aboutsummaryrefslogtreecommitdiffstats
path: root/list-observations
blob: 869e307da01d56e491125a3dcac1defea7984e9d (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
#!/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)

layerDefn = layer.GetLayerDefn()
fieldCount = layerDefn.GetFieldCount()
sum_count = 0
summary = {}
listSeparator = re.compile(r',\s*')
def printObservation(feature):
    global sum_count
    properties = {}
    for i in range(fieldCount):
        if not feature.IsFieldSet(i):
            continue
        fieldDefn = layerDefn.GetFieldDefn(i)
        if feature.IsFieldNull(i):
            val = None
        elif fieldDefn.type == ogr.OFTInteger: # booleans are there too
            val = feature.GetFieldAsInteger(i)
        elif fieldDefn.type == ogr.OFTString:
            val = feature.GetFieldAsString(i)
        elif fieldDefn.type == ogr.OFTDateTime:
            st = feature.GetFieldAsDateTime(i)
            t = (st[0], st[1], st[2], st[3], st[4], int(st[5]), st[6], -1, -1)
            val = datetime.fromtimestamp(time.mktime(t))
        else:
            raise Exception(f'{fieldDefn.name}: Unknown field type {fieldDefn.type}')
        properties[fieldDefn.name] = val

    v = properties.get('IsPositiveObservation')
    if v is not None and not v:
        return
    v = properties.get('IsNaturalOccurrence')
    if v is not None and not v:
        return

    uncertainty = properties.get('CoordinateUncertaintyInMeters')
    if uncertainty is not None and uncertainty > args.max_uncertainty:
        return

    vernacularName = properties.get('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]):
            return

    protectedByLaw = properties.get('ProtectedByLaw')
    if args.protected and (protectedByLaw is None or not protectedByLaw):
        return

    taxonIsRedlisted = properties.get('TaxonIsRedlisted')
    redlistCategory = properties.get('RedlistCategory')
    if args.redlisted is not None:
        if args.redlisted == 'TaxonIsRedlisted':
            if taxonIsRedlisted is None or not taxonIsRedlisted:
                return
        elif type(args.redlisted) == list:
            if redlistCategory is None or redlistCategory not in args.redlisted:
                return

    reportedBy = properties.get('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:
            return

    recordedBy = properties.get('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:
            return

    startDate = properties.get('StartDate')
    if args.until is not None and (startDate is None or args.until < startDate):
        return

    endDate = properties.get('EndDate')
    if args.since is not None and (endDate is None or endDate < args.since):
        return

    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:
            return

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

    v = properties.get('Sex')
    if v is not None:
        print(f'Kön:           {v}')

    v = properties.get('LifeStage')
    if v is not None:
        print(f'Ålder/stadium: {v}')

    v = properties.get('Activity')
    if v is not None:
        print(f'Aktivitet:     {v}')

    v = properties.get('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 = properties.get('Projects')
    if v is not None:
        print(f'Projects:      {v}')

    v = properties.get('OccurrenceRemarks')
    if v is not None:
        print(f'Kommentar:     {v}')

    v = properties.get('DatasetName')
    if v is not None:
        print(f'Källa:         {v}')
    v = properties.get('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(0)
    v = properties.get('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 = properties.get('TaxonIsInvasiveInSweden')
    if v2 is not None and v2:
        v.append('främmande i Sverige')
    v2 = properties.get('TaxonIsInvasiveEuRegulation')
    if v2 is not None and v2:
        v.append('invasiv enligt EU-förordning 1143/2014')
    v2 = properties.get('Natura2000HabitatsDirective')
    if v2 is not None and v2:
        v2 = []
        v3 = properties.get('Natura2000HabitatsDirectiveArticle2')
        if v3 is not None and v3:
            v3 = properties.get('Natura2000HabitatsDirectiveArticle2PrioritySpecie')
            if v3 is not None and v3:
                v2.append('II (prioriterad art)')
            else:
                v2.append('II')
        v3 = properties.get('Natura2000HabitatsDirectiveArticle4')
        if v3 is not None and v3:
            v2.append('IV')
        v3 = properties.get('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 = properties.get('TaxonIsSignalSpecie')
    if v2 is not None and v2:
        v.append('signalart enligt Skogsstyrelsen')
    v2 = properties.get('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()
while feature is not None:
    printObservation(feature)
    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')