Exemplo n.º 1
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    def load_file(self, filespec, dstobj=None, **kwargs):
        info = iohelper.get_fileinfo(filespec)
        if not info.ondisk:
            raise ValueError("File does not appear to be on disk: %s" %
                             (info.url))

        filepath = info.filepath
        if dstobj is None:
            # Put here to avoid circular import
            from ginga.RGBImage import RGBImage
            dstobj = RGBImage(logger=self.logger)

        header = Header()
        metadata = {'header': header, 'path': filepath}

        data_np = self.imload(filepath, header)

        # TODO: set up the channel order correctly
        dstobj.set_data(data_np, metadata=metadata)

        if dstobj.name is not None:
            dstobj.set(name=dstobj.name)
        else:
            name = iohelper.name_image_from_path(filepath, idx=None)
            dstobj.set(name=name)

        dstobj.set(path=filepath, idx=None, image_loader=self.load_file)
        return dstobj
Exemplo n.º 2
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    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
Exemplo n.º 3
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    def load_file(self, filespec, dstobj=None, **kwargs):
        info = iohelper.get_fileinfo(filespec)
        if not info.ondisk:
            raise ValueError("File does not appear to be on disk: %s" % (
                info.url))

        filepath = info.filepath
        if dstobj is None:
            # Put here to avoid circular import
            from ginga.RGBImage import RGBImage
            dstobj = RGBImage(logger=self.logger)

        header = Header()
        metadata = {'header': header, 'path': filepath}

        data_np = self._imload(filepath, header)

        # TODO: set up the channel order correctly
        dstobj.set_data(data_np, metadata=metadata)

        if dstobj.name is not None:
            dstobj.set(name=dstobj.name)
        else:
            name = iohelper.name_image_from_path(filepath, idx=None)
            dstobj.set(name=name)

        dstobj.set(path=filepath, idx=None, image_loader=self.load_file)
        return dstobj
Exemplo n.º 4
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    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
Exemplo n.º 5
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    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)
Exemplo n.º 6
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    def open_file(self, filespec, 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))

        self.fileinfo = info
        filepath = info.filepath

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = pyfits.open(filepath, 'readonly', memmap=memmap)
        self.fits_f = 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)))

        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)))

        idx = 0
        extver_db = {}
        self.hdu_info = []
        self.hdu_db = {}

        for tup in _hduinfo:
            name = tup[1]
            # figure out the EXTVER for this HDU
            extver = extver_db.setdefault(name, 0)
            extver += 1
            extver_db[name] = extver

            # prepare a record of pertinent info about the HDU for
            # lookups by numerical index or (NAME, EXTVER)
            d = Bunch.Bunch(index=idx, name=name, extver=extver)
            if len(tup) > 5:
                d.setvals(htype=tup[2], dtype=tup[5])
            self.hdu_info.append(d)
            # different ways of accessing this HDU:
            # by numerical index
            self.hdu_db[idx] = d
            # by (hduname, extver)
            self.hdu_db[(name, extver)] = d
            idx += 1

        self.extver_db = extver_db
Exemplo n.º 7
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def test_get_fileinfo_real_file():
    """Test behavior on real file."""
    bnch = iohelper.get_fileinfo(iohelper.__file__)
    assert bnch['ondisk']
    assert bnch['name'] == 'iohelper'
    assert bnch['numhdu'] is None
    # filepath and url are OS-dependent, hence the lax check here
    assert bnch['url'].startswith('file://')
Exemplo n.º 8
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    def load_file(self, filespec, header):
        info = iohelper.get_fileinfo(filespec)
        if not info.ondisk:
            raise ValueError("File does not appear to be on disk: %s" % (
                info.url))

        filepath = info.filepath
        return self._imload(filepath, header)
Exemplo n.º 9
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def load_data(filespec, idx=None, logger=None, **kwargs):
    """Load data from a file.

    This call is used to load a data item from a filespec (path or URL)

    Parameters
    ----------
    filespec : str
        The path of the file to load (can be a URL).

    idx : int or string (optional)
        The index or name of the data unit in the file (e.g. an HDU name)

    logger : python logger (optional)
        A logger to record progress opening the item

    All other keyword parameters are passed to the opener chosen for
    the file type.

