AeroViz 0.1.2__py3-none-any.whl → 0.1.3b0__py3-none-any.whl

AeroViz/dataProcess/Chemistry/__init__.py

@@ -2,62 +2,62 @@ from ..core import _writter, _run_process
 
 __all__ = [
 
-	'Chemistry',
+    'Chemistry',
 
 ]
 
 
 class Chemistry(_writter):
 
-	## Reconstruction
-	@_run_process('Chemistry - reconstruction basic', 'reconstrc_basic')
-	def ReConstrc_basic(self, *df_chem, df_ref=None, df_water=None, df_density=None,
-						nam_lst=['NH4+', 'SO42-', 'NO3-', 'Fe', 'Na+', 'OC', 'EC']):
-		from ._mass_volume import _basic
+    ## Reconstruction
+    @_run_process('Chemistry - reconstruction basic', 'reconstrc_basic')
+    def ReConstrc_basic(self, *df_chem, df_ref=None, df_water=None, df_density=None,
+                        nam_lst=['NH4+', 'SO42-', 'NO3-', 'Fe', 'Na+', 'OC', 'EC']):
+        from ._mass_volume import _basic
 
-		out = _basic(df_chem, df_ref, df_water, df_density, nam_lst=nam_lst)
+        out = _basic(df_chem, df_ref, df_water, df_density, nam_lst=nam_lst)
 
-		return self, out
+        return self, out
 
-	## Partition
-	@_run_process('Chemistry -  Partition', 'partition')
-	def Partition(self, *df_chem, nam_lst=['NH4+', 'SO42-', 'NO3-', 'Cl-', 'NO2', 'HNO3', 'SO2', 'NH3', 'HCl', 'temp']):
-		from ._partition import _basic
+    ## Partition
+    @_run_process('Chemistry -  Partition', 'partition')
+    def Partition(self, *df_chem, nam_lst=['NH4+', 'SO42-', 'NO3-', 'Cl-', 'NO2', 'HNO3', 'SO2', 'NH3', 'HCl', 'temp']):
+        from ._partition import _basic
 
-		out = _basic(df_chem, nam_lst=nam_lst)
+        out = _basic(df_chem, nam_lst=nam_lst)
 
-		return self, out
+        return self, out
 
-	## ISOROPIA
-	@_run_process('Chemistry - ISOROPIA', 'isoropia')
-	def ISOROPIA(self, *df_chem,
-				 nam_lst=['Na+', 'SO42-', 'NH4+', 'NO3-', 'Cl-', 'Ca2+', 'K+', 'Mg2+', 'NH3', 'HNO3', 'HCl', 'RH',
-						  'temp']):
-		from ._isoropia import _basic
+    ## ISOROPIA
+    @_run_process('Chemistry - ISOROPIA', 'isoropia')
+    def ISOROPIA(self, *df_chem,
+                 nam_lst=['Na+', 'SO42-', 'NH4+', 'NO3-', 'Cl-', 'Ca2+', 'K+', 'Mg2+', 'NH3', 'HNO3', 'HCl', 'RH',
+                          'temp']):
+        from ._isoropia import _basic
 
-		if self.path_out is None:
-			raise ValueError('Please Input "path_out" !!')
+        if self.path_out is None:
+            raise ValueError('Please Input "path_out" !!')
 
-		out = _basic(df_chem, self.path_out, nam_lst=nam_lst)
+        out = _basic(df_chem, self.path_out, nam_lst=nam_lst)
 
-		return self, out
+        return self, out
 
-	## OCEC
-	@_run_process('Chemistry - OC/EC basic', 'ocec_basic')
-	def OCEC_basic(self, df_lcres, df_res, df_mass=None, ocec_ratio=None, ocec_ratio_month=1, hr_lim=200,
-				   least_square_range=(0.1, 2.5, 0.1), WISOC_OC_range=(0.2, 0.7, 0.01), ):
-		from ._ocec import _basic
+    ## OCEC
+    @_run_process('Chemistry - OC/EC basic', 'ocec_basic')
+    def OCEC_basic(self, df_lcres, df_res, df_mass=None, ocec_ratio=None, ocec_ratio_month=1, hr_lim=200,
+                   least_square_range=(0.1, 2.5, 0.1), WISOC_OC_range=(0.2, 0.7, 0.01), ):
+        from ._ocec import _basic
 
