indexerror in longslit.go

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Marianne Heida

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Apr 17, 2014, 7:35:41 AM4/17/14
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Hi Nick,

I'm trying to reduce longslit data and calibrate them with the Ne lamps. When I get to the last step (longslit.go) the pipeline crashes with 

Traceback (most recent call last):
  File "Longslit_driver.py", line 60, in <module>
    waveops, longslit)
  File "/Users/marianne/mosdrp/MOSFIRE/Longslit.py", line 159, in go
    wavoptions).rstrip(".fits")
  File "/Users/marianne/mosdrp/MOSFIRE/Wavelength.py", line 96, in filelist_to_wavename
    end = files[-1].split('/')[-1].rstrip(".fits").split("_")[1]
IndexError: list index out of range

My path doesn't have underscores in it, so that can't be the problem. I'm using the pipeline version 3/14 (parent: 374:cf601433f89e tip). I've pasted my Ne.txt file and the pipeline output below.

Thanks in advance,
Marianne

Ne.txt:
# Created by 'marianne' on Wed Apr 16 13:25:53 2014
/Users/marianne/keck-mosfire/2013dec23 # Abs. path to files [optional]
m131223_0019.fits
m131223_0020.fits
m131223_0021.fits

pipeline output:
n192060:H marianne$ ~/mospy Longslit_driver.py 
Loading: Flat.txt
['/Users/marianne/keck-mosfire/2013dec23/m131223_0007.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0008.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0009.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0010.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0011.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0012.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0013.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0014.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0015.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0016.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0017.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0018.fits']
Attempting to combine:  ['/Users/marianne/keck-mosfire/2013dec23/m131223_0007.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0008.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0009.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0010.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0011.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0012.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0013.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0014.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0015.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0016.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0017.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0018.fits']

Apr 17 11:26: IMCOMBINE
  combine = average, scale = none, zero = none, weight = none
  reject = minmax, nlow = 1, nhigh = 1
  blank = 0.
                Images 
  /Users/marianne/keck-mosfire/2013dec23/m131223_0007.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0008.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0009.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0010.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0011.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0012.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0013.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0014.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0015.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0016.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0017.fits[0]
  /Users/marianne/keck-mosfire/2013dec23/m131223_0018.fits[0]

  Output image = combflat_2d_H.fits, ncombine = 12
Combined '['/Users/marianne/keck-mosfire/2013dec23/m131223_0007.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0008.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0009.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0010.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0011.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0012.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0013.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0014.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0015.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0016.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0017.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0018.fits']' to 'longslit'
Flat written to combflat_2d_H.fits
00] Finding Slit Edges for long ending at    1. Slit composed of 46 CSU slits
long] Bounding top/bottom: 5/2034
Producing Pixel Flat...
Pixel flat took  7.861 s

Loading: Ne.txt
combining : ['/Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits']
Maskname specified (longslit) does not match header maskname  (LONGSLIT-46x0.7).
File /Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits uses mask 'LONGSLIT-46x0.7' but the stack is of 'longslit'
File /Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits uses mask 'LONGSLIT-46x0.7' but the stack is of 'longslit'
/Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits longslit/H
Maskname specified (longslit) does not match header maskname  (LONGSLIT-46x0.7).
File /Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits uses mask 'LONGSLIT-46x0.7' but the stack is of 'longslit'
File /Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits uses mask 'LONGSLIT-46x0.7' but the stack is of 'longslit'
/Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits longslit/H
Maskname specified (longslit) does not match header maskname  (LONGSLIT-46x0.7).
File /Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits uses mask 'LONGSLIT-46x0.7' but the stack is of 'longslit'
File /Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits uses mask 'LONGSLIT-46x0.7' but the stack is of 'longslit'
/Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits longslit/H
Wrote to 'wave_stack_H_m131223_0019-0021.fits'

