Hi @tlohde,
While running region_a.order_granules(), I noticed a lot of lines like:
NSIDC returned these messages
['Granule 228833223 contained no data within the spatial and/or temporal '
'subset constraints to be processed',
'Granule 228825218 contained no data within the spatial and/or temporal '
'subset constraints to be processed',
...
which seems to indicate some data is missing. So I tried reading the ICESat-2 HDF5 files using datatree.open_datatree and it does look like some of the laser beams are missing, e.g. this one only has 2 (gt3l and gt3r) out of 6 beams:
import datatree
is2dt = datatree.open_datatree(
"icesat-2_data/processed_ATL06_20190108030055_01630205_005_01.h5",
engine="h5netcdf",
phony_dims="access",
)
print(is2dt)
DataTree('None', parent=None)
│ Dimensions: ()
│ Data variables:
│ *empty*
│ Attributes: (12/49)
│ Conventions: CF-1.6
│ Processing Parameters: This file was gernerated by the ICESa...
│ citation: Cite these data in publications as fo...
│ contributor_name: Thomas E Neumann (thomas.neumann@nasa...
│ contributor_role: Instrument Engineer, Investigator, Pr...
│ creator_name: GSFC I-SIPS > ICESat-2 Science Invest...
│ ... ...
│ summary: ATL06 provides estimates of the ice-s...
│ time_coverage_duration: 325.0
│ time_coverage_end: 2019-01-08T03:06:20.000000Z
│ time_coverage_start: 2019-01-08T03:00:55.000000Z
│ time_type: CCSDS UTC-A
│ title: ATLAS/ICESat-2 L3A Land Ice Height
├── DataTree('METADATA')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ Description: ISO19115 Structured Metadata Represented within HDF5
│ │ iso_19139_dataset_xml: <?xml version="1.0"?>\n<gmd:DS_Series xsi:schemaL...
│ │ iso_19139_series_xml: <?xml version="1.0" encoding="UTF-8"?>\n<gmd:DS_S...
│ ├── DataTree('AcquisitionInformation')
│ │ ├── DataTree('lidar')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: ATLAS on ICESat-2 determines the range between the satellit...
│ │ │ identifier: ATLAS
│ │ │ pulse_rate: 10000 pps
│ │ │ type: Laser Altimeter
│ │ │ wavelength: 532 nm
│ │ ├── DataTree('lidarDocument')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ edition: Pre-Release
│ │ │ publicationDate: 12/31/17
│ │ │ title: A document describing the ATLAS instrument will be prov...
│ │ ├── DataTree('platform')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: Ice, Cloud, and land Elevation Satellite-2
│ │ │ identifier: ICESat-2
│ │ │ type: Spacecraft
│ │ └── DataTree('platformDocument')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ edition: 31-Dec-16
│ │ publicationDate: 31-Dec-16
│ │ title: The Ice, Cloud, and land Elevation Satellite-2 (ICESat-...
│ ├── DataTree('DataQuality')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ scope: NOT_SET
│ │ ├── DataTree('CompletenessOmission')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ evaluationMethodType: directInternal
│ │ │ measureDescription: TBD
│ │ │ nameOfMeasure: TBD
│ │ │ unitofMeasure: TBD
│ │ │ value: NOT_SET
│ │ └── DataTree('DomainConsistency')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ evaluationMethodType: directInternal
│ │ measureDescription: TBD
│ │ nameOfMeasure: TBD
│ │ unitofMeasure: TBD
│ │ value: NOT_SET
│ ├── DataTree('DatasetIdentification')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes: (12/14)
│ │ VersionID: 005
│ │ abstract: ATL06 provides estimates of the ice-sheet me...
│ │ characterSet: utf8
│ │ creationDate: 2021-09-05T11:16:31.000000Z
│ │ credit: The software that generates the ATL06 produc...
│ │ fileName: ATL06_20190108030055_01630205_005_01.h5
│ │ ... ...
│ │ purpose: ATL06 provides estimates of the ice-sheet me...
