path: root/list-observations

#!/usr/bin/python3

#----------------------------------------------------------------------
# List and filter observations from Artdatabanken
# Copyright © 2023 Guilhem Moulin <guilhem@fripost.org>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
#----------------------------------------------------------------------

import argparse
from datetime import datetime
import time
import locale
import re
from pathlib import Path
from osgeo import gdal, ogr, osr
gdal.UseExceptions()

target_srs = osr.SpatialReference()
target_srs.ImportFromEPSG(3006)
target_srs.SetAxisMappingStrategy(osr.OAMS_TRADITIONAL_GIS_ORDER)

locale.setlocale(locale.LC_TIME, 'sv_SE.UTF-8')

programName = 'list-observations'

def ePath(v):
    return Path(v).expanduser()


class geometryAction(argparse.Action):
    def __init__(self, option_strings, dest, nargs=None, **kwargs):
        super().__init__(option_strings, dest, **kwargs)
    def __call__(self, parser, namespace, value, option_string=None):
        items = getattr(namespace, self.dest, None)
        if items is None:
            items = [value]
        else:
            items = items.copy()
            items.append(value)
        setattr(namespace, self.dest, items)

class redlistedAction(argparse.Action):
    def __init__(self, option_strings, dest, nargs=None, **kwargs):
        super().__init__(option_strings, dest, nargs=nargs, **kwargs)
    def __call__(self, parser, namespace, values, option_string=None):
        items = getattr(namespace, self.dest, None)
        if values is None:
            items = 'TaxonIsRedlisted'
        else:
            values = values.split(',')
            for v in values:
                if v not in ['EX', 'EW', 'RE', 'CR', 'EN', 'VU', 'NT', 'LC', 'DD', 'NE', 'NA']:
                    raise Exception(f'{v}: Invalid redlist category')
            if items is None:
                items = values
            else:
                items = items.copy()
                items.extend(values)
        setattr(namespace, self.dest, items)

class splitAndExtendAction(argparse.Action):
    def __init__(self, option_strings, dest, nargs=None, **kwargs):
        super().__init__(option_strings, dest, nargs=nargs, **kwargs)
    def __call__(self, parser, namespace, values, option_string=None):
        items = getattr(namespace, self.dest, None)
        values = values.lower().split(',')
        if items is None:
            items = values
        else:
            items = items.copy()
            items.extend(values)
        setattr(namespace, self.dest, items)

parser = argparse.ArgumentParser(
    description='List and filter observations from Artdatabanken.',
    prog = programName,
    usage='''%(prog)s [--geometry=FILE] [--max-distance=N] [--redlisted[=NT,VU,…]] OBSERVATIONS_FILE'''
)
parser.add_argument('--geometry', type=ePath, metavar='FILE', action=geometryAction,
    help='Geometry file of interest')
parser.add_argument('--max-uncertainty', metavar='N', type=int, default=250,
    help='Maximum coordinate uncertainty in meters (default: %(default)s)')
parser.add_argument('--max-distance', metavar='N', type=int,
    help='Maximum distance in meters from target geometry')
parser.add_argument('--since', metavar='YYYY-MM-DD',
    help='Start date for observations in ISO 8601 format')
parser.add_argument('--until', metavar='YYYY-MM-DD',
    help='End date for observations in ISO 8601 format')
parser.add_argument('--protected', action='store_true',
    help='Only consider taxons that are protected by law')
parser.add_argument('--redlisted', nargs='?', metavar='NT,…', action=redlistedAction,
    help='Only consider redlisted taxons')
parser.add_argument('--taxon', metavar='NAME', action=splitAndExtendAction,
    help='Only consider these taxons')
parser.add_argument('--reporter', metavar='NAME', action=splitAndExtendAction,
    help='Only consider observation by these reporters')
parser.add_argument('--observer', metavar='NAME', action=splitAndExtendAction,
    help='Only consider observation by these observers')
parser.add_argument('observations', type=ePath, metavar='OBSERVATIONS_FILE',
    help='Observations file')

args = parser.parse_args()

