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Commit 2cce57fe authored by jlaura's avatar jlaura Committed by GitHub
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Merge pull request #6 from jlaura/master 

All tests passing locally
parents eb46fd9e affbc873
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environment.yml
+ 1
− 1
View file @ 2cce57fe
......@@ -10,4 +10,4 @@ dependencies:
- pandas
- sqlalchemy
- pyyaml
- networkx
- networkx
plio/examples/loggers/logging.json
+ 19
− 19
View file @ 2cce57fe
{
"loggers": {
"my_module": {
"level": "DEBUG",
"propagate": false,
"level": "DEBUG",
"propagate": false,
"handlers": [
"console"
]
}
},
"version": 1,
"disable_existing_loggers": false,
},
"version": 1,
"disable_existing_loggers": false,
"handlers": {
"console": {
"formatter": "simple",
"class": "logging.StreamHandler",
"stream": "ext://sys.stdout",
"formatter": "simple",
"class": "logging.StreamHandler",
"stream": "ext://sys.stdout",
"level": "DEBUG"
},
},
"info_file_handler": {
"formatter": "simple",
"backupCount": 10,
"level": "INFO",
"encoding": "utf8",
"class": "logging.handlers.RotatingFileHandler",
"maxBytes": 10485760,
"formatter": "simple",
"backupCount": 10,
"level": "DEBUG",
"encoding": "utf8",
"class": "logging.handlers.RotatingFileHandler",
"maxBytes": 10485760,
"filename": "info.log"
}
},
},
"root": {
"level": "DEBUG",
"level": "DEBUG",
"handlers": [
"console",
"console",
"info_file_handler"
]
},
},
"formatters": {
"simple": {
"format": "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
......
plio/io/io_controlnetwork.py
+ 21
− 17
View file @ 2cce57fe
......@@ -145,7 +145,7 @@ class IsisStore(object):
self._path = path
if not mode:
mode = 'a' # pragma: no cover
mode = 'wb' # pragma: no cover
self._mode = mode
self._handle = None
......@@ -170,13 +170,13 @@ class IsisStore(object):
self._handle.seek(offset)
self._handle.write(data)
def create_points(self, obj, pointid_prefix, pointid_suffix):
def create_points(self, graphs, pointid_prefix, pointid_suffix):
"""
Step through a control network (C) and return protocol buffer point objects
Parameters
----------
obj : list
graphs : list
of iterable objects (dataframes) with the appropriate
attributes: point_id, point_type, serial, measure_type, x, y required.
The entries in the list must support grouping by the point_id attribute.
......@@ -197,20 +197,21 @@ class IsisStore(object):
# TODO: Rewrite using apply syntax for performance
point_sizes = []
point_messages = []
for df in obj:
for i, g in df.groupby('point_id'):
for graph in graphs:
for i, control_point_id in enumerate(graph.point_nodes):
control_point = graph.node[control_point_id]
point_spec = cnf.ControlPointFileEntryV0002()
point_spec.id = _set_pid(self.pointid)
point_spec.id = _set_pid(control_point['pointid'])
for attr, attrtype in self.point_attrs:
if attr in g.columns:
if attr in control_point.keys():
# As per protobuf docs for assigning to a repeated field.
if attr == 'aprioriCovar':
arr = g.iloc[0]['aprioriCovar']
arr = control_point['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 third argument casts the value to the correct type
setattr(point_spec, attr, attrtype(control_point[attr]))
point_spec.type = int(control_point.get('point_type', 2))
# The reference index should always be the image with the lowest index
point_spec.referenceIndex = 0
......@@ -218,16 +219,19 @@ class IsisStore(object):
# A single extend call is cheaper than many add calls to pack points
measure_iterable = []
for node_id, m in g.iterrows():
for j, control_measure_id in graph.edges(control_point_id):
control_measure = graph.node[control_measure_id]
if control_measure['node_type'] != 'correspondence':
continue
measure_spec = point_spec.Measure()
# 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 control_measure.keys():
setattr(measure_spec, attr, attrtype(control_measure[attr]))
if attr in g.columns:
setattr(measure_spec, attr, attrtype(m[attr]))
measure_spec.type = int(m.measure_type)
measure_spec.line = m.y
measure_spec.sample = m.x
measure_spec.type = int(control_measure['measure_type'])
measure_spec.line = float(control_measure['y'])
measure_spec.sample = float(control_measure['x'])
measure_iterable.append(measure_spec)
self.nmeasures += 1
point_spec.measures.extend(measure_iterable)
......
