def _bag_checks_v2_gdal_compatibility(self, grid_file: str) -> None:
if self._gdal_compatibility is False:
self._bc_report += "GDAL Compatibility [SKIP_SEC]"
self._bc_report += "All GDAL-compatibility-related checks are deactivated. [SKIP_REP]"
return
self._bc_report += "GDAL Compatibility [SECTION]"
self._bc_gdal_compatibility_errors = 0
self._bc_gdal_compatibility_warnings = 0
try:
bf = bag.BAGFile(grid_file)
# CHK: Too many refinement grids
self._bc_report += "Check for 'Too many refinement grids' GDAL error [CHECK]"
bf_rows, bf_cols = bf.elevation_shape()
if self._is_vr and ((bf_rows * bf_cols) > 10000000):
self._bc_gdal_compatibility_warnings += 1
self._bc_report += "[WARNING] Too big super-grid: %d, %d" % (bf_rows, bf_cols)
return
else:
self._bc_report += "OK"
except Exception as e:
traceback.print_exc()
self._bc_report += "Other potential issues [CHECK]"
self._bc_gdal_compatibility_errors += 1
self._bc_report += "[ERROR] Unexpected issue: %s" % e
def _bag_checks_v2_elevation(self, grid_file: str) -> None:
if self._elevation is False:
self._bc_report += "Elevation [SKIP_SEC]"
self._bc_report += "All elevation-related checks are deactivated. [SKIP_REP]"
return
self._bc_report += "Elevation [SECTION]"
self._bc_elevation_errors = 0
self._bc_elevation_warnings = 0
try:
bf = bag.BAGFile(grid_file)
# CHK: presence of elevation
self._bc_report += "Check the presence of the Elevation dataset [CHECK]"
if not bf.has_elevation():
self._bc_elevation_errors += 1
self._bc_report += "[ERROR] Missing the Elevation dataset"
return
else:
self._bc_report += "OK"
self._cur_min_depth, self._cur_max_depth = bf.depth_min_max()
logger.debug('min/max depth: %.2f/%.2f' % (self._cur_min_depth, self._cur_max_depth))
# CHK: all NaN
self._bc_report += "Check that all the values are not NaN [CHECK]"
if np.isnan(self._cur_min_depth): # all NaN case
self._bc_elevation_warnings += 1
self._bc_report += "[WARNING] All elevation values are NaN"
else:
self._bc_report += "OK"
if self._is_vr:
# CHK: presence of VR Refinements
self._bc_report += "Check the presence of the VR Refinements dataset [CHECK]"
if not bf.has_varres_refinements():
self._bc_elevation_errors += 1
self._bc_report += "[ERROR] Missing the VR Refinements dataset"
else:
self._bc_report += "OK"
self._cur_vr_min_depth, self._cur_vr_max_depth = bf.vr_depth_min_max()
logger.debug('VR min/max depth: %.2f/%.2f' % (self._cur_vr_min_depth, self._cur_vr_max_depth))
# CHK: VR depth all NaN
self._bc_report += "Check that all the VR depth values are not NaN [CHECK]"
if np.isnan(self._cur_vr_min_depth): # all NaN case
self._bc_elevation_warnings += 1
self._bc_report += "[WARNING] All VR elevation values are NaN"
else:
self._bc_report += "OK"
except Exception as e:
traceback.print_exc()
self._bc_report += "Other potential issues [CHECK]"
self._bc_elevation_errors += 1
self._bc_report += "[ERROR] Unknown issue: %s" % e
def _bag_checks_v1_tracking_list(self, grid_file: str) -> None:
if self._tracking_list is False:
self._bc_report += "Tracking List [SKIP_SEC]"
self._bc_report += "All tracking-list-related checks are deactivated. [SKIP_REP]"
return
self._bc_report += "Tracking List [SECTION]"
self._bc_tracking_list_errors = 0
self._bc_tracking_list_warnings = 0
try:
bf = bag.BAGFile(grid_file)
# CHK: presence of tracking list
self._bc_report += "Check the presence of the Tracking List dataset [CHECK]"
if not bf.has_tracking_list():
self._bc_tracking_list_errors += 1
self._bc_report += "[ERROR] Missing the Tracking List dataset"
return
else:
self._bc_report += "OK"
# CHK validity of row columns
self._bc_report += "Check the validity of 'row' columns [CHECK]"
if not bf.has_valid_row_in_tracking_list():
