diff --git a/caseExamples/NeuroML2/Case1_new_morphOnly.cell.nml b/caseExamples/NeuroML2/Case1_new_morphOnly.cell.nml
new file mode 100644
index 0000000..a17d7be
--- /dev/null
+++ b/caseExamples/NeuroML2/Case1_new_morphOnly.cell.nml
@@ -0,0 +1,98 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case1_new.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case1_orig_morphOnly.cell.nml b/caseExamples/NeuroML2/Case1_orig_morphOnly.cell.nml
new file mode 100644
index 0000000..1a90fc5
--- /dev/null
+++ b/caseExamples/NeuroML2/Case1_orig_morphOnly.cell.nml
@@ -0,0 +1,90 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case1_orig.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case2_new_morphOnly.cell.nml b/caseExamples/NeuroML2/Case2_new_morphOnly.cell.nml
new file mode 100644
index 0000000..bad8e7c
--- /dev/null
+++ b/caseExamples/NeuroML2/Case2_new_morphOnly.cell.nml
@@ -0,0 +1,87 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case2_new.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case2_orig_morphOnly.cell.nml b/caseExamples/NeuroML2/Case2_orig_morphOnly.cell.nml
new file mode 100644
index 0000000..297d6be
--- /dev/null
+++ b/caseExamples/NeuroML2/Case2_orig_morphOnly.cell.nml
@@ -0,0 +1,87 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case2_orig.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case3_new_morphOnly.cell.nml b/caseExamples/NeuroML2/Case3_new_morphOnly.cell.nml
new file mode 100644
index 0000000..aff644d
--- /dev/null
+++ b/caseExamples/NeuroML2/Case3_new_morphOnly.cell.nml
@@ -0,0 +1,76 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case3_new.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case3_orig_morphOnly.cell.nml b/caseExamples/NeuroML2/Case3_orig_morphOnly.cell.nml
new file mode 100644
index 0000000..1af37e2
--- /dev/null
+++ b/caseExamples/NeuroML2/Case3_orig_morphOnly.cell.nml
@@ -0,0 +1,148 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case3_orig.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case4_new_morphOnly.cell.nml b/caseExamples/NeuroML2/Case4_new_morphOnly.cell.nml
new file mode 100644
index 0000000..49211af
--- /dev/null
+++ b/caseExamples/NeuroML2/Case4_new_morphOnly.cell.nml
@@ -0,0 +1,108 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case4_new.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case4_orig_morphOnly.cell.nml b/caseExamples/NeuroML2/Case4_orig_morphOnly.cell.nml
new file mode 100644
index 0000000..5cc1172
--- /dev/null
+++ b/caseExamples/NeuroML2/Case4_orig_morphOnly.cell.nml
@@ -0,0 +1,108 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case4_orig.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case5_new_morphOnly.cell.nml b/caseExamples/NeuroML2/Case5_new_morphOnly.cell.nml
new file mode 100644
index 0000000..a622111
--- /dev/null
+++ b/caseExamples/NeuroML2/Case5_new_morphOnly.cell.nml
@@ -0,0 +1,102 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case5_new.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/caseExamples/NeuroML2/Case5_orig_morphOnly.cell.nml b/caseExamples/NeuroML2/Case5_orig_morphOnly.cell.nml
new file mode 100644
index 0000000..5c0ccd8
--- /dev/null
+++ b/caseExamples/NeuroML2/Case5_orig_morphOnly.cell.nml
@@ -0,0 +1,99 @@
+
+
+
+ Neuronal morphology exported in NeuroML v2.3.1 from CVapp (NeuroMorpho.org version)
+ Original file: Case5_orig.swc
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/cvapp/main.java b/src/cvapp/main.java
