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Which Format is Faster, Matlab (.mat) or NumPy (.npy)?



Announcing the arrival of Valued Associate #679: Cesar Manara
Planned maintenance scheduled April 17/18, 2019 at 00:00UTC (8:00pm US/Eastern)
2019 Moderator Election Q&A - Questionnaire
2019 Community Moderator Election ResultsMATLAB Perceptronunique column value in python numpyAppending to numpy array for creating datasetis numpy isclose function returning bad answer?Python - Converting 3D numpy array to 2DQuestion Related Numpywhy nobody uses matlabHow to make a numpy ndarray from several numpy arraysOpen image saved using python in matlabNumpy Python deep learning framework










2












$begingroup$


I am working on a deep learning problem to detect cancer in images of size 250 x 250. I have hardware limitations and I have been running out of memory.



I decided to convert my images to Matlab formatted files (".mat"), with some improvement; however, I still run out of memory. I have explored some resources that highly recommend using NumPy files (".npy").



It would be costly to convert my images to NumPy files, so I would like to make sure that converting will make a difference. I am not asking for memory enhancement algorithms (e.g. batching), just the memory difference between ".mat" and ".npy" files.










share|improve this question











$endgroup$




bumped to the homepage by Community 23 mins ago


This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.














  • $begingroup$
    Can you post your loading code? Can you post benchmarking, including memory usage?
    $endgroup$
    – Brian Spiering
    Nov 10 '18 at 18:07















2












$begingroup$


I am working on a deep learning problem to detect cancer in images of size 250 x 250. I have hardware limitations and I have been running out of memory.



I decided to convert my images to Matlab formatted files (".mat"), with some improvement; however, I still run out of memory. I have explored some resources that highly recommend using NumPy files (".npy").



It would be costly to convert my images to NumPy files, so I would like to make sure that converting will make a difference. I am not asking for memory enhancement algorithms (e.g. batching), just the memory difference between ".mat" and ".npy" files.










share|improve this question











$endgroup$




bumped to the homepage by Community 23 mins ago


This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.














  • $begingroup$
    Can you post your loading code? Can you post benchmarking, including memory usage?
    $endgroup$
    – Brian Spiering
    Nov 10 '18 at 18:07













2












2








2





$begingroup$


I am working on a deep learning problem to detect cancer in images of size 250 x 250. I have hardware limitations and I have been running out of memory.



I decided to convert my images to Matlab formatted files (".mat"), with some improvement; however, I still run out of memory. I have explored some resources that highly recommend using NumPy files (".npy").



It would be costly to convert my images to NumPy files, so I would like to make sure that converting will make a difference. I am not asking for memory enhancement algorithms (e.g. batching), just the memory difference between ".mat" and ".npy" files.










share|improve this question











$endgroup$




I am working on a deep learning problem to detect cancer in images of size 250 x 250. I have hardware limitations and I have been running out of memory.



I decided to convert my images to Matlab formatted files (".mat"), with some improvement; however, I still run out of memory. I have explored some resources that highly recommend using NumPy files (".npy").



It would be costly to convert my images to NumPy files, so I would like to make sure that converting will make a difference. I am not asking for memory enhancement algorithms (e.g. batching), just the memory difference between ".mat" and ".npy" files.







python deep-learning matlab numpy






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Nov 16 '18 at 18:07









from keras import michael

29810




29810










asked Jun 28 '18 at 10:53









Andrew NaguibAndrew Naguib

676




676





bumped to the homepage by Community 23 mins ago


This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.







bumped to the homepage by Community 23 mins ago


This question has answers that may be good or bad; the system has marked it active so that they can be reviewed.













  • $begingroup$
    Can you post your loading code? Can you post benchmarking, including memory usage?
    $endgroup$
    – Brian Spiering
    Nov 10 '18 at 18:07
















  • $begingroup$
    Can you post your loading code? Can you post benchmarking, including memory usage?
    $endgroup$
    – Brian Spiering
    Nov 10 '18 at 18:07















$begingroup$
Can you post your loading code? Can you post benchmarking, including memory usage?
$endgroup$
– Brian Spiering
Nov 10 '18 at 18:07




$begingroup$
Can you post your loading code? Can you post benchmarking, including memory usage?
$endgroup$
– Brian Spiering
Nov 10 '18 at 18:07










3 Answers
3






active

oldest

votes


















1












$begingroup$

From my research:



  • both can store data in binary format

  • both store the data type of the data

  • I am unsure about compression ratios and load time, which seems to be the subtext of your question.