    Returns
    -------
    data_obj : a data object for a ginga viewer

    """
    global loader_registry

    info = iohelper.get_fileinfo(filespec)
    filepath = info.filepath

    if idx is None:
        idx = info.numhdu

    # Assume type to be a FITS image unless the MIME association says
    # it is something different.
    try:
        typ, subtyp = iohelper.guess_filetype(filepath)

    except Exception as e:
        msg = "error determining file type of '{}': {}".format(filepath, e)
        if logger is not None:
            logger.warning(msg)
        raise ValueError(msg)

    mimetype = '%s/%s' % (typ, subtyp)
    logger.debug("determined MIME type: {}'".format(mimetype))

    openers = get_openers(mimetype)
    if len(openers) == 0:
        msg = "No openers found for type '{}'".format(mimetype)
        if logger is not None:
            logger.warning(msg)
        raise ValueError(msg)

    opener = openers[0].opener(logger)
    with opener.open_file(filepath) as opn_f:
        data_obj = opener.load_idx(idx, **kwargs)

    return data_obj
Exemplo n.º 10
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    def load_file(self, filespec, ahdr, numhdu=None, naxispath=None,
                  phdr=None):

        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

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = fitsio.FITS(filepath)

        if numhdu is None:
            found_valid_hdu = False
            for i in range(len(fits_f)):
                hdu = fits_f[i]
                info = hdu.get_info()
                #print(info)
                name = info['extname']
                extver = info['extver']

                if not ('ndims' in info) or (info['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:
                ## raise FITSError("No data HDU found that Ginga can open in '%s'" % (
                ##     filepath))
                # Just load the header
                numhdu = 0

        elif isinstance(numhdu, (int, str)):
            hdu = fits_f[numhdu]
            info = hdu.get_info()
            name = info['extname']
            extver = info['extver']
            if len(name) > 0:
                numhdu = (name, extver)

        hdu = fits_f[numhdu]

        data, naxispath = self.load_hdu(hdu, ahdr, fobj=fits_f,
                                        naxispath=naxispath)

        # Read PRIMARY header
        if phdr is not None:
            self.fromHDU(fits_f[0], phdr)

        fits_f.close()
        return (data, numhdu, naxispath)
Exemplo n.º 11
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    def load_file(self, filespec, ahdr, numhdu=None, naxispath=None,
                  phdr=None):

        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

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = fitsio.FITS(filepath)

        if numhdu is None:
            found_valid_hdu = False
            for i in range(len(fits_f)):
                hdu = fits_f[i]
                info = hdu.get_info()
                #print(info)
                name = info['extname']
                extver = info['extver']

                if not ('ndims' in info) or (info['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:
                ## raise FITSError("No data HDU found that Ginga can open in '%s'" % (
                ##     filepath))
                # Just load the header
                numhdu = 0

        elif isinstance(numhdu, (int, str)):
            hdu = fits_f[numhdu]
            info = hdu.get_info()
            name = info['extname']
            extver = info['extver']
            if len(name) > 0:
                numhdu = (name, extver)

        hdu = fits_f[numhdu]

        data, naxispath = self.load_hdu(hdu, ahdr, fobj=fits_f,
                                        naxispath=naxispath)

        # Read PRIMARY header
        if phdr is not None:
            self.fromHDU(fits_f[0], phdr)

        fits_f.close()
        return (data, numhdu, naxispath)
Exemplo n.º 12
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def load_data(filespec, idx=None, logger=None, **kwargs):
    """Load data from a file.

    This call is used to load a data item from a filespec (path or URL)

    Parameters
    ----------
    filespec : str
        The path of the file to load (can be a URL).

    idx : int or string (optional)
        The index or name of the data unit in the file (e.g. an HDU name)

    logger : python logger (optional)
        A logger to record progress opening the item

    All other keyword parameters are passed to the opener chosen for
    the file type.

