SNAP was updated last night on Windows 10 and today on Fedora 33 linux. Just “gpt -h” hangs on both systems.
There is an ongoing correction for this, a new minor version will be available.
I have same problem gpt execute never finishes (version 8.0.3)
I have the same issue in SNAP 8. I could get rid of the latest updates by cleaning the snap cache (delete .snap folder), right? But if I do so, other updates are also gone. Some of them I need (e.g. to download the precice orbit files in ApplyOrbitFile operator). So my question is: Is there an option that I select the updates which I would like to update, and deselect others or do I have to update always all available updates? Sorry to post it under that thread, but since it is related, I thought it might be OK.
Yes, you can select which updates you need in Tools -> Plugins -> Updates.
A complete cleaning of SNAP cache would mean cleaning:
C:\Users\[username]\.snap
C:\Users\[username]\AppData\Roaming\SNAP or C:\Users\[username]\AppData\Local\SNAP
C:\Users\[username]\AppData\Local\Temp\snap-[username]
(depending on what directories from the above listed ones you have)
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thanks. 
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I am having the same problem with gpt not exiting, on CentOS 7 after the recent S2TBX updates. I specifically updated to get rid of messages coming from org.esa.s2tbx.dataio.gdal.GDALInstaller when processing Back Geocoding, ESD, Coherence, etc. for Sentinel-1 data with S1TBX:
SEVERE: org.esa.s2tbx.dataio.gdal.GDALInstaller: Can't set execution permissions for executable /w2/SNAP_home/auxdata/gdal/gdal-3-0-0/share/proj/projjson.schema.json. If required, please ask an authorised user to make the file executable.
java.nio.file.FileSystemException: /w2/SNAP_home/auxdata/gdal/gdal-3-0-0/share/proj/projjson.schema.json: Operation not permitted
The GDAL modules from S2TBX are used when processing SAR with S1TBX. At one point many years ago this was apparent when after S2TBX install, SAR processing could no longer use compressed DEMs. Prior to S2TBX installation, with only S1TBX installed, we were able to use compressed DEMs.
This mostly worked for me, but I did have to restore my ~/.snap/auxdata/Orbits folder because I started having problems with applying orbit files. Thanks!
This GPT issue should be solved now by installing S2TBX 8.0.3 updates.
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software upgrade is work perfect!! thanks
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I have still met the same problem with SNAP(v9.0.0) and S2TBX (v9.0.0). What should I do in addition to updating s2tbx?
run_config.xml (1.9 KB)
Config ready; running: "E:\Program Files\snap\bin\gpt.exe" V:\01-Satellite-matchups\L02-ACPROCESSED\L02-NIGLAS\N15_15\\P65B201_赛里木湖\MSI\00_L1_SUBSET\run_config.xml
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.2 found on system. Internal GDAL 3.2.1 from distribution will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
Executing processing graph
INFO: org.esa.s2tbx.dataio.s2.ortho.S2OrthoProductReaderPlugIn: Building product reader - EPSG:32644
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [metadata_level] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [granuleidentifier] does not exist
WARNING: org.esa.snap.core.metadata.GenericXmlMetadata: Metadata: the path to element [bandid] does not exist
INFO: org.hsqldb.persist.Logger: dataFileCache open start
18%36%54%72%....82%...57544 [main] INFO serverStartup - Nc4Iosp: NetCDF-4 C library loaded (jna_path='C:\Users\optics\.snap\auxdata\netcdf_natives\9.0.1\amd64', libname='netcdf').
57549 [main] INFO serverStartup - NetcdfLoader: set log level: old=0 new=0
57549 [main] INFO serverStartup - Nc4Iosp: set log level: old=0 new=0
107% done.
INFO: org.hsqldb.persist.Logger: Database closed
Hello,
This was solved since S2TBX 8.0.3 and not reported since. Therefore maybe you have some old remainings there.
Close SNAP and try also a complete clean, see locations indicated above:
If it still does not work, fresh install with the option “delete all previous SNAP data”.
