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Fix tests to match expected sparse plate layout
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@melissalinkert
melissalinkert committed Nov 23, 2021
1 parent 75032a8 commit 293d03a
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Showing 2 changed files with 92 additions and 35 deletions.
127 changes: 92 additions & 35 deletions src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -823,7 +823,11 @@ public void testHCSMetadata() throws Exception {
int rowCount = 2;
int colCount = 3;
int fieldCount = 2;
checkPlateGroupLayout(output, rowCount, colCount, fieldCount, 512, 512);
Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
plateMap.put("0", Arrays.asList("0", "1", "2"));
plateMap.put("1", Arrays.asList("0", "1", "2"));
checkPlateGroupLayout(output, rowCount, colCount,
plateMap, fieldCount, 512, 512);

// check plate/well level metadata
Map<String, Object> plate =
Expand Down Expand Up @@ -875,7 +879,7 @@ public void testHCSMetadata() throws Exception {
*/
@Test
public void testHCSMetadataNoAcquisitions() throws Exception {
input = getTestFile("C4-H2-only-no-acqs.xml");
input = getTestFile("A1-B1-only-no-acqs.xml");
assertTool();

ZarrGroup z = ZarrGroup.open(output);
Expand All @@ -885,7 +889,11 @@ public void testHCSMetadataNoAcquisitions() throws Exception {
int fieldCount = 1;

// Only two rows are filled out with one column each (two Wells total)
checkPlateGroupLayout(output, 2, 1, fieldCount, 2, 2);
Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
plateMap.put("0", Arrays.asList("0"));
plateMap.put("1", Arrays.asList("0"));
checkPlateGroupLayout(output, rowCount, colCount,
plateMap, fieldCount, 2, 2);

// check plate/well level metadata
Map<String, Object> plate =
Expand All @@ -904,23 +912,16 @@ public void testHCSMetadataNoAcquisitions() throws Exception {
checkDimension(rows, rowCount);
checkDimension(columns, colCount);

assertEquals(rows.size() * columns.size(), wells.size());
for (int row=0; row<rows.size(); row++) {
for (int col=0; col<columns.size(); col++) {
int well = row * columns.size() + col;
assertEquals(row + "/" + col, wells.get(well).get("path"));
}
}
assertEquals(2, wells.size());
for (Map<String, Object> well : wells) {
int row = ((Number) well.get("row_index")).intValue();
int col = ((Number) well.get("column_index")).intValue();

// check well metadata
for (Map<String, Object> row : rows) {
String rowName = (String) row.get("name");
for (Map<String, Object> column : columns) {
String columnName = (String) column.get("name");
ZarrGroup wellGroup = ZarrGroup.open(
output.resolve(rowName).resolve(columnName));
checkWell(wellGroup, fieldCount);
}
String wellPath = well.get("path").toString();
assertEquals(row + "/" + col, wellPath);

ZarrGroup wellGroup = ZarrGroup.open(output.resolve(wellPath));
checkWell(wellGroup, fieldCount, -1);
}

// check OME metadata
Expand All @@ -942,6 +943,12 @@ public void testSingleWell() throws IOException {
int colCount = 12;
int fieldCount = 1;

Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
plateMap.put("4", Arrays.asList("5"));

checkPlateGroupLayout(output, rowCount, colCount,
plateMap, fieldCount, 2, 2);

// check plate/well level metadata
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
Expand Down Expand Up @@ -988,6 +995,12 @@ public void testTwoWells() throws IOException {
int colCount = 12;
int fieldCount = 1;

Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
plateMap.put("2", Arrays.asList("3"));
plateMap.put("7", Arrays.asList("1"));
checkPlateGroupLayout(output, rowCount, colCount,
plateMap, fieldCount, 2, 2);

// check plate/well level metadata
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
Expand Down Expand Up @@ -1040,6 +1053,12 @@ public void testOnePlateRow() throws IOException {
int colCount = 12;
int fieldCount = 1;

Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
plateMap.put("5", Arrays.asList(
"0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11"));
checkPlateGroupLayout(output, rowCount, colCount,
plateMap, fieldCount, 2, 2);

