UnboundLocalError in register_micro()

[smith6jt-cop]

Bug Report: UnboundLocalError in registration.py:register_micro() (v1.2.0)

Repository: https://github.com/MathOnco/valis
Version: valis-wsi 1.2.0
Severity: Crash — UnboundLocalError when calling register_micro() with a class and params

Description

Valis.register_micro() in registration.py (lines 4890-4897) has a bug where passing an uninstantiated class with parameters causes an UnboundLocalError.

Code with Bug

# registration.py lines 4890-4897
if non_rigid_registrar_cls is not None:
    if isinstance(non_rigid_registrar_cls, type):
        if non_rigid_reg_params is None:
            non_rigid_registrar_obj = non_rigid_registrar_cls()
        else:
            nr = non_rigid_registrar_obj(**non_rigid_reg_params)  # BUG
    else:
        non_rigid_registrar_obj = non_rigid_registrar_cls

Two issues on line 4896:

1. non_rigid_registrar_obj is not yet defined at this point — it's only assigned in the if non_rigid_reg_params is None branch above. This causes UnboundLocalError.
2. The result is assigned to nr instead of non_rigid_registrar_obj, so even if it didn't crash, the variable used on subsequent lines (non_rigid_registrar_obj) would still be undefined.

Expected Fix

if non_rigid_registrar_cls is not None:
    if isinstance(non_rigid_registrar_cls, type):
        if non_rigid_reg_params is None:
            non_rigid_registrar_obj = non_rigid_registrar_cls()
        else:
            non_rigid_registrar_obj = non_rigid_registrar_cls(**non_rigid_reg_params)
    else:
        non_rigid_registrar_obj = non_rigid_registrar_cls

Reproduction

from valis import registration, non_rigid_registrars

registrar = registration.Valis(
    src_dir="/path/to/edf",
    dst_dir="/path/to/output",
    non_rigid_registrar_cls=None,  # Disable coarse NR
)

registrar.register()

# This call triggers the bug:
registrar.register_micro(
    max_non_rigid_registration_dim_px=4096,
    non_rigid_registrar_cls=non_rigid_registrars.OpticalFlowWarper,  # a CLASS, not instance
    non_rigid_reg_params={"smoothing_method": "gauss", "sigma_ratio": 0.01},
)
# -> UnboundLocalError: local variable 'non_rigid_registrar_obj' referenced before assignment

Note

The same pattern is correctly implemented in serial_non_rigid.py:register() (lines 995-1001), where it properly handles both class and instance inputs. The register_micro() method appears to have been partially updated.

Context

We use register_micro() for multi-cycle immunofluorescence registration (CODEX/mIF), passing OpticalFlowWarper as a class with smoothing parameters. This is the standard usage pattern documented in VALIS tutorials.

Environment

• valis-wsi 1.2.0
• Python 3.10-3.12
• Linux (Ubuntu 24.04 / HiPerGator HPC)

[cdgatenbee]

Thanks for catching this @smith6jt-cop. Hoping to push an update this week, and will make sure this fix is in there.

Best,
-Chandler