n192060:H marianne$ ~/mospy Longslit_driver.py 
Loading: Ne.txt
['/Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits'] resolves to input files: wave_stack_H_m131223_0019-0021.fits
Extracting at 1040 
Waiting
Extract position set to 1025
z 15211.519229 1354.58715596
c 15228.8736286 1089.67889908
f 15233.2147649 -499.770642202
Fitting
STD: 2.08 MAD: 0.32
[  1.46380449e+04   1.69810663e+00  -6.94774998e-05   2.17197004e-08
  -3.80762541e-13  -5.21046422e-16]
Stored:  1
x 15235.1334915 2.65975855131
z 16039.2362968 -57.444668008
d 16049.8972895 6.04607645875
x 16023.5565968 -0.940342052314
f 16232.9979947 -0.13111167002
Fitting
STD: 0.08 MAD: 0.08
[  1.46337115e+04   1.76408017e+00  -2.33779097e-04   1.86108903e-07
  -6.56546858e-11   8.26227940e-15]
Stored:  1
n 15916.3354933 -0.0274704142012
Saving to:  lambda_center_coeffs_wave_stack_H_m131223_0019-0021.npy
Extracting at 1025 
q 16406.5565051 -0.0299112426036
Closing figure
save to:  lambda_center_coeffs_wave_stack_H_m131223_0019-0021.npy