One thing you don't seem to address is what you are loading the data into, or whether you are considering moving from a MATLAB environment to Python environment or visa-versa.



That said, I found this post useful and thought it may be helpful to you if you have not seen it already. https://stackoverflow.com/a/10997335/3259054 Perhaps you could write a small script to sample some files and see the difference.



Have you considered the HDF5 format? If you are looking to make a change, you might as well test other options too and HDF5 has a lot of momentum towards becoming the de facto standard for scientific computing.



Finally, purely out of a desire to learn, why are you concerned about the file format if you have memory constraints?






share|improve this answer









$endgroup$




















    1












    $begingroup$

    MATLAB has known for it's memory consumption. So even if you use same data for processing in Python overall system memory utilization will be less in Python.



    Based on my experience so far using Python helped me dealing more data with better performance.



    One other hand Python have many libraries/Frameworks out of box to further enhance the overall performance and Machine Learning/ Deep Learning (I am not much sure if similar Libraries & Frameworks are available in Matlab also).






    share|improve this answer











    $endgroup$




















      0












      $begingroup$

      One way to reduce in-memory bottlenecks is to more efficiently handle data processing (regardless of the on-disk format).



      There are software frameworks designed to improve the training process, especially for loading images. Dask is one such framework to scale existing Python workflows, thus mostly likely it will reduce the memory bottleneck for .npy files relative to .mat files (the only way to be sure is to benchmark).






      share|improve this answer











      $endgroup$













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        3 Answers
        3






        active

        oldest

        votes








        3 Answers
        3






        active

        oldest

        votes









        active

        oldest

        votes






        active

        oldest

        votes









        1












        $begingroup$

        From my research:



        • both can store data in binary format

        • both store the data type of the data

        • I am unsure about compression ratios and load time, which seems to be the subtext of your question.

        One thing you don't seem to address is what you are loading the data into, or whether you are considering moving from a MATLAB environment to Python environment or visa-versa.



        That said, I found this post useful and thought it may be helpful to you if you have not seen it already. https://stackoverflow.com/a/10997335/3259054 Perhaps you could write a small script to sample some files and see the difference.



        Have you considered the HDF5 format? If you are looking to make a change, you might as well test other options too and HDF5 has a lot of momentum towards becoming the de facto standard for scientific computing.



        Finally, purely out of a desire to learn, why are you concerned about the file format if you have memory constraints?






        share|improve this answer









        $endgroup$

















          1












          $begingroup$

          From my research:



          • both can store data in binary format

          • both store the data type of the data

          • I am unsure about compression ratios and load time, which seems to be the subtext of your question.

          One thing you don't seem to address is what you are loading the data into, or whether you are considering moving from a MATLAB environment to Python environment or visa-versa.



          That said, I found this post useful and thought it may be helpful to you if you have not seen it already. https://stackoverflow.com/a/10997335/3259054 Perhaps you could write a small script to sample some files and see the difference.



          Have you considered the HDF5 format? If you are looking to make a change, you might as well test other options too and HDF5 has a lot of momentum towards becoming the de facto standard for scientific computing.



          Finally, purely out of a desire to learn, why are you concerned about the file format if you have memory constraints?






          share|improve this answer









          $endgroup$















            1












            1








            1





            $begingroup$

            From my research:



            • both can store data in binary format

            • both store the data type of the data

            • I am unsure about compression ratios and load time, which seems to be the subtext of your question.

            One thing you don't seem to address is what you are loading the data into, or whether you are considering moving from a MATLAB environment to Python environment or visa-versa.



            That said, I found this post useful and thought it may be helpful to you if you have not seen it already. https://stackoverflow.com/a/10997335/3259054 Perhaps you could write a small script to sample some files and see the difference.



            Have you considered the HDF5 format? If you are looking to make a change, you might as well test other options too and HDF5 has a lot of momentum towards becoming the de facto standard for scientific computing.



            Finally, purely out of a desire to learn, why are you concerned about the file format if you have memory constraints?






            share|improve this answer









            $endgroup$



            From my research:



            • both can store data in binary format

            • both store the data type of the data

            • I am unsure about compression ratios and load time, which seems to be the subtext of your question.

            One thing you don't seem to address is what you are loading the data into, or whether you are considering moving from a MATLAB environment to Python environment or visa-versa.



