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feat: add option to keep file object open #90

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May 9, 2024
Merged

feat: add option to keep file object open #90

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38 changes: 27 additions & 11 deletions icesat2_toolkit/io/ATL03.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@
h5py = import_dependency('h5py')

# PURPOSE: read ICESat-2 ATL03 HDF5 data files
def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
def read_granule(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL03 Global Geolocated Photons data files

Expand All @@ -59,6 +59,8 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
full path to ATL03 file
ATTRIBUTES: bool, default False
read file, group and variable attributes
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -270,12 +272,14 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
IS2_atl03_attrs[att_name] = att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
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):
def interpolate_ATL09(FILENAME, pfl, dtime,
ATTRIBUTES=True, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL09 Atmospheric Characteristics data files
and interpolates a subset of variables to ATL03 segment lengths
Expand All @@ -288,8 +292,10 @@ def interpolate_ATL09(FILENAME, pfl, dtime, ATTRIBUTES=True, **kwargs):
profile for a given beam
dtime: float
ATL03 reference photon delta_time
ATTRIBUTES: bool, default False
ATTRIBUTES: bool, default True
read file, group and variable attributes
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -349,12 +355,13 @@ def interpolate_ATL09(FILENAME, pfl, dtime, ATTRIBUTES=True, **kwargs):
IS2_atl09_attrs[att_name] = att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl09_mds, IS2_atl09_attrs)

# PURPOSE: find valid beam groups within ICESat-2 ATL03 HDF5 data files
def find_beams(FILENAME, **kwargs):
def find_beams(FILENAME, KEEP=False ,**kwargs):
"""
Find valid beam groups within ICESat-2 ATL03 Global Geolocated Photons
data files
Expand All @@ -363,6 +370,8 @@ def find_beams(FILENAME, **kwargs):
----------
FILENAME: str
full path to ATL03 file
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -391,12 +400,13 @@ def find_beams(FILENAME, **kwargs):
else:
IS2_atl03_beams.append(gtx)
# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# return the list of beams
return IS2_atl03_beams

# PURPOSE: read ICESat-2 ATL03 HDF5 data files for main level variables
def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
def read_main(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL03 Global Geolocated Photons data files
for only the main-level variables and not the beam-level data
Expand All @@ -407,6 +417,8 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
full path to ATL03 file
ATTRIBUTES: bool, default False
read file, group and variable attributes
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -558,12 +570,13 @@ def read_main(FILENAME, ATTRIBUTES=False, **kwargs):
IS2_atl03_attrs[att_name] = att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
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):
def read_beam(FILENAME, gtx, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL03 Global Geolocated Photons data files
for a specific beam
Expand All @@ -583,6 +596,8 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
- ``'gt3r'``
ATTRIBUTES: bool, default False
read file, group and variable attributes
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -666,6 +681,7 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
IS2_atl03_attrs['geophys_corr'][key][att_name]=att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl03_mds, IS2_atl03_attrs)
21 changes: 15 additions & 6 deletions icesat2_toolkit/io/ATL06.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@

# PURPOSE: read ICESat-2 ATL06 HDF5 data files
def read_granule(FILENAME, ATTRIBUTES=False, HISTOGRAM=False,
QUALITY=False, **kwargs):
QUALITY=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL06 (Land Ice Along-Track Height Product) data files

Expand All @@ -62,6 +62,8 @@ def read_granule(FILENAME, ATTRIBUTES=False, HISTOGRAM=False,
read ATL06 residual_histogram variables
QUALITY: bool, default False
read ATL06 segment_quality variables
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -266,12 +268,13 @@ def read_granule(FILENAME, ATTRIBUTES=False, HISTOGRAM=False,
IS2_atl06_attrs['quality_assessment'][key][k][att_name]= att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl06_mds, IS2_atl06_attrs, IS2_atl06_beams)

# PURPOSE: find valid beam groups within ICESat-2 ATL06 HDF5 data files
def find_beams(FILENAME, **kwargs):
def find_beams(FILENAME, KEEP=False, **kwargs):
"""
Find valid beam groups within ICESat-2 ATL06 (Land Ice Along-Track
Height Product) data files
Expand All @@ -280,6 +283,8 @@ def find_beams(FILENAME, **kwargs):
----------
FILENAME: str
full path to ATL06 file
KEEP: bool, default False
keep file object open

Returns
-------
Expand All @@ -306,12 +311,13 @@ def find_beams(FILENAME, **kwargs):
else:
IS2_atl06_beams.append(gtx)
# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# return the list of beams
return IS2_atl06_beams

