def make_btl_mean(ssscc_list, debug=False):
# TODO: add (some) error handling from odf_process_bottle.py
"""
Create "bottle mean" files from continuous CTD data averaged at the bottle stops.
Parameters
----------
ssscc_list : list of str
List of stations to convert
debug : bool, optional
Display verbose messages
Returns
-------
boolean
bottle averaging of mean has finished successfully
"""
print('Generating btl_mean.pkl files')
for ssscc in ssscc_list:
if not Path(cfg.directory["bottle"] + ssscc +
"_btl_mean.pkl").exists():
imported_df = importConvertedFile(
cfg.directory["converted"] + ssscc + ".pkl", False)
bottle_df = btl.retrieveBottleData(imported_df, debug=debug)
mean_df = btl.bottle_mean(bottle_df)
saveConvertedDataToFile(
mean_df, cfg.directory["bottle"] + ssscc + "_btl_mean.pkl")
return True
def process_bottle(ssscc):
cnv_file = converted_directory + ssscc + '.pkl'
imported_df = cnv.importConvertedFile(cnv_file, False)
bottle_df = btl.retrieveBottleData(imported_df, False)
if bottle_df.empty:
#errPrint("Bottle fire data not found in converted file")
sys.exit(1)
else:
total_bottles_fired = bottle_df[btl_fire_num].iloc[-1]
bottle_num = 1
while bottle_num <= total_bottles_fired:
bottle_num += 1
mean_df = btl.bottle_mean(bottle_df)
meanfilePath = btl_data_prefix + ssscc + btl_data_postfix
cnv.saveConvertedDataToFile(mean_df, meanfilePath)
return
def main(argv):
# MK: depreciated 04/27/20, use ctdcal.convert.make_btl_mean instead
parser = argparse.ArgumentParser(
description=
'Process bottle fire data from a converted, csv-formatted text file')
parser.add_argument('cnv_file',
metavar='cnv_file',
help='the converted data file to process')
# debug messages
parser.add_argument('-d',
'--debug',
action='store_true',
help='display debug messages')
# output directory
parser.add_argument('-o',
metavar='dest_dir',
dest='outDir',
help='location to save output files')
args = parser.parse_args()
if args.debug:
global DEBUG
DEBUG = True
debugPrint("Running in debug mode")
# Verify converted exists
if not os.path.isfile(args.cnv_file):
errPrint('ERROR: Input converted file:', args.cnv_file, 'not found\n')
sys.exit(1)
# Set the default output directory to be the same directory as the hex file
outputDir = os.path.dirname(args.cnv_file)
# Used later for building output file names
filename_ext = os.path.basename(
args.cnv_file) # original filename with ext
filename_base = os.path.splitext(filename_ext)[
0] # original filename w/o ext
# Verify Output Directory exists
if args.outDir:
if os.path.isdir(args.outDir):
outputDir = args.outDir
else:
errPrint('ERROR: Output directory:', args.outDir,
'is unreachable.\n')
sys.exit(1)
debugPrint("Import converted data to dataframe... ", end='')
imported_df = cnv.importConvertedFile(args.cnv_file, False)
debugPrint("Success!")
debugPrint(imported_df.head())
#debugPrint(imported_df.dtypes)
# Retrieve the rows from the imported dataframe where the btl_fire_bool column == True
# Returns a new dataframe
bottle_df = btl.retrieveBottleData(imported_df, False)
if bottle_df.empty:
errPrint("Bottle fire data not found in converted file")
sys.exit(1)
else:
total_bottles_fired = bottle_df[BOTTLE_FIRE_NUM_COL].iloc[-1]
debugPrint(total_bottles_fired, "bottle fire(s) detected")
bottle_num = 1
while bottle_num <= total_bottles_fired:
debugPrint('Bottle:', bottle_num)
debugPrint(bottle_df.loc[bottle_df[BOTTLE_FIRE_NUM_COL] ==
bottle_num].head())
bottle_num += 1
# # Build the filename for the bottle fire data
# bottlefileName = filename_base.replace(CONVERTED_SUFFIX,'') + BOTTLE_SUFFIX + '.' + FILE_EXT
# bottlefilePath = os.path.join(outputDir, bottlefileName)
#
# # Save the bottle fire dataframe to file.
# debugPrint('Saving bottle data to:', bottlefilePath + '... ', end='')
# if not cnv.saveConvertedDataToFile(bottle_df, bottlefilePath, DEBUG):
# errPrint('ERROR: Could not save bottle fire data to file')
# else:
# debugPrint('Success!')
#
mean_df = btl.bottle_mean(bottle_df)
# Build the filename for the bottle fire mean data
# meanfileName = filename_base.replace(CONVERTED_SUFFIX,'') + BOTTLE_SUFFIX + MEAN_SUFFIX + '.' + FILE_EXT
meanfileName = filename_base.replace(
CONVERTED_SUFFIX, '') + BOTTLE_SUFFIX + MEAN_SUFFIX + '.' + EXT_PKL
meanfilePath = os.path.join(outputDir, meanfileName)
# Save the bottle fire mean dataframe to file.
debugPrint('Saving mean data to:', meanfilePath + '... ', end='')
if not cnv.saveConvertedDataToFile(mean_df, meanfilePath, DEBUG):
errPrint('ERROR: Could not save mean fire data to file')
else:
debugPrint('Success!')