Adding functions and NB for overlap connectivity check (#504) (0d22bd05) · Commits · aflab / astrogeology / Autocnet

autocnet/graph/network.py

+80 −0

Original line number	Diff line number	Diff line
		@@ -17,6 +17,7 @@ import shapely

		import geoalchemy2
		from sqlalchemy.ext.declarative.api import DeclarativeMeta
		from sqlalchemy.sql import func
		import shapely.affinity
		import shapely.geometry
		import shapely.wkt as swkt
		@@ -2221,6 +2222,85 @@ class NetworkCandidateGraph(CandidateGraph):
		"""
		self.redis_queue.flushdb()

		def empty_overlays(self, filters={'ignore': False}, size_threshold=0):
		"""
		Find overlaps that do not contain valid points. By default, valid points
		include not ignored points, but additional point properties can be used to
		further define a valid point. For example, to look at not ignored, free
		(not ground) points; filters = {'ignored': False, 'pointtype': 2}.

		Parameters
		----------
		filters: dict
		Points object properties for point filtering.

		size_threshold: float
		Minimum area requirment for returned overlaps. Units are
		determined by spatial reference system.

		Returns
		-------
		overlays: list of Overlay objects
		Model information associated with overlaps that contain no valid points

		See Also
		--------
		autocnet.io.db.model.Overlay: for description of information associated with Overlay class
		autocnet.io.db.model.Points: for description of information associated with Points class
		"""
		with self.session_scope() as session:
		# Find overlap ids that contain one or more valid points
		sq = session.query(Overlay.id).join(Points, func.ST_Contains(Overlay.geom, Points.geom))
		for attr, value in filters.items():
		sq = sq.filter(getattr(Points, attr)==value)
		sq = sq.group_by(Overlay.id)

		# find overlap information not satisfying previous query
		q = session.query(Overlay).filter(Overlay.id.notin_(sq)).filter(func.ST_Area(Overlay.geom)>=size_threshold)
		overlays = q.all()
		session.expunge_all()
		return overlays


		def connected_overlays(self, filters={'ignore': False}, size_threshold=0):
		"""
		Find overlaps that contain valid points. By default, valid points
		include not ignored points, but additional point properties can be used to
		further define a valid point. For example, to look at not ignored, free
		(not ground) points; filters = {'ignored': False, 'pointtype': 2}.

		Parameters
		----------
		filters: dict
		Points object properties for point filtering.

		size_threshold: float
		Minimum area requirment for returned overlaps. Units are
		determined by spatial reference system.

		Returns
		-------
		overlays: list of Overlay objects
		Model information associated with overlaps that contain one or more valid points

		See Also
		--------
		autocnet.io.db.model.Overlay: for description of information associated with Overlay class
		autocnet.io.db.model.Points: for description of information associated with Points class
		"""
		with self.session_scope() as session:
		# Find overlap ids that contain one or more valid points
		sq = session.query(Overlay.id).join(Points, func.ST_Contains(Overlay.geom, Points.geom))
		for attr, value in filters.items():
		sq = sq.filter(getattr(Points, attr)==value)
		sq = sq.group_by(Overlay.id)

		# find overlap information satisfying previous query
		q = session.query(Overlay).filter(Overlay.id.in_(sq)).filter(func.ST_Area(Overlay.geom)>=size_threshold)
		overlays = q.all()
		session.expunge_all()
		return overlays

		def cluster_propagate_control_network(self,
		base_cnet,
		walltime='00:20:00',

docs/users/installation.rst

+5 −5

Original line number	Diff line number	Diff line
		@@ -10,12 +10,12 @@ Via Conda
		1. [Download](https://www.continuum.io/downloads) and install the Python 3.x Miniconda installer. Respond ``Yes`` when
		prompted to add conda to your BASH profile.
		1. (Optional) We like to sequester applications in their own environments to avoid any dependency conflicts. To do this:
		* ``conda create -n <your_environment_name> python=3 && source activate <your_environment_name>``
		* ``conda create -n <your_environment_name> && source activate <your_environment_name>``
		1. Bring up a command line and add three channels to your conda config (``~/condarc``):
		* ``conda config --add channels usgs-astrogeology``
		* ``conda config --add channels conda-forge``
		* ``conda config --add channels jlaura``
		* ``conda config --add channels menpo``
		1. Finally, install autocnet: ``conda install -c jlaura autocnet-dev``
		1. Finally, install autocnet: ``conda install -c usgs-astrogeology autocnet``

		Via setup.py
		------------
		@@ -28,9 +28,9 @@ Manual Development Environment
		------------------------------
		To manually install AutoCnet (for example in a development environment) we must install the necessary dependencies.

		1. Create a virtual environment: ``conda create -n autocnet python=3.5 && source activate autocnet``
		1. Create a virtual environment: ``conda create -n autocnet && source activate autocnet``
		2. As above, add conda-forge to the channel list.
		3. To install the planetary I/O module and the OpenCV computer vision module: ``conda install -c jlaura plio opencv3``
		3. To install the planetary I/O module and the OpenCV computer vision module: ``conda install -c usgs-astrogeology plio opencv3``
		4. To install the optional VLFeature module (for SIFT): ``conda install -c conda-forge vlfeat``
		4a. To install the Cython wrapper to vlfeat: ``conda install -c menpo cyvlfeat``
		5. To install PIL and PySAL: ``pip install pillow pysal``

docs/users/tutorials/index.rst

+2 −1

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ Working With ISIS Control Networks
		-------------------------------
		.. toctree::
		:maxdepth: 1

		Ingesting from ISIS control network<isis_ingest/from_cnet.ipynb>

docs/users/tutorials/isis_ingestion/overlap_check.ipynb

0 → 100644

+236 −0

File added.

Preview size limit exceeded, changes collapsed.