    Returns
    -------
    data_obj : a data object for a ginga viewer

    """
    global loader_registry

    info = iohelper.get_fileinfo(filespec)
    filepath = info.filepath

    if idx is None:
        idx = info.numhdu

    # Assume type to be a FITS image unless the MIME association says
    # it is something different.
    try:
        typ, subtyp = iohelper.guess_filetype(filepath)

    except Exception as e:
        if logger is not None:
            logger.warning("error determining file type: %s; "
                           "assuming 'image/fits'" % (str(e)))
        # Can't determine file type: assume and attempt FITS
        typ, subtyp = 'image', 'fits'

    if logger is not None:
        logger.debug("assuming file type: %s/%s'" % (typ, subtyp))
    try:
        loader_info = loader_registry['%s/%s' % (typ, subtyp)]
        data_loader = loader_info.loader

    except KeyError:
        # for now, assume that this is an unrecognized FITS file
        data_loader = load_fits

    data_obj = data_loader(filepath, idx=idx, logger=logger,
                           **kwargs)
    return data_obj
Exemplo n.º 13
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def load_data(filespec, idx=None, logger=None, **kwargs):
    """Load data from a file.

    This call is used to load a data item from a filespec (path or URL)

    Parameters
    ----------
    filespec : str
        The path of the file to load (can be a URL).

    idx : int or string (optional)
        The index or name of the data unit in the file (e.g. an HDU name)

    logger : python logger (optional)
        A logger to record progress opening the item

    All other keyword parameters are passed to the opener chosen for
    the file type.

    Returns
    -------
    data_obj : a data object for a ginga viewer

    """
    global loader_registry

    info = iohelper.get_fileinfo(filespec)
    filepath = info.filepath

    if idx is None:
        idx = info.numhdu

    # Assume type to be a FITS image unless the MIME association says
    # it is something different.
    try:
        typ, subtyp = iohelper.guess_filetype(filepath)

    except Exception as e:
        if logger is not None:
            logger.warning("error determining file type: %s; "
                           "assuming 'image/fits'" % (str(e)))
        # Can't determine file type: assume and attempt FITS
        typ, subtyp = 'image', 'fits'

    if logger is not None:
        logger.debug("assuming file type: %s/%s'" % (typ, subtyp))
    try:
        loader_info = loader_registry['%s/%s' % (typ, subtyp)]
        data_loader = loader_info.loader

    except KeyError:
        # for now, assume that this is an unrecognized FITS file
        data_loader = load_fits

    data_obj = data_loader(filepath, idx=idx, logger=logger, **kwargs)
    return data_obj
Exemplo n.º 14
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    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)
Exemplo n.º 15
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    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)
Exemplo n.º 16
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    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)
Exemplo n.º 17
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    def open_file(self, filespec, **kwargs):
        # open the HDF5 file and make a full inventory of what is
        # available to load
        info = iohelper.get_fileinfo(filespec)
        if not info.ondisk:
            raise ValueError("File does not appear to be on disk: %s" % (
                info.url))

        self._path = info.filepath

        self.logger.debug("Loading file '%s' ..." % (self._path))
        self._f = h5py.File(self._path, 'r', **kwargs)
        return self
Exemplo n.º 18
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    def load_file(self, filespec, ahdr, numhdu=None, naxispath=None,
                  phdr=None):

        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

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = pyfits.open(filepath, 'readonly')

        # this seems to be necessary now for some fits files...
        try:
            fits_f.verify('fix')
        except Exception as e:
            raise FITSError("Error loading fits file '%s': %s" % (
                filepath, str(e)))

        if numhdu is None:
            found_valid_hdu = False
            for numhdu in range(len(fits_f)):
                hdu = fits_f[numhdu]
                if (hdu.data is None) or (0 in hdu.data.shape):
                    # non-pixel or zero-length data hdu?
                    continue
                if not isinstance(hdu.data, numpy.ndarray):
                    # We need to open a numpy array
                    continue
                #print "data type is %s" % hdu.data.dtype.kind
                # Looks good, let's try it
                found_valid_hdu = True
                break

            if not found_valid_hdu:
                ## raise FITSError("No data HDU found that Ginga can open in '%s'" % (
                ##     filepath))
                # Load just the header
                numhdu = 0

        hdu = fits_f[numhdu]

        data, naxispath = self.load_hdu(hdu, ahdr, fobj=fits_f,
                                        naxispath=naxispath)

