Python and the fits module (operating system interfaces): "IOError: [Errno 2] No such file or directory"

Question

It seems that for a script that I am attempting to use I am returning an error which is a little baffling, that is, in attempting to create a new file from an old file extension it is saying that the file that it is attempting to create does not exist? Could anyone explain why this is happening and perhaps a potential fix?

Here is the script I am using:

#Function to replace all NaNs in the exposure map by 0s and to replace the corresponding pixels in the sky and large scale sensitivity map by 0s.
def replace_nan(filename):
    #Print that all NaNs will be replaced by 0s in the exposure map and that the corresponding pixels in the sky and large scale sensitivity map will also be replaced by 0s.
    print "All NaNs will be replaced by 0s in " + filename + " and the corresponding pixels in the sky and large scale sensitivity map will also be replaced by 0s."
    #Open the exposure map, the corresponding sky and large scale sensitivity map and copy the primary headers (extension 0 of hdulist) to new hdulists.
    hdulist_ex = fits.open(filename)
    new_hdu_header_ex = fits.PrimaryHDU(header=hdulist_ex[0].header)
    new_hdulist_ex = fits.HDUList([new_hdu_header_ex])
    hdulist_sk = fits.open(filename.replace("ex","sk_corrected"))
    new_hdu_header_sk = fits.PrimaryHDU(header=hdulist_sk[0].header)
    new_hdulist_sk = fits.HDUList([new_hdu_header_sk])
    hdulist_lss = fits.open(filename.replace("ex","lss_m"))
    new_hdu_header_lss = fits.PrimaryHDU(header=hdulist_lss[0].header)
    new_hdulist_lss = fits.HDUList([new_hdu_header_lss])

    #For all frames in the image: Create the mask and run the function replace_pix.
    for i in range(1,len(hdulist_ex)):
        mask = np.isnan(hdulist_ex[i].data)
        replace_pix(hdulist_ex[i],mask,new_hdulist_ex)
        replace_pix(hdulist_sk[i],mask,new_hdulist_sk)
        replace_pix(hdulist_lss[i],mask,new_hdulist_lss)

    #Write the new hdulists to new images.
    new_hdulist_ex.writeto(filename.replace(".img","_new.img"))
    new_hdulist_sk.writeto(filename.replace("ex.img","sk_new.img"))
    new_hdulist_lss.writeto(filename.replace("ex.img","lss_new.img"))

    #Print that all NaNs are replaced by 0s in the exposure map and that the corresponding pixels in the sky and large scale sensitivity map are also replaced by 0s.
    print "All NaNs are replaced by 0s in " + filename + " and the corresponding pixels in the sky and large scale sensitivity map are also replaced by 0s."

When running:

replace_nan("/Users/.../sw00031048001uw1_ex.img")

I get the following error:

IOError: [Errno 2] No such file or directory: '/Users/.../sw00031048001uw1_sk_corrected.img'

Full traceback:

---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
<ipython-input-10-af5110b477a1> in <module>()
----> 1 replace_nan('/Users/UCL_Astronomy/Documents/UCL/PHASG199/M33_SWIFT_corrected_usnob1_spec/sw00031048001uw1_ex.img')

<ipython-input-8-ca837d8e11f7> in replace_nan(filename)
      7     new_hdu_header_ex = fits.PrimaryHDU(header=hdulist_ex[0].header)
      8     new_hdulist_ex = fits.HDUList([new_hdu_header_ex])
----> 9     hdulist_sk = fits.open(filename.replace("ex","sk_corrected"))
     10     new_hdu_header_sk = fits.PrimaryHDU(header=hdulist_sk[0].header)
     11     new_hdulist_sk = fits.HDUList([new_hdu_header_sk])

//anaconda/lib/python2.7/site-packages/astropy/io/fits/hdu/hdulist.pyc in fitsopen(name, mode, memmap, save_backup, cache, **kwargs)
    127         raise ValueError('Empty filename: %s' % repr(name))
    128 
--> 129     return HDUList.fromfile(name, mode, memmap, save_backup, cache, **kwargs)
    130 
    131 

//anaconda/lib/python2.7/site-packages/astropy/io/fits/hdu/hdulist.pyc in fromfile(cls, fileobj, mode, memmap, save_backup, cache, **kwargs)
    269 
    270         return cls._readfrom(fileobj=fileobj, mode=mode, memmap=memmap,
--> 271                              save_backup=save_backup, cache=cache, **kwargs)
    272 
    273     @classmethod

//anaconda/lib/python2.7/site-packages/astropy/io/fits/hdu/hdulist.pyc in _readfrom(cls, fileobj, data, mode, memmap, save_backup, cache, **kwargs)
    790             if not isinstance(fileobj, _File):
    791                 # instantiate a FITS file object (ffo)
--> 792                 ffo = _File(fileobj, mode=mode, memmap=memmap, cache=cache)
    793             else:
    794                 ffo = fileobj

//anaconda/lib/python2.7/site-packages/astropy/io/fits/file.pyc in __init__(self, fileobj, mode, memmap, clobber, cache)
    135             self._open_fileobj(fileobj, mode, clobber)
    136         elif isinstance(fileobj, string_types):
--> 137             self._open_filename(fileobj, mode, clobber)
    138         else:
    139             self._open_filelike(fileobj, mode, clobber)

//anaconda/lib/python2.7/site-packages/astropy/io/fits/file.pyc in _open_filename(self, filename, mode, clobber)
    438             self._open_zipfile(self.name, mode)
    439         else:
--> 440             self._file = fileobj_open(self.name, PYFITS_MODES[mode])
    441             # Make certain we're back at the beginning of the file
    442         self._file.seek(0)

//anaconda/lib/python2.7/site-packages/astropy/io/fits/util.pyc in fileobj_open(filename, mode)
    412         """
    413 
--> 414         return open(filename, mode)
    415 
    416 

Answer 1

Look at the first line of your traceback:

----> 9     hdulist_sk =     fits.open(filename.replace("ex","sk_corrected"))

You're trying to open a file with the "corrected" filename before that file exists. fits.open is only for opening existing FITS files.