│ │ shortName: ATL06
│ │ spatialRepresentationType: along-track
│ │ status: onGoing
│ │ topicCategory: geoscientificInformation
│ │ uuid: 6abf99e8-3be1-30e0-a623-28f0d12fc9b8
│ ├── DataTree('Extent')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ eastBoundLongitude: -41.329960843275046
│ │ northBoundLatitude: 80.00112360641836
│ │ rangeBeginningDateTime: 2019-01-08T03:00:54.862971Z
│ │ rangeEndingDateTime: 2019-01-08T03:05:36.716995Z
│ │ southBoundLatitude: 62.24122894734801
│ │ westBoundLongitude: -50.388809857370006
│ ├── DataTree('Lineage')
│ │ ├── DataTree('ANC06-01')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: MERIT 3 arcsec Digital Elevation Model reformatted into HDF...
│ │ │ fileName: merit_3as_20200617_001_01.h5
│ │ │ shortName: ANC06-01
│ │ │ uuid: 3db8ab65-d2ac-37c7-86db-17c762268673
│ │ │ version: 20200617
│ │ ├── DataTree('ANC06-02')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: ArcticDEM 32m Digital Elevation Model reformatted into HDF5.
│ │ │ fileName: arcticdem32m_20190611_001_01.h5
│ │ │ shortName: ANC06-02
│ │ │ uuid: ce07ef72-0bf4-353b-8475-fb568b029905
│ │ │ version: 20190611
│ │ ├── DataTree('ANC06-03')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: REMA Antarctica 100m Digital Elevation Model filled and ref...
│ │ │ fileName: atl06rema100m_20190628_001_01.h5
│ │ │ shortName: ANC06-03
│ │ │ uuid: 3e0a81bd-bbd5-35fa-b868-3254f9355b7f
│ │ │ version: 20190628
│ │ ├── DataTree('ANC17')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: Land Ice Height SNR Significance Table
│ │ │ fileName: anc17_snr_f_20170718_001_01.h5
│ │ │ shortName: ANC17
│ │ │ uuid: 52fe4165-bac0-3dc9-a9b3-921a591a7dc5
│ │ │ version: 20170718
│ │ ├── DataTree('ANC19')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: TAI to UTC leapsecond file retrieved from ftp://maia.usno.n...
│ │ │ fileName: tai_utc_2017.dat
│ │ │ shortName: ANC19
│ │ │ uuid: 7c66d365-278a-31f7-8fe4-9c80e2f012e5
│ │ │ version: 001
│ │ ├── DataTree('ANC25-06')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: HDF5 template file that defines the organization and defaul...
│ │ │ fileName: ANC25-06_20210831171721_045_01.h5
│ │ │ shortName: ANC25-06
│ │ │ uuid: d29cdb37-801e-3a00-a034-d20c51047ad6
│ │ │ version: 045
│ │ ├── DataTree('ANC26-06')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: HDF5 template file that defines the organization and defaul...
│ │ │ fileName: ANC26-06_20210831171731_045_01.h5
│ │ │ shortName: ANC26-06
│ │ │ uuid: 2093f4f5-2274-3520-8824-cae25668b08b
│ │ │ version: 045
│ │ ├── DataTree('ANC28')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: DTU Mean Sea Surface re-referenced to the WGS84 ellipsoid.
│ │ │ fileName: dtu13_20180705_001_01.nc
│ │ │ shortName: ANC28
│ │ │ uuid: 56f47040-a72e-3109-99c2-bc1658e6dda4
│ │ │ version: 20180705
│ │ ├── DataTree('ANC36-06')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: ISO 19139 XML file containing Series-level metadata informa...
│ │ │ fileName: ANC36-06_20210831170309_005_01.xml
│ │ │ shortName: ANC36-06
│ │ │ uuid: 7e1fe2fa-7a92-39a3-9f24-630dca51625a
│ │ │ version: 005
│ │ ├── DataTree('ANC38-06')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ description: ISO 19139 XML file containing DataSet-level metadata inform...
│ │ │ fileName: ANC38-06_20210831170314_005_01.xml
│ │ │ shortName: ANC38-06
│ │ │ uuid: f2325ab1-962d-3bf1-a1ef-7e66bdb9ffb3
│ │ │ version: 005
│ │ ├── DataTree('ATL03')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes: (12/15)
│ │ │ description: ICESat-2 ATLAS L2A Global Geolocated Photon data products.
