Merge 1178482 into d51a777

docs/custom_loading.rst

@@ -77,7 +77,8 @@ ensure that the data file being loaded is compatible with the loader function.
                 os.path.splitext(args[0].lower())[1] == '.fits')
 
 
-    @data_loader("my-format", identifier=identify_generic_fits)
+    @data_loader("my-format", identifier=identify_generic_fits,
+                 extensions=['fits'])
     def generic_fits(file_name, **kwargs):
         name = os.path.basename(file_name.rstrip(os.sep)).rsplit('.', 1)[0]
 
@@ -94,6 +95,10 @@ ensure that the data file being loaded is compatible with the loader function.
         return Spectrum1D(flux=data, wcs=wcs, uncertainty=uncertainty, meta=meta)
 
 
+An ``extensions`` keyword can be provided. This allows for basic filename
+extension matching in the case that the ``identifier`` function is not
+provided.
+
 After placing this python file in the user's ``~/.specutils`` directory, it
 can be utilized by referencing its name in the ``read`` method of the
 :class:`~specutils.Spectrum1D` class

specutils/io/default_loaders/apogee.py

@@ -0,0 +1,179 @@
+"""
+Loader for APOGEE spectrum files: apVisit_, apStar_, aspcapStar_ files.
+
+.. _apVisit: https://data.sdss.org/datamodel/files/APOGEE_REDUX/APRED_VERS/TELESCOPE/PLATE_ID/MJD5/apVisit.html
+.. _apStar: https://data.sdss.org/datamodel/files/APOGEE_REDUX/APRED_VERS/APSTAR_VERS/TELESCOPE/LOCATION_ID/apStar.html
+.. _aspcapStar: https://data.sdss.org/datamodel/files/APOGEE_REDUX/APRED_VERS/APSTAR_VERS/ASPCAP_VERS/RESULTS_VERS/LOCATION_ID/aspcapStar.html
+"""
+import os
+
+from astropy.io import fits
+from astropy.table import Table
+from astropy.wcs import WCS
+from astropy.units import Unit, def_unit
+from astropy.nddata import StdDevUncertainty
+
+import numpy as np
+
+from specutils.io.registers import data_loader, custom_writer
+from specutils import Spectrum1D
+
+__all__ = ['apVisit_identify', 'apStar_identify', 'aspcapStar_identify',
+           'apVisit_loader', 'apStar_loader', 'aspcapStar_loader']
+
+
+def apVisit_identify(origin, *args, **kwargs):
+    """
+    Check whether given filename is FITS. This is used for Astropy I/O
+    Registry.
+    """
+    return (isinstance(args[0], str) and
+            args[0].lower().split('.')[-1] == 'fits' and
+            args[0].startswith('apVisit'))
+
+
+def apStar_identify(origin, *args, **kwargs):
+    """
+    Check whether given filename is FITS. This is used for Astropy I/O
+    Registry.
+    """
+    return (isinstance(args[0], str) and
+            args[0].lower().split('.')[-1] == 'fits' and
+            args[0].startswith('apStar'))
+
+
+def aspcapStar_identify(origin, *args, **kwargs):
+    """
+    Check whether given filename is FITS. This is used for Astropy I/O
+    Registry.
+    """
+    return (isinstance(args[0], str) and
+            args[0].lower().split('.')[-1] == 'fits' and
+            args[0].startswith('aspcapStar'))
+
+
+@data_loader(label="APOGEE apVisit", identifier=apVisit_identify, extensions=['fits'])
+def apVisit_loader(file_name, **kwargs):
+    """
+    Loader for APOGEE apVisit files.
+
+    Parameters
+    ----------
+    file_name: str
+        The path to the FITS file
+
+    Returns
+    -------
+    data: Spectrum1DRef
+        The data.
+    """
+    name = os.path.basename(file_name.rstrip(os.sep)).rsplit('.', 1)[0]
+    hdulist = fits.open(file_name, **kwargs)
+
+    header = hdulist[0].header
+    meta = {'header': header}
+
+    # spectrum is stored in three rows (for three chips)
