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akoyabio / phenoptrReports

Create analysis reports from inForm data.
https://akoyabio.github.io/phenoptrReports
zlib License
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Spatial map viewer doesn't recognize component images #26

Closed HAL4500 closed 5 years ago

HAL4500 commented 5 years ago

Hi, I'm encountering an error when trying to use the spatial map viewer addin. After uploading the consolidated data file and selecting the directory with component and composite images exported from inForm 2.4.4 I get the following error:

No component image available for Macro_3178_IF_09_11_19_[8855,47803].im3, skipping Warning in phenoptrReports::nearest_neighbor_map(csd, field, .export_path,

The viewer itself launches in the browser albeit the images do not load. What could be the problem?

AB-Kent commented 5 years ago

The viewer is looking for a file named Macro_3178_IF_09_11_19_[8855,47803]_component_data.tif in the directory you selected; is that file present?

HAL4500 commented 5 years ago

Yes, all of the files are present in the folder.

AB-Kent commented 5 years ago

Can you run this small program and reply with the result? (Copy/paste to the RStudio console and press Return; choose your export directory; copy the results and paste to a reply here.) Thanks!

base_path = choose.dir() # Choose the same directory you chose in the spatial map viewer
component_path = file.path(base_path, 'Macro_3178_IF_09_11_19_[8855,47803]_component_data.tif')
print(file.exists(component_path))
print(phenoptr::get_field_info(component_path))
HAL4500 commented 5 years ago

I'm dumb, the images were in the folder, but each in a separate one... I grouped them all together and it's working. Thanks for the effort though!

AB-Kent commented 5 years ago

😃