for k in ['since', 'until']:
    v = getattr(args, k, None)
    if v is not None:
        d = datetime.fromisoformat(v)
        setattr(args, k, d)

geometry = None
if args.geometry is not None:
    for path in args.geometry:
        path = path.as_posix()
        ds = ogr.Open(path, update=0)

        layer = None
        for i in range(ds.GetLayerCount()):
            lyr = ds.GetLayerByIndex(i)
            if lyr.GetGeomType() in [ogr.wkbPolygon,
                                     ogr.wkbMultiPolygon,
                                     ogr.wkbPolygonM,
                                     ogr.wkbMultiPolygonM,
                                     ogr.wkbPolygonZM,
                                     ogr.wkbMultiPolygonZM,
                                     ogr.wkbPolygon25D,
                                     ogr.wkbMultiPolygon25D]:
                layer = lyr
                break
        if layer is None:
            raise Exception(f'{path}: does not have any layer of geometry type Polygon')

        source_srs = layer.GetSpatialRef()
        transform_srs = osr.CoordinateTransformation(source_srs, target_srs)

        feature = layer.GetNextFeature()
        while feature is not None:
            geom = feature.GetGeometryRef()
            geom = geom.Clone()
            geom.FlattenTo2D()
            geom.Transform(transform_srs)

            if geometry is None:
                geometry = ogr.Geometry(ogr.wkbMultiPolygon)

            geometryType = geom.GetGeometryType()
            if geometryType == ogr.wkbPolygon:
                geometry.AddGeometry(geom)
            elif geometryType == ogr.wkbMultiPolygon:
                for i in range(geom.GetGeometryCount()):
                    geom2 = geom.GetGeometryRef(i)
                    geometry.AddGeometry(geom2)
            else:
                raise Exception(f'Unsuported geometry {geometryType}')
            feature = layer.GetNextFeature()
        layer = None
        ds = None

    geometry = geometry.UnionCascaded()


path = args.observations.as_posix()
ds = ogr.Open(path, update=0)

layer = None
for i in range(ds.GetLayerCount()):
    lyr = ds.GetLayerByIndex(i)
    if lyr.GetGeomType() in [ogr.wkbPoint, ogr.wkbPointM, ogr.wkbMultiPointM, ogr.wkbPointZM, ogr.wkbMultiPointZM, ogr.wkbPoint25D]:
        layer = lyr
        break
if layer is None:
    raise Exception(f'{path}: does not have any layer of geometry type Point')

source_srs = layer.GetSpatialRef()
transform_srs = osr.CoordinateTransformation(source_srs, target_srs)

def getField(feat, name):
    idx = feature.GetFieldIndex(name)
    if idx is not None and idx >= 0:
        return feature.GetField(idx)
    return None
def getFieldAsDateTime(feat, name):
    idx = feature.GetFieldIndex(name)
    if idx is not None and idx >= 0:
        v = feature.GetFieldAsDateTime(idx)
        t = (v[0], v[1], v[2], v[3], v[4], int(v[5]), v[6], -1, -1)
        return datetime.fromtimestamp(time.mktime(t))
    return None

sum_count = 0
summary = {}
listSeparator = re.compile(r',\s*')
feature = layer.GetNextFeature()
while feature is not None:
    v = feature.GetField('IsPositiveObservation')
    if v is not None and not v:
        feature = layer.GetNextFeature()
        continue
    v = feature.GetField('IsNaturalOccurrence')
    if v is not None and not v:
        feature = layer.GetNextFeature()
        continue

    uncertainty = feature.GetField('CoordinateUncertaintyInMeters')
    if uncertainty is not None and uncertainty > args.max_uncertainty:
        feature = layer.GetNextFeature()
        continue

    vernacularName = getField(feature, 'VernacularName')
    if vernacularName is None:
        raise Exception('Missing name')
    if args.taxon is not None:
        name = vernacularName.lower()
        if not any([sub in name for sub in args.taxon]):
            feature = layer.GetNextFeature()
            continue

    protectedByLaw = feature.GetField('ProtectedByLaw')
    if args.protected and (protectedByLaw is None or not protectedByLaw):
        feature = layer.GetNextFeature()
        continue

