From 951162530f674c8c0d1a052f098bf5a80d19914b Mon Sep 17 00:00:00 2001 From: "Ankur Sinha (Ankur Sinha Gmail)" Date: Fri, 26 Jan 2024 15:04:18 +0000 Subject: [PATCH 1/9] feat(neuron/netpyne): use `%r` instead of `%e` or `%s` when writing recorded data to file. `%r` or the `repr` function gives the "official" string representation of an object, so of a float too, while the `%s` or `str` method returns the "nicely printable string representation of an object". Also, irrespective of which one we use, we must use the same for both NEURON and NetPyNE. --- src/main/java/org/neuroml/export/neuron/NeuronWriter.java | 4 ++-- src/main/resources/netpyne/run.vm | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java index 08c846388..e3e790b69 100644 --- a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java +++ b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java @@ -1433,7 +1433,7 @@ else if(cc.getComponentType().isOrExtends(NeuroMLElements.CONTINUOUS_CONNECTION_ } //columnsPostTraces.get(outfileId).add(bIndent+" f_" + outfileId + "_f2.write('%e\\t'% py_v_" + timeRef + "[i] "); - columnsPostTraces.get(outfileId).add(bIndent+" f_" + outfileId + "_f2.write('%e\\t"); + columnsPostTraces.get(outfileId).add(bIndent+" f_" + outfileId + "_f2.write('%r\\t"); writingVariables.get(outfileId).add("py_v_" + timeRef + "[i], "); ArrayList colIds = new ArrayList(); @@ -1476,7 +1476,7 @@ else if(cc.getComponentType().isOrExtends(NeuroMLElements.CONTINUOUS_CONNECTION_ /*columnsPostTraces.get(outfileId).add( " + '%e\\t'%(py_v_" + colId + "[i]) ");*/ - columnsPostTraces.get(outfileId).add("%e\\t"); + columnsPostTraces.get(outfileId).add("%r\\t"); writingVariables.get(outfileId).add("py_v_" + colId + "[i], "); } diff --git a/src/main/resources/netpyne/run.vm b/src/main/resources/netpyne/run.vm index 8ed746ee5..369c43282 100644 --- a/src/main/resources/netpyne/run.vm +++ b/src/main/resources/netpyne/run.vm @@ -175,7 +175,7 @@ class NetPyNESimulation(): dat_file_$of.name = open('$of.file_name', 'w') for i in range(len(col_${of.name}_t)): - dat_file_${of.name}.write(#foreach ($oc in $of.output_columns ) '%s\t'%(col_${of.name}_${oc.name}[i]/${oc.neuron_variable_scale}) + #end '\n') + dat_file_${of.name}.write(#foreach ($oc in $of.output_columns ) '%r\t'%(col_${of.name}_${oc.name}[i]/${oc.neuron_variable_scale}) + #end '\n') dat_file_${of.name}.close() #end @@ -201,10 +201,10 @@ class NetPyNESimulation(): if id in to_record_keys: #if ($of.spike_file_format=="ID_TIME") - spike_file_${of.name}.write('%i\t%s\n'%(to_record[id],t/1000.)) # format: $of.spike_file_format + spike_file_${of.name}.write('%i\t%r\n'%(to_record[id],t/1000.)) # format: $of.spike_file_format #else - spike_file_${of.name}.write('%s\t%i\n'%(t/1000.,to_record[id])) # format: $of.spike_file_format + spike_file_${of.name}.write('%r\t%i\n'%(t/1000.,to_record[id])) # format: $of.spike_file_format #end spike_file_${of.name}.close() From e6ef4de485da2cf92ebee54cb6e2025d57ae7452 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 1 May 2024 11:38:16 +0100 Subject: [PATCH 2/9] Test on java 21 --- .github/workflows/ci.yml | 13 +++++++++---- .github/workflows/docs.yml | 14 +++++++------- pom.xml | 4 ++-- 3 files changed, 18 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a1b56b05d..e980149b8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,14 +16,19 @@ jobs: strategy: fail-fast: false matrix: - java: [ '8', '11', '16', '17', '19'] - runs-on: [ubuntu-latest, macos-latest, windows-2019 ] + java: [ '8', '11', '16', '17', '19', '21' ] + runs-on: [ubuntu-latest, macos-latest, windows-latest] + exclude: + - runs-on: macos-latest + java: "8" + - runs-on: macos-latest + java: "16" name: Test on Java ${{ matrix.Java }} on ${{ matrix.runs-on }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up JDK ${{ matrix.Java }} - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: java-version: ${{ matrix.Java }} distribution: 'temurin' diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 2d1c5f0d4..380031c48 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -13,18 +13,18 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: nelonoel/branch-name@v1.0.1 - name: Set up JDK 11 - uses: actions/setup-java@v3 + uses: actions/setup-java@v4 with: java-version: 11 distribution: 'temurin' java-package: jdk - name: Set up Python 3.9 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: 3.9 @@ -34,14 +34,14 @@ jobs: pip install ghp-import - name: Checkout NeuroML2 - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: NeuroML/NeuroML2 ref: development path: NeuroML2 - name: Checkout org.lemsml - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: LEMS/jLEMS ref: development @@ -49,14 +49,14 @@ jobs: - name: Checkout org.neuroml.model.injectingplugin - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: NeuroML/org.neuroml.model.injectingplugin ref: development path: org.neuroml.model.injectingplugin - name: Checkout org.neuroml.model - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: repository: NeuroML/org.neuroml.model ref: development diff --git a/pom.xml b/pom.xml index c38acde79..8df75dd3a 100644 --- a/pom.xml +++ b/pom.xml @@ -91,8 +91,8 @@ maven-compiler-plugin 3.0 - 1.7 - 1.7 + 1.8 + 1.8 From 2d0159a697e185ecd735bd5eb19468db0294f0c6 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 1 May 2024 11:42:22 +0100 Subject: [PATCH 3/9] Just test on macos-12 for now... --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e980149b8..ef4d9210e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,7 +17,7 @@ jobs: fail-fast: false matrix: java: [ '8', '11', '16', '17', '19', '21' ] - runs-on: [ubuntu-latest, macos-latest, windows-latest] + runs-on: [ubuntu-latest, macos-12, windows-latest] # Note macos-12, not latest/14, due to hdf5 install issue exclude: - runs-on: macos-latest java: "8" @@ -36,7 +36,7 @@ jobs: - name: Install and test (non Win) env: main_repo_branch: ${GITHUB_REF_NAME} - if: ${{ matrix.runs-on != 'windows-2019' }} + if: ${{ matrix.runs-on != 'windows-latest' }} run: | export main_repo_branch=${{env.main_repo_branch}} if [[ ${main_repo_branch} != "master" && ${main_repo_branch} != "development" && ${main_repo_branch} != "experimental" && ${main_repo_branch} != *"osb"* ]]; then main_repo_branch=development ; fi @@ -72,7 +72,7 @@ jobs: mvn dependency:tree - name: Install and test (Win) - if: ${{ matrix.runs-on == 'windows-2019' }} + if: ${{ matrix.runs-on == 'windows-latest' }} run: | # Install org.neuroml.model.injectingplugin From faf1311f84a8fc3bc0b9c204e3c8ca127ab2eefd Mon Sep 17 00:00:00 2001 From: pgleeson Date: Wed, 1 May 2024 11:49:37 +0100 Subject: [PATCH 4/9] Back to windows-2019 --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ef4d9210e..922ab123b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,7 +17,7 @@ jobs: fail-fast: false matrix: java: [ '8', '11', '16', '17', '19', '21' ] - runs-on: [ubuntu-latest, macos-12, windows-latest] # Note macos-12, not latest/14, due to hdf5 install issue + runs-on: [ubuntu-latest, macos-12, windows-2019] # Note macos-12, not latest/14, due to hdf5 install issue exclude: - runs-on: macos-latest java: "8" @@ -36,7 +36,7 @@ jobs: - name: Install and test (non Win) env: main_repo_branch: ${GITHUB_REF_NAME} - if: ${{ matrix.runs-on != 'windows-latest' }} + if: ${{ matrix.runs-on != 'windows-2019' }} run: | export main_repo_branch=${{env.main_repo_branch}} if [[ ${main_repo_branch} != "master" && ${main_repo_branch} != "development" && ${main_repo_branch} != "experimental" && ${main_repo_branch} != *"osb"* ]]; then main_repo_branch=development ; fi @@ -72,7 +72,7 @@ jobs: mvn dependency:tree - name: Install and test (Win) - if: ${{ matrix.runs-on == 'windows-latest' }} + if: ${{ matrix.runs-on == 'windows-2019' }} run: | # Install