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Replaces deprecated np.NaN with np.nan #3

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28 changes: 14 additions & 14 deletions oceanmixedlayers/energy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -159,21 +159,21 @@ def compute_MLD(self,T_i,S_i,Rho_i,Pc,dP,Zc_i,dZ_i,energy,Debug=False):
ACTIVE[np.isnan(T_i[0,...])|np.isnan(S_i[0,...])] = False
FINISHED[np.isnan(T_i[0,...])|np.isnan(S_i[0,...])] = True

MLD_z = np.add(np.NaN,np.array(np.zeros(ND)))
MLD_z = np.add(np.nan,np.array(np.zeros(ND)))
MLD_z[ACTIVE] = 0.0
MLD_p = np.add(np.NaN,np.array(np.zeros(ND)))
MLD_p = np.add(np.nan,np.array(np.zeros(ND)))
MLD_p[ACTIVE] = 0.0
PE_x = np.add(np.NaN,np.array(np.zeros(ND)))
PE_x = np.add(np.nan,np.array(np.zeros(ND)))
PE_x[ACTIVE] = 0.0
PE_i = np.add(np.NaN,np.array(np.zeros(ND)))
PE_i = np.add(np.nan,np.array(np.zeros(ND)))
PE_i[ACTIVE] = 0.0
PE_i_above = np.add(np.NaN,np.array(np.zeros(ND)))
PE_i_above = np.add(np.nan,np.array(np.zeros(ND)))
PE_i_above[ACTIVE] = 0.0
MLDp = np.add(np.NaN,np.array(np.zeros(ND)))
MLDp = np.add(np.nan,np.array(np.zeros(ND)))
MLDp[ACTIVE] = 0.0
MLDz = np.add(np.NaN,np.array(np.zeros(ND)))
MLDz = np.add(np.nan,np.array(np.zeros(ND)))
MLDz[ACTIVE] = 0.0
IT_total = np.add(np.NaN,np.array(np.zeros(ND)))
IT_total = np.add(np.nan,np.array(np.zeros(ND)))
IT_total[ACTIVE] = 0

z=-1
Expand Down Expand Up @@ -382,17 +382,17 @@ def compute_MLD(self,Zc,dZ,Rho0_layer,dRho0dz_layer,energy,CNVG_T=1.e-5,Debug=Fa
ACTIVE[np.isnan(Rho0_layer[0,...])] = False
FINISHED[np.isnan(Rho0_layer[0,...])] = True

MLD = np.add(np.NaN,np.array(np.zeros(ND)))
MLD = np.add(np.nan,np.array(np.zeros(ND)))
MLD[ACTIVE] = 0.0
PE_after = np.add(np.NaN,np.array(np.zeros(ND)))
PE_after = np.add(np.nan,np.array(np.zeros(ND)))
PE_after[ACTIVE] = 0.0
PE_before = np.add(np.NaN,np.array(np.zeros(ND)))
PE_before = np.add(np.nan,np.array(np.zeros(ND)))
PE_before[ACTIVE] = 0.0
PE_before_above = np.add(np.NaN,np.array(np.zeros(ND)))
PE_before_above = np.add(np.nan,np.array(np.zeros(ND)))
PE_before_above[ACTIVE] = 0.0
dz_Mixed = np.add(np.NaN,np.array(np.zeros(ND)))
dz_Mixed = np.add(np.nan,np.array(np.zeros(ND)))
dz_Mixed[ACTIVE] = 0.0
IT_total = np.add(np.NaN,np.array(np.zeros(ND)))
IT_total = np.add(np.nan,np.array(np.zeros(ND)))
IT_total[ACTIVE] = 0

