BUG: force_sktiff does not work in tiff.ome_to_binary

[mhturner]

Describe the issue:

I was running into a Exception: Resource temporarily unavailable error when opening Bruker .ome.tif files on a compute cluster. I'm not sure why I was getting that error in the first place but this bug report is about my attempted workaround.

I tried to force suite2p to use tifffile.imread with force_sktiff = True however the same exception was generated the same way, so I think it is still trying to use scanimage-tiff-reader. I believe this line in tiff.ome_to_binary() may be the culprit, since it's just checking if scanimage-tiff-reader is installed and not regarding the db dictionary:

suite2p/suite2p/io/tiff.py

Line 323 in 90be895

use_sktiff = not HAS_SCANIMAGE

I'm not sure if a similar issue arises from other methods in the tiff module as well. I got around it by uninstalling scanimage-tiff-reader, and files are loading just fine using tifffile.

Reproduce the code example:

import suite2p

datadir = ...
database = {
    'data_path': [datadir],
    'input_format': 'bruker',
    'nchannels': 1,
    'nplanes': 1,
    'batch_size': 2000, 
    'functional_chan': 2,  
    'force_sktiff': 1,
}

settings = suite2p.default_settings()


output_ops = suite2p.run_s2p(settings=settings, db=database)

Example input dataset used to reproduce the issue:

No response

Error message:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/network/rit/lab/turner_lab/miniconda/envs/turnersuite/lib/python3.10/site-packages/suite2p/run_s2p.py", line 438, in run_s2p
    dbs = files_to_binary[db["input_format"]](dbs, settings, files, files_chan2)
  File "/network/rit/lab/turner_lab/miniconda/envs/turnersuite/lib/python3.10/site-packages/suite2p/io/tiff.py", line 396, in ome_to_binary
    im = read_tiff(file, tif, Ltif, ix, batch_size, use_sktiff)
  File "/network/rit/lab/turner_lab/miniconda/envs/turnersuite/lib/python3.10/site-packages/suite2p/io/tiff.py", line 126, in read_tiff
    im = tif.data(beg=ix, end=ix + nfr)
  File "/network/rit/lab/turner_lab/miniconda/envs/turnersuite/lib/python3.10/site-packages/ScanImageTiffReader/__init__.py", line 309, in data
    raise Exception(self.__ctx.log.decode("utf-8","strict"))
Exception: Resource temporarily unavailable

Version information:

suite2p v1.1.0

Context for the issue:

No response