vodex.dbmethods module

DbExporter

Transforms the information from the database into the core classes.

Source code in src\vodex\dbmethods.py
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
class DbExporter:
    """
    Transforms the information from the database into the core classes.
    """

    # TODO : make it work for annotations

    def __init__(self, db_reader: DbReader):
        self.db = db_reader

    @classmethod
    def load(cls, file_name: Union[Path, str]):
        """
        Loads a database from a file and initialises a DbExporter.

        Args:
            file_name: full path to a file to database.
        """
        db_reader = DbReader.load(file_name)
        return cls(db_reader)

    def reconstruct_file_manager(self):
        """
        Creates file manager from the database records.
        """
        data_dir = self.db.get_data_dir()
        file_names = self.db.get_file_names()
        frames_per_file = self.db.get_frames_per_file()

        fm = FileManager(data_dir, file_names=file_names, frames_per_file=frames_per_file)
        return fm

    def reconstruct_volume_manager(self):
        """
        Creates volume manager from the database records.
        """
        fm = self.reconstruct_file_manager()
        fpv = self.db.get_fpv()
        fgf = self.db.get_fgf()
        vm = VolumeManager(fpv, FrameManager(fm), fgf=fgf)
        return vm

    def reconstruct_labels(self, group):
        """
        Creates labels corresponding to the specified annotation from the database records.
        """
        state_names, state_info = self.db.get_Name_and_Description_from_AnnotationTypeLabels(group)
        labels = Labels(group, state_names, state_info=state_info)
        return labels

    def reconstruct_timeline(self, group, labels):
        import itertools
        """
        Creates timeline corresponding to the specified annotation from the database records.
        """
        # get the mapping between the names and the Ids
        label_names = self.db.get_Id_map_to_Names_from_AnnotationTypeLabels()
        # get all the labels that were used in the annotation ( does not reconstruct unused Labels )
        labels_per_frame = self.db.get_AnnotationTypeLabelId_from_Annotations(group)

        label_order = []
        duration = []
        for label_id, frames in itertools.groupby(labels_per_frame):
            label_name = label_names[label_id]
            label_order.append(labels.__getattribute__(label_name))
            duration.append(sum(1 for _ in frames))

        timeline = Timeline(label_order, duration)
        return timeline

    def reconstruct_cycle(self, group):
        """
        Creates cycle corresponding to the specified annotation from the database records.
        """
        cycle_json = self.db.get_Structure_from_Cycle(group)
        if cycle_json is not None:
            cycle = Cycle.from_json(cycle_json)
        else:
            cycle = None
        return cycle

    def reconstruct_annotations(self):

        """
        Creates annotations from the database records.
        """
        # get the names of all the available annotations from the db
        annotation_names = self.db.get_Names_from_AnnotationTypes()
        # get the total number of frames in the recording
        n_frames = FrameManager(self.reconstruct_file_manager()).n_frames

        annotations = []
        for group in annotation_names:
            # reconstruct Labels for the group
            labels = self.reconstruct_labels(group)
            # try to get a cycle
            cycle = self.reconstruct_cycle(group)
            # define the annotation type ( Cycle / Timeline)
            if cycle is not None:
                annotation = Annotation.from_cycle(n_frames, labels, cycle)
            else:
                timeline = self.reconstruct_timeline(group, labels)
                annotation = Annotation.from_timeline(n_frames, labels, timeline)

            annotations.append(annotation)

        return annotations

load(file_name) classmethod

Loads a database from a file and initialises a DbExporter.

Parameters:

Name Type Description Default
file_name Union[Path, str]

full path to a file to database.

required
Source code in src\vodex\dbmethods.py
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
@classmethod
def load(cls, file_name: Union[Path, str]):
    """
    Loads a database from a file and initialises a DbExporter.

    Args:
        file_name: full path to a file to database.
    """
    db_reader = DbReader.load(file_name)
    return cls(db_reader)

reconstruct_annotations()

Creates annotations from the database records.

Source code in src\vodex\dbmethods.py
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
def reconstruct_annotations(self):

    """
    Creates annotations from the database records.
    """
    # get the names of all the available annotations from the db
    annotation_names = self.db.get_Names_from_AnnotationTypes()
    # get the total number of frames in the recording
    n_frames = FrameManager(self.reconstruct_file_manager()).n_frames

    annotations = []
    for group in annotation_names:
        # reconstruct Labels for the group
        labels = self.reconstruct_labels(group)
        # try to get a cycle
        cycle = self.reconstruct_cycle(group)
        # define the annotation type ( Cycle / Timeline)
        if cycle is not None:
            annotation = Annotation.from_cycle(n_frames, labels, cycle)
        else:
            timeline = self.reconstruct_timeline(group, labels)
            annotation = Annotation.from_timeline(n_frames, labels, timeline)

        annotations.append(annotation)

    return annotations

reconstruct_cycle(group)

Creates cycle corresponding to the specified annotation from the database records.

Source code in src\vodex\dbmethods.py
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
def reconstruct_cycle(self, group):
    """
    Creates cycle corresponding to the specified annotation from the database records.
    """
    cycle_json = self.db.get_Structure_from_Cycle(group)
    if cycle_json is not None:
        cycle = Cycle.from_json(cycle_json)
    else:
        cycle = None
    return cycle

reconstruct_file_manager()

Creates file manager from the database records.

Source code in src\vodex\dbmethods.py
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
def reconstruct_file_manager(self):
    """
    Creates file manager from the database records.
    """
    data_dir = self.db.get_data_dir()
    file_names = self.db.get_file_names()
    frames_per_file = self.db.get_frames_per_file()

    fm = FileManager(data_dir, file_names=file_names, frames_per_file=frames_per_file)
    return fm

reconstruct_labels(group)

Creates labels corresponding to the specified annotation from the database records.

Source code in src\vodex\dbmethods.py
1352
1353
1354
1355
1356
1357
1358
def reconstruct_labels(self, group):
    """
    Creates labels corresponding to the specified annotation from the database records.
    """
    state_names, state_info = self.db.get_Name_and_Description_from_AnnotationTypeLabels(group)
    labels = Labels(group, state_names, state_info=state_info)
    return labels

reconstruct_volume_manager()

Creates volume manager from the database records.

Source code in src\vodex\dbmethods.py
1342
1343
1344
1345
1346
1347
1348
1349
1350
def reconstruct_volume_manager(self):
    """
    Creates volume manager from the database records.
    """
    fm = self.reconstruct_file_manager()
    fpv = self.db.get_fpv()
    fgf = self.db.get_fgf()
    vm = VolumeManager(fpv, FrameManager(fm), fgf=fgf)
    return vm

DbReader

Reads information from the database. Database interface that abstracts the SQLite calls.

Source code in src\vodex\dbmethods.py
 450
 451
 452
 453
 454
 455
 456
 457
 458
 459
 460
 461
 462
 463
 464
 465
 466
 467
 468
 469
 470
 471
 472
 473
 474
 475
 476
 477
 478
 479
 480
 481
 482
 483
 484
 485
 486
 487
 488
 489
 490
 491
 492
 493
 494
 495
 496
 497
 498
 499
 500
 501
 502
 503
 504
 505
 506
 507
 508
 509
 510
 511
 512
 513
 514
 515
 516
 517
 518
 519
 520
 521
 522
 523
 524
 525
 526
 527
 528
 529
 530
 531
 532
 533
 534
 535
 536
 537
 538
 539
 540
 541
 542
 543
 544
 545
 546
 547
 548
 549
 550
 551
 552
 553
 554
 555
 556
 557
 558
 559
 560
 561
 562
 563
 564
 565
 566
 567
 568
 569
 570
 571
 572
 573
 574
 575
 576
 577
 578
 579
 580
 581
 582
 583
 584
 585
 586
 587
 588
 589
 590
 591
 592
 593
 594
 595
 596
 597
 598
 599
 600
 601
 602
 603
 604
 605
 606
 607
 608
 609
 610
 611
 612
 613
 614
 615
 616
 617
 618
 619
 620
 621
 622
 623
 624
 625
 626
 627
 628
 629
 630
 631
 632
 633
 634
 635
 636
 637
 638
 639
 640
 641
 642
 643
 644
 645
 646
 647
 648
 649
 650
 651
 652
 653
 654
 655
 656
 657
 658
 659
 660
 661
 662
 663
 664
 665
 666
 667
 668
 669
 670
 671
 672
 673
 674
 675
 676
 677
 678
 679
 680
 681
 682
 683
 684
 685
 686
 687
 688
 689
 690
 691
 692
 693
 694
 695
 696
 697
 698
 699
 700
 701
 702
 703
 704
 705
 706
 707
 708
 709
 710
 711
 712
 713
 714
 715
 716
 717
 718
 719
 720
 721
 722
 723
 724
 725
 726
 727
 728
 729
 730
 731
 732
 733
 734
 735
 736
 737
 738
 739
 740
 741
 742
 743
 744
 745
 746
 747
 748
 749
 750
 751
 752
 753
 754
 755
 756
 757
 758
 759
 760
 761
 762
 763
 764
 765
 766
 767
 768
 769
 770
 771
 772
 773
 774
 775
 776
 777
 778
 779
 780
 781
 782
 783
 784
 785
 786
 787
 788
 789
 790
 791
 792
 793
 794
 795
 796
 797
 798
 799
 800
 801
 802
 803
 804
 805
 806
 807
 808
 809
 810
 811
 812
 813
 814
 815
 816
 817
 818
 819
 820
 821
 822
 823
 824
 825
 826
 827
 828
 829
 830
 831
 832
 833
 834
 835
 836
 837
 838
 839
 840
 841
 842
 843
 844
 845
 846
 847
 848
 849
 850
 851
 852
 853
 854
 855
 856
 857
 858
 859
 860
 861
 862
 863
 864
 865
 866
 867
 868
 869
 870
 871
 872
 873
 874
 875
 876
 877
 878
 879
 880
 881
 882
 883
 884
 885
 886
 887
 888
 889
 890
 891
 892
 893
 894
 895
 896
 897
 898
 899
 900
 901
 902
 903
 904
 905
 906
 907
 908
 909
 910
 911
 912
 913
 914
 915
 916
 917
 918
 919
 920
 921
 922
 923
 924
 925
 926
 927
 928
 929
 930
 931
 932
 933
 934
 935
 936
 937
 938
 939
 940
 941
 942
 943
 944
 945
 946
 947
 948
 949
 950
 951
 952
 953
 954
 955
 956
 957
 958
 959
 960
 961
 962
 963
 964
 965
 966
 967
 968
 969
 970
 971
 972
 973
 974
 975
 976
 977
 978
 979
 980
 981
 982
 983
 984
 985
 986
 987
 988
 989
 990
 991
 992
 993
 994
 995
 996
 997
 998
 999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
class DbReader:
    """
    Reads information from the database.
    Database interface that abstracts the SQLite calls.
    """

    def __init__(self, connection):
        self.connection = connection
        self.connection.execute("PRAGMA foreign_keys = 1")

    def get_n_frames(self):
        cursor = self.connection.cursor()
        try:
            cursor.execute(f"SELECT COUNT(*) FROM Frames")
            n_frames = cursor.fetchone()[0]
        except Exception as e:
            print(f"Could not get total number of frames from Frames because {e}")
            raise e
        finally:
            cursor.close()
        return n_frames