    taxonIsRedlisted = feature.GetField('TaxonIsRedlisted')
    redlistCategory = getField(feature, 'RedlistCategory')
    if args.redlisted is not None:
        if args.redlisted == 'TaxonIsRedlisted':
            if taxonIsRedlisted is None or not taxonIsRedlisted:
                feature = layer.GetNextFeature()
                continue
        elif type(args.redlisted) == list:
            if redlistCategory is None or redlistCategory not in args.redlisted:
                feature = layer.GetNextFeature()
                continue

    reportedBy = getField(feature, 'ReportedBy')
    if args.reporter is not None:
        found = False
        for r in listSeparator.split(reportedBy):
            r = r.lower()
            if any([sub in r for sub in args.reporter]):
                found = True
                break
        if not found:
            feature = layer.GetNextFeature()
            continue

    recordedBy = getField(feature, 'RecordedBy')
    if args.observer is not None:
        found = False
        for r in listSeparator.split(recordedBy):
            r = r.lower()
            if any([sub in r for sub in args.observer]):
                found = True
                break
        if not found:
            feature = layer.GetNextFeature()
            continue

    startDate = getFieldAsDateTime(feature, 'StartDate')
    if args.until is not None and (startDate is None or args.until < startDate):
        feature = layer.GetNextFeature()
        continue

    endDate = getFieldAsDateTime(feature, 'EndDate')
    if args.since is not None and (endDate is None or endDate < args.since):
        feature = layer.GetNextFeature()
        continue

    geom = feature.GetGeometryRef()
    geom = geom.Clone()
    geom.FlattenTo2D()
    geom.Transform(transform_srs)

    distance = None
    if geometry is not None and not geometry.Contains(geom):
        distance = geom.Distance(geometry)
        if distance == -1:
            raise Exception('distance')
        max_distance = 0 if args.max_distance is None else args.max_distance
        if uncertainty is not None:
            max_distance += uncertainty
        if max_distance < distance:
            feature = layer.GetNextFeature()
            continue

    if sum_count > 0:
        print('')

    print(f'Artnamn:       {vernacularName.title()}')

    name = vernacularName
    if taxonIsRedlisted is not None and taxonIsRedlisted and redlistCategory is not None:
        name += f' ({redlistCategory})'
    n = summary.get(name, 0)
    summary[name] = n + 1

    v = getField(feature, 'OrganismQuantityInt')
    if v is None:
        v = 'Noterad'
    else:
        v = str(v)
        unit = getField(feature, 'OrganismQuantityUnit')
        if unit is not None and unit != '':
            v += ' ' + unit
    print(f'Antal & enhet: {v}')

    v = getField(feature, 'Sex')
    if v is not None:
        print(f'Kön:           {v}')

    v = getField(feature, 'LifeStage')
    if v is not None:
        print(f'Ålder/stadium: {v}')

    v = getField(feature, 'Activity')
    if v is not None:
        print(f'Aktivitet:     {v}')

    v = getField(feature, 'DiscoveryMethod')
    if v is not None:
        print(f'Metod:         {v}')

    if ',' in reportedBy:
        print(f'Rapportörer:   {reportedBy}')
    else:
        print(f'Rapportör:     {reportedBy}')
    if ',' in recordedBy:
        print(f'Observatörer:  {recordedBy}')
    else:
        print(f'Observatör:    {recordedBy}')

    print(f'Startdatum:    {startDate.strftime("%-d %B %Y %H:%M")}')
    print(f'Slutdatum:     {endDate.strftime("%-d %B %Y %H:%M")}')

    v = getField(feature, 'Projects')
    if v is not None:
        print(f'Projects:      {v}')

    v = getField(feature, 'OccurrenceRemarks')
    if v is not None:
        print(f'Kommentar:     {v}')

    v = getField(feature, 'DatasetName')
    if v is not None:
        print(f'Källa:         {v}')
    v = getField(feature, 'Url')
    if v is not None:
        print(f'URL:           {v}')

