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fix: drop DIMENSION_LIST, CLASS and NAME attributes (#86)
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@tsutterley
tsutterley authored Nov 3, 2023
1 parent 6f1b9d8 commit 054fe62
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104 changes: 68 additions & 36 deletions icesat2_toolkit/io/ATL03.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python
u"""
ATL03.py (12/2022)
ATL03.py (11/2023)
Read ICESat-2 ATL03 and ATL09 data files to calculate average segment surfaces
ATL03 datasets: Global Geolocated Photons
ATL09 datasets: Atmospheric Characteristics
Expand All @@ -15,6 +15,7 @@
https://www.h5py.org/
UPDATE HISTORY:
Updated 11/2023: drop DIMENSION_LIST, CLASS and NAME attributes
Updated 12/2022: place some imports behind try/except statements
refactor ICESat-2 data product read programs under io
Updated 04/2022: updated docstrings to numpy documentation format
Expand Down Expand Up @@ -127,27 +128,32 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
IS2_atl03_attrs[gtx]['geophys_corr'] = {}
# Global Group Attributes
for att_name,att_val in fileID[gtx].attrs.items():
IS2_atl03_attrs[gtx][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[gtx][att_name] = att_val
# ICESat-2 Measurement Group
for key,val in fileID[gtx]['heights'].items():
IS2_atl03_attrs[gtx]['heights'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[gtx]['heights'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[gtx]['heights'][key][att_name]=att_val
# ICESat-2 Geolocation Group
for key,val in fileID[gtx]['geolocation'].items():
IS2_atl03_attrs[gtx]['geolocation'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[gtx]['geolocation'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[gtx]['geolocation'][key][att_name]=att_val
# ICESat-2 Background Photon Rate Group
for key,val in fileID[gtx]['bckgrd_atlas'].items():
IS2_atl03_attrs[gtx]['bckgrd_atlas'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[gtx]['bckgrd_atlas'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[gtx]['bckgrd_atlas'][key][att_name]=att_val
# ICESat-2 Geophysical Corrections Group
for key,val in fileID[gtx]['geophys_corr'].items():
IS2_atl03_attrs[gtx]['geophys_corr'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[gtx]['geophys_corr'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[gtx]['geophys_corr'][key][att_name]=att_val

# ICESat-2 spacecraft orientation at time
IS2_atl03_mds['orbit_info'] = {}
Expand All @@ -158,11 +164,13 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
if ATTRIBUTES:
# Global Group Attributes
for att_name,att_val in fileID['orbit_info'].attrs.items():
IS2_atl03_attrs['orbit_info'][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['orbit_info'][att_name] = att_val
# Variable Attributes
IS2_atl03_attrs['orbit_info'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['orbit_info'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['orbit_info'][key][att_name] = att_val

# information ancillary to the data product
# number of GPS seconds between the GPS epoch (1980-01-06T00:00:00Z UTC)
Expand All @@ -185,7 +193,8 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
# Variable Attributes
IS2_atl03_attrs['ancillary_data'][key] = {}
for att_name,att_val in fileID['ancillary_data'][key].attrs.items():
IS2_atl03_attrs['ancillary_data'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['ancillary_data'][key][att_name] = att_val

# transmit-echo-path (tep) parameters
IS2_atl03_mds['ancillary_data']['tep'] = {}
Expand All @@ -198,7 +207,8 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
# Variable Attributes
IS2_atl03_attrs['ancillary_data']['tep'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['ancillary_data']['tep'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['ancillary_data']['tep'][key][att_name] = att_val

# channel dead time and first photon bias derived from ATLAS calibration
cal1,cal2 = ('ancillary_data','calibrations')
Expand All @@ -218,12 +228,14 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
# Variable Attributes
IS2_atl03_attrs[cal1][var][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[cal1][var][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[cal1][var][key][att_name] = att_val
if isinstance(val, h5py.Group):
for k,v in val.items():
IS2_atl03_attrs[cal1][var][key][k] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[cal1][var][key][k][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[cal1][var][key][k][att_name]=att_val

# get ATLAS impulse response variables for the transmitter echo path (TEP)
tep1,tep2 = ('atlas_impulse_response','tep_histogram')
Expand All @@ -239,21 +251,24 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
if ATTRIBUTES:
# Global Group Attributes
for att_name,att_val in fileID[tep1][pce][tep2].attrs.items():
IS2_atl03_attrs[tep1][pce][tep2][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[tep1][pce][tep2][att_name] = att_val
# Variable Attributes
IS2_atl03_attrs[tep1][pce][tep2][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[tep1][pce][tep2][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[tep1][pce][tep2][key][att_name] = att_val

# Global File Attributes
if ATTRIBUTES:
for att_name,att_val in fileID.attrs.items():
IS2_atl03_attrs[att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[att_name] = att_val

# Closing the HDF5 file
fileID.close()
# Return the datasets and variables
return (IS2_atl03_mds,IS2_atl03_attrs,IS2_atl03_beams)
return (IS2_atl03_mds, IS2_atl03_attrs, IS2_atl03_beams)