org.neuroml.model.injectingplugin From 528e08ab08e10b18fdbf4c068659bc0ad3920b27 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Fri, 31 May 2024 10:26:56 +0100 Subject: [PATCH 5/9] Fixes to Neuron and Netpyne to handle case where cell has external morphology/biophysicalProperties --- .../org/lemsml/export/dlems/DLemsWriter.java | 28 ++++++++-- .../neuroml/export/info/InfoTreeCreator.java | 2 +- .../neuroml/export/netpyne/NetPyNEWriter.java | 5 ++ .../neuroml/export/neuron/NamingHelper.java | 3 +- .../neuroml/export/neuron/NeuronWriter.java | 26 ++++++---- .../org/neuroml/export/svg/Network3D.java | 9 ++-- .../org/neuroml/export/svg/SVGWriter.java | 38 ++++++++------ .../java/org/neuroml/export/utils/Utils.java | 39 ++++++++++++-- .../export/utils/support/ModelFeature.java | 51 ++++++++++--------- .../export/neuron/JsonSerializerTest.java | 2 +- 10 files changed, 141 insertions(+), 62 deletions(-) diff --git a/src/main/java/org/lemsml/export/dlems/DLemsWriter.java b/src/main/java/org/lemsml/export/dlems/DLemsWriter.java index 237c8688a..270da55bb 100644 --- a/src/main/java/org/lemsml/export/dlems/DLemsWriter.java +++ b/src/main/java/org/lemsml/export/dlems/DLemsWriter.java @@ -673,8 +673,21 @@ private void writeDLemsForComponent(JsonGenerator g, Component comp, HashMap standalones = Utils.convertLemsComponentToNeuroML(component); + LinkedHashMap standalones = Utils.convertLemsComponentToNeuroML(component, true, null); for(Standalone element : standalones.values()) { diff --git a/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java b/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java index 04b8aea0e..2df4ee025 100644 --- a/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java +++ b/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java @@ -472,6 +472,11 @@ public static void main(String[] args) throws Exception //lemsFiles.add(new File("../neuroConstruct/osb/olfactorybulb/networks/MiglioreEtAl14_OlfactoryBulb3D/NeuroML2/Channels/test/LEMS_OlfactoryTest_12.xml")); //lemsFiles.add(new File("../neuroConstruct/osb/generic/hodgkin_huxley_tutorial/Tutorial/Source/LEMS_HH_Simulation.xml")); //lemsFiles.add(new File("../git/multi/temp/LEMS_ISN_net.xml")); + //lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_ACNet2.xml")); + lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_in.xml")); + lemsFiles.add(new File("../git/morphology_include/LEMS_m_out_b_in.xml")); + lemsFiles.add(new File("../git/morphology_include/LEMS_m_out_b_out.xml")); + //lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_out.xml")); for (File lemsFile : lemsFiles) { diff --git a/src/main/java/org/neuroml/export/neuron/NamingHelper.java b/src/main/java/org/neuroml/export/neuron/NamingHelper.java index a51024d23..87df3170a 100644 --- a/src/main/java/org/neuroml/export/neuron/NamingHelper.java +++ b/src/main/java/org/neuroml/export/neuron/NamingHelper.java @@ -13,6 +13,7 @@ import org.neuroml.model.Segment; import org.neuroml.model.SegmentGroup; import org.neuroml.model.util.CellUtils; +import org.neuroml.model.util.NeuroMLException; /** * @@ -31,7 +32,7 @@ public NamingHelper(Cell cell) this.cell = cell; } - public String getNrnSectionName(Segment seg) + public String getNrnSectionName(Segment seg) throws NeuroMLException { String uniqueId = cell.getId() + ":" + seg.getId(); diff --git a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java index 08c846388..d1bad3df2 100644 --- a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java +++ b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java @@ -2071,7 +2071,7 @@ private Cell getCellFromComponent(Component cellComponent) throws LEMSException, } else { - cell = Utils.getCellFromComponent(cellComponent); + cell = Utils.getCellFromComponent(cellComponent, lems); compIdsVsCells.put(cellComponent.getID(), cell); } return cell; @@ -2105,7 +2105,11 @@ public IntracellularProperties