def getFileHistory(filePath):
# Call getGitInfo
versionInfo = getGitInfo(filePath)
if versionInfo == None:
return None
else:
# print results
#for count in range(0,len(versionInfo)):
# print count,versionInfo[count]
version_metadata = {}
version_metadata['author'] = versionInfo[4].replace('author: ','')
version_metadata['creation_date'] = versionInfo[3].replace('date: ','')
version_metadata['institution_id'] = 'PCMDI'
version_metadata['latest_tag_point'] = versionInfo[2].replace('latest_tagPoint: ','')
version_metadata['note'] = versionInfo[1].replace('note: ','')
version_metadata['previous_commit'] = versionInfo[0].replace('commit: ','')
#print version_metadata
return version_metadata
def getFileHistory(filePath):
# Call getGitInfo
versionInfo = getGitInfo(filePath)
if versionInfo == None:
return None
else:
# print results
#for count in range(0,len(versionInfo)):
# print count,versionInfo[count]
version_metadata = {}
version_metadata['author'] = versionInfo[4].replace('author: ','')
version_metadata['creation_date'] = versionInfo[3].replace('date: ','')
version_metadata['institution_id'] = 'PCMDI'
version_metadata['latest_tag_point'] = versionInfo[2].replace('latest_tagPoint: ','')
version_metadata['note'] = versionInfo[1].replace('note: ','')
version_metadata['previous_commit'] = versionInfo[0].replace('commit: ','')
#print version_metadata
return version_metadata
def makeSteric(salinity,salinityChg,temp,tempChg,outFileName,thetao,pressure):
"""
The makeSteric() function takes 3D (not temporal) arguments and creates
heat content and steric fields which are written to a specified outfile
Author: Paul J. Durack : [email protected] : @durack1.
Created on Thu Jul 18 13:03:37 2013.
Inputs:
------
- salinity(lev,lat,lon) - 3D array for the climatological period.
- salinityChg(lev,lat,lon) - 3D array for the temporal change period.
- temp(lev,lat,lon) - 3D array for the climatological period either in-situ or potential temperature.
- tempChg(lev,lat,lon) - 3D array for the temporal change period as with temp, either in-situ or potential temperature.
- outFileName(str) - output filename with full path specified.
- thetao(bool) - boolean value specifying either in-situ or potential temperature arrays provided.
- pressure(bool) - boolean value specifying whether lev-coordinate is pressure (dbar) or depth (m).
Usage:
------
>>> from makeStericLib import makeSteric
>>> makeSteric(salinity,salinityChg,thetao,thetaoChg,'outfile.nc',True,False)
Notes:
-----
- PJD 18 Jul 2013 - Validated Ishii v6.13 data against WOA94 - checks out ok. Units: dyn decimeter compared to http://www.nodc.noaa.gov/OC5/WOA94/dyn.html uses cm (not decimeter; x 10)
- PJD 18 Jul 2013 - Added attribute scrub to incoming variables (so,so_chg,temp,temp_chg) to maintain output consistency
- PJD 22 Jul 2013 - Added name attributes to so and temp variables, added units to so_chg
- PJD 22 Jul 2013 - removed duplicated code by converting repetition to function scrubNaNAndMask
- PJD 23 Jul 2013 - Further cleaned up so,so_chg,temp,temp_chg outputs specifying id/name attributes
- PJD 5 Aug 2013 - Updated python-seawater library to version 3.3.1 from github repo, git clone http://github.com/ocefpaf/python-seawater, python setup.py install --user
- PJD 7 Aug 2013 - FIXED: thetao rather than in-situ temperature propagating throughout calculations
- PJD 7 Aug 2013 - Replaced looping with 3D gpan
- PJD 7 Aug 2013 - Further code duplication cleanup
- PJD 8 Aug 2013 - FIXED: scrubNanAndMask function type/mask/grid issue - encase sw arguments in np.array() (attempt to strip cdms fluff)
- PJD 8 Aug 2013 - FIXED: removed depth variable unit edits - not all inputs are depth (m)
- PJD 15 Aug 2013 - Increased interpolated field resolution [200,300,500,700,1000,1500,1800,2000] - [5,10,20,30,40,50,75,100,125,150,200, ...]
- PJD 18 Aug 2013 - AR5 hard coded rho=1020,cp=4187 == 4.3e6 vs Ishii 1970 rho.mean=1024,cp.mean=3922 == 4.1e6 ~5% too high
- PJD 13 Jan 2014 - Corrected steric_height_anom and steric_height_thermo_anom to true anomaly fields, needed to remove climatology
- PJD 3 May 2014 - Turned off thetao conversion, although convert to numpy array rather than cdms2 transient variable
- PJD 13 Oct 2014 - Added seawater_library_version as a global attribute
- PJD 13 Oct 2014 - FIXED: bug with calculation of rho_halo variable was calculating gpan
- PJD 13 Oct 2014 - Added alternate calculation of halosteric anomaly (direct salinity anomaly calculation, rather than total-thermosteric)
- PJD 13 Oct 2014 - Added makeSteric_version as a global attribute
- TODO: Better deal with insitu vs thetao variables
- TODO: Query Charles on why *.name attributes are propagating
- TODO: validate outputs and compare to matlab versions - 10e-7 errors.
"""
# Remap all variables to short names
so = salinity
so_chg = salinityChg
temp = temp
temp_chg = tempChg
del(salinity,salinityChg,tempChg) ; gc.collect()
# Strip attributes to maintain consistency between datasets
for count,x in enumerate(so.attributes.keys()):
delattr(so,x)
#print so.listattributes() ; # Print remaining attributes
for count,x in enumerate(so_chg.attributes.keys()):
delattr(so_chg,x)
for count,x in enumerate(temp.attributes.keys()):
delattr(temp,x)
for count,x in enumerate(temp_chg.attributes.keys()):
delattr(temp_chg,x)
del(count,x)
# Create z-coordinate from salinity input
if not pressure:
z_coord = so.getAxis(0)
y_coord = so.getAxis(1)
y_coord = tile(y_coord,(so.shape[2],1)).transpose()
depth_levels = tile(z_coord.getValue(),(so.shape[2],so.shape[1],1)).transpose()
pressure_levels = sw.pres(np.array(depth_levels),np.array(y_coord))
del(z_coord,y_coord,depth_levels) ; gc.collect()
else:
pressure_levels = so.getAxis(0)
pressure_levels = transpose(tile(pressure_levels,(so.shape[2],so.shape[1],1)))
pressure_levels = cdm.createVariable(pressure_levels,id='pressure_levels')
pressure_levels.setAxis(0,so.getAxis(0))
pressure_levels.setAxis(1,so.getAxis(1))
pressure_levels.setAxis(2,so.getAxis(2))
pressure_levels.id = 'pressure_levels'
pressure_levels.units_long = 'decibar (pressure)'
pressure_levels.positive = 'down'
pressure_levels.long_name = 'sea_water_pressure'
pressure_levels.standard_name = 'sea_water_pressure'
pressure_levels.units = 'decibar'
pressure_levels.axis = 'Z'
# Cleanup depth axis attributes
depth = so.getAxis(0)
depth.id = 'depth'
depth.name = 'depth'
depth.long_name = 'depth'
depth.standard_name = 'depth'
depth.axis = 'Z'
