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Ignore secondary annotations (undefined annotations in TYPE_DCT) #25
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annotations that are not declared in TYPE_DCT. This prevents breakage of load_neuron when data contains undeclared structural annotations (eg. contours, spines). These undeclared structural annotations have not the same origin points as the soma, basal, apical, or axon (TYPE_DCT). During csr_matrix generation the annotations require to be connected with soma, therefore those undeclared annotations often break the loading of data. To block annoying error messages an verbose argument is added to suppress printing of the messages.
to be processed. Otherwise in case of LoadNeuronError the loading is stopped.
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Hi @BCJongbloets I think Travis is not running your build because of a flagged account. Could you loggin to https://travis-ci.org/ and see if you have a notification about it ? |
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Hi Benoit,
I did not have Travis enabled on this project. I now made an account with Travis and have enabled it for my forked repro. However I have no clue what pipeline to run using Travis.
Do you have a predefined .travis.yml for this project?
Bart
… On Jan 23, 2020, at 01:30, Benoit Coste ***@***.***> wrote:
Hi @BCJongbloets <https://github.com/BCJongbloets> I think Travis is not running your build because of a flagged account. Could you loggin to https://travis-ci.org/ <https://travis-ci.org/> and see if you have a notification about it ?
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Usage of reconstruction data files with structural annotations for anatomical contours fail to load
in the current TMD package. This is because those annotations usually are not connected with the
soma or any of the processes (basal, apical, axon) as defined in TYPE_DCT. To allow for loading of
the data we can remove all data that is not defined in TYPE_DCT. A 'verbose' argument is added
to allow the user to avoid superfluous printing of the warning that data was removed.
I hope you find this edit useful, also included a test file that would in the current version of TMD
cannot be read, but with the edit will be read. This file was converted from a neurolucida .DAT file to
SWCplus file with (https://neuroinformatics.nl/HBP/morphology-viewer/).
BJ2510_a1_MSaa00455_PVAi9-4473_B2_traced_BCJ.swc.txt
*had to add .txt to allow for import