convertCellWithMorphology(Component cellComponent { BiophysicalProperties bp = cell.getBiophysicalProperties(); ip = bp.getIntracellularProperties(); - bpComp = cellComponent.getChild("biophysicalProperties"); + bpComp = cellComponent.quietGetChild("biophysicalProperties"); + if (bpComp==null) + { + bpComp = lems.getComponent(bp.getId()); + } mpComp = bpComp.getChild("membraneProperties"); ipComp = bpComp.getChild("intracellularProperties"); } @@ -3936,8 +3940,8 @@ public static void main(String[] args) throws Exception ArrayList lemsFiles = new ArrayList(); - lemsFiles.add(new File("../neuroConstruct/osb/hippocampus/interneurons/WangBuzsaki1996/NeuroML2/LEMS_ComponentType/LEMS_WangBuzsaki.xml")); - lemsFiles.add(new File("../neuroConstruct/osb/generic/HindmarshRose1984/NeuroML2/LEMS_Regular_HindmarshRoseNML.xml")); + //lemsFiles.add(new File("../neuroConstruct/osb/hippocampus/interneurons/WangBuzsaki1996/NeuroML2/LEMS_ComponentType/LEMS_WangBuzsaki.xml")); + //lemsFiles.add(new File("../neuroConstruct/osb/generic/HindmarshRose1984/NeuroML2/LEMS_Regular_HindmarshRoseNML.xml")); //lemsFiles.add(new File("../neuroConstruct/osb/showcase/StochasticityShowcase/NeuroML2/LEMS_Inputs0.xml")); //lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/examples/LEMS_c302_C1_Oscillator.xml")); @@ -3947,14 +3951,14 @@ public static void main(String[] args) throws Exception //lemsFiles.add(new File("../neuroConstruct/osb/cerebellum/networks/VervaekeEtAl-GolgiCellNetwork/NeuroML2/LEMS_Pacemaking.xml")); //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml")); lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml")); - lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml")); - lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/IzhikevichModel/NeuroML2/LEMS_2007One.xml")); + //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex15_CaDynamics.xml")); + //lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/IzhikevichModel/NeuroML2/LEMS_2007One.xml")); //lemsFiles.add(new File("../org.neuroml.export/src/test/resources/examples/LEMS_SpikePass2.xml")); /* lemsFiles.add(new File("../neuroConstruct/osb/showcase/StochasticityShowcase/NeuroML2/LEMS_NoisyCurrentInput.xml")); lemsFiles.add(new File("../neuroConstruct/osb/showcase/StochasticityShowcase/NeuroML2/LEMS_OUCurrentInput_test.xml")); lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/IzhikevichModel/NeuroML2/LEMS_FiveCells.xml"));*/ - lemsFiles.add(new File("../git/ca1/NeuroML2/channels/test_Cadynamics/NeuroML2/LEMS_test_Ca.xml")); + //lemsFiles.add(new File("../git/ca1/NeuroML2/channels/test_Cadynamics/NeuroML2/LEMS_test_Ca.xml")); //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex20a_AnalogSynapsesHH.xml")); //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex20_AnalogSynapses.xml")); //lemsFiles.add(new File("../NeuroMLlite/neuromllite/LEMS_Sim_ten_cells_spikes_nest.xml")); @@ -3976,7 +3980,11 @@ public static void main(String[] args) throws Exception // // lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/multiple/PospischilEtAl2008/NeuroML2/channels/Na/LEMS_Na.xml")); // lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/multiple/PospischilEtAl2008/NeuroML2/channels/Kd/LEMS_Kd.xml")); -// lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_MediumNet.xml")); + lemsFiles.add(new File("../neuroConstruct/osb/cerebral_cortex/networks/ACnet2/neuroConstruct/generatedNeuroML2/LEMS_ACNet2.xml")); + lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_in.xml")); + lemsFiles.add(new File("../git/morphology_include/LEMS_m_out_b_in.xml")); + lemsFiles.add(new File("../git/morphology_include/LEMS_m_in_b_out.xml")); + // lemsFiles.add(new File("../OpenCortex/examples/LEMS_ACNet.xml")); // //lemsFiles.add(new File("../OpenCortex/examples/LEMS_SpikingNet.xml")); @@ -3995,7 +4003,7 @@ public static void main(String[] args) throws Exception // lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex25_MultiComp.xml")); // lemsFiles.add(new File("../neuroConstruct/osb/showcase/NetPyNEShowcase/NeuroML2/LEMS_HybridTut.xml")); // lemsFiles.add(new File("../OpenCortex/examples/LEMS_L23TraubDemo_1cells_0conns.xml")); - lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml")); + //lemsFiles.add(new File("../NeuroML2/LEMSexamples/LEMS_NML2_Ex0_IaF.xml")); //lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/examples/LEMS_c302_C1_Muscles.xml")); //lemsFiles.add(new File("../neuroConstruct/osb/invertebrate/celegans/CElegansNeuroML/CElegans/pythonScripts/c302/examples/LEMS_c302_C1_Syns.xml")); diff --git a/src/main/java/org/neuroml/export/svg/Network3D.java b/src/main/java/org/neuroml/export/svg/Network3D.java index 2cfa0ba79..59561063f 100644 --- a/src/main/java/org/neuroml/export/svg/Network3D.java +++ b/src/main/java/org/neuroml/export/svg/Network3D.java @@ -6,6 +6,7 @@ import java.util.HashMap; import java.util.List; import org.neuroml.model.util.CellUtils; +import org.neuroml.model.util.NeuroMLException; public class Network3D { @@ -19,13 +20,13 @@ public Network3D(String comment) lines = new ArrayList(100); } - public Network3D(Cell cell) + public Network3D(Cell cell) throws NeuroMLException { this.comment = "Cell: "+cell.getId(); lines = extractLines(cell, null); } - public void addCell(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor) + public void addCell(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor) throws NeuroMLException { lines.addAll(extractLines(cell, offsetX, offsetY, offsetZ, defaultColor)); } @@ -201,13 +202,13 @@ private Network3D rotate(double degreesAroundZ, double degreesAroundY) } - private ArrayList extractLines(Cell cell, String defaultColor) + private ArrayList extractLines(Cell cell, String defaultColor) throws NeuroMLException { return extractLines(cell, 0, 0, 0, defaultColor); } - private ArrayList extractLines(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor) + private ArrayList extractLines(Cell cell, float offsetX, float offsetY, float offsetZ, String defaultColor) throws NeuroMLException { ArrayList result = new ArrayList(); diff --git a/src/main/java/org/neuroml/export/svg/SVGWriter.java b/src/main/java/org/neuroml/export/svg/SVGWriter.java index 7733ead43..de92ffe5e 100644 --- a/src/main/java/org/neuroml/export/svg/SVGWriter.java +++ b/src/main/java/org/neuroml/export/svg/SVGWriter.java @@ -82,21 +82,27 @@ public String getMainScript() throws GenerationException { StringBuilder core = new StringBuilder(); - Rectangle bounds = render(core, false); - StringBuilder result = new StringBuilder(); - //Add header - result.append("\n"); - //addComment(result, "Total bounds: "+bounds.toString()); - startElement(result, "svg", "xmlns=" + SVG_NAMESPACE, - "version=" + SVG_VERSION, - "width="+bounds.width, - "height="+bounds.height, - "viewBox=0 0 "+bounds.width+" "+bounds.height); - - result.append(core.toString()); - - endElement(result, "svg"); + try { + + Rectangle bounds = render(core, false); + + //Add header + result.append("\n"); + //addComment(result, "Total bounds: "+bounds.toString()); + startElement(result, "svg", "xmlns=" + SVG_NAMESPACE, + "version=" + SVG_VERSION, + "width="+bounds.width, + "height="+bounds.height, + "viewBox=0 0 "+bounds.width+" "+bounds.height); + + result.append(core.toString()); + + endElement(result, "svg"); + } + catch (NeuroMLException ne) { + throw new GenerationException("Problem generating SVG", ne); + } return result.toString(); } @@ -107,7 +113,7 @@ public List getAllBasedOnCell(NeuroMLDocument nmlDocument) { return cells; } - public Rectangle render(StringBuilder result, boolean png) { + public Rectangle render(StringBuilder result, boolean png) throws NeuroMLException { if (nmlDocument.getNetwork().isEmpty()) { @@ -185,7 +191,7 @@ public Rectangle render(StringBuilder