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test_hsi.py
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test_hsi.py
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#!/usr/bin/env python
"""
Test the capabilities of HSI.Cube
"""
import os,os.path,sys,re,time,commands
from nose.tools import *
import peppy.vfs as vfs
import peppy.hsi.common as HSI
import peppy.hsi.ENVI as ENVI
from cStringIO import StringIO
import numpy
def localfile(name):
path = os.path.join(os.path.dirname(__file__), name)
return path
fakeNmFile="""ENVI
description = {
fake test cube}
samples = 5
lines = 4
bands = 3
header offset = 0
file type = ENVI standard
data type = 2
reflectance scale factor = 10000.000000
interleave = BIL
sensor type = AVIRIS
byte order = %d
bbl = {
1, 1, 0, 1
}
wavelength = {
369.850, 379.690, 389.530, 399.370
}
wavelength units = nm
fwhm = {
9.610, 9.580, 9.550, 9.530 }
""" % HSI.nativeByteOrder
fakeUmFile="""ENVI
description = {
fake test cube}
samples = 5
lines = 4
bands = 3
header offset = 0
file type = ENVI standard
data type = 2
reflectance scale factor = 10000.000000
interleave = BIL
sensor type = AVIRIS
byte order = %d
bbl = {
1, 1, 0, 1
}
wavelength = {
.369850, .379690, .389530, .399370
}
wavelength units = um
fwhm = {
.009610, .009580, .009550, .009530 }
""" % HSI.nativeByteOrder
def fakeCube(interleave,default=None, file=fakeNmFile):
file=StringIO(file)
h=ENVI.Header()
h.read(file)
h['interleave']=interleave
other = HSI.newCube(interleave)
h.setCubeAttributes(other)
if default is None:
data = numpy.array(numpy.arange(other.samples*other.lines*other.bands),dtype=other.data_type)
else:
data = numpy.zeros((other.samples*other.lines*other.bands),dtype=other.data_type)
data += default
cube = HSI.createCubeLike(other, data=data.tostring())
h.setCubeAttributes(cube)
return cube
def loadCube(filename):
h=ENVI.Header(filename)
cube=h.getCube()
cube.open()
return cube
class fakeFooCube(object):
def testFail(self):
self.assertRaises(ValueError,cube.newCube,'foo')
class baseCube(object):
def setUp(self):
self.pixlist=[]
self.spectralist=[]
self.spectrallines=[]
def testPixels(self):
assert(self.cube.isDataLoaded())
for line,sample,band,value in self.pixlist:
eq_(self.cube.getPixel(line,sample,band),value)
#print "%d,%d,%d: stored=%f should be=%f" % (line,sample,band,float(self.cube.getPixel(line,sample,band)),float(value))
eq_(self.cube.flatToLocation(self.cube.locationToFlat(line,sample,band)),(line,sample,band))
def testSpectra(self):
assert(self.cube.isDataLoaded())
for line,sample,spectra in self.spectralist:
eq_(self.cube.getSpectra(line,sample).tolist(),spectra)
def testLinesOfSpectra(self):
assert(self.cube.isDataLoaded())
# verify lines of spectra by looking at all the pixel data
# defined in pixlist, but getting the values using
# getLineOfSpectra and comparing the pixel values that way.
# Not terribly efficient since it may end up loading the same
# band many times, but oh well.
for line,sample,band,value in self.pixlist:
lines=self.cube.getLineOfSpectraCopy(line)
#print "band size=%s sample=%d line=%d expected=%f val=%f" % (str(plane.shape),line,sample,value,plane[sample][line])
eq_(lines.shape,(self.cube.samples,self.cube.bands))
eq_(lines[sample][band],value)
def testBands(self):
assert(self.cube.isDataLoaded())
