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Various improvements to Core data classes #140

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Jul 26, 2023
Merged

Various improvements to Core data classes #140

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7a00bb3
Added pixel_scale as an attribute of the camera. Rearranged core test…
JuanCab Jul 26, 2023
f25ec21
Fixed a bad call that used a positional argument by accident for Sour…
Jul 26, 2023
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151 changes: 74 additions & 77 deletions stellarphot/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,9 @@ class Camera:
The dark current of the camera in units such that, when multiplied by
exposure time, the unit matches the unit of the `read_noise`.

pixel_scale : `astropy.quantity.Quantity`
The pixel scale of the camera in units of arcseconds per pixel.

Attributes
----------

Expand All @@ -42,6 +45,9 @@ class Camera:
The dark current of the camera in units such that, when multiplied
by exposure time, the unit matches the unit of the `read_noise`.

pixel_scale : `astropy.quantity.Quantity`
The pixel scale of the camera in units of arcseconds per pixel.

Notes
-----
The gain, read noise, and dark current are all assumed to be constant
Expand All @@ -53,18 +59,22 @@ class Camera:
>>> from stellarphot import Camera
>>> camera = Camera(gain=1.0 * u.electron / u.adu,
... read_noise=1.0 * u.electron,
... dark_current=0.01 * u.electron / u.second)
... dark_current=0.01 * u.electron / u.second,
... pixel_scale=0.563 * u.arcsec / u.pixel)
>>> camera.gain
<Quantity 1. electron / adu>
>>> camera.read_noise
<Quantity 1. electron>
>>> camera.dark_current
<Quantity 0.01 electron / s>
>>> camera.pixel_scale
<Quantity 0.563 arcsec / pix>

"""
def __init__(self, gain=1.0 * u.electron / u.adu,
read_noise=1.0 * u.electron,
dark_current=0.01 * u.electron / u.second):
dark_current=0.01 * u.electron / u.second,
pixel_scale=1.0 * u.arcsec / u.pixel):
super().__init__()

# Check that input has units and if not crap out.
Expand All @@ -82,11 +92,16 @@ def __init__(self, gain=1.0 * u.electron / u.adu,
self.dark_current = dark_current
else:
raise TypeError("dark_current must have units.")
if isinstance(pixel_scale, u.Quantity):
self.pixel_scale = pixel_scale
else:
raise TypeError("pixel_scale must have units.")

def copy(self):
return Camera(gain=self.gain,
read_noise=self.read_noise,
dark_current=self.dark_current)
dark_current=self.dark_current,
pixel_scale=self.pixel_scale)

def __copy__(self):
return self.copy()
Expand All @@ -104,13 +119,6 @@ class BaseEnhancedTable(QTable):
Parameters
----------

table_description: dict or dict-like (Default: None)
This is a dictionary where each key is a required table column name
and the value corresponding to each key is the required dtype
(can be None). This is used to check the format of the input data
table. Columns will be output in the order of the keys in the dictionary
with any additional columns tacked on the end.

input_data: `astropy.table.QTable` (Default: None)
A table containing astronomical data of interest. This table
will be checked to make sure all columns listed in table_description
Expand All @@ -120,6 +128,13 @@ class BaseEnhancedTable(QTable):
validation will not only affect the data attribute of the instance,
the original input data is left unchanged.

table_description: dict or dict-like (Default: None)
This is a dictionary where each key is a required table column name
and the value corresponding to each key is the required dtype
(can be None). This is used to check the format of the input data
table. Columns will be output in the order of the keys in the dictionary
with any additional columns tacked on the end.

colname_map: dict, optional (Default: None)
A dictionary containing old column names as keys and new column
names as values. This is used to automatically update the column
Expand All @@ -134,12 +149,12 @@ class BaseEnhancedTable(QTable):
validation of the inputs is performed and the resulting table is returned.
"""

def __init__(self, table_description=None, input_data=None, colname_map=None,
def __init__(self, *args, input_data=None, table_description=None, colname_map=None,
**kwargs):
if (table_description is None) and (input_data is None):
# Assume user is trying to create an empty table and let QTable
# handle it
super().__init__(**kwargs)
super().__init__(*args, **kwargs)
else:
# Confirm a proper table description is passed (that is dict-like with keys
# and values)
Expand Down Expand Up @@ -186,7 +201,6 @@ def __init__(self, table_description=None, input_data=None, colname_map=None,
# Call QTable initializer to finish up
super().__init__(data=data, **kwargs)


def _validate_columns(self, data):
# Check the format of the data table matches the table_description by
# checking each column listed in table_description exists and is the
Expand All @@ -211,7 +225,6 @@ def _validate_columns(self, data):
raise ValueError(f"data['{this_col}'] is missing from input "
"data.")


