def extract(fitsfile):
outfile = pyfits.HDUList()
# Make empty HDU; no image
outfile.append(pyfits.PrimaryHDU())
for i, hdu in enumerate(fitsfile):
if (i == 0 and hdu.data != None) or isinstance(hdu, pyfits.ImageHDU):
print hdu.data.shape + (i, )
if i == 0:
print 'Image: Primary HDU (number 0) %sx%s' % hdu.data.shape
else:
print 'Image: Extension HDU (number %s) %sx%s' % tuple(
(i, ) + hdu.data.shape)
tbhdu = source_extract(image_data)
outfile.append(tbhdu)
return x, y, flux, sigma, outfile
def test_byteswap(self):
p = fits.PrimaryHDU()
l = fits.HDUList()
n = np.zeros(3, dtype='i2')
n[0] = 1
n[1] = 60000
n[2] = 2
c = fits.Column(name='foo', format='i2', bscale=1, bzero=32768,
array=n)
t = fits.BinTableHDU.from_columns([c])
l.append(p)
l.append(t)
l.writeto(self.temp('test.fits'), clobber=True)
with fits.open(self.temp('test.fits')) as p:
assert p[1].data[1]['foo'] == 60000.0
def cut_frame_with_target(myfile, ra, dec, h=4000, w=2000, debug=False):
hdulist = pf.open(myfile)[0]
img = hdulist.data * 1.
img = img.T
nx, ny = img.shape
if (ra * dec != 0):
# Get pixel coordinates of SN
wcs = pywcs.WCS(hdulist.header)
try:
target_pix = wcs.wcs_sky2pix([(np.array([ra,dec], np.float_))], 1)[0]
except:
print "ERROR when converting sky to wcs. Is astrometry in place? Default coordinates assigned."
target_pix = [+nx/2., ny/2.]
if debug: print i, target_pix
else:
target_pix = [+nx/2., ny/2.]
#If contained in the frame
if (target_pix[0] > 0 and target_pix[0]<nx) and (target_pix[1] > 0 and target_pix[1]<ny):
xmin = np.maximum(0, target_pix[0]-w/2.)
xmax = np.minimum(nx, target_pix[0]+w/2.)
ymin = np.maximum(0, target_pix[1]-h/2.)
ymax = np.minimum(ny, target_pix[1]+h/2.)
print "Target", target_pix, xmin, xmax, ymin, ymax
newhdu = pf.PrimaryHDU()
newhdu.header = hdulist.header
newhdu.data = hdulist.data[ymin:ymax,xmin:xmax]
newname = os.path.join(os.path.dirname(myfile),"out.fits")
newhdu.writeto(newname, output_verify="fix", clobber=False)
print "Extracted region around target and stored to ",newname
else:
print "Target not in the frame!"
def new_spt():
fn = commands.getoutput('ls *_flt.fits').split('\n')
dx = []
km2AU = 1.0 / 1.49598e8
Xi, Yi, Zi, minJD, maxJD = get_ephem( )
for k in fn:
#keys = commands.getoutput('gethead %s POSTNSTX POSTNSTY POSTNSTZ PSTRTIME'%(k)).split()
#keys2 = commands.getoutput('gethead %s_flt.fits EXPSTART'%(k.split('_')[0])).split()
#keys2 = commands.getoutput('gethead %s_flt.fits EXPSTART EXPEND'%(k.split('_')[0])).split()
h0 = pyfits.open('%s_flt.fits'%(k.split('_')[0]))
header0 = h0[0].header
h0.close()
keys2 = [ float(header0['EXPSTART']), float(header0['EXPEND']) ]
date_midexp = 0.5* ( float(keys2[0]) + float(keys2[1]) ) + 2400000.5 ##-- JD
if not (date_midexp > minJD)*(date_midexp<maxJD):
print k, date_midexp, (date_midexp > minJD)*(date_midexp<maxJD)
continue
dx, dy, dz = float(Xi(date_midexp)), float(Yi(date_midexp)), float(Zi(date_midexp))
#print dx, dy, dz
#d = date2jd( keys[3] )
#dx.append( [ d, float(keys[0])*km2AU, float(keys[1])*km2AU, float(keys[2])*km2AU, k.split('_')[0] ] )
prihdr = pyfits.Header()
prihdr['MIDMJD'] = date_midexp - 2400000.5
prihdr['MIDJD'] = date_midexp #- 2400000.5
prihdr['POSTNSTX'] = dx
prihdr['POSTNSTY'] = dy
prihdr['POSTNSTZ'] = dz
prihdr['COMMENT'] = 'Generated by update_spt.py on %s'%(time.ctime())
prihdu = pyfits.PrimaryHDU(header=prihdr)
prihdu.writeto('/net/frakir/raid/aparker/FullSurvey/%s_sdt.fits'%(k.split('_')[0]))
def make_image(pixels, name, type, directory, invert=False, linearize=False):
'''Create a grayscale image from an array of values. The
type flag is used to set the type of images generated.
