Changes between Version 60 and Version 61 of WikiStart


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Timestamp:
Sep 27, 2017, 11:27:09 AM (3 years ago)
Author:
steiger5na
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  • WikiStart

    v60 v61  
    150150
    151151== 5.3 How to connect to the server from home ==
    152 On Linux: 
    153 
    154 - Create a tunnel on command line: ssh -L !2222:servcalcul7a:22  username@legilnx02.legi.grenoble-inp.fr[[BR]]- Install X2GoClient (Remote desktop client) and start it[[BR]]- In upper left corner, you can create a new session. The setup for the server is: Host: localhost; Login: username; SSH port: 2222[[BR]]- Once the session is created, you can click on it, enter you password and then you are working on one of the LEGI computers.
     152On Linux:
     153
     154- Create a tunnel on command line: ssh -L !2222:servcalcul7a:22  username@legilnx02.legi.grenoble-inp.fr[[BR]]- Install X2GoClient (Remote desktop client) and start it[[BR]]- In upper left corner, you can create a new session. The setup for the server is: Host: localhost; Login: username; SSH port: 2222[[BR]]- Once the session is created, you can click on it, enter you password and then you are working on one of the LEGI computers.
    155155
    156156On Windows: As Elin!
    157157
    158158== 5.4 How to process the data ==
    159 All experiments are saved in fsnet>project>coriolis>2017>17ICESHELF>DATA>EXPXX. The  file EXPXX is for the horizontal laser sheet, EXPXX_SCAN is for the  horizontal scanning and EXPXX_VERT for the vertical sheet.  Within each EXPXX you will get three files : FALCON, PC01 and PC02.  These are the three cameras we are using during the experiments, the  FALCON is the camera for the vertical sheet and will only be used to get  the time parameters. The data from the PC01 and PC02 need to be treated  in order to perform the ''PIV''.
    160 
    161  1. '''Copy the files from the computer of the cameras'''. [[BR]]- The images from the vertical camera are saved on the local computer in G: and have to be copied into the folder FALCON in the corresponding experiment. [[BR]]- The images from PCO1 (camera at the inflow) are saved on D: of the remote desktop connection that ends with 151. The images have the be copied into the folder PCO1 of the corresponding experiment.[[BR]]- The images from PCO2 (camera above the trough) are saved on D: of the remote desktop connection that ends with 150. The images have to be copied into the folder PCO2 of the corresponding experiment.
    162  1. '''Get the .xml file with timing information'''[[BR]]In uvmat select the Run>field series then open>browse and select an experiment. Go in the folder within the FALCON and select the *.seq file. Choose "extract_rdvision_times" in the Action part, click on Input and Run. This will create a "Falcon.xml" within the FALCON folder.
    163  1. '''Convert .tif into .png[[BR]]I'''n Run>Field series you can open any .tif of the desired folder (Warning : you should not take the im.tif but any im@XXXX.tif is working). Then in the ''Action'' part you should select "extract_multitif", if the Input button is in pink you should click on it and give to the software a .xml with informations about your experiment. Once it is done you can click on RUN, don't forget to select "cluster_oar" in the run mode, the action will be much faster. When it is done a new folder called PCYY.png is created in your EXPXX folder and contains all the png.[[BR]]
    164 
    165 The next step is to use these png images in the Fields series as before, with the action ''sub_background'' that will remove all the motionless structures.  For the input you have to make sure that the 'image rescaling coefficient' is equal to 2 and then make is run. (This process takes a long time, don't forget to make it run on the cluster). The output of this action is a file PCYY.png.sback filed with png images.
     159All experiments are saved in fsnet>project>coriolis>2017>17ICESHELF>DATA>EXPXX. The  file EXPXX is for the horizontal laser sheet, EXPXX_SCAN is for the  horizontal scanning and EXPXX_VERT for the vertical sheet.  Within each EXPXX you will get three files : FALCON, PC01 and PC02.  These are the three cameras we are using during the experiments, the  FALCON is the camera for the vertical sheet and will only be used to get  the time parameters. The data from the PC01 and PC02 need to be treated  in order to perform the ''PIV''.
     160
     161 1. '''Copy the files from the computer of the cameras'''. [[BR]]- The images from the vertical camera are saved on the local computer in G: and have to be copied into the folder FALCON in the corresponding experiment. [[BR]]- The images from ''PCO1'' (camera at the inflow) are saved on D: of the remote desktop connection that ends with ''151''. The images have the be copied into the folder ''PCO1'' of the corresponding experiment.[[BR]]- The images from ''PCO2'' (camera above the trough) are saved on D: of the remote desktop connection that ends with ''150''. The images have to be copied into the folder ''PCO2'' of the corresponding experiment.
     162 1. '''Get the .xml file with timing information'''[[BR]]In uvmat select the Run>field series then open>browse and select an experiment. Go in the folder within the FALCON and select the ''.seq'' file. Choose ''extract_rdvision_times'' in the Action part, click on Input and Run. This will create a ''Falcon.xml ''within the FALCON folder.
     163 1. '''Convert .tif into .png[[BR]]'''In Run>Field series you can open any ''.tif'' of the desired folder (Warning : you should not take the im.tif but any im@XXXX.tif is working). Then in the ''Action'' part you should select ''extract_multitif'', if the Input button is in pink you should click on it and give to the software the'' Falcon.xml'' that you extracted earlier (If that doesn't exist, copy one ''.xml'' file from a previous experiment and change the seting manually. Once it is done you can click on RUN, don't forget to select ''cluster_oar'' in the run mode, the action will be much faster. When it is done a new folder called PCOY.png is created in your EXPXX folder and contains all the png. [[BR]]For''' SCANS''': Check that the right number of slices is registered! To do so, click on ''check_data_files'' in the'' Action'' part and type the right number of slices in ''nb_slices i''
     164 1. '''Remove background'''[[BR]]Browse for the right experiment again and chose the extracted ''.png'' images. The action ''sub_background'' that will remove all the motionless structures.  For the input you have to make sure that the ''image rescaling coefficient'' is equal to 2 and then make is run. (This process takes a long time, don't forget to make it run on the cluster). You can check on ''Status'', how many images are done. The output of this action is a file PCOY.png.sback filed with png images.[[BR]]For''' SCANS: '''Here, the ''image rescaling coefficient'' should be equal to 0! Also, set the ''Number of images for sliding background'' to the number of images per slice!
     165 1. '''Do PIV[[BR]]'''Browse for the images with the removed background''' '''(PCOY.png.sback.). Choose the Action ''civ_series''. For in Input, you have to import an existing .xml file to get the right parameters. You can use one .xml file from another experiment on which the piv is already done. Browse for: EXPXX/PCOY.png.sback.civ/0_XML and choose any of the img_#.xml. Make sure in the Input parameters that you chose the correct mask (right camera and with/without corner).
    166166
    167167= 6 - Organization of data files =