first test with XBT

docs/Readme-Python.txt

@@ -31,13 +31,19 @@ D={}
 D={'un': 1, "deux: 2}
 D['un']
 1
-D.has_key('deux')
+'deux' in D
 True
 D.keys()
 ['un', 'deux']
 D.values()
 [1,2]
 
+len(D)
+    Return the number of items in the dictionary d.
+
+d[key]
+    Return the item of d with key key. Raises a KeyError if key is not in the map.
+    
 d[key] = value
     Set d[key] to value.
 

file_extractor.py

@@ -13,27 +13,35 @@ class FileExtractor:
 
     '''
     This class read multiple ASCII file, extract physical parameter from ROSCOP codification at the given column
-    and fill arrays
+    and fill arrays.
+
+    Parameters
+    ----------
+    fname : file, str, pathlib.Path, list of str
+        File, filename, or list to read.
+    skip_header : int, optional
+        The number of lines to skip at the beginning of the file.
     '''
 
     # constructor with values by default
-    def __init__(self, files):
+    def __init__(self, fname, skip_header=0):
         # attibutes
         # public:
-        self.files = files
+        self.fname = fname
         self.n = 0
         self.m = 0
         # replace this constante with roscop fill value
         self.FillValue = 1e36
 
         # private:
-        self.__headeer = {}
+        self.skip_header = skip_header
+        self.__header = {}
         self.__data = {}
     # overloading operators
 
     def __str__(self):
         ''' overload string representation '''
-        return 'Class FileExtractor, file: %s, size = %d' % (self.files, len(self))
+        return 'Class FileExtractor, file: %s, size = %d' % (self.fname, len(self))
 
     def disp(self, keys):
         # for key in keys:
@@ -47,11 +55,17 @@ class FileExtractor:
 
    # first pass on file(s)
     def firstPass(self):
+        '''
+        Returns
+         ------
+        out : [n,m]
+        The size of array.
+        '''
         lineRead = 0
         filesRead = 0
         indMax = 0
 
-        for file in self.files:
+        for file in self.fname:
             with fileinput.input(
                     file, openhook=fileinput.hook_encoded("ISO-8859-1")) as f:
                 filesRead += 1
@@ -73,13 +87,32 @@ class FileExtractor:
         self.m = indMax
         return self.n, self.m
 
-    # second pass, extract data from roscop code in files and fill array
-    def secondPass(self, keys, cfg, type):
+    # second pass, extract data from roscop code in fname and fill array
+    def secondPass(self, keys, cfg, device):
+        '''
+        Read the file to its internal dict
+
+        Parameters
+        ----------
+        keys: sequence, a list of physical parameter to read.
+            ex: ['PRES', 'TEMP', 'PSAL']
+        cfg: toml.load() instance, configuration file
+        device: str, instrument
+            ex: CTD,XBT or LADCP
+        '''
         n = 0
         m = 0
 
-        # get the dictionary from toml block, type instrument is in lower case
-        hash = cfg['split'][type.lower()]
+        #print(device, cfg[device.lower()])
+        print(device)
+        # set skip_header is declared in toml section, 0 by default
+        if 'skikHeader' in cfg[device.lower()]:
+            self.skip_header = cfg[device.lower()]['skipHeader']
+        #
+        logging.debug(self.skip_header)
+
+        # get the dictionary from toml block, device must be is in lower case
+        hash = cfg['split'][device.lower()]
 
         # initialize arrays, move at the end of firstPass ?
         for key in keys:
@@ -87,10 +120,12 @@ class FileExtractor:
             # the shape parameter has to be an int or sequence of ints
             self.__data[key] = np.ones((self.n, self.m)) * self.FillValue
 
-        for file in self.files:
+        for file in self.fname:
             with fileinput.input(
                     file, openhook=fileinput.hook_encoded("ISO-8859-1")) as f:
                 for line in f:
+                    if f.filelineno() < self.skip_header + 1:
+                        continue
                     if line[0] == '#' or line[0] == '*':
                         continue
                     # split the line
@@ -129,7 +164,7 @@ if __name__ == "__main__":
                         default='tests/test.toml')
     parser.add_argument('-k', '--key', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
                         help='display dictionary for key(s), (default: %(default)s)')
-    parser.add_argument('files', nargs='*',
+    parser.add_argument('fname', nargs='*',
                         help='cnv file(s) to parse, (default: data/cnv/dfr29*.cnv)')
 
     # display extra logging info
@@ -140,8 +175,8 @@ if __name__ == "__main__":
         logging.basicConfig(
             format='%(levelname)s:%(message)s', level=logging.DEBUG)
 
