V1.0 Tasks

astropop/fits_utils.py

@@ -31,7 +31,8 @@ def string_to_header_key(string: str) -> str:
     """
     # for non hierarch keys, we will use normalized keywords (uppercase)
     if fits.Card._keywd_FSC_RE.match(string.upper()) and len(string) <= 8:
-        return string.upper()
+        string = string.upper()
+        return string
 
     # these cases should go to hierarch
     if string.casefold().startswith('hierarch '):

astropop/framedata/_compat.py

@@ -1,14 +1,14 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 """Handle compatibility between FrameData and other data formats."""
 
-import warnings
 import itertools
+import warnings
 from os import PathLike
 import copy as cp
 import numpy as np
 from astropy.io import fits
-from astropy.io.fits.verify import VerifyWarning
 from astropy.wcs import WCS, FITSFixedWarning
+from astropy.io.fits.verify import VerifyWarning
 from astropy.nddata.ccddata import CCDData
 from astropy.nddata import StdDevUncertainty, VarianceUncertainty, \
                            InverseVariance
@@ -19,17 +19,17 @@
 from ..fits_utils import imhdus, string_to_header_key
 
 
+_HDU_UNCERT = 'UNCERT'
+_HDU_MASK = 'MASK'
+_HDU_FLAGS = 'PIXFLAGS'
+_UNIT_KEY = 'BUNIT'
 _PCs = set(['PC1_1', 'PC1_2', 'PC2_1', 'PC2_2'])
 _CDs = set(['CD1_1', 'CD1_2', 'CD2_1', 'CD2_2'])
 _KEEP = set(['JD-OBS', 'MJD-OBS', 'DATE-OBS'])
 _PROCTECTED = ["SIMPLE", "XTENSION", "BITPIX", "NAXIS", "EXTEND", "PCOUNT",
                "GCOUNT", "GROUPS", "BSCALE", "BZERO", "TFIELDS"]
 _PROTECTED_N = ["TFORM", "TSCAL", "TZERO", "TNULL", "TTYPE", "TUNIT", "TDISP",
                 "TDIM", "THEAP", "TBCOL"]
-_HDU_UNCERT = 'UNCERT'
-_HDU_MASK = 'MASK'
-_HDU_FLAGS = 'PIXFLAGS'
-_UNIT_KEY = 'BUNIT'
 
 
 def _remove_sip_keys(header, wcs):
@@ -103,9 +103,12 @@
 def _normalize_and_strip_dict(meta):
     """Normalize meta keys and remove the protected ones."""
     if meta is None:
-        return {}, [], []
+        return fits.Header(), [], []
 
-    nmeta = {}
+    if not isinstance(meta, fits.Header):
+        raise TypeError('meta must be a fits.Header instance.')
+
+    nmeta = fits.Header()
     history = []
     comment = []
 
@@ -129,8 +132,8 @@
             # as dicts are case sensitive, this can happen. Raise error
             warnings.warn(f'Duplicated key {k}. First value will be used.')
         if k not in _PROCTECTED and k != '' and k not in nmeta:
-            # remove protected keys
-            nmeta[k] = v
+            # keep commentaries. Do not keep protected keys
+            nmeta.append((k, meta[k], meta.comments[k]))
 
     # remove protected keys with number
     naxis = nmeta.get('NAXIS', 0)
@@ -146,38 +149,6 @@
     return nmeta, history, comment
 
 
-def _merge_and_clean_header(meta, header, wcs):
-    """Merge meta and header and clean the WCS and spurious keys."""
-    if not isinstance(meta, (dict, fits.Header)) and meta is not None:
-        raise TypeError('meta must be a dict or fits.Header. '
-                        f'Got {type(meta)}')
-    if not isinstance(header, fits.Header) and header is not None:
-        raise TypeError('header must be a fits.Header. '
-                        f'Got {type(header)}')
-    if not isinstance(wcs, WCS) and wcs is not None:
-        raise TypeError('wcs must be a astropy.wcs.WCS. '
-                        f'Got {type(wcs)}')
-
-    history = []
-    comment = []
-    fmeta = fits.Header()
-
-    for m in [meta, header]:
-        m, h, c = _normalize_and_strip_dict(m)
-        # extract history and comments from meta
-        history.extend(h)
-        comment.extend(c)
-        # merge meta and header
-        fmeta.update(m)
-
-    # extract wcs from header
-    meta, wcs_ = extract_header_wcs(fmeta)
-    if wcs_ and wcs:
-        raise ValueError('meta and wcs offer a WCS. Use only one.')
-    wcs = wcs_ if wcs is None else wcs
-    return meta, wcs, history, comment
-
-
 def _extract_fits(obj, hdu=0, unit=None, hdu_uncertainty=_HDU_UNCERT,
                   hdu_flags=_HDU_FLAGS, hdu_mask=_HDU_MASK,
                   unit_key=_UNIT_KEY):
@@ -240,7 +211,7 @@
     if isinstance(obj, (str, bytes, PathLike)):
         hdul.close()
 
