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Merged
MarkRivers merged 3 commits into from
Mar 4, 2015
Merged

Hdf5 bugfix #71

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9efe841
Fixed Attributes not being saved for constant datasets. Fixed crash w…
Mar 2, 2015
9d8e8bd
Comment out debug messages
Mar 4, 2015
e95bd3e
Changed logic if ndattr_default is not found. It will now just skip t…
Mar 4, 2015
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183 changes: 118 additions & 65 deletions ADApp/pluginSrc/NDFileHDF5.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -392,25 +392,29 @@ asynStatus NDFileHDF5::createTree(hdf5::Group* root, hid_t h5handle)
}

// Write contant datasets to file
this->writeHdfConstDatasets(new_group, root);

getIntegerParam(NDFileHDF5_storeAttributes, &storeAttributes);
if (storeAttributes == 1){
// Set some attributes on the group
this->writeHdfAttributes(new_group, root);
}
// this->writeHdfConstDatasets(new_group, root);
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@ulrikpedersen ulrikpedersen Mar 5, 2015

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With writeHdfConstDatasets() commented out at this point, this function is not used anywhere else. Is it no longer required and can be deleted? It should not be left in the code like this if it is not used...

I must admit I've lost track a bit in these many changes so I don't have the overview to determine if this function can go...


// Create all the datasets in this group
hdf5::Group::MapDatasets_t::iterator it_dsets;
hdf5::Group::MapDatasets_t& datasets = root->get_datasets();
for (it_dsets = datasets.begin(); it_dsets != datasets.end(); ++it_dsets){
hid_t new_dset = this->createDataset(new_group, it_dsets->second);
if (new_dset <= 0) continue; // failure to create the datasets so move on to next
if (new_dset <= 0) {
//hdf5::Dataset *dset = it_dsets->second;
//asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s Failed to create dataset: %s\n", driverName, functionName, dset->get_name().c_str());
continue; // failure to create the datasets so move on to next
}
// Write the hdf attributes to the dataset
this->writeHdfAttributes( new_dset, it_dsets->second);
// Datasets are closed after data has been written
}

getIntegerParam(NDFileHDF5_storeAttributes, &storeAttributes);
if (storeAttributes == 1){
// Set some attributes on the group
this->writeHdfAttributes(new_group, root);
}

hdf5::Group::MapGroups_t::const_iterator it_group;
hdf5::Group::MapGroups_t& groups = root->get_groups();
for (it_group = groups.begin(); it_group != groups.end(); ++it_group){
Expand Down Expand Up @@ -503,6 +507,8 @@ void NDFileHDF5::writeHdfAttributes( hid_t h5_handle, hdf5::Element* element)
this->writeH5attrInt32(h5_handle, attr.get_name(), attr.source.get_src_def());
break;
default:
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::writeHdfAttributes unknown type: unable to create attribute: %s\n",
driverName, attr.get_name());
break;
}
}
Expand Down Expand Up @@ -545,10 +551,35 @@ void NDFileHDF5::writeHdfConstDatasets( hid_t h5_handle, hdf5::Group* group)
}
}

hid_t NDFileHDF5::writeHdfConstDataset( hid_t h5_handle, hdf5::Dataset* dset)
{
hdf5::DataType_t dtype = hdf5::string;

if(dset != NULL && dset->data_source().is_src_constant())
{
dtype = dset->data_source().get_datatype();
switch ( dtype )
{
case hdf5::string:
return this->writeH5dsetStr(h5_handle, dset->get_name(), dset->data_source().get_src_def());
break;
case hdf5::float64:
return this->writeH5dsetFloat64(h5_handle, dset->get_name(), dset->data_source().get_src_def());
break;
case hdf5::int32:
return this->writeH5dsetInt32(h5_handle, dset->get_name(), dset->data_source().get_src_def());
break;
default:
return -1;
break;
}
}
}