so.setAxis(0,depth)
so_chg.setAxis(0,depth)
temp.setAxis(0,depth)
temp_chg.setAxis(0,depth)
del(depth)
# Convert using python-seawater library (v3.3.1 - 130807)
if thetao:
# Process potential temperature to in-situ - default conversion sets reference pressure to 0 (surface)
#temp_chg = sw.temp(np.array(so),np.array(temp_chg),np.array(pressure_levels)); # units degrees C
#temp = sw.temp(np.array(so),np.array(temp),np.array(pressure_levels)); # units degrees C
#temp_chg = sw.ptmp(np.array(so),np.array(temp_chg),np.array(pressure_levels),np.array(pressure_levels)); # units degrees C
#temp = sw.ptmp(np.array(so),np.array(temp),np.array(pressure_levels),np.array(pressure_levels)); # units degrees C
temp_chg = np.array(temp_chg); # units degrees C
temp = np.array(temp); # units degrees C
# Climatologies - rho,cp,steric_height
rho = sw.dens(np.array(so),np.array(temp),np.array(pressure_levels)) ; # units kg m-3
cp = sw.cp(np.array(so),np.array(temp),np.array(pressure_levels)) ; # units J kg-1 C-1
steric_height = sw.gpan(np.array(so),np.array(temp),np.array(pressure_levels)) ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
# Halosteric - rho,cp
ss = map(array,(so+so_chg))
rho_halo = sw.dens(np.array(ss),np.array(temp),np.array(pressure_levels)) ; # units kg m-3
cp_halo = sw.cp(np.array(ss),np.array(temp),np.array(pressure_levels)) ; # units J kg-1 C-1
tmp = sw.gpan(np.array(ss),np.array(temp),np.array(pressure_levels)) ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
steric_height_halo_anom2 = tmp-steric_height ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
# Full steric - steric_height
tt = map(array,(temp+temp_chg))
tmp = sw.gpan(np.array(ss),np.array(tt),np.array(pressure_levels)) ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
steric_height_anom = tmp-steric_height ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
del(ss,tmp) ; gc.collect()
# Thermosteric - rho,cp,steric_height
rho_thermo = sw.dens(np.array(so),np.array(tt),np.array(pressure_levels)) ; # units kg m-3
cp_thermo = sw.cp(np.array(so),np.array(tt),np.array(pressure_levels)) ; # units J kg-1 C-1
tmp = sw.gpan(np.array(so),np.array(tt),np.array(pressure_levels)) ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
steric_height_thermo_anom = tmp-steric_height ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
del(tt,tmp) ; gc.collect()
# Halosteric - steric_height
steric_height_halo_anom = steric_height_anom-steric_height_thermo_anom ; # units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
# Create heat content
heat_content = np.array(temp)*np.array(rho)*np.array(cp) ; # units J
heat_content_sanom = np.array(temp)*np.array(rho_halo)*np.array(cp_halo) ; # units J
heat_content_tanom = np.array(temp_chg)*np.array(rho)*np.array(cp) ; # units J
#heat_content_tanom = np.array(temp_chg)*np.array(1020)*np.array(4187) ; # units J - try hard-coded - AR5 numbers
heat_content_tsanom = np.array(temp_chg)*np.array(rho_halo)*np.array(cp_halo) ; # units J
# Correct all instances of NaN values and fix masks - applied before cdms variables are created otherwise names/ids/attributes are reset
temp = scrubNaNAndMask(temp,so)
temp_chg = scrubNaNAndMask(temp_chg,so)
rho = scrubNaNAndMask(rho,so)
cp = scrubNaNAndMask(cp,so)
rho_halo = scrubNaNAndMask(rho_halo,so)
cp_halo = scrubNaNAndMask(cp_halo,so)
rho_thermo = scrubNaNAndMask(rho_thermo,so)
cp_thermo = scrubNaNAndMask(cp_thermo,so)
steric_height = scrubNaNAndMask(steric_height,so)
steric_height_anom = scrubNaNAndMask(steric_height_anom,so)
steric_height_thermo_anom = scrubNaNAndMask(steric_height_thermo_anom,so)
steric_height_halo_anom = scrubNaNAndMask(steric_height_halo_anom,so)
steric_height_halo_anom2 = scrubNaNAndMask(steric_height_halo_anom2,so)
heat_content = scrubNaNAndMask(heat_content,so)
heat_content_sanom = scrubNaNAndMask(heat_content_sanom,so)
heat_content_tanom = scrubNaNAndMask(heat_content_tanom,so)
heat_content_tsanom = scrubNaNAndMask(heat_content_tsanom,so)
# Recreate and redress variables
so.id = 'so_mean'
so.units = '1e-3'
so_chg.id = 'so_chg'
so_chg.units = '1e-3'
temp = cdm.createVariable(temp,id='temp_mean')
temp.setAxis(0,so.getAxis(0))
temp.setAxis(1,so.getAxis(1))
temp.setAxis(2,so.getAxis(2))
temp.units = 'degrees_C'
temp_chg = cdm.createVariable(temp_chg,id='temp_chg')
temp_chg.setAxis(0,so.getAxis(0))
temp_chg.setAxis(1,so.getAxis(1))
temp_chg.setAxis(2,so.getAxis(2))
temp_chg.units = 'degrees_C'
rho = cdm.createVariable(rho,id='rho')
rho.setAxis(0,so.getAxis(0))
rho.setAxis(1,so.getAxis(1))
rho.setAxis(2,so.getAxis(2))
rho.name = 'density_mean'
rho.units = 'kg m^-3'
cp = cdm.createVariable(cp,id='cp')
cp.setAxis(0,so.getAxis(0))
cp.setAxis(1,so.getAxis(1))
cp.setAxis(2,so.getAxis(2))
cp.name = 'heat_capacity_mean'
cp.units = 'J kg^-1 C^-1'
rho_halo = cdm.createVariable(rho_halo,id='rho_halo')
rho_halo.setAxis(0,so.getAxis(0))
rho_halo.setAxis(1,so.getAxis(1))
rho_halo.setAxis(2,so.getAxis(2))
rho_halo.name = 'density_mean_halo'
rho_halo.units = 'kg m^-3'
cp_halo = cdm.createVariable(cp_halo,id='cp_halo')
cp_halo.setAxis(0,so.getAxis(0))
cp_halo.setAxis(1,so.getAxis(1))
cp_halo.setAxis(2,so.getAxis(2))
cp_halo.name = 'heat_capacity_mean_halo'
cp_halo.units = 'J kg^-1 C^-1'
rho_thermo = cdm.createVariable(rho_thermo,id='rho_thermo')
rho_thermo.setAxis(0,so.getAxis(0))
rho_thermo.setAxis(1,so.getAxis(1))
rho_thermo.setAxis(2,so.getAxis(2))
rho_thermo.name = 'density_mean_thermo'
rho_thermo.units = 'kg m^-3'
cp_thermo = cdm.createVariable(cp_thermo,id='cp_thermo')
cp_thermo.setAxis(0,so.getAxis(0))
cp_thermo.setAxis(1,so.getAxis(1))
cp_thermo.setAxis(2,so.getAxis(2))
cp_thermo.name = 'heat_capacity_mean_thermo'
cp_thermo.units = 'J kg^-1 C^-1'
steric_height = cdm.createVariable(steric_height,id='steric_height')
steric_height.setAxis(0,so.getAxis(0))
steric_height.setAxis(1,so.getAxis(1))
steric_height.setAxis(2,so.getAxis(2))
steric_height.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_anom = cdm.createVariable(steric_height_anom,id='steric_height_anom')
steric_height_anom.setAxis(0,so.getAxis(0))
steric_height_anom.setAxis(1,so.getAxis(1))
steric_height_anom.setAxis(2,so.getAxis(2))
steric_height_anom.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_thermo_anom = cdm.createVariable(steric_height_thermo_anom,id='steric_height_thermo_anom')
steric_height_thermo_anom.setAxis(0,so.getAxis(0))
steric_height_thermo_anom.setAxis(1,so.getAxis(1))
