Non-Rigid Registration Error

[ewestlundicr]

Hi,

I have a set of 20 czi-images to align and merge with Valis. The majority have been working great, but in 6 of them I get the following error when I reach the non-rigid alignment step.

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Preparing images for non-rigid registration:   0%|          | 0/2 [00:00<?, ?image/s]
[c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\valis\valtils.py:25](file:///C:/Users/ewestlund/Documents/Python/Nicole_valis_merge/valis_merge_venv/lib/site-packages/valis/valtils.py:25): UserWarning: 'NoneType' object has no attribute 'pointer'
  warnings.warn(warning_msg, warning_type)
Traceback (most recent call last):
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\valis\registration.py", line 4624, in register
    non_rigid_registrar = self.non_rigid_register(rigid_registrar, slide_processors)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\valis\registration.py", line 4077, in non_rigid_register
    self.prep_images_for_large_non_rigid_registration(max_img_dim=self.max_non_rigid_registration_dim_px,
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\valis\registration.py", line 3850, in prep_images_for_large_non_rigid_registration
    vips_level_img = slide_obj.slide2vips(closest_img_level)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\valis\registration.py", line 485, in slide2vips
    vips_img = self.reader.slide2vips(level=level, series=series, xywh=xywh)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\valis\slide_io.py", line 1300, in slide2vips
    vips_slide = pyvips.Image.arrayjoin(
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\pyvips\vimage.py", line 256, in call_function
    return pyvips.Operation.call(name, *args, **kwargs)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\pyvips\voperation.py", line 282, in call
    op.set(name, intro.details[name]['flags'], match_image, value)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\pyvips\voperation.py", line 216, in set
    super(Operation, self).set(name, value)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\pyvips\vobject.py", line 117, in set
    gv.set(value)
  File "c:\Users\ewestlund\Documents\Python\Nicole_valis_merge\valis_merge_venv\lib\site-packages\pyvips\gvalue.py", line 221, in set
    gobject_lib.g_object_ref(image.pointer)
AttributeError: 'NoneType' object has no attribute 'pointer'

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This is the script I've been using

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from valis import registration

slide_src_dir = "../TMA Slide 12/TMA Slide 12 Scene 01" # Original files directory
results_dst_dir = "../TMA Slide 12/TMA Slide 12 Scene 01/registration" # Registration results saved here
merged_slide_dst_f = "../TMA Slide 12/TMA Slide 12 Scene 01/merged/TMA Slide 12 Scene 01.ome.tiff" # Where to save merged slide

registrar = registration.Valis(slide_src_dir, results_dst_dir)
rigid_registrar, non_rigid_registrar, error_df = registrar.register()

registrar.warp_and_merge_slides(merged_slide_dst_f, non_rigid=False)

registration.kill_jvm() # Kill the JVM

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I'm using Python v3.10 and Valis v1.1.0.

If anyone has any ideas of what is causing the error, I would be very grateful.

Thank you