result, boolean png) { } } - public void convertToPng(File pngFile) { + public void convertToPng(File pngFile) throws NeuroMLException { // One quick run to get bounds... Rectangle bounds = render(new StringBuilder(), false); diff --git a/src/main/java/org/neuroml/export/utils/Utils.java b/src/main/java/org/neuroml/export/utils/Utils.java index b1d26dbb6..726510814 100644 --- a/src/main/java/org/neuroml/export/utils/Utils.java +++ b/src/main/java/org/neuroml/export/utils/Utils.java @@ -30,6 +30,8 @@ import org.neuroml.export.utils.support.SupportLevelInfo; import org.neuroml.model.Cell; import org.neuroml.model.Cell2CaPools; +import org.neuroml.model.Morphology; +import org.neuroml.model.BiophysicalProperties; import org.neuroml.model.NeuroMLDocument; import org.neuroml.model.Standalone; import org.neuroml.model.util.NeuroML2Validator; @@ -401,11 +403,42 @@ public static NeuroMLDocument convertLemsComponentToNeuroMLDocument(Component co return nmlDocument; } - public static LinkedHashMap convertLemsComponentToNeuroML(Component comp) throws LEMSException, NeuroMLException + public static LinkedHashMap convertLemsComponentToNeuroML(Component comp, boolean fixExternalMorphsBiophys, Lems lems) throws LEMSException, NeuroMLException { NeuroMLDocument nmlDocument = convertLemsComponentToNeuroMLDocument(comp); LinkedHashMap els = NeuroMLConverter.getAllStandaloneElements(nmlDocument); + + if (fixExternalMorphsBiophys) + { + for (Map.Entry entry : els.entrySet()) + { + String id = entry.getKey(); + Standalone e = entry.getValue(); + if (e instanceof Cell) { + Cell cell = (Cell)e; + + if (cell.getMorphologyAttr() != null) + { + Component morphComp = lems.getComponent(cell.getMorphologyAttr()); + NeuroMLDocument nmlDocumentMorph = convertLemsComponentToNeuroMLDocument(morphComp); + Morphology m = nmlDocumentMorph.getMorphology().get(0); + cell.setMorphology(m); + cell.setMorphologyAttr(null); + els.put(id, cell); + } + if (cell.getBiophysicalPropertiesAttr() != null) + { + Component bpComp = lems.getComponent(cell.getBiophysicalPropertiesAttr()); + NeuroMLDocument nmlDocumentBp = convertLemsComponentToNeuroMLDocument(bpComp); + BiophysicalProperties bp = nmlDocumentBp.getBiophysicalProperties().get(0); + cell.setBiophysicalProperties(bp); + cell.setBiophysicalPropertiesAttr(null); + els.put(id, cell); + } + } + } + } return els; } @@ -423,9 +456,9 @@ public static Component convertNeuroMLToComponent(Standalone nmlElement) throws } } - public static Cell getCellFromComponent(Component comp) throws LEMSException, NeuroMLException + public static Cell getCellFromComponent(Component comp, Lems lems) throws LEMSException, NeuroMLException { - LinkedHashMap els = Utils.convertLemsComponentToNeuroML(comp); + LinkedHashMap els = Utils.convertLemsComponentToNeuroML(comp, true, lems); Cell cell = (Cell) els.values().iterator().next(); if (cell == null) { diff --git a/src/main/java/org/neuroml/export/utils/support/ModelFeature.java b/src/main/java/org/neuroml/export/utils/support/ModelFeature.java index 6063290cf..a15cab5b8 100644 --- a/src/main/java/org/neuroml/export/utils/support/ModelFeature.java +++ b/src/main/java/org/neuroml/export/utils/support/ModelFeature.java @@ -106,7 +106,7 @@ private static void analyseSingleComponent(Component component, ArrayList 1) @@ -116,29 +116,34 @@ private static void analyseSingleComponent(Component component, ArrayList Date: Tue, 4 Jun 2024 15:40:02 +0100 Subject: [PATCH 6/9] Added check EXT_MORPH_BIOPHYS_CELL_MODEL, just passing on Neuron & Netne --- src/main/java/org/neuroml/export/eden/EDENWriter.java | 1 + .../org/neuroml/export/netpyne/NetPyNEWriter.java | 1 + .../java/org/neuroml/export/neuron/NeuronWriter.java | 1 + src/main/java/org/neuroml/export/utils/Utils.java | 10 +++++++++- .../neuroml/export/utils/support/ModelFeature.java | 11 +++++++++++ .../export/utils/support/SupportLevelInfo.java | 4 +++- 6 files changed, 26 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/neuroml/export/eden/EDENWriter.java b/src/main/java/org/neuroml/export/eden/EDENWriter.java index e94b9260c..a812a2c2d 100644 --- a/src/main/java/org/neuroml/export/eden/EDENWriter.java +++ b/src/main/java/org/neuroml/export/eden/EDENWriter.java @@ -71,6 +71,7 @@ public void setSupportedFeatures() { sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH); + sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.NONE); sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH); diff --git a/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java b/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java index 2df4ee025..931a63310 100644 --- a/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java +++ b/src/main/java/org/neuroml/export/netpyne/NetPyNEWriter.java @@ -97,6 +97,7 @@ public void setSupportedFeatures() { sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH); + sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH); diff --git a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java index d1bad3df2..8d1d509a9 100644 --- a/src/main/java/org/neuroml/export/neuron/NeuronWriter.java +++ b/src/main/java/org/neuroml/export/neuron/NeuronWriter.java @@ -132,6 +132,7 @@ public void setSupportedFeatures() { sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.MEDIUM); sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.MEDIUM); + sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.MEDIUM); sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.LOW); sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.MEDIUM); diff --git a/src/main/java/org/neuroml/export/utils/Utils.java b/src/main/java/org/neuroml/export/utils/Utils.java index 726510814..93dd9ea76 100644 --- a/src/main/java/org/neuroml/export/utils/Utils.java +++ b/src/main/java/org/neuroml/export/utils/Utils.java @@ -556,7 +556,15 @@ public Sim importFile(File simFile) throws LEMSException { if(run) { SupportLevelInfo sli = SupportLevelInfo.getSupportLevelInfo(); - sli.checkConversionSupported(Format.LEMS, sim.getLems()); + try + { + sli.checkConversionSupported(Format.LEMS, sim.getLems()); + } + catch (ModelFeatureSupportException mfse) + { + E.info(mfse.getMessage()); + System.exit(-1); + } sim.run(); IOUtil.saveReportAndTimesFile(sim, lemsFile); E.info("Finished reading, building, running and displaying LEMS model"); diff --git a/src/main/java/org/neuroml/export/utils/support/ModelFeature.java b/src/main/java/org/neuroml/export/utils/support/ModelFeature.java index a15cab5b8..cb34f7ff7 100644 --- a/src/main/java/org/neuroml/export/utils/support/ModelFeature.java +++ b/src/main/java/org/neuroml/export/utils/support/ModelFeature.java @@ -37,6 +37,7 @@ public enum ModelFeature NETWORK_WITH_ANALOG_CONNS_MODEL("Network model with analog/continuously communicating connections between cells"), ABSTRACT_CELL_MODEL("Model with abstract (non conductance based) cell(s)"), COND_BASED_CELL_MODEL("Model with conductance based cell(s)"), + EXT_MORPH_BIOPHYS_CELL_MODEL("Model with conductance based cell(s) with morphology and/or biophysicalProperties outside cell element"), MULTICOMPARTMENTAL_CELL_MODEL("Model with multicompartmental cell(s)"), CHANNEL_POPULATIONS_CELL_MODEL("Model with channel populations"), CHANNEL_DENSITY_ON_SEGMENT("Model with channel density specified per segment (aot segmentGroup)"), @@ -106,7 +107,17 @@ private static void analyseSingleComponent(Component component, ArrayList 1) diff --git a/src/main/java/org/neuroml/export/utils/support/SupportLevelInfo.java b/src/main/java/org/neuroml/export/utils/support/SupportLevelInfo.java index 78ad709ed..6849028b9 100644 --- a/src/main/java/org/neuroml/export/utils/support/SupportLevelInfo.java +++ b/src/main/java/org/neuroml/export/utils/support/SupportLevelInfo.java @@ -41,6 +41,7 @@ private SupportLevelInfo() /* Add