        # Read PRIMARY header
        if phdr is not None:
            self.fromHDU(fits_f[0], phdr)

        fits_f.close()
        return (data, numhdu, naxispath)
Exemplo n.º 19
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    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)
Exemplo n.º 20
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    def load_image(self, filepath, idx=None):

        info = iohelper.get_fileinfo(filepath, cache_dir=self.tmpdir)
        filepfx = info.filepath
        if idx is None:
            idx = info.numhdu

        # Create an image.  Assume type to be an AstroImage unless
        # the MIME association says it is something different.
        try:
            typ, subtyp = self.guess_filetype(filepfx)

        except Exception as e:
            self.logger.warn("error determining file type: %s; assuming 'image/fits'" % (str(e)))
            # Can't determine file type: assume and attempt FITS
            typ, subtyp = 'image', 'fits'

        kwdargs = {}

        self.logger.debug("assuming file type: %s/%s'" % (typ, subtyp))
        if (typ == 'image') and (subtyp not in ('fits', 'x-fits')):
            image = RGBImage.RGBImage(logger=self.logger)
            filepath = filepfx
        else:
            inherit_prihdr = self.settings.get('inherit_primary_header', False)
            image = AstroImage.AstroImage(logger=self.logger,
                                          inherit_primary_header=inherit_prihdr)
            kwdargs.update(dict(numhdu=idx))

        try:
            self.logger.info("Loading image from %s kwdargs=%s" % (
                filepath, str(kwdargs)))
            image.load_file(filepath, **kwdargs)

        except Exception as e:
            errmsg = "Failed to load file '%s': %s" % (
                filepath, str(e))
            self.logger.error(errmsg)
            try:
                (type, value, tb) = sys.exc_info()
                tb_str = "\n".join(traceback.format_tb(tb))
            except Exception as e:
                tb_str = "Traceback information unavailable."
            self.gui_do(self.show_error, errmsg + '\n' + tb_str)
            #chinfo.fitsimage.onscreen_message("Failed to load file", delay=1.0)
            raise ControlError(errmsg)

        self.logger.debug("Successfully loaded file into image object.")
        return image
Exemplo n.º 21
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    def open_file(self, filespec, 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))

        self.fileinfo = info
        filepath = info.filepath

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = fitsio.FITS(filepath, memmap=memmap)
        self.fits_f = fits_f

        extver_db = {}
        self.extver_db = extver_db
        self.hdu_info = []
        self.hdu_db = {}

        for idx in range(len(fits_f)):
            hdu = fits_f[idx]
            hduinfo = hdu.get_info()
            name = hduinfo['extname']
            # figure out the EXTVER for this HDU
            #extver = hduinfo['extver']
            extver = extver_db.setdefault(name, 0)
            extver += 1
            extver_db[name] = extver

            # prepare a record of pertinent info about the HDU for
            # lookups by numerical index or (NAME, EXTVER)
            d = Bunch.Bunch(index=idx, name=name, extver=extver)
            hdutype = self.hdutypes.get(hduinfo['hdutype'], 'UNKNOWN')
            d.setvals(htype=hdutype,
                      dtype=str(hduinfo.get('img_type', None)))
            self.hdu_info.append(d)
            # different ways of accessing this HDU:
            # by numerical index
            self.hdu_db[idx] = d
            # by (hduname, extver)
            key = (name, extver)
            if len(name) > 0 and extver >= 0 and key not in self.hdu_db:
                self.hdu_db[key] = d

        return self
Exemplo n.º 22
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    def open_file(self, filespec, 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))

        self.fileinfo = info
        filepath = info.filepath

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = fitsio.FITS(filepath, memmap=memmap)
        self.fits_f = fits_f

        extver_db = {}
        self.extver_db = extver_db
        self.hdu_info = []
        self.hdu_db = {}

        for idx in range(len(fits_f)):
            hdu = fits_f[idx]
            hduinfo = hdu.get_info()
            name = hduinfo['extname']
            # figure out the EXTVER for this HDU
            #extver = hduinfo['extver']
            extver = extver_db.setdefault(name, 0)
            extver += 1
            extver_db[name] = extver

