Exemple #1
0
def mast2phot(source, results, units, master=None, extra_fields=None):
    """
    Convert/combine MAST record arrays to measurement record arrays.
    
    Every line in the combined array represents a measurement in a certain band.
    
    This is probably only useful if C{results} contains only information on
    one target (or you have to give 'ID' as an extra field, maybe).
    
    The standard columns are:
    
        1. C{meas}: containing the photometric measurement
        2. C{e_meas}: the error on the photometric measurement
        3. C{flag}: an optional quality flag
        4. C{unit}: the unit of the measurement
        5. C{photband}: the photometric passband (FILTER.BAND)
        6. C{source}: name of the source catalog
    
    You can add extra information from the Mast catalog via the list of keys
    C{extra_fields}.
    
    If you give a C{master}, the information will be added to a previous
    record array. If not, a new master will be created.
    
    The result is a record array with each row a measurement.
    
    @param source: name of the Mast source
    @type source: str
    @param results: results from Mast C{search}
    @type results: record array
    @param units: header of Mast catalog with key name the column name and
    key value the units of that column
    @type units: dict
    @param master: master record array to add information to
    @type master: record array
    @param extra_fields: any extra columns you want to add information from
    @type extra_fields: list of str
    @return: array with each row a measurement
    @rtype: record array
    """
    e_flag = 'e_'
    q_flag = 'q_'
    #-- basic dtypes
    dtypes = [('meas', 'f8'), ('e_meas', 'f8'), ('flag', 'a20'),
              ('unit', 'a30'), ('photband', 'a30'), ('source', 'a50')]

    #-- MAST has no unified terminology:
    translations = {
        'kepler/kgmatch': {
            '_r': "Ang Sep (')",
            '_RAJ2000': 'KIC RA (J2000)',
            '_DEJ2000': 'KIC Dec (J2000)'
        }
    }

    #-- extra can be added:
    names = list(results.dtype.names)
    if extra_fields is not None:
        if source in translations:
            translation = translations[source]
        else:
            translation = {
                '_r': '_r',
                '_RAJ2000': '_RAJ2000',
                '_DEJ2000': '_DEJ2000'
            }
        for e_dtype in extra_fields:
            try:
                dtypes.append(
                    (e_dtype,
                     results.dtype[names.index(translation[e_dtype])].str))
            except ValueError:
                if e_dtype != '_r': raise
                dtypes.append(
                    (e_dtype, results.dtype[names.index('AngSep')].str))

    #-- create empty master if not given
    newmaster = False
    if master is None or len(master) == 0:
        master = np.rec.array(
            [tuple([('f' in dt[1]) and np.nan or 'none' for dt in dtypes])],
            dtype=dtypes)
        newmaster = True

    #-- add fluxes and magnitudes to the record array
    cols_added = 0
    for key in cat_info.options(source):
        if key[:2] in [e_flag, q_flag] or '_unit' in key or key == 'bibcode':
            continue
        photband = cat_info.get(source, key)
        #-- contains measurement, error, quality, units, photometric band and
        #   source
        cols = [
            results[key][:1],
            (e_flag + key in cat_info.options(source)
             and results[cat_info.get(source, e_flag + key)][:1]
             or np.ones(len(results[:1])) * np.nan),
            (q_flag + key in cat_info.options(source)
             and results[cat_info.get(source, q_flag + key)][:1]
             or np.ones(len(results[:1])) * np.nan),
            np.array(len(results[:1]) * [units[key]], str),
            np.array(len(results[:1]) * [photband], str),
            np.array(len(results[:1]) * [source], str)
        ]
        #-- add any extra fields if desired.
        if extra_fields is not None:
            for e_dtype in extra_fields:
                cols += [
                    e_dtype in results.dtype.names and results[e_dtype][:1]
                    or np.ones(len(results[:1])) * np.nan
                ]
        #-- add to the master
        rows = []
        for i in range(len(cols[0])):
            rows.append(tuple([col[i] for col in cols]))
        master = np.core.records.fromrecords(master.tolist() + rows,
                                             dtype=dtypes)
        cols_added += 1

    #-- fix colours: we have to run through it two times to be sure to have
    #   all the colours
    N = len(master) - cols_added
    master_ = vizier._breakup_colours(master[N:])
    master_ = vizier._breakup_colours(master_)
    #-- combine and return
    master = np.core.records.fromrecords(master.tolist()[:N] +
                                         master_.tolist(),
                                         dtype=dtypes)

    #-- skip first line from building
    if newmaster: master = master[1:]
    return master
Exemple #2
0
def mast2phot(source,results,units,master=None,extra_fields=None):
    """
    Convert/combine MAST record arrays to measurement record arrays.
    