n192060:H marianne$ ~/mospy Longslit_driver.py 
Loading: Ne.txt
WAVENAMES ['/Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits']
GUESSNAMES ['/Users/marianne/keck-mosfire/2013dec23/m131223_0019.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0020.fits', '/Users/marianne/keck-mosfire/2013dec23/m131223_0021.fits']
longslit] Writing to: lambda_coeffs_wave_stack_H_m131223_0019-0021.npy
* Fitting Slit long from 976 to 1097
Computing 0 spectrum at 1040
resid ang S01 @ p 976: 0.16 rms 0.09 mad [shift 3]
resid ang S01 @ p 977: 0.13 rms 0.10 mad [shift 3]
resid ang S01 @ p 978: 0.89 rms 0.13 mad [shift 3]
resid ang S01 @ p 979: 0.84 rms 0.13 mad [shift 3]
resid ang S01 @ p 980: 1.73 rms 0.59 mad [shift 3]
resid ang S01 @ p 981: 0.56 rms 0.33 mad [shift 3]
resid ang S01 @ p 982: 0.80 rms 0.53 mad [shift 3]
resid ang S01 @ p 983: 98.93 rms 5.08 mad [shift 3]
resid ang S01 @ p 984: 0.11 rms 0.08 mad [shift 3]
resid ang S01 @ p 985: 0.29 rms 0.15 mad [shift 3]
resid ang S01 @ p 986: 0.52 rms 0.17 mad [shift 3]
resid ang S01 @ p 987: 1.04 rms 0.39 mad [shift 3]
resid ang S01 @ p 988: 0.30 rms 0.15 mad [shift 3]
resid ang S01 @ p 989: 1.10 rms 0.19 mad [shift 2]
resid ang S01 @ p 990: 0.79 rms 0.17 mad [shift 2]
resid ang S01 @ p 991: 1.20 rms 0.23 mad [shift 2]
resid ang S01 @ p 992: 1.02 rms 0.51 mad [shift 2]
resid ang S01 @ p 993: 2.51 rms 1.05 mad [shift 2]
resid ang S01 @ p 994: 0.30 rms 0.05 mad [shift 2]
resid ang S01 @ p 995: 0.21 rms 0.03 mad [shift 2]
resid ang S01 @ p 996: 0.17 rms 0.12 mad [shift 2]
resid ang S01 @ p 997: 0.19 rms 0.09 mad [shift 2]
resid ang S01 @ p 998: 0.12 rms 0.04 mad [shift 2]
resid ang S01 @ p 999: 0.21 rms 0.08 mad [shift 2]
resid ang S01 @ p1000: 0.13 rms 0.05 mad [shift 2]
resid ang S01 @ p1001: 0.09 rms 0.05 mad [shift 2]
resid ang S01 @ p1002: 0.19 rms 0.05 mad [shift 2]
resid ang S01 @ p1003: 0.18 rms 0.09 mad [shift 2]
resid ang S01 @ p1004: 0.35 rms 0.10 mad [shift 2]
resid ang S01 @ p1005: 0.31 rms 0.10 mad [shift 2]
resid ang S01 @ p1006: 2.11 rms 0.28 mad [shift 2]
resid ang S01 @ p1007: 0.14 rms 0.07 mad [shift 1]
resid ang S01 @ p1008: 0.64 rms 0.28 mad [shift 1]
resid ang S01 @ p1009: 0.22 rms 0.15 mad [shift 1]
resid ang S01 @ p1010: 0.17 rms 0.10 mad [shift 1]
resid ang S01 @ p1011: 0.76 rms 0.22 mad [shift 1]
resid ang S01 @ p1012: 0.15 rms 0.04 mad [shift 1]
resid ang S01 @ p1013: 5.70 rms 4.64 mad [shift 1]
resid ang S01 @ p1014: 0.16 rms 0.11 mad [shift 1]
resid ang S01 @ p1015: 0.86 rms 0.58 mad [shift 1]
resid ang S01 @ p1016: 0.96 rms 0.52 mad [shift 1]
resid ang S01 @ p1017: 1.15 rms 0.56 mad [shift 1]
resid ang S01 @ p1018: 0.83 rms 0.24 mad [shift 1]
resid ang S01 @ p1019: 1.08 rms 0.53 mad [shift 1]
resid ang S01 @ p1020: 0.81 rms 0.56 mad [shift 1]
resid ang S01 @ p1021: 0.30 rms 0.11 mad [shift 1]
resid ang S01 @ p1022: 0.60 rms 0.11 mad [shift 1]
resid ang S01 @ p1023: 5.35 rms 0.97 mad [shift 1]
resid ang S01 @ p1024: 0.83 rms 0.27 mad [shift 1]
resid ang S01 @ p1025: 0.19 rms 0.08 mad [shift 1]
resid ang S01 @ p1026: 0.90 rms 0.59 mad [shift 1]
resid ang S01 @ p1027: 0.10 rms 0.08 mad [shift 1]
resid ang S01 @ p1028: 0.16 rms 0.06 mad [shift 1]
resid ang S01 @ p1029: 0.17 rms 0.11 mad [shift 1]
resid ang S01 @ p1030: 0.71 rms 0.16 mad [shift 0]
resid ang S01 @ p1031: 0.64 rms 0.09 mad [shift 0]