self._bc_tracking_list_errors += 1
self._bc_report += "[ERROR] At least 1 invalid value in 'row' columns"
else:
self._bc_report += "OK"
# CHK validity of col columns
self._bc_report += "Check the validity of 'col' columns [CHECK]"
if not bf.has_valid_col_in_tracking_list():
self._bc_tracking_list_errors += 1
self._bc_report += "[ERROR] At least 1 invalid value in 'col' columns"
else:
self._bc_report += "OK"
if self._is_vr:
# CHK: presence of VR Tracking List
self._bc_report += "Check the presence of the VR Tracking List dataset [CHECK]"
if not bf.has_varres_tracking_list():
self._bc_tracking_list_errors += 1
self._bc_report += "[ERROR] Missing the VR Tracking List dataset"
else:
self._bc_report += "OK"
except Exception as e:
traceback.print_exc()
self._bc_report += "Other potential issues [CHECK]"
self._bc_tracking_list_errors += 1
self._bc_report += "[ERROR] Unexpected issue: %s" % e
def _bag_checks_v1_uncertainty(self, grid_file: str) -> None:
if self._uncertainty is False:
self._bc_report += "Uncertainty [SKIP_SEC]"
self._bc_report += "All uncertainty-related checks are deactivated. [SKIP_REP]"
return
self._bc_report += "Uncertainty [SECTION]"
self._bc_uncertainty_errors = 0
self._bc_uncertainty_warnings = 0
try:
bf = bag.BAGFile(grid_file)
# CHK: presence of uncertainty
self._bc_report += "Check the presence of the Uncertainty dataset [CHECK]"
if not bf.has_uncertainty():
self._bc_uncertainty_errors += 1
self._bc_report += "[ERROR] Missing the Uncertainty dataset"
return
else:
self._bc_report += "OK"
if self._cur_max_depth is None:
self._cur_min_depth, self._cur_max_depth = bf.depth_min_max()
logger.debug('min/max depth: %.2f/%.2f' %
(self._cur_min_depth, self._cur_max_depth))
if np.isnan(self._cur_max_depth) or (self._cur_max_depth < 0.0):
high_unc_threshold = 2.0
else:
high_unc_threshold = 2.0 + 0.05 * self._cur_max_depth
logger.debug('max uncertainty threshold: %.2f' %
(high_unc_threshold, ))
# logger.debug('min/max elevation: %s/%s' % (min_elevation, max_elevation))
min_uncertainty, max_uncertainty = bf.uncertainty_min_max()
logger.debug('min/max uncertainty: %.2f/%.2f' %
(min_uncertainty, max_uncertainty))
if self._noaa_nbs_profile:
# CHK: all NaN
self._bc_report += "Check that all the values are not NaN [CHECK]"
if np.isnan(min_uncertainty): # all NaN case
self._bc_uncertainty_warnings += 1
self._bc_report += "[WARNING] All uncertainty values are NaN"
return
else:
self._bc_report += "OK"
# CHK: negative uncertainty
self._bc_report += "Check that uncertainty values are only positive [CHECK]"
if min_uncertainty <= 0.0:
self._bc_uncertainty_errors += 1
self._bc_report += "[ERROR] At least one negative or zero value of uncertainty is present (%.3f)" \
% min_uncertainty
else:
self._bc_report += "OK"
if self._noaa_nbs_profile:
# CHK: negative uncertainty
self._bc_report += "Check that uncertainty values are not too high (<%.2fm) [CHECK]" \
% high_unc_threshold
if max_uncertainty >= high_unc_threshold:
self._bc_uncertainty_warnings += 1
self._bc_report += "[WARNING] Too high value for maximum uncertainty: %.2f" % max_uncertainty
else:
self._bc_report += "OK"
if self._is_vr:
# CHK: presence of VR Refinements
self._bc_report += "Check the presence of the VR Refinements dataset [CHECK]"
if not bf.has_varres_refinements():
self._bc_uncertainty_errors += 1
self._bc_report += "[ERROR] Missing the VR Refinements dataset"
else:
self._bc_report += "OK"
if self._cur_vr_max_depth is None:
self._cur_vr_min_depth, self._cur_vr_max_depth = bf.vr_depth_min_max(
)
logger.debug('min/max elevation: %.2f/%.2f' %
(self._cur_vr_min_depth, self._cur_vr_max_depth))
if np.isnan(self._cur_vr_max_depth) or (self._cur_vr_max_depth
< 0.0):