The invert flag is used to invert the grayscale. For
example, inverted .PNG and .FITS images:
make_image(array, 'filename', 'fp', 1)'''
# invert
if invert == 1: pixels = pixels.max() - pixels
# make fits
if 'f' in type:
if name + '.fits' in os.listdir(directory):
os.unlink(os.path.join(directory, name + '.fits'))
hdu = pf.PrimaryHDU(np.flipud(pixels))
hdulist = pf.HDUList([hdu])
hdulist.writeto(os.path.join(directory, name + '.fits'), clobber=True)
# scale to 0-255
pixels -= pixels.min()
m = pixels.max()
if m != 0:
pixels *= 255 / m
# render in linear space
if linearize == 1:
pixels /= 255
pixels = 1 - pixels
pixels = np.power(pixels, 1 / 2.2)
pixels = 1 - pixels
pixels *= 255
# make rest
image = im.fromarray(np.uint8(pixels))
if 'g' in type:
image.save(os.path.join(directory, name + '.gif'))
if 'p' in type:
image.save(os.path.join(directory, name + '.png'))
if 'e' in type:
image.save(os.path.join(directory, name + '.eps'))
def writeFITS(data, output, overwrite=True, int=True):
"""
Write out a FITS file using PyFITS. Will remove an existing file if overwrite=True.
:param data: data to write to a FITS file
:type data: ndarray
:param output: name of the output file
:type output: string
:param overwrite: removes an existing file if present before writing a new one
:type overwrite: bool
:param int: whether or not to save the data scaled to 16bit unsigned integer values
:type int: bool
:return: None
"""
if overwrite and os.path.isfile(output):
os.remove(output)
#create a new FITS file, using HDUList instance
ofd = pf.HDUList(pf.PrimaryHDU())
#new image HDU
hdu = pf.ImageHDU(data=data)
if int:
hdu.scale('int16', '', bzero=32768)
hdu.header.add_history('Scaled to unsigned 16bit integer!')
#update and verify the header
hdu.header.add_history(
'If questions, please contact Sami-Matias Niemi (smn2 at mssl.ucl.ac.uk).'
)
hdu.header.add_history(
'This file has been created with the VISsim Python Package at %s' %
datetime.datetime.isoformat(datetime.datetime.now()))
hdu.verify('fix')
ofd.append(hdu)
#write the actual file
ofd.writeto(output)
def createSigMap(self,run=True, method=2, generateDistribution=False):
"""Generates a significance map."""
if(self.plotConf['binfactor']):
suffix = "_rebin.fits"
else:
suffix = ".fits"
try:
checkForFiles(self.logger,
[self.commonConf['base']+"_CMAP"+suffix,
self.commonConf['base']+"_modelMap"+suffix])
except(FileNotFound):
self.logger.critical("One or more needed files do not exist")
return
onImage = pyfits.open(self.commonConf['base']+"_CMAP"+suffix)
onData = onImage[0].data.copy()
onHeader = onImage[0].header
offImage = pyfits.open(self.commonConf['base']+"_modelMap"+suffix)
offData = offImage[0].data.copy()
sigData = offImage[0].data.copy()
for x,row in enumerate(sigData):
for y in enumerate(row):
if method == 1:
sigData[x,y[0]] = ((onData[x,y[0]]-offData[x,y[0]])*(onData[x,y[0]]-offData[x,y[0]]))/sqrt(offData[x,y[0]])
elif method == 2:
sigData[x,y[0]] = (onData[x,y[0]]-offData[x,y[0]])/sqrt(offData[x,y[0]])
newImage = pyfits.PrimaryHDU(sigData)
newImage.header = onHeader
newImage.update_header()
hdulist = pyfits.HDUList([newImage])
hdulist.writeto(self.commonConf['base']+"_sigMap"+suffix,clobber=True)
self.logger.info("Created a significance map from "
+self.commonConf['base']+"_CMAP"+suffix+" and "
+self.commonConf['base']+"_modelMap"+suffix+".")
