Python tables.entries_from_file函数代码示例

def test_entries_from_file_time_string_parse_format():

    with pytest.raises(ValueError):
        # Error should be  raised because of the date format in GOES_DATA
        entries = list(entries_from_file(GOES_DATA))

    entries = list(entries_from_file(GOES_DATA,
                                     time_string_parse_format='%d/%m/%Y'))

    assert len(entries) == 4
    entry = entries[0]
    assert len(entry.fits_header_entries) == 17

    assert entry.observation_time_start == datetime(2011, 6, 7, 0, 0)
    assert entry.observation_time_end == datetime(2011, 6, 7, 0, 0)
    assert entry.path == GOES_DATA

 def _download_and_collect_entries(self, query_result, client=None,
         path=None, progress=False):
     if client is None:
         client = VSOClient()
     for block in query_result:
         paths = client.get([block], path).wait(progress=progress)
         for path in paths:
             qr_entry = tables.DatabaseEntry._from_query_result_block(block)
             file_entries = list(
                 tables.entries_from_file(path, self.default_waveunit))
             for entry in file_entries:
                 entry.source = qr_entry.source
                 entry.provider = qr_entry.provider
                 entry.physobs = qr_entry.physobs
                 entry.fileid = qr_entry.fileid
                 entry.observation_time_start =\
                     qr_entry.observation_time_start
                 entry.observation_time_end = qr_entry.observation_time_end
                 entry.instrument = qr_entry.instrument
                 entry.size = qr_entry.size
                 entry.wavemin = qr_entry.wavemin
                 entry.wavemax = qr_entry.wavemax
                 entry.path = path
                 entry.download_time = datetime.utcnow()
                 yield entry

    def _download_and_collect_entries(self, query_result, client=None,
            path=None, progress=False):
        if client is None:
            client = VSOClient()

        paths = client.get(query_result, path).wait(progress=progress)

        for (path, block) in zip(paths, query_result):
            qr_entry = tables.DatabaseEntry._from_query_result_block(block)

            if os.path.isfile(path):
                entries = tables.entries_from_file(path, self.default_waveunit)
            elif os.path.isdir(path):
                entries = tables.entries_from_dir(path, self.default_waveunit)
            else:
                raise ValueError('The path is neither a file nor directory')

            for entry in entries:
                entry.source = qr_entry.source
                entry.provider = qr_entry.provider
                entry.physobs = qr_entry.physobs
                entry.fileid = qr_entry.fileid
                entry.observation_time_start = qr_entry.observation_time_start
                entry.observation_time_end = qr_entry.observation_time_end
                entry.instrument = qr_entry.instrument
                entry.size = qr_entry.size
                entry.wavemin = qr_entry.wavemin
                entry.wavemax = qr_entry.wavemax
                entry.path = path
                entry.download_time = datetime.utcnow()
                yield entry