vr_high_unc_threshold = 2.0
else:
vr_high_unc_threshold = 2.0 + 0.05 * self._cur_vr_max_depth
logger.debug('VR uncertainty threshold: %.2f' %
(vr_high_unc_threshold, ))
vr_min_uncertainty, vr_max_uncertainty = bf.vr_uncertainty_min_max(
)
logger.debug('VR min/max uncertainty: %.2f/%.2f' %
(vr_min_uncertainty, vr_max_uncertainty))
if self._noaa_nbs_profile:
# CHK: all NaN
self._bc_report += "Check that all the VR values are not NaN [CHECK]"
if np.isnan(vr_min_uncertainty): # all NaN case
self._bc_uncertainty_warnings += 1
self._bc_report += "[WARNING] All uncertainty values are NaN"
return
else:
self._bc_report += "OK"
# CHK: negative uncertainty
self._bc_report += "Check that VR uncertainty values are only positive [CHECK]"
if vr_min_uncertainty <= 0.0:
self._bc_uncertainty_errors += 1
self._bc_report += "[ERROR] At least one negative or zero value of uncertainty is present (%.3f)" \
% min_uncertainty
else:
self._bc_report += "OK"
if self._noaa_nbs_profile:
# CHK: negative uncertainty
self._bc_report += "Check that VR uncertainty values are not too high (<%.2fm) [CHECK]" \
% vr_high_unc_threshold
if vr_max_uncertainty >= vr_high_unc_threshold:
self._bc_uncertainty_warnings += 1
self._bc_report += "[WARNING] Too high value for maximum uncertainty: %.2f" % vr_max_uncertainty
else:
self._bc_report += "OK"
except Exception as e:
traceback.print_exc()
self._bc_report += "Other potential issues [CHECK]"
self._bc_uncertainty_errors += 1
self._bc_report += "[ERROR] Unuspected issue: %s" % e
def _bag_checks_v1_metadata(self, grid_file: str) -> None:
if self._metadata is False:
self._bc_report += "Metadata [SKIP_SEC]"
self._bc_report += "All metadata-related checks are deactivated. [SKIP_REP]"
return
self._bc_report += "Metadata [SECTION]"
self._bc_metadata_errors = 0
self._bc_metadata_warnings = 0
try:
bf = bag.BAGFile(grid_file)
# CHK: presence of metadata
self._bc_report += "Check the presence of the Metadata dataset [CHECK]"
if not bf.has_metadata():
self._bc_metadata_errors += 1
self._bc_report += "[ERROR] Missing the Metadata dataset"
return
else:
self._bc_report += "OK"
bf.populate_metadata()
# bf.extract_metadata('test.xml')
if self._noaa_nbs_profile:
# CHK: use of projected spatial reference system
self._bc_report += "Check that the spatial reference system is projected [CHECK]"
if bf.meta.wkt_srs is None:
if b"UTM" not in bf.meta.xml_srs:
self._bc_report += "[WARNING] The spatial reference system might be NOT projected [%s...]" \
% bf.meta.xml_srs[:20]
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
else:
srs = osr.SpatialReference()
srs.ImportFromWkt(bf.meta.wkt_srs)
# check if projected coordinates
if not srs.IsProjected:
self._bc_report += "[WARNING] The spatial reference system does is NOT projected [%s...]" \
% bf.meta.wkt_srs[:20]
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
# TODO: additional checks on SRS
if self._noaa_nbs_profile:
# CHK: definition of vertical datum
self._bc_report += "Check that the vertical datum is defined [CHECK]"
if bf.meta.wkt_vertical_datum is None:
if b"Unknown" in bf.meta.xml_vertical_datum:
self._bc_report += "[WARNING] The vertical datum might be unknown [%s...]" \
% bf.meta.xml_vertical_datum[:20]
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
else:
if "unknown" in bf.meta.wkt_vertical_datum.lower():
self._bc_report += "[WARNING] The vertical datum is unknown [%s...]" \
% bf.meta.wkt_vertical_datum[:20]
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
if self._noaa_nbs_profile:
# CHK: presence of creation date
self._bc_report += "Check the presence of the creation date [CHECK]"
if bf.meta.date is None:
self._bc_report += "[WARNING] Unable to retrieve the creation date."