def convertfits(inname, stretchfactor=4, shrinkfactor=5):
outname = inname.rpartition('.')
outname = outname[0] + '_resize' + outname[1] + outname[2]
if os.path.exists(outname):
print outname + " exists and will not be remade."
return ''
infits = pyfits.open(inname)
x0 = infits[1].header['NAXIS1']
x1 = infits[1].header['NAXIS2']
if x0 % shrinkfactor:
print "Error: convertfis cannot divide axis 0 (" + str(
x0) + ") by " + str(shrinkfactor)
return 1
if x1 % shrinkfactor:
print "Error: convertfits cannot divide axis 1 (" + str(
x1) + ") by " + str(shrinkfactor)
return 1
inarr = infits[1].data
[x0, x1] = inarr.shape
if x0 % shrinkfactor:
print "Error: convertfis cannot divide axis 0 (" + str(
x0) + ") by " + str(shrinkfactor)
return 1
if x1 % shrinkfactor:
print "Error: convertfits cannot divide axis 1 (" + str(
x1) + ") by " + str(shrinkfactor)
return 1
infits[1].header['NAXIS1'] = x0 * stretchfactor / shrinkfactor
infits[1].header['NAXIS2'] = x1 * stretchfactor / shrinkfactor
infits[1].header['CDELT1'] = infits[1].header['CDELT1'] * (
1.0 * shrinkfactor / stretchfactor)
infits[1].header['CDELT2'] = infits[1].header['CDELT2'] * (
1.0 * shrinkfactor / stretchfactor)
outname = inname.rpartition('.')
outname = outname[0] + '_resize' + outname[1] + outname[2]
infits[1].data = shrink(stretch(inarr, stretchfactor), shrinkfactor)
outfits = pyfits.HDUList([
pyfits.PrimaryHDU(infits[0].data, infits[0].header),
pyfits.ImageHDU(infits[1].data, infits[1].header)
])
outfits.writeto(outname)
def _writeImpl(self, filename):
if not pyfits:
raise RuntimeError("I failed to import pyfits, so cannot write to disk")
fits = pyfits.HDUList()
hdr = pyfits.Header()
hdr['RA'] = (self.raBoresight, "Telescope boresight RA, degrees")
hdr['DEC'] = (self.decBoresight, "Telescope boresight Dec, degrees")
hdu = pyfits.PrimaryHDU(header=hdr)
hdr.update()
fits.append(hdu)
maxLength = max(len(pp) for pp in self.patch)
columns = []
for name in self._fields:
format = self._fields[name]
if format == "A":
maxLength = max(len(ss) for ss in getattr(self, name))
format = "A%d" % maxLength
columns.append(pyfits.Column(name=name, format=format, array=getattr(self, name)))
fits.append(pyfits.BinTableHDU.from_columns(columns, hdr, name=self._hduName))
numRows = sum(len(mag) for mag in self.fiberMag)
fiberId = np.array(sum(([ii]*len(mags) for ii, mags in zip(self.fiberId, self.fiberMag)), []))
fiberMag = np.array(sum((mag.tolist() for mag in self.fiberMag), []))
filterNames = sum(self.filterNames, [])
assert(len(fiberId) == numRows)
assert(len(fiberMag) == numRows)
assert(len(filterNames) == numRows)
maxLength = max(len(ff) for ff in filterNames) if filterNames else 1
fits.append(pyfits.BinTableHDU.from_columns([
pyfits.Column(name='fiberId', format='J', array=fiberId),
pyfits.Column(name='fiberMag', format='E', array=fiberMag),
pyfits.Column(name='filterName', format='A%d' % maxLength, array=filterNames),
], hdr, name='PHOTOMETRY'))
# clobber=True in writeto prints a message, so use open instead
with open(filename, "wb") as fd:
fits.writeto(fd)
def fits_logrebin(infile,outfile):
try:
import pyfits
except:
from astropy.io import fits as pyfits
f = pyfits.open(infile)
header = f[0].header
data = f[0].data.copy()
crval1 = header['crval1']
crpix = header['crpix1']
cd = header['cd1_1']
outwave,outspec = rebin_log(data,crval1,crpix,cd)
out = pyfits.PrimaryHDU(outspec)
outwv = scipy.log10(outwave)
start = outwv[0]
delt = outwv[1]-outwv[0]
out.header.update('CRVAL1',start)
out.header.update('CRPIX1',1)