def test_entries_from_file():
    entries = list(entries_from_file(MQ_IMAGE))
    assert len(entries) == 1
    entry = entries[0]
    assert len(entry.fits_header_entries) == 31
    expected_fits_header_entries = [
        FitsHeaderEntry("SIMPLE", True),
        FitsHeaderEntry("BITPIX", 16),
        FitsHeaderEntry("NAXIS", 2),
        FitsHeaderEntry("NAXIS1", 1500),
        FitsHeaderEntry("NAXIS2", 1340),
        FitsHeaderEntry("CONTACT", "[email protected]"),
        FitsHeaderEntry("DATE_OBS", "2013-08-12T08:42:53.000"),
        FitsHeaderEntry("DATE_END", "2013-08-12T08:42:53.000"),
        FitsHeaderEntry("FILENAME", "mq130812.084253.fits"),
        FitsHeaderEntry("INSTITUT", "Observatoire de Paris"),
        FitsHeaderEntry("INSTRUME", "Spectroheliograph"),
        FitsHeaderEntry("OBJECT", "FS"),
        FitsHeaderEntry("OBS_MODE", "SCAN"),
        FitsHeaderEntry("PHYSPARA", "Intensity"),
        FitsHeaderEntry("NBREG", 1),
        FitsHeaderEntry("NBLAMBD", 1),
        FitsHeaderEntry("WAVELNTH", 6563),
        FitsHeaderEntry("WAVEUNIT", "angstrom"),
        FitsHeaderEntry("POLARANG", 0),
        FitsHeaderEntry("THEMISFF", 3),
        FitsHeaderEntry("LONGTRC", 258.78),
        FitsHeaderEntry("LONGCARR", 258.78),
        FitsHeaderEntry("LONGITUD", 258.78),
        FitsHeaderEntry("LATITUD", 6.50107),
        FitsHeaderEntry("LATIRC", 6.50107),
        FitsHeaderEntry("INDLAMD", 1),
        FitsHeaderEntry("INDREG", 1),
        FitsHeaderEntry("SEQ_IND", 1),
        FitsHeaderEntry("SVECTOR", 0),
        FitsHeaderEntry("COMMENT", ""),
        FitsHeaderEntry("HISTORY", ""),
    ]
    assert entry.fits_header_entries == expected_fits_header_entries
    assert entry.fits_key_comments == [
        FitsKeyComment("SIMPLE", "Written by IDL:  Mon Aug 12 08:48:08 2013"),
        FitsKeyComment("BITPIX", "Integer*2 (short integer)"),
    ]
    assert entry.instrument == "Spectroheliograph"
    assert entry.observation_time_start == datetime(2013, 8, 12, 8, 42, 53)
    assert entry.observation_time_end == datetime(2013, 8, 12, 8, 42, 53)
    assert round(entry.wavemin, 1) == 656.3
    assert round(entry.wavemax, 1) == 656.3
    assert entry.path == MQ_IMAGE

def test_entries_from_file():
    with pytest.warns(AstropyUserWarning, match='File may have been truncated'):
        entries = list(entries_from_file(MQ_IMAGE))
    assert len(entries) == 1
    entry = entries[0]
    assert len(entry.fits_header_entries) == 31
    expected_fits_header_entries = [
        FitsHeaderEntry('SIMPLE', True),
        FitsHeaderEntry('BITPIX', 16),
        FitsHeaderEntry('NAXIS', 2),
        FitsHeaderEntry('NAXIS1', 1500),
        FitsHeaderEntry('NAXIS2', 1340),
        FitsHeaderEntry('CONTACT', '[email protected]'),
        FitsHeaderEntry('DATE_OBS', '2013-08-12T08:42:53.000'),
        FitsHeaderEntry('DATE_END', '2013-08-12T08:42:53.000'),
        FitsHeaderEntry('FILENAME', 'mq130812.084253.fits'),
        FitsHeaderEntry('INSTITUT', 'Observatoire de Paris'),
        FitsHeaderEntry('INSTRUME', 'Spectroheliograph'),
        FitsHeaderEntry('OBJECT', 'FS'),
        FitsHeaderEntry('OBS_MODE', 'SCAN'),
        FitsHeaderEntry('PHYSPARA', 'Intensity'),
        FitsHeaderEntry('NBREG', 1),
        FitsHeaderEntry('NBLAMBD', 1),
        FitsHeaderEntry('WAVELNTH', 6563),
        FitsHeaderEntry('WAVEUNIT', 'angstrom'),
        FitsHeaderEntry('POLARANG', 0),
        FitsHeaderEntry('THEMISFF', 3),
        FitsHeaderEntry('LONGTRC', 258.78),
        FitsHeaderEntry('LONGCARR', 258.78),
        FitsHeaderEntry('LONGITUD', 258.78),
        FitsHeaderEntry('LATITUD', 6.50107),
        FitsHeaderEntry('LATIRC', 6.50107),
        FitsHeaderEntry('INDLAMD', 1),
        FitsHeaderEntry('INDREG', 1),
        FitsHeaderEntry('SEQ_IND', 1),
        FitsHeaderEntry('SVECTOR', 0),
        FitsHeaderEntry('COMMENT', ''),
        FitsHeaderEntry('HISTORY', '')]
    assert entry.fits_header_entries == expected_fits_header_entries
    assert entry.fits_key_comments.sort() == [
        FitsKeyComment('SIMPLE', 'Written by IDL:  Mon Aug 12 08:48:08 2013'),
        FitsKeyComment('BITPIX', 'Integer*2 (short integer)')].sort()
    assert entry.instrument == 'Spectroheliograph'
    assert entry.observation_time_start == datetime(2013, 8, 12, 8, 42, 53)
    assert entry.observation_time_end == datetime(2013, 8, 12, 8, 42, 53)
    assert round(entry.wavemin, 1) == 656.3
    assert round(entry.wavemax, 1) == 656.3
    assert entry.path == MQ_IMAGE

