Updates to plio to support generic isis cnet writing. (d1b82e3b) · Commits · aflab / astrogeology / Plio

data/data.db

+2 KiB (55 KiB)

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plio/init.py

+8 −0

Original line number	Diff line number	Diff line
		@@ -4,8 +4,16 @@ import plio
		__version__ = "0.1.0"



		def get_data(filename):
		packagdir = plio.__path__[0]
		dirname = os.path.join(os.path.dirname(packagdir), 'data')
		fullname = os.path.join(dirname, filename)
		return fullname

		# Submodule imports
		from . import sqlalchemy_json
		from . import isis_serial_number
		from . import io_controlnetwork
		from . import io_gdal
		from . import utils

plio/io_controlnetwork.py

+51 −14

Original line number	Diff line number	Diff line
		@@ -2,6 +2,13 @@ from time import gmtime, strftime
		import pvl

		from plio import ControlNetFileV0002_pb2 as cnf
		from plio.utils import xstr

		try:
		import spiceypy
		spicey_available = True
		except:
		spicey_available = False

		VERSION = 2
		HEADERSTARTBYTE = 65536
		@@ -30,7 +37,8 @@ def to_isis(path, obj, mode='w', version=VERSION,
		headerstartbyte=HEADERSTARTBYTE,
		networkid='None', targetname='None',
		description='None', username=DEFAULTUSERNAME,
		creation_date=None, modified_date=None):
		creation_date=None, modified_date=None,
		pointid_prefix=None, pointid_suffix=None):
		"""
		Parameters
		----------
		@@ -70,6 +78,14 @@ def to_isis(path, obj, mode='w', version=VERSION,

		username : str
		The name of the user / application that created the control network

		pointid_prefix : str
		Prefix to be added to the pointid. If the prefix is 'foo_', pointids
		will be in the form 'foo_1, foo_2, ..., foo_n'

		pointid_suffix : str
		Suffix to tbe added to the point id. If the suffix is '_bar', pointids
		will be in the form '1_bar, 2_bar, ..., n_bar'.
		"""

		with IsisStore(path, mode) as store:
		@@ -77,8 +93,7 @@ def to_isis(path, obj, mode='w', version=VERSION,
		creation_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())
		if not modified_date:
		modified_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())

		point_messages, point_sizes = store.create_points(obj)
		point_messages, point_sizes = store.create_points(obj, pointid_prefix, pointid_suffix)
		points_bytes = sum(point_sizes)
		buffer_header, buffer_header_size = store.create_buffer_header(networkid,
		targetname,
		@@ -87,7 +102,6 @@ def to_isis(path, obj, mode='w', version=VERSION,
		point_sizes,
		creation_date,
		modified_date)
		print(point_sizes)
		# Write the buffer header
		store.write(buffer_header, HEADERSTARTBYTE)
		# Then write the points, so we know where to start writing, + 1 to avoid overwrite
		@@ -95,7 +109,7 @@ def to_isis(path, obj, mode='w', version=VERSION,
		for i, point in enumerate(point_messages):
		store.write(point, point_start_offset)
		point_start_offset += point_sizes[i]

		print(point_start_offset)
		header = store.create_pvl_header(version, headerstartbyte, networkid,
		targetname, description, username,
		buffer_header_size, points_bytes,
		@@ -119,6 +133,16 @@ class IsisStore(object):
		self.pointid = 0
		self.nmeasures = 0

		# Conversion from buffer types to Python types
		bt = {1: float,
		5: int,
		8: bool,
		9: str,
		11: None,
		14: None}
		self.point_attrs = [(i.name, bt[i.type]) for i in cnf._CONTROLPOINTFILEENTRYV0002.fields]
		self.measure_attrs = [(i.name, bt[i.type]) for i in cnf._CONTROLPOINTFILEENTRYV0002_MEASURE.fields]

		self._path = path
		if not mode:
		mode = 'a' # pragma: no cover
		@@ -146,7 +170,7 @@ class IsisStore(object):
		self._handle.seek(offset)
		self._handle.write(data)

		def create_points(self, obj):
		def create_points(self, obj, pointid_prefix, pointid_suffix):
		"""
		Step through a control network (C) and return protocol buffer point objects