out.header.update('CD1_1',delt)
out.header.update('DC-FLAG',1)
out.writeto(outfile)
def __init__(self):
""" Constructor: Initialize data objects and variables
"""
# call superclass constructor (calls setup)
super(StepDark, self).__init__()
# list of data and darks
self.datalist = [] # used in run() for every new input data file
# dark values
self.darkloaded = 0 # indicates if dark has been loaded
self.darks = [] # list containing arrays with dark values
self.goodpixmap = numpy.zeros(
[1, 1], dtype=numpy.int16) # array with good pixels
# dark file info and header keywords to fit
self.darkfile = '' # name of selected dark file
self.darkhead = pyfits.PrimaryHDU(
numpy.array(1)) # header of dark file
self.fitkeys = [] # FITS keywords that have to fit
self.keyvalues = [
] # values of the keywords (from the first data file)
# set configuration
self.log.debug('Init: done')
def distortion_interp_frame(frame, y, x, storeall=True, output_dir="."):
frame_ds = re.sub(".fits", "_ds.fits", frame)
flux = pyf.open(frame_ds)[-1].data
flux_dw = scipy.ndimage.map_coordinates(flux, [y, x], order=3)
header = pyf.open(frame_ds)[0].header
flux_hdu = pyf.PrimaryHDU(flux_dw, header)
fluxout = pyf.HDUList()
fluxout.append(flux_hdu)
try:
outname = re.sub(".fits", "_dw.fits", frame)
outname = re.sub(".*/", output_dir + "/", outname)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
fluxout.writeto(outname, clobber=True)
fluxout.close()
except IOError, err:
print err
sys.exit(1)
def write_fits_tile(spec_tile, filename):
'''
########################################################################################################################
#This program writes the spec_tile output from collapse_longslit to a fits file
#Input:
# spec_tile: 2D image to write
# filename: name of file to write to (without extension)
#Output:
# writes a fits file
#Called from:
# create_all_tile_files
# display_rotated_image
########################################################################################################################
'''
print filename
hdu = pyfits.PrimaryHDU(spec_tile)
hdulist = pyfits.HDUList([hdu])
#if os.path.exists('/user/bostroem/science/12465_otfr20120425/mama/%s.fits' %(filename)):
# os.remove('/user/bostroem/science/12465_otfr20120425/mama/%s.fits' %(filename))
hdulist.writeto(filename+'.fits', clobber = True)
def test_updated_file_permissions(self):
"""
Regression test for https://trac.assembla.com/pyfits/ticket/79
Tests that when a FITS file is modified in update mode, the file
permissions are preserved.
"""
filename = self.temp('test.fits')
hdul = [fits.PrimaryHDU(), fits.ImageHDU()]
hdul = fits.HDUList(hdul)
hdul.writeto(filename)
old_mode = os.stat(filename).st_mode
hdul = fits.open(filename, mode='update')
hdul.insert(1, fits.ImageHDU())
hdul.flush()
hdul.close()
assert old_mode == os.stat(filename).st_mode
def mask_from_weight(infile, outfile, value=0):
import pyfits
(data, hdr) = rfits(infile)
newdata = numpy.where(data > 0, 1, 0)
newfits = pyfits.HDUList()
hdu = pyfits.PrimaryHDU()
#hdu.data = newdata.astype("Int16") # Just as integer
hdu.data = newdata #.astype("UInt8") # Just as ushort integer
hdu.header = hdr
# Remove old version of file before
if os.path.isfile(outfile):
os.remove(outfile)
newfits.append(hdu)
newfits.writeto(outfile)
newfits.close
return
def test_writeto_append_mode_gzip(self):
"""Regression test for
https://github.com/spacetelescope/PyFITS/issues/33
Check that a new GzipFile opened in append mode can be used to write
out a new FITS file.
