public static String cleanForXML(String line) {
StringBuilder buffer = new StringBuilder();
for (int i = 0; i < line.length(); i++) {
char c = line.charAt(i);
if (c < 128 && Character.isLetter(c)) {
buffer.append(c);
} else {
buffer.append('_');
}
}
return buffer.toString();
}
/**
* Get any children that match this name or path. Similar to getChild(), but will grab multiple
* matches rather than only the first.
*
* @param name element name or path/to/element
* @return array of child elements that match
* @author processing.org
*/
public XML[] getChildren(String name) {
if (name.length() > 0 && name.charAt(0) == '/') {
throw new IllegalArgumentException("getChildren() should not begin with a slash");
}
if (name.indexOf('/') != -1) {
return getChildrenRecursive(PApplet.split(name, '/'), 0);
}
// if it's a number, do an index instead
// (returns a single element array, since this will be a single match
if (Character.isDigit(name.charAt(0))) {
return new XML[] {getChild(Integer.parseInt(name))};
}
int childCount = getChildCount();
XML[] matches = new XML[childCount];
int matchCount = 0;
for (int i = 0; i < childCount; i++) {
XML kid = getChild(i);
String kidName = kid.getName();
if (kidName != null && kidName.equals(name)) {
matches[matchCount++] = kid;
}
}
return (XML[]) PApplet.subset(matches, 0, matchCount);
}
/**
* Internal helper function for getChild(String).
*
* @param items result of splitting the query on slashes
* @param offset where in the items[] array we're currently looking
* @return matching element or null if no match
* @author processing.org
*/
protected XML getChildRecursive(String[] items, int offset) {
// if it's a number, do an index instead
if (Character.isDigit(items[offset].charAt(0))) {
XML kid = getChild(Integer.parseInt(items[offset]));
if (offset == items.length - 1) {
return kid;
} else {
return kid.getChildRecursive(items, offset + 1);
}
}
int childCount = getChildCount();
for (int i = 0; i < childCount; i++) {
XML kid = getChild(i);
String kidName = kid.getName();
if (kidName != null && kidName.equals(items[offset])) {
if (offset == items.length - 1) {
return kid;
} else {
return kid.getChildRecursive(items, offset + 1);
}
}
}
return null;
}
public void run() {
// String a =
// "http://neuromorpho.org/neuroMorpho/dableFiles/borst/CNG%20version/dCH-cobalt.CNG.swc"; //
// For developer use
if (myArgs.length == 0) {
String usage =
"\nError, missing SWC file containing morphology!\n\nUsage: \n java -cp build cvapp.main swc_file [-test]"
+ "\n or:\n ./run.sh swc_file ["
+ TEST_FLAG
+ "|"
+ TEST_NOGUI_FLAG
+ "|"
+ NEUROML1_EXPORT_FLAG
+ "|"
+ NEUROML2_EXPORT_FLAG
+ "]\n\n"
+ "where swc_file is the file name or URL of the SWC morphology file\n";
System.out.println(usage);
System.exit(0);
}
String a = myArgs[0];
File baseDir = new File(".");
if ((new File(a)).exists()) {
baseDir = (new File(a)).getParentFile();
}
try {
File root =
new File(main.class.getProtectionDomain().getCodeSource().getLocation().toURI().getPath())
.getParentFile();
if (!a.startsWith("http://") && !a.startsWith("file://")) {
a = "file://" + (new File(a)).getCanonicalPath();
}
boolean supressGui = false;
if (myArgs.length == 2
&& (myArgs[1].equals(TEST_NOGUI_FLAG)
|| myArgs[1].equals(NEUROML1_EXPORT_FLAG)
|| myArgs[1].equals(NEUROML2_EXPORT_FLAG))) {
supressGui = true;
}
neuronEditorFrame nef = null;
nef = new neuronEditorFrame(700, 600, supressGui);
// nef.validate();
nef.pack();
centerWindow(nef);
nef.setVisible(!supressGui);
nef.setReadWrite(true, true);
int indexof = a.lastIndexOf('/') + 1;
String directory = a.substring(0, indexof);
String fileName = a.substring(indexof, a.length());
URL u = new URL(a);
String sdata[] = readStringArrayFromURL(u);
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + fileName);
nef.loadFile(sdata, directory, fileName);
System.out.println("Loaded: " + fileName);
if (myArgs.length == 2 && myArgs[1].equals(TEST_ONE_FLAG)) {
// Thread.sleep(1000);
doTests(nef, fileName);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML1_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml1FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".xml"
: rootFile.getName() + ".xml";
File nml1File = new File(rootFile.getParentFile(), nml1FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File(root, "Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
System.exit(0);
} else if (myArgs.length == 2 && myArgs[1].equals(NEUROML2_EXPORT_FLAG)) {
File rootFile = (new File(baseDir, fileName)).getAbsoluteFile();
String nml2FileName =
rootFile.getName().endsWith(".swc")
? rootFile.getName().substring(0, rootFile.getName().length() - 4) + ".cell.nml"
: rootFile.getName() + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(rootFile.getParentFile(), nml2FileName);
neuronEditorPanel nep = nef.getNeuronEditorPanel();
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved the NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXML(nml2File, new File(root, "Schemas/v2/NeuroML_v2beta4.xsd"));
System.exit(0);
} else if (myArgs.length == 2
&& (myArgs[1].equals(TEST_FLAG) || (myArgs[1].equals(TEST_NOGUI_FLAG)))) {
// Thread.sleep(1000);
doTests(nef, fileName);
File exampleDir = new File("twoCylSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("spherSomaSwc");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
exampleDir = new File("caseExamples");
for (File f : exampleDir.listFiles()) {
if (f.getName().endsWith(".swc")) {
sdata = fileString.readStringArrayFromFile(f.getAbsolutePath());
nef.setTitle("3DViewer (Modified from CVAPP with permission)-Neuron: " + f.getName());
nef.loadFile(sdata, f.getParent(), f.getName());
doTests(nef, f.getAbsolutePath());
}
}
if (supressGui) System.exit(0);
}
} catch (Exception exception) {
System.err.println("Error while handling SWC file (" + a + ")");
exception.printStackTrace();
}
}
/*
* Carries out a number of tests, generates NEURON, GENESIS and NeuroML code etc.
