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Merge pull request #41 from NeuroML/experimental
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To v1.10.1; helper methods for handling when morphology/biophysProps outside cell element
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@pgleeson
pgleeson authored Jun 11, 2024
2 parents 2657ce9 + 2fbedb8 commit 124b764
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Showing 5 changed files with 194 additions and 54 deletions.
4 changes: 2 additions & 2 deletions .github/workflows/javadocs.yml
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Expand Up @@ -32,14 +32,14 @@ jobs:
uses: actions/checkout@v4
with:
repository: NeuroML/NeuroML2
ref: development
ref: ${{ github.ref }}
path: NeuroML2

- name: Checkout org.neuroml.model.injectingplugin
uses: actions/checkout@v4
with:
repository: NeuroML/org.neuroml.model.injectingplugin
ref: development
ref: ${{ github.ref }}
path: org.neuroml.model.injectingplugin

- name: Install NeuroML deps
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12 changes: 6 additions & 6 deletions pom.xml
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Expand Up @@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.neuroml.model</groupId>
<artifactId>org.neuroml.model</artifactId>
<version>1.10.0</version>
<version>1.10.1</version>
<packaging>bundle</packaging>
<properties>
<build.version2>2.3.1</build.version2>
Expand All @@ -19,12 +19,12 @@
<dependency>
<groupId>org.neuroml.model.injectingplugin</groupId>
<artifactId>org.neuroml.model.injectingplugin</artifactId>
<version>1.10.0</version>
<version>1.10.1</version>
</dependency>
<dependency>
<groupId>org.neuroml.core</groupId>
<artifactId>neuroml2-base-definitions</artifactId>
<version>1.10.0</version>
<version>1.10.1</version>
</dependency>

<dependency>
Expand Down Expand Up @@ -64,7 +64,7 @@
&lt;br /&gt;
&lt;br /&gt;
</top>
<bottom>Copyright NeuroML Contributors 2023</bottom>
<bottom>Copyright NeuroML Contributors 2024</bottom>
</configuration>
</plugin>
<plugin>
Expand Down Expand Up @@ -105,7 +105,7 @@
</goals>
<configuration>
<resourceBundles>
<resourcebundle>org.neuroml.core:neuroml2-base-definitions:1.10.0</resourcebundle>
<resourcebundle>org.neuroml.core:neuroml2-base-definitions:1.10.1</resourcebundle>
</resourceBundles>
</configuration>
</execution>
Expand Down Expand Up @@ -198,7 +198,7 @@
<plugin>
<groupId>org.neuroml.model.injectingplugin</groupId>
<artifactId>org.neuroml.model.injectingplugin</artifactId>
<version>1.10.0</version>
<version>1.10.1</version>
</plugin>
</plugins>
</configuration>
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178 changes: 148 additions & 30 deletions src/main/java/org/neuroml/model/util/CellUtils.java
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Expand Up @@ -13,6 +13,8 @@
import org.neuroml.model.Point3DWithDiam;
import org.neuroml.model.Segment;
import org.neuroml.model.SegmentGroup;
import org.neuroml.model.Morphology;
import org.neuroml.model.BiophysicalProperties;

/**
*
Expand All @@ -32,9 +34,16 @@ public static boolean isUnbranchedNonOverlapping(SegmentGroup sg) {
sg.getNeuroLexId().equals(NEUROML2_NEUROLEX_UNBRANCHED_NONOVERLAPPING_SEG_GROUP);
}

public static boolean hasUnbranchedNonOverlappingInfo(Cell cell)
@Deprecated
public static boolean hasUnbranchedNonOverlappingInfo(Cell cell) throws NeuroMLException
{
for (SegmentGroup sg : cell.getMorphology().getSegmentGroup())
return hasUnbranchedNonOverlappingInfo(cell, null);
}

public static boolean hasUnbranchedNonOverlappingInfo(Cell cell, NeuroMLDocument nml2doc) throws NeuroMLException {

