def load_file(self, filepath, numhdu=None, **kwargs):
self.logger.debug("Loading file '%s' ..." % (filepath))
self.clear_metadata()
# These keywords might be provided but not used.
kwargs.pop('allow_numhdu_override')
kwargs.pop('memmap')
info = iohelper.get_fileinfo(filepath)
if numhdu is None:
numhdu = info.numhdu
try:
with fits.open(filepath, 'readonly') as in_f:
self.load_hdu(in_f[numhdu], **kwargs)
except Exception as e:
self.logger.error("Error reading table from file: {0}".format(
str(e)))
# Set the table name if no name currently exists for this table
# TODO: should this *change* the existing name, if any?
if self.name is not None:
self.set(name=self.name)
else:
name = self.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
name += iohelper.get_hdu_suffix(numhdu)
self.set(name=name)
self.set(path=filepath, idx=numhdu)
def open_files(self, path):
"""Load file(s) -- image*.fits, image*.fits[ext].
Returns success code (True or False).
"""
paths = []
input_list = _patt.findall(path)
if not input_list:
input_list = [path]
for path in input_list:
# Strips trailing wildcard
if path.endswith('*'):
path = path[:-1]
if os.path.isdir(path):
continue
self.logger.debug('Opening files matched by {0}'.format(path))
info = iohelper.get_fileinfo(path)
ext = iohelper.get_hdu_suffix(info.numhdu)
files = glob.glob(info.filepath) # Expand wildcard
paths.extend(['{0}{1}'.format(f, ext) for f in files])
if len(paths) > 0:
self.load_paths(paths)
return True
return False
def get_hdu(self, numhdu, dstobj=None, **kwargs):
if numhdu is None:
numhdu, hdu = self.find_first_good_hdu()
elif numhdu in self.hdu_db:
d = self.hdu_db[numhdu]
hdu = self.fits_f[d.index]
# normalize the index
numhdu = (d.name, d.extver)
else:
hdu = self.fits_f[numhdu]
# normalize the hdu index, if possible
name = hdu.name
extver = hdu.ver
_numhdu = (name, extver)
if ((len(name) > 0) and (_numhdu in self.fits_f)
and hdu is self.fits_f[_numhdu]):
numhdu = _numhdu
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=self.fits_f, **kwargs)
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = self.fileinfo.name
if '[' not in name:
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=self.fileinfo.filepath, idx=numhdu)
return dstobj
def open_files(self, path):
"""Load file(s) -- image*.fits, image*.fits[ext].
Returns success code (True or False).
"""
paths = []
input_list = _patt.findall(path)
if not input_list:
input_list = [path]
for path in input_list:
# Strips trailing wildcard
if path.endswith('*'):
path = path[:-1]
if os.path.isdir(path):
continue
self.logger.debug('Opening files matched by {0}'.format(path))
info = iohelper.get_fileinfo(path)
ext = iohelper.get_hdu_suffix(info.numhdu)
files = glob.glob(info.filepath) # Expand wildcard
paths.extend(['{0}{1}'.format(f, ext) for f in files])
if len(paths) > 0:
self.load_paths(paths)
return True
return False
def load_file(self,
filepath,
numhdu=None,
naxispath=None,
allow_numhdu_override=True,
memmap=None):
self.logger.debug("Loading file '%s' ..." % (filepath))
self.clear_metadata()
ahdr = self.get_header()
info = iohelper.get_fileinfo(filepath)
if numhdu is None:
numhdu = info.numhdu
_data, numhdu_, naxispath = self.io.load_file(info.filepath,
ahdr,
numhdu=numhdu,
naxispath=naxispath,
phdr=self._primary_hdr,
memmap=memmap)
# this is a handle to the full data array
self._md_data = _data
if naxispath is None:
naxispath = []
# Drill down to 2D data slice
if len(naxispath) == 0:
naxispath = ([0] * (len(_data.shape) - 2))