    def add_from_file(self, file, ignore_already_added=False):
        """Generate as many database entries as there are FITS headers in the
        given file and add them to the database.

        Parameters
        ----------
        file : str or file-like object
            Either a path pointing to a FITS file or a an opened file-like
            object. If an opened file object, its mode must be one of the
            following rb, rb+, or ab+.

        ignore_already_added : bool, optional
            See :meth:`sunpy.database.Database.add`.

        """
        self.add_many(
            tables.entries_from_file(file, self.default_waveunit),
            ignore_already_added)

    def _download_and_collect_entries(self, query_result, **kwargs):

        client = kwargs.pop('client', None)
        path = kwargs.pop('path', None)
        progress = kwargs.pop('progress', False)
        methods = kwargs.pop('methods', ('URL-FILE_Rice', 'URL-FILE'))

        if kwargs:
            k, v = kwargs.popitem()
            raise TypeError('unexpected keyword argument {0!r}'.format(k))

        if client is None:
            client = VSOClient()

        paths = client.get(query_result, path, methods).wait(progress=progress)

        for (path, block) in zip(paths, query_result):
            qr_entry = tables.DatabaseEntry._from_query_result_block(block)

            if os.path.isfile(path):
                entries = tables.entries_from_file(path, self.default_waveunit)
            elif os.path.isdir(path):
                entries = tables.entries_from_dir(path, self.default_waveunit)
            else:
                raise ValueError('The path is neither a file nor directory')

            for entry in entries:
                entry.source = qr_entry.source
                entry.provider = qr_entry.provider
                entry.physobs = qr_entry.physobs
                entry.fileid = qr_entry.fileid
                entry.observation_time_start = qr_entry.observation_time_start
                entry.observation_time_end = qr_entry.observation_time_end
                entry.instrument = qr_entry.instrument
                entry.size = qr_entry.size
                entry.wavemin = qr_entry.wavemin
                entry.wavemax = qr_entry.wavemax
                entry.path = path
                entry.download_time = datetime.utcnow()
                yield entry

def test_entries_from_file_withoutwaveunit():
    # does not raise `WaveunitNotFoundError`, because no wavelength information
    # is present in this file
    entries_from_file(RHESSI_IMAGE).next()
    with pytest.raises(WaveunitNotFoundError):
        entries_from_file(EIT_195_IMAGE).next()

    def _download_and_collect_entries(self, query_result, **kwargs):

        client = kwargs.pop('client', None)
        path = kwargs.pop('path', None)
        progress = kwargs.pop('progress', False)
        methods = kwargs.pop('methods', ('URL-FILE_Rice', 'URL-FILE'))
        overwrite = kwargs.pop('overwrite', False)

        if kwargs:
            k, v = kwargs.popitem()
            raise TypeError('unexpected keyword argument {0!r}'.format(k))

        if client is None:
            client = VSOClient()

        remove_list = []
        delete_entries = []
        for qr in query_result:
            temp = tables.DatabaseEntry._from_query_result_block(qr)
            for database_entry in self:
                if database_entry.path is not None and temp._compare_attributes(
                    database_entry, ["source", "provider", "physobs", "fileid",
                                     "observation_time_start", "observation_time_end",
                                     "instrument", "size", "wavemin", "wavemax"]):
                    if not overwrite:
                        remove_list.append(qr)
                    else:
                        delete_entries.append(database_entry)

        for temp in remove_list:
            query_result = [x for x in query_result if x != temp]

        for temp in delete_entries:
            self.remove(temp)

        paths = client.fetch(query_result, path).wait(progress=progress)