resid ang S01 @ p1032: 1.45 rms 0.20 mad [shift 0]
resid ang S01 @ p1033: 0.56 rms 0.38 mad [shift 0]
resid ang S01 @ p1034: 0.13 rms 0.07 mad [shift 0]
resid ang S01 @ p1035: 0.29 rms 0.08 mad [shift 0]
resid ang S01 @ p1036: 1.11 rms 0.51 mad [shift 0]
resid ang S01 @ p1037: 1.06 rms 0.44 mad [shift 0]
resid ang S01 @ p1038: 3.91 rms 0.32 mad [shift 0]
resid ang S01 @ p1039: 6.86 rms 0.42 mad [shift 0]
resid ang S01 @ p1040: 0.45 rms 0.09 mad [shift 0]
resid ang S01 @ p1041: 0.82 rms 0.18 mad [shift 0]
resid ang S01 @ p1042: 1.06 rms 0.40 mad [shift 0]
resid ang S01 @ p1043: 0.30 rms 0.17 mad [shift 0]
resid ang S01 @ p1044: 6.28 rms 3.90 mad [shift 0]
resid ang S01 @ p1045: 0.49 rms 0.16 mad [shift 0]
resid ang S01 @ p1046: 0.64 rms 0.29 mad [shift 0]
resid ang S01 @ p1047: 0.51 rms 0.23 mad [shift 0]
resid ang S01 @ p1048: 0.21 rms 0.12 mad [shift 0]
resid ang S01 @ p1049: 0.32 rms 0.14 mad [shift 0]
resid ang S01 @ p1050: 0.10 rms 0.06 mad [shift-1]
resid ang S01 @ p1051: 0.13 rms 0.09 mad [shift-1]
resid ang S01 @ p1052: 0.18 rms 0.07 mad [shift-1]
resid ang S01 @ p1053: 0.11 rms 0.06 mad [shift-1]
resid ang S01 @ p1054: 0.32 rms 0.06 mad [shift-1]
resid ang S01 @ p1055: 0.25 rms 0.15 mad [shift-1]
resid ang S01 @ p1056: 0.12 rms 0.08 mad [shift-1]
resid ang S01 @ p1057: 0.18 rms 0.08 mad [shift-1]
resid ang S01 @ p1058: 0.83 rms 0.30 mad [shift-1]
resid ang S01 @ p1059: 1.39 rms 0.16 mad [shift-1]
resid ang S01 @ p1060: 1.80 rms 0.10 mad [shift-1]
resid ang S01 @ p1061: 0.87 rms 0.25 mad [shift-1]
resid ang S01 @ p1062: 0.16 rms 0.15 mad [shift-1]
resid ang S01 @ p1063: 0.95 rms 0.54 mad [shift-1]
resid ang S01 @ p1064: 0.18 rms 0.13 mad [shift-1]
resid ang S01 @ p1065: 2.08 rms 0.21 mad [shift-1]
resid ang S01 @ p1066: 0.33 rms 0.06 mad [shift-1]
resid ang S01 @ p1067: 0.38 rms 0.14 mad [shift-1]
resid ang S01 @ p1068: 0.30 rms 0.17 mad [shift-1]
resid ang S01 @ p1069: 0.26 rms 0.20 mad [shift-1]
resid ang S01 @ p1070: 1.11 rms 0.51 mad [shift-1]
resid ang S01 @ p1071: 0.26 rms 0.22 mad [shift-1]
resid ang S01 @ p1072: 0.30 rms 0.22 mad [shift-1]
resid ang S01 @ p1073: 2.69 rms 0.30 mad [shift-1]
resid ang S01 @ p1074: 5.79 rms 1.04 mad [shift-1]
resid ang S01 @ p1075: 11.71 rms 11.07 mad [shift-2]
resid ang S01 @ p1076: 0.16 rms 0.10 mad [shift-2]
resid ang S01 @ p1077: 55.68 rms 15.60 mad [shift-2]
resid ang S01 @ p1078: 1.04 rms 0.49 mad [shift-2]
resid ang S01 @ p1079: 1.55 rms 0.84 mad [shift-2]
resid ang S01 @ p1080: 0.34 rms 0.31 mad [shift-2]
resid ang S01 @ p1081: 25.14 rms 6.62 mad [shift-2]
resid ang S01 @ p1082: 4.29 rms 1.12 mad [shift-2]
resid ang S01 @ p1083: 0.22 rms 0.08 mad [shift-2]
resid ang S01 @ p1084: 0.19 rms 0.09 mad [shift-2]
resid ang S01 @ p1085: 0.15 rms 0.09 mad [shift-2]
resid ang S01 @ p1086: 0.80 rms 0.30 mad [shift-2]
resid ang S01 @ p1087: 0.16 rms 0.08 mad [shift-2]
resid ang S01 @ p1088: 0.07 rms 0.04 mad [shift-2]
resid ang S01 @ p1089: 1.19 rms 0.27 mad [shift-2]
resid ang S01 @ p1090: 0.24 rms 0.14 mad [shift-2]
resid ang S01 @ p1091: 0.77 rms 0.22 mad [shift-2]
resid ang S01 @ p1092: 0.25 rms 0.13 mad [shift-2]
resid ang S01 @ p1093: 0.23 rms 0.09 mad [shift-2]
resid ang S01 @ p1094: 0.64 rms 0.10 mad [shift-3]
resid ang S01 @ p1095: 1.26 rms 0.27 mad [shift-3]
resid ang S01 @ p1096: 1.31 rms 0.14 mad [shift-3]
S00] TOOK: 289 s
-----> Mask took 289

