From 160c1ae05ed650de443a6ec5fb0f52fa95643997 Mon Sep 17 00:00:00 2001
From: acpaquette <acp263@nau.edu>
Date: Fri, 12 Oct 2018 11:45:01 -0700
Subject: [PATCH] Small changes (#81)
* Small updates to get the scripts working.
* Fixed pradius calculations, and made some small changes.
* Removed coord transforms and made body_fix func more generic.
* Updated reproj doc string.
* General refactor to socet scripts and clean up. Simplfied input for both scripts.
* Updated conf to use conda prefix
* Fixed up __getattr__ func
* Corrected attribute error text
* Uploaded notebooks for remote access
* Updated notebooks with complete footprint function
* More or less final notebook
* Forgot to tab this in under the first except block
* Updated version.
* Removed unnecessary notebooks
* Removed previously removed module
* Removed old import
* Updates travis to use environment.yml
* Fixes issue indexing on the hcube
---
docs/conf.py | 3 +-
plio/io/hcube.py | 21 ++++++++------
plio/io/io_crism.py | 33 ++++++++++++++++++++--
plio/io/io_gdal.py | 41 ++++++++++++++++------------
plio/io/io_moon_minerology_mapper.py | 14 ++++++----
recipe/meta.yaml | 1 +
6 files changed, 77 insertions(+), 36 deletions(-)
diff --git a/docs/conf.py b/docs/conf.py
index 7ed992f..af2d4db 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!$CONDA_PREFIX/bin/python
# -*- coding: utf-8 -*-
#
# autocnet documentation build configuration file, created by
@@ -17,7 +17,6 @@ import sys
import os
from unittest.mock import MagicMock
-
autodoc_mock_imports = ['proj4', 'gdal', 'osr','ogr', 'osgeo', 'osgeo.gdal',
'osgeo.gdalconst']
diff --git a/plio/io/hcube.py b/plio/io/hcube.py
index 0d1ed9f..5c50699 100644
--- a/plio/io/hcube.py
+++ b/plio/io/hcube.py
@@ -8,7 +8,7 @@ class HCube(object):
"""
A Mixin class for use with the io_gdal.GeoDataset class
to optionally add support for spectral labels, label
- based indexing, and lazy loading for reads.
+ based indexing, and lazy loading for reads.
"""
@property
@@ -23,11 +23,11 @@ class HCube(object):
except:
self._wavelengths = []
return self._wavelengths
-
+
@property
def tolerance(self):
return getattr(self, '_tolerance', 2)
-
+
@tolerance.setter
def tolerance(self, val):
if isinstance(val, int):
@@ -43,15 +43,15 @@ class HCube(object):
def __getitem__(self, key):
i = _iLocIndexer(self)
return i[key]
-
+
@property
def loc(self):
return _LocIndexer(self)
-
+
@property
def iloc(self):
return _iLocIndexer(self)
-
+
def _read(self, key):
ifnone = lambda a, b: b if a is None else a
@@ -69,12 +69,17 @@ class HCube(object):
ystep = ystop - ystart
else:
raise TypeError("Loc style access elements must be slices, e.g., [:] or [10:100]")
-
+
pixels = (xstart, ystart, xstep, ystep)
if isinstance(key[0], (int, np.integer)):
return self.read_array(band=int(key[0]+1), pixels=pixels)
+
+ elif isinstance(key[0], slice):
+ # Given some slice iterate over the bands and get the bands and pixel space requested
+ return [self.read_array(i, pixels = pixels) for i in list(range(1, self.nbands + 1))[key[0]]]
+
else:
arrs = []
for b in key[0]:
arrs.append(self.read_array(band=int(b+1), pixels=pixels))
- return np.stack(arrs)
\ No newline at end of file
+ return np.stack(arrs)
diff --git a/plio/io/io_crism.py b/plio/io/io_crism.py
index 415ec47..a65657f 100644
--- a/plio/io/io_crism.py
+++ b/plio/io/io_crism.py
@@ -2,13 +2,42 @@ import os
import numpy as np
from .io_gdal import GeoDataset
from .hcube import HCube
+
+try:
+ from libpysat.derived import crism
+ from libpysat.derived.utils import get_derived_funcs
+ libpysat_enabled = True
+except:
+ print('No libpysat module. Unable to attach derived product functions')
+ libpysat_enabled = False
+
import gdal
class Crism(GeoDataset, HCube):
"""
- An M3 specific reader with the spectral mixin.
+ An Crism specific reader with the spectral mixin.
