Questions tagged [hdf5]
The Hierarchical Data Format version 5 (HDF5), is an open source file format that supports large, complex, heterogeneous data and uses a "file directory" like structure.
35
questions
5
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1answer
336 views
What is the schema of HEC-RAS output in HDF5 format?
I realize that HDF5 is a self describing format, and I can use a tool or programmatically find out what types of data groups exist in an HDF5 file.
What I am really looking for are the group and data ...
4
votes
2answers
607 views
Opening EOS netCDF4/HDF5 file with correct format using xarray?
I am using xarray (version 0.12.2) to work with the MODIS/Terra+Aqua MAIAC Land Aerosol Optical Depth dataset (MCD19A2.006). xarray successfully opens that dataset with the correct variables and ...
4
votes
1answer
2k views
Changing origin (top left corner) coordinates of raster using PyQGIS?
I am developing a python plugin for QGIS. The purpose of the plugin is to properly open an HDF5 dataset as a raster. Opening and displaying the raster can be done without the need for a plugin, ...
4
votes
0answers
4k views
HDF5 files in QGIS
I am working with GPM GMI precipitation data that is stored in the hdf5 data format. All I am trying to do is import and visualize the data in the QGIS environment. I can import the precipitation file ...
3
votes
3answers
2k views
HDF5 and georeferencing?
I'm doing quite heavy processing of Earth Observation data, and it appears that a lot of my workflow can be speeded up by using HDF5 for local storage. I mostly work with large stacks of raster files, ...
3
votes
1answer
4k views
Opening HDF5 satellite images in GDAL with Python? [closed]
I want to read and open HDF5 satellite images by python for batch processing.
How can I read and open both image bands and meta data?
For batch processing I need to geo-reference and read IR bands. ...
3
votes
2answers
177 views
How to use a raster dataset to store and retrieve “vectors” using Python?
For a rectangular area of about 10 by 10 km, I have to generate "displacement vectors" with a 1 meter resolution (i.e. a delta-x and delta-y value for every cell of 1 by 1 meter). I will end up with ...
3
votes
2answers
3k views
How to get value for specific coordinates in R
I have a bunch of raster files in different formats:
- NETCDF 4
- HDF 5
- GeoTIFF
Using rgal package I'm able to open any of them and use them as objects in R!
Creating stacks of them allows me to ...
3
votes
2answers
408 views
PyQGIS (3.2) and H5PY DLL problem
I am working in a project in which I need to use PyQGIS and H5PY. The problem comes when I load qgis library and h5py, for example:
import qgis
import h5py
I get this error:
from ._conv import ...
2
votes
2answers
1k views
What is the easiest way to create map using HDF-5 data subset?
I need to visualize some area using values provided in HDF-EOS version 5 file and create map using those values and other GIS layers.
Unfortunately, my QGIS do not recognize the HDF5 file.
Do I ...
2
votes
1answer
226 views
GDALwarp HDF5 Image With Unknown Projection
I have a NetCDF file that contains a series of HDF5 bands. I am looking to project one of these bands contained within this file. I've attempted to use the following command to achieve this:
gdalwarp ...
2
votes
1answer
663 views
projecting INSAT3D L1B data from HDF5 to Geotiff
I am attempting to use gdal to project a set of geostationary INSAT 3D L1B images.
I tried to follow the steps in
Unable to warp HDF5 files
I created the .vrt files using
gdal_translate -of VRT ...
2
votes
1answer
2k views
GDAL set negative values to nodata or NaN
How can I set all negative values in a raster to NaN or no data?
I've made a virtual raster to link data and coordinates from a HDF5 then using something like this:
gdalwarp -geoloc -tr 3000 3000 -...
2
votes
1answer
28 views
Gdal translate HDF5 to GeoTIFF library funtion
Im am trying to convert a radar file provided in HDF5 to a GeoTIFF using gdal.Translate() in my Python script.
An example of the HDF5 file can be downloaded here
I have already managed to get it ...
1
vote
1answer
5k views
extract value for a given coordinate from HDF5 file
I have an HDF5 file of radiation data for the Indian Ocean region. I plotted the data in Python using the following code
import h5py as h5
import matplotlib.pyplot as plt
f = h5.File("D:\Nikka\Geo ...
1
vote
2answers
87 views
Extract subfiles from a HDF5 file?
Does anyone know how to extract subfiles from a HDF5 file? The GIS remote sensing data I am getting is aggregated into a single .h5 file, but I need it separated into the component files. My aim is ...
1
vote
0answers
21 views
Load gzipped HDF5 layer without decompressing using GDAL
I am interested in loading a VIIRS raster that's contained in a gzipped H5 file, but I get an error. I am using the following command to get the info:
gdalinfo HDF5:"/vsigzip/imagery/viirs/test3/...
1
vote
1answer
49 views
Conversion of MLS/AURA RELATIVE HUMIDITY PRODUCT to correctly referenced GeoTIFF
I have downloaded the following product
https://cmr.earthdata.nasa.gov/search/concepts/C1251101764-GES_DISC.html
and it gives me a .he5file.
