diff --git a/.travis.yml b/.travis.yml
index f1d26c72f7c5d90006194c0a0409ab86638aa2f1..d38a9bda8959d1aae91654d7b3dca4b2e8c93bb1 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -4,12 +4,6 @@ branches:
only:
- master
-env:
- global:
- - BINSTAR_USER: jlaura
- matrix:
- - PYTHON_VERSION: 3.5
-
os:
- linux
- osx
@@ -43,7 +37,6 @@ install:
# Install not using env because build needs to be in root env
- conda config --add channels conda-forge
- conda config --add channels jlaura
- - conda install python=$PYTHON_VERSION
- conda install -c conda-forge gdal h5py
- conda install pandas sqlalchemy pyyaml networkx affine
- conda install -c jlaura pvl protobuf
@@ -51,22 +44,13 @@ install:
# Development installation
- conda install pytest pytest-cov sh anaconda-client
- # Straight from the menpo team
- - if [["$TRAVIS_OS_NAME" == "osx"]]; then
- curl -o condaci.py https://raw.githubusercontent.com/menpo/condaci/v0.4.8/condaci.py;
- else
- wget https://raw.githubusercontent.com/menpo/condaci/v0.4.8/condaci.py -O condaci.py;
- fi
- - python condaci.py setup
-
script:
- - pytest --cov=plio
- # After test success, package and upload to Anaconda
- - ~/miniconda/bin/python condaci.py build ./conda
+ - pytest --cov=plio
after_success:
- coveralls
+ - conda install conda-build && conda install anaconda-client && conda config --set anaconda_upload yes && conda build --token $CONDA_UPLOAD_TOKEN recipe
notifications:
webhooks:
diff --git a/plio/data/data.db b/plio/data/data.db
index e2a35c8a1100073db89ee98fe564d573b90f3a2e..c1ac0e7c5802a4222a93a6ab400dc3dbc454aeb0 100644
Binary files a/plio/data/data.db and b/plio/data/data.db differ
diff --git a/plio/geofuncs/geofuncs.py b/plio/geofuncs/geofuncs.py
index 9db0f00da7fe4c683d3d420ed72f3d2a794a30b5..bc7b0f05ff0d8ff01a79199e129847b29bf726d5 100644
--- a/plio/geofuncs/geofuncs.py
+++ b/plio/geofuncs/geofuncs.py
@@ -1,4 +1,5 @@
import json
+import warnings
import numpy as np
def intersection_to_pixels(inverse_affine, ul, ur, lr, ll):
@@ -27,6 +28,10 @@ def intersection_to_pixels(inverse_affine, ul, ur, lr, ll):
miny = np.inf
maxy = -np.inf
+ if inverse_affine == None:
+ warnings.warn('Inverse affine transformation not available.')
+ return None
+
for c in [ul, ur, lr, ll]:
px, py = map(int, inverse_affine * (c[0], c[1]))
@@ -51,7 +56,6 @@ def compute_overlap(geodata_a, geodata_b):
p1 = geodata_a.footprint
p2 = geodata_b.footprint
intersection = json.loads(p1.Intersection(p2).ExportToJson())['coordinates'][0]
-
ul, ur, lr, ll = find_four_corners(intersection)
a_intersection = intersection_to_pixels(geodata_a.inverse_affine, ul, ur, lr, ll)
@@ -120,7 +124,6 @@ def find_four_corners(coords, threshold=120):
plio.geofuncs.geofuncs.find_corners
"""
corners = find_corners(coords, threshold)
-
corners.sort(key = lambda x:x[1])
upper = corners[2:]
lower = corners[:2]
diff --git a/plio/io/io_controlnetwork.py b/plio/io/io_controlnetwork.py
index 6efe11af8f83e466c244b99a488add159dada5ab..b41ced34d512ff326b7edcb0062ed4868fca8969 100644
--- a/plio/io/io_controlnetwork.py
+++ b/plio/io/io_controlnetwork.py
@@ -9,7 +9,6 @@ VERSION = 2
HEADERSTARTBYTE = 65536
DEFAULTUSERNAME = 'None'
-
def write_filelist(lst, path="fromlist.lis"):
"""
Writes a filelist to a file so it can be used in ISIS3.