Hello, many thanks for your reply. However, I have tried both a complete cleaning of the SNAP cache and a fresh install with the option “delete all previous SNAP data”. It still does not work:sob:
Then, that’s not the reason.
What are you trying to run with gpt?
I run the gpt to resample and subset for a series of MSI data.
Some things you can try, just out of curiosity:
1/ try to run the same graph that you run with gpt, in Graph Builder
2/ what happens if you run “gpt -h” from a command line?
First, I confirmed that I ran gpt to successfully get a subset image that could be opened with SNAP and composited into RGB.
Then, I did the two operations you mentioned above:
1/ try to run the same graph that you run with gpt, in Graph Builder.
If I load the graph directly and click run, it returns an error: null.
I need to re-type the resample and subset parameters. The progress bar quickly reaches 100%, but the task is not completed, and the text above the progress bar shows “computing raster data”. And it runs successfully after ~10 min. But the file size of the output in Graph Builder was a light larger (maybe some difference in the parameters settings of resample ).
2/ After running “gpt -h”, it returns as follows.
PS C:\Users\optics> gpt -h
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Incompatible GDAL 3.4.2 found on system. Internal GDAL 3.2.1 from distribution will be used.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.
INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Internal GDAL 3.2.1 set to be used by SNAP.
Usage:
gpt <op>|<graph-file> [options] [<source-file-1> <source-file-2> ...]
Description:
This tool is used to execute SNAP raster data operators in batch-mode. The
operators can be used stand-alone or combined as a directed acyclic graph
(DAG). Processing graphs are represented using XML. More info about
processing graphs, the operator API, and the graph XML format can be found
in the SNAP documentation.
Arguments:
<op> Name of an operator. See below for the list of <op>s.
<graph-file> Operator graph file (XML format).
<source-file-i> The <i>th source product file. The actual number of source
file arguments is specified by <op>. May be optional for
operators which use the -S option.
Options:
-h Displays command usage. If <op> is given, the specific
operator usage is displayed.
-e Displays more detailed error messages. Displays a stack
trace, if an exception occurs.
-t <file> The target file. Default value is 'target.dim'.
-f <format> Output file format, e.g. 'GeoTIFF', 'HDF5',
'BEAM-DIMAP'. If not specified, format will be derived
from the target filename extension, if any, otherwise the
default format is 'BEAM-DIMAP'. Ony used, if the graph
in <graph-file> does not specify its own 'Write'
operator.
-p <file> A (Java Properties) file containing processing parameters
in the form <name>=<value> or a XML file containing a
parameter DOM for the operator. Entries in this file are
overwritten by the -P<name>=<value> command-line option
(see below). The following variables are substituted in
the parameters file:
${system.<java-sys-property>}
${operatorName} (given by the <op> argument)
${graphFile} (given by the <graph-file> argument)
${targetFile} (pull path given by the -t option)
${targetDir} (derived from -t option)
${targetName} (derived from -t option)
${targetBaseName} (derived from -t option)
${targetFormat} (given by the -f option)
-c <cache-size> Sets the tile cache size in bytes. Value can be suffixed
with 'K', 'M' and 'G'. Must be less than maximum
available heap space. If equal to or less than zero, tile
caching will be completely disabled. The default tile
cache size is '1,073,741,824M'.
-q <parallelism> Sets the maximum parallelism used for the computation,
i.e. the maximum number of parallel (native) threads.
The default parallelism is '12'.
-x Clears the internal tile cache after writing a complete
row of tiles to the target product file. This option may
be useful if you run into memory problems.
-S<source>=<file> Defines a source product. <source> is specified by the
operator or the graph. In an XML graph, all occurrences of
${<source>} will be replaced with references to a source
product located at <file>.
-P<name>=<value> Defines a processing parameter, <name> is specific for the
used operator or graph. In an XML graph, all occurrences
of ${<name>} will be replaced with <value>. Overwrites
parameter values specified by the '-p' option.
-D<name>=<value> Defines a system property for this invocation.
-v <dir> A directory containing any number of Velocity templates.
Each template generates a text output file along with the
target product. This feature has been added to support a
flexible generation of metadata files.