/**
* Write a string constant dataset.
*/
void NDFileHDF5::writeH5dsetStr(hid_t element, const std::string &name, const std::string &str_value) const
hid_t NDFileHDF5::writeH5dsetStr(hid_t element, const std::string &name, const std::string &str_value) const
{
herr_t hdfstatus = -1;
hid_t hdfdatatype = -1;
Expand All @@ -572,7 +603,7 @@ void NDFileHDF5::writeH5dsetStr(hid_t element, const std::string &name, const st
driverName, functionName, name.c_str());
H5Tclose(hdfdatatype);
H5Sclose(hdfdataspace);
return;
return -1;
}

hdfstatus = H5Dwrite(hdfdset, hdfdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, str_value.c_str());
Expand All @@ -582,17 +613,17 @@ void NDFileHDF5::writeH5dsetStr(hid_t element, const std::string &name, const st
H5Aclose (hdfdset);
H5Tclose(hdfdatatype);
H5Sclose(hdfdataspace);
return;
return -1;
}

H5Dclose (hdfdset);
//H5Dclose (hdfdset);
H5Tclose(hdfdatatype);
H5Sclose(hdfdataspace);

return;
return hdfdset;
}

void NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const std::string &str_value) const
hid_t NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const std::string &str_value) const
{
herr_t hdfstatus = -1;
hid_t hdfdatatype = -1;
Expand Down Expand Up @@ -624,7 +655,7 @@ void NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
return;
return -1;
}
epicsInt32 ival;
sscanf(str_value.c_str(), "%d", &ival);
Expand All @@ -634,7 +665,7 @@ void NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
driverName, functionName, name.c_str());
H5Dclose(hdfdset);
H5Sclose(hdfdataspace);
return;
return -1;
}
} else {
// Here we have an array of integer values
Expand All @@ -655,7 +686,7 @@ void NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
return;
return -1;
}
hdfstatus = H5Dwrite(hdfdset, hdfdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, ivalues);
delete [] ivalues;
Expand All @@ -664,16 +695,16 @@ void NDFileHDF5::writeH5dsetInt32(hid_t element, const std::string &name, const
driverName, functionName, name.c_str());
H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
return;
return -1;
}
}
H5Dclose (hdfdset);
//H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
return;
return hdfdset;

}

void NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, const std::string &str_value) const
hid_t NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, const std::string &str_value) const
{
herr_t hdfstatus = -1;
hid_t hdfdatatype = -1;
Expand Down Expand Up @@ -705,7 +736,7 @@ void NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, cons
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
return;
return -1;
}
double fval;
sscanf(str_value.c_str(), "%lf", &fval);
Expand All @@ -715,7 +746,7 @@ void NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, cons
driverName, functionName, name.c_str());
H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
return;
return -1;
}
} else {
// Here we have an array of integer values
Expand All @@ -736,7 +767,7 @@ void NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, cons
asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s unable to create dataset: %s\n",
driverName, functionName, name.c_str());
H5Sclose(hdfdataspace);
return;
return -1;
}
hdfstatus = H5Dwrite(hdfdset, hdfdatatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, fvalues);
delete [] fvalues;
Expand All @@ -745,12 +776,12 @@ void NDFileHDF5::writeH5dsetFloat64(hid_t element, const std::string &name, cons
driverName, functionName, name.c_str());
H5Dclose(hdfdset);
H5Sclose(hdfdataspace);
return;
return -1;
}
}
H5Dclose (hdfdset);
//H5Dclose (hdfdset);
H5Sclose(hdfdataspace);
return;
return hdfdset;

}

Expand All @@ -769,6 +800,9 @@ hid_t NDFileHDF5::createDataset(hid_t group, hdf5::Dataset *dset)
if (dset->data_source().is_src_detector()) {
return this->createDatasetDetector(group, dset);
}
if(dset->data_source().is_src_constant()) {
return this->writeHdfConstDataset(group, dset);
}
if (dset->data_source().is_src_ndattribute()) {
// At this time we cannot create the dataset as we do not know its type yet
return -1;
Expand Down Expand Up @@ -1941,6 +1975,13 @@ asynStatus NDFileHDF5::writePerformanceDataset()
}
}

if(perf_group == NULL)
{
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::writePerformanceDataset No default attribute group defined.\n",
driverName);
return asynError;
}

