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create database scripts

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Ruben van de Ven 2020-12-17 14:57:03 +01:00
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.gitignore vendored
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dataset/
dataset/
*.pyc

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README.md Normal file
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# Auto-accept : part of the Accept & Work series
## Install:
```bash
virtualenv --system-site-packages -p python3 venv
source venv/bin/activate
./download_dataset.sh
python tools.py create
```
To use a custom dataset version (defaults to the smaller validation 2017 set)
```bash
python tools.py create --annotations FILENAME.json --db dataset/NAME.db
```
## Server
Python server. Based on work for the [COCO dataset interface](https://git.rubenvandeven.com/plottingdata/coco) for [Plotting Data](http://plottingd.at/a).

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coco/__init__.py Normal file
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coco/coco.sql Normal file
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BEGIN TRANSACTION;
CREATE TABLE IF NOT EXISTS "segments" (
"id" INTEGER UNIQUE,
"annotation_id" INTEGER,
"points" TEXT,
PRIMARY KEY("id")
) WITHOUT ROWID;
CREATE TABLE IF NOT EXISTS "categories" (
"id" INTEGER UNIQUE,
"supercategory" TEXT,
"name" TEXT UNIQUE,
PRIMARY KEY("id")
) WITHOUT ROWID;
CREATE TABLE IF NOT EXISTS "images" (
"id" INTEGER UNIQUE,
"flickr_url" TEXT,
"coco_url" TEXT,
"width" FLOAT,
"height" FLOAT,
"date_captured" DATETIME,
PRIMARY KEY("id","id")
) WITHOUT ROWID;
CREATE TABLE IF NOT EXISTS "annotations" (
"id" INTEGER UNIQUE,
"image_id" INTEGER,
"category_id" INTEGER,
"iscrowd" BOOL,
"area" FLOAT,
"bbox_top" FLOAT,
"bbox_left" FLOAT,
"bbox_width" FLOAT,
"bbox_height" FLOAT,
"zerkine_moments" TEXT DEFAULT NULL,
PRIMARY KEY("id")
) WITHOUT ROWID;
CREATE INDEX IF NOT EXISTS "segments_annotation" ON "segments" (
"annotation_id"
);
CREATE INDEX IF NOT EXISTS "annotations_image" ON "annotations" (
"image_id"
);
CREATE INDEX IF NOT EXISTS "annotations_category" ON "annotations" (
"category_id"
);
COMMIT;