│ │ │ end_cycle: 2
│ │ │ end_geoseg: 671084
│ │ │ end_orbit: 1751
│ │ │ end_region: 5
│ │ │ end_rgt: 163
│ │ │ ... ...
│ │ │ start_geoseg: 555757
│ │ │ start_orbit: 1751
│ │ │ start_region: 5
│ │ │ start_rgt: 163
│ │ │ uuid: 6050c1de-3d15-3ad2-9f5a-b7b6d56cef26
│ │ │ version: 005
│ │ ├── DataTree('ATL09')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes: (12/15)
│ │ │ description: ICESat-2 ATLAS L3A atmosphere data products.
│ │ │ end_cycle: 2
│ │ │ end_geoseg: 2007126
│ │ │ end_orbit: 1751
│ │ │ end_region: 14
│ │ │ end_rgt: 163
│ │ │ ... ...
│ │ │ start_geoseg: 12
│ │ │ start_orbit: 1751
│ │ │ start_region: 1
│ │ │ start_rgt: 163
│ │ │ uuid: 8672b328-3422-345d-b8b9-418830801f5d
│ │ │ version: 005
│ │ └── DataTree('Control')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ description: Text-based keyword=value file generated automatically withi...
│ │ fileName: CTL_atlas_l3a_is_007739532.ctl
│ │ shortName: CNTL
│ │ version: 1
│ ├── DataTree('ProcessStep')
│ │ ├── DataTree('Browse')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ identifier: atlas_brw
│ │ │ processDescription: Browse processing is performed for each granule SIPS...
│ │ │ runTimeParameters: CTL_atlas_l3a_is_007739532.ctl
│ │ │ softwareDate: Jul 28 2021
│ │ │ softwareTitle: Creates ATLAS HDF5 browse files
│ │ │ softwareVersion: Version 2.5
│ │ │ stepDateTime: 2021-09-05T11:19:48.000000Z
│ │ ├── DataTree('Metadata')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ identifier: atlas_meta
│ │ │ processDescription: Metadata information is processed by the metadata ut...
│ │ │ runTimeParameters: CTL_atlas_l3a_is_007739532.ctl
│ │ │ softwareDate: Jul 28 2021
│ │ │ softwareTitle: Creates ATLAS XML metadata files
│ │ │ softwareVersion: Version 4.5
│ │ │ stepDateTime: 2021-09-05T11:19:59.000000Z
│ │ ├── DataTree('PGE')
│ │ │ Dimensions: ()
│ │ │ Data variables:
│ │ │ *empty*
│ │ │ Attributes:
│ │ │ ATBDDate: 12/04/2019
│ │ │ ATBDTitle: Algorithm Theoretical Basis Document (ATBD) For Land...
│ │ │ ATBDVersion: N/A
│ │ │ documentDate: Feb 2020
│ │ │ documentation: ATLAS Science Algorithm Software Design Description ...
│ │ │ identifier: atlas_l3a_is
│ │ │ processDescription: Computes surface heights for each beam, along and ac...
│ │ │ runTimeParameters: CTL_atlas_l3a_is_007739532.ctl
│ │ │ softwareDate: Jul 28 2021
│ │ │ softwareTitle: ASAS L3A Icesheet PGE
│ │ │ softwareVersion: Version 4.5
│ │ │ stepDateTime: 2021-09-05T11:16:31.000000Z
│ │ └── DataTree('QA')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ identifier: atl06_qa_util
│ │ processDescription: QA processing is performed by an external utility on...
│ │ runTimeParameters: CTL_atlas_l3a_is_007739532.ctl
│ │ softwareDate: Jul 28 2021
│ │ softwareTitle: ATL06 QA Utility
│ │ softwareVersion: Version 4.5
│ │ stepDateTime: 2021-09-05T11:19:46.000000Z
│ ├── DataTree('ProductSpecificationDocument')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ ShortName: ATL06_SDP
│ │ characterSet: utf8
│ │ edition: v4.3
│ │ language: eng
│ │ publicationDate: Feb 2020
│ │ title: ICESat-2-SIPS-SPEC-4260 - ATLAS Science Algorithm Stand...
│ ├── DataTree('QADatasetIdentification')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ abstract: An ASCII product that contains statistical information on ...