z=-1
Expand Down
14 changes: 7 additions & 7 deletions oceanmixedlayers/energy2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ def energy_anomaly_mld_density(z_c,#Central z position relative to sea surface (
energy=1.0,#energy threshold (J/m2)
threshold=1.e-5,#convergence threshold (nd)
gradient=False,
mask_val=np.NaN
mask_val=np.nan
):
"""Computes the threshold mld with a fixed vertical coordinate"""
num_coord = ptntl_rho_layer.shape[0]
Expand All @@ -40,12 +40,12 @@ def energy_anomaly_mld_density(z_c,#Central z position relative to sea surface (

mask = update_mask(ptntl_rho_layer[0,...],mask_val)
active_mask = ~mask
mld = np.add(np.NaN,np.zeros(shape_profs));mld[active_mask]=0.0
delta_energy = np.add(np.NaN,np.zeros(shape_profs));delta_energy[active_mask]=0.0
pe_mixed = np.add(np.NaN,np.zeros(shape_profs));pe_mixed[active_mask]=0.0
pe_unmixed = np.add(np.NaN,np.zeros(shape_profs));pe_unmixed[active_mask]=0.0
dz_mixed = np.add(np.NaN,np.zeros(shape_profs));dz_mixed[active_mask]=0.0
iterations = np.add(np.NaN,np.zeros(shape_profs));iterations[active_mask]=0.0
mld = np.add(np.nan,np.zeros(shape_profs));mld[active_mask]=0.0
delta_energy = np.add(np.nan,np.zeros(shape_profs));delta_energy[active_mask]=0.0
pe_mixed = np.add(np.nan,np.zeros(shape_profs));pe_mixed[active_mask]=0.0
pe_unmixed = np.add(np.nan,np.zeros(shape_profs));pe_unmixed[active_mask]=0.0
dz_mixed = np.add(np.nan,np.zeros(shape_profs));dz_mixed[active_mask]=0.0
iterations = np.add(np.nan,np.zeros(shape_profs));iterations[active_mask]=0.0

iz=0
while(iz<num_coord and np.sum(active_mask)>0):
Expand Down
8 changes: 4 additions & 4 deletions oceanmixedlayers/energy_Newton.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,13 +61,13 @@ def compute_MLD(self,Zc,dZ,Rho0_layer,dRho0dz_layer,energy,CNVG_T=1.e-5,Debug=Fa
ACTIVE[np.isnan(Rho0_layer[0,...])] = False
FINISHED[np.isnan(Rho0_layer[0,...])] = True

MLD = np.add(np.NaN,np.array(np.zeros(ND)))
MLD = np.add(np.nan,np.array(np.zeros(ND)))
MLD[ACTIVE] = 0.0
PE_after = np.add(np.NaN,np.array(np.zeros(ND)))
PE_after = np.add(np.nan,np.array(np.zeros(ND)))
PE_after[ACTIVE] = 0.0
PE_before = np.add(np.NaN,np.array(np.zeros(ND)))
PE_before = np.add(np.nan,np.array(np.zeros(ND)))
PE_before[ACTIVE] = 0.0
IT_total = np.add(np.NaN,np.array(np.zeros(ND)))
IT_total = np.add(np.nan,np.array(np.zeros(ND)))
IT_total[ACTIVE] = 0

z=-1
Expand Down
2 changes: 1 addition & 1 deletion oceanmixedlayers/extrema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ class extrema():
def __init__(self):
pass

def maxval_mld_fixedcoord(coordinate, value, mask_val=np.NaN):
def maxval_mld_fixedcoord(coordinate, value, mask_val=np.nan):
"""Computes the threshold mld with a fixed vertical coordinate"""

if (coordinate.shape != value.shape):
Expand Down
6 changes: 3 additions & 3 deletions oceanmixedlayers/gradient.py
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Expand Up @@ -10,7 +10,7 @@ def __init__(self):
pass


def gradient_mld_fixedcoord(coordinate, value, critical_gradient, mask_val=np.NaN,smooth=True):
def gradient_mld_fixedcoord(coordinate, value, critical_gradient, mask_val=np.nan,smooth=True):
"""Computes the gradient mld with a fixed vertical coordinate"""

