Updates for subpixel alignment, changes affine to projective transform to capture reflection. (a4a4eed8) · Commits · aflab / astrogeology / Autocnet

autocnet/graph/cluster_submit.py

+4 −9

Original line number	Diff line number	Diff line
		#!/usr/bin/env python

		import argparse
		import copy
		import os
		import json
		import sys
		import logging

		from io import StringIO
		from contextlib import redirect_stdout
		import sys

		from redis import StrictRedis

		from autocnet.graph.network import NetworkCandidateGraph
		from autocnet.graph.node import NetworkNode
		from autocnet.graph.edge import NetworkEdge
		from autocnet.io.db.model import Points, Measures, Overlay
		from autocnet.utils.utils import import_func
		from autocnet.utils.serializers import JsonEncoder, object_hook
		from autocnet.io.db.model import JobsHistory
		from autocnet.utils.serializers import object_hook

		logging.basicConfig(stream=sys.stdout, level=logging.INFO)
		log = logging.getLogger(__name__)

		def parse_args(): # pragma: no cover
		@@ -102,7 +97,7 @@ def process(msg):
		# For now, pass all the potential config items through
		# most funcs will simply discard the unnecessary ones.
		msg['kwargs']['ncg'] = ncg
		msg['kwargs']['Session'] = ncg.Session
		msg['kwargs']['session'] = ncg.Session

		# Now run the function.
		res = func(msg['args'], *msg['kwargs'])

autocnet/graph/cluster_submit_single.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -78,7 +78,7 @@ def process(msg):
		# For now, pass all the potential config items through
		# most funcs will simply discard the unnecessary ones.
		msg['kwargs']['ncg'] = ncg
		msg['kwargs']['Session'] = ncg.Session
		msg['kwargs']['session'] = ncg.Session

		# Now run the function.
		res = func(msg['args'], *msg['kwargs'])

autocnet/graph/network.py

+12 −9

Original line number	Diff line number	Diff line
		@@ -105,7 +105,7 @@ class CandidateGraph(nx.Graph):
		'keypoint_index' : int
		}

		def __init__(self, args, basepath=None, node_id_map=None, overlaps=False, cam_type='isis', *kwargs):
		def __init__(self, args, basepath=None, node_id_map=None, overlaps=False, *kwargs):
		super(CandidateGraph, self).__init__(args, *kwargs)

		self.graph['creationdate'] = strftime("%Y-%m-%d %H:%M:%S", gmtime())
		@@ -131,7 +131,7 @@ class CandidateGraph(nx.Graph):
		node_id = self.graph['node_counter']
		self.graph['node_counter'] += 1
		n['data'] = self.node_factory(
		image_name=i, image_path=image_path, node_id=node_id, cam_type=cam_type)
		image_name=i, image_path=image_path, node_id=node_id)

		self.graph['node_name_map'][i] = node_id

		@@ -1638,6 +1638,14 @@ class NetworkCandidateGraph(CandidateGraph):
		retries += 1
		sleep(retries ** sleeptime)

		# def _setup_nodes(self):
		# with self.session_scope() as session:
		# res = session.query(Images.path, Images.cam_type, Images.dem, Images.dem_type).all()
		# for r in res:
		# self.nodes[r[0]]['cam_type'] = r[1]
		# self.nodes[r[0]]['dem'] = r[2]
		# self.nodes[r[0]]['dem_type'] = r[3]

		def _setup_edges(self):
		with self.session_scope() as session:
		res = session.query(Edges).all()
		@@ -2089,14 +2097,10 @@ class NetworkCandidateGraph(CandidateGraph):
		if just_stage:
		return command

		if queue == None:
		queue = self.config['cluster']['queue']

		submitter = Slurm(command,
		job_name=jobname,
		mem_per_cpu=self.config['cluster']['processing_memory'],
		time=walltime,
		partition=queue,
		ntasks=ntasks,
		output=log_dir+f'/autocnet.{function}-%j')

		@@ -2461,7 +2465,7 @@ class NetworkCandidateGraph(CandidateGraph):
		if overlaps:
		self._execute_sql(sql.compute_overlaps_sql)

		def from_database(self, query_string=sql.select_pub_image, cam_type='isis'):
		def from_database(self, query_string=sql.select_pub_image):
		"""
		This is a constructor that takes the results from an arbitrary query string,
		uses those as a subquery into a standard polygon overlap query and
		@@ -2509,7 +2513,7 @@ class NetworkCandidateGraph(CandidateGraph):
		adjacency[spath].append(dpath)

		# Add nodes that do not overlap any images
		self.__init__(adjacency, node_id_map=adjacency_lookup, cam_type=cam_type)
		self.__init__(adjacency, node_id_map=adjacency_lookup)