# verify bands by looking at all the pixel data defined in
# pixlist, but getting the band using getBand and comparing
# the pixel values that way. Not terribly efficient since it
# may end up loading the same band many times, but oh well.
for line,sample,band,value in self.pixlist:
plane=self.cube.getBand(band)
#print "band size=%s sample=%d line=%d expected=%f val=%f" % (str(plane.shape),line,sample,value,plane[sample][line])
eq_(plane.shape,(self.cube.lines,self.cube.samples))
eq_(plane[line][sample],value)
class fakeBase(baseCube):
def setUp(self,interleave):
baseCube.setUp(self)
self.cube=fakeCube(interleave)
def testBandList_nm(self):
bands=self.cube.getBandListByWavelength(382.0,units='nm')
eq_(bands,[1])
bands=self.cube.getBandListByWavelength(405.0,units='nm')
eq_(bands,[1])
bands=self.cube.getBandListByWavelength(305.0,units='nm')
eq_(bands,[0])
bands=self.cube.getBandListByWavelength(372.0,405.0,units='nm')
eq_(bands,[1])
bands=self.cube.getBandListByWavelength(200.0,1000.0,units='nm')
eq_(bands,[0,1])
def testBandList_um(self):
bands=self.cube.getBandListByWavelength(.382,units='um')
eq_(bands,[1])
bands=self.cube.getBandListByWavelength(.405,units='um')
eq_(bands,[1])
bands=self.cube.getBandListByWavelength(.305,units='um')
eq_(bands,[0])
bands=self.cube.getBandListByWavelength(.372,.405,units='um')
eq_(bands,[1])
bands=self.cube.getBandListByWavelength(0.2,1.0,units='um')
eq_(bands,[0,1])
def testUnits(self):
eq_(self.cube.wavelength_units,'nm')
def testNewHeader(self):
header=ENVI.Header(self.cube)
eq_(header['data type'],'2')
class fakeUmBase(fakeBase):
def setUp(self,interleave):
# skip fakeBase and call its parent directly
baseCube.setUp(self)
self.cube=fakeCube(interleave,file=fakeUmFile)
def testUnits(self):
eq_(self.cube.wavelength_units,'um')
class testFakeBILCube(fakeBase):
def setUp(self):
super(testFakeBILCube,self).setUp('bil')
self.pixlist=[
(0,0,0, 0),
(0,0,1, 5),
(0,0,2, 10),
(3,1,0, 46),
(3,4,2, 59),
(2,3,1, 38),
]
## self.spectralist=[
## (0,0, [0,5,10])
## ]
#print self.cube.raw
class testFakeUmBILCube(fakeUmBase):
def setUp(self):
super(testFakeUmBILCube,self).setUp('bil')
self.pixlist=[
(0,0,0, 0),
(0,0,1, 5),
(0,0,2, 10),
(3,1,0, 46),
(3,4,2, 59),
(2,3,1, 38),
]
## self.spectralist=[
## (0,0, [0,5,10])
## ]
#print self.cube.raw
class testFakeBIPCube(fakeBase):
def setUp(self):
super(testFakeBIPCube,self).setUp('bip')
self.pixlist=[
(0,0,0, 0),
(0,0,1, 1),
(0,0,2, 2),
(2,3,0, 39),
(3,2,1, 52),
(1,4,2, 29),
]
#print self.cube.raw
class testFakeBSQCube(fakeBase):
def setUp(self):
super(testFakeBSQCube,self).setUp('bsq')
self.pixlist=[
(0,0,0, 0),
(0,0,1, 20),
(0,0,2, 40),
(2,3,0, 13),
(3,2,1, 37),
(1,4,2, 49),
]
#print self.cube.raw
class testFilenames(object):
def testHeader1(self):
filename = localfile('hsi/test1.bil')
urls = ENVI.findHeaders(filename)
header = vfs.normalize(localfile('hsi/test1.hdr'))
eq_(urls[0], header)
def testHeader2(self):
filename = localfile('hsi/test2.bip')
urls = ENVI.findHeaders(filename)
header = vfs.normalize(localfile('hsi/test2.bip.hdr'))
eq_(urls[0], header)
def testIdentify1(self):
filename = localfile('hsi/test1.bil')
format = HSI.HyperspectralFileFormat.identify(filename)
eq_(format.format_id, 'ENVI')
def testIdentify2(self):
filename = localfile('hsi/test2.bip')
format = HSI.HyperspectralFileFormat.identify(filename)
eq_(format.format_id, 'ENVI')
class testGuessBands(object):
def setup(self):
self.cube = HSI.newCube("bsq")
def testNormal(self):
self.cube.wavelengths = [440, 555, 670]
self.cube.bbl = [1, 1, 1]
self.cube.bands = 3
self.cube.wavelength_units = 'nm'
bands = self.cube.getBandListByWavelength(305.0,units='nm')
eq_(bands,[0])
bands = self.cube.getBandListByWavelength(450.0,units='nm')
eq_(bands,[0])
bands = self.cube.getBandListByWavelength(550.0,units='nm')
eq_(bands,[1])
bands = self.cube.getBandListByWavelength(570.0,units='nm')
eq_(bands,[1])
bands = self.cube.getBandListByWavelength(660.0,units='nm')
eq_(bands,[2])
bands = self.cube.getBandListByWavelength(680.0,units='nm')
eq_(bands,[2])
def testReverse(self):
self.cube.wavelengths = [670, 555, 440]
self.cube.bbl = [1, 1, 1]
self.cube.bands = 3
self.cube.wavelength_units = 'nm'
bands = self.cube.getBandListByWavelength(305.0,units='nm')
eq_(bands,[2])
bands = self.cube.getBandListByWavelength(450.0,units='nm')
eq_(bands,[2])
bands = self.cube.getBandListByWavelength(550.0,units='nm')
eq_(bands,[1])
bands = self.cube.getBandListByWavelength(570.0,units='nm')
eq_(bands,[1])
bands = self.cube.getBandListByWavelength(660.0,units='nm')
eq_(bands,[0])
bands = self.cube.getBandListByWavelength(680.0,units='nm')
eq_(bands,[0])
def testBadBandsAtStart(self):
self.cube.wavelengths = [200, 250, 300, 350, 400, 440, 555, 670]
self.cube.bbl = [0, 0, 0, 0, 0, 1, 1, 1]
self.cube.bands = 8
self.cube.wavelength_units = 'nm'
bands = self.cube.getBandListByWavelength(305.0,units='nm')
eq_(bands,[5])
bands = self.cube.getBandListByWavelength(450.0,units='nm')
eq_(bands,[5])
bands = self.cube.getBandListByWavelength(550.0,units='nm')
eq_(bands,[6])
bands = self.cube.getBandListByWavelength(570.0,units='nm')
eq_(bands,[6])
bands = self.cube.getBandListByWavelength(660.0,units='nm')
eq_(bands,[7])
bands = self.cube.getBandListByWavelength(680.0,units='nm')
eq_(bands,[7])