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Immediate improvements #52

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merged 4 commits into from
Sep 26, 2024
Merged

Immediate improvements #52

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d787dd8
Automated Contrast and Center 3D Images
AvocadoMoon Sep 24, 2024
568ff6f
Fix Dimension Problems
AvocadoMoon Sep 24, 2024
dfd8579
Anytime Selected First
AvocadoMoon Sep 24, 2024
f66b61c
Include Channel,Z,Time Size in Table
AvocadoMoon Sep 26, 2024
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4 changes: 4 additions & 0 deletions view-simulation-results/src/main/java/org/vcell/N5/ExportDataRepresentation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,10 @@ public static class SimulationExportDataRepresentation {
public ArrayList<String> differentParameterValues;
public String savedFileName;

public int zSlices;
public int tSlices;
public int numVariables;

public SimulationExportDataRepresentation(String exportDate, String uri, String jobID, String dataID, String simulationName,
String applicationName, String biomodelName, String variables, String startAndEndTime,
ArrayList<String> differentParameterValues, String savedFileName){
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5 changes: 5 additions & 0 deletions view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java
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Expand Up @@ -9,6 +9,8 @@
import com.amazonaws.services.s3.AmazonS3ClientBuilder;
import com.google.gson.GsonBuilder;
import ij.ImagePlus;
import ij.plugin.ContrastEnhancer;
import ij.plugin.frame.ContrastAdjuster;
import net.imglib2.cache.img.CachedCellImg;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.real.DoubleType;
Expand Down Expand Up @@ -134,6 +136,9 @@ public ImagePlus getImgPlusFromN5File() throws IOException {
setUnits(n5AmazonS3Reader, imagePlus);
imagePlus.setProperty("channelInfo", n5AmazonS3Reader.getAttribute(dataSetChosen, "channelInfo", HashMap.class));
imagePlus.setProperty("maskInfo", n5AmazonS3Reader.getAttribute(dataSetChosen, "maskMapping", HashMap.class));
imagePlus.setZ(Math.floorDiv(imagePlus.getNSlices(), 2));

new ContrastEnhancer().stretchHistogram(imagePlus, 1);
return imagePlus;
}

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12 changes: 6 additions & 6 deletions view-simulation-results/src/main/java/org/vcell/N5/UI/ImageIntoMemory.java
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Expand Up @@ -37,17 +37,17 @@ public class ImageIntoMemory extends EventListenerList implements ActionListener

private static final Logger logger = N5ImageHandler.getLogger(ImageIntoMemory.class);

public ImageIntoMemory(double cDim, double tDim, double zDim, SimResultsLoader simResultsLoader){
public ImageIntoMemory(double cDim, double zDim, double tDim, SimResultsLoader simResultsLoader){
this.simResultsLoader = simResultsLoader;
channelStartTextField = new HintTextField("1");
channelEndTextField = new HintTextField("" + (int) cDim);

timeStartTextField = new HintTextField("1");
timeEndTextField = new HintTextField("" + (int) tDim);

zStartTextField = new HintTextField("1");
zEndTextField = new HintTextField("" + (int) zDim);

timeStartTextField = new HintTextField("1");
timeEndTextField = new HintTextField("" + (int) tDim);

// Create the frame
frame = new JFrame("Select " + simResultsLoader.userSetFileName + " Dimensions");
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
Expand Down Expand Up @@ -113,8 +113,8 @@ public void actionPerformed(ActionEvent e) {
if (e.getSource().equals(okayButton)){
frame.dispose();

startC = Integer.parseInt(channelStartTextField.getText()) - 1;
endC = Integer.parseInt(channelEndTextField.getText()) - 1;
startC = Integer.parseInt(channelStartTextField.getText());
endC = Integer.parseInt(channelEndTextField.getText());
startT = Integer.parseInt(timeStartTextField.getText()) - 1;
endT = Integer.parseInt(timeEndTextField.getText()) - 1;
startZ = Integer.parseInt(zStartTextField.getText()) - 1;
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11 changes: 6 additions & 5 deletions view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java
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Expand Up @@ -236,7 +236,7 @@ private JPanel topPanel(){
includeExampleExports.setSelected(!N5ImageHandler.exportedDataExists());

GridBagConstraints gridBagConstraints = new GridBagConstraints();

JPanel topRow = new JPanel(new GridBagLayout());
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
Expand Down Expand Up @@ -271,6 +271,7 @@ private JPanel topPanel(){
monthInterval = new JCheckBox("Past Month");
yearlyInterval = new JCheckBox("Past Year");
anyInterval = new JCheckBox("Any Time");
anyInterval.setSelected(true);

ButtonGroup buttonGroup = new ButtonGroup();
buttonGroup.add(todayInterval);
Expand All @@ -281,10 +282,10 @@ private JPanel topPanel(){
JPanel filters = new JPanel();
filters.setLayout(new BorderLayout());
timeFilter = new JPanel(new GridBagLayout());
timeFilter.add(anyInterval);
timeFilter.add(todayInterval);
timeFilter.add(monthInterval);
timeFilter.add(yearlyInterval);
timeFilter.add(anyInterval);
// timeFilter.setBorder(BorderFactory.createTitledBorder(lowerEtchedBorder, " Time "));
filters.add(timeFilter, BorderLayout.NORTH);
filters.add(includeExampleExports, BorderLayout.SOUTH);
Expand Down Expand Up @@ -490,7 +491,7 @@ static class N5ExportTableModel extends AbstractTableModel {
add("BioModel");
add("Application");
add("Simulation");
add("Time Slice");
add("Channel,Z,Time");
add("Date Exported");
add("N5 File Name");
}};
Expand Down Expand Up @@ -524,8 +525,8 @@ public Object getValueAt(int rowIndex, int columnIndex) {
return data.biomodelName;
} else if (columnIndex == headers.indexOf("Simulation")) {
return data.simulationName;
} else if (columnIndex == headers.indexOf("Time Slice")) {
return data.startAndEndTime;
} else if (columnIndex == headers.indexOf("Channel,Z,Time")) {
return String.format("%s,%s,%s", data.numVariables, data.zSlices, data.tSlices);
} else if (columnIndex == headers.indexOf("Date Exported")) {
return data.exportDate;
} else if (columnIndex == headers.indexOf("N5 File Name")) {
Expand Down
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