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Merge remote-tracking branch 'origin/winnerbranch'
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@cvalenzu
cvalenzu committed Dec 16, 2016
2 parents d891d23 + f34656b commit 63507d6
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Showing 5 changed files with 418 additions and 20 deletions.
23 changes: 21 additions & 2 deletions acalib/algorithms/stacking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,33 @@


class Stacking(Algorithm):
"""
Create a stacked image using a template image and a set of different images from same object.
"""

def default_params(self):
pass
pass

def run(self, template_data, data_cont):
"""
Run the stacking algorithm given a template image and a container of images.
Parameters
----------
template_data: (M,N) numpy.ndarray
Astronomical image.
data_cont: acalib.container
An images set container
Returns
-------
result: (M,N) numpy.ndarray
Image stacked
"""

tprops = acalib.core.transform.fits_props(template_data)
scaled = acalib.core.transform.scale(data_cont, tprops['major'])
rotated, angles = acalib.core.transform.rotate(scaled, tprops['angle'])
aligned = acalib.core.transform.crop_and_align(rotated, angles)
result = mean(aligned , axis=0)
return result, signaltonoise(result)
return result
179 changes: 172 additions & 7 deletions acalib/upi/axes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,22 @@
# axes_names used in formatting
@support_nddata
def axes_names(data,wcs=None):
"""
Get the axes's names.
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
Returns
-------
result: numpy.ndarray
Numpy ndarray with the axes's names from the WCS.
"""
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
return None
Expand All @@ -18,6 +34,30 @@ def axes_names(data,wcs=None):

@support_nddata
def cut(data, wcs=None, mask=None, unit=None, lower=None, upper=None):
"""
Get the axes's names.
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
mask : numpy.ndarray
Mask for data.
unit : astropy.units.Unit
Astropy unit (http://docs.astropy.org/en/stable/units/).
lower : tuple
Start coordinate from where to cut.
upper : tuple
Coordinate to end cut.
Returns
-------
result: astropy.nddata.NDData.
data cut from lower to upper.
"""
# Check for NDDataSlicing... maybe this is already done by astropy.nddata package.
mslab = core.slab(data, lower, upper)
scube = data[mslab]
Expand All @@ -26,7 +66,26 @@ def cut(data, wcs=None, mask=None, unit=None, lower=None, upper=None):

@support_nddata
def extent(data,wcs=None,lower=None,upper=None):
""" Get axes extent """
"""
Get the axes extent.
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
lower : (M,N) or (M,N,Z) tuple of int
Start coordinate in data
upper : (M,N) or (M,N,Z) tuple of int
End coordinate in data
Returns
-------
result: (M, N) tuple of astropy.units.quantity.Quantity
Axes extent
"""
#TODO: These can be a decorator
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
Expand All @@ -43,7 +102,22 @@ def extent(data,wcs=None,lower=None,upper=None):

@support_nddata
def center(data,wcs=None):
""" Get center of the data"""
"""
Get center of the data
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
Returns
-------
result: astropy.units.quantity.Quantity
Center of the data
"""
#TODO: These can be a decorator
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
Expand All @@ -53,7 +127,22 @@ def center(data,wcs=None):

@support_nddata
def axes_units(data,wcs=None):
""" Get units of the axes"""
"""
Get units of the axes
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
Returns
-------
result: (M,N) or (M,N,Z) numpy.ndarray
Vector with the units of the axes
"""
#TODO: These can be a decorator (
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
Expand All @@ -63,7 +152,22 @@ def axes_units(data,wcs=None):

@support_nddata
def resolution(data,wcs=None):
""" Get the resolution of data"""
"""
Get the resolution of data
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
Returns
-------
result: (M,N) or (M,N,Z) numpy.ndarray
Resolution of the data
"""
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
return None
Expand All @@ -72,7 +176,30 @@ def resolution(data,wcs=None):

@support_nddata
def spectral_velocities(data,wcs=None,fqs=None,fqis=None,restfrq=None):
""" Get the spectral velocities from frequencies fqs given a rest frequency (by default search for it in the WCS). If fqs is None, then frequencies indices (fqis) need to be given.
"""
Get the spectral velocities from frequencies fqs given a rest
frequency (by default search for it in the WCS). If fqs is None,
then frequencies indices (fqis) need to be given.
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
fqs : astropy.units.quantity.Quantity
Array of frequencies with units.
fqis : list of integers
Array of frequencies indices
restfrq : astropy.units.quantity.Quantity
Rest frequency
Returns
-------
result: astropy.units.quantity.Quantity
Array of Spectral velocities.
"""
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
Expand All @@ -93,7 +220,26 @@ def spectral_velocities(data,wcs=None,fqs=None,fqis=None,restfrq=None):

@support_nddata
def features(data,wcs=None,lower=None,upper=None):
""" Creates an array with WCS axea in features format """
"""
Creates an array with WCS axea in features format
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
lower : (M,N) or (M,N,Z) tuple of integers
Start coordinate in data.
upper : (M,N) or (M,N,Z) tuple of integers
End coordinate in data.
Returns
-------
result: astropy.table.Table
Table with WCS information of a section from the data.
"""
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
return None
Expand All @@ -105,7 +251,26 @@ def features(data,wcs=None,lower=None,upper=None):
@support_nddata
# TODO: Consider using "box" structure rather than up and low
def opening(data,center,window,wcs=None):
""" Field of view (center +- window) converted to indices """
"""
Field of view (center +- window) converted to indices
Parameters
----------
data : (M,N) or (M,N,Z) numpy.ndarray or astropy.nddata.NDData
Astronomical data cube.
center : astropy.units.quantity.Quantity
Center of the field of view in WCS.
window : astropy.units.quantity.Quantity
Window for the field in WCS.
wcs : astropy.wcs.wcs.WCS
World Coordinate System to use.
Returns
-------
result: ((M1,N1,Z1),(M2,N2,Z2)) tuple of tuple of ints
"""
if wcs is None:
log.error("A world coordinate system (WCS) is needed")
return None
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