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To process a list of files listing all files with theabsolute path. #146

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To process a list of files listing all files with theabsolute path. #146

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43 changes: 23 additions & 20 deletions MOSFIRE/IO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,13 +137,13 @@ def load_lambdaslit(fnum, maskname, band, options):
"that in the edge file '%s'" % (maskname, ret[0]['maskname']))
warning("Continuing")


return readfits(fn, options)

def writefits(img, maskname, fname, options, header=None, bs=None,
overwrite=False, lossy_compress=False):
'''Convenience wrapper to write MOSFIRE drp-friendly FITS files

Args:
img: Data array to write to disk
maskname: Name of the science mask
Expand Down Expand Up @@ -185,7 +185,7 @@ def writefits(img, maskname, fname, options, header=None, bs=None,

warnings.filterwarnings('always')
if overwrite:
try:
try:
os.remove(fn)
debug("Removed old file '{0}'".format(fn))
except: pass
Expand All @@ -199,7 +199,7 @@ def writefits(img, maskname, fname, options, header=None, bs=None,


def readfits(path, use_bpm=False):
'''Read a fits file from path and return a tuple of (header, data,
'''Read a fits file from path and return a tuple of (header, data,
Target List, Science Slit List (SSL), Mechanical Slit List (MSL),
Alignment Slit List (ASL)).'''

Expand Down Expand Up @@ -286,14 +286,14 @@ def fname_to_date_tuple(fname):
if len(fname) != 17:
raise Exception("The file name '%s' is not of correct length. It "
"must be of the form mYYmmdd_nnnn.fits" % fname)

try:
fdate = fname.split("m")[1][0:6]
yr, mn, dy = "20" + fdate[0:2], fdate[2:4], int(fdate[4:6])
month = months[mn]
except:
warning("Could not parse date out of file name: %s" % (fname))

return yr, month, dy

def fname_to_path(fname, options):
Expand Down Expand Up @@ -354,10 +354,13 @@ def list_file_to_strings(fname):
inputs = np.genfromtxt(fname,dtype=str)
path = ""
start_index = 0
if inputs.size == 1:
inputs = np.array([inputs])
if len(inputs):
if os.path.isabs(inputs[0][0]):
path = inputs[0]
start_index = 1
if inputs[0][-5:] != ".fits":
if os.path.isabs(inputs[0][0]):
path = inputs[0]
start_index = 1
for i in range(start_index, len(inputs)):
output.append(os.path.join(path, inputs[i]))

Expand Down Expand Up @@ -404,7 +407,7 @@ def fix_long2pos_headers(filelist):
# assign FRAMEID to wide slits
if header['YOFFSET']==14 or header['YOFFSET']==-14:
header['FRAMEID']="A"

#reverse sign of offsets for narrow slits
if header['YOFFSET']==-21:
header['YOFFSET']=7
Expand All @@ -420,10 +423,10 @@ def fix_long2pos_headers(filelist):


def readmosfits(fname, options, extension=None):
'''Read a fits file written by MOSFIRE from path and return a tuple of
(header, data, Target List, Science Slit List (SSL), Mechanical Slit
'''Read a fits file written by MOSFIRE from path and return a tuple of
(header, data, Target List, Science Slit List (SSL), Mechanical Slit
List (MSL), Alignment Slit List (ASL)).

Note, the extension is typically not used, only used if the detector server
does not append slit extension.
'''
Expand Down Expand Up @@ -468,7 +471,7 @@ def readmosfits(fname, options, extension=None):
ssl = ssl[ssl.field("Slit_Number") != ' ']
msl = msl[msl.field("Slit_Number") != ' ']
asl = asl[asl.field("Slit_Number") != ' ']


# ELIMINATE POSITION B of the long2pos slit
ssl = ssl[ssl.field("Target_Name") != 'posB']
Expand Down Expand Up @@ -501,7 +504,7 @@ def readscitbl(path):


def parse_header_for_bars(header):
'''Parse {header} and convert to an array of CSU bar positions in mm. If
'''Parse {header} and convert to an array of CSU bar positions in mm. If
the positon is negative it means the barstat is not OK'''

poss = []
Expand All @@ -516,11 +519,11 @@ def parse_header_for_bars(header):
poss.append(pos)

if len(poss) != CSU.numbars:
error("Found %i bars instead of %i" %
error("Found %i bars instead of %i" %
(lens(poss), CSU.numbars))
raise CSU.MismatchError("Found %i bars instead of %i" %
raise CSU.MismatchError("Found %i bars instead of %i" %
(lens(poss), CSU.numbars))


return np.array(poss)

Expand Down Expand Up @@ -597,7 +600,7 @@ def imcombine(filelist, out, options, method="average", reject="none",\
mclip: use median as the function to calculate the baseline values for
sigclip rejection?
lsigma, hsigma: low and high sigma rejection thresholds.

Returns:
None

Expand Down Expand Up @@ -653,7 +656,7 @@ def imcombine(filelist, out, options, method="average", reject="none",\
warning('nlow + nhigh >= number of input images. Combining without rejection')
nlow = 0
nhigh = 0

if ccdproc.version.major >= 1 and ccdproc.version.minor >= 1\
and ccdproc.version.release:
info('Combining files using ccdproc.combine task')
Expand Down