"""
+ def __init__(self, file_name):
+
+ GeoDataset.__init__(self, file_name)
+ HCube.__init__(self)
+
+ self.derived_funcs = {}
+
+ if libpysat_enabled:
+ self.derived_funcs = get_derived_funcs(crism)
+
+ def __getattr__(self, name):
+ try:
+ func = self.derived_funcs[name]
+
+ setattr(self, name, func.__get__(self))
+ return getattr(self, name)
+
+ except KeyError as keyerr:
+ raise AttributeError("'Crism' object has no attribute '{}'".format(name)) from None
+
@property
def wavelengths(self):
if not hasattr(self, '_wavelengths'):
@@ -29,4 +58,4 @@ def open(input_data):
input_data = os.path.splitext(input_data)[:-1] + '.img'
ds = Crism(input_data)
- return ds
\ No newline at end of file
+ return ds
diff --git a/plio/io/io_gdal.py b/plio/io/io_gdal.py
index a890015..49f1210 100644
--- a/plio/io/io_gdal.py
+++ b/plio/io/io_gdal.py
@@ -269,6 +269,7 @@ class GeoDataset(object):
@property
def footprint(self):
if not hasattr(self, '_footprint'):
+ # Try to get the footprint from the image
try:
polygon_pvl = find_in_dict(self.metadata, 'Polygon')
start_polygon_byte = find_in_dict(polygon_pvl, 'StartByte')
@@ -280,28 +281,32 @@ class GeoDataset(object):
# Sloppy unicode to string because GDAL pukes on unicode
stream = str(f.read(num_polygon_bytes))
self._footprint = ogr.CreateGeometryFromWkt(stream)
- except:
- self._footprint = None
- try:
- # Get the lat lon corners
- lat = [i[0] for i in self.latlon_corners]
- lon = [i[1] for i in self.latlon_corners]
-
- # Compute a ogr geometry for the tiff which
- # provides leverage for overlaps
- ring = ogr.Geometry(ogr.wkbLinearRing)
- for point in [*zip(lon, lat)]:
- ring.AddPoint(*point)
- ring.AddPoint(lon[0], lat[0])
-
- poly = ogr.Geometry(ogr.wkbPolygon)
- poly.AddGeometry(ring)
- poly.FlattenTo2D()
- self._footprint = poly
except:
self._footprint = None
+ # If the image does not have a footprint, try getting the image from projected
+ # coordinates
+ try:
+ # Get the lat lon corners
+ lat = [i[0] for i in self.latlon_corners]
+ lon = [i[1] for i in self.latlon_corners]
+
+ # Compute a ogr geometry for the tiff which
+ # provides leverage for overlaps
+ ring = ogr.Geometry(ogr.wkbLinearRing)
+ for point in [*zip(lon, lat)]:
+ ring.AddPoint(*point)
+ ring.AddPoint(lon[0], lat[0])
+
+ poly = ogr.Geometry(ogr.wkbPolygon)
+ poly.AddGeometry(ring)
+ poly.FlattenTo2D()
+ self._footprint = poly
+
+ except:
+ self._footprint = None
+
return self._footprint
@property
diff --git a/plio/io/io_moon_minerology_mapper.py b/plio/io/io_moon_minerology_mapper.py
index de573ac..d078f85 100644
--- a/plio/io/io_moon_minerology_mapper.py
+++ b/plio/io/io_moon_minerology_mapper.py
@@ -4,11 +4,11 @@ from .io_gdal import GeoDataset
from .hcube import HCube
try:
- from libpysat.derived import m3, crism
- from libpysat.derived.utils import add_derived_funcs
+ from libpysat.derived import m3
+ from libpysat.derived.utils import get_derived_funcs
libpysat_enabled = True
except:
- print('No libpysat module. Unable to attached derived product functions')
+ print('No libpysat module. Unable to attach derived product functions')
libpysat_enabled = False
import gdal
@@ -23,8 +23,10 @@ class M3(GeoDataset, HCube):
GeoDataset.__init__(self, file_name)
HCube.__init__(self)
+ self.derived_funcs = {}
+
if libpysat_enabled:
- self.derived_funcs = add_derived_funcs(m3)
+ self.derived_funcs = get_derived_funcs(m3)
def __getattr__(self, name):
try:
@@ -33,8 +35,8 @@ class M3(GeoDataset, HCube):
setattr(self, name, func.__get__(self))
return getattr(self, name)
- except:
- raise AttributeError()
+ except KeyError as keyerr:
+ raise AttributeError("'M3' object has no attribute '{}'".format(name)) from None
@property
def wavelengths(self):
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
index d66bd95..f9b9033 100644
--- a/recipe/meta.yaml
+++ b/recipe/meta.yaml
@@ -51,6 +51,7 @@ requirements:
- usgscam
- jinja2
+
test:
imports:
- plio
--
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