public void loadFromFile(File positionFile) throws java.io.IOException { logger.logComment("Loading position records from file: " + positionFile.getAbsolutePath()); this.reset(); Reader in = new FileReader(positionFile); LineNumberReader reader = new LineNumberReader(in); String nextLine = null; String currentInputRef = null; while ((nextLine = reader.readLine()) != null) { // logger.logComment("Parsing line: "+ nextLine); if (nextLine.endsWith(":")) { currentInputRef = nextLine.substring(0, nextLine.length() - 1); logger.logComment("currentInputRef: " + currentInputRef); } else { SingleElectricalInput input = new SingleElectricalInput(nextLine); this.addSingleInput(currentInputRef, input); } } in.close(); logger.logComment("Finished loading cell info. Internal state: " + this.toString()); }
public void saveToFile(File inputsFile) throws java.io.IOException { logger.logComment( "Saving " + this.getNumberSingleInputs() + " inputs to file: " + inputsFile.getAbsolutePath()); // will create the parent dir if it doesn't exist. if (!inputsFile.exists()) { logger.logComment("File: " + inputsFile + " doesn't exist."); if (!inputsFile.getParentFile().exists()) { logger.logComment("Parent dir: " + inputsFile.getParentFile() + " doesn't exist."); // String parentDirName = inputsFile.getParentFile().getCanonicalPath(); File projectDir = inputsFile.getParentFile().getParentFile(); if (!projectDir.exists()) { throw new FileNotFoundException( "Project dir doesn't exist: " + projectDir.getAbsolutePath()); } // logger.logComment("Going to create dir: "+ parentDirName +" in dir :"+ projectDir); logger.logComment("Going to create dir: " + inputsFile.getParentFile()); inputsFile.getParentFile().mkdir(); logger.logComment("Success? " + inputsFile.getParentFile().exists()); } } FileWriter fw = new FileWriter(inputsFile); Enumeration keys = this.myElecInputs.keys(); while (keys.hasMoreElements()) { String input = (String) keys.nextElement(); ArrayList<SingleElectricalInput> inputs = getInputLocations(input); fw.write(input + ":\n"); for (int i = 0; i < inputs.size(); i++) { fw.write(inputs.get(i) + "\n"); } } logger.logComment("Finished saving data to file: " + inputsFile.getAbsolutePath()); fw.flush(); fw.close(); }
public ArrayList<SimpleXMLEntity> getNetworkMLEntities( int unitSystem, NeuroMLConstants.NeuroMLVersion version, SimpleXMLElement topLevelCompElement) throws NeuroMLException { ArrayList<SimpleXMLEntity> entities = new ArrayList<SimpleXMLEntity>(); Units timeUnits = UnitConverter.timeUnits[unitSystem]; Units currentUnits = UnitConverter.currentUnits[unitSystem]; SimpleXMLElement inputsElement = null; try { logger.logComment( "Going to save file in NeuroML format: " + this.getNumberSingleInputs() + " inputs in total"); if (getNumberSingleInputs() == 0) { SimpleXMLComment comm = new SimpleXMLComment("There are no electrical inputs present in the network"); entities.add(comm); return entities; } boolean nml2 = version.isVersion2(); boolean nml2alpha = version.isVersion2alpha(); if (!nml2) { inputsElement = new SimpleXMLElement(NetworkMLConstants.INPUTS_ELEMENT); entities.add(inputsElement); if (unitSystem == UnitConverter.GENESIS_PHYSIOLOGICAL_UNITS) { inputsElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.UNITS_ATTR, NetworkMLConstants.UNITS_PHYSIOLOGICAL)); } else if (unitSystem == UnitConverter.GENESIS_SI_UNITS) { inputsElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.UNITS_ATTR, NetworkMLConstants.UNITS_SI)); } } Enumeration keys = myElecInputs.keys(); while (keys.hasMoreElements()) { String inputReference = (String) keys.nextElement(); ArrayList<SingleElectricalInput> inputsHere = getInputLocations(inputReference); logger.logComment("Adding " + inputsHere.size() + " inputs"); StimulationSettings