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
# CHK: presence of survey start date
self._bc_report += "Check the presence of the survey start date [CHECK]"
if bf.meta.survey_start_date is None:
self._bc_report += "[WARNING] Unable to retrieve the survey start date."
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
# CHK: presence of survey end date
self._bc_report += "Check the presence of the survey end date [CHECK]"
if bf.meta.survey_end_date is None:
self._bc_report += "[WARNING] Unable to retrieve the survey end date."
self._bc_metadata_warnings += 1
else:
self._bc_report += "OK"
if self._noaa_nbs_profile:
# CHK: use of product uncertainty
self._bc_report += "Check the selection of Product Uncertainty [CHECK]"
if not bf.has_product_uncertainty():
self._bc_metadata_warnings += 1
self._bc_report += "[WARNING] The Uncertainty layer does not contain Product Uncertainty: %s" \
% bf.meta.unc_type
else:
self._bc_report += "OK"
if self._is_vr:
# CHK: presence of VR Metadata
self._bc_report += "Check the presence of the VR Metadata dataset [CHECK]"
if not bf.has_varres_metadata():
self._bc_metadata_errors += 1
self._bc_report += "[ERROR] Missing the VR Metadata dataset"
else:
self._bc_report += "OK"
except Exception as e:
traceback.print_exc()
self._bc_report += "Other potential issues [CHECK]"
self._bc_metadata_errors += 1
self._bc_report += "[ERROR] Unexpected issue: %s" % e
def _bag_checks_v1_structure(self, grid_file: str) -> None:
if self._structure is False:
self._bc_report += "Structure [SKIP_SEC]"
self._bc_report += "All structure-related checks are deactivated. [SKIP_REP]"
return
self._bc_report += "Structure [SECTION]"
self._bc_structure_errors = 0
self._bc_structure_warnings = 0
try:
bf = bag.BAGFile(grid_file)
# logger.debug('BAG version: %s' % bf.bag_version())
# CHK: presence of root
self._bc_report += "Check the presence of the BAG Root group [CHECK]"
if not bf.has_bag_root():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the BAG Root group"
else:
self._bc_report += "OK"
# CHK: presence of version
self._bc_report += "Check the presence of the BAG Version attribute [CHECK]"
if not bf.has_bag_version():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the BAG Version attribute"
else:
self._bc_report += "OK"
# CHK: presence of metadata
self._bc_report += "Check the presence of the Metadata dataset [CHECK]"
if not bf.has_metadata():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the Metadata dataset"
else:
self._bc_report += "OK"
# CHK: presence of elevation
self._bc_report += "Check the presence of the Elevation dataset [CHECK]"
if not bf.has_elevation():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the Elevation dataset"
else:
self._bc_report += "OK"
# CHK: presence of uncertainty
self._bc_report += "Check the presence of the Uncertainty dataset [CHECK]"
if not bf.has_uncertainty():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the Uncertainty dataset"
else:
self._bc_report += "OK"
# CHK: presence of tracking list
self._bc_report += "Check the presence of the Tracking List dataset [CHECK]"
if not bf.has_tracking_list():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the Tracking List dataset"
else:
self._bc_report += "OK"
if self._is_vr:
# CHK: presence of VR Metadata
self._bc_report += "Check the presence of the VR Metadata dataset [CHECK]"
if not bf.has_varres_metadata():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the VR Metadata dataset"
else:
self._bc_report += "OK"
# CHK: presence of VR Refinements
self._bc_report += "Check the presence of the VR Refinements dataset [CHECK]"
if not bf.has_varres_refinements():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the VR Refinements dataset"
else:
self._bc_report += "OK"
# CHK: presence of VR Tracking List
self._bc_report += "Check the presence of the VR Tracking List dataset [CHECK]"
if not bf.has_varres_tracking_list():
self._bc_structure_errors += 1
self._bc_report += "[ERROR] Missing the VR Tracking List dataset"
else:
self._bc_report += "OK"
except Exception as e:
traceback.print_exc()
self._bc_report += "Other potential issues [CHECK]"
self._bc_structure_errors += 1
self._bc_report += "[ERROR] %s" % e