Skip to content

Draft: add `z_nm_pattern`

payno requested to merge add_z_nm_pattern into main

overview

Add a new name file convention according to the frame z position instead of the index. For now we expect z to be provided in nano meter.

pattern looks like: "{volume_basename}_{z_mm}mm{z_um_zfill3}um{z_nm_zfill3}nm.{data_extension}"

The behavior is defined in VolumeSingleFrameBaseZNM

This feature has been implemented as extension of the the three single frame volume scheme we have at the moment: edf, tiff and jp2k. As urllib prevent from using _ we went for edf+znm, tiff+znm and jp2k+znm that I think are convenient enough.

notes

bottlenecks

z random or decreasing values

for now it save the volume according to z which is provided by _z_nm_pos and set from set_z_nm_positions. But nothing prevent from setting unordered z values or decreasing z values. But the reading and definition of data will always be made with z increasing values.

To avoid this we are now checking z values re providing 'decreasing'.

Edited by payno

Merge request reports