steric_height_thermo_anom.setAxis(2,so.getAxis(2))
steric_height_thermo_anom.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom = cdm.createVariable(steric_height_halo_anom,id='steric_height_halo_anom')
steric_height_halo_anom.setAxis(0,so.getAxis(0))
steric_height_halo_anom.setAxis(1,so.getAxis(1))
steric_height_halo_anom.setAxis(2,so.getAxis(2))
steric_height_halo_anom.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom2 = cdm.createVariable(steric_height_halo_anom2,id='steric_height_halo_anom2')
steric_height_halo_anom2.setAxis(0,so.getAxis(0))
steric_height_halo_anom2.setAxis(1,so.getAxis(1))
steric_height_halo_anom2.setAxis(2,so.getAxis(2))
steric_height_halo_anom2.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
heat_content = cdm.createVariable(heat_content,id='heat_content')
heat_content.setAxis(0,so.getAxis(0))
heat_content.setAxis(1,so.getAxis(1))
heat_content.setAxis(2,so.getAxis(2))
heat_content.units = 'J'
heat_content_sanom = cdm.createVariable(heat_content_sanom,id='heat_content_sanom')
heat_content_sanom.setAxis(0,so.getAxis(0))
heat_content_sanom.setAxis(1,so.getAxis(1))
heat_content_sanom.setAxis(2,so.getAxis(2))
heat_content_sanom.units = 'J'
heat_content_tanom = cdm.createVariable(heat_content_tanom,id='heat_content_tanom')
heat_content_tanom.setAxis(0,so.getAxis(0))
heat_content_tanom.setAxis(1,so.getAxis(1))
heat_content_tanom.setAxis(2,so.getAxis(2))
heat_content_tanom.units = 'J'
heat_content_tsanom = cdm.createVariable(heat_content_tsanom,id='heat_content_tsanom')
heat_content_tsanom.setAxis(0,so.getAxis(0))
heat_content_tsanom.setAxis(1,so.getAxis(1))
heat_content_tsanom.setAxis(2,so.getAxis(2))
heat_content_tsanom.units = 'J'
# Create model-based depth index for subset target levels
newdepth = np.array([5,10,20,30,40,50,75,100,125,150,200,300,500,700,1000,1500,1800,2000]).astype('f');
newdepth_bounds = np.array([[0,5],[5,10],[10,20],[20,30],[30,40],[40,50],[50,75],[75,100],[100,125],[125,150],
[150,200],[200,300],[300,500],[500,700],[700,1000],[1000,1500],[1500,1800],[1800,2000]]).astype('f')
#newdepth = np.array([200,300,500,700,1000,1500,1800,2000]).astype('f');
#newdepth_bounds = np.array([[0,200],[200,300],[300,500],[500,700],[700,1000],[1000,1500],[1500,1800],[1800,2000]]).astype('f')
# Interpolate to depths
so_depthInterp = cdu.linearInterpolation(so,pressure_levels,levels=newdepth)
temp_depthInterp = cdu.linearInterpolation(temp,pressure_levels,levels=newdepth)
steric_height_depthInterp = cdu.linearInterpolation(steric_height,pressure_levels,levels=newdepth)
steric_height_anom_depthInterp = cdu.linearInterpolation(steric_height_anom,pressure_levels,levels=newdepth)
steric_height_thermo_anom_depthInterp = cdu.linearInterpolation(steric_height_thermo_anom,pressure_levels,levels=newdepth)
steric_height_halo_anom_depthInterp = cdu.linearInterpolation(steric_height_halo_anom,pressure_levels,levels=newdepth)
steric_height_halo_anom2_depthInterp = cdu.linearInterpolation(steric_height_halo_anom2,pressure_levels,levels=newdepth)
heat_content_sanom_depthInterp = cdu.linearInterpolation(heat_content_sanom,pressure_levels,levels=newdepth)
heat_content_tanom_depthInterp = cdu.linearInterpolation(heat_content_tanom,pressure_levels,levels=newdepth)
heat_content_tsanom_depthInterp = cdu.linearInterpolation(heat_content_tanom,pressure_levels,levels=newdepth)
# Fix masks - applied before cdms variables are created otherwise names/ids/attributes are reset
temp_depthInterp = scrubNaNAndMask(temp_depthInterp,so_depthInterp)
steric_height_depthInterp = scrubNaNAndMask(steric_height_depthInterp,so_depthInterp)
steric_height_anom_depthInterp = scrubNaNAndMask(steric_height_anom_depthInterp,so_depthInterp)
steric_height_thermo_anom_depthInterp = scrubNaNAndMask(steric_height_thermo_anom_depthInterp,so_depthInterp)
steric_height_halo_anom_depthInterp = scrubNaNAndMask(steric_height_halo_anom_depthInterp,so_depthInterp)
steric_height_halo_anom2_depthInterp = scrubNaNAndMask(steric_height_halo_anom2_depthInterp,so_depthInterp)
heat_content_sanom_depthInterp = scrubNaNAndMask(heat_content_sanom_depthInterp,so_depthInterp)
heat_content_tanom_depthInterp = scrubNaNAndMask(heat_content_tanom_depthInterp,so_depthInterp)
heat_content_tsanom_depthInterp = scrubNaNAndMask(heat_content_tsanom_depthInterp,so_depthInterp)
# Fix bounds
newdepth = so_depthInterp.getAxis(0)
newdepth.setBounds(newdepth_bounds)
del(newdepth_bounds)
newdepth.id = 'depth2'
newdepth.units_long = 'decibar (pressure)'
newdepth.positive = 'down'
newdepth.long_name = 'sea_water_pressure'
newdepth.standard_name = 'sea_water_pressure'
newdepth.units = 'decibar'
newdepth.axis = 'Z'
# Assign corrected bounds
so_depthInterp.setAxis(0,newdepth)
temp_depthInterp.setAxis(0,newdepth)
steric_height_depthInterp.setAxis(0,newdepth)
steric_height_anom_depthInterp.setAxis(0,newdepth)
steric_height_thermo_anom_depthInterp.setAxis(0,newdepth)
steric_height_halo_anom_depthInterp.setAxis(0,newdepth)
steric_height_halo_anom2_depthInterp.setAxis(0,newdepth)
heat_content_sanom_depthInterp.setAxis(0,newdepth)
heat_content_tanom_depthInterp.setAxis(0,newdepth)
heat_content_tsanom_depthInterp.setAxis(0,newdepth)
# Average/integrate to surface - configure bounds
# Preallocate arrays
so_depthAve = np.ma.zeros([len(newdepth),shape(so)[1],shape(so)[2]])
temp_depthAve = so_depthAve.copy()
heat_content_sanom_depthInteg = so_depthAve.copy()
heat_content_tanom_depthInteg = so_depthAve.copy()
heat_content_tsanom_depthInteg = so_depthAve.copy()
for count,depth in enumerate(newdepth):
tmp = cdu.averager(so_depthInterp[0:(count+1),...],axis=0,weights='weighted',action='average')
so_depthAve[count,] = tmp;
tmp = cdu.averager(temp_depthInterp[0:(count+1),...],axis=0,weights='weighted',action='average')
temp_depthAve[count,] = tmp;
tmp = cdu.averager(heat_content_sanom_depthInterp[0:(count+1),...],axis=0,weights='weighted',action='sum')
heat_content_sanom_depthInteg[count,] = tmp
tmp = cdu.averager(heat_content_tanom_depthInterp[0:(count+1),...],axis=0,weights='weighted',action='sum')
heat_content_tanom_depthInteg[count,] = tmp
tmp = cdu.averager(heat_content_tsanom_depthInterp[0:(count+1),...],axis=0,weights='weighted',action='sum')
heat_content_tsanom_depthInteg[count,] = tmp
del(heat_content_tanom_depthInterp,heat_content_tsanom_depthInterp); gc.collect()
# Fix masks - applied before cdms variables are created otherwise names/ids/attributes are reset
so_depthAve = scrubNaNAndMask(so_depthAve,so_depthInterp)