if (coordinate.shape != value.shape):
Expand Down Expand Up @@ -84,7 +84,7 @@ def gradient_mld_fixedcoord(coordinate, value, critical_gradient, mask_val=np.Na
i_c+=1
return mld, mldi

def max_gradient(coordinate, value, critical_gradient, mask_val=np.NaN,smooth=True):
def max_gradient(coordinate, value, critical_gradient, mask_val=np.nan,smooth=True):
"""Computes the gradient mld with a fixed vertical coordinate"""

if (coordinate.shape != value.shape):
Expand Down Expand Up @@ -129,7 +129,7 @@ def max_gradient(coordinate, value, critical_gradient, mask_val=np.NaN,smooth=Tr
return mld, mldi


def linearfit_mld_fixedcoord(coordinate, value, error_tolerance, mask_val=np.NaN,smooth=True):
def linearfit_mld_fixedcoord(coordinate, value, error_tolerance, mask_val=np.nan,smooth=True):
"""
Computes the mld from fiting a linear slope to the thermocline and mixed layer
with a fixed vertical coordinate
Expand Down
8 changes: 4 additions & 4 deletions oceanmixedlayers/holtetalley.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,13 @@ def algorithm_mld(presi, sali, cnsrv_tempi, ptntl_rhoi):
for zi in range(LP):
LI = (MINDIFF==(pres[zi,...]-10.)**2)
pres[:LP-zi,LI]=(pres[zi:,LI])
pres[LP-zi:,LI]=np.NaN
pres[LP-zi:,LI]=np.nan
sal[:LP-zi,LI]=(sal[zi:,LI])
sal[LP-zi:,LI]=np.NaN
sal[LP-zi:,LI]=np.nan
ptntl_rho[:LP-zi,LI]=(ptntl_rho[zi:,LI])
ptntl_rho[LP-zi:,LI]=np.NaN
ptntl_rho[LP-zi:,LI]=np.nan
cnsrv_temp[:LP-zi,LI]=(cnsrv_temp[zi:,LI])
cnsrv_temp[LP-zi:,LI]=np.NaN
cnsrv_temp[LP-zi:,LI]=np.nan
MINDIFF[LI]=0.0

##########################################################################
Expand Down
2 changes: 1 addition & 1 deletion oceanmixedlayers/pe_anomaly.py
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Expand Up @@ -50,7 +50,7 @@ def compute(self,Rho0_layer,dRho0dz_layer,Zc,dZi,DPT):
Rho0_Mixed = np.copy(Rho0_layer)
dz_Mixed = dZ[0]

PEdelta = np.zeros(ND)+np.NaN
PEdelta = np.zeros(ND)+np.nan

ACTIVE = np.ones(ND,dtype='bool')
ACTIVE[np.isnan(Rho0_layer[0,...])] = False
Expand Down
2 changes: 1 addition & 1 deletion oceanmixedlayers/threshold.py
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Expand Up @@ -9,7 +9,7 @@ class threshold():
def __init__(self):
pass

def threshold_mld_fixedcoord(coordinate, value, delta=0.0, reference=0.0, mask_val=np.NaN, interp=True, interpsurf=True,absdiff=False):
def threshold_mld_fixedcoord(coordinate, value, delta=0.0, reference=0.0, mask_val=np.nan, interp=True, interpsurf=True,absdiff=False):
"""Computes the threshold mld with a fixed vertical coordinate"""