        # get the volumes

    def get_data_dir(self):
        """
        Get data directory
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT Value FROM Options 
                     WHERE Key = "data_dir" """
            )
            data_dir = cursor.fetchone()[0]
        except Exception as e:
            print(f"Could not get_data_dir because {e}")
            raise e
        finally:
            cursor.close()

        return data_dir

    def get_fpv(self):
        """
        Get frames per volume
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT Value FROM Options 
                     WHERE Key = "frames_per_volume" """
            )
            fpv = int(cursor.fetchone()[0])
        except Exception as e:
            print(f"Could not get_fpv because {e}")
            raise e
        finally:
            cursor.close()

        return fpv

    def get_fgf(self):
        """
        Get frames per volume
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT Value FROM Options 
                     WHERE Key = "num_head_frames" """
            )
            fdf = int(cursor.fetchone()[0])
        except Exception as e:
            print(f"Could not get_fgf because {e}")
            raise e
        finally:
            cursor.close()

        return fdf

    def get_options(self):
        """
        Gets the information from the OPTIONS table.
        Returns a dictionary with the Key: Value from the table.
        ( Keys: 'data_dir', 'frames_per_volume', 'num_head_frames', 'num_tail_frames', 'num_full_volumes' )
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT * FROM Options"""
            )
            options = {}
            for row in cursor.fetchall():
                options[row[0]] = row[1]

        except Exception as e:
            print(f"Could not get_options because {e}")
            raise e
        finally:
            cursor.close()

        return options

    def get_file_names(self):
        """
        Get the file names from the Files table.
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT FileName FROM Files ORDER BY Id ASC"""
            )
            file_names = [row[0] for row in cursor.fetchall()]
        except Exception as e:
            print(f"Could not get_file_names because {e}")
            raise e
        finally:
            cursor.close()

        return file_names

    def get_frames_per_file(self):
        """
        Get the file names from the Files table.
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT NumFrames FROM Files ORDER BY Id ASC"""
            )
            frames_per_file = [row[0] for row in cursor.fetchall()]
        except Exception as e:
            print(f"Could not get_frames_per_file because {e}")
            raise e
        finally:
            cursor.close()

        return frames_per_file

    def get_volume_list(self):
        """
        Returns a list of all the volumes.
        :return: list of all the volumes
        :rtype: [int]
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(f"SELECT DISTINCT VolumeId FROM Volumes")
            volume_ids = [volume[0] for volume in cursor.fetchall()]
        except Exception as e:
            print(f"Could not get total number of frames from Frames because {e}")
            raise e
        finally:
            cursor.close()

        return volume_ids

    @classmethod
    def load(cls, file_name):
        """
        Load the contents of a database file on disk to a
        transient copy in memory without modifying the file
        """
        disk_db = connect(file_name)
        memory_db = connect(':memory:')
        disk_db.backup(memory_db)
        disk_db.close()
        # Now use `memory_db` without modifying disk db
        return cls(memory_db)

    def choose_full_volumes(self, frames):
        """
        Chooses the frames from specified frames, that also correspond to full volumes.

        The order of the frames is not preserved!
        The result will correspond to frames sorted in increasing order !

        :param frames: a list of frame IDs
        :type frames: [int]
        :param fpv: frames per volume
        :type fpv: int
        :return: frames IDs from frames. corresponding to slices
        :rtype: [int]
        """
        # create list of frame Ids
        frame_ids = tuple(frames)
        n_frames = len(frame_ids)

        # get the volumes
        cursor = self.connection.cursor()
        try:
            # get n_volumes (frames per volume)
            cursor.execute(
                f"""SELECT Value FROM Options 
                    WHERE Key = "frames_per_volume" """
            )
            fpv = int(cursor.fetchone()[0])

            # get ids of full volumes in the provided frames
            cursor.execute(
                f"""SELECT VolumeId FROM
                    (
                    SELECT VolumeId, count(VolumeId) as N
                    FROM Volumes
                    WHERE FrameId IN ({', '.join(['?'] * n_frames)})
                    GROUP BY VolumeId
                    )
                    WHERE N = ?""", frame_ids + (fpv,)
            )
            volume_ids = [volume[0] for volume in cursor.fetchall()]
            n_volumes = len(volume_ids)

            # get all frames from frames that correspond to full volumes
            cursor.execute(
                f"""SELECT FrameId FROM Volumes
                    WHERE FrameId IN ({', '.join(['?'] * n_frames)})
                    AND VolumeId IN ({', '.join(['?'] * n_volumes)})""", frame_ids + tuple(volume_ids)
            )
            frame_ids = [frame[0] for frame in cursor.fetchall()]
        except Exception as e:
            print(f"Could not choose_full_volumes because {e}")
            raise e
        finally:
            cursor.close()

        return volume_ids, frame_ids

    def choose_frames_per_slices(self, frames, slices):
        """
        Chooses the frames from specified frames, that also correspond to the same slices (continuously)
        in different volumes.
        For example, if slices = [2,3,4] it will choose such frames from "given frames" that also correspond
        to a chunk from slice 2 to slice 4 in all the volumes.
        If there is a frame that corresponds to a slice "2" in a volume,
        but no frames corresponding to the slices "3" and "4" in the SAME volume, such frame will not be picked.

        The order of the frames is not preserved!
        The result will correspond to frames sorted in increasing order !

        :param frames: a list of frame IDs
        :type frames: [int]
        :param slices: a list of slice IDs, order will not be preserved: will be sorted in increasing order
        :type slices: [int]
        :return: frames IDs from frames. corresponding to slices
        :rtype: [int]
        """
        # create list of frame Ids
        frame_ids = tuple(frames)
        slice_ids = tuple(slices)
        n_frames = len(frame_ids)
        n_slices = len(slices)

        # get the volumes
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""SELECT FrameId FROM Volumes
                    WHERE FrameId in ({', '.join(['?'] * n_frames)})
                    AND SliceInVolume IN ({', '.join(['?'] * n_slices)})
                    AND VolumeId IN
                        (
                        SELECT VolumeId FROM
                            (
                            SELECT VolumeId, count(VolumeId) as N 
                            FROM Volumes 
                            WHERE FrameId IN ({', '.join(['?'] * n_frames)})
                            AND SliceInVolume IN ({', '.join(['?'] * n_slices)})
                            GROUP BY VolumeId
                            )
                        WHERE N = ?
                        )""", frame_ids + slice_ids + frame_ids + slice_ids + (n_slices,)
            )

            frame_ids = cursor.fetchall()
        except Exception as e:
            print(f"Could not choose_frames_per_slices because {e}")
            raise e
        finally:
            cursor.close()
        frame_ids = [frame[0] for frame in frame_ids]
        return frame_ids

    def prepare_frames_for_loading(self, frames):
        """
        Finds all the information needed
        1) to load the frames
        2) and shape them back into volumes/slices.
        For each frame returns the image file,
        frame location on the image and corresponding volume.

        The order is not preserved!
        the volume correspond to sorted volumes in increasing order !

        :param frames: a list of frame IDs
        :type frames: [int]
        :return: three lists, the length of the frames :
                data directory, file names,
                image files, frame location on the image, volumes.
        :rtype: str, [str], [str],[int],[int]
        # TODO : break into functions that get the file locations and the stuff relevant to the frames
        # TODO : make one " prepare volumes " for loading?
        """
        n_frames = len(frames)

        # get the frames
        cursor = self.connection.cursor()
        try:
            # get data directory
            cursor.execute(
                f"""SELECT Value
                    FROM Options
                    WHERE Key = "data_dir" """)
            data_dir = cursor.fetchone()[0]

            # get file_names
            cursor.execute(
                f"""SELECT FileName
                    FROM Files """)
            file_names = cursor.fetchall()

            # get info for every frame
            cursor.execute(
                f"""SELECT 
                        FileId,
                        FrameInFile,
                        VolumeId
                    FROM 
                        Frames
                        INNER JOIN Volumes 
                        ON Frames.Id = Volumes.FrameId
                    WHERE FrameId IN ({', '.join(['?'] * n_frames)})""", tuple(frames))
            frame_info = cursor.fetchall()

        except Exception as e:
            print(f"Could not prepare_frames_for_loading because {e}")
            raise e
        finally:
            cursor.close()

        file_names = [row[0] for row in file_names]

        file_ids = [row[0] for row in frame_info]
        frame_in_file = [row[1] for row in frame_info]
        volumes = [row[2] for row in frame_info]

        return data_dir, file_names, file_ids, frame_in_file, volumes

    def get_frames_per_volumes(self, volume_ids):
        """
        Finds all the frames that correspond to the specified volumes.
        The order is not preserved!
        the volume correspond to sorted volumes in increasing order !