temp_depthAve = scrubNaNAndMask(temp_depthAve,so_depthInterp)
heat_content_sanom_depthInteg = scrubNaNAndMask(heat_content_sanom_depthInteg,so_depthInterp)
heat_content_tanom_depthInteg = scrubNaNAndMask(heat_content_tanom_depthInteg,so_depthInterp)
heat_content_tsanom_depthInteg = scrubNaNAndMask(heat_content_tsanom_depthInteg,so_depthInterp)
del(so_depthInterp)
# Convert numpy arrays to cdms objects
heat_content_sanom_depthInteg = cdm.createVariable(heat_content_sanom_depthInteg,id='heat_content_sanom_depthInteg')
heat_content_sanom_depthInteg.id = 'heat_content_sanom_depthInteg'
heat_content_sanom_depthInteg.setAxis(0,newdepth)
heat_content_sanom_depthInteg.setAxis(1,so.getAxis(1))
heat_content_sanom_depthInteg.setAxis(2,so.getAxis(2))
heat_content_sanom_depthInteg.units = 'J'
heat_content_tanom_depthInteg = cdm.createVariable(heat_content_tanom_depthInteg,id='heat_content_tanom_depthInteg')
heat_content_tanom_depthInteg.id = 'heat_content_tanom_depthInteg'
heat_content_tanom_depthInteg.setAxis(0,newdepth)
heat_content_tanom_depthInteg.setAxis(1,so.getAxis(1))
heat_content_tanom_depthInteg.setAxis(2,so.getAxis(2))
heat_content_tanom_depthInteg.units = 'J'
heat_content_tsanom_depthInteg = cdm.createVariable(heat_content_tsanom_depthInteg,id='heat_content_tsanom_depthInteg')
heat_content_tsanom_depthInteg.id = 'heat_content_tsanom_depthInteg'
heat_content_tsanom_depthInteg.setAxis(0,newdepth)
heat_content_tsanom_depthInteg.setAxis(1,so.getAxis(1))
heat_content_tsanom_depthInteg.setAxis(2,so.getAxis(2))
heat_content_tsanom_depthInteg.units = 'J'
so_depthAve = cdm.createVariable(so_depthAve,id='so_depthAve')
so_depthAve.id = 'so_depthAve'
so_depthAve.setAxis(0,newdepth)
so_depthAve.setAxis(1,so.getAxis(1))
so_depthAve.setAxis(2,so.getAxis(2))
so_depthAve.units = '1e-3'
temp_depthAve = cdm.createVariable(temp_depthAve,id='temp_depthAve')
temp_depthAve.id = 'temp_depthAve'
temp_depthAve.setAxis(0,newdepth)
temp_depthAve.setAxis(1,so.getAxis(1))
temp_depthAve.setAxis(2,so.getAxis(2))
temp_depthAve.units = 'degrees_C'
steric_height_depthInterp = cdm.createVariable(steric_height_depthInterp,id='steric_height_depthInterp')
steric_height_depthInterp.setAxis(0,newdepth)
steric_height_depthInterp.setAxis(1,so.getAxis(1))
steric_height_depthInterp.setAxis(2,so.getAxis(2))
steric_height_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_anom_depthInterp = cdm.createVariable(steric_height_anom_depthInterp,id='steric_height_anom_depthInterp')
steric_height_anom_depthInterp.setAxis(0,newdepth)
steric_height_anom_depthInterp.setAxis(1,so.getAxis(1))
steric_height_anom_depthInterp.setAxis(2,rho.getAxis(2))
steric_height_anom_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_thermo_anom_depthInterp = cdm.createVariable(steric_height_thermo_anom_depthInterp,id='steric_height_thermo_anom_depthInterp')
steric_height_thermo_anom_depthInterp.setAxis(0,newdepth)
steric_height_thermo_anom_depthInterp.setAxis(1,so.getAxis(1))
steric_height_thermo_anom_depthInterp.setAxis(2,so.getAxis(2))
steric_height_thermo_anom_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom_depthInterp = cdm.createVariable(steric_height_halo_anom_depthInterp,id='steric_height_halo_anom_depthInterp')
steric_height_halo_anom_depthInterp.setAxis(0,newdepth)
steric_height_halo_anom_depthInterp.setAxis(1,so.getAxis(1))
steric_height_halo_anom_depthInterp.setAxis(2,so.getAxis(2))
steric_height_halo_anom_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom2_depthInterp = cdm.createVariable(steric_height_halo_anom2_depthInterp,id='steric_height_halo_anom2_depthInterp')
steric_height_halo_anom2_depthInterp.setAxis(0,newdepth)
steric_height_halo_anom2_depthInterp.setAxis(1,so.getAxis(1))
steric_height_halo_anom2_depthInterp.setAxis(2,so.getAxis(2))
steric_height_halo_anom2_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
# Cleanup workspace
del(newdepth) ; gc.collect()
# Write variables to file
if os.path.isfile(outFileName):
os.remove(outFileName)
filehandle = cdm.open(outFileName,'w')
# Global attributes
globalAttWrite(filehandle,options=None) ; # Use function to write standard global atts
# Write seawater version
filehandle.seawater_library_version = sw.__version__
# Write makeSteric version
makeStericPath = str(makeSteric.__code__).split(' ')[6]
makeStericPath = replace(replace(makeStericPath,'"',''),',','') ; # Clean scraped path
filehandle.makeSteric_version = ' '.join(getGitInfo(makeStericPath)[0:3])
# Master variables
filehandle.write(so.astype('float32'))
filehandle.write(so_chg.astype('float32'))
filehandle.write(so_depthAve.astype('float32'))
filehandle.write(temp.astype('float32'))
filehandle.write(temp_chg.astype('float32'))
filehandle.write(temp_depthAve.astype('float32'))
# Derived variables
filehandle.write(cp.astype('float32'))
filehandle.write(cp_halo.astype('float32'))
filehandle.write(cp_thermo.astype('float32'))
filehandle.write(rho.astype('float32'))
filehandle.write(rho_halo.astype('float32'))
filehandle.write(rho_thermo.astype('float32'))
filehandle.write(heat_content.astype('float32'))
filehandle.write(heat_content_sanom.astype('float32'))
filehandle.write(heat_content_sanom_depthInteg.astype('float32'))
filehandle.write(heat_content_tanom.astype('float32'))
filehandle.write(heat_content_tanom_depthInteg.astype('float32'))
filehandle.write(heat_content_tsanom.astype('float32'))
filehandle.write(heat_content_tsanom_depthInteg.astype('float32'))
filehandle.write(steric_height.astype('float32'))
filehandle.write(steric_height_depthInterp.astype('float32'))
filehandle.write(steric_height_anom.astype('float32'))
filehandle.write(steric_height_anom_depthInterp.astype('float32'))
filehandle.write(steric_height_halo_anom.astype('float32'))
filehandle.write(steric_height_halo_anom2.astype('float32'))
filehandle.write(steric_height_halo_anom_depthInterp.astype('float32'))
filehandle.write(steric_height_halo_anom2_depthInterp.astype('float32'))
filehandle.write(steric_height_thermo_anom.astype('float32'))
filehandle.write(steric_height_thermo_anom_depthInterp.astype('float32'))
filehandle.close()
# Cleanup workspace
del(outFileName) ; gc.collect()
def makeSteric(salinity, salinityChg, temp, tempChg, outFileName, thetao,
pressure):
"""
The makeSteric() function takes 3D (not temporal) arguments and creates
heat content and steric fields which are written to a specified outfile
Author: Paul J. Durack : [email protected] : @durack1.