│ │ creationDate: 2021-09-05T11:19:46.000000Z
│ │ fileName: ATL06_20190108030055_01630205_005_01.qa
│ └── DataTree('SeriesIdentification')
│ Dimensions: ()
│ Data variables:
│ *empty*
│ Attributes: (12/19)
│ VersionID: 005
│ abstract: ATL06 provides estimates of the ice-sh...
│ characterSet: utf8
│ credit: The software that generates the ATL06 ...
│ format: HDF
│ formatVersion: 5
│ ... ...
│ purpose: ATL06 provides estimates of the ice-sh...
│ resourceProviderOrganizationName: National Aeronautics and Space Adminis...
│ revisionDate: 2016-06-09
│ shortName: ATL06
│ status: onGoing
│ topicCategory: geoscientificInformation
├── DataTree('ancillary_data')
│ Dimensions: (phony_dim_0: 1)
│ Dimensions without coordinates: phony_dim_0
│ Data variables:
│ atlas_sdp_gps_epoch (phony_dim_0) datetime64[ns] ...
│ data_end_utc (phony_dim_0) |S27 ...
│ data_start_utc (phony_dim_0) |S27 ...
│ end_delta_time (phony_dim_0) datetime64[ns] ...
│ granule_end_utc (phony_dim_0) |S27 ...
│ granule_start_utc (phony_dim_0) |S27 ...
│ start_delta_time (phony_dim_0) datetime64[ns] ...
│ Attributes:
│ Description: Contains information ancillary to the data product. This ma...
│ data_rate: Data within this group pertain to the granule in its entirety.
├── DataTree('gt3l')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ Description: Contains subgroups organized by Ground Track (gt1l, ...
│ │ atlas_beam_type: strong
│ │ atlas_pce: pce3
│ │ atlas_spot_number: 5
│ │ atmosphere_profile: profile_3
│ │ groundtrack_id: gt3l
│ │ sc_orientation: Backward
│ └── DataTree('land_ice_segments')
│ Dimensions: (phony_dim_1: 1)
│ Dimensions without coordinates: phony_dim_1
│ Data variables:
│ h_li (phony_dim_1) float32 ...
│ latitude (phony_dim_1) float64 ...
│ longitude (phony_dim_1) float64 ...
│ Attributes:
│ Description: The land_ice_height group contains the primary set of deriv...
│ data_rate: Data within this group are sparse. Data values are provide...
├── DataTree('gt3r')
│ │ Dimensions: ()
│ │ Data variables:
│ │ *empty*
│ │ Attributes:
│ │ Description: Contains subgroups organized by Ground Track (gt1l, ...
│ │ atlas_beam_type: weak
│ │ atlas_pce: pce3
│ │ atlas_spot_number: 6
│ │ atmosphere_profile: profile_3
│ │ groundtrack_id: gt3r
│ │ sc_orientation: Backward
│ └── DataTree('land_ice_segments')
│ Dimensions: (phony_dim_2: 1)
│ Dimensions without coordinates: phony_dim_2
│ Data variables:
│ h_li (phony_dim_2) float32 ...
│ latitude (phony_dim_2) float64 ...
│ longitude (phony_dim_2) float64 ...
│ Attributes:
│ Description: The land_ice_height group contains the primary set of deriv...
│ data_rate: Data within this group are sparse. Data values are provide...
└── DataTree('orbit_info')
Dimensions: (sc_orient_time: 1)
Coordinates:
* sc_orient_time (sc_orient_time) datetime64[ns] 2019-01-07T23:30:00
Data variables:
sc_orient (sc_orient_time) int8 ...
Attributes:
Description: Contains data that are common among all beams for the granu...
data_rate: These parameters are constant for a given granule.
So to answer your questions:
You’re not necessarily doing anything wrong since the subsetter is doing its job (removing laser tracks that aren’t needed)? The unfortunate thing is that sometimes there are 2 lasers returned, sometimes 6, and the current icepyx reader can’t handle the inconsistency. Maybe using region_a.order_granules(subset=False) could allow you to keep all 6 laser tracks, but that’s a question for @JessicaS11 perhaps
Depends on how you want to combine them 
If you describe your scientific goal briefly (i.e. what you’re trying to do with the ICESat-2 elevation data), it’ll be easier for us to better advise on what’s the best way. At the moment, I can only guess that you you want to look at elevation change over time or something?