procastro package

Module contents

Framework to easily handle multiple astronomy data files

class procastro.AstroDir(*args, **kwargs)

Bases: object

Collection of AstroFile objects.

Collection can be indexed, filtered, and has several recursive methods that are applied to each AstroFile are available

files

Contains the list of all AstroFile that belong to this AstroDir.

Type:

list

props

Properties related to this object

Type:

dict

Parameters:

• path (str or list or AstroFile) – Contains information from the file list. If str, a directory+wildcard format is assumed and parsed by glob.glob

• mbias (array_like, dict or AstroFile, optional) – Master bias and flat to associate to each AstroFile (in one shared AstroCalib object)

• mflat (array_like, dict or AstroFile, optional) – Master bias and flat to associate to each AstroFile (in one shared AstroCalib object)

• mbias_header (astropy.io.fits.Header) – Headers for bias and flat

• mflat_header (astropy.io.fits.Header) – Headers for bias and flat

• calib_force (bool, optional) – If True, then force specified mbias and mflat to all files, otherwise assign it only if it doesn’t have one already.

• hdu (int, optional) – default HDU

• hdud (int, optional) – default HDU for data

• hduh (int, optional) – default HDU for the header

See also

procastro.AstroCalib

Object that holds calibration information. One of them can be shared by many AstroFile instances

procastro.AstroCalib.add_bias, procastro.AstroCalib.add_flat

add_bias(mbias)

Updates the master bias of all AstroCalib instances included on the contained AstroFile instances

Parameters:

mbias (dict indexed by exposure time, array or AstroFile) – Master Bias to use for all frames.

See also

procastro.AstroCalib.add_bias

this function is called for each unique AstroCalib object in AstroDir

add_flat(mflat)

Update Master Flats of all AstroCalib instances included on the contained AstroFile instances.

Parameters:

mflat (dict indexed by filter name, array or AstroFile) – Master Flat to use for all frames.

See also

procastro.AstroCalib.add_flat

This function is called for each unique AstroCalib object in AstroDir

sort(*args, **kwargs)

Sorts AstroFile instances inplace depending on the given header fields. After sorting the contents the method will return None to avoid problems

Parameters:

args (str) – A header field name to be used as comparison key

Raises:

ValueError – If the field given cannot be used to compare each AstroFile or if no header field was specified.

stats(*args, **kwargs)

Obtains statistical data from each AstroFile stored in this instance

Parameters:

• extra_headers (list, optional) – List of header items to include on the output

• verbose_heading (bool, optional) –

• args (Specify the stats that want to be returned) –

Returns:

The stat as returned by each of the AstroFiles

Return type:

array_like

See also

procastro.AstroFile.stats

for the available statistics

filter(*args, **kwargs)

Filter files according to those whose filter return True to the given arguments. What the filter does is type-dependent for each file.

Logical ‘and’ statements can be simulated by chaining this method multiple times.

Parameters:

**kwargs – Keyword arguments containing the name of the item and the expected value.

Returns:

Copy containing the files which were not discarded.

Return type:

procastro.AstroDir

See also

procastro.AstroFile.filter

Specifies the syntax used by the recieved arguments.

basename(joinchr=', ')

Obtains the basename each file contained.

Parameters:

joinchar (str, optional) – Character used to separate the name of each file

Returns:

Each file basename separated by the specified ‘joinchar’

Return type:

str

getheaderval(*args, **kwargs)

Gets the header values specified in ‘args’ from each file. A function can be specified to be used over the returned values for casting purposes.

Parameters:

cast (function, optional) – Function output used to cas the output

Returns:

Type depends on whether a single value or multiple tuples were given

Return type:

List of integers or tuples

setheader(**kwargs)

Sets the header values specified in ‘args’ from each of the files.

get_datacube(normalize_region=None, normalize=False, verbose=False, check_unique=None, group_by=None, trim_area_warn=0.25)

Generates a data cube with the data of each AstroFile.

Parameters:

• normalize_region – Subregion to use for normalization

• normalize (bool, optional) – If True, will normalize the data inside the data cube

• verbose (bool, optional) –

• check_unique (array_like, optional) – Receives a list of headers that need to be checked for uniqueness.

• group_by (str, optional) – Datacube will be organized based on the header item given

Returns:

Dictionary containing a data cube grouped by the given parameters, otherwise the data will be indexed to None as key

Return type:

dict

pixel_xy(xx, yy, normalize_region=None, normalize=False, check_unique=None, group_by=None)

Obtains the pixel value at the (‘xx’,’yy’) position for all frames.

Parameters:

• xx (int, int) –

• yy (int, int) –

• normalize_region – Subregion to use for normalization

• group_by – If set, then group by the specified header returning an [n_unique, n_y, n_x] array

• normalize (bool, optional) – Whether to Normalize

• check_unique (str, optional) – Check uniqueness in header

Returns:

Values of the pixel on each frame

Return type:

array_like

median(normalize_region=None, normalize=False, verbose=True, check_unique=None, group_by=None)

Calculates the median of the contained files

Parameters:

• normalize_region – Subregion to use for normalization

• normalize (bool, optional) – Whether to Normalize

• verbose (bool, optional) – Output progress indicator

• check_unique (str, optional) – Check uniqueness in header

• group_by – If set, then group by the specified header returning an [n_unique, n_y, n_x] array

Returns:

• array_like – Median between frames

• dict – If group_by is set, a dictionary keyed by this group will be returned

mean(normalize_region=None, normalize=False, verbose=True, check_unique=None, group_by=None)

Calculates the mean of the contained files

Parameters:

• normalize_region – Subregion to use for normalization

• normalize (bool, optional) – Whether to Normalize

• verbose (bool, optional) – Output progress indicator

• check_unique (str, optional) – Check uniqueness in header

• group_by – If set, then group by the specified header returning an [n_unique, n_y, n_x] array

Returns:

• ndarray – Mean between frames

• dict – If group_by is set, a dictionary keyed by this group will be returned

lin_interp(target=0, verbose=True, field='EXPTIME', check_unique=None, group_by=None)

Linear interpolate to given target value of the field ‘field’.

