inclusion of iwr process in main, fix for first guess x0 in iwr.process

README.md

@@ -75,10 +75,26 @@ Usage:
 
 ## Running the tests
 
+- For `awr` data:
+
 ```
 trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --no_clobber
 trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method M99 --name _M99 --plot --figdir ./test/fig
-trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method osoaa --name _osoaa --plot
+trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method osoaa --name _osoaa --plot --figdir ./test/fig
+trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method osoaa --ws 5 --aot=0.2 --name _osoaaws5_aot0.1 --plot --figdir ./test/fig
+trios_processing ./test/data/ 150 awr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --method temp_opt --name _optimization --plot --figdir ./test/fig
+```
+
+- For `iwr` data:
+
+```
+trios_processing ./test/data/ 150 iwr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --no_clobber --plot --figdir ./test/fig
+```
+
+- For `swr` data:
+
+```
+trios_processing ./test/data/ 150 swr --lat 42.30351823 --lon 9.462897398 --odir ./test/results --no_clobber --plot --figdir ./test/fig
 ```
 
 

test/results/Rrs_awr_2018-05-30_idpr150_M99.csv

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trios/config.py

@@ -16,3 +16,8 @@ F0_file =  os.path.join(root, '../aux/Thuillier_2003_0.3nm.dat')
 wl_step = 3
 wl_common = np.arange(320,950+wl_step,wl_step)
 
+# wavelength indexes for iwr plotting
+# for close red/IR
+# idx_list_for_plot=(165,170,175,180,185,190,195,200,205)
+# through visible/IR
+idx_list_for_plot=(28, 37, 51, 71, 91, 105, 130, 140, 170)
\ No newline at end of file

trios/main.py

@@ -3,7 +3,8 @@
 Usage:
   trios_processing <input_dir> <IDpr> <measurement_type> --lat <lat> --lon <lon> \
    [--altitude=alt] [--ofile <ofile>] [--odir <odir>] [--plot] [--figdir <figdir>] \
-   [--name <name>] [--method <method>] [--no_clobber]
+   [--name <name>] [--method <method>] [--no_clobber] \
+   [--vza <vza>] [--azi <azi>] [--ws <ws>] [--aot <aot>]
   trios_processing -h | --help
   trios_processing -v | --version
 
@@ -26,6 +27,14 @@ Options:
   --name name  Keyword to append to file name and figures [default: ]
   --method method  Keyword for the method to apply for data processing.
                    For awr: M99, M15, osoaa, temp_opt [default: M99]
+  --vza vza  Viewing zenith angle (in deg) of the awr radiometer (applicable for all awr methods)
+            [default: 40]
+  --azi azi  Relative azimuth angle (in deg) of the awr radiometer (applicable for all awr methods)
+            [default: 135]
+  --ws ws  Wind speed (in m/s) (applicable for awr methods: M99, M15, osoaa)
+           [default: 2]
+  --aot aot  Aerosol optical thickness at 550 nm (applicable for awr methods: osoaa)
+             [default: 0.1]
   --no_clobber     Do not process  <input_dir> <IDpr> files if <output_file> already exists.
 '''
 
@@ -65,6 +74,10 @@ def main():
     plot = args['--plot']
     figdir = os.path.abspath(args['--figdir'])
     noclobber = args['--no_clobber']
+    azi = float(args['--azi'])
+    vza = float(args['--vza'])
+    ws = float(args['--ws'])
+    aot = float(args['--aot'])
 
     try:
         type_ = type_list[meas_type]
@@ -103,17 +116,15 @@ def main():
                 ax.set_ylabel(r'$R_{rs}\  (sr^{-1})$')
                 ax.set_xlabel(r'Wavelength (nm)')
                 ax.set_title('ID: ' + idpr + ', ' + date + ', sza=' + str(round(df.sza.mean(), 2)))
-                fig.savefig(os.path.join(figdir, 'trios_swr_' + date + '_idpr' + idpr + name+'.png'), bbox_inches='tight')
+                fig.savefig(os.path.join(figdir, 'trios_swr_' + date + '_idpr' + idpr + name + '.png'),
+                            bbox_inches='tight')
                 plt.close()
 
     elif meas_type == 'awr':
         # -----------------------------------------------
         #   AWR processing
         # -----------------------------------------------
-        azi = 135
-        vza = 40
-        ws = 2
-        method = 'M99'
+
         uawr = u.awr_data(idpr, files)
         if uawr.Edf:
             df, wl = uawr.reader(lat, lon, alt)
@@ -127,17 +138,39 @@ def main():
                 print('Skip processing: data already processed with "--no_clobber" set')
                 return
 