getIntegerParam(NDFileNumCaptured, &numCaptured);
dims[1] = 5;
if (numCaptured < this->numPerformancePoints) dims[0] = numCaptured;
Expand Down Expand Up @@ -1987,7 +2028,7 @@ asynStatus NDFileHDF5::createAttributeDataset()
int extraDims;
hsize_t hdfdims=1;
int numCaptures = 1;
hid_t hdfgroup;
hid_t groupDefault = -1;
const char *attrNames[5] = {"NDAttrName", "NDAttrDescription", "NDAttrSourceType", "NDAttrSource", NULL};
const char *attrStrings[5] = {NULL,NULL,NULL,NULL,NULL};
int i;
Expand All @@ -2004,15 +2045,21 @@ asynStatus NDFileHDF5::createAttributeDataset()

hdf5::Root *root = this->layout.get_hdftree();
hdf5::Group* def_group = root->find_ndattr_default_group();
hid_t groupDefault = H5Gopen(this->file, def_group->get_full_name().c_str(), H5P_DEFAULT);
if (strlen(this->hostname) > 0) {
this->writeStringAttribute(groupDefault, "hostname", this->hostname);
//check for NULL
if(def_group != NULL) {
groupDefault = H5Gopen(this->file, def_group->get_full_name().c_str(), H5P_DEFAULT);
if (strlen(this->hostname) > 0) {
this->writeStringAttribute(groupDefault, "hostname", this->hostname);
}
}
else {
asynPrint(this->pasynUserSelf, ASYN_TRACE_WARNING, "%s::%s No default attribute group defined.\n",
driverName, functionName);
}

ndAttr = this->pFileAttributes->next(ndAttr); // get the first NDAttribute
while(ndAttr != NULL)
{
hdfgroup = groupDefault;

if (ndAttr->getDataType() < NDAttrString)
{
Expand Down Expand Up @@ -2073,37 +2120,38 @@ asynStatus NDFileHDF5::createAttributeDataset()
this->writeStringAttribute(hdfAttrNode->hdfdataset, attrNames[i], attrStrings[i]);
}

// Add the attribute to the list
attrList.push_back(hdfAttrNode);

} else {
hdfAttrNode->hdfdataspace = H5Screate_simple(hdfAttrNode->hdfrank, &hdfAttrNode->hdfdims, NULL);
// In here we need to create the dataset
hdfAttrNode->hdfdataset = H5Dcreate2(hdfgroup, hdfAttrNode->attrName,
hdfAttrNode->hdfdatatype, hdfAttrNode->hdfdataspace,
H5P_DEFAULT, hdfAttrNode->hdfcparm, H5P_DEFAULT);


// create a memory space of exactly one element dimension to use for writing slabs
hdfAttrNode->elementSize = 1;
hdfAttrNode->hdfmemspace = H5Screate_simple(hdfAttrNode->hdfrank, &hdfAttrNode->elementSize, NULL);

// Write some description of the NDAttribute as a HDF attribute to the dataset
for (i=0; attrNames[i] != NULL; i++)
{
size = strlen(attrStrings[i]);
if (size <= 0) continue;
this->writeStringAttribute(hdfAttrNode->hdfdataset, attrNames[i], attrStrings[i]);
if(groupDefault > -1) {
hdfAttrNode->hdfdataspace = H5Screate_simple(hdfAttrNode->hdfrank, &hdfAttrNode->hdfdims, NULL);
// In here we need to create the dataset
hdfAttrNode->hdfdataset = H5Dcreate2(groupDefault, hdfAttrNode->attrName,
hdfAttrNode->hdfdatatype, hdfAttrNode->hdfdataspace,
H5P_DEFAULT, hdfAttrNode->hdfcparm, H5P_DEFAULT);


// create a memory space of exactly one element dimension to use for writing slabs
hdfAttrNode->elementSize = 1;
hdfAttrNode->hdfmemspace = H5Screate_simple(hdfAttrNode->hdfrank, &hdfAttrNode->elementSize, NULL);