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coco/storage.py Normal file
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import logging
import os
import sqlite3
import pycocotools.coco
import ast
import copy
import svgwrite
logger = logging.getLogger('coco.storage')
class Annotation:
def __init__(self, result, storage):
self.storage = storage
self.id = result['id']
self.image_id = result['image_id']
self.category_id = result['category_id']
self.iscrowd = bool(result['iscrowd'])
self.area = result['area']
self.bbox = [result['bbox_left'], result['bbox_top'], result['bbox_width'], result['bbox_height']]
self.segments = self.fetchSegments()
self.is_normalised = False
if type(result['zerkine_moment']) is list:
self.zerkine_moment = result['zerkine_moment'] # when normalising, this is already there
else:
self.zerkine_moment = self.parseZerkineFromDB(result['zerkine_moment']) if result['zerkine_moment'] else None
@classmethod
def parseZerkineFromDB(cls, r):
z = r.split(' ')
return [float(i) for i in z]
def fetchSegments(self):
try:
cur = self.storage.con.cursor()
cur.execute("SELECT * FROM segments WHERE annotation_id = :id AND points != 'ount' AND points != 'iz'", {'id': self.id})
segments = []
for row in cur:
segments.append(Segment(row))
except Exception as e:
logger.critical(f"Invalid segment for annotation {self.id}")
logger.exception(e)
raise(e)
return segments
def getNormalised(self, width, height) -> 'Annotation':
'''
center segments in boundig box with given width and height, and on point 0,0
'''
scale = min(width/self.bbox[2], height/self.bbox[3])
logger.debug(f"Normalise from bbox: {self.bbox}")
new_width = self.bbox[2] * scale
new_height = self.bbox[3] * scale
dx = (width - new_width) / 2
dy = (height - new_height) / 2
data = self.forJson()
data['bbox_left'] = 0
data['bbox_top'] = 0
data['bbox_width'] = new_width
data['bbox_height'] = new_height
newAnn = Annotation(data, self.storage)
newAnn.is_normalised = True
newAnn.bbox_original = self.bbox
newAnn.scale = scale
for i, segment in enumerate(newAnn.segments):
newAnn.segments[i].points = [[
(p[0]-self.bbox[0]) * scale,
(p[1]-self.bbox[1]) * scale
] for p in segment.points]
return newAnn
def forJson(self):
data = self.__dict__.copy()
del data['storage']
data['image'] = self.storage.getImage(data['image_id'])
return data
def writeToDrawing(self, dwg, **pathSpecs):
for segment in self.segments:
if len(pathSpecs) == 0:
pathSpecs['fill'] = 'white'
dwg.add(svgwrite.path.Path(segment.getD(), class_=f"cat_{self.category_id}", **pathSpecs))
def getTranslationToCenter(self):
dimensions = (self.bbox[2], self.bbox[3])
targetSize = max(dimensions)
dx = (dimensions[0] - targetSize)/2
dy = (dimensions[1] - targetSize)/2
return (dx, dy)
def asSvg(self, filename, square=False, bg=None):
dimensions = (self.bbox[2], self.bbox[3])
viewbox = copy.copy(self.bbox)
if square:
targetSize = max(dimensions)
dx = (dimensions[0] - targetSize)/2
dy = (dimensions[1] - targetSize)/2
viewbox[2] = targetSize
viewbox[3] = targetSize
dimensions = (targetSize, targetSize)
viewbox[0] += dx
viewbox[1] += dy
dwg = svgwrite.Drawing(
filename,
size=dimensions,
viewBox=" ".join([str(s) for s in viewbox])
)
if bg:
dwg.add(dwg.rect(
(viewbox[0],viewbox[1]),
(viewbox[2],viewbox[3]),
fill=bg))
self.writeToDrawing(dwg)
return dwg
class Segment():
def __init__(self, result):
try:
self.points = self.asCoordinates(ast.literal_eval('['+result['points']+']'))
except Exception as e:
logger.critical(f"Exception loading segment for {result} {result['points']}")
raise
@classmethod
def asCoordinates(cls, pointList):
points = []
r = len(pointList) / 2
for i in range(int(r)):
points.append([
pointList[(i)*2],
pointList[(i)*2+1]
])
return points
def getD(self):
start = self.points[0]
d = f'M{start[0]:.4f} {start[1]:.4f} L'
for i in range(1, len(self.points)):
p = self.points[i]
d += f' {p[0]:.4f} {p[1]:.4f}'
d += " Z" # segments are always closed
return d
def forJson(self):
return self.points
class COCOStorage:
def __init__(self, filename):
self.logger = logging.getLogger('coco.storage')
self.filename = filename
if not os.path.exists(self.filename):
con = sqlite3.connect(self.filename)
cur = con.cursor()
d = os.path.dirname(os.path.realpath(__file__))
with open(os.path.join(d,'coco.sql'), 'r') as fp:
cur.executescript(fp.read())
con.close()
self.con = sqlite3.connect(self.filename)
self.con.row_factory = sqlite3.Row
def propagateFromAnnotations(self, filename):
self.logger.info(f"Load {filename}")
coco = pycocotools.coco.COCO(filename)
self.logger.info("Create categories")
cur = self.con.cursor()
cur.executemany('INSERT OR IGNORE INTO categories(id, supercategory, name) VALUES (:id, :supercategory, :name)', coco.cats.values())
self.con.commit()
self.logger.info("Images...")
cur.executemany('''
INSERT OR IGNORE INTO images(id, flickr_url, coco_url, width, height, date_captured)
VALUES (:id, :flickr_url, :coco_url, :width, :height, :date_captured)
''', coco.imgs.values())
self.con.commit()
self.logger.info("Annotations...")
def annotation_generator():
for c in coco.anns.values():
ann = c.copy()
ann['bbox_top'] = ann['bbox'][1]
ann['bbox_left'] = ann['bbox'][0]
ann['bbox_width'] = ann['bbox'][2]
ann['bbox_height'] = ann['bbox'][3]
yield ann
cur.executemany('''
INSERT OR IGNORE INTO annotations(id, image_id, category_id, iscrowd, area, bbox_top, bbox_left, bbox_width, bbox_height)
VALUES (:id, :image_id, :category_id, :iscrowd, :area, :bbox_top, :bbox_left, :bbox_width, :bbox_height)
''', annotation_generator())
self.con.commit()
self.logger.info("Segments...")
def segment_generator():
for ann in coco.anns.values():
for i, seg in enumerate(ann['segmentation']):
yield {
'id': ann['id']*10 + i, # create a uniqe segment id, supports max 10 segments per annotation
'annotation_id': ann['id'],
'points': str(seg)[1:-1],
}
cur.executemany('''
INSERT OR IGNORE INTO segments(id, annotation_id, points)
VALUES (:id, :annotation_id, :points)
''', segment_generator())
self.con.commit()
self.logger.info("Done...")
def getCategories(self):
if not hasattr(self, 'categories'):
cur = self.con.cursor()
cur.execute("SELECT * FROM categories ORDER BY id")
self.categories = [dict(cat) for cat in cur]
return self.categories
def getCategory(self, cid):
cats = self.getCategories()
cat = [c for c in cats if c['id'] == cid]
if not len(cat):
return None
return cat[0]
def getImage(self, image_id: int):
cur = self.con.cursor()
cur.execute(f"SELECT * FROM images WHERE id = ? LIMIT 1", (image_id,))
img = cur.fetchone()
return dict(img)
def getAnnotationWithoutZerkine(self):
cur = self.con.cursor()
# annotation 918 and 2206849 have 0 height. Crashing the script... exclude them
cur.execute(f"SELECT * FROM annotations WHERE zerkine_moment IS NULL AND area > 0 LIMIT 1")
ann = cur.fetchone()
if ann:
return Annotation(ann, self)
else:
return None
def countAnnotationsWithoutZerkine(self):
cur = self.con.cursor()
cur.execute(f"SELECT count(id) FROM annotations WHERE zerkine_moment IS NULL AND area > 0")
return int(cur.fetchone()[0])
def storeZerkineForAnnotation(self, annotation, moments, delayCommit = False):
m = ' '.join([str(m) for m in moments])
cur = self.con.cursor()
cur.execute(
"UPDATE annotations SET zerkine_moment = :z WHERE id = :id",
{'z': m, 'id': annotation.id}
)
if not delayCommit:
self.con.commit()
return True
def getZerkines(self):
cur = self.con.cursor()
cur.execute(f"SELECT id, zerkine_moment FROM annotations WHERE zerkine_moment IS NOT NULL")
return cur.fetchall()
def getAllAnnotationPoints(self):
cur = self.con.cursor()
cur.execute(f"SELECT annotations.id, points FROM annotations INNER JOIN segments ON segments.annotation_id = annotations.id WHERE area > 0")
return cur.fetchall()
def getAnnotationById(self, annotation_id = None, withZerkine = False):
if annotation_id == -1:
annotation_id = None
return self.getRandomAnnotation(annotation_id = annotation_id, withZerkine = withZerkine)
def getRandomAnnotation(self, annotation_id = None, category_id = None, withZerkine = False):
result = self.getRandomAnnotations(annotation_id, category_id, withZerkine, limit=1)
return result[0] if len(result) else None
def getRandomAnnotations(self, annotation_id = None, category_id = None, withZerkine = False, limit=None):
cur = self.con.cursor()
where = ""
params = []
if annotation_id:
where = "id = ?"
params.append(annotation_id)
elif category_id:
where = "category_id = ?"
params.append(category_id)
else:
where = "1=1"
if withZerkine:
where += " AND zerkine_moment IS NOT NULL"
sqlLimit = ""
if limit:
sqlLimit = f"LIMIT {int(limit)}"
cur.execute(f"SELECT * FROM annotations WHERE {where} ORDER BY RANDOM() {sqlLimit}", tuple(params))
results = []
for ann in cur:
results.append(Annotation(ann, self))
return results
# ann = cur.fetchall()
#
# if ann:
# return Annotation(ann, self)
# else:
# return None