# Set the image name if no name currently exists for this image
# TODO: should this *change* the existing name, if any?
if not (self.name is None):
self.set(name=self.name)
else:
name = self.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
if (numhdu is None) or allow_numhdu_override:
numhdu = numhdu_
name += iohelper.get_hdu_suffix(numhdu)
self.set(name=name)
self.set(path=filepath, idx=numhdu)
self.set_naxispath(naxispath)
# Try to make a wcs object on the header
# TODO: in order to do more sophisticated WCS (e.g. distortion
# correction) that requires info in additional headers we need
# to pass additional information to the wcs class
#self.wcs.load_header(hdu.header, fobj=fobj)
self.wcs.load_header(ahdr)
def popup(self, title, callfn, initialdir=None, filename=None):
"""Let user select and load file(s). This allows wildcards and
extensions, like in FBrowser.
Parameters
----------
title : str
Title for the file dialog.
callfn : func
Function used to open the file(s).
initialdir : str or `None`
Directory for file dialog.
filename : str
Filter for file dialog.
"""
self.cb = callfn
filenames = QtGui.QFileDialog.getOpenFileNames(self.parent, title,
initialdir, filename)
# Special handling for PyQt5, see
# https://www.reddit.com/r/learnpython/comments/2xhagb/pyqt5_trouble_with_openinggetting_the_name_of_the/
if ginga.toolkit.get_toolkit() == 'qt5':
filenames = filenames[0]
all_paths = []
for filename in filenames:
# Special handling for wildcard or extension.
# This is similar to open_files() in FBrowser plugin.
if '*' in filename or '[' in filename:
info = iohelper.get_fileinfo(filename)
ext = iohelper.get_hdu_suffix(info.numhdu)
files = glob.glob(info.filepath) # Expand wildcard
paths = ['{0}{1}'.format(f, ext) for f in files]
if self.all_at_once:
all_paths.extend(paths)
else:
for path in paths:
self.cb(path)
else:
# Normal load
if self.all_at_once:
all_paths.append(filename)
else:
self.cb(filename)
if self.all_at_once and len(all_paths) > 0:
self.cb(all_paths)
def popup(self, title, callfn, initialdir=None, filename=None):
"""Let user select and load file(s). This allows wildcards and
extensions, like in FBrowser.
Parameters
----------
title : str
Title for the file dialog.
callfn : func
Function used to open the file(s).
initialdir : str or `None`
Directory for file dialog.
filename : str
Filter for file dialog.
"""
self.cb = callfn
filenames = QtGui.QFileDialog.getOpenFileNames(
self.parent, title, initialdir, filename)
# Special handling for PyQt5, see
# https://www.reddit.com/r/learnpython/comments/2xhagb/pyqt5_trouble_with_openinggetting_the_name_of_the/
if ginga.toolkit.get_toolkit() == 'qt5':
filenames = filenames[0]
all_paths = []
for filename in filenames:
# Special handling for wildcard or extension.
# This is similar to open_files() in FBrowser plugin.
if '*' in filename or '[' in filename:
info = iohelper.get_fileinfo(filename)
ext = iohelper.get_hdu_suffix(info.numhdu)
files = glob.glob(info.filepath) # Expand wildcard
paths = ['{0}{1}'.format(f, ext) for f in files]
if self.all_at_once:
all_paths.extend(paths)
else:
for path in paths:
self.cb(path)
else:
# Normal load
if self.all_at_once:
all_paths.append(filename)
else:
self.cb(filename)
if self.all_at_once and len(all_paths) > 0:
self.cb(all_paths)
def load_file(self, filepath, numhdu=None, naxispath=None,
allow_numhdu_override=True, memmap=None):
self.logger.debug("Loading file '%s' ..." % (filepath))
self.clear_metadata()
ahdr = self.get_header()
info = iohelper.get_fileinfo(filepath)
if numhdu is None:
numhdu = info.numhdu
_data, numhdu_, naxispath = self.io.load_file(info.filepath, ahdr,
numhdu=numhdu,
naxispath=naxispath,
phdr=self._primary_hdr,
memmap=memmap)
# this is a handle to the full data array
self._md_data = _data
if naxispath is None:
naxispath = []
# Drill down to 2D data slice
if len(naxispath) == 0:
naxispath = ([0] * (len(_data.shape)-2))