index 9d53d88..f05e98d 100644
--- a/src/cvapp/main.java
+++ b/src/cvapp/main.java
@@ -324,13 +324,18 @@ private static void doTests(neuronEditorFrame nef, String fileName, String nmlEx
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_"+nml2FileName;
}
- File nml2File = new File(nmlExportDir, nml2FileName);
- nep.writeStringToFile(nep.getCell().writeNeuroML_v2(), nml2File.getAbsolutePath());
+ File nml2File = new File(nmlExportDir, nml2FileName);
+ nep.writeStringToFile(nep.getCell().writeNeuroML_v2(), nml2File.getAbsolutePath());
System.out.println("Saved NeuroML representation of the file to: "+nml2File.getAbsolutePath()+": "+nml2File.exists());
-
validateXMLWithURL(nml2File, LATEST_NEUROML_V2_SCHEMA);
+
+ nml2FileName = nml2FileName.replace(".cell","_morphOnly.cell");
+ File nml2FileMorph = new File(nmlExportDir, nml2FileName);
+ nep.writeStringToFile(nep.getCell().writeNeuroML_v2_morphologyOnly(), nml2FileMorph.getAbsolutePath());
+ System.out.println("Saved NeuroML representation of the file to: "+nml2FileMorph.getAbsolutePath()+": "+nml2FileMorph.exists());
+ validateXMLWithURL(nml2FileMorph, LATEST_NEUROML_V2_SCHEMA);
}
diff --git a/src/cvapp/neulucData.java b/src/cvapp/neulucData.java
index c366a52..89f630c 100644
--- a/src/cvapp/neulucData.java
+++ b/src/cvapp/neulucData.java
@@ -661,7 +661,7 @@ public String writeNeuroML_v1_8_1() {
// above also sets maxType to the maximal nlcode;
neuromlWriter nw = new neuromlWriter(points, sectionTypes, sourceFileName);
- return nw.nmlString(neuromlWriter.NeuroMLVersion.NEUROML_VERSION_1_8_1);
+ return nw.nmlString(neuromlWriter.NeuroMLVersion.NEUROML_VERSION_1_8_1, false);
}
public String writeNeuroML_v2() {
@@ -670,7 +670,15 @@ public String writeNeuroML_v2() {
// above also sets maxType to the maximal nlcode;
neuromlWriter nw = new neuromlWriter(points, sectionTypes, sourceFileName);
- return nw.nmlString(neuromlWriter.NeuroMLVersion.NEUROML_VERSION_2_3_1);
+ return nw.nmlString(neuromlWriter.NeuroMLVersion.NEUROML_VERSION_2_3_1, false);
+ }
+ public String writeNeuroML_v2_morphologyOnly() {
+ unwrite();
+ // rootpoint = maxRadiusPoint();
+ // above also sets maxType to the maximal nlcode;
+
+ neuromlWriter nw = new neuromlWriter(points, sectionTypes, sourceFileName);
+ return nw.nmlString(neuromlWriter.NeuroMLVersion.NEUROML_VERSION_2_3_1, true);
}
public String GENESISwriteHR() {
diff --git a/src/cvapp/neuromlWriter.java b/src/cvapp/neuromlWriter.java
index ef93247..a512e08 100644
--- a/src/cvapp/neuromlWriter.java
+++ b/src/cvapp/neuromlWriter.java
@@ -123,9 +123,13 @@ public boolean isVersion1()
form.setGroupingUsed(false);
}
- public String nmlString(NeuroMLVersion version) {
+ public String nmlString(NeuroMLVersion version, boolean morphologyOnly) {
if (points.size() < 2 || sectionTypes.length < 2 || !sectionTypes[1].equals("soma")) {
- System.out.println("error: null data or section types in hocWrite");
+ System.out.println("Error: null data or section types in hocWrite");
+ return "";
+ }
+ if (version.isVersion1() && morphologyOnly) {
+ System.out.println("Error: morphologyOnly option only supported by version 2");
return "";
}
@@ -209,10 +213,13 @@ public String nmlString(NeuroMLVersion version) {
INDENT+"length_units=\"micrometer\">\n\n");
} else if (version.isVersion2()) {
+ String nmlId = cellName;
+ if (morphologyOnly)
+ nmlId += "_morphology";
sbf.append("\n\n");
