add netcdf withou data

file_extractor.py

@@ -25,10 +25,11 @@ class FileExtractor:
     '''
 
     # constructor with values by defaul
-    def __init__(self, fname, separator=None, skip_header=0):
+    def __init__(self, fname, keys, separator=None, skip_header=0):
         # attibutes
         # public:
         self.fname = fname
+        self.keys = keys
         self.n = 0
         self.m = 0
 
@@ -45,12 +46,12 @@ class FileExtractor:
         ''' overload string representation '''
         return 'Class FileExtractor, file: %s, size = %d' % (self.fname, len(self))
 
-    def disp(self, keys):
+    def disp(self):
         # for key in keys:
         #     print("{}:".format(key))
         #     print(self.__data[key])
         buf = ''
-        for key in keys:
+        for key in self.keys:
             buf += "{}:\n".format(key)
             buf += "{}\n".format(self.__data[key])
         return buf
@@ -87,10 +88,10 @@ class FileExtractor:
         # the size of arrays
         self.n = filesRead
         self.m = indMax
-        return self.n, self.m
+        # return self.n, self.m
 
     # second pass, extract data from roscop code in fname and fill array
-    def secondPass(self, keys, cfg, device):
+    def secondPass(self, cfg, device):
         '''
         Read the file to its internal dict
 
@@ -116,7 +117,7 @@ class FileExtractor:
         hash = cfg['split'][device.lower()]
 
         # initialize arrays, move at the end of firstPass ?
-        for key in keys:
+        for key in self.keys:
             # mult by __fillValue next
             # the shape parameter has to be an int or sequence of ints
             self.__data[key] = np.ones((self.n, self.m)) * self.__FillValue
@@ -134,7 +135,7 @@ class FileExtractor:
 
                     str = ' '
                     # fill array with extracted value of line for eack key (physical parameter)
-                    for key in keys:
+                    for key in self.keys:
                         self.__data[key][n, m] = p[hash[key]]
                         # debug info
                         str += "{:>{width}}".format(
@@ -152,9 +153,9 @@ class FileExtractor:
 if __name__ == "__main__":
 
     # usage:
-    # > python file_extractor.py data/cnv/dfr2900[1-3].cnv -d
-    # > python file_extractor.py data/cnv/dfr2900[1-3].cnv -k PRES TEMP PSAL DOX2 DENS
-    # > python file_extractor.py data/cnv/dfr29*.cnv -d
+    # > python file_extractor.py data/CTD/cnv/dfr2900[1-3].cnv -d
+    # > python file_extractor.py data/CTD/cnv/dfr2900[1-3].cnv -k PRES TEMP PSAL DOX2 DENS
+    # > python file_extractor.py data/CTD/cnv/dfr29*.cnv -d
     parser = argparse.ArgumentParser(
         description='This class read multiple ASCII file, extract physical parameter \
             from ROSCOP codification at the given column and fill arrays ',
@@ -163,7 +164,7 @@ if __name__ == "__main__":
                         action='store_true')
     parser.add_argument('-c', '--config', help="toml configuration file, (default: %(default)s)",
                         default='tests/test.toml')
-    parser.add_argument('-k', '--key', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
+    parser.add_argument('-k', '--keys', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
                         help='display dictionary for key(s), (default: %(default)s)')
     parser.add_argument('fname', nargs='*',
                         help='cnv file(s) to parse, (default: data/cnv/dfr29*.cnv)')
@@ -176,12 +177,11 @@ if __name__ == "__main__":
         logging.basicConfig(
             format='%(levelname)s:%(message)s', level=logging.DEBUG)
 
-    fe = FileExtractor(args.fname)
+    fe = FileExtractor(args.fname, args.keys)
     print("File(s): {}, Config: {}".format(args.fname, args.config))
     cfg = toml.load(args.config)
-    [n, m] = fe.firstPass()
-    print("Indices:", n, m)
-    fe.secondPass(args.key, cfg, 'ctd')
-    # fe.secondPass(['PRES', 'TEMP', 'PSAL', 'DOX2'], cdf, 'ctd')
-    fe.disp(args.key)
-    # fe.disp(['PRES', 'TEMP', 'PSAL', 'DOX2'])
+    fe.firstPass()
+    print("Indices: {} x {}\nkeys: {}".format(fe.n, fe.m, fe.keys))
+    fe.secondPass(cfg, 'ctd')
+    # debug
+    # print(fe.disp())

netcdf.py

+import logging
 from netCDF4 import Dataset
+from numpy import arange, dtype
+from physicalParameter import Roscop
 
 
 def writeNetCDF(fileName, fe):
 
