Skip to content

Fix display for nested/vlen cmpds #474

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

Open
mattjala wants to merge 9 commits into
base: master
Choose a base branch
from
Open

Fix display for nested/vlen cmpds #474

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
feff3cf
Fix display for nested/vlen cmpds
mattjala May 20, 2026
b3093fe
Committing clang-format changes
github-actions[bot] May 20, 2026
699c5a6
Guard against unsafe writes
mattjala May 27, 2026
32e4603
Committing clang-format changes
github-actions[bot] May 27, 2026
0848e32
Fix array of varstr read
mattjala May 29, 2026
211146e
Remove support for vlen pre-allocation
mattjala Jun 4, 2026
64ccc59
Display nested types in single cell
mattjala Jun 18, 2026
3a3f0bb
Read array and vlen data the way the JNI expects
mattjala Sep 15, 2026
7155f9d
Committing clang-format changes
github-actions[bot] Sep 15, 2026
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
36 changes: 21 additions & 15 deletions hdfview/src/main/java/hdf/view/TableView/DataDisplayConverterFactory.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,7 @@ public static HDFDisplayConverter getDataDisplayConverter(final DataFormat dataO

dataFormatReference = dataObject;

Datatype dtype = dataObject.getDatatype();

// For VLEN(compound), use compound base type so CompoundDataDisplayConverter is created
if (dtype.isVLEN() && !dtype.isVarStr() && dtype.getDatatypeBase() != null &&
dtype.getDatatypeBase().isCompound()) {
dtype = dtype.getDatatypeBase();
}

HDFDisplayConverter converter = getDataDisplayConverter(dtype);
HDFDisplayConverter converter = getDataDisplayConverter(dataObject.getDatatype());

return converter;
}
Expand Down Expand Up @@ -237,7 +229,7 @@ private static class CompoundDataDisplayConverter extends HDFDisplayConverter {
CompoundDataFormat compoundFormat = (CompoundDataFormat)dataFormatReference;

List<Datatype> localSelectedTypes =
DataFactoryUtils.filterNonSelectedMembers(compoundFormat, dtype);
DataFactoryUtils.filterNonSelectedMembers(compoundFormat, dtype, false);

log.trace("setting up {} base HDFDisplayConverters", localSelectedTypes.size());

Expand Down Expand Up @@ -331,10 +323,15 @@ public Object canonicalToDisplayValue(Object value)
Object curObject = cmpdList.get(i);
if (curObject instanceof List)
buffer.append(memberTypeConverters[i].canonicalToDisplayValue(curObject));
else {
else if (curObject != null && curObject.getClass().isArray()) {
// Array-of-compound: the member is indexed by row.
Object dataArrayValue = Array.get(curObject, cellRowIdx);
buffer.append(memberTypeConverters[i].canonicalToDisplayValue(dataArrayValue));
}
else {
// A single compound element: the member is already the value.
buffer.append(memberTypeConverters[i].canonicalToDisplayValue(curObject));
}
}
buffer.append("}");
}
Expand Down Expand Up @@ -469,7 +466,9 @@ public Object canonicalToDisplayValue(Object value)
try {
Object obj;
Object convertedValue;
int arrLen = Array.getLength(value);

// An array's elements may arrive as a List, nested arrays included.
int arrLen = (value instanceof List) ? ((List<?>)value).size() : Array.getLength(value);

log.trace("canonicalToDisplayValue({}): array length={}", value, arrLen);

Expand All @@ -480,7 +479,7 @@ public Object canonicalToDisplayValue(Object value)
if (i > 0)
buffer.append(", ");

obj = Array.get(value, i);
obj = (value instanceof List) ? ((List<?>)value).get(i) : Array.get(value, i);

convertedValue = baseTypeConverter.canonicalToDisplayValue(obj);

Expand Down Expand Up @@ -610,7 +609,14 @@ public Object canonicalToDisplayValue(Object value)
try {
Object obj;
Object convertedValue;
int arrLen = Array.getLength(value);

// A scalar cell defers to the base converter.
if (!value.getClass().isArray() && !(value instanceof List)) {
buffer.append(baseTypeConverter.canonicalToDisplayValue(value));
return buffer;
}

int arrLen = (value instanceof List) ? ((List<?>)value).size() : Array.getLength(value);

log.trace("canonicalToDisplayValue({}): array length={}", value, arrLen);

Expand All @@ -621,7 +627,7 @@ public Object canonicalToDisplayValue(Object value)
if (i > 0)
buffer.append(", ");

obj = Array.get(value, i);
obj = (value instanceof List) ? ((List<?>)value).get(i) : Array.get(value, i);

convertedValue = baseTypeConverter.canonicalToDisplayValue(obj);

Expand Down
89 changes: 65 additions & 24 deletions hdfview/src/main/java/hdf/view/TableView/DataFactoryUtils.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,36 @@ public class DataFactoryUtils {
/** the CMPD_START_IDX_MAP_INDEX value. */
public static final int CMPD_START_IDX_MAP_INDEX = 1;