-		out = _basic(df_lcres, df_res, df_mass, ocec_ratio, ocec_ratio_month, hr_lim, least_square_range,
-					 WISOC_OC_range)
+        out = _basic(df_lcres, df_res, df_mass, ocec_ratio, ocec_ratio_month, hr_lim, least_square_range,
+                     WISOC_OC_range)
 
-		return self, out
+        return self, out
 
-	## TEOM
-	@_run_process('Chemistry - TEOM basic', 'teom_basic')
-	def TEOM_basic(self, df_teom, df_check=None):
-		from ._teom import _basic
+    ## TEOM
+    @_run_process('Chemistry - TEOM basic', 'teom_basic')
+    def TEOM_basic(self, df_teom, df_check=None):
+        from ._teom import _basic
 
-		out = _basic(df_teom, df_check)
+        out = _basic(df_teom, df_check)
 
-		return self, out
+        return self, out

AeroViz/dataProcess/Chemistry/_calculate.py

@@ -1,27 +1,27 @@
-from pandas import concat, DataFrame
+from pandas import concat
 
 # parameter
 _mol_wg = {
-	'SO42-': 96.06,
-	'NO3-': 62.00,
-	'Cl-': 35.4,
+    'SO42-': 96.06,
+    'NO3-': 62.00,
+    'Cl-': 35.4,
 
-	'Ca2+': 40.078,
-	'K+': 39.098,
-	'Mg2+': 24.305,
-	'Na+': 22.99,
-	'NH4+': 18.04,
+    'Ca2+': 40.078,
+    'K+': 39.098,
+    'Mg2+': 24.305,
+    'Na+': 22.99,
+    'NH4+': 18.04,
 }
 
 
 # ug -> umol
 def _ug2umol(_df):
-	_pt_ky = list(set(_df.keys()) & set(_mol_wg.keys()))
-	_gas_ky = list(set(_df.keys()) - set(_mol_wg.keys()) - set(['temp', 'RH']))
+    _pt_ky = list(set(_df.keys()) & set(_mol_wg.keys()))
+    _gas_ky = list(set(_df.keys()) - set(_mol_wg.keys()) - set(['temp', 'RH']))
 
-	_par = (_df['temp'].to_frame() + 273.15) * .082
+    _par = (_df['temp'].to_frame() + 273.15) * .082
 
-	_df_pt = concat([(_df[_ky] / _mol_wg[_ky]).copy() for _ky in _pt_ky], axis=1)
-	_df_gas = _df[_gas_ky] / _par.values
+    _df_pt = concat([(_df[_ky] / _mol_wg[_ky]).copy() for _ky in _pt_ky], axis=1)
+    _df_gas = _df[_gas_ky] / _par.values
 
-	return concat([_df_pt, _df_gas], axis=1)
+    return concat([_df_pt, _df_gas], axis=1)

AeroViz/dataProcess/Chemistry/_isoropia.py

@@ -1,99 +1,100 @@
+from pathlib import Path
 from subprocess import Popen, PIPE
-from pandas import date_range, concat, DataFrame, to_numeric, read_csv
-from ._calculate import _ug2umol
+
 import numpy as np
+from pandas import concat, DataFrame, to_numeric, read_csv
 
-from pathlib import Path
+from ._calculate import _ug2umol
 
 
 def _basic(df_che, path_out, nam_lst):
-	# parameter
-	df_all = concat(df_che, axis=1)
-	index = df_all.index.copy()
-	df_all.columns = nam_lst
+    # parameter
+    df_all = concat(df_che, axis=1)
+    index = df_all.index.copy()
+    df_all.columns = nam_lst
 
-	df_umol = _ug2umol(df_all)
+    df_umol = _ug2umol(df_all)
 
-	## output
-	## Na, SO4, NH3, NO3, Cl, Ca, K, Mg, RH, TEMP
-	df_input = DataFrame(index=index)
-	df_out = DataFrame(index=index)
+    ## output
+    ## Na, SO4, NH3, NO3, Cl, Ca, K, Mg, RH, TEMP
+    df_input = DataFrame(index=index)
+    df_out = DataFrame(index=index)
 
-	pth_input = path_out / '_temp_input.txt'
-	pth_output = path_out / '_temp_input.dat'
+    pth_input = path_out / '_temp_input.txt'
+    pth_output = path_out / '_temp_input.dat'
 