// Write some description of the NDAttribute as a HDF attribute to the dataset
for (i=0; attrNames[i] != NULL; i++)
{
size = strlen(attrStrings[i]);
if (size <= 0) continue;
this->writeStringAttribute(hdfAttrNode->hdfdataset, attrNames[i], attrStrings[i]);
}
// Add the attribute to the list
attrList.push_back(hdfAttrNode);
}

}

// Add the attribute to the list
attrList.push_back(hdfAttrNode);

}
// if the NDArray attribute is a string we attach it as an HDF attribute to the meta data group.
else if (ndAttr->getDataType() == NDAttrString)
{
hid_t dsetgroup;
hid_t dsetgroup = -1;
hdf5::Dataset *dset = NULL;
int closeGroup = 0;
// Search for the dataset of the NDAttribute. If it exists then we use it
Expand All @@ -2114,16 +2162,19 @@ asynStatus NDFileHDF5::createAttributeDataset()
// Here we must close the group after writing the attribute
closeGroup = 1;
} else {
dsetgroup = hdfgroup;
if(groupDefault > -1)
dsetgroup = groupDefault;
}
// Write some description of the NDAttribute as a HDF attribute to the dataset
ndAttr->getValueInfo(&ndAttrDataType, &size);
char * attrDataTypeStr = (char*)calloc(size, sizeof(char));
ndAttr->getValue(ndAttrDataType, attrDataTypeStr, size);
if (size > 0) this->writeStringAttribute(dsetgroup, ndAttr->getName(), attrDataTypeStr);
free(attrDataTypeStr);
if (closeGroup == 1){
H5Gclose(dsetgroup);
if(dsetgroup > -1) {
// Write some description of the NDAttribute as a HDF attribute to the dataset
ndAttr->getValueInfo(&ndAttrDataType, &size);
char * attrDataTypeStr = (char*)calloc(size, sizeof(char));
ndAttr->getValue(ndAttrDataType, attrDataTypeStr, size);
if (size > 0) this->writeStringAttribute(dsetgroup, ndAttr->getName(), attrDataTypeStr);
free(attrDataTypeStr);
if (closeGroup == 1){
H5Gclose(dsetgroup);
}
}
}
ndAttr = this->pFileAttributes->next(ndAttr);
Expand Down Expand Up @@ -2161,8 +2212,10 @@ asynStatus NDFileHDF5::writeAttributeDataset(hdf5::When_t whenToSave)
continue;
}
//check if when to save matches.
if (hdfAttrNode->whenToSave != whenToSave)
if (hdfAttrNode->whenToSave != whenToSave) {
//asynPrint(this->pasynUserSelf, ASYN_TRACE_ERROR, "%s::%s WARNING: NDAttribute named \'%s\' when to save miss match\n", driverName, functionName, hdfAttrNode->attrName);
continue;
}

// find the data based on datatype
ret = ndAttr->getValue(ndAttr->getDataType(), datavalue, 8);
Expand Down
7 changes: 4 additions & 3 deletions ADApp/pluginSrc/NDFileHDF5.h
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Original file line number Diff line number Diff line change
Expand Up @@ -85,9 +85,10 @@ class epicsShareClass NDFileHDF5 : public NDPluginFile
asynStatus createHardLinks(hdf5::Group* root);

void writeHdfConstDatasets( hid_t h5_handle, hdf5::Group* group);
void writeH5dsetStr(hid_t element, const std::string &name, const std::string &str_value) const;
void writeH5dsetInt32(hid_t element, const std::string &name, const std::string &str_value) const;
void writeH5dsetFloat64(hid_t element, const std::string &name, const std::string &str_value) const;
hid_t writeHdfConstDataset( hid_t h5_handle, hdf5::Dataset* dset);
hid_t writeH5dsetStr(hid_t element, const std::string &name, const std::string &str_value) const;
hid_t writeH5dsetInt32(hid_t element, const std::string &name, const std::string &str_value) const;
hid_t writeH5dsetFloat64(hid_t element, const std::string &name, const std::string &str_value) const;

void writeHdfAttributes( hid_t h5_handle, hdf5::Element* element);
hid_t createDataset(hid_t group, hdf5::Dataset *dset);
Expand Down