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requirements.txt Normal file
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tornado
coloredlogs
pycocotools
numpy
mahotas
svgwrite

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tools.py Normal file
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import argparse
from coco.storage import COCOStorage
import logging
import pycocotools.coco
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger("tools")
def create(args):
con = args.storage.con
cur = con.cursor()
cur.executemany('INSERT OR IGNORE INTO categories(id, supercategory, name) VALUES (:id, :supercategory, :name)', args.coco.cats.values())
con.commit()
logger.info("Images...")
cur.executemany('''
INSERT OR IGNORE INTO images(id, flickr_url, coco_url, width, height, date_captured)
VALUES (:id, :flickr_url, :coco_url, :width, :height, :date_captured)
''', args.coco.imgs.values())
con.commit()
logger.info("Annotations...")
def annotation_generator():
for c in args.coco.anns.values():
ann = c.copy()
ann['bbox_top'] = ann['bbox'][1]
ann['bbox_left'] = ann['bbox'][0]
ann['bbox_width'] = ann['bbox'][2]
ann['bbox_height'] = ann['bbox'][3]
yield ann
cur.executemany('''
INSERT OR IGNORE INTO annotations(id, image_id, category_id, iscrowd, area, bbox_top, bbox_left, bbox_width, bbox_height)
VALUES (:id, :image_id, :category_id, :iscrowd, :area, :bbox_top, :bbox_left, :bbox_width, :bbox_height)
''', annotation_generator())
con.commit()
logger.info("Segments...")
def segment_generator():
for ann in args.coco.anns.values():
for i, seg in enumerate(ann['segmentation']):
yield {
'id': ann['id']*10 + i, # create a uniqe segment id, supports max 10 segments per annotation
'annotation_id': ann['id'],
'points': str(seg)[1:-1],
}
cur.executemany('''
INSERT OR IGNORE INTO segments(id, annotation_id, points)
VALUES (:id, :annotation_id, :points)
''', segment_generator())
con.commit()
logger.info("Done...")
if __name__ == "__main__":
parser = argparse.ArgumentParser()
subparsers = parser.add_subparsers(title = 'subcommands', help="Use command -h for specific help")
parser_create = subparsers.add_parser('create')
parser_create.add_argument(
'--annotations',
metavar="JSON_FILENAME",
type=pycocotools.coco.COCO,
dest='coco',
default='dataset/annotations/instances_val2017.json'
)
parser_create.add_argument(
'--db',
type=COCOStorage,
metavar='DATABASE',
dest='storage',
help='SQLite db filename, will be created if not existing',
default='dataset/instances_val2017.db'
)
parser_create.set_defaults(target = create)
# parser_build = subparsers.add_parser('build')
args = parser.parse_args()
if 'target' in args:
args.target(args)
else:
parser.print_help()
exit(1)