+    data = np.concatenate([hdulist[1].data[0, :],
+                           hdulist[1].data[1, :],
+                           hdulist[1].data[2, :]])
+    unit = Unit('1e-17 erg / (Angstrom cm2 s)')
+
+    stdev = np.concatenate([hdulist[2].data[0, :],
+                           hdulist[2].data[1, :],
+                           hdulist[2].data[2, :]])
+    uncertainty = StdDevUncertainty(stdev * unit)
+
+    # Dispersion is not a simple function in these files.  There's a
+    # look-up table instead.
+    dispersion = np.concatenate([hdulist[4].data[0, :],
+                                 hdulist[4].data[1, :],
+                                 hdulist[4].data[2, :]])
+    dispersion_unit = Unit('Angstrom')
+    hdulist.close()
+
+    return Spectrum1D(data=data * unit,
+                      uncertainty=uncertainty,
+                      dispersion=dispersion * dispersion_unit,
+                      meta=meta)
+
+
+@data_loader(label="APOGEE apStar", identifier=apStar_identify, extensions=['fits'])
+def apStar_loader(file_name, **kwargs):
+    """
+    Loader for APOGEE apStar files.
+
+    Parameters
+    ----------
+    file_name: str
+        The path to the FITS file
+
+    Returns
+    -------
+    data: Spectrum1DRef
+        The data.
+    """
+    name = os.path.basename(file_name.rstrip(os.sep)).rsplit('.', 1)[0]
+    hdulist = fits.open(file_name, **kwargs)
+
+    header = hdulist[0].header
+    meta = {'header': header}
+    wcs = WCS(hdulist[1].header)
+
+    data = hdulist[1].data[0, :]  # spectrum in the first row of the first extension
+    unit = Unit('1e-17 erg / (Angstrom cm2 s)')
+
+    uncertainty = StdDevUncertainty(hdulist[2].data[0, :])
+
+    # dispersion from the WCS but convert out of logspace
+    # dispersion = 10**wcs.all_pix2world(np.arange(data.shape[0]), 0)[0]
+    dispersion = 10**wcs.all_pix2world(np.vstack((np.arange(data.shape[0]),
+                                                  np.zeros((data.shape[0],)))).T,
+                                       0)[:, 0]
+    dispersion_unit = Unit('Angstrom')
+    hdulist.close()
+
+    return Spectrum1D(data=data * unit,
+                      uncertainty=uncertainty,
+                      dispersion=dispersion * dispersion_unit,
+                      meta=meta,
+                      wcs=wcs)
+
+
+@data_loader(label="APOGEE aspcapStar", identifier=aspcapStar_identify, extensions=['fits'])
+def aspcapStar_loader(file_name, **kwargs):
+    """
+    Loader for APOGEE aspcapStar files.
+
+    Parameters
+    ----------
+    file_name: str
+        The path to the FITS file
+
+    Returns
+    -------
+    data: Spectrum1DRef
+        The data.
+    """
+    name = os.path.basename(file_name.rstrip(os.sep)).rsplit('.', 1)[0]
+    hdulist = fits.open(file_name, **kwargs)
+
+    header = hdulist[0].header
+    meta = {'header': header}
+    wcs = WCS(hdulist[1].header)
+
+    data = hdulist[1].data # spectrum in the first extension
+    unit = def_unit('arbitrary units')
+
+    uncertainty = StdDevUncertainty(hdulist[2].data)
+
+    # dispersion from the WCS but convert out of logspace
+    dispersion = 10**wcs.all_pix2world(np.arange(data.shape[0]), 0)[0]
+    dispersion_unit = Unit('Angstrom')
+    hdulist.close()
+
+    return Spectrum1D(data=data * unit,
+                      uncertainty=uncertainty,
+                      dispersion=dispersion * dispersion_unit,
+                      meta=meta,
+                      wcs=wcs)

