Closed Gibbsdavidl closed 1 year ago
Going to try converting them to ome.tiffs first.
After converting the images to ome.tiffs with bfconvert, it made it through one file, but then crashed again:
==== Measuring error
100%|██████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:05<00:00, 1.59it/s] 0%| | 0/9 [00:00<?, ?it/s]Converting slide to pyvips image 100%|████████████████████████████████████████████████████████████████████████████████████| 240/240 [00:00<00:00, 1290.72it/s]saving /users/dgibbs/res0/img/ctl_indiv/reg/20230322_9-968277_FLC_72hCTL-2_2C_B01_w4.ome.tiff (39205 x 38957 and 1 channels)] [====================================================================================================] 100.0% in 1.031 minute[====================================================================================================] 100.0% in 1.347 minutes Complete
11%|██████████ | 1/9 [01:26<11:33, 86.74s/it]Converting slide to pyvips image
100%|█████████████████████████████████████████████████████████████████████████████████████| 240/240 [00:00<00:00, 323676.19it/s]
11%|██████████ | 1/9 [01:29<11:58, 89.80s/it]/s]
Traceback (most recent call last):
File "/users/dgibbs/code/valis_code/valis_reg.py", line 18, in
Looks like the same error as before.
resolved. not sure what the problem was. somehow the local environment was "bad".
Hi there,
I'm registering 7 tiffs following the examples given in the readthedocs, but the script is failing at the warp and save slides step.
It's failing in both warp_and_save_slides and warp_and_merge_slides attempts.
For merging, I'm creating a channel dictionary in (nearly) the same way, so each file in registrar.original_img_list has a channel name. Not sure what's going wrong.
Thank you!!
========================================================================= ERROR FOR warp and save slides:
11%|████████████ | 1/9 [01:40<13:22, 100.32s/it]/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/slide_io.py:1587: FutureWarning: Unlike other reduction functions (e.g.
registrar.warp_and_save_slides(reg_slide_dst_f, crop="overlap")
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/valtils.py", line 29, in wrapper
return f(*args, kwargs)
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/registration.py", line 4332, in warp_and_save_slides
slide_obj.warp_and_save_slide(dst_f=dst_f, level = level,
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/valtils.py", line 29, in wrapper
return f(*args, *kwargs)
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/registration.py", line 983, in warp_and_save_slide
ome_xml_obj = slide_io.update_xml_for_new_img(current_ome_xml_str=slide_meta.original_xml,
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/valtils.py", line 29, in wrapper
return f(args, kwargs)
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/slide_io.py", line 2644, in update_xml_for_new_img
temp_new_ome = create_ome_xml(new_xyzct, bf_dtype, is_rgb, pixel_physical_size_xyu, channel_names, colormap=colormap)
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/valtils.py", line 29, in wrapper
return f(*args, **kwargs)
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/slide_io.py", line 2568, in create_ome_xml
channels = [create_channel(i, name=channel_names[i], color=colormap[channel_names[i]]) for i in range(c)]
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/slide_io.py", line 2568, in
channels = [create_channel(i, name=channel_names[i], color=colormap[channel_names[i]]) for i in range(c)]
KeyError: 'None'
skew
,kurtosis
), the default behavior ofmode
typically preserves the axis it acts along. In SciPy 1.11.0, this behavior will change: the default value ofkeepdims
will become False, theaxis
over which the statistic is taken will be eliminated, and the value None will no longer be accepted. Setkeepdims
to True or False to avoid this warning. most_common_channel_count = stats.mode(all_channels)[0][0] 11%|████████████ | 1/9 [01:40<13:23, 100.46s/it] Traceback (most recent call last): File "/users/dgibbs/code/valis_code/valis_reg.py", line 20, in============================================================================= ERROR FOR warp and merge slides:
..... ==== Performing microregistration
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 8/8 [01:58<00:00, 14.81s/it]
======== Non-rigid registration complete in 1.989 minutes
==== Measuring error
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████| 9/9 [00:05<00:00, 1.59it/s]
/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/slide_io.py:1587: FutureWarning: Unlike other reduction functions (e.g.
skew
,kurtosis
), the default behavior ofmode
typically preserves the axis it acts along. In SciPy 1.11.0, this behavior will change: the default value ofkeepdims
will become False, theaxis
over which the statistic is taken will be eliminated, and the value None will no longer be accepted. Setkeepdims
to True or False to avoid this warning.most_common_channel_count = stats.mode(all_channels)[0][0]
Traceback (most recent call last): File "/users/dgibbs/code/valis_code/valis_merge.py", line 33, in
merged_img, channel_names, ome_xml = registrar.warp_and_merge_slides(merged_slide_dst_f,
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/valtils.py", line 29, in wrapper
return f(*args, **kwargs)
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/registration.py", line 4442, in warp_and_merge_slides
keep_channels = [warped_slide[c] for c in keep_idx]
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/valis/registration.py", line 4442, in
keep_channels = [warped_slide[c] for c in keep_idx]
File "/users/dgibbs/anaconda3/envs/valis_env/lib/python3.9/site-packages/pyvips/vimage.py", line 1418, in getitem
i = range(self.bands)[arg]
IndexError: range object index out of range