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NeuGen's pseudo-backend: Improved comments - the pseudo-backend can b…
…e used to generate networks and export them. Anything further has to be implemented if necessary.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -87,10 +87,12 @@ | |
| import org.neugen.utils.Utils; | ||
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| /** | ||
| * @brief provide some backend functionality | ||
| * @brief NeuGen's backend | ||
| * Note: This pseudo-backend attempts to disentangle the interweaved | ||
| * GUI and backend components of NeuGen. Therefore this pseudo-backend | ||
| * may be considered as a hack. Some functionality is available, cf. | ||
| * below, however this backend needs to be enhanced for desired functionality. | ||
| * @author stephanmg <[email protected]> | ||
| * | ||
| * @note maybe a configuration builder (SettingsBuilder) is a good choice | ||
| */ | ||
| public final class NGBackend { | ||
| /// public static members | ||
|
|
@@ -119,8 +121,7 @@ public NGBackend(boolean with_gui) { | |
| } | ||
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| /** | ||
| * @brief executes just the project | ||
| * | ||
| * @brief executes the project | ||
| * @param projectType | ||
| */ | ||
| public void execute(String projectType) { | ||
|
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@@ -129,12 +130,11 @@ public void execute(String projectType) { | |
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| /** | ||
| * @brief loads the initial parameters from project directory | ||
| * | ||
| * @param file | ||
| * @param root | ||
| * @return | ||
| * @return parameter list | ||
| */ | ||
| @SuppressWarnings("CallToPrintStackTrace") | ||
| @SuppressWarnings({"CallToPrintStackTrace", "CallToThreadDumpStack"}) | ||
| private XMLObject loadParam(File file) { | ||
| XMLObject root = null; | ||
| try { | ||
|
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@@ -150,10 +150,10 @@ private XMLObject loadParam(File file) { | |
| } | ||
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| /** | ||
| * @brief get's the project property | ||
| * | ||
| * @brief get the project property | ||
| * @param projectPath | ||
| * @param projectType | ||
| * @return list of properties | ||
| */ | ||
| private Properties getProjectProp(String projectPath, String projectType) { | ||
| Properties prop = new Properties(); | ||
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@@ -177,13 +177,12 @@ private Properties getProjectProp(String projectPath, String projectType) { | |
| } | ||
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| /** | ||
| * @brief creates a project | ||
| * | ||
| * @brief creates a NeuGen project | ||
| * @param projectPath | ||
| * @param projectType | ||
| * @param force | ||
| * @param open_only - if specified opens only the project | ||
| * @return | ||
| * @return parameters as a map | ||
| */ | ||
| @SuppressWarnings("NestedAssignment") | ||
| public Map<String, XMLObject> create_and_open_project(String projectPath, String projectType, boolean force, boolean open_only) { | ||
|
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@@ -309,8 +308,7 @@ public Map<String, XMLObject> create_and_open_project(String projectPath, String | |
| } | ||
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| /** | ||
| * @brief saves the PARAM parameters | ||
| * | ||
| * @brief saves the PARAM parameters (NeuGen parameters) | ||
| * @param currentRoot | ||
| * @param projectDirPath | ||
| */ | ||
|
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@@ -319,8 +317,7 @@ private void save_param(XMLNode currentRoot, String projectDirPath) { | |
| } | ||
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| /** | ||
| * @brief saves the INTERNA parameters | ||
| * | ||
| * @brief saves the INTERNA parameters (NeuGen parameters) | ||
| * @param currentRoot | ||
| * @param projectDirPath | ||
| */ | ||
|
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@@ -330,7 +327,6 @@ private void save_interna(XMLNode currentRoot, String projectDirPath) { | |
|
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| /** | ||
| * @brief save all params | ||
| * | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| */ | ||
|
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@@ -340,8 +336,7 @@ public void save(Map<String, XMLObject> paramTrees, String projectDirPath) { | |
| } | ||
|
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| /** | ||
| * @brief saves INTERNA or PARAM parameters | ||
| * | ||
| * @brief saves INTERNA or PARAM parameters (NeuGen parameters) | ||
| * @param currentRoot | ||
| * @param projectDirPath | ||
| * @param param | ||
|
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@@ -350,7 +345,7 @@ private void save(XMLNode currentRoot, String projectDirPath, String param) { | |
