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@shaunwbell
shaunwbell committed Nov 25, 2019
1 parent 09e29b3 commit 0a66271
Showing 1 changed file with 95 additions and 65 deletions.
160 changes: 95 additions & 65 deletions OnCruiseRoutines/CTD2NC.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,12 +33,12 @@
from CTD_Vis import ctd
from CTD_Vis import ncprocessing

__author__ = 'Shaun Bell'
__email__ = '[email protected]'
__created__ = datetime.datetime(2014, 01, 29)
__author__ = "Shaun Bell"
__email__ = "[email protected]"
__created__ = datetime.datetime(2014, 01, 29)
__modified__ = datetime.datetime(2014, 10, 13)
__version__ = "0.2.0"
__status__ = "Development"
__version__ = "0.2.0"
__status__ = "Development"

"""-------------------------------Work Flow--------------------------------------------"""
"""
Expand All @@ -50,20 +50,21 @@
"""
"""------------------------------- Data Pointer----------------------------------------"""

def data_processing(user_in, user_out, pressure_varname = 'prDM'):

def data_processing(user_in, user_out, pressure_varname="prDM"):
"""
Change pressure_var to prDM for
most 9/11 and prSM for sbe25 in following line or
prdM for sbe19pV2
"""
#add ability to ingest entire directory
# add ability to ingest entire directory
if os.path.isdir(user_in):
user_in = [user_in] + [fi for fi in os.listdir(user_in) if fi.endswith('.cnv')]
user_in = [user_in] + [fi for fi in os.listdir(user_in) if fi.endswith(".cnv")]

else:
user_in = user_in.split(',')
user_in = user_in.split(",")

for i, filein in enumerate(user_in):
if i == 0 and len(user_in) > 1:
Expand All @@ -73,34 +74,40 @@ def data_processing(user_in, user_out, pressure_varname = 'prDM'):
path = filein.strip()
else:
filein = path + filein.strip()
#read in .cnv file generate pandas dataframe... includes some preprocessing
#Todo: incorporate PMEL header information from cast logs (either as a '@' comment in the cnv file or from a separate text file)

# read in .cnv file generate pandas dataframe... includes some preprocessing
# Todo: incorporate PMEL header information from cast logs (either as a '@' comment in the cnv file or from a separate text file)
cast = ctd.from_cnv(filein, pressure_varname=pressure_varname)

timeclass = ctd.DataTimes(time_str=cast.time_str)
sfc_extend = 'Extrapolated to SFC from ' + str(cast.SFC_EXTEND) + 'm'
sfc_extend = "Extrapolated to SFC from " + str(cast.SFC_EXTEND) + "m"

# make sure save path exists
savefile=(user_out)
savefile = user_out
if not os.path.exists(savefile):
os.makedirs(savefile)

print "Working on Cast {cast_file}".format(cast_file=filein)

#PMEL EPIC Conventions
ncinstance = ncprocessing.CTD_NC(savefile=(savefile + cast.name.replace('_ctd', 'c') + '_ctd.nc'), data=cast)

# PMEL EPIC Conventions
ncinstance = ncprocessing.CTD_NC(
savefile=(savefile + cast.name.replace("_ctd", "c") + "_ctd.nc"), data=cast
)
ncinstance.file_create()
ncinstance.sbeglobal_atts() #
ncinstance.sbeglobal_atts() #
ncinstance.PMELglobal_atts(sfc_extend=sfc_extend)
ncinstance.dimension_init()
ncinstance.variable_init()
ncinstance.add_data()
ncinstance.add_coord_data(pressure_var=pressure_varname, time1=timeclass.get_EPIC_date()[0], time2=timeclass.get_EPIC_date()[1])
ncinstance.add_coord_data(
pressure_var=pressure_varname,
time1=timeclass.get_EPIC_date()[0],
time2=timeclass.get_EPIC_date()[1],
)
ncinstance.close()
#COARDS/CF Style Conventions
'''

# COARDS/CF Style Conventions
"""
ncinstance = ncprocessing.CF_CTD_NC(savefile=(savefile + cast.name.replace('_ctd', 'c') + '_cf_ctd.nc'), data=cast)
ncinstance.file_create()
ncinstance.sbeglobal_atts()
Expand All @@ -110,24 +117,25 @@ def data_processing(user_in, user_out, pressure_varname = 'prDM'):
ncinstance.add_data()
ncinstance.add_coord_data( time=timeclass.get_python_date() )
ncinstance.close()
'''
"""
processing_complete = True
return processing_complete

def IPHC_data_processing(user_in, user_out, pressure_varname = 'prdM'):

def IPHC_data_processing(user_in, user_out, pressure_varname="prdM"):
"""
Change pressure_var to prDM for
most 9/11 and prSM for sbe25 in following line or
prdM for sbe19pV2
"""
#add ability to ingest entire directory
# add ability to ingest entire directory
if os.path.isdir(user_in):
user_in = [user_in] + [fi for fi in os.listdir(user_in) if fi.endswith('.cnv')]
user_in = [user_in] + [fi for fi in os.listdir(user_in) if fi.endswith(".cnv")]

else:
user_in = user_in.split(',')
user_in = user_in.split(",")

for i, filein in enumerate(user_in):
if i == 0 and len(user_in) > 1:
Expand All @@ -137,19 +145,21 @@ def IPHC_data_processing(user_in, user_out, pressure_varname = 'prdM'):
path = filein.strip()
else:
filein = path + filein.strip()
#read in .cnv file generate pandas dataframe... includes some preprocessing
#Todo: incorporate PMEL header information from cast logs (either as a '@' comment in the cnv file or from a separate text file)