Can anyone help me in correctly geo-referencing the file ...
1
vote
0answers
56 views
Loading MOPITT data into QGIS?
I have a problem importing Terra MOPITT data into QGIS (2.18) correctly.
The data is in hdf5(HDFEOS) format. QGIS/GDAL imports the data, but the image is rotated by 90° and shifted.
QGIS error: CRS ...
1
vote
0answers
116 views
Adding HDF data to a mosaic dataset
I am trying to add a couple of HDF rasters into a mosaic dataset, however no matter what I do I keep getting this error:
This is a screenshot of my inputs:
The raster processing and mosaic post-...
1
vote
0answers
685 views
Patch processing of multiple HDF5 files using Python and Gdal (gdalwarp)
I am trying to extend this process
http://geoinformaticstutorial.blogspot.com/2014/06/reading-and-map-projecting-amsr-2-data.html
wherein a set of raster data with separate geolocation arrays are ...
1
vote
0answers
225 views
Multiple HDF5 files in single GDAL virtual raster
Does anyone know how to generate a single GDAL virtual raster linking multiple HDF5 files to each other? Each file represents different swaths of the globe with different lat/lon coordinates and data ...
1
vote
1answer
2k views
How to open SMAP's Surface Moisture data files
I downloaded surface moisture data from Nasa's Soil Moisture Active Passive (SMAP) sensor website (https://nsidc.org/data/smap/smap-data.html).
For each processing level (1-4), three types of files ...
0
votes
1answer
91 views
Write to GDAL raster to HDF5
Is there a way to write a GDAL raster to a HDF4 or HDF5 dataset using GDAL? I have found many examples that show how to read HDF datasets, but none on how to write them.
0
votes
2answers
532 views
Concatenate/combine specific data from multiple HDF5 files into a single CSV file in Python(with code for converting single hdf file to csv file) [closed]
Suppose I have multiple HDF5 files in my E:\NASA directory and want to compile/concatenate the lat (path in HDF5: xxx.HDF5/XS/FLG/latitude), long (path in HDF5: xxx.HDF5/XS/FLG/longitude) and ...
0
votes
1answer
32 views
gdal_translate outputs coordinates in metres, but I need degrees
I wish to convert a HDF5 file into NetCDF, with the output NetCDF containing the selected band(s) and the latitudes and longitudes.
The data provider gives this info about the original file:
Table 2. ...
0
votes
1answer
258 views
Displaying hdf5 file at correct location? [closed]
I have downloaded the INSAT-K1 VHR INSOLATION PRODUCT (https://mosdac.gov.in/catalog/doi/36). This is satellite data in hdf5 format. When I display the raster in either ArcGIS or QGIS it appears at ...
0
votes
1answer
65 views
Correct projection for LAI Copernicus?
I download data from http://land.copernicus.eu/global/products/lai?qt-lai_characteristics=5 and when I visualize it in ArcGIS I set epsg 3857, but scale is wrong and measure show pixel with ...
0
votes
0answers
11 views
Check if a line shapefile is in side a raster in Python using GDAL? [closed]
I have an H5 file that including multiple storm tracks. I want to select the tracks across Haiti (which is my research area).
Is there any suggestion of how should I do this in Python?
Tracks data: H5 ...
0
votes
0answers
10 views
Extract HDF5 group name and apply it as a variable name using R
I'm new to using HDF5 files and need to extract information from several thousand such files, each with 6 groups of interest (e.g., ('/gt1l', '/gt1r', '/gt2l', '/gt2r', '/gt3l', '/gt3r'). I would ...
0
votes
0answers
7 views
How can I merge multiple .h5 files while I just want to extract one single band in output in Google Colab using gdal?
I have 366 .h5 files in a drive over Google Colab. I can read single .h5 file using 'gdalinfo'. But I have to extract only a same single layer (subdataset) from all of those .h5 files and extract as ...
0
votes
0answers
38 views
Mismatch between two methods projecting hdf5 using GDAL
I want to convert subdataset from h5 to tiff format and project the data with WGS84.
The product is https://www.geo.vu.nl/~gwerf/GFED/GFED4/ name is GFED4.1s_2010.hdf5 and the subdataset is sd39 ...
0
votes
0answers
15 views
spatially extract global hdf5 to subregion
I need to download some SMAP L4 soil moisture data from https://nsidc.org/data/SPL4SMAU/versions/4 .
The interface allows for spatial filtering to select a subregion of the global domain either by ...
0
votes
1answer
32 views
Determining Appropriate DBDB-V Subdataset
I am using DBDB-V v6.2 and GDAL, specifically the dbdbv6_level0c.h5 HDF5 file and the GDAL 2.3.3 C# binaries.
Using these lines of code I can easily find the full list of Subdatasets used in the ...
0
votes
1answer
631 views
Plotting and/or exporting VIIRS SDR DNB data as GeoTIFF in R?
I already asked this question @stackoverflow however, perhaps it fits better here, due to the spatial nature of VIIRS data and the hdf5-eos file format.
Im looking into how to handle .h5 (hdf-eos) ...