specutils/io/default_loaders/ascii.py

@@ -0,0 +1,114 @@
+import os
+
+import astropy.units as u
+from astropy.nddata import StdDevUncertainty
+from astropy.table import Table
+
+from specutils import Spectrum1D
+from specutils.io.registers import data_loader
+
+__all__ = ['ascii_identify', 'ascii_loader', 'ipac_identify', 'ipac_loader']
+
+
+def ascii_identify(origin, *args, **kwargs):
+    """Check if it's an ASCII file."""
+    name = os.path.basename(args[0])
+
+    if name.lower().split('.')[-1] in ['txt', 'ascii']:
+       return True
+
+    return False
+
+
+@data_loader(label="ASCII", identifier=ascii_identify, extensions=['txt', 'ascii'])
+def ascii_loader(file_name, **kwargs):
+    """
+    Load spectrum from ASCII file
+
+    Parameters
+    ----------
+    file_name: str
+        The path to the ASCII file
+
+    Returns
+    -------
+    data: Spectrum1D
+        The data.
+    """
+    table = Table.read(file_name, format='ascii')
+
+    flux = None
+    dispersion = None
+    uncertainty = None
+
+    # If there are more than two columns, assume that the first is wavelength,
+    # and the second is flux
+    if len(table.columns) > 1:
+        disp_unit = u.Unit("Angstrom")
+        dispersion = table.columns[0] * disp_unit
+
+        unit = u.Unit("Jy")
+        flux = table.columns[1] * unit
+
+        # If there are more than two columns, assume the third is uncertainty
+        if len(table.columns) >= 2:
+            uncertainty = StdDevUncertainty(table.columns[2] * unit)
+    # If there is only one column, assume it's just flux.
+    elif len(table.columns) == 1:
+        unit = u.Unit("Jy")
+        flux = table.columns[0] * unit
+
+    return Spectrum1D(flux=flux,
+                      spectral_axis=dispersion,
+                      meta=table.meta,
+                      uncertainty=uncertainty)
+
+
+def ipac_identify(*args, **kwargs):
+    """Check if it's an ASCII file."""
+    name = os.path.basename(args[0])
+
+    if name.lower().split('.')[-1] in ['txt', 'dat']:
+        return True
+
+    return False
+
+
+@data_loader(label="IPAC", identifier=ipac_identify, extensions=['txt', 'dat'])
+def ipac_loader(file_name, **kwargs):
+    """
+    Load spectrum from ASCII file
+
+    Parameters
+    ----------
+    file_name: str
+        The path to the ASCII file
+
+    Returns
+    -------
+    data: Spectrum1D
+        The data.
+    """
+    table = Table.read(file_name, format='ascii.ipac')
+
+    flux = None
+    dispersion = None
+    uncertainty = None
+
+    # If there are more than two columns, assume that the first is wavelength,
+    # and the second is flux
+    if len(table.columns) > 1:
+        dispersion = u.Quantity(table.columns[0])
+        flux = u.Quantity(table.columns[1])
+
+        # If there are more than two columns, assume the third is uncertainty
+        if len(table.columns) >= 2:
+            uncertainty = StdDevUncertainty(u.Quantity(table.columns[2]))
+    # If there is only one column, assume it's just flux.
+    elif len(table.columns) == 1:
+        flux = u.Quantity(table.columns[0])
+
+    return Spectrum1D(flux=flux,
+                      spectral_axis=dispersion,
+                      meta=table.meta,
+                      uncertainty=uncertainty)

specutils/io/default_loaders/cube_reader.py

@@ -25,7 +25,7 @@ def identify_generic_fits(origin, *args, **kwargs):
             fits.getheader(args[0])['NAXIS'] == 3)
 
 
-@data_loader("cubetest1", identifier=identify_generic_fits)
+@data_loader("cubetest1", identifier=identify_generic_fits, extensions=['fits'])
 def generic_fits(file_name, **kwargs):
     name = os.path.basename(file_name.rstrip(os.sep)).rsplit('.', 1)[0]
 

specutils/io/default_loaders/ecsv.py

@@ -0,0 +1,45 @@
+import os
+
+from astropy.table import Table
+
+from specutils.io.registers import data_loader, custom_writer
+from specutils import Spectrum1D
+
+__all__ = ['ecsv_identify', 'ecsv_spectrum_loader']
+
+
+def ecsv_identify(origin, *args, **kwargs):
+    """Check if it's an ECSV file."""
+    name = os.path.basename(args[0])
+
+    if name.lower().split('.')[-1] == 'ecsv':
+       return True
+
+    return False
+
+
+@data_loader(label="Spectrum ECSV", identifier=ecsv_identify, extensions=['ecsv'])
+def ecsv_spectrum_loader(file_name, **kwargs):
+    """
+    Load spectrum from ECSV file
+
+    Parameters
+    ----------
+    file_name: str
+        The path to the ECSV file
+
+    Returns
+    -------
+    data: Spectrum1D
+        The data.
+    """
+    table = Table.read(file_name, format='ascii.ecsv')
+
+    unit = table['Intensity'].unit
+    disp_unit = table['Wavelength'].unit
+    flux = table['Intensity'] * unit
+    dispersion = table['Wavelength'] * disp_unit
+
+    return Spectrum1D(flux=flux,
+                      spectral_axis=dispersion,
+                      meta=table.meta)