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Adds option to export cells with just the <morphology> element
FYI @sanjayankur31 Note the morphOnly cells here are mostly valid, but can't be visualised by PlotMorphologyVispy.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" | ||
| id="Case1_new_morphology"> | ||
|
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| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case1_new.swc </notes> | ||
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| <morphology id="morphology_Case1_new"> | ||
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| <!-- First point is of a multi point soma => not spherical! --> | ||
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| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
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| <!-- Cylindrical soma... --> | ||
| <proximal x="0" y="-10" z="0" diameter="20"/> | ||
| <distal x="0" y="0" z="0" diameter="20"/> | ||
| </segment> | ||
|
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| <segment id="1" name="Seg_1"> <!-- "Cable" is 0--> | ||
| <parent segment="0"/> | ||
| <distal x="0" y="10" z="0" diameter="20"/> | ||
| </segment> | ||
|
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| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
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| <segment id="2" name="Seg_2"> <!-- "Cable" is 1--> | ||
| <parent segment="0"/> | ||
| <proximal x="10" y="0" z="0" diameter="4"/> | ||
| <distal x="30" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
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| <segment id="3" name="Seg_3"> <!-- "Cable" is 2--> | ||
| <parent segment="2"/> | ||
| <proximal x="30" y="0" z="0" diameter="4"/> | ||
| <distal x="40" y="10" z="0" diameter="4"/> | ||
| </segment> | ||
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| <segment id="4" name="Seg_4"> <!-- "Cable" is 3--> | ||
| <parent segment="2"/> | ||
| <proximal x="30" y="0" z="0" diameter="4"/> | ||
| <distal x="40" y="-10" z="0" diameter="4"/> | ||
| </segment> | ||
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| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| <member segment="1"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="Cable_1" > | ||
| <member segment="2"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="Cable_2" > | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="Cable_3" > | ||
| <member segment="4"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="color_white" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="dendrite_group" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="soma_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="basal_dendrite" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="color_green" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
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| </morphology> | ||
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| </neuroml> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" | ||
| id="Case1_orig_morphology"> | ||
|
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| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case1_orig.swc </notes> | ||
|
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| <morphology id="morphology_Case1_orig"> | ||
|
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| <!-- First point is of a multi point soma => not spherical! --> | ||
|
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| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
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| <!-- Cylindrical soma... --> | ||
| <proximal x="-10" y="10" z="0" diameter="0.2"/> | ||
| <distal x="10" y="10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
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| <segment id="1" name="Seg_1"> <!-- "Cable" is 0--> | ||
| <parent segment="0"/> | ||
| <distal x="10" y="-10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
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||
| <segment id="2" name="Seg_2"> <!-- "Cable" is 0--> | ||
| <parent segment="1"/> | ||
| <distal x="-10" y="-10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
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| <segment id="3" name="Seg_3"> <!-- "Cable" is 0--> | ||
| <parent segment="2"/> | ||
| <distal x="-10" y="10" z="0" diameter="0.2"/> | ||
| </segment> | ||
|
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||
| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
|
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| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
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| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
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| <!-- Parent point is on soma! Not creating 'real' segment --> | ||
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| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| <member segment="1"/> | ||
| <member segment="2"/> | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="dendrite_group" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="soma_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="color_green" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="basal_dendrite" > | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| <include segmentGroup="Cable_4"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="color_white" > | ||
| <include segmentGroup="Cable_0"/> | ||
| </segmentGroup> | ||
|
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| </morphology> | ||
|
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| </neuroml> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" | ||
| id="Case2_new_morphology"> | ||
|
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| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case2_new.swc </notes> | ||
|
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| <morphology id="morphology_Case2_new"> | ||
|
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| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
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| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="0" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="1" name="Seg_1"> <!-- "Cable" is 1--> | ||
| <parent segment="0"/> | ||
| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="20" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="2" name="Seg_2"> <!-- "Cable" is 2--> | ||
| <parent segment="0"/> | ||
| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="0" y="20" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="3" name="Seg_3"> <!-- "Cable" is 2--> | ||
| <parent segment="2"/> | ||
| <distal x="0" y="30" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="4" name="Seg_4"> <!-- "Cable" is 3--> | ||
| <parent segment="0"/> | ||
| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="0" y="-20" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="5" name="Seg_5"> <!-- "Cable" is 3--> | ||
| <parent segment="4"/> | ||
| <distal x="0" y="-30" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="Cable_1" > | ||
| <member segment="1"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="Cable_2" > | ||
| <member segment="2"/> | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="Cable_3" > | ||
| <member segment="4"/> | ||
| <member segment="5"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="axon_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="color_grey" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| </morphology> | ||
|
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| </neuroml> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
| xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
| xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" | ||
| id="Case2_orig_morphology"> | ||
|
|
||
| <notes> | ||
| Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version) | ||
| Original file: Case2_orig.swc </notes> | ||
|
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| <morphology id="morphology_Case2_orig"> | ||
|
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| <segment id="0" name="Seg_0"> <!-- "Cable" is 0--> | ||
|
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| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="0" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="1" name="Seg_1"> <!-- "Cable" is 1--> | ||
| <parent segment="0"/> | ||
| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="20" y="0" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="2" name="Seg_2"> <!-- "Cable" is 2--> | ||
| <parent segment="0"/> | ||
| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="0" y="20" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="3" name="Seg_3"> <!-- "Cable" is 2--> | ||
| <parent segment="2"/> | ||
| <distal x="0" y="30" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segment id="4" name="Seg_4"> <!-- "Cable" is 3--> | ||
| <parent segment="0"/> | ||
| <proximal x="0" y="0" z="0" diameter="4"/> | ||
| <distal x="0" y="-20" z="0" diameter="4"/> | ||
| </segment> | ||
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| <segment id="5" name="Seg_5"> <!-- "Cable" is 3--> | ||
| <parent segment="4"/> | ||
| <distal x="0" y="-30" z="0" diameter="4"/> | ||
| </segment> | ||
|
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| <segmentGroup id="Cable_0" > | ||
| <member segment="0"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="Cable_1" > | ||
| <member segment="1"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="Cable_2" > | ||
| <member segment="2"/> | ||
| <member segment="3"/> | ||
| </segmentGroup> | ||
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| <segmentGroup id="Cable_3" > | ||
| <member segment="4"/> | ||
| <member segment="5"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="axon_group" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="all" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
|
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| <segmentGroup id="color_grey" > | ||
| <include segmentGroup="Cable_0"/> | ||
| <include segmentGroup="Cable_1"/> | ||
| <include segmentGroup="Cable_2"/> | ||
| <include segmentGroup="Cable_3"/> | ||
| </segmentGroup> | ||
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| </morphology> | ||
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| </neuroml> |
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