[BUG] Cannot find a valid transformation file in 'elastix_resampled_to_auto'

[Mtkostecki]

Operating System

Linux

OS Version

Ubuntu 24.04

Code Version

v2.1.4

How are you using the application?

Old scripts

Expected Behavior

I run the analysis code and get the error below - it seems that in the elastix_resampled_to_auto folder I cannot see the tiff files created. What might be a problem? I got only IterationInfo.0.R0.txt there and elastix.log

Actual Behavior

No files in elastix_to_auto

Steps to Reproduce

1. I run the analysis code and get the error below - it seems that in the elastix_resampled_to_auto folder I cannot see the tiff files created. What might be a problem? I got only IterationInfo.0.R0.txt there and elastix.log

Logs and Screenshots

Traceback (most recent call last):
  File "/home/pne/Downloads/CellMap_template_MagdaMGR.py", line 253, in <module>
    coordinates_transformed = transformation(coordinates);
  File "/home/pne/Downloads/CellMap_template_MagdaMGR.py", line 238, in transformation
    coordinates = elx.transform_points(
  File "/home/pne/miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Elastix.py", line 951, in transform_points
    transform_parameter_dir, transform_parameter_file = transform_directory_and_file(transform_parameter_file = transform_parameter_file, transform_directory = transform_directory)
  File "/home/pne/miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Elastix.py", line 280, in transform_directory_and_file
    transform_parameter_file = transform_file(transform_parameter_dir)
  File "/home/pne/miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/ClearMap2-2.1.4-py3.9-linux-x86_64.egg/ClearMap/Alignment/Elastix.py", line 249, in transform_file
    raise RuntimeError('Cannot find a valid transformation file in %r!' % result_directory)
RuntimeError: Cannot find a valid transformation file in '/home/pne/MAteusz/Rescaled/Mouse2/elastix_resampled_to_auto'!
/home/pne/miniconda3/envs/ClearMapUi39/lib/python3.9/site-packages/torch/distributed/distributed_c10d.py:181: UserWarning: torch.distributed.reduce_op is deprecated, please use torch.distributed.ReduceOp instead
  warnings.warn(