    if geom.GetGeometryType() != ogr.wkbPoint:
        raise Exception('Not a point')
    x, y = geom.GetPoint_2D(i)
    v = getField(feature, 'Locality')
    if v is not None:
        print(f'Lokalnamn:     {v}')
    coords = f'Koordinater:   N{y:.0f}, Ö{x:.0f} (±{uncertainty:.0f}m) {target_srs.GetName()}'

    if geometry is not None:
        if distance is None:
            dist = 'i'
        else:
            dist = f'{distance:.0f}m från'
        coords += f'; {dist} målgeometrin'
    print(coords)

    if redlistCategory is None:
        v = '—'
    elif redlistCategory == 'EX':
        v = 'Utdöd (EX)'
    elif redlistCategory == 'EW':
        v = 'Utdöd i vilt tillstånd (EW)'
    elif redlistCategory == 'RE':
        v = 'Nationellt utdöd (RE)'
    elif redlistCategory == 'CR':
        v = 'Akut hotad (CR)'
    elif redlistCategory == 'EN':
        v = 'Starkt hotad (EN)'
    elif redlistCategory == 'VU':
        v = 'Sårbar (VU)'
    elif redlistCategory == 'NT':
        v = 'Nära hotad (NT)'
    elif redlistCategory == 'LC':
        v = 'Livskraftig (LC)'
    elif redlistCategory == 'DD':
        v = 'Kunskapsbrist (DD)'
    elif redlistCategory == 'NE':
        v = 'Ej bedömd (NE)'
    elif redlistCategory == 'NA':
        v = 'Ej tillämplig (NA)'
    else:
        v = redlistCategory
    print(f'Rödlistning:   {v}')

    v = []
    if protectedByLaw is not None and protectedByLaw:
        v.append('nationellt fridlyst')
    v2 = getField(feature, 'TaxonIsInvasiveInSweden')
    if v2 is not None and v2:
        v.append('främmande i Sverige')
    v2 = getField(feature, 'TaxonIsInvasiveEuRegulation')
    if v2 is not None and v2:
        v.append('invasiv enligt EU-förordning 1143/2014')
    v2 = getField(feature, 'Natura2000HabitatsDirective')
    if v2 is not None and v2:
        v2 = []
        v3 = getField(feature, 'Natura2000HabitatsDirectiveArticle2')
        if v3 is not None and v3:
            v3 = getField(feature, 'Natura2000HabitatsDirectiveArticle2PrioritySpecie')
            if v3 is not None and v3:
                v2.append('II (prioriterad art)')
            else:
                v2.append('II')
        v3 = getField(feature, 'Natura2000HabitatsDirectiveArticle4')
        if v3 is not None and v3:
            v2.append('IV')
        v3 = getField(feature, 'Natura2000HabitatsDirectiveArticle5')
        if v3 is not None and v3:
            v2.append('V')
        if len(v2) == 0:
            v.append('habitatdirektivet')
        elif len(v2) == 1:
            v.append('habitatdirektivets bilaga ' + v2[0])
        else:
            v.append('habitatdirektivets bilagor ' + ', '.join(v2[0:-1]) + ' & ' + v2[-1])
    v2 = getField(feature, 'TaxonIsSignalSpecie')
    if v2 is not None and v2:
        v.append('signalart enligt Skogsstyrelsen')
    v2 = getField(feature, 'BirdDirective')
    if v2 is not None and v2:
        v.append('fågeldirektivet')
    if len(v) > 0:
        v[0] = v[0][0].upper() + v[0][1:]
        v = '; '.join(v)
    else:
        v = '—'
    print(f'Naturvård:     {v}')

    sum_count += 1
    feature = layer.GetNextFeature()

if sum_count == 0:
    print('No matching observations found!')
    exit(0)

max_count = max(summary.values())
width = len(str(max_count))

print('\n\nSummary\n-------')
for name, n in sorted(summary.items(), key=lambda x: (-x[1], x[0])):
    print('{0:{width}d}×  {1}'.format(n, name, width=width))
print('-' * (width+1))
print(f'{sum_count} matching observations')