Support single z-stack tif file for input

[matham]

This is part of this PR: brainglobe/cellfinder#397 and brainglobe/brainglobe-utils#67.

I had to fix this manually for the tests to pass. But this is an issue with the repo, not these changes:

ImportError while importing test module 'D:\code\cellcount\brainglobe-workflows\tests\brainmapper\test_unit\test_prep.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
C:\Prog\Python\Python310\lib\importlib\__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests\brainmapper\test_unit\test_prep.py:6: in <module>
    from brainglobe_workflows.brainmapper import prep
brainglobe_workflows\brainmapper\prep.py:25: in <module>
    import brainglobe_workflows.brainmapper.parser as parser
brainglobe_workflows\brainmapper\parser.py:25: in <module>
    from cellfinder.core.tools.source_files import source_custom_config_cellfinder
E   ImportError: cannot import name 'source_custom_config_cellfinder' from 'cellfinder.core.tools.source_files' (D:\code\cellcount\cellfinder\cellfinder\core\tools\source_files.py)

Then is succeded except of these tests, which I don't think are related to this PR

========================================================================================================== short test summary info =========================================================================================================== FAILED tests/brainmapper/test_integration/test_detection.py::test_detection_full - OSError: Unable to synchronously open file (truncated file: eof = 66060288, sblock->base_addr = 0, stored_eof = 184831728)
FAILED tests/cellfinder_core/test_integration/test_cellfinder.py::test_main - FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Matthew Einhorn\\.brainglobe-tests\\.cellfinder\\cellfinder.conf.custom'
FAILED tests/cellfinder_core/test_integration/test_cellfinder.py::test_main_w_inputs[config_local_json] - FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Matthew Einhorn\\.brainglobe-tests\\.cellfinder\\cellfinder.conf.custom'
FAILED tests/cellfinder_core/test_integration/test_cellfinder.py::test_main_w_inputs[config_GIN_json] - FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Matthew Einhorn\\.brainglobe-tests\\.cellfinder\\cellfinder.conf.custom'
FAILED tests/cellfinder_core/test_integration/test_cellfinder.py::test_entry_point_help - FileNotFoundError: [WinError 2] The system cannot find the file specified
FAILED tests/cellfinder_core/test_unit/test_cellfinder.py::test_run_workflow_from_cellfinder_run[default_input_config_cellfinder] - FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Matthew Einhorn\\.brainglobe-tests\\.cellfinder\\cellfinder.conf.custom'
FAILED tests/cellfinder_core/test_unit/test_cellfinder.py::test_run_workflow_from_cellfinder_run[config_local_json] - FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Matthew Einhorn\\.brainglobe-tests\\.cellfinder\\cellfinder.conf.custom'
FAILED tests/cellfinder_core/test_unit/test_cellfinder.py::test_run_workflow_from_cellfinder_run[config_GIN_json] - FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Matthew Einhorn\\.brainglobe-tests\\.cellfinder\\cellfinder.conf.custom'
================================================================================ 8 failed, 14 passed, 1 skipped, 1 xfailed, 39 warnings in 407.22s (0:06:47) =================================================================================

[adamltyson]

Thanks for this @matham. Just to let you know we should get back to you with a review next week.

[K-Meech]

Looks good to me! I added a few small comments below to make it clearer that dask or numpy arrays may now be returned.

The test failures you encountered should hopefully have been fixed with #89. Could you pull the latest changes from main into this branch? Hopefully that will then fix the CI.

Merging this PR will require brainglobe/brainglobe-utils#67 and brainglobe/cellfinder#397 to be merged first.

[alessandrofelder]

Many thanks @matham !
I'll merge this now, and aim to make a release of various recent changes on Monday (Friday afternoon releases are dangerous 😆 )

[codecov]

Codecov Report

Attention: Patch coverage is 85.71429% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 85.69%. Comparing base (918ac9f) to head (ae9297d).

Files	Patch %	Lines
brainglobe_workflows/brainmapper/main.py	75.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #88   +/-   ##
=======================================
  Coverage   85.69%   85.69%           
=======================================
  Files          16       16           
  Lines         839      839           
=======================================
  Hits          719      719           
  Misses        120      120           

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[alessandrofelder]

benchmark test failure expected as we have not released cellfinder with the required new API yet. Other tests pass.