[BUG] TIFFConverter.__init__() got an unexpected keyword argument 'data_type'

[tlambert03]

Summary and expected behavior

Code for reproduction (using python script or command line interface)

Can't do it with code at the moment ... was following your guide for phase from brightfield

Screenshots or steps for reproduction (using napari GUI)

Include relevant logs which are created next to the output dir, name of the dataset, yaml file(s) if encountering reconstruction errors.

11:46:35 : INFO : Dummy-10 : Running Acquisition...
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File ~\dev\waveorder\waveorder\plugin\main_widget.py:674, in MainWidget._handle_acq_error(self=<waveorder.plugin.main_widget.MainWidget object>, exc=TypeError("TIFFConverter.__init__() got an 
unexpected keyword argument 'data_type'"))
    673 def _handle_acq_error(self, exc):
--> 674     raise exc
        exc = TypeError("TIFFConverter.__init__() got an unexpected keyword argument 'data_type'")
File c:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\superqt\utils\_qthreading.py:175, in WorkerBase.run(self=<waveorder.acq.acquisition_workers.BFAcquisitionWorker object>)
    173     warnings.filterwarnings("always")
    174     warnings.showwarning = lambda *w: self.warned.emit(w)
--> 175     result = self.work()
        self = <waveorder.acq.acquisition_workers.BFAcquisitionWorker object at 0x0000022D91253250>    176 if isinstance(result, Exception):
    177     if isinstance(result, RuntimeError):
    178         # The Worker object has likely been deleted.
    179         # A deleted wrapped C/C++ object may result in a runtime
    180         # error that will cause segfault if we try to do much other
    181         # than simply notify the user.

File ~\dev\waveorder\waveorder\acq\acquisition_workers.py:270, in BFAcquisitionWorker.work(self=<waveorder.acq.acquisition_workers.BFAcquisitionWorker object>)
    267 self._check_abort()
    269 # Cleanup acquisition by closing window, converting to zarr, and deleting temp directory
--> 270 self._cleanup_acq()
        self = <waveorder.acq.acquisition_workers.BFAcquisitionWorker object at 0x0000022D91253250>    272 # Reconstruct snapped images
    273 self.n_slices = stack.shape[2]

File ~\dev\waveorder\waveorder\acq\acquisition_workers.py:352, in BFAcquisitionWorker._cleanup_acq(self=<waveorder.acq.acquisition_workers.BFAcquisitionWorker object>)
    350 try:
    351     self.latest_out_path = self.snap_dir / "raw_data.zarr"
--> 352     converter = TIFFConverter(
        dir_ = 'C:\\Users\\Admin\\Desktop\\New Folder\\snap_1'
        prefix = 'snap_1'
        self = <waveorder.acq.acquisition_workers.BFAcquisitionWorker object at 0x0000022D91253250>
        self.latest_out_path = WindowsPath('C:/Users/Admin/Desktop/New Folder/snap_1/raw_data.zarr')    353         str(Path(dir_) / prefix),
    354         str(self.latest_out_path),
    355         data_type="ometiff",
    356         grid_layout=False,
    357     )
    358     converter.run()
    359     shutil.rmtree(Path(dir_) / prefix)

TypeError: TIFFConverter.__init__() got an unexpected keyword argument 'data_type'

Environment:

Operating system: windows
Python version: 3.12
Python environment (command line, IDE, Jupyter notebook, etc):
Micro-Manager/pycromanager version:

iohub 0.2.2
waveorder sha 96872f5
pycromanager 0.27.2

[tlambert03]

pinning 'iohub<0.2' brings back the data_type kwarg ... but causes a bunch of other errors with napari and pydantic:

(waveorder) PS C:\Users\Admin\dev\waveorder> uv pip install 'iohub<0.2'  
Resolved 42 packages in 352ms
Prepared 4 packages in 874ms
Uninstalled 4 packages in 86ms
Installed 4 packages in 168ms
 - iohub==0.2.0
 + iohub==0.1.0
 - pydantic==2.11.7
 + pydantic==1.10.22
 - tifffile==2025.5.10
 + tifffile==2023.2.28
 - zarr==2.18.7
 + zarr==2.15.0
(waveorder) PS C:\Users\Admin\dev\waveorder> napari -w waveorder
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\Users\Admin\dev\waveorder\.venv\Scripts\napari.exe\__main__.py", line 4, in <module>
  File "C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\napari\__main__.py", line 17, in <module>
    from napari import Viewer
  File "C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\lazy_loader\__init__.py", line 82, in __getattr__
    submod = importlib.import_module(submod_path)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Admin\AppData\Roaming\uv\python\cpython-3.12.7-windows-x86_64-none\Lib\importlib\__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\napari\viewer.py", line 8, in <module>
    from napari.components.viewer_model import ViewerModel
  File "C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\napari\components\__init__.py", line 17, in <module>
    from napari.components.camera import Camera
  File "C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\napari\components\camera.py", line 6, in <module>
    from napari._pydantic_compat import validator
  File "C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\napari\_pydantic_compat.py", line 33, in <module>
    from pydantic.v1.error_wrappers import ErrorWrapper, display_errors
ImportError: cannot import name 'display_errors' from 'pydantic.v1.error_wrappers' (C:\Users\Admin\dev\waveorder\.venv\Lib\site-packages\pydantic\v1\error_wrappers.py)

(and clearly doesn't jive with the "iohub>=0.2,<0.3", listed in pyproject.toml)

[tlambert03]

slightly confused because #448 specifically bumped that iohub version, but BFAquisitionWorker and PolarizationAqcuisitionWorker still use the v0.1 API

[talonchandler]

Apologies, this is a code path that we're planning to hide/deprecate.

See this comment for recommended way to reconstruct, and see this issue for docs discussion.