def _update_colnames(self, colname_map, data):
# Change column names as desired, done before validating the columns,
# which is why we work on _orig_data
Expand Down Expand Up @@ -241,16 +254,16 @@ class PhotometryData(BaseEnhancedTable):
Parameters
----------

input_data: `astropy.table.QTable`, optional (Default: None)
A table containing all the instrumental aperture photometry results
to be validated.

observatory: `astropy.coordinates.EarthLocation`, optional (Default: None)
The location of the observatory.

camera: `stellarphot.Camera`, optional (Default: None)
A description of the CCD used to perform the photometry.

input_data: `astropy.table.QTable`, optional (Default: None)
A table containing all the instrumental aperture photometry results
to be validated.

colname_map: dict, optional (Default: None)
A dictionary containing old column names as keys and new column
names as values. This is used to automatically update the column
Expand All @@ -268,25 +281,11 @@ class PhotometryData(BaseEnhancedTable):

Attributes
----------
gain : float
The gain of the camera in units such that the unit of the product `gain`
times the image data matches the unit of the `read_noise`.

read_noise : float
The read noise of the camera with units.

dark_current : float
The dark current of the camera in units such that, when multiplied by
exposure time, the unit matches the unit of the `read_noise`.

lat: float
The location of the observatory in degrees North.

lon: float
The location of the observatory in degrees East.
camera: `stellarphot.Camera`
A description of the CCD used to perform the photometry.

height: float
Altitute of the observatory in meters.
observatory: `astropy.coordinates.EarthLocation`
The location of the observatory.

Notes
-----
Expand Down Expand Up @@ -377,21 +376,20 @@ class PhotometryData(BaseEnhancedTable):
observatory = None
camera = None

def __init__(self, observatory=None, camera=None, input_data=None,
def __init__(self, *args, input_data=None, observatory=None, camera=None,
colname_map=None, passband_map=None, retain_user_computed=False,
**kwargs):
if (observatory is None) and (camera is None) and (input_data is None):
super().__init__(**kwargs)
super().__init__(*args, **kwargs)
else:
# Save passband filter name mapping
self._passband_map = passband_map.copy()

# Perform input validation
if not isinstance(observatory, EarthLocation):
raise TypeError("observatory must be an "
"astropy.coordinates.EarthLocation object.")
"astropy.coordinates.EarthLocation object instead "
f"of type {type(observatory)}.")
if not isinstance(camera, Camera):
raise TypeError("camera must be a stellarphot.Camera object.")
raise TypeError("camera must be a stellarphot.Camera object instead "
f"of type {type(camera)}.")

# Check the time column is correct format and scale
try:
Expand All @@ -405,9 +403,8 @@ def __init__(self, observatory=None, camera=None, input_data=None,
"astropy.time.Time entries.")

# Convert input data to QTable (while also checking for required columns)
super().__init__(table_description=self.phot_descript,
input_data=input_data, colname_map=colname_map,
**kwargs)
super().__init__(input_data=input_data, table_description=self.phot_descript,
colname_map=colname_map, **kwargs)

# Add the TableAttributes directly to meta (and adding attribute
# functions below) since using TableAttributes results in a
Expand All @@ -419,6 +416,7 @@ def __init__(self, observatory=None, camera=None, input_data=None,
self.meta['gain'] = camera.gain
self.meta['read_noise'] = camera.read_noise
self.meta['dark_current'] = camera.dark_current
self.meta['pixel_scale'] = camera.pixel_scale

# Check for consistency of counts-related columns
counts_columns = ['aperture_sum', 'annulus_sum', 'sky_per_pix_avg',
Expand Down Expand Up @@ -467,7 +465,7 @@ def __init__(self, observatory=None, camera=None, input_data=None,
- LocalTime.ymdhms.second*u.s
shift = Column(data = delta, name='shift')
# Compute MJD at local noon before the evening of this
# observation
# observation.
self['night'] = Column(data=
np.array((Time(self['date-obs'])
+ shift).to_value('mjd'),
Expand All @@ -480,8 +478,10 @@ def __init__(self, observatory=None, camera=None, input_data=None,

