def __init__(self,
s57: S57File,
profile: int = 0,
version: str = "2021",
survey_area: int = Checks.survey_areas["Pacific Coast"],
use_mhw: bool = False,
mhw_value: float = 0.0,
sorind: Optional[str] = None,
sordat: Optional[str] = None,
multimedia_folder: Optional[str] = None,
check_image_names: bool = False):
self.type = 'FEATURE_SCAN_v11'
self.s57 = s57
self.flags = Flags()
self.report = Report(lib_name=lib_info.lib_name,
lib_version=lib_info.lib_version)
self.checks = Checks(flags=self.flags,
report=self.report,
all_features=self.s57.rec10s,
survey_area=survey_area,
version=version,
sorind=sorind,
sordat=sordat,
profile=profile,
use_mhw=use_mhw,
mhw_value=mhw_value,
check_image_names=check_image_names,
multimedia_folder=multimedia_folder)
def __init__(self, s57):
self.type = scan_algos["BASE"]
# inputs
self.s57 = s57
# outputs
self.flagged_features = [[], [], []]
# report
self.report = Report(lib_name=lib_info.lib_name,
lib_version=lib_info.lib_version)
def __init__(self, root, opr):
self.type = submission_algos["BASE"]
self.version = specs_vers["BASE"]
self.opr = opr
# inputs
if not os.path.exists(root):
raise RuntimeError("The passed root path does not exist: %s" %
root)
self.root = os.path.abspath(root)
self.root_is_project = False
self.root_is_survey = False
self.root_is_report = False
# identify project folder
if self.is_valid_project_folder(self.root, opr=self.opr)[0]:
self.project = os.path.basename(self.root)
self.project_path = self.root
self.root_is_project = True
elif self.is_valid_survey_folder(self.root, opr=self.opr)[0]:
self.project_path = os.path.abspath(
os.path.join(self.root, os.pardir))
self.project = os.path.basename(self.project_path)
self.root_is_survey = True
elif self.is_valid_report_folder(self.root, opr=self.opr)[0]:
self.project_path = os.path.abspath(
os.path.join(self.root, os.pardir))
self.project = os.path.basename(self.project_path)
self.root_is_report = True
else:
raise RuntimeError(
"Unable to identify the kind of root folder: %s" % self.root)
logger.debug("project folder: %s" % self.project_path)
self.xnnnnns = list()
self.xnnnnn_paths = list()
self.cur_xnnnnn = None
self.cur_xnnnnn_path = None
self.pr_path = None
# outputs
self.errors = list()
self.warnings = list()
# report
self.report = Report(lib_name=lib_info.lib_name,
lib_version=lib_info.lib_version)
def __init__(self, s57, grids):
self.type = valsou_algos["BASE"]
self.version = specs_vers["BASE"]
# inputs
self.s57 = s57
# inputs
self.grids = grids
# outputs
self.flagged_features = list()
# report
self.report = Report(lib_name=lib_info.lib_name,
lib_version=lib_info.lib_version)
def __init__(self, s57, ss, progress=None):
self.type = scan_algos["BASE"]
self.version = specs_vers["BASE"]
# inputs
self.s57 = s57
self.ss = ss
# outputs
self.flagged_features = [[], [], []]
# report
self.report = Report(lib_name=lib_info.lib_name, lib_version=lib_info.lib_version)
# progress bar
self.progress = progress
def test_init(self):
# noinspection PyArgumentList
if not QtWidgets.QApplication.instance():
QtWidgets.QApplication([])
li = LibInfo()
rep = Report(lib_name=li.lib_name, lib_version=li.lib_version)
rep += "Test [CHECK]"
rep += "OK"
rep += "Test [CHECK]"
rep += "test"
rep += "test"
rep += "test"
rep += "test [SKIP_CHK]"
rep += "skip [SKIP_REP]"
rep += "End [TOTAL]"
rep += "Check 1 - Test"
rep += "Check 2 - Test"
rep.display()
rep.generate_pdf(path=str(
self.testing.output_data_folder().joinpath('test.pdf')),
title="Test Document",
use_colors=True,
small=True)
def __init__(self, ss, s57, cs, sounding_unit, progress=None):
self.type = triangle_algos["BASE"]
# inputs
self.ss = ss
self.cs = cs
self.s57 = s57
# criteria
self.csu = sounding_unit