            # prepare a record of pertinent info about the HDU for
            # lookups by numerical index or (NAME, EXTVER)
            d = Bunch.Bunch(index=idx, name=name, extver=extver)
            hdutype = self.hdutypes.get(hduinfo['hdutype'], 'UNKNOWN')
            d.setvals(htype=hdutype, dtype=str(hduinfo.get('img_type', None)))
            self.hdu_info.append(d)
            # different ways of accessing this HDU:
            # by numerical index
            self.hdu_db[idx] = d
            # by (hduname, extver)
            key = (name, extver)
            if len(name) > 0 and extver >= 0 and key not in self.hdu_db:
                self.hdu_db[key] = d

        return self
Exemplo n.º 23
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    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
Exemplo n.º 24
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    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])
Exemplo n.º 25
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def test_get_fileinfo_dummy_file():
    """Test behavior on dummy file."""

    # pathlib behaves differently depending on OS.
    if IS_WINDOWS:
        filename = r'C:\mypath\dummyfile.fits[1]'
        filepath = 'C:\\mypath\\dummyfile.fits'
        url = 'file:///C:/mypath/dummyfile.fits'
    else:
        filename = '/mypath/dummyfile.fits[1]'
        filepath = '/mypath/dummyfile.fits'
        url = 'file:///mypath/dummyfile.fits'

    bnch = iohelper.get_fileinfo(filename)
    assert not bnch['ondisk']
    assert bnch['name'] == 'dummyfile[1]'
    assert bnch['numhdu'] == 1
    assert bnch['filepath'] == filepath
    assert bnch['url'] == url
Exemplo n.º 26
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    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
Exemplo n.º 27
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    def load_file(self, filespec, ahdr, numhdu=None, naxispath=None,
                  phdr=None):

        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

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = fitsio.FITS(filepath)

        if numhdu is None:
            found_valid_hdu = False
            for numhdu in range(len(fits_f)):
                hdu = fits_f[numhdu]
                info = hdu.get_info()
                if not ('ndims' in info) or (info['ndims'] == 0):
                    # compressed FITS file or non-pixel data hdu?
                    continue
                #print "data type is %s" % hdu.data.dtype.kind
                # Looks good, let's try it
                found_valid_hdu = True
                break

            if not found_valid_hdu:
                ## raise FITSError("No data HDU found that Ginga can open in '%s'" % (
                ##     filepath))
                # Just load the header
                numhdu = 0

        hdu = fits_f[numhdu]

        data, naxispath = self.load_hdu(hdu, ahdr, fobj=fits_f,
                                        naxispath=naxispath)

        # Read PRIMARY header
        if phdr is not None:
            self.fromHDU(fits_f[0], phdr)

        fits_f.close()
        return (data, numhdu, naxispath)
Exemplo n.º 28
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def get_fileinfo(self, filespec, dldir=None):
    """Break down a file specification into its components.

    Parameters
    ----------
    filespec : str
        The path of the file to load (can be a URL).

    dldir

    Returns
    -------
    res : `~ginga.misc.Bunch.Bunch`

    """
    if dldir is None:
        dldir = self.tmpdir

    # Get information about this file/URL
    info = iohelper.get_fileinfo(filespec, cache_dir=dldir)
Exemplo n.º 29
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def get_fileinfo(self, filespec, dldir=None):
    """Break down a file specification into its components.