# PURPOSE: read ICESat-2 ATL06 HDF5 data files for beam variables
def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
def read_beam(FILENAME, gtx, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL06 (Land Ice Along-Track Height Product) data files
for a specific beam
Expand All @@ -335,6 +341,8 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
read ATL06 residual_histogram variables
QUALITY: bool, default False
read ATL06 segment_quality variables
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -404,6 +412,7 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
IS2_atl06_attrs[gtx]['land_ice_segments'][key][k][att_name] = att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl06_mds, IS2_atl06_attrs)
21 changes: 15 additions & 6 deletions icesat2_toolkit/io/ATL07.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@
h5py = import_dependency('h5py')

# PURPOSE: read ICESat-2 ATL07 HDF5 data files
def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
def read_granule(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL07 (Sea Ice Height) data files

Expand All @@ -50,6 +50,8 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
full path to ATL07 file
ATTRIBUTES: bool, default False
read HDF5 attributes for groups and variables
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -210,19 +212,22 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
IS2_atl07_attrs['quality_assessment'][key][k][att_name]= att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl07_mds, IS2_atl07_attrs, IS2_atl07_beams)

# PURPOSE: find valid beam groups within ICESat-2 ATL07 HDF5 data files
def find_beams(FILENAME, **kwargs):
def find_beams(FILENAME, KEEP=False, **kwargs):
"""
Find valid beam groups within ICESat-2 ATL07 (Sea Ice Height) data files

Parameters
----------
FILENAME: str
full path to ATL07 file
KEEP: bool, default False
keep file object open

Returns
-------
Expand All @@ -249,12 +254,13 @@ def find_beams(FILENAME, **kwargs):
else:
IS2_atl07_beams.append(gtx)
# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# return the list of beams
return IS2_atl07_beams

# PURPOSE: read ICESat-2 ATL07 HDF5 data files for beam variables
def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
def read_beam(FILENAME, gtx, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL07 (Sea Ice Height) data files for a specific beam

Expand All @@ -273,6 +279,8 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
- ``'gt3r'``
ATTRIBUTES: bool, default False
read HDF5 attributes for groups and variables
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -340,6 +348,7 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
IS2_atl07_attrs[gtx]['sea_ice_segments'][key][k][att_name] = att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl07_mds, IS2_atl07_attrs)
21 changes: 15 additions & 6 deletions icesat2_toolkit/io/ATL10.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
h5py = import_dependency('h5py')

# PURPOSE: read ICESat-2 ATL10 HDF5 data files
def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
def read_granule(FILENAME, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL10 (Sea Ice Freeboard) data files

Expand All @@ -45,6 +45,8 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
full path to ATL10 file
ATTRIBUTES: bool, default False
read HDF5 attributes for groups and variables
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -208,19 +210,22 @@ def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):
IS2_atl10_attrs['quality_assessment'][key][k][att_name]= att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl10_mds, IS2_atl10_attrs, IS2_atl10_beams)

# PURPOSE: find valid beam groups within ICESat-2 ATL10 HDF5 data files
def find_beams(FILENAME, **kwargs):
def find_beams(FILENAME, KEEP=False, **kwargs):
"""
Find valid beam groups within ICESat-2 ATL10 (Sea Ice Freeboard) data files

Parameters
----------
FILENAME: str
full path to ATL10 file
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -248,12 +253,13 @@ def find_beams(FILENAME, **kwargs):
else:
IS2_atl10_beams.append(gtx)
# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# return the list of beams
return IS2_atl10_beams

# PURPOSE: read ICESat-2 ATL10 HDF5 data files for beam variables
def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
def read_beam(FILENAME, gtx, ATTRIBUTES=False, KEEP=False, **kwargs):
"""
Reads ICESat-2 ATL10 (Sea Ice Freeboard) data files for a specific beam

Expand All @@ -272,6 +278,8 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
- ``'gt3r'``
ATTRIBUTES: bool, default False
read HDF5 attributes for groups and variables
KEEP: bool, default False
keep file object open

Returns
-------
Expand Down Expand Up @@ -341,6 +349,7 @@ def read_beam(FILENAME, gtx, ATTRIBUTES=False, **kwargs):
IS2_atl10_attrs[gtx][group][key][k][att_name] = att_val

# Closing the HDF5 file
fileID.close()
if not KEEP:
fileID.close()
# Return the datasets and variables
return (IS2_atl10_mds, IS2_atl10_attrs)
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