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Add more options for ASC and SWC loaders #431
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I did not add options for all checks, just for the ones that might be needed for TMD. Also, I did not change the HDF5 reader at all for two reasons:
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@eleftherioszisis and @mgeplf WDYT? |
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@matz-e @eleftherioszisis @mgeplf |
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I am in favor of adding these options if they aid in processing morphologies with artifacts. However, my main concern is about the repercussions of using these options and then converting between formats. I believe we need way more tests to ensure that the converters will not break when using these options. |
I think they will because the HDF5 format is very strict and I did not change much in this one because I think the HDF5 files are mainly created using MorphIO, even though they could be created in another way (and also because the HDF5 part of MorphIO is harder to change 😇 ). |
Same. Also, this should not create any illusion that all our software can run with non-fixed morphologies. We have a pretty rigid idea of how a morphology should look like (exactly 1 soma, e.g.) |
That's why I added warnings in all irregular cases, but you think it's not enough? To be more clear I improved the conversion test to check that morphologies that can be written can then be read without any specific option. This means that the irregular morphologies can be loaded with the new options BUT when they can be written (mainly for soma issues) they are automatically fixed (not in a smart way but just to make it work). This only happens for weird somata (e.g. multiple somata or somata with bifuractions). So the user gets a warning but if he is able to write it, whether he manually fixes the morphology or he lets MorphIO to fix it automatically if it is possible, then MorphIO will be able to load it with the default loader afterwards. |
I'm more concerned. Let's hope it's enough. People being aware helps a lot already. |
Ok :) |
Do you have any other comment or any suggestion before merging? |
Anything about this PR? @matz-e @mgeplf @eleftherioszisis |
Add soma bifurcation for ASC files Add new options and tests Use proper warnings and fix tests Rename single point section into root bifurcation Add bindings Cleaning Clean tests Apply clang-format Improve readability of enum Option Remove duplicated test Restore add_test in else() block Add option for root point not equal to -1 in SWC files Add Python bindings for custom root id Add tests for conversions Check that converted files can be read
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@mgeplf @eleftherioszisis @matz-e |
Thanks, I'm still far behind on fixing things :( I will add it to the list of things to do.... |
Ahah no problem, at least now it will be in your todo list 😜 |
Fixes #427