        :param volume_ids: a list of volume IDs
        :type volume_ids: [int]
        :return: frame IDs
        :rtype: [int]
        """
        ids = list_of_int(volume_ids)

        # get the frames
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT FrameId FROM Volumes 
                    WHERE VolumeId IN ({', '.join(['?'] * len(ids))})""", tuple(ids))
            frame_ids = cursor.fetchall()
        except Exception as e:
            print(f"Could not _get_FrameId_from_Volumes because {e}")
            raise e
        finally:
            cursor.close()
        # TODO : get rid of list of tuples?
        #  https://www.reddit.com/r/Python/comments/2iiqri/quick_question_why_are_sqlite_fields_returned_as/
        frame_ids = [frame[0] for frame in frame_ids]
        return frame_ids

    def get_and_frames_per_annotations(self, conditions):
        """
        Chooses the frames that correspond to the specified conditions on annotation. Using "and" logic. Example : if
        you ask for frames corresponding to condition 1 and condition 2 , it will return such frames that both
        condition 1 and condition 2 are True AT THE SAME TIME

        :param conditions: a list of conditions on the annotation labels
        in a form [(group, name),(group, name), ...] where group is a string for the annotation type
        and name is the name of the label of that annotation type. For example [('light', 'on'), ('shape','c')]
        :type conditions: [tuple]
        :return: list of frame Ids that satisfy all the conditions, if there are no such frames, an empty list
        :rtype: list
        """
        # create list of label Ids
        labels_ids = []
        for label_info in conditions:
            labels_ids.append(self._get_Id_from_AnnotationTypeLabels(label_info))
        labels_ids = tuple(labels_ids)
        n_labels = len(labels_ids)

        # get the frames
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT FrameId FROM 
                    (SELECT FrameId, count(FrameId) as N 
                    FROM Annotations 
                    WHERE AnnotationTypeLabelId IN ({', '.join(['?'] * n_labels)})
                    GROUP BY FrameId)
                    WHERE N = {n_labels}""", labels_ids)
            frame_ids = cursor.fetchall()
        except Exception as e:
            print(f"Could not _get_and_FrameId_from_Annotations because {e}")
            raise e
        finally:
            cursor.close()
        # TODO : get rid of list of tuples?
        #  https://www.reddit.com/r/Python/comments/2iiqri/quick_question_why_are_sqlite_fields_returned_as/
        frame_ids = [frame[0] for frame in frame_ids]
        return frame_ids

    def get_or_frames_per_annotations(self, conditions):
        """
        Chooses the frames that correspond to the specified conditions on annotation. Using "or" logic. Example : if
        you ask for frames corresponding to condition 1 and condition 2 , it will return such frames that either
        condition 1 is true OR condition 2 is True OR both are true.

        :param conditions: a list of conditions on the annotation labels
        in a form [(group, name),(group, name), ...] where group is a string for the annotation type
        and name is the name of the label of that annotation type. For example [('light', 'on'), ('shape','c')]
        :type conditions: [tuple]
        :return:
        :rtype:
        """
        # create list of label Ids
        labels_ids = []
        for label_info in conditions:
            labels_ids.append(self._get_Id_from_AnnotationTypeLabels(label_info))
        labels_ids = tuple(labels_ids)
        n_labels = len(labels_ids)

        # get the frames
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT FrameId FROM Annotations 
                    WHERE AnnotationTypeLabelId IN ({', '.join(['?'] * n_labels)})
                    GROUP BY FrameId""", labels_ids)
            frame_ids = cursor.fetchall()
        except Exception as e:
            print(f"Could not _get_or_FrameId_from_Annotations because {e}")
            raise e
        finally:
            cursor.close()
        # TODO : get rid of list of tuples?
        #  https://www.reddit.com/r/Python/comments/2iiqri/quick_question_why_are_sqlite_fields_returned_as/
        frame_ids = [frame[0] for frame in frame_ids]
        return frame_ids

    def get_conditionIds_per_cycle_per_volumes(self, annotation_name):
        """
        Returns a list of condition IDs that correspond to each volume, list of corresponding volumes
        and a count of the volume-condition pairs
        annotation_name: str
        """
        # TODO : check if empty
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT VolumeId, AnnotationTypeLabelId, count(VolumeId) FROM
                    CycleIterations 
                    INNER JOIN Volumes ON CycleIterations.FrameId = Volumes.FrameId 
                    INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                    WHERE AnnotationTypeLabelId in 
                        (
                        SELECT Id from AnnotationTypeLabels 
                        WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                        )
                    AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    AND CycleIteration = 0
                    GROUP BY VolumeId, AnnotationTypeLabelId
                    ORDER BY VolumeId""", (annotation_name, annotation_name))
            info = cursor.fetchall()
            # TODO : check if empty
            volume_ids = [row[0] for row in info]
            condition_ids = [row[1] for row in info]
            count = [row[2] for row in info]

        except Exception as e:
            print(f"Could not get_conditions_per_cycle_per_volumes because {e}")
            raise e
        finally:
            cursor.close()

        return volume_ids, condition_ids, count

    def get_conditionIds_per_cycle_per_frame(self, annotation_name):
        """
        Returns a list of condition IDs that correspond to each frame, list of corresponding frames.
        annotation_name: str
        """
        # TODO : check if empty
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT CycleIterations.FrameId, AnnotationTypeLabelId FROM
                    CycleIterations 
                    INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                    WHERE AnnotationTypeLabelId in 
                        (
                        SELECT Id from AnnotationTypeLabels 
                        WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                        )
                    AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    AND CycleIteration = 0
                    ORDER BY CycleIterations.FrameId""", (annotation_name, annotation_name))
            info = cursor.fetchall()
            # TODO : check if empty
            frame_ids = [row[0] for row in info]
            condition_ids = [row[1] for row in info]

        except Exception as e:
            print(f"Could not get_conditionIds_per_cycle_per_frame because {e}")
            raise e
        finally:
            cursor.close()

        return frame_ids, condition_ids

    def get_cycleIterations_per_volumes(self, annotation_name):
        """
        Returns a list of cycleIterations that correspond to each volume, list of corresponding volumes
        and a count of the volume-iteration pairs
        annotation_name: str
        """
        # TODO : check if empty
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT VolumeId, CycleIteration, count(VolumeId) FROM
                    CycleIterations 
                    INNER JOIN Volumes ON CycleIterations.FrameId = Volumes.FrameId 
                    INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                    WHERE AnnotationTypeLabelId in 
                        (
                        SELECT Id from AnnotationTypeLabels 
                        WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                        )
                    AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    GROUP BY VolumeId
                    ORDER BY VolumeId""", (annotation_name, annotation_name))
            info = cursor.fetchall()
            # TODO : check if empty
            volume_ids = [row[0] for row in info]
            cycle_its = [row[1] for row in info]
            count = [row[2] for row in info]

        except Exception as e:
            print(f"Could not get_cycleIterations_per_volumes because {e}")
            raise e
        finally:
            cursor.close()

        return volume_ids, cycle_its, count

    def get_cycleIterations_per_frame(self, annotation_name):
        """
        Returns a list of cycle iterations that correspond to each frame, list of corresponding frames.
        annotation_name: str
        """
        # TODO : check if empty
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT CycleIterations.FrameId, CycleIteration FROM
                    CycleIterations 
                    INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                    WHERE AnnotationTypeLabelId in 
                        (
                        SELECT Id from AnnotationTypeLabels 
                        WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                        )
                    AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    ORDER BY CycleIterations.FrameId""", (annotation_name, annotation_name))
            info = cursor.fetchall()
            # TODO : check if empty
            frame_ids = [row[0] for row in info]
            condition_ids = [row[1] for row in info]

        except Exception as e:
            print(f"Could not get_conditionIds_per_cycle_per_frame because {e}")
            raise e
        finally:
            cursor.close()

        return frame_ids, condition_ids

    def get_Names_from_AnnotationTypes(self):
        """
        Returns the names of all the available annotations.
        """
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute("""SELECT Name FROM AnnotationTypes""")
            names = [name[0] for name in cursor.fetchall()]
        except Exception as e:
            print(f"Could not _get_Name_from_AnnotationTypes because {e}")
            raise e
        finally:
            cursor.close()
        return names

    def get_Structure_from_Cycle(self, group):
        """
        Returns cycle Structure if the annotation has a cycle entry or None otherwise.
        """
        group = (group,)
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute("""SELECT Structure FROM Cycles WHERE AnnotationTypeId = 
                             (SELECT Id FROM AnnotationTypes WHERE Name = ?)""", group)
            info = cursor.fetchone()
            if info:
                cycle = info[0]
            else:
                cycle = None
        except Exception as e:
            print(f"Could not get_Structure_from_Cycle because {e}")
            raise e
        finally:
            cursor.close()
        return cycle

    def get_Name_and_Description_from_AnnotationTypeLabels(self, group):
        """
        Returns the Name and description for the labels that correspond to the annotation
        with the provided group name.
        """
        group = (group,)
        names = []
        descriptions = {}