@@ -86,7 +85,6 @@ def to_isis(path, obj, serials, mode='wb', version=VERSION,
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:
if not creation_date:
creation_date = strftime("%Y-%m-%d %H:%M:%S", gmtime())
@@ -128,8 +126,8 @@ class IsisStore(object):
"""
def __init__(self, path, mode=None, **kwargs):
- self.pointid = 0
self.nmeasures = 0
+ self.npoints = 0
# Conversion from buffer types to Python types
bt = {1: float,
@@ -196,9 +194,15 @@ class IsisStore(object):
point_sizes = []
point_messages = []
for i, g in df.groupby('point_id'):
+
+ # Get the point specification from the protobuf
point_spec = cnf.ControlPointFileEntryV0002()
- point_spec.id = _set_pid(i)
+ # Set the ID and then loop over all of the attributes that the
+ # point has and check for corresponding columns in the group and
+ # set with the correct type
+ #point_spec.id = _set_pid(i)
+ point_spec.id = _set_pid(i)
for attr, attrtype in self.point_attrs:
if attr in g.columns:
# As per protobuf docs for assigning to a repeated field.
@@ -217,23 +221,25 @@ class IsisStore(object):
for node_id, m in g.iterrows():
measure_spec = point_spec.Measure()
- measure_spec.serialnumber = serials[m.image_index]
# 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.serialnumber = serials[m.image_index]
measure_spec.sample = m.x
measure_spec.line = m.y
measure_spec.type = 2
measure_iterable.append(measure_spec)
self.nmeasures += 1
- point_spec.measures.extend(measure_iterable)
+ self.npoints += 1
+
+ point_spec.measures.extend(measure_iterable)
point_message = point_spec.SerializeToString()
point_sizes.append(point_spec.ByteSize())
point_messages.append(point_message)
- self.pointid += 1
return point_messages, point_sizes
def create_buffer_header(self, networkid, targetname,
@@ -342,7 +348,7 @@ class IsisStore(object):
('Created', creation_date),
('LastModified', modified_date),
('Description', description),
- ('NumberOfPoints', self.pointid),
+ ('NumberOfPoints', self.npoints),
('NumberOfMeasures', self.nmeasures),
('Version', version)
])
diff --git a/plio/io/io_gdal.py b/plio/io/io_gdal.py
index 44a54913251eb6b41579d4ae0c63ed1221cc9584..5522171d467998859e1854826f59e34ef72beb13 100644
--- a/plio/io/io_gdal.py
+++ b/plio/io/io_gdal.py
@@ -200,6 +200,9 @@ class GeoDataset(object):
@property
def inverse_affine(self):
+ # If det(A) == 0, the transformation is degenerate
+ if self.forward_affine.is_degenerate:
+ return None
self._ia = ~self.forward_affine
return self._ia
@@ -475,10 +478,9 @@ class GeoDataset(object):
# Check that the read start is not outside of the image
xstart, ystart, xcount, ycount = pixels
xmax, ymax = map(int, self.xy_extent[1])
-
# If the image is south up, flip the roi
if self.north_up == False:
- ystart = ymax - ystart - ycount
+ ystart = ymax - (ystart + ycount)
if xstart < 0:
xstart = 0
@@ -488,10 +490,11 @@ class GeoDataset(object):
if xstart + xcount > xmax:
xcount = xmax - xstart
- if ystart + ycount > ymax:
+ if ystart + ycount > ymax:
ycount = ymax - ystart
-
array = band.ReadAsArray(xstart, ystart, xcount, ycount).astype(dtype)
+ #if self.north_up == False:
+ # array = np.flipud(array)
return array
def compute_overlap(self, geodata, **kwargs):
diff --git a/plio/io/isis_serial_number.py b/plio/io/isis_serial_number.py
index 92ea721c4485b2f71c18d3ffd566e98946a36609..0c187abff1a0ea0fbe70fe3781dca7fc092f035f 100644
--- a/plio/io/isis_serial_number.py
+++ b/plio/io/isis_serial_number.py
@@ -38,7 +38,6 @@ def get_isis_translation(label):
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()
-
# Try and pull an instrument identifier
try:
instrumentid = find_in_dict(label, 'InstrumentId').capitalize()
@@ -51,7 +50,6 @@ def get_isis_translation(label):
Translations.instrument==instrumentid):
# Convert the JSON back to a PVL object
translation = PVLModule(row.translation)
-
return translation
@@ -75,6 +73,7 @@ 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
@@ -91,11 +90,11 @@ def generate_serial_number(label):
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():
serial_entry = search_translation[serial_entry]
elif '*' in search_translation.keys() and search_translation['*'] != '*':
serial_entry = search_translation['*']
-
serial_number.append(serial_entry)
except:
pass
diff --git a/conda/meta.yaml b/recipe/meta.yaml
similarity index 100%
rename from conda/meta.yaml
rename to recipe/meta.yaml