Fixing NetworkCandidateGraph.from_cnet() (#498) (2110895f) · Commits · aflab / astrogeology / Autocnet

autocnet/graph/network.py

+111 −38

Original line number	Diff line number	Diff line
		@@ -1844,7 +1844,7 @@ class NetworkCandidateGraph(CandidateGraph):
		session.commit()

		@classmethod
		def from_filelist(cls, filelist, clear_db=False):
		def from_filelist(cls, filelist, config, clear_db=False):
		"""
		Parse a filelist to add nodes to the database. Using the
		information in the database, then instantiate a complete,
		@@ -1856,11 +1856,47 @@ class NetworkCandidateGraph(CandidateGraph):
		If a list, this is a list of paths. If a str, this is
		a path to a file containing a list of image paths
		that is newline ("\\n") delimited.
		config : dict, str
		configuration information; either a path to a yaml
		file or a dictionary.

		clear_db : boolean
		truncates all tables in the active database.

		Returns
		-------
		ncg : object
		A network candidate graph object

		See Also:
		--------
		config_from_dict: config documentation
		"""
		obj = cls()

		if isinstance(config, str):
		config = parse_config(config)
		obj.config_from_dict(config)

		if clear_db:
		obj.clear_db()

		obj.add_from_filelist(filelist, clear_db=clear_db)

		return obj

		def add_from_filelist(self, filelist, clear_db=False):
		"""
		Parse a filelist to add nodes to the database.

		Parameters
		----------
		filelist : list, str
		If a list, this is a list of paths. If a str, this is
		a path to a file containing a list of image paths
		that is newline ("\\n") delimited.
		clear_db : boolean
		truncates all tables in the active database.
		"""
		if isinstance(filelist, list):
		pass
		@@ -1870,7 +1906,7 @@ class NetworkCandidateGraph(CandidateGraph):
		warnings.warn('Unable to parse the passed filelist')

		if clear_db:
		cls.clear_db()
		self.clear_db()

		total=len(filelist)
		for cnt, f in enumerate(filelist):
		@@ -1878,12 +1914,28 @@ class NetworkCandidateGraph(CandidateGraph):
		# images in the DB
		print('loading {} of {}'.format(cnt+1, total))
		image_name = os.path.basename(f)
		NetworkNode(image_path=f, image_name=image_name)
		node = NetworkNode(image_path=f, image_name=image_name)
		node.parent = self
		node.populate_db()

		obj = cls.from_database()
		self.from_database()
		# Execute the computation to compute overlapping geometries
		obj._execute_sql(compute_overlaps_sql)
		return obj
		self._execute_sql(compute_overlaps_sql)

		def add_image(self, img_path):
		"""
		Upload a single image to NetworkCandidateGraph associated DB.

		Parameters
		----------
		img_path: str
		absolute path to image
		"""
		image_name = os.path.basename(img_path)
		node = NetworkNode(image_path=f, image_name=image_name)
		node.parent = self
		node.populate_db()


		def copy_images(self, newdir):
		"""
		@@ -1942,11 +1994,6 @@ class NetworkCandidateGraph(CandidateGraph):
		An optional string to select a subset of the images in the
		database specified in the config.

		Returns
		-------
		obj : obj
		A network candidate graph.

		Example
		-------
		>>> ncg = NetworkCandidateGraph()
		@@ -2043,8 +2090,7 @@ class NetworkCandidateGraph(CandidateGraph):
		# Setup the edges
		self._setup_edges()

		@staticmethod
		def clear_db(tables=None):
		def clear_db(self, tables=None):
		"""
		Truncate all of the database tables and reset any
		autoincrement columns to start with 1.
		@@ -2054,8 +2100,7 @@ class NetworkCandidateGraph(CandidateGraph):
		table : str or list of str, optional
		the table name of a list of table names to truncate
		"""
		session = Session()
		session.rollback() # In case any transactions are not done
		with self.session_scope() as session:
		if tables:
		if isinstance(tables, str):
		tables = [tables]
		@@ -2064,13 +2109,14 @@ class NetworkCandidateGraph(CandidateGraph):