    Parameters
    ----------
    filespec : str
        The path of the file to load (can be a URL).

    dldir

    Returns
    -------
    res : `~ginga.misc.Bunch.Bunch`

    """
    if dldir is None:
        dldir = self.tmpdir

    # Get information about this file/URL
    info = iohelper.get_fileinfo(filespec, cache_dir=dldir)
Exemplo n.º 30
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    def open_file(self, filespec, **kwargs):

        info = iohelper.get_fileinfo(filespec)
        if not info.ondisk:
            raise ImageError("File does not appear to be on disk: %s" %
                             (info.url))

        self.fileinfo = info
        filepath = info.filepath

        self._path = filepath
        self.rgb_f = PILimage.open(filepath)

        idx = 0
        extver_db = {}
        self.hdu_info = []
        self.hdu_db = {}
        numframes = getattr(self.rgb_f, 'n_frames', 1)
        self.logger.info("number of frames: {}".format(numframes))

        for idx in range(numframes):
            name = "frame{}".format(idx)
            extver = 0
            # prepare a record of pertinent info about the HDU for
            # lookups by numerical index or (NAME, EXTVER)
            d = Bunch.Bunch(index=idx,
                            name=name,
                            extver=extver,
                            dtype='uint8',
                            htype='N/A')
            self.hdu_info.append(d)
            # different ways of accessing this HDU:
            # by numerical index
            self.hdu_db[idx] = d
            # by (hduname, extver)
            key = (name, extver)
            if key not in self.hdu_db:
                self.hdu_db[key] = d

        self.extver_db = extver_db
        return self
Exemplo n.º 31
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    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])
Exemplo n.º 32
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    def get_fileinfo(self, filespec, dldir=None):
        """
        Break down a file specification into its components.

        Parameters
        ----------
        `filespec`: string
            the path of the file to load (can be a URL)

        Returns
        -------
        res:
            a Bunch object
        """
        if dldir is None:
            dldir = self.tmpdir

        # Get information about this file/URL
        info = iohelper.get_fileinfo(filespec, cache_dir=dldir)

        if (not info.ondisk) and (info.url is not None) and \
               (not info.url.startswith('file:')):
            # Download the file if a URL was passed
            def  _dl_indicator(count, blksize, totalsize):
                pct = float(count * blksize) / float(totalsize)
                msg = "Downloading: %%%.2f complete" % (pct*100.0)
                self.gui_do(self.showStatus, msg)

            # Try to download the URL.  We press our generic URL server
            # into use as a generic file downloader.
            try:
                dl = catalog.URLServer(self.logger, "downloader", "dl",
                                       info.url, "")
                filepath = dl.retrieve(info.url, filepath=info.filepath,
                                       cb_fn=_dl_indicator)
            finally:
                self.gui_do(self.showStatus, "")

        return info
Exemplo n.º 33
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    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])
Exemplo n.º 34
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    def get_fileinfo(self, filespec, dldir='/tmp'):

        # Get information about this file/URL
        info = iohelper.get_fileinfo(filespec, cache_dir=dldir)

        if (not info.ondisk) and (info.url is not None) and \
               (not info.url.startswith('file:')):
            # Download the file if a URL was passed
            def  _dl_indicator(count, blksize, totalsize):
                pct = float(count * blksize) / float(totalsize)
                msg = "Downloading: %%%.2f complete" % (pct*100.0)
                self.viewer.onscreen_message(msg, delay=1.0)

            # Try to download the URL.  We press our generic URL server
            # into use as a generic file downloader.
            try:
                dl = catalog.URLServer(self.logger, "downloader", "dl",
                                       info.url, "")
                filepath = dl.retrieve(info.url, filepath=info.filepath,
                                       cb_fn=_dl_indicator)
            finally:
                self.viewer.clear_onscreen_message()

        return info
Exemplo n.º 35
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    def load_file(self,
                  filespec,
                  ahdr,
                  numhdu=None,
                  naxispath=None,
                  phdr=None,
                  memmap=None):

        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

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = pyfits.open(filepath, 'readonly', memmap=memmap)