-    fe = FileExtractor(args.files)
-    print("File(s): {}, Config: {}".format(args.files, args.config))
+    fe = FileExtractor(args.fname)
+    print("File(s): {}, Config: {}".format(args.fname, args.config))
     cfg = toml.load(args.config)
     [n, m] = fe.firstPass()
     print("Indices:", n, m)

oceano.py

@@ -51,13 +51,17 @@ def process(args, cfg, ti):
 if __name__ == "__main__":
     '''
     usage:
-    > python oceano.py data/cnv/dfr2900[1-3].cnv -d
-    > python oceano.py data/cnv/dfr2900[1-3].cnv -k PRES TEMP PSAL DOX2 DENS
-    > python oceano.py data/cnv/dfr29*.cnv -d
+    > python oceano.py data/CTD/cnv/dfr2900[1-3].cnv -d
+    > python oceano.py data/CTD/cnv/dfr2900[1-3].cnv -k PRES TEMP PSAL DOX2 DENS
+    > python oceano.py data/CTD/cnv/dfr29*.cnv -d
     '''
     parser = argparse.ArgumentParser(
         description='This program read multiple ASCII file, extract physical parameter \
-                following ROSCOP codification at the given column, fill arrays, write header file',
+                following ROSCOP codification at the given column, fill arrays, write header file ',
+        usage='\npython oceano.py data/CTD/cnv/dfr2900[1-3].cnv -i CTD -d\n'
+        'python oceano.py data/CTD/cnv/dfr2900[1-3].cnv -i CTD -k PRES TEMP PSAL DOX2 DENS\n'
+        'python oceano.py data/CTDcnv/dfr29*.cnv -d\n'
+        'python oceano.py data/XBT/T7_000*.cnv -i XBT -k DEPTH TEMP SVEL\n',
         epilog='J. Grelet IRD US191 - March 2019')
     parser.add_argument('-d', '--debug', help='display debug informations',
                         action='store_true')
@@ -83,8 +87,9 @@ if __name__ == "__main__":
 
     # read config Toml file and get the physical parameter list (Roscop code) for the specified instrument
     cfg = toml.load(args.config)
-    instru = args.instrument[0]
-    keys = cfg['split'][instru.lower()].keys()
+    device = str(args.instrument[0])  # convert one element list to str
+    print(device)
+    keys = cfg['split'][device.lower()].keys()
 
     # test arguements from sys.argv, args is never to None with default option set
     if args.gui or len(sys.argv) == 1:
@@ -99,11 +104,9 @@ if __name__ == "__main__":
                              enable_events=True),
                     sg.FilesBrowse(key='_HIDDEN_',
                                    tooltip='Choose one or more files',
-                                   initial_folder='data/{}'.format(ti[instru]),
-                                   file_types=(("{} files".format(ti[instru]), "*.{}".format(ti[instru])),))],
-                   [sg.Input(key='_COMBO_', visible=False,
-                             enable_events=True),
-                    sg.Combo(['CTD', 'XBT', 'LADCP', 'TSG'],
+                                   initial_folder='data/{}'.format(ti[device]),
+                                   file_types=(("{} files".format(ti[device]), "*.{}".format(ti[device])),))],
+                   [sg.Combo(ti.keys(), enable_events=True,
                              key='_COMBO_', tooltip='Select the instrument')],
                    * [[sg.Checkbox(k, key=k,
                                    tooltip='Select the extract the physical parameter {}'.format(k))] for k in keys],
@@ -119,7 +122,7 @@ if __name__ == "__main__":
         while True:
            # display the main windows
             event, values = window.Read()
-            print(event, values)
+            # print(event, values)
 
             if event is 'Cancel' or event == None:
                 raise SystemExit("Cancelling: user exit")
@@ -128,8 +131,14 @@ if __name__ == "__main__":
                 break
 
             if event is '_COMBO_':
-                window.FindElement('_HIDDEN_').File_types = (
-                    ("{} files".format(ti[values['_COMBO_']]), "*.{}".format(ti[values['_COMBO_']])),)
+                e = window.Rows[1][2]
+                # print(e.FileTypes)
+                e.FileTypes = (("{} files".format(
+                    ti[values['_COMBO_']]), "*.{}".format(ti[values['_COMBO_']])),)
+                window.Finalize
+                # print(e.FileTypes)
+                # window.FindElement('_HIDDEN_').File_types = (
+                #    ("{} files".format(ti[values['_COMBO_']]), "*.{}".format(ti[values['_COMBO_']])),)
 
             if event is '_HIDDEN_':
                 window.Element('_IN_').Update(
@@ -177,6 +186,6 @@ if __name__ == "__main__":
             parser.print_help(sys.stderr)
             sys.exit(1)
         # in command line mode (console)
-        fe, n, m = process(args, cfg, ti[instru])
+        fe, n, m = process(args, cfg, device)
         print("Dimensions: {} x {}".format(m, n))
         print(fe.disp(args.key))

tests/test.toml

@@ -41,7 +41,7 @@ comment        = "CTD bottles water sampling with temperature, salinity and oxyg
 
 cruisePrefix   = "fr29"
 stationPrefixLength  = 3
-header = 40
+skipHeader = 40
 acquisitionSoftware = "WinMK21"
 acquisitionVersion = "2.10.1" 
 processingSoftware = ""