Created on Thu Jul 18 13:03:37 2013.
Inputs:
------
- salinity(lev,lat,lon) - 3D array for the climatological period.
- salinityChg(lev,lat,lon) - 3D array for the temporal change period.
- temp(lev,lat,lon) - 3D array for the climatological period either in-situ or potential temperature.
- tempChg(lev,lat,lon) - 3D array for the temporal change period as with temp, either in-situ or potential temperature.
- outFileName(str) - output filename with full path specified.
- thetao(bool) - boolean value specifying either in-situ or potential temperature arrays provided.
- pressure(bool) - boolean value specifying whether lev-coordinate is pressure (dbar) or depth (m).
Usage:
------
>>> from makeStericLib import makeSteric
>>> makeSteric(salinity,salinityChg,thetao,thetaoChg,'outfile.nc',True,False)
Notes:
-----
- PJD 18 Jul 2013 - Validated Ishii v6.13 data against WOA94 - checks out ok. Units: dyn decimeter compared to http://www.nodc.noaa.gov/OC5/WOA94/dyn.html uses cm (not decimeter; x 10)
- PJD 18 Jul 2013 - Added attribute scrub to incoming variables (so,so_chg,temp,temp_chg) to maintain output consistency
- PJD 22 Jul 2013 - Added name attributes to so and temp variables, added units to so_chg
- PJD 22 Jul 2013 - removed duplicated code by converting repetition to function scrubNaNAndMask
- PJD 23 Jul 2013 - Further cleaned up so,so_chg,temp,temp_chg outputs specifying id/name attributes
- PJD 5 Aug 2013 - Updated python-seawater library to version 3.3.1 from github repo, git clone http://github.com/ocefpaf/python-seawater, python setup.py install --user
- PJD 7 Aug 2013 - FIXED: thetao rather than in-situ temperature propagating throughout calculations
- PJD 7 Aug 2013 - Replaced looping with 3D gpan
- PJD 7 Aug 2013 - Further code duplication cleanup
- PJD 8 Aug 2013 - FIXED: scrubNanAndMask function type/mask/grid issue - encase sw arguments in np.array() (attempt to strip cdms fluff)
- PJD 8 Aug 2013 - FIXED: removed depth variable unit edits - not all inputs are depth (m)
- PJD 15 Aug 2013 - Increased interpolated field resolution [200,300,500,700,1000,1500,1800,2000] - [5,10,20,30,40,50,75,100,125,150,200, ...]
- PJD 18 Aug 2013 - AR5 hard coded rho=1020,cp=4187 == 4.3e6 vs Ishii 1970 rho.mean=1024,cp.mean=3922 == 4.1e6 ~5% too high
- PJD 13 Jan 2014 - Corrected steric_height_anom and steric_height_thermo_anom to true anomaly fields, needed to remove climatology
- PJD 3 May 2014 - Turned off thetao conversion, although convert to numpy array rather than cdms2 transient variable
- PJD 13 Oct 2014 - Added seawater_library_version as a global attribute
- PJD 13 Oct 2014 - FIXED: bug with calculation of rho_halo variable was calculating gpan
- PJD 13 Oct 2014 - Added alternate calculation of halosteric anomaly (direct salinity anomaly calculation, rather than total-thermosteric)
- PJD 13 Oct 2014 - Added makeSteric_version as a global attribute
- TODO: Better deal with insitu vs thetao variables
- TODO: Query Charles on why *.name attributes are propagating
- TODO: validate outputs and compare to matlab versions - 10e-7 errors.
"""
# Remap all variables to short names
so = salinity
so_chg = salinityChg
temp = temp
temp_chg = tempChg
del (salinity, salinityChg, tempChg)
gc.collect()
# Strip attributes to maintain consistency between datasets
for count, x in enumerate(so.attributes.keys()):
delattr(so, x)
#print so.listattributes() ; # Print remaining attributes
for count, x in enumerate(so_chg.attributes.keys()):
delattr(so_chg, x)
for count, x in enumerate(temp.attributes.keys()):
delattr(temp, x)
for count, x in enumerate(temp_chg.attributes.keys()):
delattr(temp_chg, x)
del (count, x)
# Create z-coordinate from salinity input
if not pressure:
z_coord = so.getAxis(0)
y_coord = so.getAxis(1)
y_coord = tile(y_coord, (so.shape[2], 1)).transpose()
depth_levels = tile(z_coord.getValue(),
(so.shape[2], so.shape[1], 1)).transpose()
pressure_levels = sw.pres(np.array(depth_levels), np.array(y_coord))
del (z_coord, y_coord, depth_levels)
gc.collect()
else:
pressure_levels = so.getAxis(0)
pressure_levels = transpose(
tile(pressure_levels, (so.shape[2], so.shape[1], 1)))
pressure_levels = cdm.createVariable(pressure_levels, id='pressure_levels')
pressure_levels.setAxis(0, so.getAxis(0))
pressure_levels.setAxis(1, so.getAxis(1))
pressure_levels.setAxis(2, so.getAxis(2))
pressure_levels.id = 'pressure_levels'
pressure_levels.units_long = 'decibar (pressure)'
pressure_levels.positive = 'down'
pressure_levels.long_name = 'sea_water_pressure'
pressure_levels.standard_name = 'sea_water_pressure'
pressure_levels.units = 'decibar'
pressure_levels.axis = 'Z'
# Cleanup depth axis attributes
depth = so.getAxis(0)
depth.id = 'depth'
depth.name = 'depth'
depth.long_name = 'depth'
depth.standard_name = 'depth'
depth.axis = 'Z'
so.setAxis(0, depth)
so_chg.setAxis(0, depth)
temp.setAxis(0, depth)
temp_chg.setAxis(0, depth)
del (depth)
# Convert using python-seawater library (v3.3.1 - 130807)
if thetao:
# Process potential temperature to in-situ - default conversion sets reference pressure to 0 (surface)
#temp_chg = sw.temp(np.array(so),np.array(temp_chg),np.array(pressure_levels)); # units degrees C
#temp = sw.temp(np.array(so),np.array(temp),np.array(pressure_levels)); # units degrees C
#temp_chg = sw.ptmp(np.array(so),np.array(temp_chg),np.array(pressure_levels),np.array(pressure_levels)); # units degrees C
#temp = sw.ptmp(np.array(so),np.array(temp),np.array(pressure_levels),np.array(pressure_levels)); # units degrees C
temp_chg = np.array(temp_chg)
# units degrees C
temp = np.array(temp)
# units degrees C
# Climatologies - rho,cp,steric_height
rho = sw.dens(np.array(so), np.array(temp), np.array(pressure_levels))
# units kg m-3
cp = sw.cp(np.array(so), np.array(temp), np.array(pressure_levels))
# units J kg-1 C-1
steric_height = sw.gpan(np.array(so), np.array(temp),
np.array(pressure_levels))
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
# Halosteric - rho,cp
ss = map(array, (so + so_chg))
rho_halo = sw.dens(np.array(ss), np.array(temp), np.array(pressure_levels))
