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Merge pull request #23 from FrancisCrickInstitute/alpha_feedback
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Alpha feedback
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@JonathanCSmith
JonathanCSmith authored Oct 9, 2024
2 parents 202493b + 1ff8918 commit 20331df
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Showing 2 changed files with 146 additions and 14 deletions.
4 changes: 4 additions & 0 deletions src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,9 @@ public class TWOMBLIRunner implements Command {
@Parameter(type=ItemIO.OUTPUT)
public ImagePlus gapImage;

@Parameter(type=ItemIO.OUTPUT)
public boolean complete = false;

// Magic number declarations
private static final double HIGH_CONTRAST_THRESHOLD = 120.0;
private static final double LOW_CONTRAST_THRESHOLD = 0.0;
Expand Down Expand Up @@ -202,6 +205,7 @@ public void run() {
this.maskImage = maskImage;
this.hdmImage = IJ.openImage(hdmDirectory + File.separator + this.filePrefix + "_hdm.png");
this.gapImage = IJ.openImage(gapAnalysisDirectory + File.separator + this.filePrefix + "_gap.png");
this.complete = true;
}

private void detectRidges(ImagePlus inputImage, String maskImage) {
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156 changes: 142 additions & 14 deletions src/main/java/uk/ac/franciscrickinstitute/twombli/TWOMBLIWindow.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import ij.gui.ImageCanvas;
import ij.gui.StackWindow;
import ij.process.ImageProcessor;
import io.scif.img.IO;
import org.scijava.command.CommandModule;

// Logservice integration
Expand All @@ -48,6 +49,8 @@ public class TWOMBLIWindow extends StackWindow implements ProgressCancelListener
private final JCheckBox gapAnalysisCheckbox;
private final JFormattedTextField gapAnalysisDiameterField;
private final JButton anamorfButton;
private final JButton saveConfigButton;
private final JButton loadConfigButton;
private final JButton infoButton;
private final JButton changePreviewButton;
private final JLabel selectedPreviewPathField;
Expand Down Expand Up @@ -246,6 +249,16 @@ public TWOMBLIWindow(TWOMBLIConfigurator plugin, ImagePlus previewImage, ImagePl
ActionListener anamorfListener = e -> this.getAnamorfProperties();
this.anamorfButton.addActionListener(anamorfListener);

// Save config button
this.saveConfigButton = new JButton("Save Configuration");
this.saveConfigButton.setToolTipText("Save the current TWOMBLI configuration to a file.");
this.saveConfigButton.addActionListener(e -> this.saveConfiguration());

// Load config button
this.loadConfigButton = new JButton("Load Configuration");
this.loadConfigButton.setToolTipText("Load the current TWOMBLI configuration to a file.");
this.loadConfigButton.addActionListener(e -> this.loadConfiguration());

// Run Preview button
this.runPreviewButton = new JButton("Run Preview");
this.runPreviewButton.setToolTipText("Run TWOMBLI with the current configuration on the preview image.");
Expand Down Expand Up @@ -332,6 +345,14 @@ public TWOMBLIWindow(TWOMBLIConfigurator plugin, ImagePlus previewImage, ImagePl
configPanelConstraints.gridy++;
configPanel.add(gapAnalysisDiameterPanel, configPanelConstraints);

// Save config
configPanelConstraints.gridy++;
configPanel.add(this.saveConfigButton, configPanelConstraints);

// Load Config
configPanelConstraints.gridy++;
configPanel.add(this.loadConfigButton, configPanelConstraints);

// Sidebar panel
GridBagLayout sidePanelLayout = new GridBagLayout();
JPanel sidePanel = new JPanel();
Expand Down Expand Up @@ -695,6 +716,106 @@ private void getAnamorfProperties() {
this.anamorfPropertiesFile = potential;
}

private void saveConfiguration() {
String potentialSavePath = IJ.getDirectory("Save TWOMBLI Configuration");
if (potentialSavePath == null || !Files.isDirectory(Paths.get(potentialSavePath))) {
return;
}

Path savePath = Paths.get(potentialSavePath, "twombli_configuraiton.txt");
try (BufferedWriter configWriter = Files.newBufferedWriter(savePath, StandardOpenOption.CREATE_NEW)) {
configWriter.write("MINIMUM_LINE_WIDTH:" + Integer.valueOf(this.minimumLineWidthField.getText()));
configWriter.write("MAXIMUM_LINE_WIDTH:" + Integer.valueOf(this.maximumLineWidthField.getText()));
configWriter.write("DARK_LINES:" + this.darklinesCheckbox.isSelected());
configWriter.write("MINIMUM_BRANCH_LENGTH:" + Integer.valueOf(this.minimumBranchLengthField.getText()));
configWriter.write("MINIMUM_CURVATURE_WINDOW:" + Integer.valueOf(this.minimumCurvatureWindowField.getText()));
configWriter.write("MAXIMUM_CURVATURE_WINDOW:" + Integer.valueOf(this.maximumCurvatureWindowField.getText()));
configWriter.write("CURVATURE_WINDOW_STEP_SIZE:" + Integer.valueOf(this.curvatureStepSizeField.getText()));
configWriter.write("MAXIMUM_DISPLAY_HDM:" + Integer.valueOf(this.maximumDisplayHDMField.getText()));
configWriter.write("CONTRAST_SATURATION:" + Float.valueOf(this.contrastSaturationField.getText()));
configWriter.write("PERFORM_GAP_ANALYSIS:" + this.gapAnalysisCheckbox.isSelected());
configWriter.write("MINIMUM_GAP_DIAMETER:" + Integer.valueOf(this.gapAnalysisDiameterField.getText()));

if (this.anamorfPropertiesFile != null) {
configWriter.write("ANAMORF_FILE:" + this.anamorfPropertiesFile);
}
}

catch (IOException e) {
e.printStackTrace();
}
}

private void loadConfiguration() {
String potentialSaveFile = IJ.getFilePath("Load TWOMBLI Configuration");
if (potentialSaveFile == null) {
return;
}