# PURPOSE: read ICESat-2 ATL09 HDF5 data file for specific variables
def interpolate_ATL09(FILENAME, pfl, dtime, ATTRIBUTES=True, **kwargs):
Expand Down Expand Up @@ -311,22 +326,25 @@ def interpolate_ATL09(FILENAME, pfl, dtime, ATTRIBUTES=True, **kwargs):
IS2_atl09_attrs[pfl] = dict(high_rate={})
# Global Group Attributes
for att_name,att_val in fileID[pfl].attrs.items():
IS2_atl09_attrs[pfl][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl09_attrs[pfl][att_name] = att_val
# Variable Attributes
for key in high_rate_keys:
IS2_atl09_attrs[pfl]['high_rate'][key] = {}
for att_name,att_val in fileID[pfl]['high_rate'][key].attrs.items():
IS2_atl09_attrs[pfl]['high_rate'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl09_attrs[pfl]['high_rate'][key][att_name] = att_val

# Global File Attributes
if ATTRIBUTES:
for att_name,att_val in fileID.attrs.items():
IS2_atl09_attrs[att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl09_attrs[att_name] = att_val

# Closing the HDF5 file
fileID.close()
# Return the datasets and variables
return (IS2_atl09_mds,IS2_atl09_attrs)
return (IS2_atl09_mds, IS2_atl09_attrs)

# PURPOSE: find valid beam groups within ICESat-2 ATL03 HDF5 data files
def find_beams(FILENAME, **kwargs):
Expand Down Expand Up @@ -425,11 +443,13 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
if ATTRIBUTES:
# Global Group Attributes
for att_name,att_val in fileID['orbit_info'].attrs.items():
IS2_atl03_attrs['orbit_info'][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['orbit_info'][att_name] = att_val
# Variable Attributes
IS2_atl03_attrs['orbit_info'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['orbit_info'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['orbit_info'][key][att_name] = att_val

# information ancillary to the data product
# number of GPS seconds between the GPS epoch (1980-01-06T00:00:00Z UTC)
Expand All @@ -452,7 +472,8 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
# Variable Attributes
IS2_atl03_attrs['ancillary_data'][key] = {}
for att_name,att_val in fileID['ancillary_data'][key].attrs.items():
IS2_atl03_attrs['ancillary_data'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['ancillary_data'][key][att_name] = att_val

# transmit-echo-path (tep) parameters
IS2_atl03_mds['ancillary_data']['tep'] = {}
Expand All @@ -465,7 +486,8 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
# Variable Attributes
IS2_atl03_attrs['ancillary_data']['tep'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['ancillary_data']['tep'][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['ancillary_data']['tep'][key][att_name] = att_val

# channel dead time and first photon bias derived from ATLAS calibration
cal1,cal2 = ('ancillary_data','calibrations')
Expand All @@ -485,12 +507,14 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
# Variable Attributes
IS2_atl03_attrs[cal1][var][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[cal1][var][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[cal1][var][key][att_name] = att_val
if isinstance(val, h5py.Group):
for k,v in val.items():
IS2_atl03_attrs[cal1][var][key][k] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[cal1][var][key][k][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[cal1][var][key][k][att_name]=att_val

# get ATLAS impulse response variables for the transmitter echo path (TEP)
tep1,tep2 = ('atlas_impulse_response','tep_histogram')
Expand All @@ -506,21 +530,24 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
if ATTRIBUTES:
# Global Group Attributes
for att_name,att_val in fileID[tep1][pce][tep2].attrs.items():
IS2_atl03_attrs[tep1][pce][tep2][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[tep1][pce][tep2][att_name] = att_val
# Variable Attributes
IS2_atl03_attrs[tep1][pce][tep2][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs[tep1][pce][tep2][key][att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[tep1][pce][tep2][key][att_name] = att_val

# Global File Attributes
if ATTRIBUTES:
for att_name,att_val in fileID.attrs.items():
IS2_atl03_attrs[att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[att_name] = att_val

# Closing the HDF5 file
fileID.close()
# Return the datasets and variables
return (IS2_atl03_mds,IS2_atl03_attrs,IS2_atl03_beams)
return (IS2_atl03_mds, IS2_atl03_attrs, IS2_atl03_beams)

# PURPOSE: read ICESat-2 ATL03 HDF5 data files for beam variables
def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
Expand Down Expand Up @@ -595,29 +622,34 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
IS2_atl03_attrs['Atlas_impulse_response'] = {}
# Global Group Attributes
for att_name,att_val in fileID[gtx].attrs.items():
IS2_atl03_attrs[att_name] = att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs[att_name] = att_val
# ICESat-2 Measurement Group
for key,val in fileID[gtx]['heights'].items():
IS2_atl03_attrs['heights'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['heights'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['heights'][key][att_name]=att_val
# ICESat-2 Geolocation Group
for key,val in fileID[gtx]['geolocation'].items():
IS2_atl03_attrs['geolocation'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['geolocation'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['geolocation'][key][att_name]=att_val
# ICESat-2 Background Photon Rate Group
for key,val in fileID[gtx]['bckgrd_atlas'].items():
IS2_atl03_attrs['bckgrd_atlas'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['bckgrd_atlas'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['bckgrd_atlas'][key][att_name]=att_val
# ICESat-2 Geophysical Corrections Group
for key,val in fileID[gtx]['geophys_corr'].items():
IS2_atl03_attrs['geophys_corr'][key] = {}
for att_name,att_val in val.attrs.items():
IS2_atl03_attrs['geophys_corr'][key][att_name]=att_val
if att_name not in ('DIMENSION_LIST','CLASS','NAME'):
IS2_atl03_attrs['geophys_corr'][key][att_name]=att_val

# Closing the HDF5 file
fileID.close()
# Return the datasets and variables
return (IS2_atl03_mds,IS2_atl03_attrs)
return (IS2_atl03_mds, IS2_atl03_attrs)
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