# units kg m-3
cp_halo = sw.cp(np.array(ss), np.array(temp), np.array(pressure_levels))
# units J kg-1 C-1
tmp = sw.gpan(np.array(ss), np.array(temp), np.array(pressure_levels))
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
steric_height_halo_anom2 = tmp - steric_height
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
# Full steric - steric_height
tt = map(array, (temp + temp_chg))
tmp = sw.gpan(np.array(ss), np.array(tt), np.array(pressure_levels))
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
steric_height_anom = tmp - steric_height
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
del (ss, tmp)
gc.collect()
# Thermosteric - rho,cp,steric_height
rho_thermo = sw.dens(np.array(so), np.array(tt), np.array(pressure_levels))
# units kg m-3
cp_thermo = sw.cp(np.array(so), np.array(tt), np.array(pressure_levels))
# units J kg-1 C-1
tmp = sw.gpan(np.array(so), np.array(tt), np.array(pressure_levels))
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
steric_height_thermo_anom = tmp - steric_height
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
del (tt, tmp)
gc.collect()
# Halosteric - steric_height
steric_height_halo_anom = steric_height_anom - steric_height_thermo_anom
# units m3 kg-1 Pa == m2 s-2 == J kg-1 (dynamic decimeter)
# Create heat content
heat_content = np.array(temp) * np.array(rho) * np.array(cp)
# units J
heat_content_sanom = np.array(temp) * np.array(rho_halo) * np.array(
cp_halo)
# units J
heat_content_tanom = np.array(temp_chg) * np.array(rho) * np.array(cp)
# units J
#heat_content_tanom = np.array(temp_chg)*np.array(1020)*np.array(4187) ; # units J - try hard-coded - AR5 numbers
heat_content_tsanom = np.array(temp_chg) * np.array(rho_halo) * np.array(
cp_halo)
# units J
# Correct all instances of NaN values and fix masks - applied before cdms variables are created otherwise names/ids/attributes are reset
temp = scrubNaNAndMask(temp, so)
temp_chg = scrubNaNAndMask(temp_chg, so)
rho = scrubNaNAndMask(rho, so)
cp = scrubNaNAndMask(cp, so)
rho_halo = scrubNaNAndMask(rho_halo, so)
cp_halo = scrubNaNAndMask(cp_halo, so)
rho_thermo = scrubNaNAndMask(rho_thermo, so)
cp_thermo = scrubNaNAndMask(cp_thermo, so)
steric_height = scrubNaNAndMask(steric_height, so)
steric_height_anom = scrubNaNAndMask(steric_height_anom, so)
steric_height_thermo_anom = scrubNaNAndMask(steric_height_thermo_anom, so)
steric_height_halo_anom = scrubNaNAndMask(steric_height_halo_anom, so)
steric_height_halo_anom2 = scrubNaNAndMask(steric_height_halo_anom2, so)
heat_content = scrubNaNAndMask(heat_content, so)
heat_content_sanom = scrubNaNAndMask(heat_content_sanom, so)
heat_content_tanom = scrubNaNAndMask(heat_content_tanom, so)
heat_content_tsanom = scrubNaNAndMask(heat_content_tsanom, so)
# Recreate and redress variables
so.id = 'so_mean'
so.units = '1e-3'
so_chg.id = 'so_chg'
so_chg.units = '1e-3'
temp = cdm.createVariable(temp, id='temp_mean')
temp.setAxis(0, so.getAxis(0))
temp.setAxis(1, so.getAxis(1))
temp.setAxis(2, so.getAxis(2))
temp.units = 'degrees_C'
temp_chg = cdm.createVariable(temp_chg, id='temp_chg')
temp_chg.setAxis(0, so.getAxis(0))
temp_chg.setAxis(1, so.getAxis(1))
temp_chg.setAxis(2, so.getAxis(2))
temp_chg.units = 'degrees_C'
rho = cdm.createVariable(rho, id='rho')
rho.setAxis(0, so.getAxis(0))
rho.setAxis(1, so.getAxis(1))
rho.setAxis(2, so.getAxis(2))
rho.name = 'density_mean'
rho.units = 'kg m^-3'
cp = cdm.createVariable(cp, id='cp')
cp.setAxis(0, so.getAxis(0))
cp.setAxis(1, so.getAxis(1))
cp.setAxis(2, so.getAxis(2))
cp.name = 'heat_capacity_mean'
cp.units = 'J kg^-1 C^-1'
rho_halo = cdm.createVariable(rho_halo, id='rho_halo')
rho_halo.setAxis(0, so.getAxis(0))
rho_halo.setAxis(1, so.getAxis(1))
rho_halo.setAxis(2, so.getAxis(2))
rho_halo.name = 'density_mean_halo'
rho_halo.units = 'kg m^-3'
cp_halo = cdm.createVariable(cp_halo, id='cp_halo')
cp_halo.setAxis(0, so.getAxis(0))
cp_halo.setAxis(1, so.getAxis(1))
cp_halo.setAxis(2, so.getAxis(2))
cp_halo.name = 'heat_capacity_mean_halo'
cp_halo.units = 'J kg^-1 C^-1'
rho_thermo = cdm.createVariable(rho_thermo, id='rho_thermo')
rho_thermo.setAxis(0, so.getAxis(0))
rho_thermo.setAxis(1, so.getAxis(1))
rho_thermo.setAxis(2, so.getAxis(2))
rho_thermo.name = 'density_mean_thermo'
rho_thermo.units = 'kg m^-3'
cp_thermo = cdm.createVariable(cp_thermo, id='cp_thermo')
cp_thermo.setAxis(0, so.getAxis(0))
cp_thermo.setAxis(1, so.getAxis(1))
cp_thermo.setAxis(2, so.getAxis(2))
cp_thermo.name = 'heat_capacity_mean_thermo'
cp_thermo.units = 'J kg^-1 C^-1'
steric_height = cdm.createVariable(steric_height, id='steric_height')
steric_height.setAxis(0, so.getAxis(0))
steric_height.setAxis(1, so.getAxis(1))
steric_height.setAxis(2, so.getAxis(2))
steric_height.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_anom = cdm.createVariable(steric_height_anom,
id='steric_height_anom')
steric_height_anom.setAxis(0, so.getAxis(0))
steric_height_anom.setAxis(1, so.getAxis(1))
steric_height_anom.setAxis(2, so.getAxis(2))
steric_height_anom.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_thermo_anom = cdm.createVariable(
steric_height_thermo_anom, id='steric_height_thermo_anom')
steric_height_thermo_anom.setAxis(0, so.getAxis(0))
steric_height_thermo_anom.setAxis(1, so.getAxis(1))
steric_height_thermo_anom.setAxis(2, so.getAxis(2))
steric_height_thermo_anom.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom = cdm.createVariable(steric_height_halo_anom,
id='steric_height_halo_anom')
steric_height_halo_anom.setAxis(0, so.getAxis(0))
steric_height_halo_anom.setAxis(1, so.getAxis(1))
steric_height_halo_anom.setAxis(2, so.getAxis(2))
steric_height_halo_anom.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom2 = cdm.createVariable(
steric_height_halo_anom2, id='steric_height_halo_anom2')
steric_height_halo_anom2.setAxis(0, so.getAxis(0))
steric_height_halo_anom2.setAxis(1, so.getAxis(1))
steric_height_halo_anom2.setAxis(2, so.getAxis(2))
steric_height_halo_anom2.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