Morphology morphology = getCellMorphology(cell, nml2doc);
for (SegmentGroup sg : morphology.getSegmentGroup())
{
if (isUnbranchedNonOverlapping(sg))
{
Expand All @@ -44,6 +53,49 @@ public static boolean hasUnbranchedNonOverlappingInfo(Cell cell)
return false;
}

public static Morphology getCellMorphology(Cell cell, NeuroMLDocument nml2doc) throws NeuroMLException {

if (cell.getMorphology()!=null) {
return cell.getMorphology();
}
else if (cell.getMorphologyAttr() !=null)
{
for (Morphology m: nml2doc.getMorphology())
{
if (m.getId().equals(cell.getMorphologyAttr()))
return m;
}
throw new NeuroMLException("Cannot find morphology: "+cell.getMorphologyAttr()+" specified as an attribute in cell: "+cell.getId());
}
else if (nml2doc==null)
{
return null;
// Cannot get any morphology attribute
}
return null; // may be expected...
}

public static BiophysicalProperties getCellBiophysicalProperties(Cell cell, NeuroMLDocument nml2doc) {

if (cell.getBiophysicalProperties()!=null) {

return cell.getBiophysicalProperties();
}

else if (cell.getBiophysicalPropertiesAttr() !=null)
{
for (BiophysicalProperties bp: nml2doc.getBiophysicalProperties()) {
if (bp.getId().equals(cell.getBiophysicalPropertiesAttr()))
return bp;
}
}
return null;
}

/**
* @deprecated use getIdsVsSegments(Cell cell, NeuroMLDocument nml2doc) instead.
*/
@Deprecated
public static LinkedHashMap<Integer, Segment> getIdsVsSegments(Cell cell) {

LinkedHashMap<Integer, Segment> idsVsSegments = new LinkedHashMap<Integer, Segment>();
Expand All @@ -53,6 +105,16 @@ public static LinkedHashMap<Integer, Segment> getIdsVsSegments(Cell cell) {
return idsVsSegments;
}

public static LinkedHashMap<Integer, Segment> getIdsVsSegments(Cell cell, NeuroMLDocument nml2doc) throws NeuroMLException {

LinkedHashMap<Integer, Segment> idsVsSegments = new LinkedHashMap<Integer, Segment>();
Morphology morphology = getCellMorphology(cell, nml2doc);
for (Segment seg : morphology.getSegment()) {
idsVsSegments.put(seg.getId(), seg);
}
return idsVsSegments;
}

public static SegmentGroup getSegmentGroup(Cell cell, String id) throws NeuroMLException {
for (SegmentGroup sg: cell.getMorphology().getSegmentGroup()) {
if (sg.getId().equals(id))
Expand All @@ -61,8 +123,13 @@ public static SegmentGroup getSegmentGroup(Cell cell, String id) throws NeuroMLE
throw new NeuroMLException("No SegmentGroup with id: "+id+" in cell with id: "+cell.getId());
}

@Deprecated
public static Segment getSegmentWithId(Cell cell, int segmentId) throws NeuroMLException {
List<Segment> segments = cell.getMorphology().getSegment();
return getSegmentWithId(cell, null, segmentId);
}

public static Segment getSegmentWithId(Cell cell, NeuroMLDocument nml2doc, int segmentId) throws NeuroMLException {
List<Segment> segments = getCellMorphology(cell, nml2doc).getSegment();
if (segments.size()>segmentId) {
Segment guess = segments.get(segmentId);
if (guess.getId()==segmentId)
Expand All @@ -75,16 +142,21 @@ public static Segment getSegmentWithId(Cell cell, int segmentId) throws NeuroMLE
throw new NeuroMLException("No Segment with id: "+segmentId+" in cell with id: "+cell.getId());
}

public static LinkedHashMap<String, SegmentGroup> getNamesVsSegmentGroups(Cell cell) {
public static LinkedHashMap<String, SegmentGroup> getNamesVsSegmentGroups(Cell cell, NeuroMLDocument nml2doc) throws NeuroMLException {

LinkedHashMap<String, SegmentGroup> namesVsSegmentGroups = new LinkedHashMap<String, SegmentGroup>();
for (SegmentGroup sg : cell.getMorphology().getSegmentGroup()) {
for (SegmentGroup sg : getCellMorphology(cell, nml2doc).getSegmentGroup()) {
namesVsSegmentGroups.put(sg.getId(), sg);
}
return namesVsSegmentGroups;
}

public static ArrayList<Integer> getSegmentIdsInGroup(Cell cell, String segmentGroup) {
public static LinkedHashMap<String, SegmentGroup> getNamesVsSegmentGroups(Cell cell) throws NeuroMLException {

return getNamesVsSegmentGroups(cell, null);
}

public static ArrayList<Integer> getSegmentIdsInGroup(Cell cell, String segmentGroup) throws NeuroMLException {

for (SegmentGroup sg : cell.getMorphology().getSegmentGroup()) {
if (sg.getId().equals(segmentGroup)) {
Expand Down Expand Up @@ -121,34 +193,45 @@ public static boolean hasSegmentGroup(Cell cell, String segmentGroup) {
return false;
}