# Set the image name if no name currently exists for this image
# TODO: should this *change* the existing name, if any?
if not (self.name is None):
self.set(name=self.name)
else:
name = self.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
if (numhdu is None) or allow_numhdu_override:
numhdu = numhdu_
name += iohelper.get_hdu_suffix(numhdu)
self.set(name=name)
self.set(path=filepath, idx=numhdu)
self.set_naxispath(naxispath)
# Try to make a wcs object on the header
# TODO: in order to do more sophisticated WCS (e.g. distortion
# correction) that requires info in additional headers we need
# to pass additional information to the wcs class
#self.wcs.load_header(hdu.header, fobj=fobj)
self.wcs.load_header(ahdr)
def set_hdu(self, idx):
self.logger.debug("Loading fits hdu #%d" % (idx))
# determine canonical index of this HDU
info = self.file_obj.hdu_info[idx]
aidx = (info.name, info.extver)
if aidx not in self.file_obj.hdu_db:
aidx = idx
sfx = get_hdu_suffix(aidx)
# See if this HDU is still in the channel's datasrc
imname = self.name_pfx + sfx
chname = self.chname
chinfo = self.channel
if imname in chinfo.datasrc:
self.curhdu = idx
image = chinfo.datasrc[imname]
self.fv.switch_name(chname, imname)
return
# Nope, we'll have to load it
self.logger.debug("HDU %d not in memory; refreshing from file" % (idx))
try:
self.curhdu = idx
dims = [0, 0]
info = self.file_obj.hdu_info[idx]
image = self.file_obj.get_hdu(idx)
# create a future for reconstituting this HDU
future = Future.Future()
future.freeze(self.fv.load_image, self.img_path, idx=aidx)
image.set(path=self.img_path,
idx=aidx,
name=imname,
image_future=future)
self.fv.add_image(imname, image, chname=chname)
self.logger.debug("HDU #%d loaded." % (idx))
except Exception as e:
errmsg = "Error loading FITS HDU #%d: %s" % (idx, str(e))
self.logger.error(errmsg)
self.fv.show_error(errmsg, raisetab=True)
def open_files(self, path):
"""Load file(s) -- image*.fits, image*.fits[ext].
Returns success code (True or False).
"""
# Strips trailing wildcard
if path.endswith('*'):
path = path[:-1]
if os.path.isdir(path):
return False
self.logger.debug('Opening files matched by {0}'.format(path))
info = iohelper.get_fileinfo(path)
ext = iohelper.get_hdu_suffix(info.numhdu)
files = glob.glob(info.filepath) # Expand wildcard
paths = ['{0}{1}'.format(f, ext) for f in files]
self.fv.gui_do(self.fitsimage.make_callback, 'drag-drop', paths)
return True
def open_files(self, path):
"""Load file(s) -- image*.fits, image*.fits[ext].
Returns success code (True or False).