info on formats supported in jLEMS */ addSupportInfo(Format.LEMS, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH); addSupportInfo(Format.LEMS, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH); + addSupportInfo(Format.LEMS, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.NONE); addSupportInfo(Format.LEMS, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH); addSupportInfo(Format.LEMS, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH); addSupportInfo(Format.LEMS, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH); @@ -135,11 +136,12 @@ public void checkConversionSupported(Format format, Lems lems) throws ModelFeatu if(!supp.equals(SUPPORTED)) { passed = false; - report.append("Feature not supported in " + format + ": " + mf + "\n " + myInstance.isSupported(format, mf) + "\n"); + report.append("Feature is not supported in " + format + ": " + mf + "\n " + myInstance.isSupported(format, mf) + "\n"); } } if(!passed) { + report.insert(0, "Error! Some features of the model are not supported by that simulator.\n\n"); report.append("\nInfo on supported features:\n" + myInstance); throw new ModelFeatureSupportException(report.toString()); } From c4d3ae993e33a0dd92c6117fb67e11998fefbfe6 Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 11 Jun 2024 10:38:54 +0100 Subject: [PATCH 7/9] Eden supports external morphology/bioPhys --- src/main/java/org/neuroml/export/eden/EDENWriter.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/neuroml/export/eden/EDENWriter.java b/src/main/java/org/neuroml/export/eden/EDENWriter.java index a812a2c2d..427e3aace 100644 --- a/src/main/java/org/neuroml/export/eden/EDENWriter.java +++ b/src/main/java/org/neuroml/export/eden/EDENWriter.java @@ -71,7 +71,7 @@ public void setSupportedFeatures() { sli.addSupportInfo(format, ModelFeature.ABSTRACT_CELL_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.COND_BASED_CELL_MODEL, SupportLevelInfo.Level.HIGH); - sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.NONE); + sli.addSupportInfo(format, ModelFeature.EXT_MORPH_BIOPHYS_CELL_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.SINGLE_COMP_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.NETWORK_MODEL, SupportLevelInfo.Level.HIGH); sli.addSupportInfo(format, ModelFeature.MULTI_CELL_MODEL, SupportLevelInfo.Level.HIGH); From 7f7590e407ca8e8bfd81d6fd8675f365558b6b04 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 11 Jun 2024 12:01:34 +0100 Subject: [PATCH 8/9] To v1.10.1 --- pom.xml | 6 +++--- src/main/java/org/neuroml/export/utils/Utils.java | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pom.xml b/pom.xml index 8df75dd3a..4664358ef 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.neuroml.export org.neuroml.export bundle - 1.10.0 + 1.10.1 org.neuroml.export http://maven.apache.org @@ -18,12 +18,12 @@ org.neuroml.model org.neuroml.model - 1.10.0 + 1.10.1 org.lemsml jlems - 0.11.0 + 0.11.1 org.apache.velocity diff --git a/src/main/java/org/neuroml/export/utils/Utils.java b/src/main/java/org/neuroml/export/utils/Utils.java index 93dd9ea76..96b88c52c 100644 --- a/src/main/java/org/neuroml/export/utils/Utils.java +++ b/src/main/java/org/neuroml/export/utils/Utils.java @@ -44,7 +44,7 @@ public class Utils private static Lems lemsWithNML2CompTypes; - public static String ORG_NEUROML_EXPORT_VERSION = "1.10.0"; + public static String ORG_NEUROML_EXPORT_VERSION = "1.10.1"; public static final String ARCH_I686 = "i686"; public static final String ARCH_I386 = "i386"; From 11aabc96f27dcab9bb9b29a0a04fab49a249113e Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Tue, 11 Jun 2024 12:18:08 +0100 Subject: [PATCH 9/9] Bump year in docs --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 4664358ef..96bf28ef9 100644 --- a/pom.xml +++ b/pom.xml @@ -49,7 +49,7 @@ <br /> <br /> - Copyright NeuroML Contributors 2023 + Copyright NeuroML Contributors 2024