"""
# Note: when opening a GzipFile the 'b+' is superfluous, but this was
# still how the original test case looked
# Note: with statement not supported on GzipFile in older Python
# versions
fileobj = gzip.GzipFile(self.temp('test.fits.gz'), 'ab+')
h = fits.PrimaryHDU()
try:
h.writeto(fileobj)
finally:
fileobj.close()
with fits.open(self.temp('test.fits.gz')) as hdul:
assert hdul[0].header == h.header
def test_insert_groupshdu_to_non_empty_list(self):
"""Tests inserting a Simple GroupsHDU to an empty HDUList."""
hdul = fits.HDUList()
hdu = fits.PrimaryHDU(np.arange(100, dtype=np.int32))
hdul.insert(0, hdu)
hdu = fits.GroupsHDU()
assert_raises(ValueError, hdul.insert, 1, hdu)
info = [(0, 'PRIMARY', 'GroupsHDU', 8, (), '',
'1 Groups 0 Parameters'),
(1, '', 'ImageHDU', 6, (100,), 'int32', '')]
hdul.insert(0, hdu)
assert hdul.info(output=False) == info
hdul.writeto(self.temp('test-insert.fits'))
assert fits.info(self.temp('test-insert.fits'), output=False) == info
def extract_field_from_moscaic(mydir, myfilter, nfields=None, origname=False):
if np.isscalar(nfields):
nfields = np.array([nfields])
for i, f in enumerate(glob.glob(mydir + "/" + myfilter)):
hdulist = pf.open(f)
if nfields==None:
nfields = np.arange(len(hdulist)-1)+1
for n in nfields:
hdu = hdulist[n]
hdu.header = hdulist[0].header + hdulist[n].header
hduheader = pf.PrimaryHDU()
hduheader.header = hdu.header
hduheader.data = hdu.data
hdulist1 = pf.HDUList([hduheader, hdu])
if origname:
name = os.path.basename(f)
name = name.replace(".fits", "_%d.fits")
hdulist1.writeto(name%(n), output_verify="fix", clobber=True)
else:
hdulist1.writeto("out%d_%d.fits"%(i,n), output_verify="fix", clobber=True)
def main(args=sys.argv):
parser = OptionParser(usage=usage)
parser.add_option('-o',
'--outfile',
help='output catalog name',
dest='outfile')
parser.add_option('-s',
'--saturation',
help='Saturation Pixel Level',
dest='saturation')
parser.add_option('-i', '--instrum', help='Instrument tag', dest='instrum')
parser.add_option('-m',
'--mastercat',
help='Master catalog to pull non Flux columns from',
dest='mastercat')
options, catfiles = parser.parse_args()
if options.outfile is None or \
options.saturation is None:
parser.error('Must specify outfile and saturation level')
catlist = [ldac.openObjectFile(catfile) for catfile in catfiles]
mastercat = None
if options.mastercat:
mastercat = ldac.openObjectFile(options.mastercat)
combinedcat = combineCats(catlist,
options.saturation,
instrum=options.instrum,
mastercat=mastercat)
hdus = [pyfits.PrimaryHDU(), combinedcat.hdu]
if mastercat:
hdus.extend(_transferOtherHDUs(options.mastercat))
else:
hdus.extend(_transferOtherHDUs(catfiles[0]))
hdulist = pyfits.HDUList(hdus)
hdulist.writeto(options.outfile, clobber=True)
def mergecat_fits(outcat, dirs, root='run*m_udf_z8', bands=['H','B','V','I','Z','Y','J'],\
inputband='H',inputcols_dic=def_inputcols,inputcols_int=['gtype'],paramfile=None):
# collects the results from all the simulation catalogs and write to a *FITS* table
# collect the results
if len(glob.glob(outcat)) > 0:
raise ValueError, "%s already exists." % outcat
md, allcolumns, allformats = mergeoutput(dirs,
