Comments (9)
rimmartin
commented on July 22, 2024
native hdf5 1.10?
hdf5.node 0.3.1?
They are wrapped in an Int64 object in the latest versions. If you continue you would see it gets the next child members
const members2 = group.getMemberNames();
console.dir(members2);
yields [ 'OSBS' ]
I'll look into adding to the toString of Int64 to display the value yet the user should never need to operate on these values without the wrapper. I did this because hdf5 1.10 went to 64 bit id's and javascript doesn't support such a large bit field for integers
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rimmartin
commented on July 22, 2024
Now
console.log(file.id.toString());
console.log(group.id.toString());
does display the id as a string since there is no javascript 64 bit integer
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tonyferreira
commented on July 22, 2024
I tried to npm install the 0.3.2 package straight from Github, but the install threw an error in node-gyp, so I tried again with the 0.3.1 package.
Running on Node
~ » node -v
v7.5.0
brew formula for natives
~ » brew info hdf5
homebrew/science/hdf5: stable 1.10.0-patch1 (bottled)
0.3.1 of hdf5.node
~ » npm view hdf5 version
0.3.1
When I run the following to open a dataset
const file = new hdf5.File('NEONDSTowerTemperatureData.hdf5', Access.ACC_RDONLY);
const boom_3 = file.openGroup(`Domain_10/STER/min_30/boom_3/`);
const ds = h5lt.readDataset(boom_3.id, 'temperature');
I get
const ds = h5lt.readDataset(boom_3.id, 'temperature');
SyntaxError: unsupported data type
at Object.<anonymous> (<path to js file omitted>)
at Module._compile (module.js:571:32)
at Object.Module._extensions..js (module.js:580:10)
at Module.load (module.js:488:32)
at tryModuleLoad (module.js:447:12)
at Function.Module._load (module.js:439:3)
at Module.runMain (module.js:605:10)
at run (bootstrap_node.js:418:7)
at startup (bootstrap_node.js:139:9)
at bootstrap_node.js:533:3
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rimmartin
commented on July 22, 2024
You'll need the table interface: http://hdf-ni.github.io/hdf5.node/ref/tables.html. Nice set of data in tabular form.
const h5tb = require('hdf5').h5tb;
....
var boom_3 = file.openGroup(`Domain_10/STER/min_30/boom_3/`);
var temperatureTable=h5tb.readTable(boom_3.id, "temperature");
console.dir(temperatureTable);
If you are working with an unknown hierarchy you can find out what it is with
var HLType = require('hdf5/lib/globals.js').HLType;
...
var hlType=boom_3.getDatasetType("temperature");
switch(hlType){
case HLType.HL_TYPE_LITE:
break;
case HLType.HL_TYPE_IMAGE:
break;
case HLType.HL_TYPE_TABLE:
console.dir("I'm a table.");
break;
case HLType.HL_TYPE_PACKET_TABLE:
break;
case HLType.HL_TYPE_DIMENSION_SCALES:
break;
case HLType.HL_TYPE_OPTIMIZED_FUNCTIONS:
break;
case HLType.HL_TYPE_EXTENSIONS:
break;
default: //HL_TYPE_UNKNOWN
break;
}
yields
'I'm a table.'
http://hdf-ni.github.io/hdf5.node/ref/globals.html#hltype
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rimmartin
commented on July 22, 2024
for(var column in temperatureTable){
console.dir(temperatureTable[column].name);
}
yields
'date'
'numPts'
'mean'
'min'
'max'
'variance'
'stdErr'
'uncertainty'
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tonyferreira
commented on July 22, 2024
Thank you for the quick responses. I was able to retrieve the datasets from the sample file using h5tb.readTable, however, I'm getting a node abort when trying to read datasets from the following file:
const h5lt = require('hdf5').h5lt;
const H5OType = require('hdf5/lib/globals.js').H5OType;
const HLType = require('hdf5/lib/globals.js').HLType;
const Access = require('hdf5/lib/globals').Access;
const hdf5 = require('hdf5').hdf5;
const h5tb = require('hdf5').h5tb;
const file = new hdf5.File('20170331.h5', Access.ACC_RDONLY);
const group = file.openGroup('ROOT/PARAMS/A1/');
const data = h5tb.readTable(group.id, 'Values');
console.dir(data);
Node:
[1] 67409 abort node <filename>.js
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rimmartin
commented on July 22, 2024
I tested with nodejs v7.5.0 & hdf5 native hdf5-1.10.0-patch1
Reading it successfully. Not sure what the error means.
try a try catch
try{
const file = new hdf5.File('20170331.h5', Access.ACC_RDONLY);
const group = file.openGroup('ROOT/PARAMS/A1/');
const data = h5tb.readTable(group.id, 'Values');
catch(err) {
console.dir(err.message);
}
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rimmartin
commented on July 22, 2024
when pulling directly from github in your package json's dependencies have
"hdf5" : "HDF-NI/hdf5.node"
then your npm line needs to tell it where hdf5 native is
npm install –hdf5_home_mac=<your hdf5 base directory>
where this is your dependent project's install
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tonyferreira
commented on July 22, 2024
Thanks for looking into it. Looks like it's specific to my system. I'm running macOS Sierra 10.12.3 with the brew version of the natives. I'll try it on a windows machine.
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