# outputs
self.flagged_features = [[], [], []]
# report
self.report = Report(lib_name=lib_info.lib_name,
lib_version=lib_info.lib_version)
# progress bar
self.progress = progress
import sys import logging from PySide2 import QtWidgets from hyo2.abc.app.report import Report from hyo2.abc.lib.lib_info import LibInfo from hyo2.abc.lib.logging import set_logging logger = logging.getLogger(__name__) set_logging(ns_list=["hyo2.abc"]) app = QtWidgets.QApplication([]) li = LibInfo() r = Report(lib_name=li.lib_name, lib_version=li.lib_version) # sys.exit(app.exec_())
import logging
from PySide2 import QtWidgets
from hyo2.abc.app.report import Report
from hyo2.abc.lib.lib_info import LibInfo
from hyo2.abc.lib.logging import set_logging
from hyo2.abc.lib.testing import Testing
logger = logging.getLogger(__name__)
set_logging(ns_list=["hyo2.abc"])
app = QtWidgets.QApplication([])
li = LibInfo()
r = Report(lib_name=li.lib_name, lib_version=li.lib_version)
t = Testing()
output_pdf = os.path.join(
t.output_data_folder(),
"%s.pdf" % os.path.splitext(os.path.basename(__file__))[0])
if os.path.exists(output_pdf):
os.remove(output_pdf)
logger.debug('output pdf: %s' % output_pdf)
r += "Section 1 [SECTION]"
r += "Check 1 [CHECK]"
r += "OK"
r += "Check 2 [CHECK]"
class BagChecksV1:
def __init__(self,
grid_list: List[str],
output_folder: str,
output_project_folder: bool,
output_subfolders: bool,
use_nooa_nbs_profile: bool = False,
check_structure: bool = False,
check_metadata: bool = False,
check_elevation: bool = False,
check_uncertainty: bool = False,
check_tracking_list: bool = False,
progress: AbstractProgress = CliProgress(),
open_output_folder: bool = True):
self.grid_list = grid_list
self.output_folder = output_folder
self.output_project_folder = output_project_folder
self.output_subfolders = output_subfolders
self.open_output_folder = open_output_folder
self._noaa_nbs_profile = use_nooa_nbs_profile
self._structure = check_structure
self._metadata = check_metadata
self._elevation = check_elevation
self._uncertainty = check_uncertainty
self._tracking_list = check_tracking_list
self._msg = str()
self._bc_structure_errors = 0 # type: int
self._bc_structure_warnings = 0 # type: int
self._bc_metadata_errors = 0 # type: int
self._bc_metadata_warnings = 0 # type: int
self._bc_elevation_errors = 0 # type: int
self._bc_elevation_warnings = 0 # type: int
self._bc_uncertainty_errors = 0 # type: int
self._bc_uncertainty_warnings = 0 # type: int
self._bc_tracking_list_errors = 0 # type: int
self._bc_tracking_list_warnings = 0 # type: int
self._bc_report = None
self._bc_pdf = str()
self._cur_min_depth = None # type: Optional[float]
self._cur_max_depth = None # type: Optional[float]
self._cur_vr_min_depth = None # type: Optional[float]
self._cur_vr_max_depth = None # type: Optional[float]
self.progress = progress
self._is_vr = False
self._survey = str()
self._grid_basename = str()
@property
def msg(self) -> str:
return self._msg
def run(self):
self.progress.start(title="BAG Checks v1", text="Loading")
if not self._structure and not self._metadata and not self._elevation and not self._uncertainty \
and not self._tracking_list:
raise RuntimeError('At least one check needs to be selected')
logger.info(
'BAG Checks v1 -> Structure: %s, Metadata: %s, Elevation: %s, Uncertainty: %s, Tracking List: %s'
% (self._structure, self._metadata, self._elevation,
self._uncertainty, self._tracking_list))
if self._noaa_nbs_profile:
logger.info('Using the NOAA NBS profile')
else:
logger.info('Using the general profile')
# Check if the grid list is empty
if len(self.grid_list) == 0:
raise RuntimeError("The grid list is empty")
try:
start_time = time.time()
# for each file in the project grid list
self._msg = "Checks results per input:\n"
