Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add check for new columns and handle empty ROI list in TableWrapper #71

Merged
merged 4 commits into from
Jul 27, 2023
Merged

Add check for new columns and handle empty ROI list in TableWrapper #71

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f800b49
Check table columns before adding rows
ppouchin Jul 27, 2023
3904648
Fix ROI column creation when ROI list is empty
ppouchin Jul 27, 2023
ec087e9
Add test
ppouchin Jul 27, 2023
4a09725
Revert some changes
ppouchin Jul 27, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 23 additions & 8 deletions src/main/java/fr/igred/omero/annotations/TableWrapper.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutionException;
Expand Down Expand Up @@ -394,18 +395,18 @@ private static ROIData[] createROIColumn(ResultsTable results,
safeParseLong(r.getProperty(roiIdProperty))))
.filter(p -> p.getKey() != null)
.filter(p -> p.getValue() != null)
.collect(toMap(SimpleEntry::getKey,
p -> id2roi.get(p.getValue()),
(x1, x2) -> x1));
.collect(HashMap::new,
(m, v) -> m.put(v.getKey(), id2roi.get(v.getValue())),
HashMap::putAll);

Map<String, ROIData> shape2roi = ijRois.stream()
.map(r -> new SimpleEntry<>(r.getName(),
safeParseLong(r.getProperty(roiIdProperty))))
.filter(p -> p.getKey() != null)
.filter(p -> p.getValue() != null)
.collect(toMap(SimpleEntry::getKey,
p -> id2roi.get(p.getValue()),
(x1, x2) -> x1));
.collect(HashMap::new,
(m, v) -> m.put(v.getKey(), id2roi.get(v.getValue())),
HashMap::putAll);
String colToDelete = "";
if (results.columnExists(roiIdProperty)) {
Variable[] roiCol = results.getColumnAsVariables(roiIdProperty);
Expand Down Expand Up @@ -440,6 +441,20 @@ private static ROIData[] createROIColumn(ResultsTable results,
}


/**
* Checks if the new columns match the existing ones.
*
* @param nColumns The number of columns in the current Results Table.
* @param offset The offset in the current Results Table.
*/
private boolean checkColumns(int nColumns, int offset) {
boolean match = offset + nColumns == columnCount;
if (offset > 0 && !columns[0].getType().equals(ImageData.class)) match = false;
if (offset > 1 && !columns[1].getType().equals(ROIData.class)) match = false;
return match;
}


/**
* Sets the information about a given column.
*
Expand Down Expand Up @@ -522,8 +537,8 @@ public void addRows(Client client, ResultsTable results, Long imageId, List<? ex
String[] headings = rt.getHeadings();

int nColumns = headings.length;
if (nColumns + offset != columnCount) {
throw new IllegalArgumentException("Number of columns mismatch");
if (!checkColumns(nColumns, offset)) {
throw new IllegalArgumentException("Number or type of columns mismatch");
}

int n = rt.size();
Expand Down
38 changes: 38 additions & 0 deletions src/test/java/fr/igred/omero/annotations/ImageJTableTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assumptions.assumeFalse;

Expand Down Expand Up @@ -722,4 +723,41 @@ void testSaveTableAs() throws Exception {
Files.deleteIfExists(file.toPath());
}


@Test
void testAddRowsWithMismatch() throws Exception {
List<ROIWrapper> rois = new ArrayList<>(2);
rois.add(new ROIWrapper());
rois.add(new ROIWrapper());

rois.get(0).setImage(image);
rois.get(1).setImage(image);

for (int i = 0; i < 4; i++) {
RectangleWrapper rectangle = new RectangleWrapper();
rectangle.setText(String.valueOf(10 + i % 2));
rectangle.setCoordinates(i * 2, i * 2, 10, 10);
rectangle.setZ(i);
rectangle.setT(0);
rectangle.setC(0);

if (i % 2 == 1) rois.get(0).addShape(rectangle);
else rois.get(1).addShape(rectangle);
}

List<ROIWrapper> newROIs = image.saveROIs(client, rois);
List<Roi> ijRois = ROIWrapper.toImageJ(newROIs);

String label1 = image.getName() + ":" + newROIs.get(0).getShapes().get(0).getText() + ":4";
String label2 = image.getName() + ":" + newROIs.get(1).getShapes().get(0).getText() + ":10";

ResultsTable results1 = createOneRowResultsTable(label1, volume1, unit1);
ResultsTable results2 = createOneRowResultsTable(label2, volume2, unit2);

TableWrapper table = new TableWrapper(client, results1, IMAGE1.id, ijRois);

assertThrows(IllegalArgumentException.class,
() -> table.addRows(client, results2, null, ijRois));
}

}