UnboundLocalError: local variable 'slide_dimensions' referenced before assignment

[melanieloth]

Hi,

I am trying to register five .tif images by running the following code:

import time
import os
from valis import registration
from valis.slide_io import BioFormatsSlideReader

# the images for this script are all the h and e images
# This script is testing the ordering function for valis
# inital test to make sure that the script was working for registration
slide_src_dir = "./Demo1/"
results_dst_dir = "./01_demo"


# Create a Valis object and use it to register the slides in slide_src_dir
start = time.time()
registrar = registration.Valis(slide_src_dir, results_dst_dir)
registrar_rigid, registrar_nonrigid, error_df = registrar.register(reader_cls=BioFormatsSlideReader)
stop = time.time()
elapsed = stop - start
print(f"regisration time is {elapsed/60} minutes")


# Check results in registered_slide_dst_dir. If they look good, export the registered slides
registered_slide_dst_dir = os.path.join("./01_demo/registered_slides", registrar.name)
#start = time.time()
registrar.warp_and_save_slides(registered_slide_dst_dir)
#stop = time.time()
#elapsed = stop - start
#print(f"saving {registrar.size} slides took {elapsed/60} minutes")



# Shutdown the JVM
registration.kill_jvm()

This code yields the following error:

Exception origin:
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/interpolation/splines/eval_splines.py", line 116, in __eval_spline
    kk = (order).literal_value

  return _eval_cubic(*args)
^M  0%|          | 0/5 [00:00<?, ?it/s]^M 40%|████	| 2/5 [00:00<00:00, 15.57it/s]^M 80%|████████  | 4/5 [00:00<00:00, 12.69it/s]^M100%|██████████| 5/5 [$
^M  0%|          | 0/5 [00:00<?, ?it/s]^M  0%|          | 0/5 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "/home/mloth/Humam/01_demo.py", line 25, in <module>
    registrar.warp_and_save_slides(registered_slide_dst_dir)
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/valtils.py", line 121, in wrapper
    return f(*args, **kwargs)
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/registration.py", line 3789, in warp_and_save_slides
    slide_obj.warp_and_save_slide(dst_f=dst_f, level = level,
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/valtils.py", line 121, in wrapper
    return f(*args, **kwargs)
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/registration.py", line 931, in warp_and_save_slide
    warped_slide = self.warp_slide(level=level, non_rigid=non_rigid,
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/valtils.py", line 121, in wrapper
    return f(*args, **kwargs)
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/registration.py", line 862, in warp_slide
    warped_slide = slide_tools.warp_slide(src_f, M=self.M,
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/slide_tools.py", line 266, in warp_slide
    reader_cls = slide_io.get_slide_reader(src_f, series=series)
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/slide_io.py", line 2003, in get_slide_reader
    is_flattened_tiff, bf_reads_flat = check_flattened_pyramid_tiff(src_f)[0:2]
  File "/home/mloth/miniconda3/envs/valis_wsi_update/lib/python3.9/site-packages/valis/slide_io.py", line 494, in check_flattened_pyramid_tiff
    can_use_bf = bf_levels >= len(slide_dimensions) and bf_channels == n_channels
UnboundLocalError: local variable 'slide_dimensions' referenced before assignment

[cdgatenbee]

Hi @melanieloth,
Apologies for the delay in getting back to you. I think I'll be removing the interpolation package in the next release (1.0.3), which will hopefully resolve this issue. I've also been working on improving the slide read/write functions, which I think will also solve your other issue. I'll let you know when the new release is available, but I hope to have it out sometime this week.

Best,
-Chandler

[cdgatenbee]

Hi @melanieloth,
I just pushed the update (1.0.3) that I think will resolve the issues you've been running into. Please try updating valis and let me know if the new version is working better for you.

Best,
-Chandler