| logger.info("leaf count: " + currentRoot.getLeafCount()); | ||
|
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| /** | ||
| * @todo brief: tied to GUI! | ||
| * @todo brief: tied to GUI! (implement the pseudocode below - more reasonable) | ||
| * workaround: 1) alter parameters in project file before generating the net | ||
| * 2) generate net | ||
| * 3) save the file in a gui-independent way (i. e. | ||
|
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@@ -378,56 +373,52 @@ private void save(XMLNode currentRoot, String projectDirPath, String param) { | |
| } | ||
|
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| /** | ||
| * @brief init param table | ||
| * | ||
| * @brief inits param table | ||
| * @param paramTrees | ||
| * @param paramPath | ||
| * @param internaPath | ||
| * @return map of parameters | ||
| */ | ||
| private Map<String, XMLObject> initParamTable(Map<String, XMLObject> paramTrees, String paramPath, String internaPath) { | ||
| XMLObject param = paramTrees.get(NeuGenConstants.PARAM); | ||
| XMLObject interna = paramTrees.get(NeuGenConstants.INTERNA); | ||
| Map<String, XMLObject> allParam = new HashMap<String, XMLObject>(); | ||
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| allParam.put(paramPath, param); | ||
| allParam.put(internaPath, interna); | ||
| return allParam; | ||
| } | ||
|
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| /** | ||
| * @brief init all parameters | ||
| * | ||
| * @brief inits all parameters | ||
| * @param dirPath | ||
| * @param projectType | ||
| * @return map of all parameters | ||
| */ | ||
| private Map<String, XMLObject> initProjectParam(String dirPath, String projectType) { | ||
| File param = new File(dirPath + System.getProperty("file.separator") + NeuGenConstants.PARAM_FNAME); | ||
| File interna = new File(dirPath + System.getProperty("file.separator") + NeuGenConstants.INTERNA_FNAME); | ||
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| Map<String, XMLObject> paramTrees = new HashMap<String, XMLObject>(); | ||
| XMLObject paramRoot = loadParam(param); | ||
| XMLObject internaRoot = loadParam(interna); | ||
| paramTrees.put(NeuGenConstants.PARAM, paramRoot); | ||
| paramTrees.put(NeuGenConstants.INTERNA, internaRoot); | ||
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| NeuGenLib.initParamData(initParamTable(paramTrees, param.getPath(), interna.getPath()), projectType); | ||
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| return paramTrees; | ||
| } | ||
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| /** | ||
| * @brief generates the net actually | ||
| * | ||
| * @brief generates the NeuGen net | ||
| * @param projectType | ||
| */ | ||
| public void generate_network(String projectType) { | ||
| ngLib.run(projectType); | ||
| /// not necessary: | ||
| /// ngLib.getNet().destroy(); | ||
| /// ngLib.destroy(); | ||
| } | ||
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| /** | ||
| * @brief saves and closes project | ||
| * @brief saves and closes the NeuGen project | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| */ | ||
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@@ -446,12 +437,10 @@ public void save_and_close_project(Map<String, XMLObject> paramTrees, String pro | |
| } | ||
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| /** | ||
| * @brief exports a network | ||
| * | ||
| * @brief exports the NeuGen network | ||
| * Note: Enhance this function by needs, i. e. if you | ||
| * need another exporter, like HOC or something else, you | ||
| * may add it here | ||
| * | ||
| * @param type | ||
| * @param file | ||
| * @param withCellType | ||
|
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@@ -476,7 +465,6 @@ public void export_network(String type, String file, boolean withCellType) { | |
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| /** | ||
| * @brief modify the project params and set them | ||
| * | ||
| * @param paramTrees; | ||
| * @param projectDirPath | ||
| */ | ||
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@@ -492,8 +480,7 @@ public void modifyProject(Map<String, XMLObject> paramTrees, String projectDirPa | |
| } | ||
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| /** | ||
| * @brief modifies n parts density | ||
| * | ||
| * @brief modifies n parts density (NeuGen property) | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| * @param density | ||
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@@ -578,8 +565,7 @@ public void modifyNPartsDensity(Map<String, XMLObject> paramTrees, String projec | |
| } | ||
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| /** | ||
| * @brief correct synapse dist to custom value | ||
| * | ||
| * @brief correct synapse dist to custom value (NeuGen property) | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| * @param dist_synapse | ||
