Skip to content

Commit

Permalink
Improved handling of cells with external morphology/biophysics
Browse files Browse the repository at this point in the history
  • Loading branch information
@pgleeson
pgleeson committed May 31, 2024
1 parent 23132a9 commit 72c56e1
Show file tree
Hide file tree
Showing 2 changed files with 121 additions and 39 deletions.
157 changes: 119 additions & 38 deletions src/main/java/org/neuroml/model/util/CellUtils.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +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 @@ -46,21 +53,26 @@ public static boolean hasUnbranchedNonOverlappingInfo(Cell cell)
return false;
}

public static Morphology getCellMorphology(Cell cell, NeuroMLDocument nml2doc) {
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()) {
{
for (Morphology m: nml2doc.getMorphology())
{
if (m.getId().equals(cell.getMorphologyAttr()))
return m;
}
}
return null;
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) {
Expand All @@ -80,7 +92,10 @@ else if (cell.getBiophysicalPropertiesAttr() !=null)
return null;
}


/**
* @deprecated use LinkedHashMap<Integer, Segment> 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 @@ -90,6 +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 @@ -98,8 +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 @@ -112,16 +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 @@ -158,34 +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 @@ -199,13 +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 @@ -272,30 +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 nml2doc = conv.loadNeuroML(new File(test));

Cell cell = nml2doc.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<Integer, Segment> ids = getIdsVsSegments(cell, nml2doc);

LinkedHashMap<SegmentGroup, ArrayList<Integer>> sgVsSegId = getSegmentGroupsVsSegIds(cell);
for (SegmentGroup sg: sgVsSegId.keySet()) {
System.out.println("SG "+sg.getId()+": "+sgVsSegId.get(sg));
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
3 changes: 2 additions & 1 deletion src/main/java/org/neuroml/model/util/NeuroML2Validator.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -560,7 +560,8 @@ public static void main(String[] args) throws Exception {
//File f = new File("../git/morphology_include/pyr_soma_m_in_b_in.cell.nml");
//File f = new File("../git/morphology_include/pyr_soma_m_out_b_in.cell.nml");
//File f = new File("../git/morphology_include/pyr_soma_m_in_b_out.cell.nml");
File f = new File("../git/morphology_include/pyr_soma_m_out_b_out.cell.nml");
//File f = new File("../git/morphology_include/pyr_soma_m_out_b_out.cell.nml");
File f = new File("../NeuroML2/examples/NML2_FullNeuroML.nml");
//File f = new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/pyr_4_sym.cell.nml");
//File f = new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/MediumNet.net.nml");
//File f = new File("../OpenCortex/examples/Deterministic.net.nml");
Expand Down

0 comments on commit 72c56e1

Please sign in to comment.