@Deprecated
public static ArrayList<Segment> getSegmentsInGroup(Cell cell, String segmentGroup) throws NeuroMLException {
return getSegmentsInGroup(cell, null, segmentGroup);
}

for (SegmentGroup sg : cell.getMorphology().getSegmentGroup()) {
public static ArrayList<Segment> getSegmentsInGroup(Cell cell, NeuroMLDocument nml2doc, String segmentGroup) throws NeuroMLException {

for (SegmentGroup sg : CellUtils.getCellMorphology(cell, nml2doc).getSegmentGroup()) {
if (sg.getId().equals(segmentGroup)) {
LinkedHashMap<String, SegmentGroup> namesVsSegmentGroups = getNamesVsSegmentGroups(cell);
return getSegmentsInGroup(cell, namesVsSegmentGroups, sg);
LinkedHashMap<String, SegmentGroup> namesVsSegmentGroups = getNamesVsSegmentGroups(cell, nml2doc);
return getSegmentsInGroup(cell, nml2doc, namesVsSegmentGroups, sg);
}
}
throw new NeuroMLException("No SegmentGroup: "+segmentGroup+" in cell with id: "+cell.getId());
}


public static ArrayList<Segment> getSegmentsInGroup(Cell cell, LinkedHashMap<String, SegmentGroup> namesVsSegmentGroups, SegmentGroup segmentGroup) throws NeuroMLException {

return getSegmentsInGroup(cell, null, namesVsSegmentGroups, segmentGroup);
}

public static ArrayList<Segment> getSegmentsInGroup(Cell cell, NeuroMLDocument nml2doc, LinkedHashMap<String, SegmentGroup> namesVsSegmentGroups, SegmentGroup segmentGroup) throws NeuroMLException {

ArrayList<Segment> segsHere = new ArrayList<Segment>();

for (Member memb : segmentGroup.getMember()) {
segsHere.add(getSegmentWithId(cell, memb.getSegment()));
segsHere.add(getSegmentWithId(cell, nml2doc, memb.getSegment()));
}
for (Include inc : segmentGroup.getInclude()) {
String sg = inc.getSegmentGroup();
ArrayList<Segment> segs = getSegmentsInGroup(cell, namesVsSegmentGroups, namesVsSegmentGroups.get(sg));
ArrayList<Segment> segs = getSegmentsInGroup(cell, nml2doc, namesVsSegmentGroups, namesVsSegmentGroups.get(sg));
segsHere.addAll(segs);
}

return segsHere;
}

public static LinkedHashMap<SegmentGroup, ArrayList<Integer>> getSegmentGroupsVsSegIds(Cell cell) {
public static LinkedHashMap<SegmentGroup, ArrayList<Integer>> getSegmentGroupsVsSegIds(Cell cell) throws NeuroMLException {

LinkedHashMap<SegmentGroup, ArrayList<Integer>> sgVsSegId = new LinkedHashMap<SegmentGroup, ArrayList<Integer>>();

Expand All @@ -162,13 +245,33 @@ public static LinkedHashMap<SegmentGroup, ArrayList<Integer>> getSegmentGroupsVs
return sgVsSegId;
}

public static LinkedHashMap<SegmentGroup, ArrayList<Integer>> getSegmentGroupsVsSegIds(Cell cell, NeuroMLDocument nml2doc) throws NeuroMLException {

LinkedHashMap<SegmentGroup, ArrayList<Integer>> sgVsSegId = new LinkedHashMap<SegmentGroup, ArrayList<Integer>>();

Morphology morphology = getCellMorphology(cell, nml2doc);

LinkedHashMap<String, SegmentGroup> namesVsSegmentGroups = getNamesVsSegmentGroups(cell, nml2doc);

for (SegmentGroup sg : morphology.getSegmentGroup()) {
ArrayList<Integer> segsHere = getSegmentIdsInGroup(namesVsSegmentGroups, sg);
sgVsSegId.put(sg, segsHere);
}

return sgVsSegId;
}

public static double distance(Point3DWithDiam p, Point3DWithDiam d) {
return Math.sqrt( Math.pow(p.getX()-d.getX(),2) + Math.pow(p.getY()-d.getY(),2) + Math.pow(p.getZ()-d.getZ(),2) );
}

public static double getFractionAlongSegGroupLength(Cell cell, String segmentGroup, int segmentId, float fractAlongSegment) throws NeuroMLException {
return getFractionAlongSegGroupLength(cell, null, segmentGroup, segmentId, fractAlongSegment);
}

public static double getFractionAlongSegGroupLength(Cell cell, NeuroMLDocument nml2doc, String segmentGroup, int segmentId, float fractAlongSegment) throws NeuroMLException {