root=root,
bands=bands,
inputband=inputband,
inputcols_dic=inputcols_dic,
inputcols_int=inputcols_int,
paramfile=paramfile)
# now build the FITS table
fitscols = []
for i in range(len(allcolumns)):
colname = allcolumns[i]
format = allformats[i]
if type(md[colname]) == type(array([])):
fitscols += [
pyfits.Column(name=colname, format=format, array=md[colname])
]
else:
for b in bands:
bcolname = b + '_' + colname
fitscols += [
pyfits.Column(name=bcolname,
format=format,
array=md[colname][b])
]
fitscols += [
pyfits.Column(name='number',
format='K',
array=arange(0, len(md['detect'])))
]
cols = pyfits.ColDefs(fitscols)
tbhdu = pyfits.new_table(cols)
hdu = pyfits.PrimaryHDU(array([]))
thdulist = pyfits.HDUList([hdu, tbhdu])
thdulist.writeto(outcat)
def join_cats(cs, outputfile):
import pyfits
tables = {}
i = 0
cols = []
seqnr = 0
for c in cs:
print c
if len(c) > 1:
TAB = c[1]
c = c[0]
else:
TAB = 'STDTAB'
i += 1
print c
tables[str(i)] = pyfits.open(c)
for column in tables[str(i)][TAB].columns:
if column.name == 'SeqNr':
if not seqnr:
seqnr += 1
else:
column.name = column.name + '_' + str(seqnr)
seqnr += 1
cols.append(column)
print cols
print len(cols)
hdu = pyfits.PrimaryHDU()
hduSTDTAB = pyfits.new_table(cols)
hdulist = pyfits.HDUList([hdu])
hduFIELDS = pyfits.open(cs[1][0])['FIELDS']
hdulist.append(hduFIELDS)
hdulist.append(hduSTDTAB)
hdulist[1].header.update('EXTNAME', 'FIELDS')
hdulist[2].header.update('EXTNAME', 'STDTAB')
import os
os.system('rm ' + outputfile)
print outputfile
hdulist.writeto(outputfile)
def calculateCM(SynthObj, solarWl, rebinnedSpectrum, nominalWave,
nominalSpectrum):
IM = numpy.zeros((SynthObj.lineList.numLines + 2, len(solarWl)))
for i in range(SynthObj.lineList.numLines):
SynthObj.lineList.perturbLine(i, 0.3)
wave, flux = SynthObj.run()
plus = SpectralTools.binSpectrum(flux, wave, solarWl)
SynthObj.lineList.perturbLine(i, -0.3)
wave, flux = SynthObj.run()
minus = SpectralTools.binSpectrum(flux, wave, solarWl)
IM[i, :] = (plus - minus) / 0.6
#Continuum Level
plus = rebinnedSpectrum.copy() + 0.005
minus = rebinnedSpectrum.copy() - 0.005
IM[-1, :] = (plus - minus) / 0.01
plus = SpectralTools.binSpectrum(nominalSpectrum, nominalWave + 0.1,
solarWl)
minus = SpectralTools.binSpectrum(nominalSpectrum, nominalWave - 0.1,
solarWl)
edges = (plus != 0) & (minus != 0)
IM[-2, edges] = (plus[edges] - minus[edges]) / (0.2)
nFilt = Synth.lineList.numLines - 10
dims = IM.shape
U, S, V = scipy.linalg.svd(IM)
D = 1.0 / (S[0:-nFilt])
S[-nFilt:] = 0.0
newS = numpy.zeros((dims[0], dims[1]))
I = [i for i in range(dims[1])]
for i in range(len(D)):
newS[i][i] = D[i]
S = newS.copy()
CM = numpy.array(scipy.matrix(V.T.dot(S.T.dot(U.T)),
dtype=numpy.float32)).T
hdu = pyfits.PrimaryHDU(CM)
hdu.writeto('CommandMatrix_new.fits', clobber=True)
def writefits2d(a, fitsfile):
""" writefits2d -- write out an array to a fits file
a -- array (numarray or Numeric)
fitsfile -- output filename
"""
fitsobj = pyfits.HDUList()
hdu = pyfits.PrimaryHDU()
hdr = hdu.header
hdr.update('crval1', 0.)
hdr.update('crval2', 0.)
hdr.update('crpix1', a.shape[0] / 2.)
hdr.update('crpix2', a.shape[1] / 2.)