# read in .cnv file generate pandas dataframe... includes some preprocessing
# Todo: incorporate PMEL header information from cast logs (either as a '@' comment in the cnv file or from a separate text file)
cast = ctd.from_cnv(filein, pressure_varname=pressure_varname)
#tried subroutine in ctd.py but dataframe reassignment was odd
cast.drop(cast.index[cast['flag'] == True], inplace=True)

# tried subroutine in ctd.py but dataframe reassignment was odd
cast.drop(cast.index[cast["flag"] == True], inplace=True)

timeclass = ctd.DataTimes(time_str=cast.time_str)
sfc_extend = 'Extrapolated to SFC from ' + str(cast.SFC_EXTEND) + 'm'

#parse header files for '** ' lines which have IPHC relevant meta in them
sfc_extend = "Extrapolated to SFC from " + str(cast.SFC_EXTEND) + "m"

# parse header files for '** ' lines which have IPHC relevant meta in them

for entry in cast.header:
entry_lower = entry.lower()
"""* <![CDATA[
** latitude: 580104
** longitude: 1491283
Expand All @@ -160,21 +170,29 @@ def IPHC_data_processing(user_in, user_out, pressure_varname = 'prdM'):
** region: GP
** CSF bottom depth(m): 150
* ]]>"""
if ('** latitude:' in entry) or ('** Latitude:' in entry):
IPHC_Lat = float(entry.split()[-1][:2]) + float(entry.split()[-1][2:]) / 6000.
if ('** longitude:' in entry) or ('** Longitude:' in entry):
IPHC_Lon = -1 * (float(entry.split()[-1][:3]) + float(entry.split()[-1][3:]) / 6000. )
if ('** setno:' in entry) or ('** Setno:' in entry):
if ("** latitude:" in entry_lower) or ("** Latitude:" in entry_lower):
IPHC_Lat = (
float(entry.split()[-1][:2]) + float(entry.split()[-1][2:]) / 6000.0
)
if ("** longitude:" in entry_lower) or ("** Longitude:" in entry_lower):
IPHC_Lon = -1 * (
float(entry.split()[-1][:3]) + float(entry.split()[-1][3:]) / 6000.0
)
if ("** setno:" in entry_lower) or ("** Setno:" in entry_lower):
setno = entry.split()[-1]
if ('** stnno:' in entry) or ('** Stnno:' in entry):

if ("** stnno:" in entry_lower) or ("** Stnno:" in entry_lower):
stnno = entry.split()[-1]
if ('** trpno:' in entry) or ('** Trpno:' in entry):

if ("** trpno:" in entry_lower) or ("** Trpno:" in entry_lower):
trpno = entry.split()[-1]
if ('** vslcde:' in entry) | ('** vslcde' in entry):
if ("** vslcde:" in entry_lower) | ("** vslcde" in entry_lower):
vslcde = entry.split()[-1]
if '** region:' in entry:

if "** region:" in entry_lower:
region = entry.split()[-1]
if ('** CSF' in entry) or ('** csf' in entry):

if ("** CSF" in entry_lower) or ("** csf" in entry_lower):
CSFbottomdepth = float(entry.split()[-1])

print "IPHC Lat: {lat}".format(lat=IPHC_Lat)
Expand All @@ -184,35 +202,47 @@ def IPHC_data_processing(user_in, user_out, pressure_varname = 'prdM'):
print "IPHC TrpNo: {trpno}".format(trpno=trpno)
print "IPHC VSL CDE: {vslcde}".format(vslcde=vslcde)
print "IPHC Region: {region}".format(region=region)
print "IPHC CSF Bottom Depth: {CSFbottomdepth}".format(CSFbottomdepth=CSFbottomdepth)
print "IPHC CSF Bottom Depth: {CSFbottomdepth}".format(
CSFbottomdepth=CSFbottomdepth
)
# make sure save path exists
savefile=(user_out)
savefile = user_out
if not os.path.exists(savefile):
os.makedirs(savefile)

print "Working on Cast {cast_file}".format(cast_file=filein)

#PMEL EPIC Conventions
ncinstance = ncprocessing.CTD_IPHC(savefile=(savefile + filein.split('/')[-1].replace('.cnv', '.nc')), data=cast)

# PMEL EPIC Conventions
ncinstance = ncprocessing.CTD_IPHC(
savefile=(savefile + filein.split("/")[-1].replace(".cnv", ".nc")),
data=cast,
)
ncinstance.file_create()
ncinstance.sbeglobal_atts() #
ncinstance.IPHC_atts(vslcde=vslcde, setno=setno, stnno=stnno,
trpno=trpno, region=region)
ncinstance.sbeglobal_atts() #
ncinstance.IPHC_atts(
vslcde=vslcde, setno=setno, stnno=stnno, trpno=trpno, region=region
)
ncinstance.PMELglobal_atts(sfc_extend=sfc_extend, Water_Depth=CSFbottomdepth)
ncinstance.dimension_init()
ncinstance.variable_init()
ncinstance.add_data()
ncinstance.add_coord_data(pressure_var=pressure_varname,
time1=timeclass.get_EPIC_date()[0],
time2=timeclass.get_EPIC_date()[1],
latitude=IPHC_Lat, longitude=IPHC_Lon, CastLog=True)
ncinstance.add_coord_data(
pressure_var=pressure_varname,
time1=timeclass.get_EPIC_date()[0],
time2=timeclass.get_EPIC_date()[1],
latitude=IPHC_Lat,
longitude=IPHC_Lon,
CastLog=True,
)
ncinstance.close()

processing_complete = True
return processing_complete


if __name__ == '__main__':
if __name__ == "__main__":

user_in = raw_input("Please enter the abs path to the .cnv file: or \n path, file1, file2: ")
data_processing()
user_in = raw_input(
"Please enter the abs path to the .cnv file: or \n path, file1, file2: "
)
data_processing()

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