See http://velocity.apache.org/ and option -m.
-m <file> A (Java Properties) file containing (constant) metadata
in the form <name>=<value> or any XML file. Its primary
usage is to provide an additional context to be used
from within the Velocity templates. See option -v.
--diag Displays version and diagnostic information.
Operators:
Aatsr.SST Computes sea surface temperature (SST) from (A)ATSR products.
AATSR.Ungrid Ungrids (A)ATSR L1B products and extracts geolocation and pixel field of view data.
AdaptiveThresholding Detect ships using Constant False Alarm Rate detector.
AddElevation Creates a DEM band
AddLandCover Creates a land cover band
ALOS-Deskewing Deskewing ALOS product
Apply-Orbit-File Apply orbit file
Arc.SST Computes sea surface temperature (SST) from (A)ATSR and SLSTR products.
ArviOp Atmospherically Resistant Vegetation Index belongs to a family of indices with built-in atmospheric corrections.
Azimuth-Shift-Estimation-ESD Estimate azimuth offset for the whole image
AzimuthFilter Azimuth Filter
Back-Geocoding Bursts co-registration using orbit and DEM
BandMaths Create a product with one or more bands using mathematical expressions.
BandMerge Allows copying raster data from any number of source products to a specified 'master' product.
BandPassFilter Creates a basebanded SLC based on a subband of 1/3 the original bandwidth
BandsDifferenceOp No description available.
BandSelect Creates a new product with only selected bands
BandsExtractorOp Creates a new product out of the source product containing only the indexes bands given
Bi2Op The Brightness index represents the average of the brightness of a satellite image.
This index is sensitive to the brightness of soils which is highly correlated with the humidity and the presence of salts in surface
Binning Performs spatial and temporal aggregation of pixel values into cells ('bins') of a planetary grid
BiOp The Brightness index represents the average of the brightness of a satellite image.
Biophysical10mOp The 'Biophysical Processor' operator retrieves LAI from atmospherically corrected Sentinel-2 products
BiophysicalLandsat8Op The 'Biophysical Processor' operator retrieves LAI from atmospherically corrected Landsat8 products
BiophysicalOp The 'Biophysical Processor' operator retrieves LAI from atmospherically corrected Sentinel-2 products
c2rcc.landsat8 Performs atmospheric correction and IOP retrieval with uncertainties on Landsat-8 L1 data products.
c2rcc.meris Performs atmospheric correction and IOP retrieval with uncertainties on MERIS L1b data products.
c2rcc.meris4 Performs atmospheric correction and IOP retrieval with uncertainties on MERIS L1b data products from the 4th reprocessing.
c2rcc.modis Performs atmospheric correction and IOP retrieval on MODIS L1C_LAC data products.
c2rcc.msi Performs atmospheric correction and IOP retrieval with uncertainties on Sentinel-2 MSI L1C data products.
c2rcc.olci Performs atmospheric correction and IOP retrieval with uncertainties on SENTINEL-3 OLCI L1B data products.
c2rcc.seawifs Performs atmospheric correction and IOP retrieval on SeaWifs L1C data products.
c2rcc.viirs Performs atmospheric correction and IOP retrieval on Viirs L1C data products.
Calibration Calibration of products
Change-Detection Change Detection.
ChangeVectorAnalysisOp The 'Change Vector Analysis' between two dual bands at two differents dates.
CiOp Colour Index was developed to differentiate soils in the field.
In most cases the CI gives complementary information with the BI and the NDVI.
Used for diachronic analyses, they help for a better understanding of the evolution of soil surfaces.
CloudProb Applies a clear sky conservative cloud detection algorithm.
Coherence Estimate coherence from stack of coregistered images
Collocate Collocates two products based on their geo-codings.
Compactpol-Radar-Vegetation-Index Compact-pol Radar Vegetation Indices generation
Compute-Slope-Aspect Compute Slope and Aspect from DEM
Convert-Datatype Convert product data type
CoregistrationOp Coregisters two rasters, not considering their location
CP-Decomposition Perform Compact Polarimetric decomposition of a given product
CP-Simulation Simulation of Compact Pol data from Quad Pol data
CP-Stokes-Parameters Generates compact polarimetric Stokes child parameters
CreateStack Collocates two or more products based on their geo-codings.