plio/io/io_gdal.py
+ 9
− 5
View file @ 2cce57fe
......@@ -198,6 +198,12 @@ class GeoDataset(object):
self._gcs = self._srs.CloneGeogCS()
return self._srs
@property
def nbands(self):
if not getattr(self, '_nbands', None):
self._nbands = self.dataset.RasterCount
return self._nbands
@property
def geospatial_coordinate_system(self):
if not getattr(self, '_gcs', None):
......@@ -321,10 +327,8 @@ class GeoDataset(object):
@property
def coordinate_transformation(self):
if not getattr(self, '_ct', None):
print('Getting CT')
self._ct = osr.CoordinateTransformation(self.spatial_reference,
self.geospatial_coordinate_system)
print('CT', self._ct)
return self._ct
@property
......@@ -332,7 +336,6 @@ class GeoDataset(object):
if not getattr(self, '_ict', None):
self._ict = osr.CoordinateTransformation(self.geospatial_coordinate_system,
self.spatial_reference)
print(self._ict)
return self._ict
@property
......@@ -558,6 +561,7 @@ def match_rasters(match_to, match_from, destination,
GRA_Cubic, GRA_CubicSpline, GRA_Lanczos, GRA_Average,
GRA_Mode}
"""
import gdalconst # import here so Sphinx can build the docos, mocking is not working
# TODO: If a destination is not provided create an in-memory GeoDataSet object
match_to_srs = match_to.dataset.GetProjection()
......@@ -567,8 +571,8 @@ def match_rasters(match_to, match_from, destination,
match_from__srs = match_from.dataset.GetProjection()
match_from__gt = match_from.geotransform
dst = gdal.GetDriverByName('GTiff').Create(destination, width, height, match_from.RasterCount,
gdalconst.GDT_Float32)
dst = gdal.GetDriverByName('GTiff').Create(destination, width, height, 1,
gdalconst.GDT_Float64)
dst.SetGeoTransform(match_to_gt)
dst.SetProjection(match_to_srs)
......
plio/io/io_krc.py
+ 6
− 3
View file @ 2cce57fe
......@@ -364,9 +364,9 @@ class ReadBin52(object):
self.nseasons)
caseidx = np.repeat(np.arange(self.ncases), self.nseasons)
seasonidx = np.repeat(np.arange(self.nseasons), self.ncases)
flt_seasitems = seasitems.reshape(len(self.vlabels),
flt_seasitems = seasitems.reshape(len(columns),
self.ncases * self.nseasons)
self.seasons = pd.DataFrame(flt_seasitems,
self.seasons = pd.DataFrame(flt_seasitems.T,
index=[caseidx,seasonidx],
columns=columns)
self.seasons.index.names = ['Case', 'Season']
......@@ -432,6 +432,9 @@ class ReadBin52(object):
#Extract the hourly temperature data
hourly2dataframe()
# Extract the seasons
season2dataframe()
# Extract by layer data from the data cube
layeritems = self.bin52data[: , self.ndx: , : , 5: 7, : ]
latitems2dataframe()
......@@ -458,4 +461,4 @@ class ReadTds(object):
self.filename = filename
self.readbin5(headerlen)
print(self.ncases)
assert(self.ncases == self.bin52data.shape[0])
\ No newline at end of file
assert(self.ncases == self.bin52data.shape[0])
plio/io/tests/test_io_controlnetwork.py
+ 25
− 29
View file @ 2cce57fe
......@@ -3,6 +3,7 @@ import sys
import unittest
from time import strftime, gmtime
import networkx as nx
import pandas as pd
import pvl
......@@ -23,38 +24,33 @@ class TestWriteIsisControlNetwork(unittest.TestCase):
cls.serials = ['APOLLO15/METRIC/{}'.format(i) for i in serial_times.values()]
columns = ['point_id', 'point_type', 'serialnumber', 'measure_type', 'x', 'y', 'node_id']
data = []
G = nx.Graph()
G.add_node(0, node_type='image')
G.add_node(1, node_type='image')
G.add_edge(0,1)
G.point_nodes = []
for i in range(cls.npts):
data.append((i, 2, cls.serials[0], 2, 0, 0, 0))