"""
# Strips trailing wildcard
if path.endswith('*'):
path = path[:-1]
if os.path.isdir(path):
return False
self.logger.debug('Opening files matched by {0}'.format(path))
info = iohelper.get_fileinfo(path)
ext = iohelper.get_hdu_suffix(info.numhdu)
files = glob.glob(info.filepath) # Expand wildcard
paths = ['{0}{1}'.format(f, ext) for f in files]
self.load_paths(paths)
return True
def gui_load_file(self, initialdir=None):
if self.filesel.exec_():
filename = list(map(str, list(self.filesel.selectedFiles())))[0]
# Normal load
if os.path.isfile(filename):
self.logger.debug('Loading {0}'.format(filename))
self.load_file(filename)
# Fancy load (first file only)
# TODO: If load all the matches, might get QPainter errors
else:
info = iohelper.get_fileinfo(filename)
ext = iohelper.get_hdu_suffix(info.numhdu)
paths = ['{0}{1}'.format(fname, ext)
for fname in glob.iglob(info.filepath)]
self.logger.debug(
'Found {0} and only loading {1}'.format(paths, paths[0]))
self.load_file(paths[0])
def set_hdu(self, idx):
self.logger.debug("Loading fits hdu #%d" % (idx))
# determine canonical index of this HDU
info = self.file_obj.hdu_info[idx]
aidx = (info.name, info.extver)
if aidx not in self.file_obj.hdu_db:
aidx = idx
sfx = iohelper.get_hdu_suffix(aidx)
# See if this HDU is still in the channel's datasrc
imname = self.name_pfx + sfx
chname = self.chname
chinfo = self.channel
if imname in chinfo.datasrc:
self.curhdu = idx
image = chinfo.datasrc[imname]
self.fv.switch_name(chname, imname)
return
# Nope, we'll have to load it
self.logger.debug("HDU %d not in memory; refreshing from file" % (idx))
try:
self.curhdu = idx
info = self.file_obj.hdu_info[idx]
image = self.file_obj.get_hdu(idx)
# create a future for reconstituting this HDU
future = Future.Future()
future.freeze(self.fv.load_image, self.img_path, idx=aidx)
image.set(path=self.img_path, idx=aidx, name=imname,
image_future=future)
self.fv.add_image(imname, image, chname=chname)
self.logger.debug("HDU #%d loaded." % (idx))
except Exception as e:
errmsg = "Error loading FITS HDU #%d: %s" % (
idx, str(e))
self.logger.error(errmsg)
self.fv.show_error(errmsg, raisetab=True)
def load_file_cb(self, w, rsp):
w.hide()
if rsp == 0:
return
filename = w.selected_files()[0]
# Normal load
if os.path.isfile(filename):
self.logger.debug('Loading {0}'.format(filename))
self.load_file(filename)
# Fancy load (first file only)
# TODO: If load all the matches, might get (Qt) QPainter errors
else:
info = iohelper.get_fileinfo(filename)
ext = iohelper.get_hdu_suffix(info.numhdu)
paths = ['{0}{1}'.format(fname, ext)
for fname in glob.iglob(info.filepath)]
self.logger.debug(
'Found {0} and only loading {1}'.format(paths, paths[0]))
self.load_file(paths[0])
def get_hdu(self, numhdu, dstobj=None, **kwargs):
if numhdu is None:
numhdu, hdu = self.find_first_good_hdu()
elif numhdu in self.hdu_db:
d = self.hdu_db[numhdu]
hdu = self.fits_f[d.index]
# normalize the index
numhdu = (d.name, d.extver)
else:
hdu = self.fits_f[numhdu]
# normalize the hdu index, if possible
hduinfo = hdu.get_info()
name = hduinfo['extname']
extver = hduinfo['extver']
_numhdu = (name, extver)
if ((len(name) > 0) and (_numhdu in self.fits_f) and
hdu is self.fits_f[_numhdu]):
numhdu = _numhdu
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=self.fits_f,
**kwargs)
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = self.fileinfo.name
if '[' not in name:
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=self.fileinfo.filepath, idx=numhdu)
return dstobj
def load_file_cb(self, w, rsp):
w.hide()
if rsp == 0:
return
filename = w.selected_files()[0]
# Normal load
if os.path.isfile(filename):
self.logger.debug('Loading {0}'.format(filename))
self.load_file(filename)
# Fancy load (first file only)
# TODO: If load all the matches, might get (Qt) QPainter errors
else:
info = iohelper.get_fileinfo(filename)
ext = iohelper.get_hdu_suffix(info.numhdu)
paths = [
'{0}{1}'.format(fname, ext)
for fname in glob.iglob(info.filepath)
]
self.logger.debug('Found {0} and only loading {1}'.format(
paths, paths[0]))
self.load_file(paths[0])
def load_file(self,
filespec,
numhdu=None,
dstobj=None,
memmap=None,
**kwargs):
info = iohelper.get_fileinfo(filespec)
if not info.ondisk:
raise FITSError("File does not appear to be on disk: %s" %
(info.url))
filepath = info.filepath
if numhdu is None:
numhdu = info.numhdu
self.logger.debug("Loading file '%s' ..." % (filepath))
fits_f = fitsio.FITS(filepath, memmap=memmap)
try:
if numhdu is None:
found_valid_hdu = False
for i in range(len(fits_f)):
hdu = fits_f[i]
hduinfo = hdu.get_info()
#print(hduinfo)
name = hduinfo['extname']
extver = hduinfo['extver']
if not ('ndims' in hduinfo) or (hduinfo['ndims'] == 0):