# Check if we already have a numarray array, if not convert
x = N.arange(2)
print type(a)
if type(a) != type(x):
hdu.data = N.array(a.tolist())
else:
hdu.data = a.copy()
fitsobj.append(hdu)
fitsobj.writeto(fitsfile)
def test_nonstandard_hdu(self):
"""
Regression test for https://trac.assembla.com/pyfits/ticket/157
Tests that "Nonstandard" HDUs with SIMPLE = F are read and written
without prepending a superfluous and unwanted standard primary HDU.
"""
data = np.arange(100, dtype=np.uint8)
hdu = fits.PrimaryHDU(data=data)
hdu.header['SIMPLE'] = False
hdu.writeto(self.temp('test.fits'))
info = [(0, '', 'NonstandardHDU', 5, (), '', '')]
with fits.open(self.temp('test.fits')) as hdul:
assert hdul.info(output=False) == info
# NonstandardHDUs just treat the data as an unspecified array of
# bytes. The first 100 bytes should match the original data we
# passed in...the rest should be zeros padding out the rest of the
# FITS block
assert (hdul[0].data[:100] == data).all()
assert (hdul[0].data[100:] == 0).all()
def fitsout(s3d, plane, smoothx=0, smoothy=0, name='', unit=''):
""" Write the given plane into a fits file. Uses header of the original
data. Returns nothing, but write a fits file.
Parameters
----------
plane : np.array
data to store in fits file
smoothx : int
possible Gaussian smoothing length in x-coordinate (default 0)
smoothy : int
possible Gaussian smoothing length in y-coordinate (default 0)
name : str
Name to use in fits file name
"""
planeout = '%s_%s_%s.fits' % (s3d.inst, s3d.output, name)
if smoothx > 0:
plane = blur_image(plane, smoothx, smoothy)
if os.path.isfile(planeout):
os.remove(planeout)
hdu = pyfits.HDUList()
headimg = s3d.head.copy()
headimgprim = s3d.headprim.copy()
headimg['NAXIS'] = 2
for delhead in [
'NAXIS3', 'CD3_3', 'CD1_3', 'CD2_3', 'CD3_1', 'CD3_2', 'CRPIX3',
'CRVAL3', 'CTYPE3', 'CUNIT3'
]:
del headimg[delhead],
if unit != '':
headimg['BUNIT'] = unit
headimgprim['BUNIT'] = unit
hdu.append(pyfits.PrimaryHDU(header=headimgprim))
hdu.append(pyfits.ImageHDU(data=plane, header=headimg))
hdu.writeto(planeout)
def write_slits(spectra, crpix, crval, scale, out_prefix, slitnum):
num = 1
for spec in spectra:
for item in spec:
if item.size == 4:
hdu = pyfits.PrimaryHDU()
hdu.header.update('CENTER', item[2])
hdu.header.update('WIDTH', item[3])
hdulist = pyfits.HDUList([hdu])
else:
thdu = pyfits.ImageHDU(item)
thdu.header.update('CRVAL1', crval)
thdu.header.update('CD1_1', scale)
thdu.header.update('CRPIX1', crpix)
thdu.header.update('CRVAL2', 1)
thdu.header.update('CD2_2', 1)
thdu.header.update('CRPIX2', 1)
thdu.header.update('CTYPE1', 'LINEAR')
hdulist.append(thdu)
outname = out_prefix + "_spec_%02d_%02d.fits" % (slitnum, num)
hdulist.writeto(outname)
num += 1
def Data_2_Fits(FileFolder,
FitsName,
Header,
Wavelength,
Intensity,
NewKeyWord=None):
Primary_HDU = pyfits.PrimaryHDU(header=Header)
if NewKeyWord != None:
Primary_HDU.header.update(NewKeyWord[0], NewKeyWord[1])
Column1 = pyfits.Column(name='Wave', format='E', array=Wavelength)
Column2 = pyfits.Column(name='Int', format='E', array=Intensity)
Columns = pyfits.ColDefs([Column1, Column2])
Table_HDU = pyfits.new_table(Columns)
HDU_list = pyfits.HDUList([Primary_HDU, Table_HDU])
HDU_list.writeto(FileFolder + FitsName, clobber=True)
return
def write_fitsfile(objname,field,Lobj,Lobjerr,Lfieldlim,Lfieldlimerr,Llimsig,
outputname='./balff_data/objects_info.fits',verbose=True):
