Merge pull request #6 from jlaura/master

All tests passing locally

plio/examples/loggers/logging.json

@@ -20,7 +20,7 @@
     "info_file_handler": {
       "formatter": "simple",
       "backupCount": 10,
-      "level": "INFO", 
+      "level": "DEBUG", 
       "encoding": "utf8",
       "class": "logging.handlers.RotatingFileHandler",
       "maxBytes": 10485760,

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)

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)
 

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()

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

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",