*/
private static void doTests(neuronEditorFrame nef, String fileName) {
System.out.println(
"Testing Cvapp/NeuroMorpho.Org by generating NEURON, GENESIS and NeuroML files for "
+ fileName);
File tempDir = new File("temp");
if (!tempDir.exists()) tempDir.mkdir();
neuronEditorPanel nep = nef.getNeuronEditorPanel();
String rootFileName = fileName;
if (rootFileName.toLowerCase().endsWith(".swc")) {
rootFileName = rootFileName.substring(0, rootFileName.length() - 4);
}
if (rootFileName.lastIndexOf(System.getProperty("file.separator")) > 0) {
rootFileName =
rootFileName.substring(
rootFileName.lastIndexOf(System.getProperty("file.separator")) + 1);
}
// NEURON save...
String neuronFileName = rootFileName + ".hoc";
File neuronFile = new File(tempDir, neuronFileName);
File neuronTestFile = new File(tempDir, rootFileName + "_test.hoc");
nep.writeStringToFile(nep.getCell().HOCwriteNS(), neuronFile.getAbsolutePath());
StringBuilder sbNeuTest = new StringBuilder();
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/nCtools.hoc\")\n");
sbNeuTest.append("load_file(\"../neuronUtils/cellCheck.hoc\")\n");
sbNeuTest.append("load_file(\"nrngui.hoc\")\n");
sbNeuTest.append("load_file(\"" + neuronFileName + "\")\n\n");
sbNeuTest.append("forall morph()\n");
System.out.println("--------------------------------------------------------------");
nep.writeStringToFile(sbNeuTest.toString(), neuronTestFile.getAbsolutePath());
System.out.println(
"Saved NEURON representation of the file to: "
+ neuronFile.getAbsolutePath()
+ ": "
+ neuronFile.exists());
System.out.println("--------------------------------------------------------------");
// GENESIS save...
String genesisFileName = rootFileName + ".p";
File genesisFile = new File(tempDir, genesisFileName);
File genesisTestFile = new File(tempDir, rootFileName + "_test.g");
nep.writeStringToFile(nep.getCell().GENESISwriteHR(), genesisFile.getAbsolutePath());
StringBuilder sbGenTest = new StringBuilder();
sbGenTest.append("include compartments \n");
sbGenTest.append("create neutral /library\n");
sbGenTest.append("disable /library\n");
sbGenTest.append("ce /library\n");
sbGenTest.append("make_cylind_compartment\n");
sbGenTest.append("make_cylind_symcompartment\n");
sbGenTest.append("make_sphere_compartment\n");
sbGenTest.append("ce /\n");
sbGenTest.append(
"echo \"Prototype compartments created, reading cell from " + genesisFileName + "\"\n");
sbGenTest.append("readcell " + genesisFileName + " /mycell\n\n");
sbGenTest.append("create xform /form [0,0,400,400] -nolabel\n");
sbGenTest.append(
"create xdraw /form/draw [0,0,100%,100%] -wx 0.002 -wy 0.002 -transform ortho3d -bg white\n");
sbGenTest.append(
"setfield /form/draw xmin -3.0E-4 xmax 3.0E-4 ymin -3.0E-4 ymax 3.0E-4 vx 0.0 vy 0.0 vz -0.002\n");
sbGenTest.append(
"create xcell /form/draw/cell -path \"/mycell/##[][TYPE=compartment],/mycell/##[][TYPE=symcompartment]\" -colfield Vm -colmin -0.07 -colmax 0.03 -diarange -5\n");
sbGenTest.append("xcolorscale hot\n");
sbGenTest.append("xshow /form\n\n");
sbGenTest.append("showfield /mycell/##[][TYPE=compartment] **\n\n");
nep.writeStringToFile(sbGenTest.toString(), genesisTestFile.getAbsolutePath());
System.out.println(
"Saved GENESIS representation of the file to: "
+ genesisFile.getAbsolutePath()
+ ": "
+ genesisFile.exists());
System.out.println("--------------------------------------------------------------");
// NeuroML save...
String nml1FileName = rootFileName + ".xml";
File nml1File = new File(tempDir, nml1FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v1_8_1(), nml1File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml1File.getAbsolutePath()
+ ": "
+ nml1File.exists());
File v1schemaFile = new File("Schemas/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd");
validateXML(nml1File, v1schemaFile);
String nml2FileName = rootFileName + ".cell.nml";
if (Character.isDigit(nml2FileName.charAt(0))) {
nml2FileName = "Cell_" + nml2FileName;
}
File nml2File = new File(tempDir, nml2FileName);
nep.writeStringToFile(nep.getCell().writeNeuroML_v2beta(), nml2File.getAbsolutePath());
System.out.println(
"Saved NeuroML representation of the file to: "
+ nml2File.getAbsolutePath()
+ ": "
+ nml2File.exists());
validateXMLWithURL(nml2File, "Schemas/v2/NeuroML_v2beta4.xsd");
}