-	pth_input.unlink(missing_ok=True)
-	pth_output.unlink(missing_ok=True)
+    pth_input.unlink(missing_ok=True)
+    pth_output.unlink(missing_ok=True)
 
-	## header
-	_header = 'Input units (0=umol/m3, 1=ug/m3)\n' + '0\n\n' + \
-			  'Problem type (0=forward, 1=reverse); Phase state (0=solid+liquid, 1=metastable)\n' + '0, 1\n\n' + \
-			  'NH4-SO4 system case\n'
+    ## header
+    _header = 'Input units (0=umol/m3, 1=ug/m3)\n' + '0\n\n' + \
+              'Problem type (0=forward, 1=reverse); Phase state (0=solid+liquid, 1=metastable)\n' + '0, 1\n\n' + \
+              'NH4-SO4 system case\n'
 
-	## software
-	path_iso = Path(__file__).parent / 'isrpia2.exe'
+    ## software
+    path_iso = Path(__file__).parent / 'isrpia2.exe'
 
-	# make input file and output temp input (without index)
-	## NH3
-	df_input['NH3'] = df_umol['NH4+'].fillna(0).copy() + df_umol['NH3']
+    # make input file and output temp input (without index)
+    ## NH3
+    df_input['NH3'] = df_umol['NH4+'].fillna(0).copy() + df_umol['NH3']
 
-	## NO3
-	df_input['NO3'] = df_umol['HNO3'].fillna(0).copy() + df_umol['NO3-']
+    ## NO3
+    df_input['NO3'] = df_umol['HNO3'].fillna(0).copy() + df_umol['NO3-']
 
-	## Cl
-	df_input['Cl'] = df_umol['HCl'].fillna(0).copy() + df_umol['Cl-']
+    ## Cl
+    df_input['Cl'] = df_umol['HCl'].fillna(0).copy() + df_umol['Cl-']
 
-	## temp, RH
-	df_input['RH'] = df_all['RH'] / 100
-	df_input['TEMP'] = df_all['temp'] + 273.15
+    ## temp, RH
+    df_input['RH'] = df_all['RH'] / 100
+    df_input['TEMP'] = df_all['temp'] + 273.15
 
-	df_input[['Na', 'SO4', 'Ca', 'K', 'Mg']] = df_umol[['Na+', 'SO42-', 'Ca2+', 'K+', 'Mg2+']].copy()
+    df_input[['Na', 'SO4', 'Ca', 'K', 'Mg']] = df_umol[['Na+', 'SO42-', 'Ca2+', 'K+', 'Mg2+']].copy()
 
-	df_input = df_input[['Na', 'SO4', 'NH3', 'NO3', 'Cl', 'Ca', 'K', 'Mg', 'RH', 'TEMP']].fillna('-').copy()
+    df_input = df_input[['Na', 'SO4', 'NH3', 'NO3', 'Cl', 'Ca', 'K', 'Mg', 'RH', 'TEMP']].fillna('-').copy()
 
-	## output the input data
-	df_input.to_csv(pth_input, index=False)
-	with (pth_input).open('r+', encoding='utf-8', errors='ignore') as _f:
-		_cont = _f.read()
-		_f.seek(0)
+    ## output the input data
+    df_input.to_csv(pth_input, index=False)
+    with (pth_input).open('r+', encoding='utf-8', errors='ignore') as _f:
+        _cont = _f.read()
+        _f.seek(0)
 
-		_f.write(_header)
-		_f.write(_cont)
+        _f.write(_header)
+        _f.write(_cont)
 
-	# use ISOROPIA2
-	run = Popen([path_iso], stdin=PIPE, stdout=PIPE, stderr=PIPE)
-	scrn_res, run_res = run.communicate(input=str(pth_input.resolve()).encode())
+    # use ISOROPIA2
+    run = Popen([path_iso], stdin=PIPE, stdout=PIPE, stderr=PIPE)
+    scrn_res, run_res = run.communicate(input=str(pth_input.resolve()).encode())
 
-	# read dat file and transform to the normal name
-	cond_idx = df_all[['SO42-', 'NH4+', 'NO3-']].dropna().index
+    # read dat file and transform to the normal name
+    cond_idx = df_all[['SO42-', 'NH4+', 'NO3-']].dropna().index
 