            That said, I found this post useful and thought it may be helpful to you if you have not seen it already. https://stackoverflow.com/a/10997335/3259054 Perhaps you could write a small script to sample some files and see the difference.



            Have you considered the HDF5 format? If you are looking to make a change, you might as well test other options too and HDF5 has a lot of momentum towards becoming the de facto standard for scientific computing.



            Finally, purely out of a desire to learn, why are you concerned about the file format if you have memory constraints?







            share|improve this answer












            share|improve this answer



            share|improve this answer










            answered Nov 9 '18 at 14:42









            SkiddlesSkiddles

            695210




            695210





















                1












                $begingroup$

                MATLAB has known for it's memory consumption. So even if you use same data for processing in Python overall system memory utilization will be less in Python.



                Based on my experience so far using Python helped me dealing more data with better performance.



                One other hand Python have many libraries/Frameworks out of box to further enhance the overall performance and Machine Learning/ Deep Learning (I am not much sure if similar Libraries & Frameworks are available in Matlab also).






                share|improve this answer











                $endgroup$

















                  1












                  $begingroup$

                  MATLAB has known for it's memory consumption. So even if you use same data for processing in Python overall system memory utilization will be less in Python.



                  Based on my experience so far using Python helped me dealing more data with better performance.



                  One other hand Python have many libraries/Frameworks out of box to further enhance the overall performance and Machine Learning/ Deep Learning (I am not much sure if similar Libraries & Frameworks are available in Matlab also).






                  share|improve this answer











                  $endgroup$















                    1












                    1








                    1





                    $begingroup$

                    MATLAB has known for it's memory consumption. So even if you use same data for processing in Python overall system memory utilization will be less in Python.



                    Based on my experience so far using Python helped me dealing more data with better performance.



                    One other hand Python have many libraries/Frameworks out of box to further enhance the overall performance and Machine Learning/ Deep Learning (I am not much sure if similar Libraries & Frameworks are available in Matlab also).






                    share|improve this answer











                    $endgroup$



                    MATLAB has known for it's memory consumption. So even if you use same data for processing in Python overall system memory utilization will be less in Python.



                    Based on my experience so far using Python helped me dealing more data with better performance.



                    One other hand Python have many libraries/Frameworks out of box to further enhance the overall performance and Machine Learning/ Deep Learning (I am not much sure if similar Libraries & Frameworks are available in Matlab also).







                    share|improve this answer














                    share|improve this answer



                    share|improve this answer








                    edited Nov 13 '18 at 3:11









                    Stephen Rauch

                    1,52551330




                    1,52551330










                    answered Nov 13 '18 at 2:27









                    mannumannu

                    745




                    745





















                        0












                        $begingroup$

                        One way to reduce in-memory bottlenecks is to more efficiently handle data processing (regardless of the on-disk format).



                        There are software frameworks designed to improve the training process, especially for loading images. Dask is one such framework to scale existing Python workflows, thus mostly likely it will reduce the memory bottleneck for .npy files relative to .mat files (the only way to be sure is to benchmark).






                        share|improve this answer











                        $endgroup$

















                          0












                          $begingroup$

                          One way to reduce in-memory bottlenecks is to more efficiently handle data processing (regardless of the on-disk format).



                          There are software frameworks designed to improve the training process, especially for loading images. Dask is one such framework to scale existing Python workflows, thus mostly likely it will reduce the memory bottleneck for .npy files relative to .mat files (the only way to be sure is to benchmark).






                          share|improve this answer











                          $endgroup$















                            0












                            0








                            0





                            $begingroup$

                            One way to reduce in-memory bottlenecks is to more efficiently handle data processing (regardless of the on-disk format).



                            There are software frameworks designed to improve the training process, especially for loading images. Dask is one such framework to scale existing Python workflows, thus mostly likely it will reduce the memory bottleneck for .npy files relative to .mat files (the only way to be sure is to benchmark).






                            share|improve this answer











                            $endgroup$



                            One way to reduce in-memory bottlenecks is to more efficiently handle data processing (regardless of the on-disk format).



                            There are software frameworks designed to improve the training process, especially for loading images. Dask is one such framework to scale existing Python workflows, thus mostly likely it will reduce the memory bottleneck for .npy files relative to .mat files (the only way to be sure is to benchmark).







                            share|improve this answer














                            share|improve this answer



                            share|improve this answer








                            edited Nov 10 '18 at 18:03

























                            answered Nov 10 '18 at 17:51









                            Brian SpieringBrian Spiering

                            4,2781129




                            4,2781129



























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