#for cc in range(channels):
# bg=num.median(IRspecData[cc,:,:][IRBGPixels])
# print bg
# IRspecData[cc,:,:]-=bg
waterDepth=[]
siliDepth=[]
for l in range(A):
waterDepth.append([])
siliDepth.append([])
for s in range(B):
(w,spec)=specAnalysis.getSpec(IRspecData,l=l,s=s)
med=num.nanmedian(spec)
if med>0.0025: #could probably put this at 0.0025
wat=specAnalysis.water(w,spec)
sil=max(0.0,specAnalysis.silicate(w,spec))
if wat>0:
waterDepth[len(waterDepth)-1].append(wat)
else:
waterDepth[len(waterDepth)-1].append(0.0)
siliDepth[len(siliDepth)-1].append(sil)
else:
waterDepth[len(waterDepth)-1].append(0.0)
siliDepth[len(siliDepth)-1].append(0.0)
waterDepth=num.array(waterDepth)
siliDepth=num.array(siliDepth)
x=[]
y=[]
z=[]
print 'swaitch'
specData=specData[:,::-1,::-1]
(channels,A,B)=specData.shape
waterDepth=[]
for l in range(A):
waterDepth.append([])
for s in range(B):
(w,spec)=specAnalysis.getSpec(specData,l=l,s=s)
med=num.nanmedian(spec)
#print l,s,med,imData[1,l,s]
if med>0.0005:
(h,junk)=specAnalysis.water(w,spec)
if h>0.0:
waterDepth[len(waterDepth)-1].append(h)
else: waterDepth[len(waterDepth)-1].append(0.0)
else:
waterDepth[len(waterDepth)-1].append(0.0)
waterDepth=num.array(waterDepth)
"""
for i in range(len(waterDepth)):
for j in range(len(waterDepth[i])):
if len(vertsInPixelIR[i][j])>0:
print i,j
print
for i in range(len(waterDepth)):
for j in range(len(waterDepth[i])):
