ckrawczyk / gz3d_production Goto Github PK

Marvin says ```AttributeError: 'Map' object has no 'header' member```

Presumably another change in Marvin. 

MarvinDeprecationError                    Traceback (most recent call last)
<ipython-input-5-50dda1424bbf> in <module>
      4 data.get_bpt()
      5 data.make_all_spaxel_masks()
----> 6 data.get_mean_spectra(inv=True)

/raid5/homes/klmasters/Galaxy Zoo 3D/gz3d_fits.py in get_mean_spectra(self, inv)
    226         if self.cube != 'no_data':
    227             self.make_all_spaxel_masks()
--> 228             self.mean_bar = self._stack_spectra('bar_mask_spaxel')
    229             self.mean_spiral = self._stack_spectra('spiral_mask_spaxel')
    230             self.mean_center = self._stack_spectra('center_mask_spaxel')

/gz3d_fits.py in _stack_spectra(self, mask_name, inv)
    212         if len(mdx[0] > 0):
    213             weights = mask[mdx]
--> 214             spaxels = self.cube[mdx]
    215             spectra = np.array([s.spectrum for s in spaxels])
    216             if len(spectra) == 1:

marvin_subclass.py in __getitem__(self, xy)
    111     def __getitem__(self, xy):
    112         """Returns the spaxel for ``(x, y)`` without propserties"""
--> 113         spaxel = self.getSpaxel(x=xy[0], y=xy[1], properties=False, xyorig='lower')
    114         if isinstance(spaxel, list):
    115             for s in spaxel:

/packages/python3.6.8/lib/python3.6/site-packages/marvin/tools/cube.py in getSpaxel(self, x, y, ra, dec, maps, modelcube, **kwargs)
    576                 raise marvin.core.exceptions.MarvinDeprecationError(
    577                     'the {0} parameter has been deprecated. '
--> 578                     'Use maps or modelcube.'.format(old_param))
    579 
    580         return marvin.utils.general.general.getSpaxel(x=x, y=y, ra=ra, dec=dec,

MarvinDeprecationError: the properties parameter has been deprecated. Use maps or modelcube.
You can submit this error to Marvin GitHub Issues (https://github.com/sdss/marvin/issues/new).
Fill out a subject and some text describing the error that just occurred.
If able, copy and paste the full traceback information into the issue as well.```

INFO: No release version set. Setting default to MPL-6
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-43d72828a907> in <module>()
----> 1 from gz3d_fits import gz3d_fits
      2 
      3 data = gz3d_fits('/Volumes/Work/GZ3D/MPL5_fits/1-167242_127_5679242.fits.gz')
      4 data.get_bpt()
      5 data.make_all_spaxel_masks()

/raid5/homes/sshamsi/Untitled Folder/gz3d_fits.py in <module>()
      8 import json
      9 from marvin import config
---> 10 from marvin_subclass import CubeFast, Suppressor
     11 import marvin.utils.dap.bpt as bpt
     12 

/raid5/homes/sshamsi/Untitled Folder/marvin_subclass.py in <module>()
----> 1 from marvin.tools.spectrum import Spectrum
      2 from marvin.tools.cube import Cube
      3 import numpy as np
      4 import sys
      5 import traceback

ImportError: No module named 'marvin.tools.spectrum'

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-2-43d72828a907> in <module>()
      1 from gz3d_fits import gz3d_fits
      2 
----> 3 data = gz3d_fits('/Volumes/Work/GZ3D/MPL5_fits/1-167242_127_5679242.fits.gz')
      4 data.get_bpt()
      5 data.make_all_spaxel_masks()

/raid5/homes/sshamsi/Untitled Folder/gz3d_fits.py in __init__(self, filename)
     51         self.subject_id = filename.split('/')[-1].split('_')[-1].split('.')[0]
     52         # read in the fits file
---> 53         self.hdulist = fits.open(filename)
     54         # grab the wcs
     55         self.wcs = WCS(self.hdulist[1].header)

~/.local/lib/python3.5/site-packages/astropy/io/fits/hdu/hdulist.py in fitsopen(name, mode, memmap, save_backup, cache, lazy_load_hdus, **kwargs)
    162 
    163     return HDUList.fromfile(name, mode, memmap, save_backup, cache,
--> 164                             lazy_load_hdus, **kwargs)
    165 
    166 

~/.local/lib/python3.5/site-packages/astropy/io/fits/hdu/hdulist.py in fromfile(cls, fileobj, mode, memmap, save_backup, cache, lazy_load_hdus, **kwargs)
    398         return cls._readfrom(fileobj=fileobj, mode=mode, memmap=memmap,
    399                              save_backup=save_backup, cache=cache,
--> 400                              lazy_load_hdus=lazy_load_hdus, **kwargs)
    401 
    402     @classmethod

~/.local/lib/python3.5/site-packages/astropy/io/fits/hdu/hdulist.py in _readfrom(cls, fileobj, data, mode, memmap, save_backup, cache, lazy_load_hdus, **kwargs)
    985             if not isinstance(fileobj, _File):
    986                 # instantiate a FITS file object (ffo)
--> 987                 fileobj = _File(fileobj, mode=mode, memmap=memmap, cache=cache)
    988             # The Astropy mode is determined by the _File initializer if the
    989             # supplied mode was None

~/.local/lib/python3.5/site-packages/astropy/utils/decorators.py in wrapper(*args, **kwargs)
    486                         # one with the name of the new argument to the function
    487                         kwargs[new_name[i]] = value
--> 488             return function(*args, **kwargs)
    489 
    490         return wrapper

~/.local/lib/python3.5/site-packages/astropy/io/fits/file.py in __init__(self, fileobj, mode, memmap, overwrite, cache)
    173             self._open_fileobj(fileobj, mode, overwrite)
    174         elif isinstance(fileobj, str):
--> 175             self._open_filename(fileobj, mode, overwrite)
    176         else:
    177             self._open_filelike(fileobj, mode, overwrite)

~/.local/lib/python3.5/site-packages/astropy/io/fits/file.py in _open_filename(self, filename, mode, overwrite)
    525         ext = os.path.splitext(self.name)[1]
    526 
--> 527         if not self._try_read_compressed(self.name, magic, mode, ext=ext):
    528             self._file = fileobj_open(self.name, IO_FITS_MODES[mode])
    529             self.close_on_error = True

~/.local/lib/python3.5/site-packages/astropy/io/fits/file.py in _try_read_compressed(self, obj_or_name, magic, mode, ext)
    423             else:
    424                 kwargs['fileobj'] = obj_or_name
--> 425             self._file = gzip.GzipFile(**kwargs)
    426             self.compression = 'gzip'
    427         elif ext == '.zip' or magic.startswith(PKZIP_MAGIC):

~/.local/lib/python3.5/site-packages/marvin/tools/spaxel.py in spaxel_factory(cls, *args, **kwargs)
     70 
     71     if cls is not SpaxelBase:
---> 72         return type.__call__(cls, *args, **kwargs)
     73 
     74     cube = kwargs.pop('cube', None)

/usr/lib/python3.5/gzip.py in __init__(self, filename, mode, compresslevel, fileobj, mtime)
    161             mode += 'b'
    162         if fileobj is None:
--> 163             fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
    164         if filename is None:
    165             filename = getattr(fileobj, 'name', '')

FileNotFoundError: [Errno 2] No such file or directory: '/Volumes/Work/GZ3D/MPL5_fits/1-167242_127_5679242.fits.gz'