the data only once, reading data is expensive.

– Cris Luengo
Nov 22 '18 at 19:10

add a comment |

2

Have you tried profiling this function? You can do that by setting up a script which calls the function, and pressing "Run and Time" in the top bar. That'll tell you which parts of your function are the most time consuming. Run that, then edit the question to contain the result and investigate from there.

– Adriaan
Nov 22 '18 at 14:31

Second the suggestion on profiling, also - how much total data is there? Would it make more sense to read the file once and get the data in memory, then process it?

– paisanco
Nov 22 '18 at 14:32

I solve the problem with the suggestion of Adriaan, thank you very very much

– Sara Savio
Nov 22 '18 at 14:46

Sara, if you solved the problem, please post an answer here, and accept it. Thanks!

– Cris Luengo
Nov 22 '18 at 19:09

I bet your problem is in importdata. I’d suggest reading in the data only once, reading data is expensive.

– Cris Luengo
Nov 22 '18 at 19:10

Have you tried profiling this function? You can do that by setting up a script which calls the function, and pressing "Run and Time" in the top bar. That'll tell you which parts of your function are the most time consuming. Run that, then edit the question to contain the result and investigate from there.

– Adriaan
Nov 22 '18 at 14:31

Second the suggestion on profiling, also - how much total data is there? Would it make more sense to read the file once and get the data in memory, then process it?

– paisanco
Nov 22 '18 at 14:32

I solve the problem with the suggestion of Adriaan, thank you very very much

– Sara Savio
Nov 22 '18 at 14:46

Sara, if you solved the problem, please post an answer here, and accept it. Thanks!

– Cris Luengo
Nov 22 '18 at 19:09

I bet your problem is in importdata. I’d suggest reading in the data only once, reading data is expensive.

– Cris Luengo
Nov 22 '18 at 19:10

add a comment |

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