Generalize photosynthesis filenaming

[wurDevTim]

Describe your changes
Phenovation changed the naming convention over time. Some small changes where made to add support for the new files.
The new code is tested with data from both new and old cropreporters.

Type of update
Is this an update of the cropreporter filenaming to make the OJIP analysis work with old and new cropreporters.

Associated issues
#978

Additional context
The current git only contains files which uses the 'old' metadata format.
I have some test images with the new format, who can send these to? Or where to upload?
Maybe also add a test for these new files?

For the reviewer
See this page for instructions on how to review the pull request.

• PR functionality reviewed in a Jupyter Notebook
• All tests pass
• Test coverage remains 100%
• Documentation tested
• New documentation pages added to plantcv/mkdocs.yml
• Changes to function input/output signatures added to updating.md
• Code reviewed
• PR approved

[codecov]

Codecov Report

Merging #984 (484a55d) into release-4.0 (f6c6937) will not change coverage.
The diff coverage is 100.00%.

@@              Coverage Diff              @@
##           release-4.0      #984   +/-   ##
=============================================
  Coverage       100.00%   100.00%           
=============================================
  Files              171       171           
  Lines             7528      7540   +12     
=============================================
+ Hits              7528      7540   +12     

Flag	Coverage Δ
unittests	100.00% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
...lantcv/plantcv/photosynthesis/read_cropreporter.py	100.00% <100.00%> (ø)

[HaleySchuhl]

Hi @wurDevTim thanks for opening this PR. The code looks good, but the additional functionality at L78 - L80 and L121-L123 are not getting hit by the new test. Also a clarification sentence added to the documentation for photosynthesis_read_cropreporter would be good too!

[wurDevTim]

@HaleySchuhl, I see, to hit those lines I have to add testdata from our cropreporter (the new file format).
The current ones are called PSII_PSD_supopt_temp_btx623_22_rep1.DAT and PSII_PSD_supopt_temp_btx623_22_rep1.INF.
Is there a naming preference for the new files? To make it easy to keep the two version apart or can I use any name I like?

[HaleySchuhl]

@wurDevTim pretty much any name you'd like!

[wurDevTim]

@HaleySchuhl Added the files by making subfolders for the different cropreporter versions. Also updated the docs, let me know if there are any other things you like me to change.

[wurDevTim]

After quite some mails back and forth to phenovation we figured out that when 'SaveAllFrames' is set to '0' it only returns 3 frames: Fdark, F0, Fm for the PSD and Flight, Fp, Fmp for the PSL.

However, the framelabels are not updated. therefore the code below tries to set frame labels to frames which don't exist:

elif 'FqFmFrameFsp' in metadata:
   fsp_frame = int(metadata["FqFmFrameFsp"]) + 1
   fmp_frame = int(metadata["FqFmFrameFmp"]) + 1            
elif 'LtOjipFrameFsp' in metadata:
   fsp_frame = int(metadata["LtOjipFrameFsp"]) + 1
   fmp_frame = int(metadata["LtOjipFrameFmp"]) + 1

To make plantcv robust against this bug I changed the code to:

if metadata['SaveAllFrames'] == '0':
   fsp_frame = 1
   fmp_frame = 2
elif 'FqFmFrameFsp' in metadata:
   fsp_frame = int(metadata["FqFmFrameFsp"]) + 1
   fmp_frame = int(metadata["FqFmFrameFmp"]) + 1            
elif 'LtOjipFrameFsp' in metadata:
   fsp_frame = int(metadata["LtOjipFrameFsp"]) + 1
   fmp_frame = int(metadata["LtOjipFrameFmp"]) + 1

[nfahlgren]

Hi @wurDevTim, sorry for the long delay. I think this looks great, I just have a few suggestions for simplifying the code a bit

Tests were updated to achieve 100% coverage