list index out of range

[dr-sayyadhury]

Hi there,

I am running into lots of issues with trying to save the output after image registration. I finally thought i fixed it when i made sure the initial images that I used for registration were of the 'ome-tiff' format. And I can see that its converting the slide to an image (which has never hapenned berfore). BUt now it seems to indicate an error in the series and it says list index out of rnage.

Below is the error message and after which, I have written my code...Would be really grateful if you can help me with this.

Many thanks.

---

Error

Attributes of one: ['M', 'class', 'delattr', 'dict', 'dir', 'doc', 'eq', 'format', 'ge', 'getattribute', 'gt', 'hash', 'init', 'init_subclass', 'le', 'lt', 'module', 'ne', 'new', 'reduce', 'reduce_ex', 'repr', 'setattr', 'sizeof', 'slotnames', 'str', 'subclasshook', 'weakref', '_bk_dxdy_f', '_bk_dxdy_np', '_fwd_dxdy_f', '_fwd_dxdy_np', 'aligned_slide_shape_rc', 'bg_color', 'bg_px_pos_rc', 'bk_dxdy', 'check_if_empty', 'crop', 'fixed_slide', 'fwd_dxdy', 'get_aligned_to_ref_slide_crop_xywh', 'get_bg_color_px_pos', 'get_bk_dxdy', 'get_crop_method', 'get_crop_xywh', 'get_displacement_f', 'get_fwd_dxdy', 'get_overlap_crop_xywh', 'image', 'img_type', 'is_empty', 'is_rgb', 'name', 'non_rigid_reg_img_f', 'non_rigid_reg_mask', 'nr_rigid_reg_img_f', 'original_xml', 'processed_img', 'processed_img_f', 'processed_img_shape_rc', 'reader', 'reg_img_shape_rc', 'resolution', 'rigid_reg_img_f', 'rigid_reg_mask', 'series', 'set_bk_dxdy', 'set_fwd_dxdy', 'slide2image', 'slide2vips', 'slide_dimensions_wh', 'slide_shape_rc', 'src_f', 'stack_idx', 'stored_dxdy', 'units', 'update_results_img_paths', 'val_obj', 'warp_and_save_slide', 'warp_geojson', 'warp_geojson_from_to', 'warp_img', 'warp_img_from_to', 'warp_slide', 'warp_xy', 'warp_xy_from_to', 'xy_in_prev', 'xy_in_prev_in_bbox', 'xy_matched_to_prev', 'xy_matched_to_prev_in_bbox']
Converting slide to pyvips image
100%|██████████| 1521/1521 [03:46<00:00, 6.71it/s]
No series provided. Selecting series with largest image, which is series 0
No series provided. Selecting series with largest image, which is series 0
An error occurred with slide one: list index out of range
Attributes of C03030A6_dup1: ['M', 'class', 'delattr', 'dict', 'dir', 'doc', 'eq', 'format', 'ge', 'getattribute', 'gt', 'hash', 'init', 'init_subclass', 'le', 'lt', 'module', 'ne', 'new', 'reduce', 'reduce_ex', 'repr', 'setattr', 'sizeof', 'slotnames', 'str', 'subclasshook', 'weakref', '_bk_dxdy_f', '_bk_dxdy_np', '_fwd_dxdy_f', '_fwd_dxdy_np', 'aligned_slide_shape_rc', 'bg_color', 'bg_px_pos_rc', 'bk_dxdy', 'check_if_empty', 'crop', 'fixed_slide', 'fwd_dxdy', 'get_aligned_to_ref_slide_crop_xywh', 'get_bg_color_px_pos', 'get_bk_dxdy', 'get_crop_method', 'get_crop_xywh', 'get_displacement_f', 'get_fwd_dxdy', 'get_overlap_crop_xywh', 'image', 'img_type', 'is_empty', 'is_rgb', 'name', 'non_rigid_reg_img_f', 'non_rigid_reg_mask', 'nr_rigid_reg_img_f', 'original_xml', 'processed_img', 'processed_img_f', 'processed_img_shape_rc', 'reader', 'reg_img_shape_rc', 'resolution', 'rigid_reg_img_f', 'rigid_reg_mask', 'series', 'set_bk_dxdy', 'set_fwd_dxdy', 'slide2image', 'slide2vips', 'slide_dimensions_wh', 'slide_shape_rc', 'src_f', 'stack_idx', 'stored_dxdy', 'units', 'update_results_img_paths', 'val_obj', 'warp_and_save_slide', 'warp_geojson', 'warp_geojson_from_to', 'warp_img', 'warp_img_from_to', 'warp_slide', 'warp_xy', 'warp_xy_from_to', 'xy_in_prev', 'xy_in_prev_in_bbox', 'xy_matched_to_prev', 'xy_matched_to_prev_in_bbox']
Converting slide to pyvips image
100%|██████████| 441/441 [00:22<00:00, 19.65it/s]
No series provided. Selecting series with largest image, which is series 0
No series provided. Selecting series with largest image, which is series 0
An error occurred with slide C03030A6_dup1: list index out of range

