Is it possible to read from io.BytesIO?

[WaterKnight1998]

I am going to use this util in Flask backend. However, I would like to use pims_nd2 in io.BytesIO.

Is it possible? Or should I save file locally?

[caspervdw]

Hi,

Sorry, the open only works with actual file paths. As this project is merely wrapping the ND2 reading library from Nikon, we don’t have much control.

You could try virtual file systems if you want to stay in memory, but it depends on your OS how that works. I don’t have experience with that.

Or, try a pure Python alternative like https://github.com/rbnvrw/nd2reader

[WaterKnight1998]

Hi,

Sorry, the open only works with actual file paths. As this project is merely wrapping the ND2 reading library from Nikon, we don’t have much control.

You could try virtual file systems if you want to stay in memory, but it depends on your OS how that works. I don’t have experience with that.

Or, try a pure Python alternative like https://github.com/rbnvrw/nd2reader

Thank you! What is the approach with virtual file system?

[WaterKnight1998]

@caspervdw I have created a temporal file in /dev/shm from which nd2reader read contents. However, after clossing reader, and deleting temporal file. It is still there. So I think your library closes bad the file. Do you maintain any reference inside it?

[lurch]

@caspervdw There's more context in PyFilesystem/pyfilesystem2#402 (comment)

[WaterKnight1998]

@caspervdw There's more context in PyFilesystem/pyfilesystem2#402 (comment)

Right!

[caspervdw]

Hi,
I do think this library properly closes the reader. The correct ND2SDK function is called at reader.close(). Even if you do not call reader.close(), it should still be done when the reader goes out of scope. It happens at

pims_nd2/pims_nd2/nd2reader.py

Line 173 in 00acf8c

def close(self):