        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute("""SELECT Name, Description FROM AnnotationTypeLabels WHERE AnnotationTypeId = 
                             (SELECT Id FROM AnnotationTypes WHERE Name = ?)""", group)
            info = cursor.fetchall()
            for row in info:
                name = row[0]
                names.append(name)
                descriptions[name] = row[1]
        except Exception as e:
            print(f"Could not get_Name_and_Description_from_AnnotationTypeLabels because {e}")
            raise e
        finally:
            cursor.close()
        return names, descriptions

    def _get_Names_from_AnnotationTypeLabels(self):
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute("""SELECT Name FROM AnnotationTypeLabels ORDER BY Id ASC""")
            names = [name[0] for name in cursor.fetchall()]
        except Exception as e:
            print(f"Could not _get_Name_from_AnnotationTypeLabels because {e}")
            raise e
        finally:
            cursor.close()
        return names

    def get_Id_map_to_Names_from_AnnotationTypeLabels(self):
        """
        Returns a dictionary with Ids as keys and names as values.
        """
        cursor = self.connection.cursor()
        mapping = {}
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute("""SELECT Id, Name FROM AnnotationTypeLabels ORDER BY Id ASC""")
            info = cursor.fetchall()
            for row in info:
                mapping[row[0]] = row[1]
        except Exception as e:
            print(f"Could not get_Id_map_to_Names_from_AnnotationTypeLabels because {e}")
            raise e
        finally:
            cursor.close()
        return mapping

    def _get_Id_from_AnnotationTypeLabels(self, label_info):
        """
        Returns the AnnotationTypeLabels.Id for a label , searching by its name and group name.
        :param label_info: (group, name), where group is the AnnotationType.Name
                            and name is AnnotationTypeLabels.Name
        :type label_info: tuple
        :return: AnnotationLabels.Id
        :rtype: int
        """
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT Id FROM AnnotationTypeLabels 
                    WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    and Name = ?""", label_info)
            label_id = cursor.fetchone()
            assert label_id is not None, f"Could not find a label from group {label_info[0]} " \
                                         f"with name {label_info[1]}. " \
                                         f"Are you sure it's been added into the database? "
        except Exception as e:
            print(f"Could not _get_AnnotationLabelId because {e}")
            raise e
        finally:
            cursor.close()
        return label_id[0]

    def _get_Ids_from_AnnotationTypeLabels(self, group):
        """
        Returns the AnnotationTypeLabels.Id for all labels , searching by their group name.
        :param group: AnnotationType.Name
        :type group: str
        :return: AnnotationLabels.Id
        :rtype: [(int,),(int,) ... ]
        """
        group = (group,)
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT Id FROM AnnotationTypeLabels 
                    WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)""", group)
            label_ids = cursor.fetchall()
            assert label_ids is not None, f"Could not find labels from group {group} " \
                                          "Are you sure it's been added into the database? "
        except Exception as e:
            print(f"Could not _get_AnnotationLabelIds because {e}")
            raise e
        finally:
            cursor.close()
        return label_ids

    def get_AnnotationTypeLabelId_from_Annotations(self, group):
        """
        Returns the AnnotationTypeLabelIds for all labels in the order according to the FrameId,
         searching by their group name.
        :param group: AnnotationType.Name
        :type group: str
        :return: AnnotationLabels.Id
        :rtype: [int]
        """
        group = (group,)
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f""" SELECT AnnotationTypeLabelId FROM Annotations WHERE AnnotationTypeLabelId IN
                            (SELECT Id FROM AnnotationTypeLabels 
                            WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?))
                            ORDER BY FrameId ASC""", group)
            label_ids = [label[0] for label in cursor.fetchall()]
            assert label_ids is not None, f"Could not find labels from group {group} " \
                                          "Are you sure it's been added into the database? "
        except Exception as e:
            print(f"Could not _get_AnnotationTypeLabelId_from_Annotations because {e}")
            raise e
        finally:
            cursor.close()
        return label_ids

    def _get_SliceInVolume_from_Volumes(self, frames):
        """
        Chooses the slices that correspond to the specified frames.
        The order of the frames is not preserved!
        the volume correspond to frames sorted in increasing order !

        :param frames: a list of frame IDs
        :type frames: [int]
        :return: volume IDs
        :rtype: [int]
        """
        # create list of frame Ids
        frame_ids = tuple(frames)
        n_frames = len(frame_ids)

        # get the volumes
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT SliceInVolume FROM Volumes 
                    WHERE FrameId IN ({', '.join(['?'] * n_frames)})""", frame_ids)
            slice_ids = cursor.fetchall()
        except Exception as e:
            print(f"Could not _get_SliceInVolume_from_Volumes because {e}")
            raise e
        finally:
            cursor.close()
        slice_ids = [slice_id[0] for slice_id in slice_ids]
        return slice_ids

    def _get_VolumeId_from_Volumes(self, frames):
        """
        Chooses the volumes that correspond to the specified frames.
        The order is not preserved!
        the volume correspond to sorted frames in increasing order !

        :param frames: a list of frame IDs
        :type frames: [int]
        :return: volume IDs
        :rtype: [int]
        """
        # create list of frame Ids
        frame_ids = tuple(frames)
        n_frames = len(frame_ids)

        # get the volumes
        cursor = self.connection.cursor()
        try:
            # create a parameterised query with variable number of parameters
            cursor.execute(
                f"""SELECT VolumeId FROM Volumes 
                    WHERE FrameId IN ({', '.join(['?'] * n_frames)})""", frame_ids)
            volume_ids = cursor.fetchall()
        except Exception as e:
            print(f"Could not _get_VolumeId_from_Volumes because {e}")
            raise e
        finally:
            cursor.close()
        volume_ids = [volume[0] for volume in volume_ids]
        return volume_ids

    def delete_annotation(self, name: str):
        """
        Deletes annotation from all the tables.
        Deletion by "ON DELETE CASCADE" from AnnotationTypes, AnnotationTypeLabels, Annotations,
        Cycles, CycleIterations.
        """
        name = (name,)
        # get the volumes
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                f"""DELETE FROM AnnotationTypes 
                            WHERE Name = ?""", name)
        except Exception as e:
            print(f"Could not delete_annotation because {e}")
            raise e
        finally:
            cursor.close()

choose_frames_per_slices(frames, slices)

Chooses the frames from specified frames, that also correspond to the same slices (continuously) in different volumes. For example, if slices = [2,3,4] it will choose such frames from "given frames" that also correspond to a chunk from slice 2 to slice 4 in all the volumes. If there is a frame that corresponds to a slice "2" in a volume, but no frames corresponding to the slices "3" and "4" in the SAME volume, such frame will not be picked.

The order of the frames is not preserved! The result will correspond to frames sorted in increasing order !

:param frames: a list of frame IDs :type frames: [int] :param slices: a list of slice IDs, order will not be preserved: will be sorted in increasing order :type slices: [int] :return: frames IDs from frames. corresponding to slices :rtype: [int]

Source code in src\vodex\dbmethods.py
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
def choose_frames_per_slices(self, frames, slices):
    """
    Chooses the frames from specified frames, that also correspond to the same slices (continuously)
    in different volumes.
    For example, if slices = [2,3,4] it will choose such frames from "given frames" that also correspond
    to a chunk from slice 2 to slice 4 in all the volumes.
    If there is a frame that corresponds to a slice "2" in a volume,
    but no frames corresponding to the slices "3" and "4" in the SAME volume, such frame will not be picked.

    The order of the frames is not preserved!
    The result will correspond to frames sorted in increasing order !

    :param frames: a list of frame IDs
    :type frames: [int]
    :param slices: a list of slice IDs, order will not be preserved: will be sorted in increasing order
    :type slices: [int]
    :return: frames IDs from frames. corresponding to slices
    :rtype: [int]
    """
    # create list of frame Ids
    frame_ids = tuple(frames)
    slice_ids = tuple(slices)
    n_frames = len(frame_ids)
    n_slices = len(slices)

    # get the volumes
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT FrameId FROM Volumes
                WHERE FrameId in ({', '.join(['?'] * n_frames)})
                AND SliceInVolume IN ({', '.join(['?'] * n_slices)})
                AND VolumeId IN
                    (
                    SELECT VolumeId FROM
                        (
                        SELECT VolumeId, count(VolumeId) as N 
                        FROM Volumes 
                        WHERE FrameId IN ({', '.join(['?'] * n_frames)})
                        AND SliceInVolume IN ({', '.join(['?'] * n_slices)})
                        GROUP BY VolumeId
                        )
                    WHERE N = ?
                    )""", frame_ids + slice_ids + frame_ids + slice_ids + (n_slices,)
        )

        frame_ids = cursor.fetchall()
    except Exception as e:
        print(f"Could not choose_frames_per_slices because {e}")
        raise e
    finally:
        cursor.close()
    frame_ids = [frame[0] for frame in frame_ids]
    return frame_ids

choose_full_volumes(frames)

Chooses the frames from specified frames, that also correspond to full volumes.

The order of the frames is not preserved! The result will correspond to frames sorted in increasing order !

:param frames: a list of frame IDs :type frames: [int] :param fpv: frames per volume :type fpv: int :return: frames IDs from frames. corresponding to slices :rtype: [int]

Source code in src\vodex\dbmethods.py
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
def choose_full_volumes(self, frames):
    """
    Chooses the frames from specified frames, that also correspond to full volumes.

    The order of the frames is not preserved!
    The result will correspond to frames sorted in increasing order !

    :param frames: a list of frame IDs
    :type frames: [int]
    :param fpv: frames per volume
    :type fpv: int
    :return: frames IDs from frames. corresponding to slices
    :rtype: [int]
    """
    # create list of frame Ids
    frame_ids = tuple(frames)
    n_frames = len(frame_ids)

    # get the volumes
    cursor = self.connection.cursor()
    try:
        # get n_volumes (frames per volume)
        cursor.execute(
            f"""SELECT Value FROM Options 
                WHERE Key = "frames_per_volume" """
        )
        fpv = int(cursor.fetchone()[0])

        # get ids of full volumes in the provided frames
        cursor.execute(
            f"""SELECT VolumeId FROM
                (
                SELECT VolumeId, count(VolumeId) as N
                FROM Volumes
                WHERE FrameId IN ({', '.join(['?'] * n_frames)})
                GROUP BY VolumeId
                )
                WHERE N = ?""", frame_ids + (fpv,)
        )
        volume_ids = [volume[0] for volume in cursor.fetchall()]
        n_volumes = len(volume_ids)

        # get all frames from frames that correspond to full volumes
        cursor.execute(
            f"""SELECT FrameId FROM Volumes
                WHERE FrameId IN ({', '.join(['?'] * n_frames)})
                AND VolumeId IN ({', '.join(['?'] * n_volumes)})""", frame_ids + tuple(volume_ids)
        )
        frame_ids = [frame[0] for frame in cursor.fetchall()]
    except Exception as e:
        print(f"Could not choose_full_volumes because {e}")
        raise e
    finally:
        cursor.close()

    return volume_ids, frame_ids

delete_annotation(name)

Deletes annotation from all the tables. Deletion by "ON DELETE CASCADE" from AnnotationTypes, AnnotationTypeLabels, Annotations, Cycles, CycleIterations.

