def main():
logger = logging.getLogger()
logger.setLevel(logging.NOTSET)
import argparse
from hydroffice.bag import BAGFile, is_bag, __version__
app_name = "bag_metadata"
app_info = "Extraction of XML metadata from an OpenNS BAG file, using hydroffice.bag r%s" % __version__
parser = argparse.ArgumentParser(prog=app_name, description=app_info)
parser.add_argument("bag_file", type=str, help="a valid BAG file from which to extract metadata")
parser.add_argument("-x", "--xml_file", help="the output XML metadata file", type=str)
parser.add_argument("-v", "--verbose", help="increase output verbosity", action="store_true")
args = parser.parse_args()
if args.verbose:
print("> verbosity: ON")
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
if args.verbose:
print("> input: %s" % args.bag_file)
if args.xml_file:
args.xml_file = os.path.abspath(args.xml_file)
print("> output: %s" % args.xml_file)
else:
args.xml_file = os.path.abspath(BAGFile.default_metadata_file)
print("> output: %s [default]" % args.xml_file)
if not os.path.exists(args.bag_file):
parser.exit(1, "ERROR: the input valid does not exist: %s" % args.bag_file)
if not is_bag(args.bag_file):
parser.exit(1, "ERROR: the input valid does not seem a BAG file: %s" % args.bag_file)
bf = BAGFile(args.bag_file)
try:
bf.extract_metadata(args.xml_file)
except Exception as e:
parser.exit(1, "ERROR: %s" % e)
if args.verbose:
print("> DONE")
def main():
logger = logging.getLogger()
logger.setLevel(logging.NOTSET)
import argparse
from hydroffice.bag import BAGFile, is_bag, __version__
app_name = "bag_bbox"
app_info = "Extraction of bounding box from an OpenNS BAG file, using hydroffice.bag r%s" % __version__
formats = ['gjs', 'gml', 'kml', 'shp']
parser = argparse.ArgumentParser(prog=app_name, description=app_info)
parser.add_argument("bag_file", type=str, help="a valid BAG file from which to extract metadata")
parser.add_argument("-f", "--format", help="one of the available file format: " + ", ".join(formats),
choices=formats, default="kml", metavar='')
parser.add_argument("-o", "--output", help="the output file", type=str)
parser.add_argument("-v", "--verbose", help="increase output verbosity", action="store_true")
args = parser.parse_args()
if args.verbose:
print("> verbosity: ON")
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
if args.verbose:
print("> input: %s" % args.bag_file)
if args.output:
args.output = os.path.abspath(args.output)
print("> output: %s" % args.output)
else:
args.output = None
print("> output: [default]")
print("> format: %s" % args.format)
if not os.path.exists(args.bag_file):
parser.exit(1, "ERROR: the input valid does not exist: %s" % args.bag_file)
if not is_bag(args.bag_file):
parser.exit(1, "ERROR: the input valid does not seem a BAG file: %s" % args.bag_file)
bf = BAGFile(args.bag_file)
try:
bag_meta = bf.populate_metadata()
except Exception as e:
parser.exit(1, "ERROR: issue in metadata population: %s" % e)
try:
from hydroffice.bag.bbox import Bbox2Gdal
Bbox2Gdal(bag_meta, fmt=args.format, title=os.path.basename(args.bag_file), out_file=args.output)
except Exception as e:
parser.exit(1, "ERROR: issue in output creation: %s" % e)
if args.verbose:
print("> DONE")
logger.setLevel(logging.NOTSET)
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
bag_file = os.path.join(Helper.samples_folder(), "bdb_00.bag")
if os.path.exists(bag_file):
print("- file_bag_0: %s" % bag_file)
bag = BAGFile(bag_file)
bag_meta = bag.populate_metadata()
print(bag_meta)
bag_uncertainty = bag.uncertainty(mask_nan=True)
print(type(bag.elevation(mask_nan=True)), bag.elevation(mask_nan=True).shape, bag.elevation(mask_nan=True).dtype)
from hydroffice.bag.uncertainty import Uncertainty2Gdal
Uncertainty2Gdal(bag_uncertainty=bag_uncertainty, bag_meta=bag_meta, fmt="ascii", epsg=4326)
Uncertainty2Gdal(bag_uncertainty=bag_uncertainty, bag_meta=bag_meta, fmt="geotiff", epsg=4326)
Uncertainty2Gdal(bag_uncertainty=bag_uncertainty, bag_meta=bag_meta, fmt="xyz", epsg=4326)
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import logging
from matplotlib import pyplot as plt