opened_folders = list()
nr_of_files = len(self.grid_list)
for i, grid_file in enumerate(self.grid_list):
self._cur_min_depth = None
self._cur_max_depth = None
self._cur_vr_min_depth = None
self._cur_vr_max_depth = None
success = self._bag_checks_v1(grid_file=grid_file,
idx=i,
total=nr_of_files)
if success:
if self.cur_bag_checks_passed:
self._msg += "- %s: pass\n" % self._grid_basename
else:
self._msg += "- %s: fail\n" % self._grid_basename
if self.open_output_folder:
# open the output folder (if not already open)
if self.bagchecks_output_folder not in opened_folders:
self.open_bagchecks_output_folder()
opened_folders.append(self.bagchecks_output_folder)
else:
self._msg += "- %s: skip\n" % self._grid_basename
logger.info("BAG Checks v1 -> execution time: %.3f s" %
(time.time() - start_time))
except Exception as e:
traceback.print_exc()
self._msg = None
self.progress.end()
raise e
self.progress.end()
def _bag_checks_v1(self, grid_file: str, idx: int, total: int) -> bool:
quantum = 100.0 / total
cur_quantum = quantum * idx
self.progress.update(value=cur_quantum + quantum * 0.05,
text="[%d/%d] File opening" % (idx + 1, total))
# we want to be sure that the label is based on the name of the new file input
self._survey = BaseProject.make_survey_label_from_path(grid_file)
self._grid_basename = os.path.basename(grid_file)
# skip CSAR
if not bag.BAGFile.is_bag(bag_path=grid_file): # skip CSAR
logger.debug('not a BAG file: %s' % grid_file)
return False
self._is_vr = bag.BAGFile.is_vr(bag_path=grid_file)
if self._is_vr:
logger.debug('detected VR BAG')
self._bc_report = Report(lib_name=lib_name, lib_version=lib_version)
self.progress.update(value=cur_quantum + quantum * 0.15,
text="[%d/%d] Structure checking" %
(idx + 1, total))
self._bag_checks_v1_structure(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.3,
text="[%d/%d] Metadata checking" %
(idx + 1, total))
self._bag_checks_v1_metadata(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.5,
text="[%d/%d] Elevation checking" %
(idx + 1, total))
self._bag_checks_v1_elevation(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.7,
text="[%d/%d] Uncertainty checking" %
(idx + 1, total))
self._bag_checks_v1_uncertainty(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.85,
text="[%d/%d] Tracking list checking" %
(idx + 1, total))
self._bag_checks_v1_tracking_list(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.95,
text="[%d/%d] Summary" % (idx + 1, total))
self._bag_checks_v1_summary()
output_pdf = os.path.join(
self.bagchecks_output_folder, "%s.BCv1.%s.pdf" %
(self._grid_basename, datetime.now().strftime("%Y%m%d.%H%M%S")))
if self._noaa_nbs_profile:
title_pdf = "BAG Checks v1 - Tests against NOAA OCS Profile"
else:
title_pdf = "BAG Checks v1 - Tests against General Profile"
if self._bc_report.generate_pdf(output_pdf, title_pdf,
use_colors=True):
self._bc_pdf = output_pdf
return True
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
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_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_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_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_summary(self) -> None:
self._bc_report += "Summary [SECTION]"
if self._structure:
self._bc_report += "Structure [CHECK]"
self._bc_report += "Errors: %d" % self._bc_structure_errors
self._bc_report += "Warnings: %d" % self._bc_structure_warnings
if self._metadata:
self._bc_report += "Metadata [CHECK]"
self._bc_report += "Errors: %d" % self._bc_metadata_errors
self._bc_report += "Warnings: %d" % self._bc_metadata_warnings
if self._elevation:
self._bc_report += "Elevation [CHECK]"