    Every line in the combined array represents a measurement in a certain band.
    
    This is probably only useful if C{results} contains only information on
    one target (or you have to give 'ID' as an extra field, maybe).
    
    The standard columns are:
    
        1. C{meas}: containing the photometric measurement
        2. C{e_meas}: the error on the photometric measurement
        3. C{flag}: an optional quality flag
        4. C{unit}: the unit of the measurement
        5. C{photband}: the photometric passband (FILTER.BAND)
        6. C{source}: name of the source catalog
    
    You can add extra information from the Mast catalog via the list of keys
    C{extra_fields}.
    
    If you give a C{master}, the information will be added to a previous
    record array. If not, a new master will be created.
    
    The result is a record array with each row a measurement.
    
    @param source: name of the Mast source
    @type source: str
    @param results: results from Mast C{search}
    @type results: record array
    @param units: header of Mast catalog with key name the column name and
    key value the units of that column
    @type units: dict
    @param master: master record array to add information to
    @type master: record array
    @param extra_fields: any extra columns you want to add information from
    @type extra_fields: list of str
    @return: array with each row a measurement
    @rtype: record array
    """
    e_flag = 'e_'
    q_flag = 'q_'
    #-- basic dtypes
    dtypes = [('meas','f8'),('e_meas','f8'),('flag','a20'),
                  ('unit','a30'),('photband','a30'),('source','a50')]
    
    #-- MAST has no unified terminology:
    translations = {'kepler/kgmatch':{'_r':"Ang Sep (')",
                                      '_RAJ2000':'KIC RA (J2000)',
                                      '_DEJ2000':'KIC Dec (J2000)'}}
    
    #-- extra can be added:
    names = list(results.dtype.names)
    if extra_fields is not None:
        if source in translations:
            translation = translations[source]
        else:
            translation = {'_r':'_r','_RAJ2000':'_RAJ2000','_DEJ2000':'_DEJ2000'}
        for e_dtype in extra_fields:
            try:
                dtypes.append((e_dtype,results.dtype[names.index(translation[e_dtype])].str))
            except ValueError:
                if e_dtype != '_r': raise
                dtypes.append((e_dtype,results.dtype[names.index('AngSep')].str))
                
    
    #-- create empty master if not given
    newmaster = False
    if master is None or len(master)==0:
        master = np.rec.array([tuple([('f' in dt[1]) and np.nan or 'none' for dt in dtypes])],dtype=dtypes)
        newmaster = True
    
    #-- add fluxes and magnitudes to the record array
    cols_added = 0
    for key in cat_info.options(source):
        if key[:2] in [e_flag,q_flag] or '_unit' in key or key=='bibcode':
            continue
        photband = cat_info.get(source,key)
        #-- contains measurement, error, quality, units, photometric band and
        #   source
        cols = [results[key][:1],
                (e_flag+key in cat_info.options(source) and results[cat_info.get(source,e_flag+key)][:1] or np.ones(len(results[:1]))*np.nan),
                (q_flag+key in cat_info.options(source) and results[cat_info.get(source,q_flag+key)][:1] or np.ones(len(results[:1]))*np.nan),
                np.array(len(results[:1])*[units[key]],str),
                np.array(len(results[:1])*[photband],str),
                np.array(len(results[:1])*[source],str)]
        #-- add any extra fields if desired.
        if extra_fields is not None:
            for e_dtype in extra_fields:
                cols += [e_dtype in results.dtype.names and results[e_dtype][:1] or np.ones(len(results[:1]))*np.nan]
        #-- add to the master
        rows = []
        for i in range(len(cols[0])):
            rows.append(tuple([col[i] for col in cols]))
        master = np.core.records.fromrecords(master.tolist()+rows,dtype=dtypes)
        cols_added += 1
    
    #-- fix colours: we have to run through it two times to be sure to have
    #   all the colours
    N = len(master)-cols_added
    master_ = vizier._breakup_colours(master[N:])
    master_ = vizier._breakup_colours(master_)
    #-- combine and return
    master = np.core.records.fromrecords(master.tolist()[:N]+master_.tolist(),dtype=dtypes)
    
    #-- skip first line from building 
    if newmaster: master = master[1:]
    return master
Exemple #3
0
def gcpd2phot(source,results,units,master=None,e_flag='e_',q_flag='q_',extra_fields=None):
    """
    Convert/combine GCPD record arrays to measurement record arrays.
    