logger = logging.getLogger()
logger.setLevel(logging.NOTSET)
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
from hydroffice.bag.tracklist import TrackList2Csv
bag_file = os.path.join(Helper.samples_folder(), "bdb_00.bag")
bag = BAGFile(bag_file)
tl = bag.tracking_list()
tl2csv = TrackList2Csv(tl)
bag_file = os.path.join(Helper.samples_folder(), "bdb_02.bag")
bag = BAGFile(bag_file)
tl = bag.tracking_list()
tl_fields = bag.tracking_list_fields()
print(tl_fields)
tl2csv = TrackList2Csv(track_list=tl, header=tl_fields)
logger.setLevel(logging.NOTSET)
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
bag_file = os.path.join(Helper.samples_folder(), "bdb_00.bag")
if os.path.exists(bag_file):
print("- file_bag_0: %s" % bag_file)
bag = BAGFile(bag_file)
bag_meta = bag.populate_metadata()
print(bag_meta)
print("has elevation? %s" % bag.has_elevation())
bag_elevation = bag.elevation(mask_nan=False)
print(type(bag.elevation()), bag.elevation().shape, bag.elevation().dtype)
from hydroffice.bag.elevation import Elevation2Gdal
Elevation2Gdal(bag_elevation=bag_elevation, bag_meta=bag_meta, fmt="ascii")
Elevation2Gdal(bag_elevation=bag_elevation, bag_meta=bag_meta, fmt="geotiff")
Elevation2Gdal(bag_elevation=bag_elevation, bag_meta=bag_meta, fmt="xyz")
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter("%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s")
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
# bag_file = os.path.join(Helper.samples_folder(), "bdb_00.bag")
# bag_file = "C:/Users/gmasetti/Google Drive/QC Tools/test data/H12730/H12730_MB_1m_MLLW.bag"
bag_file = "C:/Users/gmasetti/Google Drive/QC Tools/test data/H12657/H12657_MB_2m_MLLW.bag"
if os.path.exists(bag_file):
print("- file_bag_0: %s" % bag_file)
bag = BAGFile(bag_file)
bag_meta = bag.populate_metadata()
print(bag_meta)
print("has density? %s" % bag.has_density())
bag_density = bag.density(mask_nan=True)
print(type(bag.density(mask_nan=True)), bag.density(mask_nan=True).shape, bag.density(mask_nan=True).dtype)
print("min: %s" % np.nanmin(bag_density))
print("max: %s" % np.nanmax(bag_density))
# from hydroffice.bag.density import Density2Gdal
# Density2Gdal(bag_density=bag_density, bag_meta=bag_meta, fmt="ascii")
# Density2Gdal(bag_density=bag_density, bag_meta=bag_meta, fmt="geotiff")
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
# Example that use bag.BAGFile to:
# - open a BAG file
# - read the whole elevation and uncertainty layers
# - read a selected range of rows for the elevation and uncertainty layers
file_bag_0 = os.path.join(Helper.samples_folder(), "bdb_00.bag")
if os.path.exists(file_bag_0):
logger.debug("- file_bag_0: %s" % file_bag_0)
# - open a file
bag_0 = BAGFile(file_bag_0)
logger.debug("\n%s\n" % bag_0)
# - get elevation shape
logger.info("elevation shape: %s" % (bag_0.elevation_shape(), ))
# - read the full elevation
full_elevation = bag_0.elevation(mask_nan=True)
logger.info("elevation array:\n type: %s\n shape: %s\n dtype: %s"
% (type(full_elevation), full_elevation.shape, full_elevation.dtype))
ax = plt.contourf(full_elevation)
plt.colorbar(ax)
plt.show()
# - read the first 10 rows of the elevation layers
selection_slice = slice(0, 10)
sliced_elevation = bag_0.elevation(mask_nan=True, row_range=selection_slice)
logger.info("sliced elevation array:\n type: %s\n shape: %s\n dtype: %s"
def __init__(self, url):
if not self.can_handle(url):
raise ValueError(url)
self._url = url
path = url2path(url)
self.f = BAGFile(path, 'r')
class BAGStore(compass_model.Store):
""" Data store implementation using a BAG file (closely mimicking HDF5Store).
Keys are the full names of objects in the file.
"""
@staticmethod
def plugin_name():
return "BAG"
@staticmethod
def plugin_description():
return """A plugin used to browse Open Navigation Surface BAG files.
It provides additional features that are not available with the general HDF5 plugin:
- View of metadata information as XML (+ content validation).
- Plot of elevation and uncertainty using their geographic extent/
The plugin is developed and maintained by G.Masetti [[email protected]].