        # this seems to be necessary now for some fits files...
        try:
            fits_f.verify('fix')
        except Exception as e:
            raise FITSError("Error loading fits file '%s': %s" %
                            (filepath, str(e)))

        if numhdu is None:

            info = fits_f.info(output=False)
            extver_db = {}

            found_valid_hdu = False
            for i in range(len(fits_f)):
                hdu = fits_f[i]
                tup = info[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)
                        or isinstance(hdu, pyfits.PrimaryHDU)):
                    # Don't open tables, etc.
                    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

                #print "data type is %s" % hdu.data.dtype.kind
                # 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:
                ## raise FITSError("No data HDU found that Ginga can open in '%s'" % (
                ##     filepath))
                # Load just the header
                hdu = fits_f[0]
                name = hdu.name
                extver = hdu.ver
                if len(name) == 0:
                    numhdu = 0
                else:
                    numhdu = (name, extver)

        elif isinstance(numhdu, (int, str)):
            hdu = fits_f[numhdu]
            name = hdu.name
            extver = hdu.ver
            if len(name) > 0:
                numhdu = (name, extver)

        hdu = fits_f[numhdu]

        data, naxispath = self.load_hdu(hdu,
                                        ahdr,
                                        fobj=fits_f,
                                        naxispath=naxispath)

        # Read PRIMARY header
        if phdr is not None:
            self.fromHDU(fits_f[0], phdr)

        fits_f.close()
        return (data, numhdu, naxispath)
Exemplo n.º 36
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    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
Exemplo n.º 37
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    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
Exemplo n.º 38
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    def load_file(self, filespec, ahdr, numhdu=None, naxispath=None,
                  phdr=None):

        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

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = pyfits.open(filepath, 'readonly')

        # this seems to be necessary now for some fits files...
        try:
            fits_f.verify('fix')
        except Exception as e:
            raise FITSError("Error loading fits file '%s': %s" % (
                filepath, str(e)))

        if numhdu is None:

            info = fits_f.info(output=False)
            extver_db = {}

            found_valid_hdu = False
            for i in range(len(fits_f)):
                hdu = fits_f[i]
                tup = info[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) or
                        isinstance(hdu, pyfits.PrimaryHDU)):
                    # Don't open tables, etc.
                    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

                #print "data type is %s" % hdu.data.dtype.kind
                # 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:
                ## raise FITSError("No data HDU found that Ginga can open in '%s'" % (
                ##     filepath))
                # Load just the header
                numhdu = 0

        elif isinstance(numhdu, (int, str)):
            hdu = fits_f[numhdu]
            name = hdu.name
            extver = hdu.ver
            if len(name) > 0:
                numhdu = (name, extver)

        hdu = fits_f[numhdu]

        data, naxispath = self.load_hdu(hdu, ahdr, fobj=fits_f,
                                        naxispath=naxispath)

        # Read PRIMARY header
        if phdr is not None:
            self.fromHDU(fits_f[0], phdr)

        fits_f.close()
        return (data, numhdu, naxispath)
Exemplo n.º 39
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    def open_file(self, filespec, 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))

        self.fileinfo = info
        filepath = info.filepath

        self.logger.debug("Loading file '%s' ..." % (filepath))
        fits_f = pyfits.open(filepath, 'readonly', memmap=memmap)
        self.fits_f = 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)))

        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)))

        idx = 0
        extver_db = {}
        self.hdu_info = []
        self.hdu_db = {}

        for tup in _hduinfo:
            name = tup[1]
            # figure out the EXTVER for this HDU
            extver = extver_db.setdefault(name, 0)
            extver += 1
            extver_db[name] = extver

            # prepare a record of pertinent info about the HDU for
            # lookups by numerical index or (NAME, EXTVER)
            d = Bunch.Bunch(index=idx, name=name, extver=extver)
            if len(tup) > 5:
                d.setvals(htype=tup[3], dtype=tup[6])
            self.hdu_info.append(d)
            # different ways of accessing this HDU:
            # by numerical index
            self.hdu_db[idx] = d
            # by (hduname, extver)
            key = (name, extver)
            if key not in self.hdu_db:
                self.hdu_db[key] = d
            idx += 1

        self.extver_db = extver_db
        return self
Exemplo n.º 40
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    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
Exemplo n.º 41
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    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