/**
* Number of flat leaf names a Datatype contributes to the list produced by
* H5Datatype.extractCompoundInfo: a compound sums its children, an
* array-of-compound adds a header entry, anything else counts once.
*/
public static int countLeafNames(Datatype t)
{
if (t == null)
return 1;
if (t.isCompound()) {
int sum = 0;
List<Datatype> children = t.getCompoundMemberTypes();
if (children != null)
for (Datatype child : children)
sum += countLeafNames(child);
return sum;
}
if (t.isArray()) {
Datatype base = t.getDatatypeBase();
if (base != null && base.isCompound()) {
int sum = 1;
for (Datatype child : base.getCompoundMemberTypes())
sum += countLeafNames(child);
return sum;
}
return 1;
}
return 1;
}

/**
* Given a CompoundDataFormat, as well as a compound datatype, removes the
* non-selected datatypes from the List of datatypes inside the compound
Expand All @@ -62,34 +92,31 @@ public class DataFactoryUtils {
public static List<Datatype> filterNonSelectedMembers(CompoundDataFormat dataFormat,
final Datatype compoundType)
{
return filterNonSelectedMembers(dataFormat, compoundType, true);
}

/**
* As above, but an inner compound keeps every member: the dataset's selected-member
* list enumerates only top-level leaves, so filtering against it would drop them all.
*/
public static List<Datatype> filterNonSelectedMembers(CompoundDataFormat dataFormat,
final Datatype compoundType, boolean isTopLevel)
{
List<Datatype> selectedTypes = new ArrayList<>(compoundType.getCompoundMemberTypes());
if (!isTopLevel)
return selectedTypes;

List<Datatype> allSelectedTypes = Arrays.asList(dataFormat.getSelectedMemberTypes());
if (allSelectedTypes == null) {
log.debug("filterNonSelectedMembers(): selected compound member datatype list is null");
return null;
}

/*
* Make sure to make a copy of the compound datatype's member list, as we will
* make modifications to the list when members aren't selected.
*/
List<Datatype> selectedTypes = new ArrayList<>(compoundType.getCompoundMemberTypes());

/*
* Among the datatypes within this compound type, only keep the ones that are
* actually selected in the dataset.
*/
Iterator<Datatype> localIt = selectedTypes.iterator();
while (localIt.hasNext()) {
Datatype curType = localIt.next();

/*
* Since the passed in allSelectedMembers list is a flattened out datatype
* structure, we want to leave the nested compound Datatypes inside our local
* list of datatypes.
*/
if (curType.isCompound())
continue;

if (!allSelectedTypes.contains(curType))
localIt.remove();
}
Expand Down Expand Up @@ -191,24 +218,28 @@ else if (base.isArray()) {
}

if (nestedCompoundType != null) {
List<Datatype> cmpdSelectedTypes = filterNonSelectedMembers(dataFormat, nestedCompoundType);
List<Datatype> cmpdSelectedTypes =
filterNonSelectedMembers(dataFormat, nestedCompoundType, false);

/*
* For Array/Vlen of Compound types, we repeat the compound members n times,
* where n is the number of array elements of variable-length elements.
* Therefore, we repeat our mapping for these types n times.
* For Array of Compound types, repeat the compound members once per
* array element.
*/
for (int j = 0; j < arrSize; j++) {
buildColIdxToProviderMap(outMap, dataFormat, cmpdSelectedTypes, curMapIndex,
curProviderIndex, depth + 1);
}
}
else if (curType.isCompound()) {
List<Datatype> cmpdSelectedTypes = filterNonSelectedMembers(dataFormat, curType);
List<Datatype> cmpdSelectedTypes = filterNonSelectedMembers(dataFormat, curType, false);

buildColIdxToProviderMap(outMap, dataFormat, cmpdSelectedTypes, curMapIndex, curProviderIndex,
depth + 1);
}
else if (curType.isVLEN() && !curType.isVarStr()) {
// A vlen is one column: it holds the whole sequence.
outMap.put(curMapIndex[0]++, curProviderIndex[0]);
}
else
outMap.put(curMapIndex[0]++, curProviderIndex[0]);

Expand Down Expand Up @@ -299,7 +330,8 @@ else if (base.isArray()) {
}

if (nestedCompoundType != null) {
List<Datatype> cmpdSelectedTypes = filterNonSelectedMembers(dataFormat, nestedCompoundType);
List<Datatype> cmpdSelectedTypes =
filterNonSelectedMembers(dataFormat, nestedCompoundType, false);

/*
* For Array/Vlen of Compound types, we repeat the compound members n times,
Expand All @@ -318,11 +350,20 @@ else if (curType.isCompound()) {
if (depth == 0)
curStartIdx[0] = curMapIndex[0];

List<Datatype> cmpdSelectedTypes = filterNonSelectedMembers(dataFormat, curType);
List<Datatype> cmpdSelectedTypes = filterNonSelectedMembers(dataFormat, curType, false);

buildRelColIdxToStartIdxMap(outMap, dataFormat, cmpdSelectedTypes, curMapIndex, curStartIdx,
depth + 1);
}
else if (curType.isVLEN() && !curType.isVarStr()) {
// A vlen is one column: it holds the whole sequence.
if (depth == 0) {
outMap.put(curMapIndex[0], curMapIndex[0]);
curMapIndex[0]++;
}
else
outMap.put(curMapIndex[0]++, curStartIdx[0]);
}
else {
if (depth == 0) {
outMap.put(curMapIndex[0], curMapIndex[0]);
Expand Down
Loading
Loading