AttributeError: module 'ark.utils.plot_utils' has no attribute 'plot_pixel_cell_cluster'
Closed this issue · 4 comments
Running cell from Pixie_Clustering notebook as follows returns error. Other functions (e.g. plot_utils.save_colored_masks in the cell above) from this module import and run during the same session in the same notebook.
Function should be imported and callable.
Using Docker, WSL, and installation as documented.
AttributeError Traceback (most recent call last)
Cell In[51], line 11
1 for pixel_fov in subset_pixel_fovs:
2 pixel_cluster_mask = load_utils.load_imgs_from_dir(
3 data_dir=os.path.join(base_dir, pixel_output_dir, "pixel_masks"),
4 files=[pixel_fov + "_pixel_mask.tiff"],
(...)
8 xr_channel_names=None,
9 )
---> 11 plot_utils.plot_pixel_cell_cluster(
12 pixel_cluster_mask,
13 [pixel_fov],
14 os.path.join(base_dir, pixel_meta_cluster_remap_name),
15 metacluster_colors=raw_cmap,
16 figsize=(5, 5),
17 dpi=150
18 )
AttributeError: module 'ark.utils.plot_utils' has no attribute 'plot_pixel_cell_cluster'
dir(plot_utils)
['Dict',
'EXTENSION_TYPES',
'List',
'Literal',
'MetaclusterColormap',
'Optional',
'Tuple',
'Union',
'builtins',
'cached',
'doc',
'file',
'loader',
'name',
'package',
'spec',
'cm',
'colors',
'contains',
'create_mantis_dir',
'create_overlay',
'dataclass',
'field',
'find_boundaries',
'image_utils',
'io_utils',
'load_utils',
'make_axes_locatable',
'misc_utils',
'natsort',
'np',
'os',
'pathlib',
'pd',
'plot_neighborhood_cluster_result',
'plot_pixel_cell_cluster_overlay',
'plt',
'rescale_intensity',
'save_colored_masks',
'set_minimum_color_for_colormap',
'shutil',
'tif_overlay_preprocess',
'tqdm',
'xr']