    Every line in the combined array represents a measurement in a certain band.
    
    The standard columns are:
    
        1. C{meas}: containing the photometric measurement
        2. C{e_meas}: the error on the photometric measurement
        3. C{flag}: an optional quality flag
        4. C{unit}: the unit of the measurement
        5. C{photband}: the photometric passband (FILTER.BAND)
        6. C{source}: name of the source catalog
    
    If you give a C{master}, the information will be added to a previous
    record array. If not, a new master will be created.
    
    Colors will be expanded, derived from the other columns and added to the
    master.
    
    The result is a record array with each row a measurement.
    
    Extra fields are not available for the GCPD, they will be filled in with
    nans.
    
    @param source: name of the VizieR source
    @type source: str
    @param results: results from VizieR C{search}
    @type results: record array
    @param units: header of Vizier catalog with key name the column name and
    key value the units of that column
    @type units: dict
    @param master: master record array to add information to
    @type master: record array
    @param e_flag: flag denoting the error on a column
    @type e_flag: str
    @param q_flag: flag denoting the quality of a measurement
    @type q_flag: str
    @param extra_fields: any extra columns you want to add information from
    @type extra_fields: list of str
    @return: array with each row a measurement
    @rtype: record array
    """
    if cat_info.has_option(source,'e_flag'):
        e_flag = cat_info.get(source,'e_flag')
    
    #-- basic dtypes
    dtypes = [('meas','f8'),('e_meas','f8'),('flag','a20'),
                  ('unit','a30'),('photband','a30'),('source','a50')]
    
    #-- extra can be added, but only if a master is already given!! The reason
    #   is that thre GCPD actually does not contain any extra information, so
    #   we will never be able to add it and will not know what dtype the extra
    #   columns should be   
    #-- extra can be added:
    names = list(results.dtype.names)
    if extra_fields is not None:
        for e_dtype in extra_fields:
            dtypes.append((e_dtype,'f8'))
     
    #-- create empty master if not given
    newmaster = False
    if master is None or len(master)==0:
        master = np.rec.array([tuple([('f' in dt[1]) and np.nan or 'none' for dt in dtypes])],dtype=dtypes)
        newmaster = True
    
    #-- add fluxes and magnitudes to the record array
    cols_added = 0
    for key in cat_info.options(source):
        if key[:2] =='e_' or key=='bibcode':
            continue
        photband = cat_info.get(source,key)
        #-- contains measurement, error, quality, units, photometric band and
        #   source
        cols = [results[key][:1],
                (e_flag+key in cat_info.options(source) and results[cat_info.get(source,e_flag+key)][:1] or np.ones(len(results[:1]))*np.nan),
                (q_flag+key in results.dtype.names and results[q_flag+key][:1] or np.ones(len(results[:1]))*np.nan),
                np.array(len(results[:1])*[units[key]],str),
                np.array(len(results[:1])*[photband],str),
                np.array(len(results[:1])*['GCPD'],str)]
        #-- add any extra fields if desired.
        if extra_fields is not None:
            for e_dtype in extra_fields:
                cols += [e_dtype in results.dtype.names and results[e_dtype][:1] or np.ones(len(results[:1]))*np.nan]
        #-- add to the master
        rows = []
        for i in range(len(cols[0])):
            rows.append(tuple([col[i] for col in cols]))
        master = np.core.records.fromrecords(master.tolist()+rows,dtype=dtypes)
        cols_added += 1
    
    #-- fix colours: we have to run through it two times to be sure to have
    #   all the colours
    N = len(master)-cols_added
    master_ = vizier._breakup_colours(master[N:])
    for i in range(5):
        master_ = vizier._breakup_colours(master_)
    #-- combine and return
    master = np.core.records.fromrecords(master.tolist()[:N]+master_.tolist(),dtype=dtypes)
    
    #-- skip first line from building 
    if newmaster: master = master[1:]
    return master
Exemple #4
0
def gcpd2phot(source,
              results,
              units,
              master=None,
              e_flag='e_',
              q_flag='q_',
              extra_fields=None):
    """
    Convert/combine GCPD record arrays to measurement record arrays.
    