-	with (pth_output).open('r', encoding='utf-8', errors='ignore') as f:
-		df_res = read_csv(f, delimiter='\s+').apply(to_numeric, errors='coerce').set_index(index)
+    with (pth_output).open('r', encoding='utf-8', errors='ignore') as f:
+        df_res = read_csv(f, delimiter='\s+').apply(to_numeric, errors='coerce').set_index(index)
 
-	df_out['H'] = df_res['HLIQ'] / (df_res['WATER'] / 1000)
+    df_out['H'] = df_res['HLIQ'] / (df_res['WATER'] / 1000)
 
-	df_out.loc[cond_idx, 'pH'] = -np.log10(df_out['H'].loc[cond_idx])
-	df_out['pH'] = df_out['pH'].where((df_all['RH'] <= 95) & (df_all['RH'] >= 20))
+    df_out.loc[cond_idx, 'pH'] = -np.log10(df_out['H'].loc[cond_idx])
+    df_out['pH'] = df_out['pH'].where((df_all['RH'] <= 95) & (df_all['RH'] >= 20))
 
-	cond_idx = df_out['pH'].dropna().index
-	df_out.loc[cond_idx, 'ALWC'] = df_res['WATER'].loc[cond_idx]
+    cond_idx = df_out['pH'].dropna().index
+    df_out.loc[cond_idx, 'ALWC'] = df_res['WATER'].loc[cond_idx]
 
-	df_out[['NH3', 'HNO3', 'HCl', 'NH4+', 'NO3-', 'Cl-']] = df_res[
-		['GNH3', 'GHNO3', 'GHCL', 'NH4AER', 'NO3AER', 'CLAER']]
+    df_out[['NH3', 'HNO3', 'HCl', 'NH4+', 'NO3-', 'Cl-']] = df_res[
+        ['GNH3', 'GHNO3', 'GHCL', 'NH4AER', 'NO3AER', 'CLAER']]
 
-	# calculate partition
-	# df_out['epls_NO3-'] = df_umol['NO3-'] / (df_umol['NO3-'] + df_umol['HNO3'])
-	# df_out['epls_NH4+'] = df_umol['NH4+'] / (df_umol['NH4+'] + df_umol['NH3'])
-	# df_out['epls_Cl-']  = df_umol['Cl-'] / (df_umol['Cl-'] + df_umol['HCl'])
+    # calculate partition
+    # df_out['epls_NO3-'] = df_umol['NO3-'] / (df_umol['NO3-'] + df_umol['HNO3'])
+    # df_out['epls_NH4+'] = df_umol['NH4+'] / (df_umol['NH4+'] + df_umol['NH3'])
+    # df_out['epls_Cl-']  = df_umol['Cl-'] / (df_umol['Cl-'] + df_umol['HCl'])
 
-	# remove _temp file (input and output)
-	pth_input.unlink(missing_ok=True)
-	pth_output.unlink(missing_ok=True)
+    # remove _temp file (input and output)
+    pth_input.unlink(missing_ok=True)
+    pth_output.unlink(missing_ok=True)
 
-	# output input and output
-	out = {
-		'input': df_input,
-		'output': df_out,
-	}
+    # output input and output
+    out = {
+        'input': df_input,
+        'output': df_out,
+    }
 
-	return out
+    return out

AeroViz/dataProcess/Chemistry/_mass_volume.py

@@ -1,175 +1,175 @@
-from pandas import date_range, concat, DataFrame, to_numeric
+from pandas import concat, DataFrame
 