nextStim = project.elecInputInfo.getStim(inputReference); ElectricalInput myElectricalInput = nextStim.getElectricalInput(); SimpleXMLElement inputElement = new SimpleXMLElement(NetworkMLConstants.INPUT_ELEMENT); inputElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_NAME_ATTR, inputReference)); if (myElectricalInput instanceof IClamp) { IClamp ic = (IClamp) myElectricalInput; float delay = ic.getDel().getNominalNumber(); float duration = ic.getDur().getNominalNumber(); float amplitude = ic.getAmp().getNominalNumber(); SimpleXMLElement inputTypeElement = new SimpleXMLElement(NetworkMLConstants.PULSEINPUT_ELEMENT); float del = (float) UnitConverter.getTime(delay, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); float dur = (float) UnitConverter.getTime(duration, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); float amp = (float) UnitConverter.getCurrent( amplitude, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_DELAY_ATTR, del + "")); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_DUR_ATTR, dur + "")); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_AMP_ATTR, amp + "")); inputElement.addChildElement(inputTypeElement); inputElement.addContent("\n "); if (nml2) { SimpleXMLElement pulseGenElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_PULSE_GEN_ELEMENT); pulseGenElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, inputReference); pulseGenElement.addAttribute( NetworkMLConstants.INPUT_DELAY_ATTR, del + timeUnits.getNeuroML2Symbol()); pulseGenElement.addAttribute( NetworkMLConstants.INPUT_DUR_ATTR, dur + timeUnits.getNeuroML2Symbol()); pulseGenElement.addAttribute( NetworkMLConstants.INPUT_AMP_ATTR, amp + currentUnits.getNeuroML2Symbol()); topLevelCompElement.addContent("\n\n "); topLevelCompElement.addChildElement(pulseGenElement); topLevelCompElement.addContent("\n\n "); } } else if (myElectricalInput instanceof RandomSpikeTrain) { RandomSpikeTrain rst = (RandomSpikeTrain) myElectricalInput; float stimFreq = rst.getRate().getNominalNumber(); String stimMech = rst.getSynapseType(); SimpleXMLElement inputTypeElement = new SimpleXMLElement(NetworkMLConstants.RANDOMSTIM_ELEMENT); float rate = (float) UnitConverter.getRate(stimFreq, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); inputTypeElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.RND_STIM_FREQ_ATTR, (float) UnitConverter.getRate( stimFreq, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem) + "")); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.RND_STIM_MECH_ATTR, stimMech)); inputElement.addChildElement(inputTypeElement); inputElement.addContent("\n "); if (nml2 && !nml2alpha) { SimpleXMLElement spikeGenElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_SPIKE_GEN_POISSON_ELEMENT); spikeGenElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, inputReference); spikeGenElement.addAttribute( NetworkMLConstants.NEUROML2_SPIKE_GEN_POISSON_RATE_ATTR, rate + " " + UnitConverter.rateUnits[UnitConverter.NEUROCONSTRUCT_UNITS] .getNeuroML2Symbol() + ""); topLevelCompElement.addContent("\n\n "); topLevelCompElement.addChildElement(spikeGenElement); topLevelCompElement.addContent("\n\n "); } } else { throw new NeuroMLException( "Error trying to save input " + inputReference + ". Cannot save in NeuroML an input of type: " + myElectricalInput.getType()); } SimpleXMLElement inputTargetElement = new SimpleXMLElement(NetworkMLConstants.INPUT_TARGET_ELEMENT); inputTargetElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.INPUT_TARGET_POPULATION_ATTR, nextStim.getCellGroup())); inputElement.addChildElement(inputTargetElement); inputTargetElement.addContent("\n "); SimpleXMLElement inputTargetSitesElement = new