"""
file_extensions = {'BAG File': ['*.bag']}
def __contains__(self, key):
return key in self.f
@property
def url(self):
return self._url
@property
def display_name(self):
return op.basename(self.f.filename)
@property
def root(self):
return self['/']
@property
def valid(self):
return bool(self.f)
@staticmethod
def can_handle(url):
if not url.startswith('file://'):
log.debug("able to handle %s? no, invalid url" % url)
return False
path = url2path(url)
if not is_bag(path):
log.debug("able to handle %s? no, not a BAG" % url)
return False
log.debug("able to handle %s? yes" % url)
return True
def __init__(self, url):
if not self.can_handle(url):
raise ValueError(url)
self._url = url
path = url2path(url)
self.f = BAGFile(path, 'r')
def close(self):
self.f.close()
def get_parent(self, key):
# HDFCompass requires the parent of the root container be None
if key == "" or key == "/":
return None
p_key = pp.dirname(key)
if p_key == "":
p_key = "/"
return self[p_key]
def main():
logger = logging.getLogger()
logger.setLevel(logging.NOTSET)
import argparse
from hydroffice.bag import BAGFile, is_bag, __version__
app_name = "bag_tracklist"
app_info = "Extraction the tracklist from an OpenNS BAG file, using hydroffice.bag r%s" % __version__
formats = ['csv']
parser = argparse.ArgumentParser(prog=app_name, description=app_info)
parser.add_argument("bag_file", type=str, help="a valid BAG file from which to extract metadata")
parser.add_argument("-f", "--format", help="one of the available file format: " + ", ".join(formats),
choices=formats, default="csv", metavar='')
parser.add_argument("-o", "--output", help="the output file", type=str)
parser.add_argument("-hd", "--header", help="add an header", action="store_true")
parser.add_argument("-v", "--verbose", help="increase output verbosity", action="store_true")
args = parser.parse_args()
if args.verbose:
print("> verbosity: ON")
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
if args.verbose:
print("> input: %s" % args.bag_file)
if args.output:
args.output = os.path.abspath(args.output)
print("> output: %s" % args.output)
else:
args.output = None
print("> output: [default]")
print("> format: %s" % args.format)
print("> header: %s" % args.header)
if not os.path.exists(args.bag_file):
parser.exit(1, "ERROR: the input valid does not exist: %s" % args.bag_file)
if not is_bag(args.bag_file):
parser.exit(1, "ERROR: the input valid does not seem a BAG file: %s" % args.bag_file)
bf = BAGFile(args.bag_file)
tl = None
try:
tl = bf.tracking_list()
except Exception as e:
parser.exit(1, "ERROR: issue in tracking-list recovery: %s" % e)
tlf = ""
if args.header:
try:
tlf = bf.tracking_list_fields()
except Exception as e:
parser.exit(1, "ERROR: issue in tracking-list fields recovery: %s" % e)
try:
from hydroffice.bag.tracklist import TrackList2Csv
TrackList2Csv(track_list=tl, csv_file=args.output, header=tlf)
except Exception as e:
parser.exit(1, "ERROR: issue in output creation: %s" % e)
if args.verbose:
print("> DONE")
logger.setLevel(logging.NOTSET)
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter("%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s")
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
bag_file = os.path.join(Helper.samples_folder(), "bdb_00.bag")
if os.path.exists(bag_file):
print("- file_bag_0: %s" % bag_file)
bag = BAGFile(bag_file)
bag_meta = bag.populate_metadata()
print(bag_meta)
print("has uncertainty? %s" % bag.has_uncertainty())
print("has product uncertainty? %s" % bag.has_product_uncertainty())
bag_uncertainty = bag.uncertainty(mask_nan=True)
print(type(bag.elevation(mask_nan=True)), bag.elevation(mask_nan=True).shape, bag.elevation(mask_nan=True).dtype)
from hydroffice.bag.uncertainty import Uncertainty2Gdal
Uncertainty2Gdal(bag_uncertainty, bag_meta, fmt="ascii")
Uncertainty2Gdal(bag_uncertainty, bag_meta, fmt="geotiff")
Uncertainty2Gdal(bag_uncertainty, bag_meta, fmt="xyz")
logger.setLevel(logging.NOTSET)
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG) # change to WARNING to reduce verbosity, DEBUG for high verbosity
ch_formatter = logging.Formatter('%(levelname)-9s %(name)s.%(funcName)s:%(lineno)d > %(message)s')
ch.setFormatter(ch_formatter)
logger.addHandler(ch)
from hydroffice.bag import BAGFile
from hydroffice.bag import BAGError
from hydroffice.bag.helper import Helper
file_bag_0 = os.path.join(Helper.samples_folder(), "bdb_00.bag")
if os.path.exists(file_bag_0):
print("- file_bag_0: %s" % file_bag_0)
bag_0 = BAGFile(file_bag_0)
print(bag_0)
print(type(bag_0.elevation(mask_nan=True)), bag_0.elevation(mask_nan=True).shape, bag_0.elevation(mask_nan=True).dtype)
# ax =plt.contourf(bag_0.elevation(mask_nan=True))
# plt.colorbar(ax)
# plt.show()
bag_meta = bag_0.populate_metadata()
print(bag_meta)
from hydroffice.bag.bbox import Bbox2Gdal
Bbox2Gdal(bag_meta, fmt="gjs", title=os.path.basename(file_bag_0))
Bbox2Gdal(bag_meta, fmt="gml", title=os.path.basename(file_bag_0))
Bbox2Gdal(bag_meta, fmt="kml", title=os.path.basename(file_bag_0))
Bbox2Gdal(bag_meta, fmt="shp", title=os.path.basename(file_bag_0))