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OpenChemistry / tomviz

Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data
https://tomviz.org/
BSD 3-Clause "New" or "Revised" License
323 stars 86 forks source link

Resize data at load time #1986

Open anderskaestner opened 4 years ago

anderskaestner commented 4 years ago

Is your feature request related to a problem? Please describe. Tomviz tends to crash when I load and work with large data sets (close to the limits given by the available memory)

Describe the solution you would like Usually, it is not needed to work with the full data set. Therefore it would make sense to have a dialog at load time that allows the user to crop and downsize the data before loading. This would reduce the stress on the available memory.

Describe alternatives you have considered None

Additional context None

cryos commented 4 years ago

If you try the latest nightly builds we have this implemented for HDF5-based formats - supporting subvolumes or striding. How large is the data you mention, what format are you using?

anderskaestner commented 4 years ago

The data I used was 2600 tiff images (1200x1200pixels, 16-bit) ~ 8Gb on a machine with 32Gb RAM. The data opened, but Tomviz crashed soon after the display of a volume rendering. BTW, we rarely have hdf5 files (this will change, but for now tiff slices are what we have)

cryos commented 4 years ago

If you have HDF5 with a volume we now have a generalized 3D array interface discussed here, and you can even resample. We have not generalized it to TIFF, it is something I would like to assess in the future but we were able to reuse the HDF5 routines here.

It would be good to try and understand the crash, is this the latest version of Tomviz? I don't think I have anything with quite so many projections.

anderskaestner commented 4 years ago

Yes šŸ˜Š This is what Iā€™m looking for.

From: "Marcus D. Hanwell" notifications@github.com Reply-To: OpenChemistry/tomviz reply@reply.github.com Date: Monday, 4 November 2019 at 16:05 To: OpenChemistry/tomviz tomviz@noreply.github.com Cc: Kaestner Anders anders.kaestner@psi.ch, Author author@noreply.github.com Subject: Re: [OpenChemistry/tomviz] Resize data at load time (#1986)

If you have HDF5 with a volume we now have a generalized 3D array interface discussed herehttps://tomviz.readthedocs.io/en/latest/data/#hdf5-subsampling, and you can even resample. We have not generalized it to TIFF, it is something I would like to assess in the future but we were able to reuse the HDF5 routines here.

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