n192060:H marianne$ ~/mospy Longslit_driver.py 
Loading: Ne.txt
2d wavelengths: Slit 1/1
longslit: writing lambda
Wrote to 'lambda_solution_wave_stack_H_m131223_0019-0021.fits'
longslit: writing sigs
Wrote to 'sigs_solution_wave_stack_H_m131223_0019-0021.fits'
longslit: rectifying
Wrote to 'rectified_wave_stack_H_m131223_0019-0021.fits'

n192060:H marianne$ ~/mospy Longslit_driver.py 
Traceback (most recent call last):
  File "Longslit_driver.py", line 60, in <module>
    waveops, longslit)
  File "/Users/marianne/mosdrp/MOSFIRE/Longslit.py", line 159, in go
    wavoptions).rstrip(".fits")
  File "/Users/marianne/mosdrp/MOSFIRE/Wavelength.py", line 96, in filelist_to_wavename
    end = files[-1].split('/')[-1].rstrip(".fits").split("_")[1]
IndexError: list index out of range

Nick Konidaris

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Apr 17, 2014, 9:29:07 AM4/17/14
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Hi Marianne, 

Thanks for the report. Can you paste in Longslit_driver.py?

thanks
n


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marian...@gmail.com

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Apr 17, 2014, 10:26:14 AM4/17/14
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Sure.

Longslit_driver.py:

# Help, bugs to: http://mosfire.googlecode.com
#
# Instructions
# 1. edit band = '' to band = 'Y' or 'J' or 'H' or 'K'
# e.g. band = 'J'
# 2. edit [709, 1350] to be the pixel values at the beginning and end
# of the long slit. Look at the raw data.
# 3. edit row_position to be a location where the standard star is not.
# 4. Decide if you want to use sky lines or Neon lamps for lambda calibration
# 5. Uncomment one line at a time and run mospy on the driver file
#

import os, time
import MOSFIRE

from MOSFIRE import Background, Combine, Detector, Flats, IO, Options, Rectify
from MOSFIRE import Wavelength, Longslit

import numpy as np, pylab as pl, pyfits as pf

np.seterr(all="ignore")

maskname = 'longslit'
band = 'H'

flatops = Options.flat
waveops = Options.wavelength

longslit = {'yrange': [974, 1099], 'row_position': 1025}

obsfiles = ['Offset_5.txt', 'Offset_-5.txt']

#Flats.handle_flats('Flat.txt', maskname, band, flatops)

# SKY LINES
# Use sky lines for wavelength calibration
# Use either Sky lines or Neon lines.
#Wavelength.imcombine(obsfiles, maskname, band, waveops)
#Wavelength.fit_lambda_interactively(maskname, band, obsfiles, waveops, longslit=longslit)
#Wavelength.fit_lambda(maskname, band, obsfiles, obsfiles, waveops, longslit=longslit)
#Wavelength.apply_lambda_simple(maskname, band, obsfiles, waveops, longslit=longslit, smooth=True)

# Update the following line after the apply_lambda_simple step
#Longslit.go(maskname, band, obsfiles ,
# 'lambda_solution_wave_stack_....',
# waveops, longslit)


# NEON
# Use neon for wavelength calibrations
#Wavelength.imcombine('Ne.txt', maskname, band, waveops)
#Wavelength.fit_lambda_interactively(maskname, band, 'Ne.txt', waveops, longslit=longslit, neon=True)
#Wavelength.fit_lambda(maskname, band, 'Ne.txt', 'Ne.txt', waveops, longslit=longslit)
#Wavelength.apply_lambda_simple(maskname, band, 'Ne.txt', waveops, longslit=longslit, smooth=True)

# Update the following line after the apply_lambda_simple step
Longslit.go(maskname, band, 'Ne.txt',
'lambda_solution_wave_stack_H_m131223_0019-0021.fits',
waveops, longslit)

Nick Konidaris

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Apr 17, 2014, 10:35:19 AM4/17/14
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Looks like there's a documentation bug. 

Longslit.go(maskname, band, 'Ne.txt',
    'lambda_solution_wave_stack_H_m131223_0019-0021.fits',
    waveops, longslit)

should be

Longslit.go(maskname, band, obsfiles,
    'lambda_solution_wave_stack_H_m131223_0019-0021.fits',
    waveops, longslit)

Thanks for pointing out the bug. I've corrected it for the next release.
~n


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marian...@gmail.com

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Apr 17, 2014, 10:43:12 AM4/17/14
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Thanks! That actually makes a lot more sense...
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