     # TODO: extract flags
 
     return res
 
@@ -331,7 +302,7 @@
             mask_h = fits.Header()
             hdul.append(fits.ImageHDU(mask, header=mask_h, name=hdu_mask))
 
     # TODO: add flags
 
     return hdul
 

astropop/framedata/framedata.py

@@ -18,7 +18,8 @@
 from ..flags import mask_from_flags
 from ._memmap import create_array_memmap, delete_array_memmap, \
                      reset_memmap_array
-from ._compat import _merge_and_clean_header, _to_hdu, _to_ccddata, _write_fits
+from ._compat import _to_hdu, _to_ccddata, _write_fits, \
+                     _normalize_and_strip_dict, extract_header_wcs
 from .._unit_property import unit_property
 
 
@@ -183,10 +184,11 @@ class FrameData:
         Pixel flags for the frame. See `~astropop.FrameData.PixelMaskFlags`.
         for values.
     wcs : `dict`, `~astropy.fits.Header` or `~astropy.wcs.WCS` (optional)
-        World Coordinate System of the image.
+        World Coordinate System of the image. If meta or header keys already
+        contain WCS informations, an error will be raised.
     meta or header: `dict` or `astropy.fits.Header` (optional)
-        Metadata (header) of the frame. If both set, they will be merged.
-        `header` priority.
+        Metadata (header) of the frame. Only one accepted. If both are passed,
+        error will be raised.
     cache_folder : string, `~pathlib.Path` or `None` (optional)
         Place to store the cached `FrameData`
     cache_filename : string, `~pathlib.Path` or `None` (optional)
@@ -221,9 +223,9 @@ class FrameData:
     cache_filename = None
 
     def __init__(self, data, unit=None, dtype=None, uncertainty=None,
-                 mask=None, flags=None, wcs=None, meta=None, header=None,
+                 mask=None, flags=None, use_memmap_backend=False,
                  cache_folder=None, cache_filename=None, origin_filename=None,
-                 use_memmap_backend=False):
+                 **kwargs):
         # setup names
         setup_filename(self, cache_folder, cache_filename)
         self._origin = origin_filename
@@ -268,19 +270,41 @@ def __init__(self, data, unit=None, dtype=None, uncertainty=None,
         self._history = []
         self._comments = []
         self._meta = fits.Header()
-        self._header_update(header, meta, wcs)
-
-    def _header_update(self, header, meta=None, wcs=None):
-        # merge header and meta. meta with higher priority
-        meta, wcs, history, comment = _merge_and_clean_header(meta, header,
-                                                              wcs)
+        if 'meta' in kwargs and 'header' in kwargs:
+            raise ValueError('Only one of meta or header can be set.')
+        if 'meta' not in kwargs:
+            kwargs['meta'] = kwargs.pop('header', None)
+        self._meta_update(kwargs.pop('meta', None),
+                          kwargs.pop('wcs', None))
+
+    def _meta_update(self, meta, wcs=None):
+        # simplify things by enforcing meta type
+        if not isinstance(meta, (dict, fits.Header, type(None))):
+            raise TypeError('meta must be a dict, Header or None.')
+
+        # force fits compliant header
+        try:
+            if meta is not None:
+                hdr = fits.Header(meta)
+            else:
+                hdr = fits.Header()
+        except Exception as e:
+            raise ValueError('meta or header must be compilant with FITS '
+                             'standard. Got error when tried to convert to '
+                             f'fits.Header: {e}')
+
+        header, history, comment = _normalize_and_strip_dict(hdr)
         if len(history) > 0:
             self.history = history
         if len(comment) > 0:
             self.comment = comment
-        if wcs is not None:
-            self._wcs = wcs
-        self._meta = meta
+
+        header, _wcs = extract_header_wcs(header)
+        if _wcs is not None and wcs is not None:
+            raise ValueError('wcs and meta/wcs cannot be set at the same '
+                             'time.')
+        self._wcs = _wcs or wcs
+        self._meta = header
 
     @property
     def origin_filename(self):
@@ -325,7 +349,7 @@ def meta(self):
 
     @meta.setter
     def meta(self, value):
-        self._header_update(None, value)
+        self._meta_update(value)
 
     @property
     def header(self):

astropop/image/_tools.py

@@ -6,7 +6,6 @@
 
 from ..logger import logger
 from ..framedata._compat import _normalize_and_strip_dict
-from ..fits_utils import string_to_header_key
 
 __all__ = ['merge_header', 'merge_flag']
 
@@ -22,8 +21,8 @@
         Method to merge the headers. 'only_equal' will merge only the keywords
         with the same value in all headers. 'first' will use the first
         header as the result. 'selected_keys' will merge only the keywords
-        in the list `header_merge_keys`. 'no_merge' will return an empty
-        header.
+        in the list `header_merge_keys`, prioritizing the first appearence.
+        'no_merge' will return an empty header.
     selected_keys: list of str
         List of keywords to be merged. Used only if method is
         'selected_keys'.
@@ -43,7 +42,7 @@
         raise ValueError('selected_keys must be provided if method is '
                          'selected_keys.')
 
