From 8e4a0856c62d978f70db27f6b47ba20428a18928 Mon Sep 17 00:00:00 2001
From: jlaura <jlaura@usgs.gov>
Date: Thu, 19 Apr 2018 10:27:25 -0700
Subject: [PATCH] Updates Indexing Issues (#34)
* Makes gdal an optional dependency
* Refactors all bae I/O into a single namespace.
* typos
* Fixes the gdal dependency test
* Adds tests for the JSON
* Tests fail without test data
* Updates for comments from @thareUSGS
* Adds ISIS3 V2 ControlNetwork Reader
* Adds hcube mixin object
* Updates to support tif M3, and fixes indexing issues
---
plio/io/hcube.py | 19 ++++++++++++-------
plio/io/io_moon_minerology_mapper.py | 11 +++++++++--
plio/utils/indexing.py | 11 +++++++----
3 files changed, 28 insertions(+), 13 deletions(-)
diff --git a/plio/io/hcube.py b/plio/io/hcube.py
index 9b41a71..0d1ed9f 100644
--- a/plio/io/hcube.py
+++ b/plio/io/hcube.py
@@ -1,6 +1,9 @@
import numpy as np
import gdal
+from ..utils.indexing import _LocIndexer, _iLocIndexer
+
+
class HCube(object):
"""
A Mixin class for use with the io_gdal.GeoDataset class
@@ -27,7 +30,6 @@ class HCube(object):
@tolerance.setter
def tolerance(self, val):
- wv = self.wavelengths
if isinstance(val, int):
self._tolerance = val
self._reindex()
@@ -39,7 +41,8 @@ class HCube(object):
self._wavelengths = np.round(self._original_wavelengths, decimals=self.tolerance)
def __getitem__(self, key):
- return _iLocIndexer(self)
+ i = _iLocIndexer(self)
+ return i[key]
@property
def loc(self):
@@ -54,7 +57,6 @@ class HCube(object):
y = key[1]
x = key[2]
-
if isinstance(x, slice):
xstart = ifnone(x.start,0)
xstop = ifnone(x.stop,self.raster_size[0])
@@ -68,8 +70,11 @@ class HCube(object):
else:
raise TypeError("Loc style access elements must be slices, e.g., [:] or [10:100]")
- pixels = (xstart, ystart, xstop, ystop)
- arrs = []
- for b in key[0]:
- arrs.append(self.read_array(band=int(b+1), pixels=pixels))
+ pixels = (xstart, ystart, xstep, ystep)
+ if isinstance(key[0], (int, np.integer)):
+ return self.read_array(band=int(key[0]+1), pixels=pixels)
+ 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
diff --git a/plio/io/io_moon_minerology_mapper.py b/plio/io/io_moon_minerology_mapper.py
index 3093c2c..c28a7dc 100644
--- a/plio/io/io_moon_minerology_mapper.py
+++ b/plio/io/io_moon_minerology_mapper.py
@@ -14,8 +14,15 @@ class M3(GeoDataset, HCube):
if not hasattr(self, '_wavelengths'):
try:
info = gdal.Info(self.file_name, format='json')
- wavelengths = [float(j) for i, j in sorted(info['metadata'][''].items(),
- key=lambda x: float(x[0].split('_')[-1]))]
+ if 'Resize' in info['metadata']['']['Band_1']:
+ wavelengths = [float(j.split(' ')[-1].replace('(','').replace(')', '')) for\
+ i,j in sorted(info['metadata'][''].items(),
+ key=lambda x: float(x[0].split('_')[-1]))]
+ # This is a geotiff translated from the PDS IMG
+ else:
+ # This is a PDS IMG
+ wavelengths = [float(j) for i, j in sorted(info['metadata'][''].items(),
+ key=lambda x: float(x[0].split('_')[-1]))]
self._original_wavelengths = wavelengths
self._wavelengths = np.round(wavelengths, self.tolerance)
except:
diff --git a/plio/utils/indexing.py b/plio/utils/indexing.py
index 50fa17a..9dc7c93 100644
--- a/plio/utils/indexing.py
+++ b/plio/utils/indexing.py
@@ -35,7 +35,7 @@ def expanded_indexer(key, ndim):
class _LocIndexer(object):
def __init__(self, data_array):
self.data_array = data_array
-
+
def __getitem__(self, key):
# expand the indexer so we can handle Ellipsis
key = expanded_indexer(key, 3)
@@ -43,8 +43,11 @@ class _LocIndexer(object):
ifnone = lambda a, b: b if a is None else a
if isinstance(sl, slice):
sl = list(range(ifnone(sl.start, 0), self.data_array.nbands, ifnone(sl.step, 1)))
-
- idx = [self._get_idx(s) for s in sl]
+
+ if isinstance(sl, (int, float)):
+ idx = self._get_idx(sl)
+ else:
+ idx = [self._get_idx(s) for s in sl]
key = (idx, key[1], key[2])
return self.data_array._read(key)
@@ -52,7 +55,7 @@ class _LocIndexer(object):
vals = np.abs(self.data_array.wavelengths-value)
minidx = np.argmin(vals)
if vals[minidx] >= tolerance:
- warning.warn("Absolute difference between requested value and found values is {}".format(vals[minidx]))
+ warnings.warn("Absolute difference between requested value and found values is {}".format(vals[minidx]))
return minidx
class _iLocIndexer(object):
--
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