"""
Create a (minimal) fits file containg data array of objects found in the fields
described in ./balff_data/fields_info.txt on the format expected by balff_mpd.py
--- INPUT ---
objname Name of objects (list of strings)
field Field the object was found in (list of strings)
Lobj Absolute luminoisity of object. Can be obtained from observed apparent magnitude with
balff_utilities.Mabs2L( balff_utilities.magapp2abs(magapp,zobj,Av=Avval,band=magband) )
Lobjerr Uncertainty on absolute Lobj
Lfieldlim Absolute luminosity corresponding to the limiting magnitude for the filed provided in
./balff_data/fields_info.txt
Lfieldlimerr Uncertainty on Lfieldlim
Llimsig Number of sigmas the limitng luminoisity Lfieldlim corresponds to
--- EXAMPLE OF USE ---
see bcda.test_write_fitsfile_onBoRG() below
"""
if verbose: print ' - Setting up output file '
col1 = pyfits.Column(name='OBJNAME' , format='A30', array=objname)
col2 = pyfits.Column(name='FIELD' , format='A30', array=field)
col3 = pyfits.Column(name='LOBJ' , format='D' , array=Lobj)
col4 = pyfits.Column(name='LOBJERR' , format='D' , array=Lobjerr)
col5 = pyfits.Column(name='LFIELDLIM' , format='D' , array=Lfieldlim)
col6 = pyfits.Column(name='LFIELDLIMERR' , format='D' , array=Lfieldlimerr)
cols = pyfits.ColDefs([col1 ,col2 ,col3 ,col4 ,col5 ,col6])
tbhdu = pyfits.new_table(cols) # creating table header
# writing hdrkeys: '---KEY--', '----------------MAX LENGTH COMMENT-------------'
tbhdu.header.append(('LLIMSIG ',Llimsig ,'Sigmas field limiting lum. corresponds to'),end=True)
if verbose: print ' - Writing simulated data to fits table '+outputname
hdu = pyfits.PrimaryHDU() # creating primary (minimal) header
thdulist = pyfits.HDUList([hdu, tbhdu]) # combine primary and table header to hdulist
thdulist.writeto(outputname,clobber=True) # write fits file (clobber=True overwrites excisting file)
return outputname
def test_update_with_truncated_header(self):
"""
Regression test for https://trac.assembla.com/pyfits/ticket/148
Test that saving an update where the header is shorter than the
original header doesn't leave a stump from the old header in the file.
"""
data = np.arange(100)
hdu = fits.PrimaryHDU(data=data)
idx = 1
while len(hdu.header) < 34:
hdu.header['TEST%d' % idx] = idx
idx += 1
hdu.writeto(self.temp('temp.fits'), checksum=True)
with fits.open(self.temp('temp.fits'), mode='update') as hdul:
# Modify the header, forcing it to be rewritten
hdul[0].header['TEST1'] = 2
with fits.open(self.temp('temp.fits')) as hdul:
assert (hdul[0].data == data).all()
def Math():
global Operand_1
Operator = OP.get()
SOP = Second_Operand()
for f in Operand_1:
print("Operand 1")
try:
Data, Header = (read_file(f, 1, 1))
except IOError:
print("Can't open file:", f)
try:
if (Operator == 1):
Data = Data + SOP
Name = "Add"
elif (Operator == 2):
Data = Data - SOP
Name = "Subtract"
elif (Operator == 3):
Data = Data * SOP
Name = "Multiply"
elif (Operator == 4):
Data = Data / SOP
Name = "Divide"
except:
print("Math error")
print("Result of " + Name)
Get_Stat(Data)
if Show_frame.get(): Draw_pic(Data, Name, 3)
Data = np.float32(Data)
new_name, extension = os.path.splitext(f)
new_name = new_name + '_' + Name + '.fits'
Header['HISTORY'] = Name
hdu = pyfits.PrimaryHDU(Data, Header)
hdulist = pyfits.HDUList([hdu])
hdulist.writeto(new_name, clobber=True, output_verify='ignore')
print("Data saved to " + new_name)
print('\r')