diff --git a/environment.yml b/environment.yml
index f51c74af88f78d0d7468b559581c862cc1172c07..e269724b9a77c1a9f4532b798dbf80dcc28fdb83 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,4 +10,4 @@ dependencies:
- pandas
- sqlalchemy
- pyyaml
- - networkx
+ - networkx
diff --git a/plio/examples/loggers/logging.json b/plio/examples/loggers/logging.json
index b5661386806ac33386e2bcceabe880e3dba03d2f..9492a40719086be7a5ae41e64af359fc8a21eb26 100644
--- a/plio/examples/loggers/logging.json
+++ b/plio/examples/loggers/logging.json
@@ -1,39 +1,39 @@
{
"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"
diff --git a/plio/io/io_controlnetwork.py b/plio/io/io_controlnetwork.py
index b120bd6a89923e3a09e710c430cf6f280605689c..280b9ff63f4fab31923777b52c54ee8450abd0f3 100644
--- a/plio/io/io_controlnetwork.py
+++ b/plio/io/io_controlnetwork.py
@@ -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)
diff --git a/plio/io/io_gdal.py b/plio/io/io_gdal.py
index 372b118f3da56a8324d2f23f13077a4df7955360..51834c6dc4f8f587c47abde8ae944da22863b499 100644
--- a/plio/io/io_gdal.py
+++ b/plio/io/io_gdal.py
@@ -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)
diff --git a/plio/io/io_krc.py b/plio/io/io_krc.py
index 978ae8e8ddbcc384971579e691121408ee753a24..3831b3f7615c94fdcc6722a68ec318b006ca5043 100644
--- a/plio/io/io_krc.py
+++ b/plio/io/io_krc.py
@@ -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])
diff --git a/plio/io/tests/test_io_controlnetwork.py b/plio/io/tests/test_io_controlnetwork.py
index 0e38111e3302f2917ee9076716fd5683544719cf..6efe026cdf20cd15afb347f74de1043d440200fc 100644
--- a/plio/io/tests/test_io_controlnetwork.py
+++ b/plio/io/tests/test_io_controlnetwork.py
@@ -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
diff --git a/setup.py b/setup.py
index ca82517062677bfeed26e5018d5a51770cf169a7..9a3ee825e049d9fd13ec70ab06674c764e7ed2b8 100644
--- a/setup.py
+++ b/setup.py
@@ -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",