heat_content = cdm.createVariable(heat_content, id='heat_content')
heat_content.setAxis(0, so.getAxis(0))
heat_content.setAxis(1, so.getAxis(1))
heat_content.setAxis(2, so.getAxis(2))
heat_content.units = 'J'
heat_content_sanom = cdm.createVariable(heat_content_sanom,
id='heat_content_sanom')
heat_content_sanom.setAxis(0, so.getAxis(0))
heat_content_sanom.setAxis(1, so.getAxis(1))
heat_content_sanom.setAxis(2, so.getAxis(2))
heat_content_sanom.units = 'J'
heat_content_tanom = cdm.createVariable(heat_content_tanom,
id='heat_content_tanom')
heat_content_tanom.setAxis(0, so.getAxis(0))
heat_content_tanom.setAxis(1, so.getAxis(1))
heat_content_tanom.setAxis(2, so.getAxis(2))
heat_content_tanom.units = 'J'
heat_content_tsanom = cdm.createVariable(heat_content_tsanom,
id='heat_content_tsanom')
heat_content_tsanom.setAxis(0, so.getAxis(0))
heat_content_tsanom.setAxis(1, so.getAxis(1))
heat_content_tsanom.setAxis(2, so.getAxis(2))
heat_content_tsanom.units = 'J'
# Create model-based depth index for subset target levels
newdepth = np.array([
5, 10, 20, 30, 40, 50, 75, 100, 125, 150, 200, 300, 500, 700, 1000,
1500, 1800, 2000
]).astype('f')
newdepth_bounds = np.array([[0, 5], [5, 10], [10, 20], [20, 30], [30, 40],
[40, 50], [50, 75], [75, 100], [100, 125],
[125, 150], [150, 200], [200, 300], [300, 500],
[500, 700], [700, 1000], [1000, 1500],
[1500, 1800], [1800, 2000]]).astype('f')
#newdepth = np.array([200,300,500,700,1000,1500,1800,2000]).astype('f');
#newdepth_bounds = np.array([[0,200],[200,300],[300,500],[500,700],[700,1000],[1000,1500],[1500,1800],[1800,2000]]).astype('f')
# Interpolate to depths
so_depthInterp = cdu.linearInterpolation(so,
pressure_levels,
levels=newdepth)
temp_depthInterp = cdu.linearInterpolation(temp,
pressure_levels,
levels=newdepth)
steric_height_depthInterp = cdu.linearInterpolation(steric_height,
pressure_levels,
levels=newdepth)
steric_height_anom_depthInterp = cdu.linearInterpolation(
steric_height_anom, pressure_levels, levels=newdepth)
steric_height_thermo_anom_depthInterp = cdu.linearInterpolation(
steric_height_thermo_anom, pressure_levels, levels=newdepth)
steric_height_halo_anom_depthInterp = cdu.linearInterpolation(
steric_height_halo_anom, pressure_levels, levels=newdepth)
steric_height_halo_anom2_depthInterp = cdu.linearInterpolation(
steric_height_halo_anom2, pressure_levels, levels=newdepth)
heat_content_sanom_depthInterp = cdu.linearInterpolation(
heat_content_sanom, pressure_levels, levels=newdepth)
heat_content_tanom_depthInterp = cdu.linearInterpolation(
heat_content_tanom, pressure_levels, levels=newdepth)
heat_content_tsanom_depthInterp = cdu.linearInterpolation(
heat_content_tanom, pressure_levels, levels=newdepth)
# Fix masks - applied before cdms variables are created otherwise names/ids/attributes are reset
temp_depthInterp = scrubNaNAndMask(temp_depthInterp, so_depthInterp)
steric_height_depthInterp = scrubNaNAndMask(steric_height_depthInterp,
so_depthInterp)
steric_height_anom_depthInterp = scrubNaNAndMask(
steric_height_anom_depthInterp, so_depthInterp)
steric_height_thermo_anom_depthInterp = scrubNaNAndMask(
steric_height_thermo_anom_depthInterp, so_depthInterp)
steric_height_halo_anom_depthInterp = scrubNaNAndMask(
steric_height_halo_anom_depthInterp, so_depthInterp)
steric_height_halo_anom2_depthInterp = scrubNaNAndMask(
steric_height_halo_anom2_depthInterp, so_depthInterp)
heat_content_sanom_depthInterp = scrubNaNAndMask(
heat_content_sanom_depthInterp, so_depthInterp)
heat_content_tanom_depthInterp = scrubNaNAndMask(
heat_content_tanom_depthInterp, so_depthInterp)
heat_content_tsanom_depthInterp = scrubNaNAndMask(
heat_content_tsanom_depthInterp, so_depthInterp)
# Fix bounds
newdepth = so_depthInterp.getAxis(0)
newdepth.setBounds(newdepth_bounds)
del (newdepth_bounds)
newdepth.id = 'depth2'
newdepth.units_long = 'decibar (pressure)'
newdepth.positive = 'down'
newdepth.long_name = 'sea_water_pressure'
newdepth.standard_name = 'sea_water_pressure'
newdepth.units = 'decibar'
newdepth.axis = 'Z'
# Assign corrected bounds
so_depthInterp.setAxis(0, newdepth)
temp_depthInterp.setAxis(0, newdepth)
steric_height_depthInterp.setAxis(0, newdepth)
steric_height_anom_depthInterp.setAxis(0, newdepth)
steric_height_thermo_anom_depthInterp.setAxis(0, newdepth)
steric_height_halo_anom_depthInterp.setAxis(0, newdepth)
steric_height_halo_anom2_depthInterp.setAxis(0, newdepth)
heat_content_sanom_depthInterp.setAxis(0, newdepth)
heat_content_tanom_depthInterp.setAxis(0, newdepth)
heat_content_tsanom_depthInterp.setAxis(0, newdepth)
# Average/integrate to surface - configure bounds
# Preallocate arrays
so_depthAve = np.ma.zeros([len(newdepth), shape(so)[1], shape(so)[2]])
temp_depthAve = so_depthAve.copy()
heat_content_sanom_depthInteg = so_depthAve.copy()
heat_content_tanom_depthInteg = so_depthAve.copy()
heat_content_tsanom_depthInteg = so_depthAve.copy()
for count, depth in enumerate(newdepth):
tmp = cdu.averager(so_depthInterp[0:(count + 1), ...],
axis=0,
weights='weighted',
action='average')
so_depthAve[count, ] = tmp
tmp = cdu.averager(temp_depthInterp[0:(count + 1), ...],
axis=0,
weights='weighted',
action='average')
temp_depthAve[count, ] = tmp
tmp = cdu.averager(heat_content_sanom_depthInterp[0:(count + 1), ...],
axis=0,
weights='weighted',
action='sum')
heat_content_sanom_depthInteg[count, ] = tmp
tmp = cdu.averager(heat_content_tanom_depthInterp[0:(count + 1), ...],
axis=0,
weights='weighted',
action='sum')
heat_content_tanom_depthInteg[count, ] = tmp
tmp = cdu.averager(heat_content_tsanom_depthInterp[0:(count + 1), ...],
axis=0,
weights='weighted',
action='sum')
heat_content_tsanom_depthInteg[count, ] = tmp
del (heat_content_tanom_depthInterp, heat_content_tsanom_depthInterp)
gc.collect()
# Fix masks - applied before cdms variables are created otherwise names/ids/attributes are reset
so_depthAve = scrubNaNAndMask(so_depthAve, so_depthInterp)
temp_depthAve = scrubNaNAndMask(temp_depthAve, so_depthInterp)
heat_content_sanom_depthInteg = scrubNaNAndMask(
heat_content_sanom_depthInteg, so_depthInterp)