		# Setup the edges
		self._setup_edges()
		@@ -2877,7 +2881,6 @@ class NetworkCandidateGraph(CandidateGraph):
		job_name='cross_instrument_matcher',
		mem_per_cpu=config['cluster']['processing_memory'],
		time=walltime,
		partition=config['cluster']['queue'],
		output=config['cluster']['cluster_log_dir']+'/autocnet.cim-%j')
		job_counter = len(groups.items())
		submitter.submit(array='1-{}'.format(job_counter))

autocnet/graph/node.py

+1 −82

Original line number	Diff line number	Diff line
		@@ -116,13 +116,11 @@ class Node(dict, MutableMapping):
		NodeID: {}
		Image Name: {}
		Image PATH: {}
		Number Keypoints: {}
		Available Masks : {}
		Type: {}
		Sensor Model Type: {}
		DEM: {}
		""".format(self['node_id'], self['image_name'], self['image_path'],
		self.nkeypoints, self.masks, self.__class__,
		self.__class__,
		self['cam_type'], self['dem'])

		def __hash__(self): #pragma: no cover
		@@ -630,55 +628,6 @@ class NetworkNode(Node):
		res = self._from_db(Keypoints)
		return res.nkeypoints if res is not None else 0

		def create_camera(self, url):
		"""
		Creates a CSM sensor for the node and serializes the state
		to the DB,

		Parameters
		----------
		url : str
		The URI to a service that can create an ISD to instantiate
		a sensor.
		"""
		raise NotImplementedError

		# TODO: This should pass the straight metadata and not mess with mundging it.
		label = pvl.dumps(self.geodata.metadata).decode()
		response = requests.post(url, json={'label':label})
		response = response.json()
		model_name = response.get('name_model', None)
		if model_name is None:
		return
		isdpath = os.path.splitext(self['image_path'])[0] + '.json'
		try:
		with open(isdpath, 'w') as f:
		json.dump(response, f)
		except Exception as e:
		log.warning('Failed to write JSON ISD for image {}.\n{}'.format(self['image_path'], e))
		isd = csmapi.Isd(self['image_path'])
		plugin = csmapi.Plugin.findPlugin('UsgsAstroPluginCSM')
		self._camera = plugin.constructModelFromISD(isd, model_name)
		serialized_camera = self._camera.getModelState()

		cam = Cameras(camera=serialized_camera, image_id=self['node_id'])
		return cam

		@property
		def camera(self):
		"""
		Get the camera object from the database.
		"""
		# TODO: This should use knoten once it is stable.
		import csmapi
		if not getattr(self, '_camera', None):
		res = self._from_db(Cameras)
		plugin = csmapi.Plugin.findPlugin('UsgsAstroPluginCSM')
		if res is not None:
		self._camera = plugin.constructModelFromState(res.camera)
		return self._camera


		def footprint_from_database(self):
		with self.parent.session_scope() as session:
		res = session.query(Images).filter(Images.id == self['node_id']).first()
		@@ -696,36 +645,6 @@ class NetworkNode(Node):
		cam_type = 'isis'
		return footprint_latlon, cam_type

		def footprint_from_csm(self):
		boundary = generate_boundary(self.geodata.raster_size[::-1]) # yx to xy
		footprint_latlon = generate_latlon_footprint(self.camera,
		boundary,
		dem=parent.dem)
		footprint_latlon.FlattenTo2D()
		cam_type = 'csm'
		return footprint_latlon, cam_type

		def generate_footprint(self, exist_check=True):
		footprint_latlon = cam_type = None

		if exist_check:
		footprint_latlon, cam_type = self.footprint_from_database()

		# not in database, create footprint
		if footprint_latlon is None and cam_type is None:
		if utils.find_in_dict(self.geodata.metadata, "Polygon"):
		# get ISIS footprint if possible
		t1 = time.time()
		footprint_latlon, cam_type = self.footprint_from_isis()
		t2 = time.time()
		else:
		# Get CSM footprint
		t1 = time.time()
		footprint_latlon, cam_type = self.footprint_from_csm()
		t2 = time.time()

		return footprint_latlon, cam_type

		@property
		def footprint(self):
		if not hasattr(self, '_footprint'):

autocnet/io/db/model.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -565,7 +565,7 @@ class Points(Base, BaseMixin):
		apriori=point_geom,
		adjusted=point_geom,
		pointtype=point_type, # Would be 3 or 4 for ground
		cam_type='isis',
		cam_type=reference_node['cam_type'],
		reference_index=0)

		# Create the measure for the reference image and add it to the point