Source code in src\vodex\dbmethods.py
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
def delete_annotation(self, name: str):
    """
    Deletes annotation from all the tables.
    Deletion by "ON DELETE CASCADE" from AnnotationTypes, AnnotationTypeLabels, Annotations,
    Cycles, CycleIterations.
    """
    name = (name,)
    # get the volumes
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""DELETE FROM AnnotationTypes 
                        WHERE Name = ?""", name)
    except Exception as e:
        print(f"Could not delete_annotation because {e}")
        raise e
    finally:
        cursor.close()

get_AnnotationTypeLabelId_from_Annotations(group)

Returns the AnnotationTypeLabelIds for all labels in the order according to the FrameId, searching by their group name. :param group: AnnotationType.Name :type group: str :return: AnnotationLabels.Id :rtype: [int]

Source code in src\vodex\dbmethods.py
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
def get_AnnotationTypeLabelId_from_Annotations(self, group):
    """
    Returns the AnnotationTypeLabelIds for all labels in the order according to the FrameId,
     searching by their group name.
    :param group: AnnotationType.Name
    :type group: str
    :return: AnnotationLabels.Id
    :rtype: [int]
    """
    group = (group,)
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f""" SELECT AnnotationTypeLabelId FROM Annotations WHERE AnnotationTypeLabelId IN
                        (SELECT Id FROM AnnotationTypeLabels 
                        WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?))
                        ORDER BY FrameId ASC""", group)
        label_ids = [label[0] for label in cursor.fetchall()]
        assert label_ids is not None, f"Could not find labels from group {group} " \
                                      "Are you sure it's been added into the database? "
    except Exception as e:
        print(f"Could not _get_AnnotationTypeLabelId_from_Annotations because {e}")
        raise e
    finally:
        cursor.close()
    return label_ids

get_Id_map_to_Names_from_AnnotationTypeLabels()

Returns a dictionary with Ids as keys and names as values.

Source code in src\vodex\dbmethods.py
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
def get_Id_map_to_Names_from_AnnotationTypeLabels(self):
    """
    Returns a dictionary with Ids as keys and names as values.
    """
    cursor = self.connection.cursor()
    mapping = {}
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute("""SELECT Id, Name FROM AnnotationTypeLabels ORDER BY Id ASC""")
        info = cursor.fetchall()
        for row in info:
            mapping[row[0]] = row[1]
    except Exception as e:
        print(f"Could not get_Id_map_to_Names_from_AnnotationTypeLabels because {e}")
        raise e
    finally:
        cursor.close()
    return mapping

get_Name_and_Description_from_AnnotationTypeLabels(group)

Returns the Name and description for the labels that correspond to the annotation with the provided group name.

Source code in src\vodex\dbmethods.py
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
def get_Name_and_Description_from_AnnotationTypeLabels(self, group):
    """
    Returns the Name and description for the labels that correspond to the annotation
    with the provided group name.
    """
    group = (group,)
    names = []
    descriptions = {}

    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute("""SELECT Name, Description FROM AnnotationTypeLabels WHERE AnnotationTypeId = 
                         (SELECT Id FROM AnnotationTypes WHERE Name = ?)""", group)
        info = cursor.fetchall()
        for row in info:
            name = row[0]
            names.append(name)
            descriptions[name] = row[1]
    except Exception as e:
        print(f"Could not get_Name_and_Description_from_AnnotationTypeLabels because {e}")
        raise e
    finally:
        cursor.close()
    return names, descriptions

get_Names_from_AnnotationTypes()

Returns the names of all the available annotations.

Source code in src\vodex\dbmethods.py
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
def get_Names_from_AnnotationTypes(self):
    """
    Returns the names of all the available annotations.
    """
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute("""SELECT Name FROM AnnotationTypes""")
        names = [name[0] for name in cursor.fetchall()]
    except Exception as e:
        print(f"Could not _get_Name_from_AnnotationTypes because {e}")
        raise e
    finally:
        cursor.close()
    return names

get_Structure_from_Cycle(group)

Returns cycle Structure if the annotation has a cycle entry or None otherwise.

Source code in src\vodex\dbmethods.py
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
def get_Structure_from_Cycle(self, group):
    """
    Returns cycle Structure if the annotation has a cycle entry or None otherwise.
    """
    group = (group,)
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute("""SELECT Structure FROM Cycles WHERE AnnotationTypeId = 
                         (SELECT Id FROM AnnotationTypes WHERE Name = ?)""", group)
        info = cursor.fetchone()
        if info:
            cycle = info[0]
        else:
            cycle = None
    except Exception as e:
        print(f"Could not get_Structure_from_Cycle because {e}")
        raise e
    finally:
        cursor.close()
    return cycle

get_and_frames_per_annotations(conditions)

Chooses the frames that correspond to the specified conditions on annotation. Using "and" logic. Example : if you ask for frames corresponding to condition 1 and condition 2 , it will return such frames that both condition 1 and condition 2 are True AT THE SAME TIME

:param conditions: a list of conditions on the annotation labels in a form [(group, name),(group, name), ...] where group is a string for the annotation type and name is the name of the label of that annotation type. For example [('light', 'on'), ('shape','c')] :type conditions: [tuple] :return: list of frame Ids that satisfy all the conditions, if there are no such frames, an empty list :rtype: list

Source code in src\vodex\dbmethods.py
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
def get_and_frames_per_annotations(self, conditions):
    """
    Chooses the frames that correspond to the specified conditions on annotation. Using "and" logic. Example : if
    you ask for frames corresponding to condition 1 and condition 2 , it will return such frames that both
    condition 1 and condition 2 are True AT THE SAME TIME

    :param conditions: a list of conditions on the annotation labels
    in a form [(group, name),(group, name), ...] where group is a string for the annotation type
    and name is the name of the label of that annotation type. For example [('light', 'on'), ('shape','c')]
    :type conditions: [tuple]
    :return: list of frame Ids that satisfy all the conditions, if there are no such frames, an empty list
    :rtype: list
    """
    # create list of label Ids
    labels_ids = []
    for label_info in conditions:
        labels_ids.append(self._get_Id_from_AnnotationTypeLabels(label_info))
    labels_ids = tuple(labels_ids)
    n_labels = len(labels_ids)

    # get the frames
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT FrameId FROM 
                (SELECT FrameId, count(FrameId) as N 
                FROM Annotations 
                WHERE AnnotationTypeLabelId IN ({', '.join(['?'] * n_labels)})
                GROUP BY FrameId)
                WHERE N = {n_labels}""", labels_ids)
        frame_ids = cursor.fetchall()
    except Exception as e:
        print(f"Could not _get_and_FrameId_from_Annotations because {e}")
        raise e
    finally:
        cursor.close()
    # TODO : get rid of list of tuples?
    #  https://www.reddit.com/r/Python/comments/2iiqri/quick_question_why_are_sqlite_fields_returned_as/
    frame_ids = [frame[0] for frame in frame_ids]
    return frame_ids

get_conditionIds_per_cycle_per_frame(annotation_name)

Returns a list of condition IDs that correspond to each frame, list of corresponding frames. annotation_name: str

Source code in src\vodex\dbmethods.py
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
def get_conditionIds_per_cycle_per_frame(self, annotation_name):
    """
    Returns a list of condition IDs that correspond to each frame, list of corresponding frames.
    annotation_name: str
    """
    # TODO : check if empty
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT CycleIterations.FrameId, AnnotationTypeLabelId FROM
                CycleIterations 
                INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                WHERE AnnotationTypeLabelId in 
                    (
                    SELECT Id from AnnotationTypeLabels 
                    WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    )
                AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                AND CycleIteration = 0
                ORDER BY CycleIterations.FrameId""", (annotation_name, annotation_name))
        info = cursor.fetchall()
        # TODO : check if empty
        frame_ids = [row[0] for row in info]
        condition_ids = [row[1] for row in info]

    except Exception as e:
        print(f"Could not get_conditionIds_per_cycle_per_frame because {e}")
        raise e
    finally:
        cursor.close()

    return frame_ids, condition_ids

get_conditionIds_per_cycle_per_volumes(annotation_name)

Returns a list of condition IDs that correspond to each volume, list of corresponding volumes and a count of the volume-condition pairs annotation_name: str

Source code in src\vodex\dbmethods.py
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
def get_conditionIds_per_cycle_per_volumes(self, annotation_name):
    """
    Returns a list of condition IDs that correspond to each volume, list of corresponding volumes
    and a count of the volume-condition pairs
    annotation_name: str
    """
    # TODO : check if empty
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT VolumeId, AnnotationTypeLabelId, count(VolumeId) FROM
                CycleIterations 
                INNER JOIN Volumes ON CycleIterations.FrameId = Volumes.FrameId 
                INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                WHERE AnnotationTypeLabelId in 
                    (
                    SELECT Id from AnnotationTypeLabels 
                    WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    )
                AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                AND CycleIteration = 0
                GROUP BY VolumeId, AnnotationTypeLabelId
                ORDER BY VolumeId""", (annotation_name, annotation_name))
        info = cursor.fetchall()
        # TODO : check if empty
        volume_ids = [row[0] for row in info]
        condition_ids = [row[1] for row in info]
        count = [row[2] for row in info]

    except Exception as e:
        print(f"Could not get_conditions_per_cycle_per_volumes because {e}")
        raise e
    finally:
        cursor.close()

    return volume_ids, condition_ids, count

get_cycleIterations_per_frame(annotation_name)

Returns a list of cycle iterations that correspond to each frame, list of corresponding frames. annotation_name: str

Source code in src\vodex\dbmethods.py
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
def get_cycleIterations_per_frame(self, annotation_name):
    """
    Returns a list of cycle iterations that correspond to each frame, list of corresponding frames.
    annotation_name: str
    """
    # TODO : check if empty
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT CycleIterations.FrameId, CycleIteration FROM
                CycleIterations 
                INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                WHERE AnnotationTypeLabelId in 
                    (
                    SELECT Id from AnnotationTypeLabels 
                    WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    )
                AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                ORDER BY CycleIterations.FrameId""", (annotation_name, annotation_name))
        info = cursor.fetchall()
        # TODO : check if empty
        frame_ids = [row[0] for row in info]
        condition_ids = [row[1] for row in info]

    except Exception as e:
        print(f"Could not get_conditionIds_per_cycle_per_frame because {e}")
        raise e
    finally:
        cursor.close()

    return frame_ids, condition_ids

get_cycleIterations_per_volumes(annotation_name)

