KeyError: 'extra_metadata' when running 'setup_puncta_analysis.jpynb'
To Reproduce
Steps to reproduce the behavior:
Install punctatols via conda create -n python=3.8 (packages are installed individually to get rid of bioformat error).
Image converted via option 2 (run macro in Fiji).
Try to run through 'setup_puncta_analysis.jpynb', and then key error 'extra_metadata' cannot be resolved.
(punctatools) u2173688@01-G3-80424-21 ~ % python
Python 3.8.18 (default, Sep 11 2023, 08:17:33)
[Clang 14.0.6 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
import json
import os
import numpy as np
import intake_io
from skimage.feature import blob_log
from skimage.segmentation import watershed
from scipy import ndimage
import pylab as plt
from am_utils.utils import walk_dir
from punctatools.lib.segment import calculate_background_image, centers_to_markers, threshold_puncta, filter_laplace
from punctatools.lib.utils import show_dataset, show_imgs, display_blobs
from punctatools.lib.utils import crop_dataset, convert_params
input_dir = "/Users/u2173688/Desktop/input/test/DM4_a"
roi_segmentation = False
output_dir = "/Users/u2173688/Desktop/puncta_analysis"
print(rf"Input directory: {input_dir}")
Input directory: /Users/u2173688/Desktop/input/test/DM4_a
if not roi_segmentation:
... print('No cell segmentation provided')
...
No cell segmentation provided
samples = walk_dir(input_dir)
print(f'\n{len(samples)} images were found:')
1 images were found:
for i in range(len(samples)):
... print(i, samples[i])
...
0 /Users/u2173688/Desktop/input/test/DM4_a/DM4_a_test.tif
sample_index = 0
if sample_index is None:
... sample_index = np.random.randint(len(samples))
...
sample = samples[sample_index]
dataset = intake_io.imload(sample)
Traceback (most recent call last):
File "", line 1, in
File "/Users/u2173688/miniconda3/envs/punctatools/lib/python3.8/site-packages/intake_io/io.py", line 62, in imload
with _autodetect(uri, **kwargs) as src:
File "/Users/u2173688/miniconda3/envs/punctatools/lib/python3.8/site-packages/intake/source/base.py", line 245, in enter
self._load_metadata()
File "/Users/u2173688/miniconda3/envs/punctatools/lib/python3.8/site-packages/intake/source/base.py", line 88, in _load_metadata
self.metadata.update(self._schema.extra_metadata)
File "/Users/u2173688/miniconda3/envs/punctatools/lib/python3.8/site-packages/intake/source/base.py", line 18, in getattr
return self[item]
KeyError: 'extra_metadata'
Expected behavior
Expected to running through 'setup_puncta_analysis.jpynb'
Environment
Operation System: Zsh on osx-64 Mac
conda version (conda --version): conda 24.1.2
pip version (pip --version): pip 23.3.1
punctatools version: 0.2.0
Additional context
Could I ask if anyone has any idea to figure out this issue, please?
🐛 Bug
KeyError: 'extra_metadata' when running 'setup_puncta_analysis.jpynb'
To Reproduce
Steps to reproduce the behavior:
(punctatools) u2173688@01-G3-80424-21 ~ % python Python 3.8.18 (default, Sep 11 2023, 08:17:33) [Clang 14.0.6 ] :: Anaconda, Inc. on darwin Type "help", "copyright", "credits" or "license" for more information.
1 images were found:
Expected behavior
Expected to running through 'setup_puncta_analysis.jpynb'
Environment
conda --version): conda 24.1.2pip --version): pip 23.3.1Additional context
Could I ask if anyone has any idea to figure out this issue, please?