 
 def _basic(df_che, df_ref, df_water, df_density, nam_lst):
-	df_all = concat(df_che, axis=1)
-	index = df_all.index.copy()
-	df_all.columns = nam_lst
-
-	## parameter
-	mol_A, mol_S, mol_N = df_all['NH4+'] / 18, df_all['SO42-'] / 96, df_all['NO3-'] / 62
-	df_all['status'] = (mol_A) / (2 * mol_S + mol_N)
-
-	convert_nam = {'AS': 'SO42-',
-				   'AN': 'NO3-',
-				   'OM': 'OC',
-				   'Soil': 'Fe',
-				   'SS': 'Na+',
-				   'EC': 'EC',
-				   }
-
-	mass_coe = {'AS': 1.375,
-				'AN': 1.29,
-				'OM': 1.8,
-				'Soil': 28.57,
-				'SS': 2.54,
-				'EC': 1,
-				}
-
-	vol_coe = {'AS': 1.76,
-			   'AN': 1.73,
-			   'OM': 1.4,
-			   'Soil': 2.6,
-			   'SS': 2.16,
-			   'EC': 1.5,
-			   }
-
-	RI_coe = {'550': {'ALWC': 1.333 + 0j,
-					  'AS': 1.53 + 0j,
-					  'AN': 1.55 + 0j,
-					  'OM': 1.55 + 0.0163j,
-					  'Soil': 1.56 + 0.006j,
-					  'SS': 1.54 + 0j,
-					  'EC': 1.80 + 0.72j,
-					  },
-
-			  ## m + kj -> m value is same as 550 current
-			  '450': {'ALWC': 1.333 + 0j,
-					  'AS': 1.57 + 0j,
-					  'AN': 1.57 + 0j,
-					  'OM': 1.58 + 0.056,
-					  'Soil': 1.56 + 0.009j,
-					  'SS': 1.54 + 0j,
-					  'EC': 1.80 + 0.79j,
-					  },
-			  }
-
-	## mass
-	## NH4 Enough
-	df_mass = DataFrame()
-	df_enough = df_all.where(df_all['status'] >= 1).dropna().copy()
-
-	for _mass_nam, _coe in mass_coe.items():
-		df_mass[_mass_nam] = df_all[convert_nam[_mass_nam]] * _coe
-
-	## NH4 Deficiency
-	defic_idx = df_all['status'] < 1
-
-	if defic_idx.any():
-		residual = mol_A - 2 * mol_S
-
-		## residual > 0
-		_status = residual > 0
-		if _status.any():
-			_cond = _status & (residual <= mol_N)
-			df_mass.loc[_cond, 'AN'] = residual.loc[_cond] * 80
-
-			_cond = _status & (residual > mol_N)
-			df_mass.loc[_cond, 'AN'] = mol_N.loc[_cond] * 80
-
-		## residual < 0
-		_status = residual <= 0
-		if _status.any():
-			df_mass.loc[_status, 'AN'] = 0
-
-			_cond = _status & (mol_A <= 2 * mol_S)
-			df_mass.loc[_cond, 'AS'] = mol_A.loc[_cond] / 2 * 132
-
-			_cond = _status & (mol_A > 2 * mol_S)
-			df_mass.loc[_cond, 'AS'] = mol_S.loc[_cond] * 132
-
-	df_mass_cal = df_mass.dropna().copy()
-	df_mass['total'] = df_mass.sum(axis=1, min_count=6)
-
-	qc_ratio = df_mass['total'] / df_ref
-	qc_cond = (qc_ratio >= 0.7) & (qc_ratio <= 1.3)
-
-	## volume
-	df_vol = DataFrame()
-	for _vol_nam, _coe in vol_coe.items():
-		df_vol[_vol_nam] = df_mass_cal[_vol_nam] / _coe
-
-	if df_water is not None:
-		df_vol['ALWC'] = df_water
-		df_vol = df_vol.dropna()
-		df_vol['total_wet'] = df_vol.sum(axis=1, min_count=6)
-
-	df_vol['total_dry'] = df_vol[vol_coe.keys()].sum(axis=1, min_count=6)
-
-	## density
-	df_vol_cal = DataFrame()
-	df_den_rec = df_mass['total'] / df_vol['total_dry']
-	if df_density is not None:
-		df_den_all = concat([df_all[['SO42-', 'NO3-', 'NH4+', 'EC']], df_density, df_mass['OM']], axis=1).dropna()
-
-		df_vol_cal = (df_den_all[['SO42-', 'NO3-', 'NH4+']].sum(axis=1) / 1.75) + \
-					 df_den_all['Cl-'] / 1.52 + \
-					 df_den_all['OM'] / 1.4 + df_den_all['EC'] / 1.77
-
-		df_den = df_den_all.sum(axis=1, min_count=6) / df_vol_cal
-	# df_den = df_den_all.sum(axis=1) / df_vol_cal
-	# df_den = df_mass['total'].loc[df_den_all.index] / df_vol_cal
-
-	## refractive index
-	ri_dic = {}
-	for _lambda, _coe in RI_coe.items():
-
-		df_RI = DataFrame()
-
-		for _ky, _df in df_vol.items():
-			if 'total' in _ky: continue
-			df_RI[_ky] = (_df * _coe[_ky])
-
-		df_RI['RI_wet'] = None
-		if df_water is not None:
-			df_RI['RI_wet'] = (df_RI / df_vol['total_wet'].to_frame().values).sum(axis=1)
+    df_all = concat(df_che, axis=1)
+    index = df_all.index.copy()
+    df_all.columns = nam_lst
+
+    ## parameter
+    mol_A, mol_S, mol_N = df_all['NH4+'] / 18, df_all['SO42-'] / 96, df_all['NO3-'] / 62
+    df_all['status'] = (mol_A) / (2 * mol_S + mol_N)
+
+    convert_nam = {'AS': 'SO42-',
+                   'AN': 'NO3-',
+                   'OM': 'OC',