self._bc_report += "Errors: %d" % self._bc_elevation_errors
self._bc_report += "Warnings: %d" % self._bc_elevation_warnings
if self._uncertainty:
self._bc_report += "Uncertainty [CHECK]"
self._bc_report += "Errors: %d" % self._bc_uncertainty_errors
self._bc_report += "Warnings: %d" % self._bc_uncertainty_warnings
if self._tracking_list:
self._bc_report += "Tracking List [CHECK]"
self._bc_report += "Errors: %d" % self._bc_tracking_list_errors
self._bc_report += "Warnings: %d" % self._bc_tracking_list_warnings
@property
def cur_bag_checks_passed(self) -> bool:
if self._structure:
if (self._bc_structure_errors > 0) or (self._bc_structure_warnings
> 0):
return False
if self._metadata:
if (self._bc_metadata_errors > 0) or (self._bc_metadata_warnings >
0):
return False
if self._elevation:
if (self._bc_elevation_errors > 0) or (self._bc_elevation_warnings
> 0):
return False
if self._uncertainty:
if (self._bc_uncertainty_errors >
0) or (self._bc_uncertainty_warnings > 0):
return False
if self._tracking_list:
if (self._bc_tracking_list_errors >
0) or (self._bc_tracking_list_warnings > 0):
return False
return True
def open_bagchecks_output_folder(self):
logger.info("open %s" % self.bagchecks_output_folder)
Helper.explore_folder(self.bagchecks_output_folder)
@property
def bagchecks_output_folder(self):
# make up the output folder (creating it if it does not exist)
if self.output_project_folder:
output_folder = os.path.join(self.output_folder, self._survey)
else:
output_folder = self.output_folder
if self.output_subfolders:
output_folder = os.path.join(output_folder, "bag_checks")
else:
output_folder = os.path.join(output_folder)
if not os.path.exists(output_folder):
os.makedirs(output_folder)
return output_folder
def _bag_checks_v1(self, grid_file: str, idx: int, total: int) -> bool:
quantum = 100.0 / total
cur_quantum = quantum * idx
self.progress.update(value=cur_quantum + quantum * 0.05,
text="[%d/%d] File opening" % (idx + 1, total))
# we want to be sure that the label is based on the name of the new file input
self._survey = BaseProject.make_survey_label_from_path(grid_file)
self._grid_basename = os.path.basename(grid_file)
# skip CSAR
if not bag.BAGFile.is_bag(bag_path=grid_file): # skip CSAR
logger.debug('not a BAG file: %s' % grid_file)
return False
self._is_vr = bag.BAGFile.is_vr(bag_path=grid_file)
if self._is_vr:
logger.debug('detected VR BAG')
self._bc_report = Report(lib_name=lib_name, lib_version=lib_version)
self.progress.update(value=cur_quantum + quantum * 0.15,
text="[%d/%d] Structure checking" %
(idx + 1, total))
self._bag_checks_v1_structure(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.3,
text="[%d/%d] Metadata checking" %
(idx + 1, total))
self._bag_checks_v1_metadata(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.5,
text="[%d/%d] Elevation checking" %
(idx + 1, total))
self._bag_checks_v1_elevation(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.7,
text="[%d/%d] Uncertainty checking" %
(idx + 1, total))
self._bag_checks_v1_uncertainty(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.85,
text="[%d/%d] Tracking list checking" %
(idx + 1, total))
self._bag_checks_v1_tracking_list(grid_file=grid_file)
self.progress.update(value=cur_quantum + quantum * 0.95,
text="[%d/%d] Summary" % (idx + 1, total))
self._bag_checks_v1_summary()
output_pdf = os.path.join(
self.bagchecks_output_folder, "%s.BCv1.%s.pdf" %
(self._grid_basename, datetime.now().strftime("%Y%m%d.%H%M%S")))
if self._noaa_nbs_profile:
title_pdf = "BAG Checks v1 - Tests against NOAA OCS Profile"
else:
title_pdf = "BAG Checks v1 - Tests against General Profile"
if self._bc_report.generate_pdf(output_pdf, title_pdf,
use_colors=True):
self._bc_pdf = output_pdf
return True