Cross-Channel-SNR-Correction Compute general polarimetric parameters
Cross-Correlation Automatic Selection of Ground Control Points
CrossResampling Estimate Resampling Polynomial using SAR Image Geometry, and Resample Input Images
DarkObjectSubtraction Performs dark object subtraction for spectral bands in source product.
DeburstWSS Debursts an ASAR WSS product
DecisionTree Perform decision tree classification
DEM-Assisted-Coregistration Orbit and DEM based co-registration
Demodulate Demodulation and deramping of SLC data
Double-Difference-Interferogram Compute double difference interferogram
DviOp Difference Vegetation Index retrieves the Isovegetation lines parallel to soil line
EAP-Phase-Correction EAP Phase Correction
Ellipsoid-Correction-GG GG method for orthorectification
Ellipsoid-Correction-RD Ellipsoid correction with RD method and average scene height
EMClusterAnalysis Performs an expectation-maximization (EM) cluster analysis.
Enhanced-Spectral-Diversity Estimate constant range and azimuth offsets for a stack of images
Faraday-Rotation-Correction Perform Faraday-rotation correction for quad-pol product
Fill-DEM-Hole Fill holes in given DEM product file.
FlhMci Computes fluorescence line height (FLH) or maximum chlorophyll index (MCI).
Flip flips a product horizontal/vertical
ForestCoverChangeOp Creates forest change masks out of two source products
FUB.Water MERIS FUB-CSIRO Coastal Water Processor to retrieve case II water properties and atmospheric properties
FuClassification Colour classification based on the discrete Forel-Ule scale
GemiOp This retrieves the Global Environmental Monitoring Index (GEMI).
Generalized-Radar-Vegetation-Index Generalized Radar Vegetation Indices generation
GenericRegionMergingOp The 'Generic Region Merging' operator computes the distinct regions from a product
GLCM Extract Texture Features
GndviOp Green Normalized Difference Vegetation Index
GoldsteinPhaseFiltering Phase Filtering
GRD-Post Applies GRD post-processing
HorizontalVerticalMotion Computation of Horizontal/Vertical Motion Components
IEM-Hybrid-Inversion Performs IEM inversion using Hybrid approach
IEM-Multi-Angle-Inversion Performs IEM inversion using Multi-angle approach
IEM-Multi-Pol-Inversion Performs IEM inversion using Multi-polarization approach
Image-Filter Common Image Processing Filters
Import-Vector Imports a shape file into a product
IntegerInterferogram Create integer interferogram
Interferogram Compute interferograms from stack of coregistered S-1 images
IonosphericCorrection Estimation of Ionospheric Phase Screens
IpviOp Infrared Percentage Vegetation Index retrieves the Isovegetation lines converge at origin
IreciOp Inverted red-edge chlorophyll index
KDTree-KNN-Classifier KDTree KNN classifier
KMeansClusterAnalysis Performs a K-Means cluster analysis.
KNN-Classifier K-Nearest Neighbour classifier
Land-Cover-Mask Perform decision tree classification
Land-Sea-Mask Creates a bitmask defining land vs ocean.
LandWaterMask Operator creating a target product with a single band containing a land/water-mask.
LinearToFromdB Converts bands to/from dB
Maximum-Likelihood-Classifier Maximum Likelihood classifier
McariOp Modified Chlorophyll Absorption Ratio Index, developed to be responsive to chlorophyll variation
Mci.s2 Computes maximum chlorophyll index (MCI) for Sentinel-2 MSI.
Merge Allows merging of several source products by using specified 'master' as reference product.
Meris.Adapt.4To3 Provides the adaptation of MERIS L1b products from 4th to 3rd reprocessing.
Meris.CorrectRadiometry Performs radiometric corrections on MERIS L1b data products.