ArrayList<Segment> segs = getSegmentsInGroup(cell, segmentGroup);
ArrayList<Segment> segs = getSegmentsInGroup(cell, nml2doc, segmentGroup);
if (segs.size()==1)
{
if(segs.get(0).getId()!=segmentId)
Expand Down Expand Up @@ -235,30 +338,45 @@ public static double getFractionAlongSegGroupLength(Cell cell, String segmentGro

public static void main(String[] args) throws Exception {
NeuroMLConverter conv = new NeuroMLConverter();
//String test = "/home/padraig/neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/bask.cell.nml";


ArrayList<String> cellFiles = new ArrayList<String>();
cellFiles.add("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/bask.cell.nml");
//String test = "/home/padraig/neuroConstruct/osb/hippocampus/networks/nc_superdeep/neuroConstruct/generatedNeuroML2/pvbasketcell.cell.nml";
String test = "/Users/padraig/neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/pyr_4_sym.cell.nml";
test = "/Users/padraig/git/GoC_Varied_Inputs/Cells/Golgi/GoC.cell.nml";
cellFiles.add("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/pyr_4_sym.cell.nml");
//test = "/Users/padraig/git/GoC_Varied_Inputs/Cells/Golgi/GoC.cell.nml";
//test = "/home/padraig/neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/bask_soma.cell.nml";
NeuroMLDocument nml2 = conv.loadNeuroML(new File(test));

Cell cell = nml2.getCell().get(0);
System.out.println("cell: " + cell.getId());
cellFiles.add("../git/morphology_include/pyr_soma_m_out_b_in.cell.nml");

LinkedHashMap<Integer, Segment> ids = getIdsVsSegments(cell);
for(String cellFile : cellFiles)
{
NeuroMLDocument nml2doc = conv.loadNeuroML(new File(cellFile), true, true);

System.out.println("getIdsVsSegments: ");
for (Integer id: ids.keySet()) {
System.out.println("ID "+id+": "+ids.get(id));
}
Cell cell = nml2doc.getCell().get(0);
System.out.println("-------- Cell loaded: " + cell.getId()+" from "+cellFile);

LinkedHashMap<SegmentGroup, ArrayList<Integer>> sgVsSegId = getSegmentGroupsVsSegIds(cell);
for (SegmentGroup sg: sgVsSegId.keySet()) {
System.out.println("SG "+sg.getId()+": "+sgVsSegId.get(sg));
LinkedHashMap<Integer, Segment> ids = getIdsVsSegments(cell, nml2doc);

System.out.println("getIdsVsSegments: ");
for (Integer id: ids.keySet()) {
System.out.println("ID "+id+": "+ids.get(id));
}

System.out.println("hasUnbranchedNonOverlappingInfo: "+hasUnbranchedNonOverlappingInfo(cell, nml2doc));
System.out.println("getSegmentWithId: "+getSegmentWithId(cell, nml2doc, 0));

System.out.println("getSegmentsInGroup: "+getSegmentsInGroup(cell, nml2doc, "soma_group"));

System.out.println("getFractionAlongSegGroupLength: "+getFractionAlongSegGroupLength(cell, nml2doc, "soma_group", 0, 0.1f));

LinkedHashMap<SegmentGroup, ArrayList<Integer>> sgVsSegId = getSegmentGroupsVsSegIds(cell, nml2doc);
for (SegmentGroup sg: sgVsSegId.keySet()) {
System.out.println("SG "+sg.getId()+": "+sgVsSegId.get(sg));
}
//getFractionAlongSegGroupLength(cell, "basal2", 8, 0.1f);
//getFractionAlongSegGroupLength(cell, "some_apicals", 2, 0.5f);
}
getFractionAlongSegGroupLength(cell, "soma_group", 0, 0.1f);
//getFractionAlongSegGroupLength(cell, "basal2", 8, 0.1f);
//getFractionAlongSegGroupLength(cell, "some_apicals", 2, 0.5f);

}

Expand Down
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