		@@ -165,13 +189,27 @@ class IsisStore(object):
		point_sizes : list
		of integer point sizes
		"""
		def _set_pid(pointid):
		return '{}{}{}'.format(xstr(pointid_prefix),
		pointid,
		xstr(pointid_suffix))

		# TODO: Rewrite using apply syntax for performance
		point_sizes = []
		point_messages = []
		for df in obj:
		for i, g in df.groupby('point_id'):
		point_spec = cnf.ControlPointFileEntryV0002()
		point_spec.id = str(self.pointid)
		point_spec.id = _set_pid(self.pointid)

		for attr, attrtype in self.point_attrs:
		if attr in g.columns:
		# As per protobuf docs for assigning to a repeated field.
		if attr == 'aprioriCovar':
		arr = g.iloc[0]['aprioriCovar']
		point_spec.aprioriCovar.extend(arr.ravel().tolist())
		else:
		setattr(point_spec, attr, attrtype(g.iloc[0][attr]))
		point_spec.type = int(g.point_type.iat[0])

		# The reference index should always be the image with the lowest index
		@@ -182,13 +220,11 @@ class IsisStore(object):

		for node_id, m in g.iterrows():
		measure_spec = point_spec.Measure()
		try:
		measure_spec.serialnumber = m.serialnumber
		except:
		measure_spec.serialnumber = str(m.serialnumber)
		measure_spec.type = m.measure_type
		measure_spec.sample = float(m.x)
		measure_spec.line = float(m.y)
		# For all of the attributes, set if they are an dict accessible attr of the obj.
		for attr, attrtype in self.measure_attrs:
		if attr in g.columns:
		setattr(measure_spec, attr, attrtype(m[attr]))
		measure_spec.type = int(m.measure_type)

		measure_iterable.append(measure_spec)
		self.nmeasures += 1
		@@ -234,6 +270,7 @@ class IsisStore(object):
		header_message_size : int
		The size of the serialized header, in bytes
		"""
		print('NID', networkid)
		raw_header_message = cnf.ControlNetFileHeaderV0002()
		raw_header_message.created = creation_date
		raw_header_message.lastModified = modified_date

plio/io_db.py

+1 −0

Original line number	Diff line number	Diff line
		import plio
		from sqlalchemy import Column, Integer, String, create_engine, orm
		from sqlalchemy.ext import declarative

plio/isis_serial_number.py

+6 −2

Original line number	Diff line number	Diff line
		import warnings
		import plio
		from plio import get_data
		from plio.io_db import Translations, StringToMission, setup_db_session
		@@ -34,7 +35,6 @@ def get_isis_translation(label):

		# Grab the spacecraft name and run it through the ISIS lookup
		spacecraft_name = find_in_dict(label, 'SpacecraftName')

		for row in plio.data_session.query(StringToMission).filter(StringToMission.key==spacecraft_name):
		spacecraft_name = row.value.lower()

		@@ -44,6 +44,7 @@ def get_isis_translation(label):
		except:
		instrumentid = None

		translation = None
		# Grab the translation PVL object using the lookup
		for row in plio.data_session.query(Translations).filter(Translations.mission==spacecraft_name,
		Translations.instrument==instrumentid):
		@@ -73,6 +74,10 @@ def generate_serial_number(label):
		label = pvl.load(label, cls=SerialNumberDecoder)
		# Get the translation information
		translation = get_isis_translation(label)
		if not translation:
		warnings.warn('Unable to load an appropriate image translation.')
		return

		serial_number = []

		# Sort the keys to ensure proper iteration order
		@@ -83,7 +88,6 @@ def generate_serial_number(label):
		search_key = group['InputKey']
		search_position = group['InputPosition']
		search_translation = {group['Translation'][1]:group['Translation'][0]}

		sub_group = find_nested_in_dict(label, search_position)
		serial_entry = sub_group[search_key]
		if serial_entry in search_translation.keys():