Meris.N1Patcher Copies an existing N1 file and replaces the data for the radiance bands
Minimum-Distance-Classifier Minimum Distance classifier
MndwiOp Modified Normalized Difference Water Index, allowing for the measurement of surface water extent
Mosaic Creates a mosaic out of a set of source products.
MphChl This operator computes maximum peak height of chlorophyll (MPH/CHL).
Msavi2Op This retrieves the second Modified Soil Adjusted Vegetation Index (MSAVI2).
MsaviOp This retrieves the Modified Soil Adjusted Vegetation Index (MSAVI).
MtciOp The Meris Terrestrial Chlorophyll Index, aims at estimating the Red Edge Position (REP).
This is the maximum slant point in the red and near-infrared region of the vegetal spectral reflectance.
It is useful for observing the chlorophyll contents, vegetation senescence, and stress for water and nutritional deficiencies, but it is less suitable for land classification
Multi-size Mosaic Creates a multi-size mosaic out of a set of source products.
Multi-Temporal-Speckle-Filter Speckle Reduction using Multitemporal Filtering
Multilook Averages the power across a number of lines in both the azimuth and range directions
MultiMasterInSAR Multi-master InSAR processing
MultiMasterStackGenerator Generates a set of master-slave pairs from a coregistered stack for use in SBAS processing
Multitemporal-Compositing Compute composite image from multi-temporal RTCs
Ndi45Op Normalized Difference Index using bands 4 and 5
NdpiOp The normalized differential pond index, combines the short-wave infrared band-I and the green band
NdtiOp Normalized difference turbidity index, allowing for the measurement of water turbidity
NdviOp The retrieves the Normalized Difference Vegetation Index (NDVI).
Ndwi2Op The Normalized Difference Water Index, allowing for the measurement of surface water extent
NdwiOp The Normalized Difference Water Index was developed for the extraction of water features
Object-Discrimination Remove false alarms from the detected objects.
Offset-Tracking Create velocity vectors from offset tracking
Oil-Spill-Clustering Remove small clusters from detected area.
Oil-Spill-Detection Detect oil spill.
OlciAnomalyFlagging Adds a flagging band indicating saturated pixels and altitude data overflows
OlciO2aHarmonisation Performs O2A band harmonisation on OLCI L1b product. Implements update v4 of R.Preusker, June 2020.
OlciSensorHarmonisation Performs sensor harmonisation on OLCI L1b product. Implements algorithm described in 'OLCI A/B Tandem Phase Analysis'
Orientation-Angle-Correction Perform polarization orientation angle correction for given coherency matrix
Oversample Oversample the datset
OWTClassification Performs an optical water type classification based on atmospherically corrected reflectances.
PCA Performs a Principal Component Analysis.
PduStitching Stitches multiple SLSTR L1B product dissemination units (PDUs) of the same orbit to a single product.
PhaseToDisplacement Phase To Displacement Conversion along LOS
PhaseToElevation DEM Generation
PhaseToHeight Phase to Height conversion
PixEx Extracts pixels from given locations and source products.
Polarimetric-Classification Perform Polarimetric classification of a given product
Polarimetric-Decomposition Perform Polarimetric decomposition of a given product
Polarimetric-Matrices Generates covariance or coherency matrix for given product
Polarimetric-Parameters Compute general polarimetric parameters
Polarimetric-Speckle-Filter Polarimetric Speckle Reduction
PpeFiltering Performs Prompt Particle Event (PPE) filtering on OLCI L1B
Principle-Components Principle Component Analysis
ProductSet-Reader Adds a list of sources
PssraOp Pigment Specific Simple Ratio, chlorophyll index
PviOp Perpendicular Vegetation Index retrieves the Isovegetation lines parallel to soil line. Soil line has an arbitrary slope and passes through origin
Rad2Refl Provides conversion from radiances to reflectances or backwards.
Radar-Vegetation-Index Dual-pol Radar Vegetation Indices generation
Random-Forest-Classifier Random Forest based classifier
RangeFilter Range Filter
RayleighCorrection Performs radiometric corrections on OLCI, MERIS L1B and S2 MSI L1C data products.