    Every line in the combined array represents a measurement in a certain band.
    
    The standard columns are:
    
        1. C{meas}: containing the photometric measurement
        2. C{e_meas}: the error on the photometric measurement
        3. C{flag}: an optional quality flag
        4. C{unit}: the unit of the measurement
        5. C{photband}: the photometric passband (FILTER.BAND)
        6. C{source}: name of the source catalog
    
    If you give a C{master}, the information will be added to a previous
    record array. If not, a new master will be created.
    
    Colors will be expanded, derived from the other columns and added to the
    master.
    
    The result is a record array with each row a measurement.
    
    Extra fields are not available for the GCPD, they will be filled in with
    nans.
    
    @param source: name of the VizieR source
    @type source: str
    @param results: results from VizieR C{search}
    @type results: record array
    @param units: header of Vizier catalog with key name the column name and
    key value the units of that column
    @type units: dict
    @param master: master record array to add information to
    @type master: record array
    @param e_flag: flag denoting the error on a column
    @type e_flag: str
    @param q_flag: flag denoting the quality of a measurement
    @type q_flag: str
    @param extra_fields: any extra columns you want to add information from
    @type extra_fields: list of str
    @return: array with each row a measurement
    @rtype: record array
    """
    if cat_info.has_option(source, 'e_flag'):
        e_flag = cat_info.get(source, 'e_flag')

    #-- basic dtypes
    dtypes = [('meas', 'f8'), ('e_meas', 'f8'), ('flag', 'a20'),
              ('unit', 'a30'), ('photband', 'a30'), ('source', 'a50')]

    #-- extra can be added, but only if a master is already given!! The reason
    #   is that thre GCPD actually does not contain any extra information, so
    #   we will never be able to add it and will not know what dtype the extra
    #   columns should be
    #-- extra can be added:
    names = list(results.dtype.names)
    if extra_fields is not None:
        for e_dtype in extra_fields:
            dtypes.append((e_dtype, 'f8'))

    #-- create empty master if not given
    newmaster = False
    if master is None or len(master) == 0:
        master = np.rec.array(
            [tuple([('f' in dt[1]) and np.nan or 'none' for dt in dtypes])],
            dtype=dtypes)
        newmaster = True

    #-- add fluxes and magnitudes to the record array
    cols_added = 0
    for key in cat_info.options(source):
        if key[:2] == 'e_' or key == 'bibcode':
            continue
        photband = cat_info.get(source, key)
        #-- contains measurement, error, quality, units, photometric band and
        #   source
        cols = [
            results[key][:1],
            (e_flag + key in cat_info.options(source)
             and results[cat_info.get(source, e_flag + key)][:1]
             or np.ones(len(results[:1])) * np.nan),
            (q_flag + key in results.dtype.names and results[q_flag + key][:1]
             or np.ones(len(results[:1])) * np.nan),
            np.array(len(results[:1]) * [units[key]], str),
            np.array(len(results[:1]) * [photband], str),
            np.array(len(results[:1]) * ['GCPD'], str)
        ]
        #-- add any extra fields if desired.
        if extra_fields is not None:
            for e_dtype in extra_fields:
                cols += [
                    e_dtype in results.dtype.names and results[e_dtype][:1]
                    or np.ones(len(results[:1])) * np.nan
                ]
        #-- add to the master
        rows = []
        for i in range(len(cols[0])):
            rows.append(tuple([col[i] for col in cols]))
        master = np.core.records.fromrecords(master.tolist() + rows,
                                             dtype=dtypes)
        cols_added += 1

    #-- fix colours: we have to run through it two times to be sure to have
    #   all the colours
    N = len(master) - cols_added
    master_ = vizier._breakup_colours(master[N:])
    for i in range(5):
        master_ = vizier._breakup_colours(master_)
    #-- combine and return
    master = np.core.records.fromrecords(master.tolist()[:N] +
                                         master_.tolist(),
                                         dtype=dtypes)

    #-- skip first line from building
    if newmaster: master = master[1:]
    return master