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V4 #1111
V4 #1111
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* A heterogeneous morphology consists of zero or more homogeneous and at least one heterogeneous neurite trees extending from the soma; * 'heterogeneous neurite trees ' is called a 'mixed subtree' for brevity * this is a breaking change with how NeuroM<=3.x works * this will fix #975
Remove deprecated modules and deprecation warning. viewer module was not included to be treated separately
Switch to using the morphio readonly morphology instead of mut Co-authored-by: Mike Gevaert <[email protected]>
Removes viewer deprecated module and hides plot_tree, plot_tree3d, plot_soma, plot_soma3d from neurom.view Co-authored-by: Zisis Eleftherios <[email protected]>
…oint (#1030) Use soma center as a reference point for morphology-level radial distance features. Radial distance features on the morphology level were using as reference point the root of each neurite. While this is ok when per-neurite features are calculated, it is incorrect when the radial distance features are calculated for the entire cell. This change renders soma as the reference point for calculating the radial distances, not the root of each neurite. When the same features are used per-neurite the old behavior of using the neurite root is still the same. Co-authored-by: Adrien Berchet <[email protected]>
* Updating copyright year (#1028) Co-authored-by: Alexander Dietz <[email protected]> * Updating copyright year (#1029) Co-authored-by: Alexander Dietz <[email protected]> * Remove duplicated deps jinja, sphinx (#1043) Co-authored-by: bbpgithubaudit <[email protected]> Co-authored-by: Alexander Dietz <[email protected]> Co-authored-by: stefanoantonel <[email protected]>
Co-authored-by: Adrien Berchet <[email protected]>
Make file paths absolute in Population init, but not resolve symlinks. Co-authored-by: Adrien Berchet <[email protected]>
* Maintain mut/immut after transformation * Add tests Co-authored-by: Eleftherios Zisis <[email protected]>
* Updating copyright year (#1028) Co-authored-by: Alexander Dietz <[email protected]> * Updating copyright year (#1029) Co-authored-by: Alexander Dietz <[email protected]> * Remove duplicated deps jinja, sphinx (#1043) * remove single point contour somas in h5 and asc tests (#1045) * this is in prep for MorphIO to be more consistent and picky with contour somas * Fix view cli (#1051) * Fix coverage (#1056) Co-authored-by: bbpgithubaudit <[email protected]> Co-authored-by: Alexander Dietz <[email protected]> Co-authored-by: stefanoantonel <[email protected]> Co-authored-by: MikeG <[email protected]> Co-authored-by: Alexis Arnaudon <[email protected]>
--------- Co-authored-by: Eleftherios Zisis <[email protected]>
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1111 +/- ##
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Coverage 100.00% 100.00%
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Files 36 35 -1
Lines 2473 2610 +137
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+ Hits 2473 2610 +137 |
The register/unregister in NeuriteType enum in this branch is quite fragile because it tries to bend the immutability of the python enums: @classmethod
def register(cls, name, value):
"""Register a new value in the Enum class."""
value = _int_or_tuple(value)
if hasattr(cls, name):
existing = getattr(cls, name)
raise ValueError(f"NeuriteType '{name}' is already registered as {repr(existing)}")
try:
existing = cls(value)
except ValueError:
existing = None
if existing:
raise ValueError(f"NeuriteType '{name}' is already registered as {repr(existing)}")
obj = _create_neurite_type(cls, value, name=name)
cls._value2member_map_[value] = obj
cls._member_map_[name] = obj
cls._member_names_.append(name)
return obj
@classmethod
def unregister(cls, name):
"""Unregister a value in the Enum class."""
if name not in cls._member_names_:
raise ValueError(
f"The NeuriteType '{name}' is not registered so it can not be unregistered"
)
value = cls._member_map_[name].value
del cls._value2member_map_[value]
del cls._member_map_[name]
cls._member_names_.remove(name) Therefore, it is no surprise that some of the functionality we relied upon is now broken in 3.12 because they tried to make them safer: https://docs.python.org/3/whatsnew/3.12.html#enum In addition, we rely on protected variables to make it work, which is also not great. In the end, the use cases for which registration is needed are not so many. To make an int type usable, it has to also exist in MorphiIO as a SectionType and all section types are already available as neurite types. That leaves us with registering new composite types that combine existing section types. As we don't have use cases where other type combinations are needed apart from axon-on-dendrite, which is already defined in NeuriteType, I suggest we remove the registration of neurite types and revisit them in the future when solid cases for this functionality appear. |
* Fix NeuriteType for Python 3.12.3 * Coverage
…_segments (#1054) * Improve iter_segments and add segment methods in core objects * Rename iterator_type into section_iterator * Remove iter_* methods and use consistent properties * Use iter_sections instead of obj.sections in check.morphtree * Update doc
* Expose soma methods as free functions. * Allow using both morphio and neurom soma in soma functions. * Keep backward compatibility with the soma methods. * Disallow storing soma values to avoid issues with mutation of soma. --------- Co-authored-by: Adrien Berchet <[email protected]>
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I've read a lot of it, and it all looks good to me.
If converting our other tools hasn't produced any large WAT
moments, I think we should go with this.
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