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.

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Cannot use PROJ4 with gdal.Translate in Python

I'm trying to convert MCD12Q1 HDF5 product to GeoTiff. I extracted metadata from the file, and from this user guide I found the projection information as PROJ4: '+proj=sinu +a=6371007.181 +b=6371007....
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How to georeference HDF5 file with missing or wrong metadata

I'm trying to access data in a HDF5 file. I can access the data itself but the metadata, in particular the information to georeference the information, is still a problem. I had partial success in ...
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Storing NDVI values from MODIS datasets in variables in R

There is a MODIS dataset called MCD14ML (collection 5), which contains some information about observed hotspots. In particular, I'm working with a subset of the dataset that is concerned with hotspots ...
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How to properly convert HDF5 file with 3K+ GCPs?

I am trying to create a GeoTiff from NOAA's Global RTOFS files for sea surface temperature, which have over 3000 GCPs, and any attempts at conversion using GDAL have resulted in slightly distorted ...
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1answer
158 views

How to convert from HDF5 to GeoTIFF with Python

I'm coming from Reading metadata in HDF5 file. I have a HDF5 file with some radar information. I'd like to read this data and geospatial metadata contained in the file to produce a GeoTIFF. Using the ...
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1answer
400 views

Reading metadata in HDF5 file

I have a HDF5 file with a field of radar observations. I'd like to read this data and produce a GeoTiff that contains the spatial metadata. I can access the data, but I can't access the geographical ...
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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 ...
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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 ...
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1answer
254 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 ...
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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 ...
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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/...
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1answer
114 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. ...
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1answer
233 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.
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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 ...
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2answers
132 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 ...
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1answer
51 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 ...
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2answers
926 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 ...
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1answer
296 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 ...
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1answer
42 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 ...
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1answer
452 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 ...
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2answers
484 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 ...
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1answer
342 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 ...
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1answer
748 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) ...
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1answer
6k 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 ...
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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 ...
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1answer
703 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 ...
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0answers
125 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-...
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1answer
67 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 ...
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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 ...
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2answers
2k 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 ...
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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, ...
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734 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 ...
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0answers
5k 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 ...
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0answers
253 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 ...
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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 -...
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2answers
197 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 ...
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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 ...
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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. ...
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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, ...