AttributeError: module 'plantcv.plantcv' has no attribute 'fluor_fvfm'

[cstephens0991]

Hi, I am very interested in adapting your ImagingPAMProcess scripts to process our PAM images. I have downloaded your repository and am trying to run the script on some TIFF images we have generated from ImagingWin software. Unfortunately, I have hit the following error, which I am not certain of a way around:

AttributeError Traceback (most recent call last)
File ~\Documents\Chris\Experiments\WP1-001_Arabidopsis_screen\PAM\ImagingWin_automation\ImagingPAMProcessing-master\scripts\ProcessImages.py:390
387 grplist = []
388 for grp, grpdf in dfgrps:
389 # print(grp)#'%s ---' % (grp))
--> 390 grplist.append(image_avg(grpdf))
391 df_avg = pd.concat(grplist)
394 # %% Add genotype information to the processing results

File ~\Documents\Chris\Experiments\WP1-001_Arabidopsis_screen\PAM\ImagingWin_automation\ImagingPAMProcessing-master\scripts\ProcessImages.py:169, in image_avg(fundf)
166 newmask = np.zeros_like(mask)
168 # compute fv/fm and save to file
--> 169 Fv, hist_fvfm = pcv.fluor_fvfm(
170 fdark=fdark, fmin=imgmin, fmax=img, mask=mask, bins=128)
171 YII = np.divide(Fv, img, out=out_flt.copy(),
172 where=np.logical_and(mask > 0, img > 0))
173 cv2.imwrite(os.path.join(fmaxdir, outfn + '_fvfm.tif'), YII)

AttributeError: module 'plantcv.plantcv' has no attribute 'fluor_fvfm'

It appears that one of the internal functions, "image_avg()" is utilising a function sourced from the plantcv package which is not recognised. I did identify the quoted package "fluor_fvfm" in the plantcv documentation (https://plantcv.readthedocs.io/en/v3.7/fluor_fvfm/), but it does not appear to feature in more recent iterations of plantcv.

I have contacted plantcv directly to ask if this function is deprecated, and if there is a replacement function. But in any case, should this be an issue for other users of your package then I thought you should be aware. Thank you very much for your help! I sincerely apologise if this is a simple error on my part - I am somewhat new to coding.

For other information, I am running in Windows 10 and using a conda environment based on the .yml file "environment_current.yml". My Python version (within the "environment_current" environment) is 3.10.8. I have also tried generating an environment using the "environment_manuscript.yml" file - which utilises an older version of plantcv, but I run into the following conflicts:

conda env create -f environment_manuscript.yml
Collecting package metadata (repodata.json): done
Solving environment: |
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python_abi conflicts for:
jupyter -> python_abi[version='3.10.|3.8.|3.9.|3.11.|3.7.|3.6.',build='_cp36m|_cp39|_cp310|_cp38|_cp311|_cp37m']
jupyter -> python[version='>=3.8,<3.9.0a0'] -> python_abi[version='3.7|3.8|3.9',build='_pypy37_pp73|_pypy39_pp73|*_pypy38_pp73']

Package openssl conflicts for:
jupyter -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1s,<1.1.2a|>=3.0.7,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1q,<1.1.2a|>=3.0.5,<4.0a0|>=3.0.3,<4.0a0|>=1.1.1o,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a']
plantcv=3.6 -> python -> openssl[version='>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1k,<1.1.2a|>=1.1.1l,<1.1.2a|>=1.1.1n,<1.1.2a|>=1.1.1o,<1.1.2a|>=1.1.1q,<1.1.2a|>=3.0.5,<4.0a0|>=1.1.1s,<1.1.2a|>=3.0.7,<4.0a0|>=3.0.3,<4.0a0|>=3.0.2,<4.0a0|>=3.0.0,<4.0a0|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a']

Package python conflicts for:
jupyter -> ipykernel -> python[version='3.10.|3.4.|>=3.7|>=3.8|>=3.3|>=3.6|>=3.5|3.8.|3.9.|3.11.|3.7.']
jupyter -> python[version='2.7.|3.5.|3.6.*|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.11,<3.12.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0']The following specifications were found to be incompatible with your system:

• feature:/win-64::__win==0=0
• jupyter -> ipykernel -> __osx
• jupyter -> ipykernel -> __win

Your installed version is: not available

Note that strict channel priority may have removed packages required for satisfiability.

I am sorry if there is redundant information here, I just wanted to make sure was thorough.

Thanks again for your help - I really appreciate it!

[dschneiderch]

Try adding python==3.7 to the manuscript.yml file.

I think there were some updates to plantcv that won't be compatible but if you can install an older version than it should work. I don't work with this anymore so I don't plan to update it.