if (coordinate.shape != value.shape):
Expand Down
28 changes: 14 additions & 14 deletions tests/Argo_Batch.ipynb
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Expand Up @@ -66,11 +66,11 @@
"outputs": [],
"source": [
"def mld_dataset(LP):\n",
" OUT = xr.Dataset(data_vars={'mld':(('prof'), np.add(np.NaN,np.zeros([LP]))),\n",
" 'pe_anom':(('prof'), np.add(np.NaN,np.zeros([LP]))),\n",
" 'latitude':(('prof'), np.add(np.NaN,np.zeros([LP]))),\n",
" 'longitude':(('prof'), np.add(np.NaN,np.zeros([LP]))),\n",
" 'julian_day':(('prof'), np.add(np.NaN,np.zeros([LP]))),\n",
" OUT = xr.Dataset(data_vars={'mld':(('prof'), np.add(np.nan,np.zeros([LP]))),\n",
" 'pe_anom':(('prof'), np.add(np.nan,np.zeros([LP]))),\n",
" 'latitude':(('prof'), np.add(np.nan,np.zeros([LP]))),\n",
" 'longitude':(('prof'), np.add(np.nan,np.zeros([LP]))),\n",
" 'julian_day':(('prof'), np.add(np.nan,np.zeros([LP]))),\n",
" 'file':(''),\n",
" 'dac':(''),\n",
" 'argo_id':(''),\n",
Expand Down Expand Up @@ -108,15 +108,15 @@
"\n",
" NP = hndl.N_PROF.size\n",
" NZ = hndl.N_LEVELS.size\n",
" Z_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" dZ_2d = np.zeros([NP,NZ])+np.NaN\n",
" P_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" dP_2d = np.zeros([NP,NZ])+np.NaN\n",
" CT_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" PSal_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" dRho0dz_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" Rho0_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" Rho_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" Z_c_2d = np.zeros([NP,NZ])+np.nan\n",
" dZ_2d = np.zeros([NP,NZ])+np.nan\n",
" P_c_2d = np.zeros([NP,NZ])+np.nan\n",
" dP_2d = np.zeros([NP,NZ])+np.nan\n",
" CT_c_2d = np.zeros([NP,NZ])+np.nan\n",
" PSal_c_2d = np.zeros([NP,NZ])+np.nan\n",
" dRho0dz_c_2d = np.zeros([NP,NZ])+np.nan\n",
" Rho0_c_2d = np.zeros([NP,NZ])+np.nan\n",
" Rho_c_2d = np.zeros([NP,NZ])+np.nan\n",
" GOOD = np.zeros([NP],dtype=bool)\n",
" for p in range(NP):\n",
" DayQC = float(hndl.JULD_QC[p])\n",
Expand Down
16 changes: 8 additions & 8 deletions tests/Argo_Examples.ipynb
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Expand Up @@ -69,21 +69,21 @@
" # effectively mimicing an ocean model vertical grid\n",
" \n",
" #> Central depth of layers\n",
" Z_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" Z_c_2d = np.zeros([NP,NZ])+np.nan\n",
" #> Thickness of layers\n",
" dZ_2d = np.zeros([NP,NZ])+np.NaN\n",
" dZ_2d = np.zeros([NP,NZ])+np.nan\n",
" # Central pressure of layers\n",
" P_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" P_c_2d = np.zeros([NP,NZ])+np.nan\n",
" # Thickness of layers in pressure space\n",
" dP_2d = np.zeros([NP,NZ])+np.NaN\n",
" dP_2d = np.zeros([NP,NZ])+np.nan\n",
" # Mean conservative temperature of layer\n",
" CT_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" CT_c_2d = np.zeros([NP,NZ])+np.nan\n",
" # Mean practical salinity of layer\n",
" PSal_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" PSal_c_2d = np.zeros([NP,NZ])+np.nan\n",
" # Mean potential density (p=0) of layer\n",
" Rho0_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" Rho0_c_2d = np.zeros([NP,NZ])+np.nan\n",
" # Gradient of potential density over layer\n",
" dRho0dz_c_2d = np.zeros([NP,NZ])+np.NaN\n",
" dRho0dz_c_2d = np.zeros([NP,NZ])+np.nan\n",
" # A quality control flag for determining which floats to use\n",
" GOOD = np.zeros([NP],dtype=bool)\n",
" \n",
Expand Down