SimpleXMLElement(NetworkMLConstants.INPUT_TARGET_SITES_ELEMENT); inputTargetSitesElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.INPUT_SITES_SIZE_ATTR, inputsHere.size() + "")); inputTargetElement.addChildElement(inputTargetSitesElement); SimpleXMLElement stimProjElement = null; if (version.isVersion2betaOrLater()) { if (myElectricalInput instanceof IClamp) { SimpleXMLElement inputListElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_INPUT_LIST_ELEMENT); entities.add(inputListElement); inputListElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, nextStim.getReference()); inputListElement.addAttribute( NetworkMLConstants.NEUROML2_INPUT_COMPONENT, inputReference); inputListElement.addAttribute( NetworkMLConstants.NEUROML2_INPUT_POPULATION, nextStim.getCellGroup()); // inputElement.addContent("\n "); inputTargetSitesElement = inputListElement; } else if (myElectricalInput instanceof RandomSpikeTrain) { SimpleXMLElement popElement = new SimpleXMLElement(NetworkMLConstants.POPULATION_ELEMENT); entities.add(0, popElement); popElement.addAttribute( NeuroMLConstants.NEUROML_ID_V2, nextStim.getReference() + "_population"); popElement.addAttribute( NetworkMLConstants.NEUROML2_POPULATION_COMPONENT, nextStim.getReference() + "_population"); popElement.addAttribute( NetworkMLConstants.NEUROML2_POPULATION_SIZE, inputsHere.size() + ""); stimProjElement = new SimpleXMLElement(NetworkMLConstants.PROJECTION_ELEMENT); stimProjElement.addAttribute( NeuroMLConstants.NEUROML_ID_V2, nextStim.getReference() + "_projection"); entities.add(stimProjElement); } } // Iterate around the list of sites for (int i = 0; i < inputsHere.size(); i++) { inputTargetSitesElement.addContent("\n "); SingleElectricalInput sei = inputsHere.get(i); SimpleXMLElement inputTargetSiteElement = new SimpleXMLElement(NetworkMLConstants.INPUT_TARGET_SITE_ELEMENT); inputTargetSiteElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.INPUT_SITE_CELLID_ATTR, sei.getCellNumber() + "")); inputTargetSiteElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.INPUT_SITE_SEGID_ATTR, sei.getSegmentId() + "")); inputTargetSiteElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.INPUT_SITE_FRAC_ATTR, sei.getFractionAlong() + "")); if (!nml2) inputTargetSitesElement.addChildElement(inputTargetSiteElement); if (nml2 && !nml2alpha) { if (myElectricalInput instanceof RandomSpikeTrain) { String connElName = NetworkMLConstants.CONNECTION_ELEMENT; SimpleXMLElement connElement = new SimpleXMLElement(connElName); connElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.CONNECTION_ID_ATTR, i + "")); stimProjElement.addContent("\n "); stimProjElement.addChildElement(connElement); stimProjElement.addContent("\n "); } } if (sei.getInstanceProps() != null) { inputTargetSiteElement.addContent("\n "); inputTargetSiteElement.addComment("Adding the site specific props"); if (sei.getInstanceProps() instanceof IClampInstanceProps) { IClampInstanceProps ic = (IClampInstanceProps) sei.getInstanceProps(); float delay = (float) UnitConverter.getTime( ic.getDelay(), UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); float duration = (float) UnitConverter.getTime( ic.getDuration(), UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); float amp = (float) UnitConverter.getCurrent( ic.getAmplitude(), UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem); if (!nml2) { SimpleXMLElement inputTypeElement = new SimpleXMLElement(NetworkMLConstants.PULSEINPUT_INSTANCE_ELEMENT); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_DELAY_ATTR, delay + "")); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_DUR_ATTR, duration + "")); // System.out.println("Converted "+amp+" to "+ a); inputTypeElement.addAttribute( new SimpleXMLAttribute(NetworkMLConstants.INPUT_AMP_ATTR, amp + "")); inputTargetSiteElement.addContent(" "); inputTargetSiteElement.addChildElement(inputTypeElement); inputTargetSiteElement.addContent("\n "); } else { SimpleXMLElement pulseGenElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_PULSE_GEN_ELEMENT); pulseGenElement.addAttribute( NeuroMLConstants.NEUROML_ID_V2, inputReference + "__" + i); pulseGenElement.addAttribute( NetworkMLConstants.INPUT_DELAY_ATTR, delay + timeUnits.getNeuroML2Symbol()); pulseGenElement.addAttribute( NetworkMLConstants.INPUT_DUR_ATTR, duration + timeUnits.getNeuroML2Symbol()); pulseGenElement.addAttribute( NetworkMLConstants.INPUT_AMP_ATTR, amp + currentUnits.getNeuroML2Symbol()); topLevelCompElement.addContent("\n\n "); topLevelCompElement.addChildElement(pulseGenElement); topLevelCompElement.addContent("\n\n "); if (version.isVersion2alpha()) { String target = nextStim.getCellGroup() + "[" + sei.getCellNumber() + "]"; SimpleXMLElement expInputElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_EXP_INPUT_ELEMENT); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_INPUT_ATTR, inputReference + "__" + i); entities.add(expInputElement); } else { String target = "../" + nextStim.getCellGroup() + "/" + sei.getCellNumber() + "/" + project.cellGroupsInfo.getCellType(nextStim.getCellGroup()); SimpleXMLElement expInputElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_INPUT_LIST_ELEMENT); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_INPUT_ATTR, inputReference + "__" + i); entities.add(expInputElement); } } } else if (sei.getInstanceProps() instanceof RandomSpikeTrainInstanceProps) { RandomSpikeTrainInstanceProps rst = (RandomSpikeTrainInstanceProps) sei.getInstanceProps(); float stimFreq = rst.getRate(); // String stimMech = rst.get; SimpleXMLElement inputTypeElement = new SimpleXMLElement(NetworkMLConstants.RANDOMSTIM_INSTANCE_ELEMENT); inputTypeElement.addAttribute( new SimpleXMLAttribute( NetworkMLConstants.RND_STIM_FREQ_ATTR, (float) UnitConverter.getRate( stimFreq, UnitConverter.NEUROCONSTRUCT_UNITS, unitSystem) + "")); // inputTypeElement.addAttribute(new // SimpleXMLAttribute(NetworkMLConstants.RND_STIM_MECH_ATTR, stimMech)); inputTargetSiteElement.addContent(" "); inputTargetSiteElement.addChildElement(inputTypeElement); inputTargetSiteElement.addContent("\n "); } else { throw new NeuroMLException( "Error trying to save input " + inputReference + ". Cannot save in NeuroML an input of type: " + myElectricalInput.getType()); } } else { if (nml2) { if (version.isVersion2alpha()) { String target = nextStim.getCellGroup() + "[" + sei.getCellNumber() + "]"; SimpleXMLElement expInputElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_EXP_INPUT_ELEMENT); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_INPUT_ATTR, inputReference); entities.add(expInputElement); } else { String target = "../" + nextStim.getCellGroup() + "/" + sei.getCellNumber() + "/" + project.cellGroupsInfo.getCellType(nextStim.getCellGroup()); SimpleXMLElement expInputElement = new SimpleXMLElement(NetworkMLConstants.NEUROML2_INPUT_ELEMENT); expInputElement.addAttribute(NeuroMLConstants.NEUROML_ID_V2, i + ""); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_EXP_INPUT_TARGET_ATTR, target); expInputElement.addAttribute( NetworkMLConstants.NEUROML2_INPUT_DESTINATION, NetworkMLConstants.NEUROML2_INPUT_DESTINATION_DEFAULT); inputTargetSitesElement.addChildElement(expInputElement); } } } if (i == inputsHere.size() - 1) inputTargetSitesElement.addContent("\n "); // Next Site } inputTargetElement.addContent("\n "); if (!nml2) { inputsElement.addChildElement(inputElement); inputElement.addContent("\n "); } } logger.logComment("Finished saving data to inputs element"); } catch (Exception ex) { ex.printStackTrace(); throw new NeuroMLException("Problem creating inputs element file", ex); } return entities; }