+ INDENT+"id=\""+nmlId+"\">\n\n");
}
String metaPrefix="";
@@ -222,7 +229,7 @@ public String nmlString(NeuroMLVersion version) {
sbf.append(INDENT+INDENT+"\n");
metaPrefix = "meta:";
- } else if (version.isVersion2()){
+ } else if (version.isVersion2() && !morphologyOnly){
sbf.append(INDENT+"| \n");
}
@@ -277,9 +284,12 @@ public String nmlString(NeuroMLVersion version) {
{
sbf.append(INDENT+INDENT+INDENT+"\n\n");
- sbf.append(INDENT+"\n\n");
+ if (!morphologyOnly)
+ {
+ sbf.append(INDENT+"\n\n");
- sbf.append(INDENT+" | \n");
+ sbf.append(INDENT+" | \n");
+ }
}
sbf.append("\n");
diff --git a/src/cvapp/neuronEditorPanel.java b/src/cvapp/neuronEditorPanel.java
index 9b450de..dde8331 100644
--- a/src/cvapp/neuronEditorPanel.java
+++ b/src/cvapp/neuronEditorPanel.java
@@ -76,7 +76,8 @@ class neuronEditorPanel extends JPanel implements ActionListener, ItemListener {
protected final static String SAVE_GENESIS = "GENESIS";
protected final static String SAVE_NEUROML_v1 = "NeuroML v1.8.1";
protected final static String SAVE_NEUROML_v2alpha = "NeuroML v2alpha";
- protected final static String SAVE_NEUROML_v2 = "NeuroML v2";
+ protected final static String SAVE_NEUROML_v2_cell = "NeuroML v2 ";
+ protected final static String SAVE_NEUROML_v2_morphOnly = "NeuroML v2 ";
protected final static String CENTER = "Center";
@@ -577,14 +578,24 @@ public void processNameEvent(String sarg) {
} else {
System.out.println("file writing not allowed ");
}
- } else if (sarg.startsWith(neuronEditorPanel.SAVE_NEUROML_v2)) {
+ } else if (sarg.startsWith(neuronEditorPanel.SAVE_NEUROML_v2_cell)) {
if (canWriteFiles) {
File f = fileString.getFileToSave(this, fdir, "Select NeuroML file");
if (f != null) {
blockingMessageOn("formatting as NeuroML");
writeStringToFile(cell.writeNeuroML_v2(), f.getAbsolutePath());
}
+ } else {
+ System.out.println("file writing not allowed ");
+ }
+ } else if (sarg.startsWith(neuronEditorPanel.SAVE_NEUROML_v2_morphOnly)) {
+ if (canWriteFiles) {
+ File f = fileString.getFileToSave(this, fdir, "Select NeuroML file");
+ if (f != null) {
+ blockingMessageOn("formatting as NeuroML");
+ writeStringToFile(cell.writeNeuroML_v2_morphologyOnly(), f.getAbsolutePath());
+ }
} else {
System.out.println("file writing not allowed ");
}
@@ -702,7 +713,8 @@ class ModifiedOptionBar extends JPanel implements ItemListener, ActionListener {
options.addItem(neuronEditorPanel.SAVE_NEURON);
options.addItem(neuronEditorPanel.SAVE_GENESIS);
options.addItem(neuronEditorPanel.SAVE_NEUROML_v1);
- options.addItem(neuronEditorPanel.SAVE_NEUROML_v2);
+ options.addItem(neuronEditorPanel.SAVE_NEUROML_v2_cell);
+ options.addItem(neuronEditorPanel.SAVE_NEUROML_v2_morphOnly);
add(saveLabel);
add(options);
@@ -761,8 +773,10 @@ public void actionPerformed(ActionEvent e) {
neupan.processNameEvent("save as Genesis - hierarchical");
} else if (sarg.equals(neuronEditorPanel.SAVE_NEUROML_v1)) {
neupan.processNameEvent(neuronEditorPanel.SAVE_NEUROML_v1);
- } else if (sarg.equals(neuronEditorPanel.SAVE_NEUROML_v2)) {
- neupan.processNameEvent(neuronEditorPanel.SAVE_NEUROML_v2);
+ } else if (sarg.equals(neuronEditorPanel.SAVE_NEUROML_v2_cell)) {
+ neupan.processNameEvent(neuronEditorPanel.SAVE_NEUROML_v2_cell);
+ } else if (sarg.equals(neuronEditorPanel.SAVE_NEUROML_v2_morphOnly)) {
+ neupan.processNameEvent(neuronEditorPanel.SAVE_NEUROML_v2_morphOnly);
} else if (sarg.equals("Center")) {
neupan.neucan.find();
} else {
|