Returns a list of cycleIterations that correspond to each volume, list of corresponding volumes and a count of the volume-iteration pairs annotation_name: str

Source code in src\vodex\dbmethods.py
 982
 983
 984
 985
 986
 987
 988
 989
 990
 991
 992
 993
 994
 995
 996
 997
 998
 999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
def get_cycleIterations_per_volumes(self, annotation_name):
    """
    Returns a list of cycleIterations that correspond to each volume, list of corresponding volumes
    and a count of the volume-iteration pairs
    annotation_name: str
    """
    # TODO : check if empty
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT VolumeId, CycleIteration, count(VolumeId) FROM
                CycleIterations 
                INNER JOIN Volumes ON CycleIterations.FrameId = Volumes.FrameId 
                INNER JOIN Annotations ON CycleIterations.FrameId = Annotations.FrameId 
                WHERE AnnotationTypeLabelId in 
                    (
                    SELECT Id from AnnotationTypeLabels 
                    WHERE AnnotationTypeId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                    )
                AND CycleId = (SELECT Id from AnnotationTypes WHERE Name = ?)
                GROUP BY VolumeId
                ORDER BY VolumeId""", (annotation_name, annotation_name))
        info = cursor.fetchall()
        # TODO : check if empty
        volume_ids = [row[0] for row in info]
        cycle_its = [row[1] for row in info]
        count = [row[2] for row in info]

    except Exception as e:
        print(f"Could not get_cycleIterations_per_volumes because {e}")
        raise e
    finally:
        cursor.close()

    return volume_ids, cycle_its, count

get_data_dir()

Get data directory

Source code in src\vodex\dbmethods.py
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
def get_data_dir(self):
    """
    Get data directory
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT Value FROM Options 
                 WHERE Key = "data_dir" """
        )
        data_dir = cursor.fetchone()[0]
    except Exception as e:
        print(f"Could not get_data_dir because {e}")
        raise e
    finally:
        cursor.close()

    return data_dir

get_fgf()

Get frames per volume

Source code in src\vodex\dbmethods.py
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
def get_fgf(self):
    """
    Get frames per volume
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT Value FROM Options 
                 WHERE Key = "num_head_frames" """
        )
        fdf = int(cursor.fetchone()[0])
    except Exception as e:
        print(f"Could not get_fgf because {e}")
        raise e
    finally:
        cursor.close()

    return fdf

get_file_names()

Get the file names from the Files table.

Source code in src\vodex\dbmethods.py
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
def get_file_names(self):
    """
    Get the file names from the Files table.
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT FileName FROM Files ORDER BY Id ASC"""
        )
        file_names = [row[0] for row in cursor.fetchall()]
    except Exception as e:
        print(f"Could not get_file_names because {e}")
        raise e
    finally:
        cursor.close()

    return file_names

get_fpv()

Get frames per volume

Source code in src\vodex\dbmethods.py
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
def get_fpv(self):
    """
    Get frames per volume
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT Value FROM Options 
                 WHERE Key = "frames_per_volume" """
        )
        fpv = int(cursor.fetchone()[0])
    except Exception as e:
        print(f"Could not get_fpv because {e}")
        raise e
    finally:
        cursor.close()

    return fpv

get_frames_per_file()

Get the file names from the Files table.

Source code in src\vodex\dbmethods.py
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
def get_frames_per_file(self):
    """
    Get the file names from the Files table.
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT NumFrames FROM Files ORDER BY Id ASC"""
        )
        frames_per_file = [row[0] for row in cursor.fetchall()]
    except Exception as e:
        print(f"Could not get_frames_per_file because {e}")
        raise e
    finally:
        cursor.close()

    return frames_per_file

get_frames_per_volumes(volume_ids)

Finds all the frames that correspond to the specified volumes. The order is not preserved! the volume correspond to sorted volumes in increasing order !

:param volume_ids: a list of volume IDs :type volume_ids: [int] :return: frame IDs :rtype: [int]

Source code in src\vodex\dbmethods.py
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
def get_frames_per_volumes(self, volume_ids):
    """
    Finds all the frames that correspond to the specified volumes.
    The order is not preserved!
    the volume correspond to sorted volumes in increasing order !

    :param volume_ids: a list of volume IDs
    :type volume_ids: [int]
    :return: frame IDs
    :rtype: [int]
    """
    ids = list_of_int(volume_ids)

    # get the frames
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT FrameId FROM Volumes 
                WHERE VolumeId IN ({', '.join(['?'] * len(ids))})""", tuple(ids))
        frame_ids = cursor.fetchall()
    except Exception as e:
        print(f"Could not _get_FrameId_from_Volumes because {e}")
        raise e
    finally:
        cursor.close()
    # TODO : get rid of list of tuples?
    #  https://www.reddit.com/r/Python/comments/2iiqri/quick_question_why_are_sqlite_fields_returned_as/
    frame_ids = [frame[0] for frame in frame_ids]
    return frame_ids

get_options()

Gets the information from the OPTIONS table. Returns a dictionary with the Key: Value from the table. ( Keys: 'data_dir', 'frames_per_volume', 'num_head_frames', 'num_tail_frames', 'num_full_volumes' )

Source code in src\vodex\dbmethods.py
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
def get_options(self):
    """
    Gets the information from the OPTIONS table.
    Returns a dictionary with the Key: Value from the table.
    ( Keys: 'data_dir', 'frames_per_volume', 'num_head_frames', 'num_tail_frames', 'num_full_volumes' )
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(
            f"""SELECT * FROM Options"""
        )
        options = {}
        for row in cursor.fetchall():
            options[row[0]] = row[1]

    except Exception as e:
        print(f"Could not get_options because {e}")
        raise e
    finally:
        cursor.close()

    return options

get_or_frames_per_annotations(conditions)

Chooses the frames that correspond to the specified conditions on annotation. Using "or" logic. Example : if you ask for frames corresponding to condition 1 and condition 2 , it will return such frames that either condition 1 is true OR condition 2 is True OR both are true.

:param conditions: a list of conditions on the annotation labels in a form [(group, name),(group, name), ...] where group is a string for the annotation type and name is the name of the label of that annotation type. For example [('light', 'on'), ('shape','c')] :type conditions: [tuple] :return: :rtype:

Source code in src\vodex\dbmethods.py
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
def get_or_frames_per_annotations(self, conditions):
    """
    Chooses the frames that correspond to the specified conditions on annotation. Using "or" logic. Example : if
    you ask for frames corresponding to condition 1 and condition 2 , it will return such frames that either
    condition 1 is true OR condition 2 is True OR both are true.

    :param conditions: a list of conditions on the annotation labels
    in a form [(group, name),(group, name), ...] where group is a string for the annotation type
    and name is the name of the label of that annotation type. For example [('light', 'on'), ('shape','c')]
    :type conditions: [tuple]
    :return:
    :rtype:
    """
    # create list of label Ids
    labels_ids = []
    for label_info in conditions:
        labels_ids.append(self._get_Id_from_AnnotationTypeLabels(label_info))
    labels_ids = tuple(labels_ids)
    n_labels = len(labels_ids)

    # get the frames
    cursor = self.connection.cursor()
    try:
        # create a parameterised query with variable number of parameters
        cursor.execute(
            f"""SELECT FrameId FROM Annotations 
                WHERE AnnotationTypeLabelId IN ({', '.join(['?'] * n_labels)})
                GROUP BY FrameId""", labels_ids)
        frame_ids = cursor.fetchall()
    except Exception as e:
        print(f"Could not _get_or_FrameId_from_Annotations because {e}")
        raise e
    finally:
        cursor.close()
    # TODO : get rid of list of tuples?
    #  https://www.reddit.com/r/Python/comments/2iiqri/quick_question_why_are_sqlite_fields_returned_as/
    frame_ids = [frame[0] for frame in frame_ids]
    return frame_ids

get_volume_list()

Returns a list of all the volumes. :return: list of all the volumes :rtype: [int]

Source code in src\vodex\dbmethods.py
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
def get_volume_list(self):
    """
    Returns a list of all the volumes.
    :return: list of all the volumes
    :rtype: [int]
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(f"SELECT DISTINCT VolumeId FROM Volumes")
        volume_ids = [volume[0] for volume in cursor.fetchall()]
    except Exception as e:
        print(f"Could not get total number of frames from Frames because {e}")
        raise e
    finally:
        cursor.close()

    return volume_ids

load(file_name) classmethod

Load the contents of a database file on disk to a transient copy in memory without modifying the file

Source code in src\vodex\dbmethods.py
608
609
610
611
612
613
614
615
616
617
618
619
@classmethod
def load(cls, file_name):
    """
    Load the contents of a database file on disk to a
    transient copy in memory without modifying the file
    """
    disk_db = connect(file_name)
    memory_db = connect(':memory:')
    disk_db.backup(memory_db)
    disk_db.close()
    # Now use `memory_db` without modifying disk db
    return cls(memory_db)

prepare_frames_for_loading(frames)

Finds all the information needed 1) to load the frames 2) and shape them back into volumes/slices. For each frame returns the image file, frame location on the image and corresponding volume.

The order is not preserved! the volume correspond to sorted volumes in increasing order !

:param frames: a list of frame IDs :type frames: [int] :return: three lists, the length of the frames : data directory, file names, image files, frame location on the image, volumes. :rtype: str, [str], [str],[int],[int]

TODO : break into functions that get the file locations and the stuff relevant to the frames

TODO : make one " prepare volumes " for loading?

Source code in src\vodex\dbmethods.py
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
def prepare_frames_for_loading(self, frames):
    """
    Finds all the information needed
    1) to load the frames
    2) and shape them back into volumes/slices.
    For each frame returns the image file,
    frame location on the image and corresponding volume.