// check plate/well level metadata
Map<String, Object> plate =
(Map<String, Object>) z.getAttributes().get("plate");
Expand Down Expand Up @@ -1266,29 +1285,60 @@ public void testChunkSizeToBig() throws Exception {
}
}

/**
* @param root dataset root path
* @param rowCount total rows the plate could contain
* @param colCount total columns the plate could contain
* @param validPaths array of row/column paths containing data
* @param fieldCount number of fields per well
* @param x image width
* @param y image height
*/
private void checkPlateGroupLayout(Path root, int rowCount, int colCount,
int fieldCount, int x, int y)
Map<String, List<String>> validPaths, int fieldCount, int x, int y)
throws IOException
{
// check valid group layout
// OME (OME-XML metadata) folder, .zattrs (Plate), .zgroup (Plate) and rows
assertEquals(rowCount + 3, Files.list(root).toArray().length);
assertEquals(validPaths.size() + 3, Files.list(root).toArray().length);

// for every row in the overall plate,
// if there are any wells with data in the row, the row path must exist
// if there are no wells with data in the row, the row path cannot exist
for (int row=0; row<rowCount; row++) {
Path rowPath = root.resolve(Integer.toString(row));
// .zgroup (Row) and columns
assertEquals(colCount + 1, Files.list(rowPath).toArray().length);
for (int col=0; col<colCount; col++) {
Path colPath = rowPath.resolve(Integer.toString(col));
ZarrGroup colGroup = ZarrGroup.open(colPath);
// .zattrs (Column/Image), .zgroup (Column/Image) and fields
assertEquals(fieldCount + 2, Files.list(colPath).toArray().length);
for (int field=0; field<fieldCount; field++) {
// append resolution index
ZarrArray series0 = colGroup.openArray(field + "/0");
assertArrayEquals(new int[] {1, 1, 1, y, x}, series0.getShape());
assertArrayEquals(new int[] {1, 1, 1, y, x}, series0.getChunks());
String rowString = Integer.toString(row);
if (validPaths.containsKey(rowString)) {
Path rowPath = root.resolve(rowString);
// .zgroup (Row) and columns
List<String> validColumns = validPaths.get(rowString);
assertEquals(validColumns.size() + 1,
Files.list(rowPath).toArray().length);

// for every column in the overall plate,
// if this row/column is a well with data, the column path must exist
// otherwise, the column path cannot exist
for (int col=0; col<colCount; col++) {
String colString = Integer.toString(col);
if (validColumns.contains(colString)) {
Path colPath = rowPath.resolve(colString);
ZarrGroup colGroup = ZarrGroup.open(colPath);
// .zattrs (Column/Image), .zgroup (Column/Image) and fields
assertEquals(fieldCount + 2, Files.list(colPath).toArray().length);
for (int field=0; field<fieldCount; field++) {
// append resolution index
ZarrArray series0 = colGroup.openArray(field + "/0");
assertArrayEquals(new int[] {1, 1, 1, y, x}, series0.getShape());
assertArrayEquals(new int[] {1, 1, 1, y, x}, series0.getChunks());
}
}
else {
assertFalse(rowPath.resolve(colString).toFile().exists());
}
}
}
else {
assertFalse(root.resolve(rowString).toFile().exists());
}
}
}

Expand All @@ -1303,6 +1353,13 @@ private void checkDimension(List<Map<String, Object>> dims, int dimCount)

private void checkWell(ZarrGroup wellGroup, int fieldCount)
throws IOException
{
checkWell(wellGroup, fieldCount, 0);
}


private void checkWell(ZarrGroup wellGroup, int fieldCount, int acquisition)
throws IOException
{
Map<String, Object> well =
(Map<String, Object>) wellGroup.getAttributes().get("well");
Expand All @@ -1313,7 +1370,7 @@ private void checkWell(ZarrGroup wellGroup, int fieldCount)
for (int i=0; i<fieldCount; i++) {
Map<String, Object> field = images.get(i);
assertEquals(field.get("path"), String.valueOf(i));
assertEquals(0, field.get("acquisition"));
assertEquals(acquisition, field.get("acquisition"));
}
}

Expand Down
0 ...ioformats2raw/test/C4-H2-only-no-acqs.xml → ...ioformats2raw/test/A1-B1-only-no-acqs.xml
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