		for t in tables:
		if t != 'spatial_ref_sys':
		try:
		session.execute(f'TRUNCATE TABLE {t} CASCADE')
		except Exception as e:
		raise RuntimeError(f'Failed to truncate table {t}, {t} not modified').with_traceback(e.__traceback__)
		try:
		session.execute(f'ALTER SEQUENCE {t}_id_seq RESTART WITH 1')
		except Exception as e:
		warnings.warn(f'Failed to truncate table {t}, {t} not modified')
		session.rollback()
		session.commit()
		session.close()
		warnings.warn(f'Failed to reset primary id sequence for table {t}')

		def place_points_from_cnet(self, cnet):
		semi_major, semi_minor = self.config["spatial"]["semimajor_rad"], self.config["spatial"]["semiminor_rad"]
		@@ -2121,13 +2167,39 @@ class NetworkCandidateGraph(CandidateGraph):
		session.close()

		@classmethod
		def from_cnet(cls, cnet, filelist):
		def from_cnet(cls, cnet, filelist, config):
		"""
		Instantiates and populates a NetworkCandidateGraph from an
		ISIS control network and corresponding cube list.

		Parameters
		----------
		cnet: str
		path to control network file from which you want to populate
		the NetworkCandidateGraph.

		filelist: str
		path to file containing list of cubes associated with
		the control network file.

		config : dict, str
		configuration information; either a path to a yaml
		file or a dictionary.

		Returns
		-------
		obj: NetworkCandidateGraph
		The NetworkCandidateGraph populated with the points and measures
		from the control network and the images from the filelist.

		See Also:
		--------
		config_from_dict: config documentation
		"""
		networkobj = cls.from_filelist(filelist)
		networkobj.place_points_from_cnet(cnet)
		return networkobj
		obj = cls.from_filelist(filelist, config)
		obj.place_points_from_cnet(cnet)

		return obj

		@property
		def measures(self):
		@@ -2137,10 +2209,11 @@ class NetworkCandidateGraph(CandidateGraph):
		@property
		def queue_length(self):
		"""
		Returns the length of the processing queue. Jobs are left on the
		queue if a cluster job is cancelled. Those cancelled jobs are then
		called on next cluster job launch, causing failures. This method provides
		a quick check for left over jobs.
		Returns the length of the processing queue.

		Jobs are left on the queue if a cluster job is cancelled. Those cancelled
		jobs are then called on next cluster job launch, causing failures. This
		method provides a check for left over jobs.
		"""
		llen = self.redis_queue.llen(self.config['redis']['processing_queue'])
		return llen

autocnet/graph/node.py

+11 −12

Original line number	Diff line number	Diff line
		@@ -514,7 +514,7 @@ class NetworkNode(Node):

		def populate_db(self):
		with self.parent.session_scope() as session:
		res = session.query(Images).filter(Images.path == kwargs['image_path']).first()
		res = session.query(Images).filter(Images.path == self['image_path']).first()
		if res:
		# Image already exists
		return
		@@ -529,17 +529,16 @@ class NetworkNode(Node):
		warnings.warn('Unable to generate image footprint.\n{}'.format(e))
		fp = None
		# Create the image
		i = Images(name=kwargs['image_name'],
		path=kwargs['image_path'],
		i = Images(name=self['image_name'],
		path=self['image_path'],
		geom=fp,
		keypoints=kps,
		#cameras=cam,
		serial=self.isis_serial,
		cam_type=cam_type)

		session = self.parent.Session()
		i.create(session)
		session.close()
		with self.parent.session_scope() as session:
		session.add(i)

		def _from_db(self, table_obj, key='image_id'):
		"""

autocnet/io/db/model.py

+1 −6

Original line number	Diff line number	Diff line
		@@ -200,15 +200,10 @@ class Images(BaseMixin, Base):
		measures = relationship("Measures")

		def __repr__(self):
		try:
		footprint = to_shape(self.geom).__geo_interface__
		except:
		footprint = None
		return json.dumps({'id':self.id,
		'name':self.name,
		'path':self.path,
		'geom':footprint,
		'footprint_bodyfixed':self.footprint_bodyfixed})
		'geom':self.geom.wkt})

		@hybrid_property
		def geom(self):