code

from valis import registration
import os

Iterate over slides and inspect them

for slide_name, slide_obj in registrar.slide_dict.items():
try:
# Inspect the Slide object
print(f"Attributes of {slide_name}: {dir(slide_obj)}")

    # Replace the following line with the correct way to access metadata
    metadata = slide_obj.original_xml

    # Example warp and save operation (update as needed)
    dst_f = os.path.join(registered_slide_dst_dir, f"{slide_name}.ome.tiff")
    slide_obj.warp_and_save_slide(dst_f=dst_f, crop="overlap", level=0)

except Exception as e:
    print(f"An error occurred with slide {slide_name}: {e}")

[cdgatenbee]

Hi @dr-sayyadhury,
Sorry to hear you've been running into issues. I've just pushed an update (1.0.3), which should have more robust slide read/write methods, and may solve this issue. Could you please try updating valis to see if those fixes resolve this issue for you?

Best,
-Chandler

[dr-sayyadhury]

Dear Chandler, Thank you for responding so quickly. Yes it worked after I updated the package. However now I am getting another error and I believe this has something to do with my tif files and it format. Is it possible if I can send you a representative tiff file set (2 files) for you to check what is wrong with the format? There are some ome.tif files that work and some that don’t. Not sure why.. Thank you. With regards, Shamini A From: Chandler Gatenbee ***@***.***> Date: Friday, January 26, 2024 at 2:08 PM To: MathOnco/valis ***@***.***> Cc: Shamini Ayyadhury ***@***.***>, Mention ***@***.***> Subject: Re: [MathOnco/valis] list index out of range (Issue #96) You don't often get email from ***@***.*** Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi @dr-sayyadhury<https://github.com/dr-sayyadhury>, Sorry to hear you've been running into issues. I've just pushed an update (1.0.3), which should have more robust slide read/write methods, and may solve this issue. Could you please try updating valis to see if those fixes resolve this issue for you? Best, -Chandler — Reply to this email directly, view it on GitHub<#96 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARBV4F65Z6URTRFACKCWYSDYQP5KJAVCNFSM6AAAAABCLGDMHKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJSGU2TIOJWGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[cdgatenbee]

Hi @dr-sayyadhury,
Glad to hear the update fixed one issue, but sorry you're having this other one. I'd be more than happy to take a look at some images to see if I can figure out what the problem is though. If you'd prefer to share them privately, you can send a link to my e-mail at Chandler[dot]Gatenbee[at]moffitt[dot]org.

Best,
-Chandler

[dr-sayyadhury]

HI so sorry i took so long. I am running into new issues. Anyway, I finally found the time to put together a few images and just sent you an email.

Hope we can work this one out soon.

Thank you.

[cdgatenbee]

Hi @dr-sayyadhury,
Thank you for sharing the images! I'll take a look and see if I can figure out what is causing the issue.

Best,
-Chandler