+    data = {}
+    dims = ['TIME', 'LATITUDE', 'LONGITUDE', 'DEPTH']
+    vars = dims.copy()
+
+    # move to main after tests
+    r = Roscop("code_roscop.csv")
+
     # create netcdf file
     nc = Dataset(fileName, "w", format="NETCDF3_CLASSIC")
-    print(nc.data_model)
+    logging.debug(' ' + nc.data_model)
 
     # create dimensions
-    depth = nc.createDimension("DEPTH", None)
-    time = nc.createDimension("TIME", None)
-    lat = nc.createDimension("LATITUDE", 73)
-    lon = nc.createDimension("LONGITUDE", 144)
+    # n is number of profiles, m the max size of profiles
+    time = nc.createDimension("TIME", fe.n)
+    lat = nc.createDimension("LATITUDE", fe.n)
+    lon = nc.createDimension("LONGITUDE", fe.n)
+    depth = nc.createDimension('DEPTH', fe.m)
+
+    logging.debug(" depth: {}, time: {}, lat: {}, lon: {}".format(
+        len(depth), len(time), len(lat), len(lon)))
+
+    # create variables
+    # add dimensions before variables list
+    for k in fe.keys:
+        vars.append(k)
+    for key in vars:
+        # for each variables get the attributes list
+        hash = r.returnCode(key)
+        # _FillValue attribute must be set when variable is created
+        # (using fill_value keyword to createVariable)
+        if '_FillValue' in hash:
+            fillvalue = hash['_FillValue']
+            # remove from the dictionary
+            hash.pop('_FillValue')
+        else:
+            fillvalue = None
+        # create the variable
+        data[key] = nc.createVariable(
+            key, dtype(hash['types']).char, dims, fill_value=fillvalue)
+        # remove from the dictionary
+        hash.pop('types')
+        # create dynamically variable attributes
+        for k in hash.keys():
+            setattr(data[key], k, hash[k])
+
+    # debug
+    for key in vars:
+        print(data[key])

oceano.py

@@ -38,7 +38,7 @@ def processArgs():
                         default='tests/test.toml')
     parser.add_argument('-i', '--instrument', nargs='?', choices=ti.keys(),
                         help='specify the instrument that produce files, eg CTD, XBT, TSG, LADCP')
-    parser.add_argument('-k', '--key', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
+    parser.add_argument('-k', '--keys', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
                         help='display dictionary for key(s), (default: %(default)s)')
     parser.add_argument('-g', '--gui', action='store_true',
                         help='use GUI interface')
@@ -122,17 +122,17 @@ def process(args, cfg, ti):
 
     # check if no file selected or cancel button pressed
     logging.debug("File(s): {}, config: {}, Keys: {}".format(
-        args.files, args.config, args.key))
+        args.files, args.config, args.keys))
 
     # fileExtractor
-    fe = FileExtractor(args.files)
+    fe = FileExtractor(args.files, args.keys)
 
     # cfg = toml.load(args.config)
-    [n, m] = fe.firstPass()
+    fe.firstPass()
     # fe.secondPass(['PRES', 'TEMP', 'PSAL', 'DOX2'], cfg, 'ctd')
-    fe.secondPass(args.key, cfg, ti)
+    fe.secondPass(cfg, ti)
     # fe.disp(['PRES', 'TEMP', 'PSAL', 'DOX2'])
-    return fe, n, m
+    return fe
 
 
 if __name__ == "__main__":
@@ -224,15 +224,15 @@ if __name__ == "__main__":
         for k in values.keys():
             if k[0] == '_' or values[k] == False:
                 del new_values[k]
-        args.key = new_values.keys()
+        args.keys = new_values.keys()
 
         # process of files start here
-        fe, n, m = process(args, cfg, values['_COMBO_'])
+        fe = process(args, cfg, values['_COMBO_'])
 
         # display result in popup GUI
         dims = "Dimensions: {} x {}".format(n, m)
         sg.PopupScrolled('Oceano2python', dims,
-                         fe.disp(args.key),  size=(80, 40))
+                         fe.disp(args.keys),  size=(80, 40))
 
         # It will output to a debug window. Bug ? debug windows xas closed before exiting program
         # print = sg.Print
@@ -264,7 +264,7 @@ if __name__ == "__main__":
 
         keys = cfg['split'][device.lower()].keys()
         # in command line mode (console)
-        fe, n, m = process(args, cfg, device)
-        print("Dimensions: {} x {}".format(m, n))
-        print(fe.disp(args.key))
-        netcdf.writeNetCDF( 'test.nc', fe)
+        fe = process(args, cfg, device)
+        print("Dimensions: {} x {}".format(fe.m, fe.n))
+        print(fe.disp())
+        netcdf.writeNetCDF( 'output/test.nc', fe)

odv/.emptydir

-Do not delete this file.
\ No newline at end of file