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@@ -609,7 +595,7 @@ public void modifySynapseDistance(Map<String, XMLObject> paramTrees, String proj | |
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| /** | ||
| * @brief modifies a Neuron and Interna parameter | ||
| * @brief modifies a Neuron and INTERNA parameter | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| * @param param | ||
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@@ -623,7 +609,7 @@ public void modifyAllParameter(Map<String, XMLObject> paramTrees, String project | |
| } | ||
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| /** | ||
| * @brief modifies a Neuron or Interna parameter | ||
| * @brief modifies a Neuron or INTERNA parameter | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| * @param param | ||
|
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@@ -642,7 +628,7 @@ private void modifyParameter(Map<String, XMLObject> paramTrees, String projectDi | |
| } | ||
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| /** | ||
| * @brief modify's an Interna parameter | ||
| * @brief modifies an INTERNA parameter (NeuGen parameter) | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| * @param param | ||
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@@ -653,7 +639,7 @@ public void modifyInternaParameter(Map<String, XMLObject> paramTrees, String pro | |
| } | ||
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| /** | ||
| * @brief modify's a Neuron parameter | ||
| * @brief modifies a Neuron parameter (NeuGen parameter) | ||
| * @param paramTrees | ||
| * @param projectDirPath | ||
| * @param param | ||
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@@ -664,7 +650,7 @@ public void modifyNeuronParameter(Map<String, XMLObject> paramTrees, String proj | |
| } | ||
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| /** | ||
| * @brief modifies some NEURON parameter recursively | ||
| * @brief modifies some Neuron parameter recursively (NeuGen parameter) | ||
| * @param paramTree | ||
| * @param projectDirPath | ||
| * @param param | ||
|
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@@ -693,7 +679,7 @@ private void modifyParameter(XMLObject paramTree, String projectDirPath, double | |
| } | ||
|
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| /** | ||
| * @brief modifies some NEURON parameter recursively | ||
| * @brief modifies some Neuron parameter recursively (NeuGen parameter) | ||
| * @param root | ||
| * @param param | ||
| * @param identifier | ||
|
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@@ -718,10 +704,9 @@ private void modifyParameter_rec(XMLNode root, double param, ArrayList<String> i | |
| } | ||
|
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| /** | ||
| * @brief replaces content of a given node specified by identifier with | ||
| * replacement | ||
| * @brief replaces content of a given node. | ||
| * The replacement is specified by identifier. | ||
| * @author stephanmg <[email protected]> | ||
| * | ||
| * @param child | ||
| * @param identifier | ||
| * @param replacement | ||
|
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@@ -752,7 +737,7 @@ private void correct_siblings(XMLNode child, String identifier, double replaceme | |
|
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| /** | ||
| * @brief returns the project type | ||
| * @return | ||
| * @return project type | ||
| */ | ||
| public String getProjectType() { | ||
| if (Region.isCa1Region()) { | ||
|
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@@ -765,22 +750,20 @@ public String getProjectType() { | |
| } | ||
|
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| /** | ||
| * @brief test | ||
| * | ||
| * @brief main method | ||
| * @param args | ||
| */ | ||
| @SuppressWarnings("CallToPrintStackTrace") | ||
| @SuppressWarnings({"CallToPrintStackTrace", "CallToThreadDumpStack"}) | ||
| public static void main(String... args) { | ||
| /** | ||
| * @brief todo works - test remaining functionality... | ||
| */ | ||
| try { | ||
| NGBackend back = new NGBackend(); | ||
| Map<String, XMLObject> params = back.create_and_open_project("foo24", NeuGenConstants.NEOCORTEX_PROJECT, true, false); | ||
| back.modifyNPartsDensity(params, "foo24/Neocortex", 0.1); | ||
| back.generate_network(NeuGenConstants.NEOCORTEX_PROJECT); | ||
| back.export_network("NGX", "foo24.ngx", false); | ||
| back.save_and_close_project(params, "foo26"); | ||
| /// TODO: fix for save_and_close_project necessary | ||
| /// back.save_and_close_project(params, "foo26"); | ||
|
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| } catch (Exception e) { | ||
| logger.fatal("Make sure you selected a valid project directory: " + e); | ||
| e.printStackTrace(); | ||
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