data.append((i, 2, cls.serials[1], 2, 0, 0, 1))
i += 1
G.point_nodes.append(i*100)
G.add_node(i * 100, node_type='point', pointid = i * 100, subpixel=False)
G.add_edge(i*100, 0)
G.add_edge(i*100, 1)
# Add a single correspondence
G.add_node(i * 1000, x=i*.5, y=i*.5, id=i*1000, node_type='correspondence', measure_type=2, serialnumber=cls.serials[0])
G.add_edge(i*1000, i*100)
# Add a second correspondence
G.add_node(i * 2000, x=i*.5, y=i*.5, id=i*2000, node_type='correspondence', measure_type=2, serialnumber=cls.serials[1])
G.add_edge(i * 2000, i*100)
dfs = [pd.DataFrame(data, columns=columns)]
cls.creation_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())
cls.modified_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())
io_controlnetwork.to_isis('test.net', dfs, mode='wb', targetname='Moon')
io_controlnetwork.to_isis('test.net', [G], mode='wb', targetname='Moon')
cls.header_message_size = 78
cls.point_start_byte = 65609 # 66949
cls.point_start_byte = 65614 # 66949
def test_create_buffer_header(self):
self.npts = 5
serial_times = {295: '1971-07-31T01:24:11.754',
296: '1971-07-31T01:24:36.970'}
self.serials = ['APOLLO15/METRIC/{}'.format(i) for i in serial_times.values()]
columns = ['point_id', 'point_type', 'serialnumber', 'measure_type', 'x', 'y', 'node_id']
data = []
for i in range(self.npts):
data.append((i, 2, self.serials[0], 2, 0, 0, 0))
data.append((i, 2, self.serials[1], 2, 0, 0, 1))
dfs = [pd.DataFrame(data, columns=columns)]
self.creation_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())
self.modified_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())
io_controlnetwork.to_isis('test.net', dfs, mode='wb', targetname='Moon')
self.header_message_size = 78
self.point_start_byte = 66104 # 66949
......@@ -73,17 +69,16 @@ class TestWriteIsisControlNetwork(unittest.TestCase):
self.assertEqual('None', header_protocol.description)
self.assertEqual(self.modified_date, header_protocol.lastModified)
#Repeating
self.assertEqual([99] * self.npts, header_protocol.pointMessageSizes)
self.assertEqual([137] * self.npts, header_protocol.pointMessageSizes)
def test_create_point(self):
with open('test.net', 'rb') as f:
f.seek(self.point_start_byte)
for i, length in enumerate([99] * self.npts):
for i, length in enumerate(5*[137]):
point_protocol = cnf.ControlPointFileEntryV0002()
raw_point = f.read(length)
point_protocol.ParseFromString(raw_point)
self.assertEqual(str(i), point_protocol.id)
self.assertEqual(str((i + 1) * 100), point_protocol.id)
self.assertEqual(2, point_protocol.type)
for m in point_protocol.measures:
self.assertTrue(m.serialnumber in self.serials)
......@@ -99,11 +94,12 @@ class TestWriteIsisControlNetwork(unittest.TestCase):
self.assertEqual(10, mpoints)
points_bytes = find_in_dict(pvl_header, 'PointsBytes')
self.assertEqual(495, points_bytes)
self.assertEqual(685, points_bytes)
points_start_byte = find_in_dict(pvl_header, 'PointsStartByte')
self.assertEqual(self.point_start_byte, points_start_byte)
@classmethod
def tearDownClass(cls):
os.remove('test.net')
#os.remove('test.net')
pass
setup.py
+ 1
− 2
View file @ 2cce57fe
......@@ -42,11 +42,10 @@ def setup_package():
'pvl',
'protobuf==3.0.0b2',
'h5py',
'icu',
'pandas',
'sqlalchemy',
'pyyaml',
'certifi'],
'networkx'],
classifiers=[
"Development Status :: 3 - Alpha",
"Topic :: Utilities",
......
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