    The order is not preserved!
    the volume correspond to sorted volumes in increasing order !

    :param frames: a list of frame IDs
    :type frames: [int]
    :return: three lists, the length of the frames :
            data directory, file names,
            image files, frame location on the image, volumes.
    :rtype: str, [str], [str],[int],[int]
    # TODO : break into functions that get the file locations and the stuff relevant to the frames
    # TODO : make one " prepare volumes " for loading?
    """
    n_frames = len(frames)

    # get the frames
    cursor = self.connection.cursor()
    try:
        # get data directory
        cursor.execute(
            f"""SELECT Value
                FROM Options
                WHERE Key = "data_dir" """)
        data_dir = cursor.fetchone()[0]

        # get file_names
        cursor.execute(
            f"""SELECT FileName
                FROM Files """)
        file_names = cursor.fetchall()

        # get info for every frame
        cursor.execute(
            f"""SELECT 
                    FileId,
                    FrameInFile,
                    VolumeId
                FROM 
                    Frames
                    INNER JOIN Volumes 
                    ON Frames.Id = Volumes.FrameId
                WHERE FrameId IN ({', '.join(['?'] * n_frames)})""", tuple(frames))
        frame_info = cursor.fetchall()

    except Exception as e:
        print(f"Could not prepare_frames_for_loading because {e}")
        raise e
    finally:
        cursor.close()

    file_names = [row[0] for row in file_names]

    file_ids = [row[0] for row in frame_info]
    frame_in_file = [row[1] for row in frame_info]
    volumes = [row[2] for row in frame_info]

    return data_dir, file_names, file_ids, frame_in_file, volumes

DbWriter

Writes information to the database. Database interface that abstracts the SQLite calls.

Learning resources

sql: https://www.devdungeon.com/content/python-sqlite3-tutorial https://www.sqlitetutorial.net/sqlite-python/creating-tables/ try-catch : https://softwareengineering.stackexchange.com/questions/64180/good-use-of-try-catch-blocks

Parameters:

Name Type Description Default
connection

connection to the SQL database

required
Source code in src\vodex\dbmethods.py
  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
class DbWriter:
    """
    Writes information to the database.
    Database interface that abstracts the SQLite calls.

    Learning resources:
        sql:
        https://www.devdungeon.com/content/python-sqlite3-tutorial
        https://www.sqlitetutorial.net/sqlite-python/creating-tables/
        try-catch :
        https://softwareengineering.stackexchange.com/questions/64180/good-use-of-try-catch-blocks

    Args:
        connection: connection to the SQL database
    """

    def __init__(self, connection):
        self.connection = connection
        self.connection.execute("PRAGMA foreign_keys = 1")

    def save(self, file_name: str):
        """
        Backup a database to a file.
        Will CLOSE connection to the database in memory!
        Args:
            file_name : the name of the file to save database to, EX.: 'databasename.db'
        """

        def progress(status, remaining, total):
            print(f'Copied {total - remaining} of {total} pages...')

        backup_db = connect(file_name)
        with backup_db:
            self.connection.backup(backup_db, progress=progress)
        # self.connection.close()
        backup_db.close()

    @classmethod
    def create(cls):
        """
        Creates an empty DB for the experiment in memory.
        """
        # TODO : figure out how to type-annotate classmethod
        # For an in-memory only database:
        memory_db = connect(':memory:')
        return cls(memory_db)

    @classmethod
    def load(cls, file_name: str):
        """
        Load the contents of a database file on disk to a
        transient copy in memory without modifying the file.
        """
        disk_db = connect(file_name)
        memory_db = connect(':memory:')
        disk_db.backup(memory_db)
        disk_db.close()
        # Now use `memory_db` without modifying disk db
        return cls(memory_db)

    def populate(self, volumes: VolumeManager = None, annotations: List[Annotation] = None):
        """
        Creates the tables if they don't exist and fills with the provided data.
        Args:
            volumes: mapping of frames to volumes, and to slices in volumes, frames per volume
            annotations: mapping of frames to labels, list of annotations
        """
        # TODO : add warnings when you are trying to write the same data again
        # TODO : How to type annotate vodex classes from core ?

        # will only create if they don't exist
        self._create_tables()
        # TODO : write cases for files and frames not None

        if volumes is not None:
            self._populate_Options(volumes.file_manager, volumes)
            self._populate_Files(volumes.file_manager)
            self._populate_Frames(volumes.frame_manager)
            self._populate_Volumes(volumes)

        if annotations is not None:
            self.add_annotations(annotations)

    def add_annotations(self, annotations: List[Annotation]):
        """
        Adds a list of annotations to the database.
        Does NOT save the database after adding.
        To keep this change in the future, you need to save the database after adding.
        Args:
            annotations: mapping of frames to labels, list of annotations
        """
        # TODO : add list checking
        for annotation in annotations:
            self._populate_AnnotationTypes(annotation)
            self._populate_AnnotationTypeLabels(annotation)
            self._populate_Annotations(annotation)
            if annotation.cycle is not None:
                self._populate_Cycles(annotation)
                self._populate_CycleIterations(annotation)

    def get_n_frames(self) -> int:
        """
        Queries and returns the total number of frames in the experiment.
        """
        cursor = self.connection.cursor()
        try:
            cursor.execute(f"SELECT COUNT(*) FROM Frames")
            n_frames = cursor.fetchone()[0]
        except Exception as e:
            print(f"Could not get total number of frames from Frames because {e}")
            raise e
        finally:
            cursor.close()
        return n_frames

    def _create_tables(self):

        # TODO : change UNIQUE(a, b)
        # into primary key over both columns a and b where appropriate

        db_cursor = self.connection.cursor()

        sql_create_Options_table = """
            CREATE TABLE IF NOT EXISTS "Options" (
            "Key"	TEXT NOT NULL UNIQUE,
            "Value"	TEXT NOT NULL,
            "Description"	TEXT,
            PRIMARY KEY("Key")
            )
            """
        db_cursor.execute(sql_create_Options_table)

        sql_create_Files_table = """
            CREATE TABLE IF NOT EXISTS "Files" (
            "Id"	INTEGER NOT NULL UNIQUE,
            "FileName"	TEXT NOT NULL UNIQUE,
            "NumFrames"	INTEGER NOT NULL,
            PRIMARY KEY("Id" AUTOINCREMENT)
            )
            """
        db_cursor.execute(sql_create_Files_table)

        sql_create_AnnotationTypes_table = """
            CREATE TABLE IF NOT EXISTS "AnnotationTypes" (
            "Id"	INTEGER NOT NULL UNIQUE,
            "Name"	TEXT NOT NULL UNIQUE,
            "Description"	TEXT,
            PRIMARY KEY("Id" AUTOINCREMENT)
            )
            """
        db_cursor.execute(sql_create_AnnotationTypes_table)

        sql_create_Frames_table = """
            CREATE TABLE IF NOT EXISTS "Frames" (
            "Id"	INTEGER NOT NULL UNIQUE,
            "FrameInFile"	INTEGER NOT NULL,
            "FileId"	INTEGER NOT NULL,
            PRIMARY KEY("Id" AUTOINCREMENT),
            FOREIGN KEY("FileId") REFERENCES "Files"("Id")
            )
            """
        db_cursor.execute(sql_create_Frames_table)

        sql_create_Cycles_table = """
            CREATE TABLE IF NOT EXISTS "Cycles" (
            "Id"	INTEGER NOT NULL UNIQUE,
            "AnnotationTypeId"	INTEGER NOT NULL UNIQUE,
            "Structure"	TEXT NOT NULL,
            FOREIGN KEY("AnnotationTypeId") REFERENCES "AnnotationTypes"("Id") ON DELETE CASCADE,
            PRIMARY KEY("Id" AUTOINCREMENT)
            )
            """
        db_cursor.execute(sql_create_Cycles_table)

        sql_create_AnnotationTypeLabels_table = """
            CREATE TABLE IF NOT EXISTS "AnnotationTypeLabels" (
            "Id"	INTEGER NOT NULL UNIQUE,
            "AnnotationTypeId"	INTEGER NOT NULL,
            "Name"	TEXT NOT NULL,
            "Description"	TEXT,
            PRIMARY KEY("Id" AUTOINCREMENT),
            FOREIGN KEY("AnnotationTypeId") REFERENCES "AnnotationTypes"("Id") ON DELETE CASCADE,
            UNIQUE("AnnotationTypeId","Name")
            )
            """
        db_cursor.execute(sql_create_AnnotationTypeLabels_table)

        sql_create_Annotations_table = """
            CREATE TABLE IF NOT EXISTS "Annotations" (
            "FrameId"	INTEGER NOT NULL,
            "AnnotationTypeLabelId"	INTEGER NOT NULL,
            FOREIGN KEY("FrameId") REFERENCES "Frames"("Id"),
            FOREIGN KEY("AnnotationTypeLabelId") REFERENCES "AnnotationTypeLabels"("Id") ON DELETE CASCADE,
            UNIQUE("FrameId","AnnotationTypeLabelId")
            )
            """
        db_cursor.execute(sql_create_Annotations_table)

        sql_create_CycleIterations_table = """
            CREATE TABLE IF NOT EXISTS "CycleIterations" (
            "FrameId"	INTEGER NOT NULL,
            "CycleId"	INTEGER NOT NULL,
            "CycleIteration"	INTEGER NOT NULL,
            FOREIGN KEY("CycleId") REFERENCES "Cycles"("Id") ON DELETE CASCADE,
            FOREIGN KEY("FrameId") REFERENCES "Frames"("Id")
            )
            """
        db_cursor.execute(sql_create_CycleIterations_table)

        sql_create_Volumes_table = """
            CREATE TABLE IF NOT EXISTS "Volumes" (
            "FrameId"	INTEGER NOT NULL UNIQUE,
            "VolumeId"	INTEGER NOT NULL,
            "SliceInVolume"	INTEGER NOT NULL,
            PRIMARY KEY("FrameId" AUTOINCREMENT),
            FOREIGN KEY("FrameId") REFERENCES "Frames"("Id")
            UNIQUE("VolumeId","SliceInVolume")
            )
            """
        db_cursor.execute(sql_create_Volumes_table)

        db_cursor.close()

    def _populate_Options(self, file_manager: FileManager, volume_manager: VolumeManager):
        """
        Populates the Options table (a dictionary with key - value pairs).
        Learning resources:
            another way of dealing with Errors : ( more pretty ??? )
            https://www.w3resource.com/python-exercises/sqlite/python-sqlite-exercise-6.php
        Args:
            file_manager: FileManager object that provides the data to populate the tables.
            volume_manager: VolumeManager object that provides the data to populate the tables.
        """
        row_data = [("data_dir", file_manager.data_dir.as_posix()),
                    ("frames_per_volume", volume_manager.fpv),
                    ("num_head_frames", volume_manager.n_head),
                    ("num_tail_frames", volume_manager.n_tail),
                    ("num_full_volumes", volume_manager.full_volumes)]