+                   'Soil': 'Fe',
+                   'SS': 'Na+',
+                   'EC': 'EC',
+                   }
+
+    mass_coe = {'AS': 1.375,
+                'AN': 1.29,
+                'OM': 1.8,
+                'Soil': 28.57,
+                'SS': 2.54,
+                'EC': 1,
+                }
+
+    vol_coe = {'AS': 1.76,
+               'AN': 1.73,
+               'OM': 1.4,
+               'Soil': 2.6,
+               'SS': 2.16,
+               'EC': 1.5,
+               }
+
+    RI_coe = {'550': {'ALWC': 1.333 + 0j,
+                      'AS': 1.53 + 0j,
+                      'AN': 1.55 + 0j,
+                      'OM': 1.55 + 0.0163j,
+                      'Soil': 1.56 + 0.006j,
+                      'SS': 1.54 + 0j,
+                      'EC': 1.80 + 0.72j,
+                      },
+
+              ## m + kj -> m value is same as 550 current
+              '450': {'ALWC': 1.333 + 0j,
+                      'AS': 1.57 + 0j,
+                      'AN': 1.57 + 0j,
+                      'OM': 1.58 + 0.056,
+                      'Soil': 1.56 + 0.009j,
+                      'SS': 1.54 + 0j,
+                      'EC': 1.80 + 0.79j,
+                      },
+              }
+
+    ## mass
+    ## NH4 Enough
+    df_mass = DataFrame()
+    df_enough = df_all.where(df_all['status'] >= 1).dropna().copy()
+
+    for _mass_nam, _coe in mass_coe.items():
+        df_mass[_mass_nam] = df_all[convert_nam[_mass_nam]] * _coe
+
+    ## NH4 Deficiency
+    defic_idx = df_all['status'] < 1
+
+    if defic_idx.any():
+        residual = mol_A - 2 * mol_S
+
+        ## residual > 0
+        _status = residual > 0
+        if _status.any():
+            _cond = _status & (residual <= mol_N)
+            df_mass.loc[_cond, 'AN'] = residual.loc[_cond] * 80
+
+            _cond = _status & (residual > mol_N)
+            df_mass.loc[_cond, 'AN'] = mol_N.loc[_cond] * 80
+
+        ## residual < 0
+        _status = residual <= 0
+        if _status.any():
+            df_mass.loc[_status, 'AN'] = 0
+
+            _cond = _status & (mol_A <= 2 * mol_S)
+            df_mass.loc[_cond, 'AS'] = mol_A.loc[_cond] / 2 * 132
+
+            _cond = _status & (mol_A > 2 * mol_S)
+            df_mass.loc[_cond, 'AS'] = mol_S.loc[_cond] * 132
+
+    df_mass_cal = df_mass.dropna().copy()
+    df_mass['total'] = df_mass.sum(axis=1, min_count=6)
+
+    qc_ratio = df_mass['total'] / df_ref
+    qc_cond = (qc_ratio >= 0.7) & (qc_ratio <= 1.3)
+
+    ## volume
+    df_vol = DataFrame()
+    for _vol_nam, _coe in vol_coe.items():
+        df_vol[_vol_nam] = df_mass_cal[_vol_nam] / _coe
+
+    if df_water is not None:
+        df_vol['ALWC'] = df_water
+        df_vol = df_vol.dropna()
+        df_vol['total_wet'] = df_vol.sum(axis=1, min_count=6)
+
+    df_vol['total_dry'] = df_vol[vol_coe.keys()].sum(axis=1, min_count=6)
+
+    ## density
+    df_vol_cal = DataFrame()
+    df_den_rec = df_mass['total'] / df_vol['total_dry']
+    if df_density is not None:
+        df_den_all = concat([df_all[['SO42-', 'NO3-', 'NH4+', 'EC']], df_density, df_mass['OM']], axis=1).dropna()
+
+        df_vol_cal = (df_den_all[['SO42-', 'NO3-', 'NH4+']].sum(axis=1) / 1.75) + \
+                     df_den_all['Cl-'] / 1.52 + \
+                     df_den_all['OM'] / 1.4 + df_den_all['EC'] / 1.77
+
+        df_den = df_den_all.sum(axis=1, min_count=6) / df_vol_cal
+    # df_den = df_den_all.sum(axis=1) / df_vol_cal
+    # df_den = df_mass['total'].loc[df_den_all.index] / df_vol_cal
+
+    ## refractive index
+    ri_dic = {}
+    for _lambda, _coe in RI_coe.items():
+
+        df_RI = DataFrame()
+
+        for _ky, _df in df_vol.items():
+            if 'total' in _ky: continue
+            df_RI[_ky] = (_df * _coe[_ky])
+
+        df_RI['RI_wet'] = None
+        if df_water is not None:
+            df_RI['RI_wet'] = (df_RI / df_vol['total_wet'].to_frame().values).sum(axis=1)
 