Read Reads a data product from a given file location.
ReflectanceToRadianceOp The 'Reflectance To Radiance Processor' operator retrieves the radiance from reflectance using Sentinel-2 products
ReipOp The red edge inflection point index
Remodulate Remodulation and reramping of SLC data
RemoteExecutionOp The Remote Execution Processor executes on the remote machines a slave graph and then on the host machine it executes a master graph using the products created by the remote machines.
Remove-GRD-Border-Noise Mask no-value pixels for GRD product
RemoveAntennaPattern Remove Antenna Pattern
ReplaceMetadata Replace the metadata of the first product with that of the second
Reproject Reprojection of a source product to a target Coordinate Reference System.
Resample Resampling of a multi-size source product to a single-size target product.
RiOp The Redness Index was developed to identify soil colour variations.
RviOp Ratio Vegetation Index retrieves the Isovegetation lines converge at origin
S2repOp Sentinel-2 red-edge position index
S2Resampling Specific S2 resample algorithm
SAR-Mosaic Mosaics two or more products based on their geo-codings.
SAR-Simulation Rigorous SAR Simulation
SARSim-Terrain-Correction Orthorectification with SAR simulation
SaviOp This retrieves the Soil-Adjusted Vegetation Index (SAVI).
SetNoDataValue Set NoDataValueUsed flag and NoDataValue for all bands
SliceAssembly Merges Sentinel-1 slice products
SM-Dielectric-Modeling Performs SM inversion using dielectric model
SmacOp Applies the Simplified Method for Atmospheric Corrections of Envisat MERIS/(A)ATSR measurements.
SnaphuExport Export data and prepare conf file for SNAPHU processing
SnaphuImport Ingest SNAPHU results into InSAR product.
Speckle-Divergence Detect urban area.
Speckle-Filter Speckle Reduction
SpectralAngleMapperOp Classifies a product using the spectral angle mapper algorithm
SRGR Converts Slant Range to Ground Range
Stack-Averaging Averaging multi-temporal images
Stack-Split Writes all bands to files.
StampsExport Export data for StaMPS processing
StatisticsOp Computes statistics for an arbitrary number of source products.
SubGraph Encapsulates a graph within a graph.
Subset Create a spatial and/or spectral subset of a data product.
Supervised-Wishart-Classification Perform supervised Wishart classification
TemporalPercentile Computes percentiles over a given time period.
Terrain-Correction RD method for orthorectification
Terrain-Flattening Terrain Flattening
Terrain-Mask Terrain Mask Generation
ThermalNoiseRemoval Removes thermal noise from products
Three-passDInSAR Differential Interferometry
TileCache Experimental Operator which provides a dedicated cache for its source product.
A guide on how this operator is used is provided at https://senbox.atlassian.net/wiki/x/VQCTLw.
TileWriter Writes a data product to a tiles.
TndviOp Transformed Normalized Difference Vegetation Index retrieves the Isovegetation lines parallel to soil line
ToolAdapterOp Tool Adapter Operator
TopoPhaseRemoval Compute and subtract TOPO phase
TOPSAR-Deburst Debursts a Sentinel-1 TOPSAR product
TOPSAR-DerampDemod Bursts co-registration using orbit and DEM
TOPSAR-Merge Merge subswaths of a Sentinel-1 TOPSAR product
TOPSAR-Split Creates a new product with only the selected subswath
TsaviOp This retrieves the Transformed Soil Adjusted Vegetation Index (TSAVI).
Undersample Undersample the datset
Unmix Performs a linear spectral unmixing.
Update-Geo-Reference Update Geo Reference
Warp Create Warp Function And Get Co-registrated Images
WdviOp Weighted Difference Vegetation Index retrieves the Isovegetation lines parallel to soil line. Soil line has an arbitrary slope and passes through origin
Wind-Field-Estimation Estimate wind speed and direction
Write Writes a data product to a file.
For the “gpt -h” I was curious if, at the end, the prompter “C:\Users\optics>” appears or not, in order to figure out if a simple gpt command finishes.
Yes, it appears at the end.