heat_content_tanom_depthInteg = scrubNaNAndMask(
heat_content_tanom_depthInteg, so_depthInterp)
heat_content_tsanom_depthInteg = scrubNaNAndMask(
heat_content_tsanom_depthInteg, so_depthInterp)
del (so_depthInterp)
# Convert numpy arrays to cdms objects
heat_content_sanom_depthInteg = cdm.createVariable(
heat_content_sanom_depthInteg, id='heat_content_sanom_depthInteg')
heat_content_sanom_depthInteg.id = 'heat_content_sanom_depthInteg'
heat_content_sanom_depthInteg.setAxis(0, newdepth)
heat_content_sanom_depthInteg.setAxis(1, so.getAxis(1))
heat_content_sanom_depthInteg.setAxis(2, so.getAxis(2))
heat_content_sanom_depthInteg.units = 'J'
heat_content_tanom_depthInteg = cdm.createVariable(
heat_content_tanom_depthInteg, id='heat_content_tanom_depthInteg')
heat_content_tanom_depthInteg.id = 'heat_content_tanom_depthInteg'
heat_content_tanom_depthInteg.setAxis(0, newdepth)
heat_content_tanom_depthInteg.setAxis(1, so.getAxis(1))
heat_content_tanom_depthInteg.setAxis(2, so.getAxis(2))
heat_content_tanom_depthInteg.units = 'J'
heat_content_tsanom_depthInteg = cdm.createVariable(
heat_content_tsanom_depthInteg, id='heat_content_tsanom_depthInteg')
heat_content_tsanom_depthInteg.id = 'heat_content_tsanom_depthInteg'
heat_content_tsanom_depthInteg.setAxis(0, newdepth)
heat_content_tsanom_depthInteg.setAxis(1, so.getAxis(1))
heat_content_tsanom_depthInteg.setAxis(2, so.getAxis(2))
heat_content_tsanom_depthInteg.units = 'J'
so_depthAve = cdm.createVariable(so_depthAve, id='so_depthAve')
so_depthAve.id = 'so_depthAve'
so_depthAve.setAxis(0, newdepth)
so_depthAve.setAxis(1, so.getAxis(1))
so_depthAve.setAxis(2, so.getAxis(2))
so_depthAve.units = '1e-3'
temp_depthAve = cdm.createVariable(temp_depthAve, id='temp_depthAve')
temp_depthAve.id = 'temp_depthAve'
temp_depthAve.setAxis(0, newdepth)
temp_depthAve.setAxis(1, so.getAxis(1))
temp_depthAve.setAxis(2, so.getAxis(2))
temp_depthAve.units = 'degrees_C'
steric_height_depthInterp = cdm.createVariable(
steric_height_depthInterp, id='steric_height_depthInterp')
steric_height_depthInterp.setAxis(0, newdepth)
steric_height_depthInterp.setAxis(1, so.getAxis(1))
steric_height_depthInterp.setAxis(2, so.getAxis(2))
steric_height_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_anom_depthInterp = cdm.createVariable(
steric_height_anom_depthInterp, id='steric_height_anom_depthInterp')
steric_height_anom_depthInterp.setAxis(0, newdepth)
steric_height_anom_depthInterp.setAxis(1, so.getAxis(1))
steric_height_anom_depthInterp.setAxis(2, rho.getAxis(2))
steric_height_anom_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_thermo_anom_depthInterp = cdm.createVariable(
steric_height_thermo_anom_depthInterp,
id='steric_height_thermo_anom_depthInterp')
steric_height_thermo_anom_depthInterp.setAxis(0, newdepth)
steric_height_thermo_anom_depthInterp.setAxis(1, so.getAxis(1))
steric_height_thermo_anom_depthInterp.setAxis(2, so.getAxis(2))
steric_height_thermo_anom_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom_depthInterp = cdm.createVariable(
steric_height_halo_anom_depthInterp,
id='steric_height_halo_anom_depthInterp')
steric_height_halo_anom_depthInterp.setAxis(0, newdepth)
steric_height_halo_anom_depthInterp.setAxis(1, so.getAxis(1))
steric_height_halo_anom_depthInterp.setAxis(2, so.getAxis(2))
steric_height_halo_anom_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
steric_height_halo_anom2_depthInterp = cdm.createVariable(
steric_height_halo_anom2_depthInterp,
id='steric_height_halo_anom2_depthInterp')
steric_height_halo_anom2_depthInterp.setAxis(0, newdepth)
steric_height_halo_anom2_depthInterp.setAxis(1, so.getAxis(1))
steric_height_halo_anom2_depthInterp.setAxis(2, so.getAxis(2))
steric_height_halo_anom2_depthInterp.units = 'm^3 kg^-1 Pa (dynamic decimeter)'
# Cleanup workspace
del (newdepth)
gc.collect()
# Write variables to file
if os.path.isfile(outFileName):
os.remove(outFileName)
filehandle = cdm.open(outFileName, 'w')
# Global attributes
globalAttWrite(filehandle, options=None)
# Use function to write standard global atts
# Write seawater version
filehandle.seawater_library_version = sw.__version__
# Write makeSteric version
makeStericPath = str(makeSteric.__code__).split(' ')[6]
makeStericPath = replace(replace(makeStericPath, '"', ''), ',', '')
# Clean scraped path
filehandle.makeSteric_version = ' '.join(getGitInfo(makeStericPath)[0:3])
# Master variables
filehandle.write(so.astype('float32'))
filehandle.write(so_chg.astype('float32'))
filehandle.write(so_depthAve.astype('float32'))
filehandle.write(temp.astype('float32'))
filehandle.write(temp_chg.astype('float32'))
filehandle.write(temp_depthAve.astype('float32'))
# Derived variables
filehandle.write(cp.astype('float32'))
filehandle.write(cp_halo.astype('float32'))
filehandle.write(cp_thermo.astype('float32'))
filehandle.write(rho.astype('float32'))
filehandle.write(rho_halo.astype('float32'))
filehandle.write(rho_thermo.astype('float32'))
filehandle.write(heat_content.astype('float32'))
filehandle.write(heat_content_sanom.astype('float32'))
filehandle.write(heat_content_sanom_depthInteg.astype('float32'))
filehandle.write(heat_content_tanom.astype('float32'))
filehandle.write(heat_content_tanom_depthInteg.astype('float32'))
filehandle.write(heat_content_tsanom.astype('float32'))
filehandle.write(heat_content_tsanom_depthInteg.astype('float32'))
filehandle.write(steric_height.astype('float32'))
filehandle.write(steric_height_depthInterp.astype('float32'))
filehandle.write(steric_height_anom.astype('float32'))
filehandle.write(steric_height_anom_depthInterp.astype('float32'))
filehandle.write(steric_height_halo_anom.astype('float32'))
filehandle.write(steric_height_halo_anom2.astype('float32'))
filehandle.write(steric_height_halo_anom_depthInterp.astype('float32'))
filehandle.write(steric_height_halo_anom2_depthInterp.astype('float32'))
filehandle.write(steric_height_thermo_anom.astype('float32'))
filehandle.write(steric_height_thermo_anom_depthInterp.astype('float32'))
filehandle.close()
# Cleanup workspace
del (outFileName)
gc.collect()