-    meta = {}
+    meta = Header()
     if method == 'no_merge':
         return meta
 
@@ -52,39 +51,36 @@
     if method == 'first':
         return headers[0].copy()
 
-    summary = None
+    first_hdr = headers[0]
+    if method == 'first':
+        return first_hdr.copy()
+
     for hdr in headers:
         hdr, _, _ = _normalize_and_strip_dict(hdr)
-        hdr = Header(hdr)
-        if summary is None:
-            summary = {k: [v] for k, v in hdr.items()}
-        for key in hdr.keys():
-            if key not in summary.keys():
-                # avoid only_equal problems
-                summary[key] = [None]
-            if hdr[key] not in summary[key]:
-                summary[key].append(hdr[key])
-
-    if method == 'selected_keys':
-        keys = selected_keys
-    else:
-        keys = summary.keys()
-
-    for k in keys:
-        # do not use np.unique to avoid problems with None
-        k = string_to_header_key(k)
-        uniq = list(set(summary[k]))
-        if len(uniq) == 1:
-            meta[k] = uniq[0]
+        if method == 'only_equal':
+            # only keeps equal keys. If is the first header, add it
+            # to the meta. If the key is different, remove it from
+            # the meta.
+            for key in hdr:
+                if key not in meta and hdr == first_hdr:
+                    meta.append((key, hdr[key], hdr.comments[key]))
+                    continue
+                if key not in meta:
+                    continue
+                if meta[key] != hdr[key]:
+                    del meta[key]
+            # remove all keys that are not in this header, since it will be not
+            # equal
+            for key in meta:
+                if key not in hdr:
+                    del meta[key]
         elif method == 'selected_keys':
-            logger.debug('Keyword %s is different across headers. '
-                         'Unsing first one.', k)
-            meta[k] = summary[k][0]
-        else:
-            logger.debug('Keyword %s is different across headers. '
-                         'Skipping.', k)
-
-    return dict(meta)
+            # only keeps the keys in the selected_keys list
+            for key in hdr:
+                if key in selected_keys and key not in meta:
+                    meta.append((key, hdr[key], hdr.comments[key]))
+
+    return meta
 
 
 def merge_flag(*flags, method='or'):

astropop/image/imarith.py

@@ -129,8 +129,8 @@ def imarith(operand1, operand2, operation, inplace=False,
     ccd.flags = merge_flag(f1, f2, method=merge_flags)
 
     # Perform merging headers operation only if both operands have headers
-    h1 = getattr(operand1, 'header', {})
-    h2 = getattr(operand2, 'header', {})
+    h1 = getattr(operand1, 'header', None)
+    h2 = getattr(operand2, 'header', None)
     keys = kwargs.get('selected_keys', None)
     ccd.meta = merge_header(h1, h2, method=merge_headers, selected_keys=keys)
 

astropop/image/processing.py

@@ -14,7 +14,7 @@
            'subtract_dark', 'flat_correct', 'trim_image']
 
 
 # TODO: replace ccdproc functions by built-in, skiping units
 # block_reduce = ccdproc.block_reduce
 # block_replicate = ccdproc.block_replicate
 
@@ -36,8 +36,7 @@
     Parameters
     ----------
     frame: `~astropop.framedata.FrameData` compatible
-        Values to perform the operation. `~astropy.units.Quantity`, numerical
-        values and `~astropy.nddata.CCDData` are also suported.
+        2D image to clean with LACosmic.
     inplace: bool, optional
         If True, the operations will be performed inplace in the `frame`.
     logger: `~logging.Logger`
@@ -49,8 +48,8 @@
         New cosmic-rays corrected `FrameData` instance if not `inplace`,
         else the `image` `~astropop.framedata.FrameData` instance.
     """
-    # As lacosmic removes and replace the cosmics pixels, no need to
-    # update the mask
+    frame = check_framedata(frame)
+
     mask, dat = astroscrappy.detect_cosmics(frame.data, **lacosmic_kwargs)
 
     if inplace:
@@ -291,12 +290,7 @@
 
     # fix WCS if existing
     if image.wcs is not None:
-        wcs = image.wcs.copy()
-        wcs.wcs.crpix[0] -= x_slice.start
-        wcs.wcs.crpix[1] -= y_slice.start
-        # FIXME: this should work but is getting wrong results
-        # image.wcs = wcs.slice(section[::-1])
-        image.wcs = wcs
+        image.wcs = image.wcs.slice(section)
 
     str_slice = ''
     for s in section[::-1]: