[Bug]: AFMReader SPM module unable to handle common units

[SylviaWhittle]

Describe the bug

Tobi found a bug in TopoStats where some .spm files fail. The issue appears to be that pm is not a valid unit when unpacking the pixel_to_nm_scaling factor. I compared TopoStats' spm loading code to AFMReader's and found that TopoStats has a unit dictionary of:

  unit_dict = {
      "pm": 1e-3,
      "nm": 1,
      "um": 1e3,
      "mm": 1e6,
  }

and AFMReader has:

  unit_dict = {
      "nm": 1,
      "um": 1e3,
  }

This needs updating ASAP. I'll do it.

Tobi's output log is attached below for evidence.

Copy of the output

Traceback (most recent call last):
  File "/Users/t/miniconda3/envs/main_topostats/bin/topostats", line 8, in <module>
    sys.exit(entry_point())
  File "/Users/t/Documents/topostats/main_topostats/TopoStats/topostats/entry_point.py", line 1204, in entry_point
    args.func(args)
  File "/Users/t/Documents/topostats/main_topostats/TopoStats/topostats/run_modules.py", line 231, in process
    all_scan_data.get_data()
  File "/Users/t/Documents/topostats/main_topostats/TopoStats/topostats/io.py", line 790, in get_data
    self.image, self.pixel_to_nm_scaling = suffix_to_loader[suffix]()
  File "/Users/t/Documents/topostats/main_topostats/TopoStats/topostats/io.py", line 640, in load_spm
    return spm.load_spm(file_path=self.img_path, channel=self.channel)
  File "/Users/t/miniconda3/envs/main_topostats/lib/python3.10/site-packages/AFMReader/spm.py", line 102, in load_spm
    return (image, spm_pixel_to_nm_scaling(filename, channel_data))
  File "/Users/t/miniconda3/envs/main_topostats/lib/python3.10/site-packages/AFMReader/spm.py", line 38, in spm_pixel_to_nm_scaling
    px_to_real[1][0] * unit_dict[px_to_real[1][1]],
KeyError: 'pm'
(main_topostats) t@dyn232037 430 minicircles topostats test for Niel % 

To Reproduce

The file is not shared as I presume it's secret, but ask Tobi for the .spm file and run TopoStats using it.

AFMReader Version

0.1.0

Python Version

3.11

Operating System

MacOS M1/M2 (post-2021)

Python Packages

N/A, need to be fast

[ns-rse]

I had clocked these units in the _spm_pixel_to_nm_scaling() function but didn't fully appreciate the implications on loading files and thought it was a method that was used elsewhere (I've a vague recollection that this might have been added after a user wanted a more comprehensive set of units).

Sorry for not copying that over. If this is to be improved here in AFMReader we should also remove _spm_pixel_to_nm_scaling() from TopoStats (captured in #1036).