        for (path, block) in zip(paths, query_result):
            qr_entry = tables.DatabaseEntry._from_query_result_block(block)

            if os.path.isfile(path):
                entries = tables.entries_from_file(path, self.default_waveunit)
            elif os.path.isdir(path):
                entries = tables.entries_from_dir(path, self.default_waveunit)
            else:
                raise ValueError('The path is neither a file nor directory')

            for entry in entries:
                entry.source = qr_entry.source
                entry.provider = qr_entry.provider
                entry.physobs = qr_entry.physobs
                entry.fileid = qr_entry.fileid
                entry.observation_time_start = qr_entry.observation_time_start
                entry.observation_time_end = qr_entry.observation_time_end
                entry.instrument = qr_entry.instrument
                entry.size = qr_entry.size
                entry.wavemin = qr_entry.wavemin
                entry.wavemax = qr_entry.wavemax
                entry.path = path
                entry.download_time = datetime.utcnow()
                yield entry

    def download(self, *query, **kwargs):
        """download(*query, client=sunpy.net.vso.VSOClient(), path=None, progress=False)
        Search for data using the VSO interface (see
        :meth:`sunpy.net.vso.VSOClient.query`). If querying the VSO results in
        no data, no operation is performed. Concrete, this means that no entry
        is added to the database and no file is downloaded. Otherwise, the
        retrieved search result is used to download all files that belong to
        this search result. After that, all the gathered information (the one
        from the VSO query result and the one from the downloaded FITS files)
        is added to the database in a way that each FITS header is represented
        by one database entry.

        """
        if not query:
            raise TypeError('at least one attribute required')
        client = kwargs.pop('client', None)
        path = kwargs.pop('path', None)
        progress = kwargs.pop('progress', False)
        if kwargs:
            k, v = kwargs.popitem()
            raise TypeError('unexpected keyword argument {0!r}'.format(k))
        if client is None:
            client = VSOClient()
        qr = client.query(*query)
        # don't do anything if querying the VSO results in no data
        if not qr:
            return
        entries = []
        for block in qr:
            paths = client.get([block], path).wait(progress=progress)
            for path in paths:
                qr_entry = tables.DatabaseEntry._from_query_result_block(block)
                file_entries = list(
                    tables.entries_from_file(path, self.default_waveunit))
                for entry in file_entries:
                    entry.source = qr_entry.source
                    entry.provider = qr_entry.provider
                    entry.physobs = qr_entry.physobs
                    entry.fileid = qr_entry.fileid
                    entry.observation_time_start =\
                        qr_entry.observation_time_start
                    entry.observation_time_end = qr_entry.observation_time_end
                    entry.instrument = qr_entry.instrument
                    entry.size = qr_entry.size
                    entry.wavemin = qr_entry.wavemin
                    entry.wavemax = qr_entry.wavemax
                    entry.path = path
                    entry.download_time = datetime.utcnow()
                entries.extend(file_entries)
        dump = serialize.dump_query(and_(*query))
        (dump_exists,), = self.session.query(
            exists().where(tables.JSONDump.dump == tables.JSONDump(dump).dump))
        if dump_exists:
            # dump already exists in table jsondumps -> edit instead of add
            # update all entries with the fileid `entry.fileid`
            for entry in entries:
                old_entry = self.session.query(
                    tables.DatabaseEntry).filter_by(fileid=entry.fileid).first()
                if old_entry is not None:
                    attrs = [
                        'source', 'provider', 'physobs',
                        'observation_time_start', 'observation_time_end',
                        'instrument', 'size', 'wavemin', 'wavemax',
                        'download_time']
                    kwargs = dict((k, getattr(entry, k)) for k in attrs)
                    cmd = commands.EditEntry(old_entry, **kwargs)
                    if self._enable_history:
                        self._command_manager.do(cmd)
                    else:
                        cmd()
        else:
            self.add_many(entries)
            # serialize the query and save the serialization in the database
            # for two reasons:
            #   1. to avoid unnecessary downloading in future calls of
            #      ``fetch``
            #   2. to know whether to add or to edit entries in future calls of
            #      ``download`` (this method)
            self.session.add(tables.JSONDump(dump))