Path savePath = Paths.get(potentialSaveFile);
if (!Files.isRegularFile(savePath)) {
return;
}

try (BufferedReader configReader = Files.newBufferedReader(savePath)) {
String line;
while ((line = configReader.readLine()) != null) {
String[] config = line.split(":");

if (config.length != 2) {
continue; // Skip invalid lines
}

String key = config[0];
String value = config[1];

switch (key) {
case "MINIMUM_LINE_WIDTH":
this.minimumLineWidthField.setText(value);
break;
case "MAXIMUM_LINE_WIDTH":
this.maximumLineWidthField.setText(value);
break;
case "DARK_LINES":
this.darklinesCheckbox.setSelected(Boolean.parseBoolean(value));
break;
case "MINIMUM_BRANCH_LENGTH":
this.minimumBranchLengthField.setText(value);
break;
case "MINIMUM_CURVATURE_WINDOW":
this.minimumCurvatureWindowField.setText(value);
break;
case "MAXIMUM_CURVATURE_WINDOW":
this.maximumCurvatureWindowField.setText(value);
break;
case "CURVATURE_WINDOW_STEP_SIZE":
this.curvatureStepSizeField.setText(value);
break;
case "MAXIMUM_DISPLAY_HDM":
this.maximumDisplayHDMField.setText(value);
break;
case "CONTRAST_SATURATION":
this.contrastSaturationField.setText(value);
break;
case "PERFORM_GAP_ANALYSIS":
this.gapAnalysisCheckbox.setSelected(Boolean.parseBoolean(value));
break;
case "MINIMUM_GAP_DIAMETER":
this.gapAnalysisDiameterField.setText(value);
break;
case "ANAMORF_FILE":
this.anamorfPropertiesFile = value;
break;
default:
// Unknown configuration key, can log or ignore
break;
}
}
} catch (IOException e) {
e.printStackTrace();
}
}

private void getBatchDirectory() {
String potential = IJ.getDirectory("Get Batch Folder");
if (potential == null) {
Expand Down Expand Up @@ -862,6 +983,7 @@ public void handleFutureComplete(Future<CommandModule> future, boolean isPreview
this.fibreImage = (ImagePlus) output.getOutput("maskImage");
this.micRadioButton.setEnabled(true);
this.micImage = (ImagePlus) output.getOutput("gapImage");
this.fibreRadioButton.setState(true);
this.handleFibreButtonPressed();
}

Expand All @@ -888,28 +1010,34 @@ public void handleFutureComplete(Future<CommandModule> future, boolean isPreview
IJ.showProgress(1, 1);
this.customProgressBar.dispose();
this.generateSummaries();

// Reopen us because someone closed everything with a hammer?
this.setVisible(true);
this.closed = false;
}
}

private void generateSummaries() {
// Loop through our results and generate a summary
Path gapsOutputPath = Paths.get(this.outputDirectory, "gaps_summary.csv");
Path twombliOutputPath = Paths.get(this.outputDirectory, "twombli_summary.csv");
Path successLog = Paths.get(this.outputDirectory, "success.log");
boolean doHeader = true;
for (CommandModule output : this.finishedFutures) {
// Gather our basic info
String filePrefix = (String) output.getInput("filePrefix");
double alignment = (double) output.getOutput("alignment");
int dimension = (int) output.getOutput("dimension");
Path anamorfSummaryPath = Paths.get(this.outputDirectory, "masks", filePrefix + "_results.csv");
Path hdmSummaryPath = Paths.get(this.outputDirectory, "hdm_csvs", filePrefix + "_ResultsHDM.csv");
Path gapAnalysisPath = Paths.get(this.outputDirectory, "gap_analysis", filePrefix + "_gaps.csv");
Outputs.generateSummaries(twombliOutputPath, alignment, dimension, anamorfSummaryPath, hdmSummaryPath, gapAnalysisPath, doHeader, this.gapAnalysisCheckbox.isSelected(), gapsOutputPath);
doHeader = false;

try (BufferedWriter successWriter = Files.newBufferedWriter(successLog, StandardOpenOption.CREATE_NEW)) {
for (CommandModule output : this.finishedFutures) {
// Gather our basic info
String filePrefix = (String) output.getInput("filePrefix");
boolean success = (boolean) output.getOutput("complete");
double alignment = (double) output.getOutput("alignment");
int dimension = (int) output.getOutput("dimension");
Path anamorfSummaryPath = Paths.get(this.outputDirectory, "masks", filePrefix + "_results.csv");
Path hdmSummaryPath = Paths.get(this.outputDirectory, "hdm_csvs", filePrefix + "_ResultsHDM.csv");
Path gapAnalysisPath = Paths.get(this.outputDirectory, "gap_analysis", filePrefix + "_gaps.csv");
Outputs.generateSummaries(twombliOutputPath, alignment, dimension, anamorfSummaryPath, hdmSummaryPath, gapAnalysisPath, doHeader, this.gapAnalysisCheckbox.isSelected(), gapsOutputPath);
doHeader = false;
successWriter.write(filePrefix + ": " + success + "\n");
}
}

catch (IOException e) {
e.printStackTrace();
}
}

Expand Down

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