-            awr = awr_process(df, wl, name, idpr)
-
             if plot:
-                figfile = os.path.join(figdir, 'trios_awr_' + date + '_idpr' + idpr + name +'.png')
+                figfile = os.path.join(figdir, 'trios_awr_' + date + '_idpr' + idpr + name + '.png')
             else:
                 figfile = ""
 
-            Rrs = awr.call_process(method, ofile, vza=vza, azi=azi, plot_file=figfile)
+            awr = awr_process(df, wl, name, idpr)
+            Rrs = awr.call_process(method, ofile, vza=vza, azi=azi, ws=ws, aot=aot, plot_file=figfile)
 
     elif meas_type == 'iwr':
-        pass
+        # -----------------------------------------------
+        #   IWR processing
+        # -----------------------------------------------
+
+        uiwr = u.iwr_data(idpr, files)
+        if uiwr.file:
+            df, wl = uiwr.reader(lat, lon, alt)
+            date = df.index[0].date().__str__()
+            if ofile:
+                ofile = os.path.join(odir, ofile)
+            else:
+                ofile = os.path.join(odir, 'Rrs_iwr_' + date + '_idpr' + idpr + name + '.csv')
+
+            if noclobber and os.path.exists(ofile):
+                print('Skip processing: data already processed with "--no_clobber" set')
+                return
+
+            if plot:
+                figfile = os.path.join(figdir, 'trios_iwr_' + date + '_idpr' + idpr + name + '.pdf')
+            else:
+                figfile = ""
+
+            iwr = iwr_process(df, wl, name, idpr)
+            results = iwr.call_process(ofile, plot_file=figfile)
 
 
 if __name__ == "__main__":

trios/process.py

+# standard lib
 import pandas as pd
 from scipy import interpolate, integrate
 import scipy.optimize as so
 
+# for plotting pruposes
+import cmocean
 import plotly.graph_objs as go
-
+from matplotlib.backends.backend_pdf import PdfPages
 import matplotlib as mpl
 import matplotlib.pyplot as plt
 
 plt.rcParams.update({'font.size': 18})
 
+# package
 from trios.utils.utils import plot as up
 import trios.utils.utils as uu
 from trios.utils.utils import reshape as r
@@ -92,7 +96,7 @@ class awr_process:
     def call_process(self, method='M99', ofile="", vza=40, azi=135, ws=2, aot=0.1, plot_file=""):
 
         wl = self.wl
-        vza, azi, ws = [vza], [azi], [ws]  # formatting for interpolation functions
+        vza, azi, ws, aot = [vza], [azi], [ws], [aot]  # formatting for interpolation functions
 
         # ------------------
         # filtering
@@ -111,7 +115,7 @@ class awr_process:
         elif method == 'osoaa':
             Rrs, rho = self.process_wrapper(wl, clean, clean.sza, vza=vza, azi=azi, ws=ws, aot=aot, method=method)
         elif method == 'temp_opt':
-            Rrs, Rrs_opt_std = self.process_optimization(wl, Lt, Lsky, Ed, sza, vza=vza, azi=azi)
+            Rrs, rho, Rrs_opt, Rrs_opt_std = self.process_optimization(wl, Lt, Lsky, Ed, sza, vza=vza, azi=azi)
 
         self.Rrs = Rrs
 
@@ -121,7 +125,6 @@ class awr_process:
             Rrs_stat = Rrs_stat.T
             Rrs_stat.to_csv(ofile)
 
-
         if plot_file:
             # ------------------
             # plotting
@@ -155,21 +158,21 @@ class awr_process:
             up.add_curve(ax, wl, Lt.mean(axis=0), Lt.std(axis=0),
                          label=r'$L_t$', c='black')
             up.add_curve(ax, wl, Lsky.mean(axis=0) * rho, Lsky.std(axis=0) * rho,
-                         label=method+' (' + str(round(rho, 4)) + ')', c='violet')
+                         label=method + ' (' + str(round(rho, 4)) + ')', c='violet')
             ax.set_ylabel(r'$L_t\ or L_{surf}$')
             ax.set_xlabel(r'Wavelength (nm)')
 
