operations with hdf files #48

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opened 2022-01-21 14:51:29 +01:00 by usov_i · 5 comments
usov_i commented 2022-01-21 14:51:29 +01:00 (Migrated from gitlab.psi.ch)

Created by: zaharko

Combine (add) and subtract hdf files in a separate tab for this functionality.

  1. When combining the files the following situations are the most common:
    1a. the metadata of the files are identical (they were measured to improve statistics)
    Then the addition of counts should happen and estimated standard deviation should be recalculated
    1b. One file is a continuation of the other (scanning motor values overlap in several points, but otherwise not)
    Then the total scanning area should be plotted, as presently hdf viewer does for one file
    1c. More complicated cases (step is not the same, etc) should not be treated, but warning or error message communicated.

There should be an option to save the combined/subtracted file in the user's computer

*Created by: zaharko* Combine (add) and subtract hdf files in a separate tab for this functionality. 1. When combining the files the following situations are the most common: 1a. the metadata of the files are identical (they were measured to improve statistics) Then the addition of counts should happen and estimated standard deviation should be recalculated 1b. One file is a continuation of the other (scanning motor values overlap in several points, but otherwise not) Then the total scanning area should be plotted, as presently hdf viewer does for one file 1c. More complicated cases (step is not the same, etc) should not be treated, but warning or error message communicated. There should be an option to save the combined/subtracted file in the user's computer
usov_i commented 2022-01-24 15:17:54 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

This functionality sounds almost exactly like the .ccl/.dat scans merging, but for hdf5 files. As a first question, does it make sense to, instead of having a tab for adding/subtracting files -> downloading them, have a tab where multiple hdf5 files can be open at the same time, similar to ccl_integrate?

*Created by: ivan-usov* This functionality sounds almost exactly like the .ccl/.dat scans merging, but for hdf5 files. As a first question, does it make sense to, instead of having a tab for adding/subtracting files -> downloading them, have a tab where multiple hdf5 files can be open at the same time, similar to ccl_integrate?
usov_i commented 2022-01-24 16:55:20 +01:00 (Migrated from gitlab.psi.ch)

Created by: zaharko

Actually, yes
I just do not know how it is from the point of view of memory. The files are not giant, so opening a number of files is not going to affect the performance?

On 24 Jan 2022, at 15:18, Ivan Usov @.@.>> wrote:

This functionality sounds almost exactly like the .ccl/.dat scans merging, but for hdf5 files. As a first question, does it make sense to, instead of having a tab for adding/subtracting files -> downloading them, have a tab where multiple hdf5 files can be open at the same time, similar to ccl_integrate?


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*Created by: zaharko* Actually, yes I just do not know how it is from the point of view of memory. The files are not giant, so opening a number of files is not going to affect the performance? On 24 Jan 2022, at 15:18, Ivan Usov ***@***.******@***.***>> wrote: This functionality sounds almost exactly like the .ccl/.dat scans merging, but for hdf5 files. As a first question, does it make sense to, instead of having a tab for adding/subtracting files -> downloading them, have a tab where multiple hdf5 files can be open at the same time, similar to ccl_integrate? — Reply to this email directly, view it on GitHub<https://github.com/paulscherrerinstitute/pyzebra/issues/48#issuecomment-1020147881>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMBMFVGIFVBDTUQFJASCCA3UXVNR5ANCNFSM5MPSNGTA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "https://github.com/paulscherrerinstitute/pyzebra/issues/48#issuecomment-1020147881", "url": "https://github.com/paulscherrerinstitute/pyzebra/issues/48#issuecomment-1020147881", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]
usov_i commented 2022-01-24 17:47:01 +01:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

I don't think that memory will be a problem. And in case of appending files, the resulting file will also be large, so there will be not much difference between both methods anyways.

Ok, so a solution based on hdf_viewer and extended with options to open multiple files, could be a good starting point. At some point we might need to review the rules for merging hdf scans, but for now I'll apply the same rules as for .ccl/.dat files

*Created by: ivan-usov* I don't think that memory will be a problem. And in case of appending files, the resulting file will also be large, so there will be not much difference between both methods anyways. Ok, so a solution based on hdf_viewer and extended with options to open multiple files, could be a good starting point. At some point we might need to review the rules for merging hdf scans, but for now I'll apply the same rules as for .ccl/.dat files
usov_i commented 2022-01-24 17:49:00 +01:00 (Migrated from gitlab.psi.ch)

Created by: zaharko

Sounds good!

On 24 Jan 2022, at 17:47, Ivan Usov @.@.>> wrote:

I don't think that memory will be a problem. And in case of appending files, the resulting file will also be large, so there will be not much difference between both methods anyways.

Ok, so a solution based on hdf_viewer and extended with options to open multiple files, could be a good starting point. At some point we might need to review the rules for merging hdf scans, but for now I'll apply the same rules as for .ccl/.dat files


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*Created by: zaharko* Sounds good! On 24 Jan 2022, at 17:47, Ivan Usov ***@***.******@***.***>> wrote: I don't think that memory will be a problem. And in case of appending files, the resulting file will also be large, so there will be not much difference between both methods anyways. Ok, so a solution based on hdf_viewer and extended with options to open multiple files, could be a good starting point. At some point we might need to review the rules for merging hdf scans, but for now I'll apply the same rules as for .ccl/.dat files — Reply to this email directly, view it on GitHub<https://github.com/paulscherrerinstitute/pyzebra/issues/48#issuecomment-1020305322>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMBMFVD75D62PCL43VX42MLUXV7BTANCNFSM5MPSNGTA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "https://github.com/paulscherrerinstitute/pyzebra/issues/48#issuecomment-1020305322", "url": "https://github.com/paulscherrerinstitute/pyzebra/issues/48#issuecomment-1020305322", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]
usov_i commented 2022-04-20 13:21:00 +02:00 (Migrated from gitlab.psi.ch)

Created by: ivan-usov

The test server now should use an optimized version of hdf scans merging (098314e30d), bringing the time from minutes down to under a second.

*Created by: ivan-usov* The test server now should use an optimized version of hdf scans merging (https://github.com/paulscherrerinstitute/pyzebra/commit/098314e30dfd5ed5281da62ffe6d24c83e1972b2), bringing the time from minutes down to under a second.
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Reference: zebra/pyzebra#48
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