search

python-microscope / microscope

Python library for control of microscope devices, supporting hardware triggers and distribution of devices over the network for performance and flexibility.
https://www.python-microscope.org
GNU General Public License v3.0
67 stars 39 forks source link

Remove camera transforms and data processing #177

Closed dstoychev closed 3 years ago

dstoychev commented 3 years ago

I think data processing is outside of the scope of python-microscope. Currently, the Camera abc includes the _process_data method, which flips and rotates the data according to the _transform attribute. This attribute is configured by the "transform" setting and also internally by the pvcam implementation via the _set_readout_transform method. I believe both can safely be removed, with the pvcam stuff seemingly being unnecessary and maybe even obsolete.

If you agree, I can provide a PR for the necessary changes, as well as a PR for Cockpit to add the ability for post-processing of image data.

mickp commented 3 years ago

The motivation for this was so that cameras can give the same view of a region regardless of configuration changes - e.g. changing the readout mode can flip an image. Not all cameras implement transforms in hardware or their libraries, so the functionality is included as part of microscope. Where a camera does implement transforms, _process_data can simply be a passthrough.

iandobbie commented 3 years ago

dstoychev notifications@github.com writes:

I think data processing is outside of the scope of python-microscope. Currently, the Camera abc includes the _process_data method, which flips and rotates the data according to the _transform attribute. This attribute is configured by the "transform" setting and also internally by the pvcam implementation via the _set_readout_transform method. I believe both can safely be removed, with the pvcam stuff seemingly being unnecessary and maybe even obsolete.

If you agree, I can provide a PR for the necessary changes, as well as a PR for Cockpit to add the ability for post-processing of image data.

No there was a fundamental reason for having a camera rotation in microscope, If you have 50 cameras on 5 machines, do you really want to force the master cockpit machines to deal with all those rotations?

Also most EMCCD cameras return images with different orientations in conventional and EM mode. As a function of the device microscope can know about this and deal with it, putting this in cockpit is wrong.

However we also still need orations in cockpit as different beam paths might produce images at different rotations. I know this is code duplication but not much and I think there are cases where both are the right place to do it.

Ian

dstoychev commented 3 years ago

Thanks to both of you for the feedback. It seems post-processing is needed to some degree in python-microscope. I will close the issue here for now and focus on post-processing in Cockpit.