             # ---- Proportion o(Lt - Lsurf ) /Lt
             ax = axs[0, 2]
             up.add_curve(ax, wl, Lsky.mean(axis=0) * rho / Ltm, Lsky.std(axis=0) * rho,
-                         label=method+' (' + str(round(rho, 4)) + ')', c='violet')
+                         label=method + ' (' + str(round(rho, 4)) + ')', c='violet')
             ax.set_ylabel(r'$L_{surf}/L_t$')
             ax.set_xlabel(r'Wavelength (nm)')
 
             # ---- Lw
             ax = axs[1, 0]
             up.add_curve(ax, wl, Rrs.mean(axis=0) * Edm, Rrs.std(axis=0) * Edm,
-                         label=method+' (' + str(round(rho, 4)) + ')', c='violet')
+                         label=method + ' (' + str(round(rho, 4)) + ')', c='violet')
 
             ax.set_ylabel(r'$L_{w}\  (sr^{-1})$')
             ax.set_xlabel(r'Wavelength (nm)')
@@ -177,7 +180,7 @@ class awr_process:
             # ---- Rrs
             ax = axs[1, 1]
             up.add_curve(ax, wl, Rrs.transpose().mean(axis=1), Rrs.transpose().std(axis=1),
-                         label=method+' (' + str(round(rho, 4)) + ')', c='violet')
+                         label=method + ' (' + str(round(rho, 4)) + ')', c='violet')
 
             ax.set_ylabel(r'$R_{rs}\  (sr^{-1})$')
             ax.set_xlabel(r'Wavelength (nm)')
@@ -263,7 +266,7 @@ class awr_process:
         # initialization of mean/median values
         # ------------------------------
         Rrs, rho = self.process(wl, Lt, Lsky, Ed, sza, ws=ws, azi=azi)
-        Rrs_bar = Rrs.mean(axis=0)
+        Rrs_bar = np.nanmedian(Rrs, axis=0)
 
         # -----------------------------
         # non-linear optimization
@@ -288,7 +291,9 @@ class awr_process:
                 print(res_lsq.x, res_lsq.cost)
             Rrs_bar = np.mean(Rrs_est, axis=0)
             Rrs_std = np.std(Rrs_est, axis=0)
-        return Rrs_bar, Rrs_std
+            Rrs_est = pd.DataFrame(Rrs_est)
+            Rrs_est.columns = pd.MultiIndex.from_product([['Rrs'], wl], names=['param', 'wl'])
+        return Rrs_est, np.mean(rho_est, axis=0), Rrs_bar, Rrs_std
 
     @classmethod
     def filtering(cls, Lt, Lsky, Ed, **kargs):
@@ -400,9 +405,256 @@ class swr_process:
 
 
 class iwr_process:
-    def __init__(self, df=None, wl=None, ):
+    def __init__(self, df=None, wl=None, name="", idpr=""):
         self.df = df
         self.wl = wl
+        self.name = name
+        self.idpr = idpr
+
+    def call_process(self, ofile="", plot_file=""):
+
+        # ---------------------------
+        # Data formatting
+        # ---------------------------
+        df = self.df
+        wl = self.wl
+
+        # set pandas dataframes with data and parameters
+        df['rounded_depth', ''] = df.prof_Edz.round(1)
+
+        # data filtering
+        df[df.rounded_depth < -0.05] = np.nan
+        # df[df == 0] = np.nan
+
+        mean = df.groupby('rounded_depth').mean()
+        median = df.groupby('rounded_depth').median()
+        std = df.groupby('rounded_depth').std()
+        q25 = df.groupby('rounded_depth').quantile(0.25)
+        q75 = df.groupby('rounded_depth').quantile(0.75)
+
+        # ---------------------------
+        # Data processing
+        # ---------------------------
+        res = self.process(mean, std)
+        res_w = self.process(mean, std, mode='log')
+        res_med = self.process(median, std)
+        res_lsq = self.process(mean, std, mode='lsq')
+
+        Kd = res_lsq.popt[:, 0]
+        Edm = res_lsq.popt[:, 1]
+        Es = mean.Ed.mean()