# Apply the filter/passband name update
if passband_map is not None:
self._passband_map = passband_map.copy()
self._update_passbands()


def add_bjd_col(self, observatory):
"""
Returns a astropy column of barycentric Julian date times corresponding to
Expand All @@ -502,28 +502,16 @@ def add_bjd_col(self, observatory):
return Time(time_barycenter + self['exposure'] / 2, scale='tdb')

@property
def lat(self):
return self.meta['lat']

@property
def lon(self):
return self.meta['lon']

@property
def height(self):
return self.meta['height']

@property
def gain(self):
return self.meta['gain']

@property
def read_noise(self):
return self.meta['read_noise']
def camera(self):
return Camera(gain=self.meta['gain'],
read_noise=self.meta['read_noise'],
dark_current=self.meta['dark_current'],
pixel_scale=self.meta['pixel_scale'])

@property
def dark_current(self):
return self.meta['dark_current']
def observatory(self):
return EarthLocation(lat=self.meta['lat'], lon=self.meta['lon'],
height=self.meta['height'])

class CatalogData(BaseEnhancedTable):
"""
Expand Down Expand Up @@ -559,6 +547,15 @@ class CatalogData(BaseEnhancedTable):
AAVSO passband names as values. This is used to automatically
update the passband column to AAVSO standard names if desired.

Attributes
----------
catalog_name: str
User readable name for the catalog.

catalog_source: str
User readable designation for the source of the catalog (could be a
URL or a journal reference).

Notes
-----
For validation of inputs, you must provide input_data, catalog_name, and
Expand Down Expand Up @@ -596,11 +593,10 @@ class CatalogData(BaseEnhancedTable):
catalog_name = None
catalog_source = None

def __init__(self, input_data=None, catalog_name=None, catalog_source=None,
colname_map=None, passband_map=None,
**kwargs):
def __init__(self, *args, input_data=None, catalog_name=None, catalog_source=None,
colname_map=None, passband_map=None, **kwargs):
if (input_data is None) and (catalog_name is None) and (catalog_source is None):
super().__init__(**kwargs)
super().__init__(*args, **kwargs)
else:
self._passband_map = passband_map

Expand All @@ -617,13 +613,14 @@ def __init__(self, input_data=None, catalog_name=None, catalog_source=None,
self.meta['catalog_name'] = str(catalog_name)
self.meta['catalog_source'] = str(catalog_source)

# Apply the filter/passband name update
if passband_map is not None:
self._passband_map = passband_map.copy()
self._update_passbands()

else:
raise ValueError("You must provide input_data to CatalogData.")

# Apply the filter/passband name update
if passband_map is not None:
self._update_passbands()

@property
def catalog_name(self):
return self.meta['catalog_name']
Expand Down Expand Up @@ -700,9 +697,9 @@ class SourceListData(BaseEnhancedTable):
'ycenter' : u.pix
}

def __init__(self, input_data=None, colname_map=None, **kwargs):
def __init__(self, *args, input_data=None, colname_map=None, **kwargs):
if (input_data is None):
super().__init__(**kwargs)
super().__init__(*args, **kwargs)
else:
# Check data before copying to avoid recusive loop and non-QTable
# data input.
Expand Down
5 changes: 4 additions & 1 deletion stellarphot/notebooks/photometry/03-photometry-template.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,10 @@
"inner_annulus = aperture + 15\n",
"outer_annulus = inner_annulus + 15\n",
"\n",
"feder_cg_16m = Camera(gain=1.5, read_noise=10.0, dark_current=0.01)\n",
"feder_cg_16m = Camera(gain = 1.5 * u.electron / u.adu,\n",
" read_noise = 10.0 * u.electron,\n",
" dark_current=0.01 * u.electron / u.second,\n",
" pixel_scale = 0.563 * u.arcsec / u.pix)\n",
"\n",
"max_adu = 50000"
]
Expand Down
2 changes: 1 addition & 1 deletion stellarphot/photometry/source_detection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -286,7 +286,7 @@ def source_detection(ccd, fwhm=8, sigma=3.0, iters=5,
'xcentroid' : 'xcenter',
'ycentroid' : 'ycenter'}

sl_data = SourceListData(sources, colname_map=colnamemap)
sl_data = SourceListData(input_data=sources, colname_map=colnamemap)
return sl_data


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