# compressed FITS file or non-pixel data hdu?
continue
#print(dir(hdu))
# Looks good, let's try it
found_valid_hdu = True
if len(name) == 0:
numhdu = i
else:
numhdu = (name, extver)
break
if not found_valid_hdu:
# Just load the header
hdu = fits_f[0]
hduinfo = hdu.get_info()
name = hduinfo['extname']
extver = hduinfo['extver']
if len(name) == 0:
numhdu = 0
else:
numhdu = (name, extver)
elif isinstance(numhdu, (int, str)):
hdu = fits_f[numhdu]
hduinfo = hdu.get_info()
name = hduinfo['extname']
extver = hduinfo['extver']
if len(name) > 0:
numhdu = (name, extver)
self.logger.debug("HDU index looks like: %s" % str(numhdu))
hdu = fits_f[numhdu]
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=fits_f, **kwargs)
# Read PRIMARY header
#self.fromHDU(fits_f[0], phdr)
finally:
fits_f.close()
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=filepath, idx=numhdu)
return dstobj
def set_hdu(self, idx):
self.logger.debug("Loading fits hdu #%d" % (idx))
# determine canonical index of this HDU
info = self.hdu_info[idx]
aidx = (info.name, info.extver)
if aidx not in self.fits_f:
aidx = idx
sfx = get_hdu_suffix(aidx)
# See if this HDU is still in the channel's datasrc
imname = self.name_pfx + sfx
chname = self.chname
chinfo = self.channel
if imname in chinfo.datasrc:
self.curhdu = idx
self.image = chinfo.datasrc[imname]
self.fv.switch_name(chname, imname)
# Still need to build datacube profile
hdu = self.fits_f[idx]
if hdu.data is not None:
dims = list(hdu.data.shape)
dims.reverse()
self.build_naxis(dims)
return
# Nope, we'll have to load it
self.logger.debug("HDU %d not in memory; refreshing from file" % (idx))
try:
self.curhdu = idx
dims = [0, 0]
hdu = self.fits_f[idx]
image = self.fv.fits_opener.load_hdu(hdu, fobj=self.fits_f)
self.image = image
if hdu.data is None:
# <- empty data part to this HDU
self.logger.warning("Empty data part in HDU #%d" % (idx))
elif info['htype'].lower() in ('bintablehdu', 'tablehdu',):
dims = [0, 0]
elif info['htype'].lower() not in ('imagehdu', 'primaryhdu'):
self.logger.warning("HDU #%d is not an image" % (idx))
else:
dims = list(hdu.data.shape)
dims.reverse()
image.load_hdu(hdu, fobj=self.fits_f)
# create a future for reconstituting this HDU
future = Future.Future()
future.freeze(self.fv.load_image, self.path, idx=aidx)
image.set(path=self.path, idx=aidx, name=imname,
image_future=future)
self.fv.add_image(imname, image, chname=chname)
self.build_naxis(dims)
self.logger.debug("HDU #%d loaded." % (idx))
except Exception as e:
errmsg = "Error loading FITS HDU #%d: %s" % (
idx, str(e))
self.logger.error(errmsg)
self.fv.show_error(errmsg, raisetab=False)
def load_file(self,
filespec,
numhdu=None,
dstobj=None,
memmap=None,
**kwargs):
info = iohelper.get_fileinfo(filespec)
if not info.ondisk:
raise FITSError("File does not appear to be on disk: %s" %
(info.url))
filepath = info.filepath
if numhdu is None:
numhdu = info.numhdu
self.logger.debug("Loading file '%s' ..." % (filepath))
with pyfits.open(filepath, 'readonly', memmap=memmap) as fits_f:
# this seems to be necessary now for some fits files...
try:
fits_f.verify('fix')
except Exception as e:
# Let's hope for the best!
self.logger.warn("Problem verifying fits file '%s': %s" %
(filepath, str(e)))
if numhdu is None:
hduinfo = fits_f.info(output=False)
extver_db = {}
found_valid_hdu = False
for i in range(len(fits_f)):
hdu = fits_f[i]
tup = hduinfo[i]
name = tup[1]
# figure out the EXTVER for this HDU
extver = extver_db.setdefault(name, 0)
extver += 1
extver_db[name] = extver
# rule out HDUs we can't deal with
if not isinstance(hdu, (
pyfits.ImageHDU,
pyfits.PrimaryHDU,
pyfits.TableHDU,
pyfits.BinTableHDU,
)):
continue
if not isinstance(hdu.data, numpy.ndarray):
# We need to open a numpy array
continue
if 0 in hdu.data.shape:
# non-pixel or zero-length data hdu?
continue
# Looks good, let's try it
found_valid_hdu = True
_numhdu = (name, extver)
if (len(name) == 0) or (_numhdu not in fits_f):
numhdu = i
else:
numhdu = _numhdu
break
if not found_valid_hdu:
# Load just the header
hdu = fits_f[0]
name = hdu.name
extver = hdu.ver
_numhdu = (name, extver)
if (len(name) == 0) or (_numhdu not in fits_f):
numhdu = 0
else:
numhdu = _numhdu
elif isinstance(numhdu, (int, str)):
hdu = fits_f[numhdu]
name = hdu.name
extver = hdu.ver
_numhdu = (name, extver)
if (len(name) > 0) and (_numhdu in fits_f):
numhdu = _numhdu
self.logger.debug("HDU index looks like: %s" % str(numhdu))
hdu = fits_f[numhdu]
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=fits_f, **kwargs)
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
## if (numhdu is None) or allow_numhdu_override:
## numhdu = numhdu_
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=filepath, idx=numhdu)
return dstobj
def load_file(self, filespec, numhdu=None, dstobj=None, memmap=None,
**kwargs):
info = iohelper.get_fileinfo(filespec)
if not info.ondisk:
raise FITSError("File does not appear to be on disk: %s" % (
info.url))
filepath = info.filepath
if numhdu is None:
numhdu = info.numhdu
self.logger.debug("Loading file '%s' ..." % (filepath))
fits_f = fitsio.FITS(filepath, memmap=memmap)
try:
if numhdu is None:
found_valid_hdu = False
for i in range(len(fits_f)):
hdu = fits_f[i]
hduinfo = hdu.get_info()
#print(hduinfo)
name = hduinfo['extname']
extver = hduinfo['extver']
if not ('ndims' in hduinfo) or (hduinfo['ndims'] == 0):
# compressed FITS file or non-pixel data hdu?
continue
#print(dir(hdu))
# Looks good, let's try it
found_valid_hdu = True
if len(name) == 0:
numhdu = i
else:
numhdu = (name, extver)
break
if not found_valid_hdu:
# Just load the header
hdu = fits_f[0]
hduinfo = hdu.get_info()
name = hduinfo['extname']
extver = hduinfo['extver']
if len(name) == 0:
numhdu = 0
else:
numhdu = (name, extver)
elif isinstance(numhdu, (int, str)):
hdu = fits_f[numhdu]
hduinfo = hdu.get_info()
name = hduinfo['extname']
extver = hduinfo['extver']
if len(name) > 0:
numhdu = (name, extver)
self.logger.debug("HDU index looks like: %s" % str(numhdu))
hdu = fits_f[numhdu]
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=fits_f,
**kwargs)
# Read PRIMARY header
#self.fromHDU(fits_f[0], phdr)
finally:
fits_f.close()
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=filepath, idx=numhdu)
return dstobj
def load_file(self, filespec, numhdu=None, dstobj=None, memmap=None,
**kwargs):
info = iohelper.get_fileinfo(filespec)
if not info.ondisk:
raise FITSError("File does not appear to be on disk: %s" % (
info.url))
filepath = info.filepath
if numhdu is None:
numhdu = info.numhdu
self.logger.debug("Loading file '%s' ..." % (filepath))
with pyfits.open(filepath, 'readonly', memmap=memmap) as fits_f:
# this seems to be necessary now for some fits files...
try:
fits_f.verify('fix')
except Exception as e:
# Let's hope for the best!
self.logger.warn("Problem verifying fits file '%s': %s" % (
filepath, str(e)))
if numhdu is None:
try:
# this can fail for certain FITS files, with a "name undefined"
# error bubbling up from astropy
hduinfo = fits_f.info(output=False)
except Exception as e:
# if so, this insures that name will be translated into the
# HDU index below
hduinfo = tuple((None, '') for i in range(len(fits_f)))
extver_db = {}
found_valid_hdu = False
for i in range(len(fits_f)):
hdu = fits_f[i]
tup = hduinfo[i]
name = tup[1]
# figure out the EXTVER for this HDU
extver = extver_db.setdefault(name, 0)
extver += 1
extver_db[name] = extver
# rule out HDUs we can't deal with
if not isinstance(hdu, (pyfits.ImageHDU,
pyfits.PrimaryHDU,
pyfits.TableHDU,
pyfits.BinTableHDU,
)):
continue
if not isinstance(hdu.data, numpy.ndarray):
# We need to open a numpy array
continue
if 0 in hdu.data.shape:
# non-pixel or zero-length data hdu?
continue
# Looks good, let's try it
found_valid_hdu = True
_numhdu = (name, extver)
if (len(name) == 0) or (_numhdu not in fits_f):
numhdu = i
else:
numhdu = _numhdu
break
if not found_valid_hdu:
# Load just the header
hdu = fits_f[0]
name = hdu.name
extver = hdu.ver
_numhdu = (name, extver)
if (len(name) == 0) or (_numhdu not in fits_f):
numhdu = 0
else:
numhdu = _numhdu
elif isinstance(numhdu, (int, str)):
hdu = fits_f[numhdu]
name = hdu.name
extver = hdu.ver
_numhdu = (name, extver)
if (len(name) > 0) and (_numhdu in fits_f):
numhdu = _numhdu
self.logger.debug("HDU index looks like: %s" % str(numhdu))
hdu = fits_f[numhdu]
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=fits_f,
**kwargs)
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = info.name
if ('[' not in name):
## if (numhdu is None) or allow_numhdu_override:
## numhdu = numhdu_
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=filepath, idx=numhdu)
return dstobj
def get_hdu(self, numhdu, dstobj=None, **kwargs):
if numhdu is None:
found_valid_hdu = False
for i, d in enumerate(self.hdu_info):
name = d.name
extver = d.extver
hdu = self.fits_f[i]
hduinfo = hdu.get_info()
if not ('ndims' in hduinfo) or (hduinfo['ndims'] == 0):
# compressed FITS file or non-pixel data hdu?
continue
if not hasattr(hdu, 'read'):
continue
data = hdu.read()
if not isinstance(data, np.ndarray):
# We need to open a numpy array
continue
if 0 in data.shape:
# non-pixel or zero-length data hdu?
continue
# Looks good, let's try it
found_valid_hdu = True
if len(name) == 0:
numhdu = i
else:
numhdu = (name, extver)
break
if not found_valid_hdu:
# Just load the header
hdu = self.fits_f[0]
d = self.hdu_info[0]
name = d.name
extver = d.extver
if len(name) == 0:
numhdu = 0
else:
numhdu = (name, extver)
elif isinstance(numhdu, (int, str)):
hdu = self.fits_f[numhdu]
hduinfo = hdu.get_info()
name = hduinfo['extname']
extver = hduinfo['extver']
if len(name) > 0:
numhdu = (name, extver)
self.logger.debug("HDU index looks like: %s" % str(numhdu))
hdu = self.fits_f[numhdu]
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=self.fits_f, **kwargs)
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = self.fileinfo.name
if '[' not in name:
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=self.fileinfo.filepath, idx=numhdu)
return dstobj
def get_hdu(self, numhdu, dstobj=None, **kwargs):
if numhdu is None:
found_valid_hdu = False
for i, d in enumerate(self.hdu_info):
name = d.name
hdu = self.fits_f[i]
# rule out HDUs we can't deal with
if not isinstance(hdu, (
pyfits.ImageHDU,
pyfits.CompImageHDU,
pyfits.PrimaryHDU,
pyfits.TableHDU,
pyfits.BinTableHDU,
)):
continue
if not isinstance(hdu.data, np.ndarray):
# We need to open a numpy array
continue
if 0 in hdu.data.shape:
# non-pixel or zero-length data hdu?
continue
# Looks good, let's try it
found_valid_hdu = True
extver = d.extver
_numhdu = (name, extver)
if (len(name) == 0) or (_numhdu not in self.fits_f):
numhdu = i
else:
numhdu = _numhdu
break
if not found_valid_hdu:
# Load just the header
hdu = self.fits_f[0]
d = self.hdu_info[0]
name = d.name
extver = d.extver
_numhdu = (name, extver)
if (len(name) == 0) or (_numhdu not in self.fits_f):
numhdu = 0
else:
numhdu = _numhdu
elif isinstance(numhdu, (int, str)):
hdu = self.fits_f[numhdu]
name = hdu.name
extver = hdu.ver
_numhdu = (name, extver)
if (len(name) > 0) and (_numhdu in self.fits_f):
numhdu = _numhdu
self.logger.debug("HDU index looks like: %s" % str(numhdu))
if numhdu not in self.fits_f:
info = self.hdu_db[numhdu]
hdu = self.fits_f[info.index]
else:
hdu = self.fits_f[numhdu]
dstobj = self.load_hdu(hdu, dstobj=dstobj, fobj=self.fits_f, **kwargs)
# Set the name if no name currently exists for this object
# TODO: should this *change* the existing name, if any?
name = dstobj.get('name', None)
if name is None:
name = self.fileinfo.name
if '[' not in name:
name += iohelper.get_hdu_suffix(numhdu)
dstobj.set(name=name)
dstobj.set(path=self.fileinfo.filepath, idx=numhdu)
return dstobj
def set_hdu(self, idx):
self.logger.debug("Loading fits hdu #%d" % (idx))
# determine canonical index of this HDU
info = self.hdu_info[idx]
aidx = (info.name, info.extver)
if aidx not in self.fits_f:
aidx = idx
sfx = get_hdu_suffix(aidx)
# See if this HDU is still in the channel's datasrc
imname = self.name_pfx + sfx
chname = self.chname
chinfo = self.channel
if imname in chinfo.datasrc:
self.curhdu = idx
self.image = chinfo.datasrc[imname]
self.fv.switch_name(chname, imname)
# Still need to build datacube profile
hdu = self.fits_f[idx]
if hdu.data is not None:
dims = list(hdu.data.shape)
dims.reverse()
self.build_naxis(dims)
return
# Nope, we'll have to load it
self.logger.debug("HDU %d not in memory; refreshing from file" % (idx))
try:
self.curhdu = idx
dims = [0, 0]
hdu = self.fits_f[idx]
image = self.fv.fits_opener.load_hdu(hdu, fobj=self.fits_f)
self.image = image
if hdu.data is None:
# <- empty data part to this HDU
self.logger.warning("Empty data part in HDU #%d" % (idx))
elif info['htype'].lower() in ('bintablehdu', 'tablehdu',):
dims = [0, 0]
elif info['htype'].lower() not in ('imagehdu', 'primaryhdu'):
self.logger.warning("HDU #%d is not an image" % (idx))
else:
dims = list(hdu.data.shape)
dims.reverse()
image.load_hdu(hdu, fobj=self.fits_f)
# create a future for reconstituting this HDU
future = Future.Future()
future.freeze(self.fv.load_image, self.path, idx=aidx)
image.set(path=self.path, idx=aidx, name=imname,
image_future=future)
self.fv.add_image(imname, image, chname=chname)
self.build_naxis(dims)
self.logger.debug("HDU #%d loaded." % (idx))
except Exception as e:
errmsg = "Error loading FITS HDU #%d: %s" % (
idx, str(e))
self.logger.error(errmsg)
self.fv.show_error(errmsg, raisetab=False)