        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO Options (Key, Value) VALUES (?, ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to Options because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_Files(self, file_manager: FileManager):
        """
        Populates the Files table with
        file_name : list with filenames per file (str), and
        num_frames : list with number of frames per file (int)
        Args:
            file_manager: FileManager object that provides the data to populate the tables.
        """
        row_data = [(filename, frames) for
                    filename, frames in zip(file_manager.file_names, file_manager.num_frames)]

        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO Files (FileName, NumFrames) VALUES (?, ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to Files because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_Frames(self, frame_manager: FrameManager):
        """
        Populates the Frames table with
        frame_in_file and frame_to_file mapping.

        Learning Resourses:
            Something like
            insert into tab2 (id_customers, value)
            values ((select id from tab1 where customers='john'), 'alfa');
            but in SQLite
            https://www.tutorialspoint.com/sqlite/sqlite_insert_query.htm

        Args:
            frame_manager: FrameManager object that provides the data to populate the tables.
        """
        # adding +1 since the frame_to_file is indexing files from 0 and sqlite gave files IDs from 1
        row_data = [(frame_in_file, frame_to_file + 1) for
                    frame_in_file, frame_to_file in zip(frame_manager.frame_in_file, frame_manager.frame_to_file)]

        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO Frames (FrameInFile, FileId) VALUES (?, ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to Frames because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_Volumes(self, volume_manager: VolumeManager):
        """
        Populates the Volumes table with
        volume_id and slice_in_volume mapping.

        Args:
            volume_manager: VolumeManager object that provides the data to populate the tables.
        """
        row_data = [(volume_id, slice_in_volume) for
                    volume_id, slice_in_volume in zip(volume_manager.frame_to_vol, volume_manager.frame_to_z)]

        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO Volumes (VolumeId, SliceInVolume) VALUES (?, ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to Volumes because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_AnnotationTypes(self, annotation: Annotation):
        """
        Populates the AnnotationTypes table with
        annotation.name, annotation.info mapping.

        Args:
            volume_manager: VolumeManager object that provides the data to populate the tables.
        """
        row_data = (annotation.name, annotation.info)
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                "INSERT INTO AnnotationTypes (Name, Description) VALUES (?, ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to AnnotationTypes because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_AnnotationTypeLabels(self, annotation):

        row_data = [(label.group, label.name, label.description)
                    for label in annotation.labels.states]

        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO AnnotationTypeLabels (AnnotationTypeId, Name, Description) " +
                "VALUES((SELECT Id FROM AnnotationTypes WHERE Name = ?), ?, ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to AnnotationTypeLabels because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_Annotations(self, annotation):
        n_frames = self.get_n_frames()
        assert n_frames == annotation.n_frames, f"Number of frames in the annotation, {annotation.n_frames}," \
                                                f"doesn't match" \
                                                f" the expected number of frames {n_frames}"
        frames = range(n_frames)
        row_data = [(frame + 1, label.name, label.group)
                    for frame, label in zip(frames, annotation.frame_to_label)]
        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO Annotations (FrameId, AnnotationTypeLabelId) " +
                "VALUES(?, (SELECT Id FROM AnnotationTypeLabels "
                "WHERE Name = ? " +
                "AND AnnotationTypeId = (SELECT Id FROM AnnotationTypes " +
                "WHERE Name = ?)))",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write group {annotation.name} to Annotations because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_Cycles(self, annotation):
        """
        """
        row_data = (annotation.name, annotation.cycle.to_json())
        cursor = self.connection.cursor()
        try:
            cursor.execute(
                "INSERT INTO Cycles (AnnotationTypeId, Structure) " +
                "VALUES((SELECT Id FROM AnnotationTypes WHERE Name = ?), ?)",
                row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write to Cycles because {e}")
            raise e
        finally:
            cursor.close()

    def _populate_CycleIterations(self, annotation):
        n_frames = self.get_n_frames()
        assert n_frames == annotation.n_frames, f"Number of frames in the annotation, {annotation.n_frames}," \
                                                f"doesn't match" \
                                                f" the expected number of frames {n_frames}"
        # get cycle id by annotation type
        cursor = self.connection.cursor()
        cursor.execute(
            "SELECT Id FROM Cycles " +
            "WHERE AnnotationTypeId = (SELECT Id FROM AnnotationTypes " +
            "WHERE Name = ?)", (annotation.name,))
        cycle_id = cursor.fetchone()[0]
        cursor.close()

        # prepare rows
        frames = range(n_frames)
        row_data = [(frame + 1, cycle_id, iteration)
                    for frame, iteration in zip(frames, annotation.frame_to_cycle)]

        # insert into CycleIterations
        cursor = self.connection.cursor()
        try:
            cursor.executemany(
                "INSERT INTO CycleIterations (FrameId, CycleId, CycleIteration) " +
                "VALUES(?, ?,?)", row_data)
            self.connection.commit()
        except Exception as e:
            print(f"Could not write group {annotation.name} to CycleIterations because {e}")
            raise e
        finally:
            cursor.close()

add_annotations(annotations)

Adds a list of annotations to the database. Does NOT save the database after adding. To keep this change in the future, you need to save the database after adding.

Parameters:

Name Type Description Default
annotations List[Annotation]

mapping of frames to labels, list of annotations

required
Source code in src\vodex\dbmethods.py
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
def add_annotations(self, annotations: List[Annotation]):
    """
    Adds a list of annotations to the database.
    Does NOT save the database after adding.
    To keep this change in the future, you need to save the database after adding.
    Args:
        annotations: mapping of frames to labels, list of annotations
    """
    # TODO : add list checking
    for annotation in annotations:
        self._populate_AnnotationTypes(annotation)
        self._populate_AnnotationTypeLabels(annotation)
        self._populate_Annotations(annotation)
        if annotation.cycle is not None:
            self._populate_Cycles(annotation)
            self._populate_CycleIterations(annotation)

create() classmethod

Creates an empty DB for the experiment in memory.

Source code in src\vodex\dbmethods.py
46
47
48
49
50
51
52
53
54
@classmethod
def create(cls):
    """
    Creates an empty DB for the experiment in memory.
    """
    # TODO : figure out how to type-annotate classmethod
    # For an in-memory only database:
    memory_db = connect(':memory:')
    return cls(memory_db)

get_n_frames()

Queries and returns the total number of frames in the experiment.

Source code in src\vodex\dbmethods.py
109
110
111
112
113
114
115
116
117
118
119
120
121
122
def get_n_frames(self) -> int:
    """
    Queries and returns the total number of frames in the experiment.
    """
    cursor = self.connection.cursor()
    try:
        cursor.execute(f"SELECT COUNT(*) FROM Frames")
        n_frames = cursor.fetchone()[0]
    except Exception as e:
        print(f"Could not get total number of frames from Frames because {e}")
        raise e
    finally:
        cursor.close()
    return n_frames

load(file_name) classmethod

Load the contents of a database file on disk to a transient copy in memory without modifying the file.

Source code in src\vodex\dbmethods.py
56
57
58
59
60
61
62
63
64
65
66
67
@classmethod
def load(cls, file_name: str):
    """
    Load the contents of a database file on disk to a
    transient copy in memory without modifying the file.
    """
    disk_db = connect(file_name)
    memory_db = connect(':memory:')
    disk_db.backup(memory_db)
    disk_db.close()
    # Now use `memory_db` without modifying disk db
    return cls(memory_db)

populate(volumes=None, annotations=None)

Creates the tables if they don't exist and fills with the provided data.

Parameters:

Name Type Description Default
volumes VolumeManager

mapping of frames to volumes, and to slices in volumes, frames per volume

None
annotations List[Annotation]

mapping of frames to labels, list of annotations

None
Source code in src\vodex\dbmethods.py
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
def populate(self, volumes: VolumeManager = None, annotations: List[Annotation] = None):
    """
    Creates the tables if they don't exist and fills with the provided data.
    Args:
        volumes: mapping of frames to volumes, and to slices in volumes, frames per volume
        annotations: mapping of frames to labels, list of annotations
    """
    # TODO : add warnings when you are trying to write the same data again
    # TODO : How to type annotate vodex classes from core ?

    # will only create if they don't exist
    self._create_tables()
    # TODO : write cases for files and frames not None

    if volumes is not None:
        self._populate_Options(volumes.file_manager, volumes)
        self._populate_Files(volumes.file_manager)
        self._populate_Frames(volumes.frame_manager)
        self._populate_Volumes(volumes)

    if annotations is not None:
        self.add_annotations(annotations)

save(file_name)

Backup a database to a file. Will CLOSE connection to the database in memory!

Parameters:

Name Type Description Default
file_name

the name of the file to save database to, EX.: 'databasename.db'

required
Source code in src\vodex\dbmethods.py
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
def save(self, file_name: str):
    """
    Backup a database to a file.
    Will CLOSE connection to the database in memory!
    Args:
        file_name : the name of the file to save database to, EX.: 'databasename.db'
    """

    def progress(status, remaining, total):
        print(f'Copied {total - remaining} of {total} pages...')

    backup_db = connect(file_name)
    with backup_db:
        self.connection.backup(backup_db, progress=progress)
    # self.connection.close()
    backup_db.close()