-		df_RI['RI_dry'] = (df_RI[vol_coe.keys()] / df_vol['total_dry'].to_frame().values).sum(axis=1)
+        df_RI['RI_dry'] = (df_RI[vol_coe.keys()] / df_vol['total_dry'].to_frame().values).sum(axis=1)
 
-		ri_dic[f'RI_{_lambda}'] = df_RI[['RI_dry', 'RI_wet']]
+        ri_dic[f'RI_{_lambda}'] = df_RI[['RI_dry', 'RI_wet']]
 
-	## mole and equivalent
-	df_eq = concat((mol_A, mol_S, mol_N, mol_A * 1, mol_S * 2, mol_N * 1), axis=1)
-	df_eq.columns = ['mol_NH4', 'mol_SO4', 'mol_NO3', 'eq_NH4', 'eq_SO4', 'eq_NO3', ]
+    ## mole and equivalent
+    df_eq = concat((mol_A, mol_S, mol_N, mol_A * 1, mol_S * 2, mol_N * 1), axis=1)
+    df_eq.columns = ['mol_NH4', 'mol_SO4', 'mol_NO3', 'eq_NH4', 'eq_SO4', 'eq_NO3', ]
 
-	## out
-	out = {'mass': df_mass,
-		   'volume': df_vol,
-		   'vol_cal': df_vol_cal,
-		   'eq': df_eq,
-		   'density_mat': df_den,
-		   'density_rec': df_den_rec,
-		   }
-	out.update(ri_dic)
+    ## out
+    out = {'mass': df_mass,
+           'volume': df_vol,
+           'vol_cal': df_vol_cal,
+           'eq': df_eq,
+           'density_mat': df_den,
+           'density_rec': df_den_rec,
+           }
+    out.update(ri_dic)
 
-	for _ky, _df in out.items():
-		out[_ky] = _df.reindex(index).where(qc_cond)
+    for _ky, _df in out.items():
+        out[_ky] = _df.reindex(index).where(qc_cond)
 
-	return out
+    return out
 
 
 # '''
 
 
 def mass_ratio(_df):
-	if _df['PM25'] >= _df['total_mass']:
-		_df['others'] = _df['PM25'] - _df['total_mass']
-		for _val, _species in zip(_df.values, _df.index):
-			_df[f'{_species}_ratio'] = _val / _df['PM25'].__round__(3)
+    if _df['PM25'] >= _df['total_mass']:
+        _df['others'] = _df['PM25'] - _df['total_mass']
+        for _val, _species in zip(_df.values, _df.index):
+            _df[f'{_species}_ratio'] = _val / _df['PM25'].__round__(3)
 
-	if _df['PM25'] < _df['total_mass']:
-		_df['others'] = 0
-		for _val, _species in zip(_df.values, _df.index):
-			_df[f'{_species}_ratio'] = _val / _df['PM25'].__round__(3)
+    if _df['PM25'] < _df['total_mass']:
+        _df['others'] = 0
+        for _val, _species in zip(_df.values, _df.index):
+            _df[f'{_species}_ratio'] = _val / _df['PM25'].__round__(3)
 
-	return _df['others':].drop(labels=['PM25_ratio', 'total_mass_ratio'])
+    return _df['others':].drop(labels=['PM25_ratio', 'total_mass_ratio'])