Parameters:

• target (int, optional) – Target value for the interpolation

• verbose (bool, optional) – Output progress indicator

• field (str, optional) – Name of the header item which will be used to interpolate each frame

• group_by – If set, then group by the specified header returning an [n_unique, n_y, n_x] array

• check_unique (str, optional) – Check uniqueness in header

Returns:

• ndarray – Linear Interpolation between frames with the specified target

• dict – If group_by is set, a dictionary keyed by this group will be returned

std(normalize_region=None, normalize=False, verbose=True, check_unique=None, group_by=None)

Get pixel by pixel standard deviation within files.

Parameters:

• normalize_region – Subregion to use for normalization

• normalize (bool, optional) – Whether to Normalize

• verbose (bool, optional) – Output progress indicator

• check_unique (str, optional) – Check uniqueness in header

• group_by – If set, then group by the specified header returning an [n_unique, n_y, n_x] array

Returns:

• ndarray – Standard deviation between frames

• dict – If group_by is set, a dictionary keyed by this group will be returned

jd_from_ut(target='jd', source='date-obs', return_only_clean=False)

Add jd in header’s cache to keyword ‘target’ using ut on keyword ‘source’

Parameters:

• target (str) – Target keyword for JD storage

• source (str or list) – Location of the input value on UT format

See also

procastro.AstroFile.jd_from_ut

For individual file implementation

merger(start=1, end=None, verbose=None)

Merges HDUImage data for all files contained in this object

Parameters:

• verbose (str) – a single character to be repeated unbuffered for every AstroFile

• start (int, optional) – HDU unit from which the method starts joining

• int (end ;) – Last ImageHDU unit to be included, if None will stop at the last hdu found

• optional – Last ImageHDU unit to be included, if None will stop at the last hdu found

See also

procastro.AstroFile.merger

For individual file implementation

class procastro.AstroFile(*args, **kwargs)

Bases: object

Representation of an astronomical data file, contains information related to the file’s data. Currently supports usage of arrays and .fit files

Parameters:

• filename (str or procastro.AstroFile) – If AstroFile, then it does not duplicate the information, but uses that object directly.

• mbias (dict indexed by exposure time, array or AstroFile, optional) – Default Master bias

• mflat (dict indexed by filter name, array or AstroFile, optional) – Default Master flat

• exists (boolean, optional) – Represents if the given pathname has an existing file

• mbias_header (astropy.io.fits.Header) –

• mflat_header (astropy.io.fits.Header) –

• hdu (int, optional) – Default hdu slot used for collection, if “hduh” or “hdud” are not specified, this parameter will override them.

• hduh (int, optional) – hdu slot containing the header information to be collected

• hdud (int, optional) – hdu slot containing astronomical data to be collected

• read_keywords (list, optional) – Read all specified keywords at creation time and store them in the header cache

• auto_trim (str, optional) – Header field name which is used to cut a portion of the data. This field should contain the dimensions of the section to be cut. (i.e. TRIMSEC = ‘[1:1992,1:1708]’)

• ron (float, str, astropy quantity, optional) – Read-out-noise value or header keyword. Only consulted if either mbias or mflat are not CCDData. If unit not specified, photon/ADU is used as default unit; if not set at all, uses 1.0 (with warning)

• gain (float, str, astropy quantity, optional) – Gain value or header keyword. Only consulted if either mbias or mflat are not CCDData. If unit not specified, photon/ADU is used as default unit; if not set at all, uses 1.0 (with warning)

• unit (astropy.unit, optional) – Specifies the unit for the data

shape

Shape of the data contained on the file

Type:

tuple

header_cache

Data contained on the most recently read header

Type:

dict

sortkey

Header Item used when sorting this object

Type:

str

type

File extension

Type:

str

get_trims()

“Get trim limits, returning in python-style YX

add_bias(mbias)

Includes a Master Bias to this instance

Parameters:

mbias (dict indexed by exposure time, array or AstroFile) –

add_flat(master_flat)

Includes a Master Bias to this instance

Parameters:

master_flat (dict indexed by filter name time, array or AstroFile) –

default_hdu_dh()

Returns default HDU for data and header collection

checktype(*args, **kwargs)

Verifies if the filename given corresponds to an existing file

Returns:

“array” : If AstroFile represents a scipy array “fits” : If AstroFile points to an existing .fits file None : Otherwise

Return type:

str

plot(*args, **kwargs)

Generates a 1D plot based on a cross-section of the current data.

Parameters:

• args (list) – unnamed arguments passed to procastro.plot()

• kwargs (dict) – named arguments passed to procastro.plot()

add_sortkey(key)

Sets a header item used for sorting comparisons

Parameters:

key (str) –

imshowz(*args, **kwargs)

Plots frame after being processed using a zscale algorithm

See also

misc_graph.imshowz

For details on what keyword arguments are available

filter(**kwargs)

Compares if the expected value of the given header item matches the value stored in this file header.

Filtering can be customized by including one of the following options after the item name, separated by an underscore.

• Strings:

  • BEGIN: True if value starts with the given string

  • END: True if value ends with the given string

  • ICASE: Case unsensitive match

  • MATCH: Case sensitive match

• Numeric values:

  • LT: True if current value is lower than the given number

  • GT: True if current value is greater than the given number

  • EQUAL: True if both values are the same

• Other:

  • NOT: Logical Not

Its possible to include multiple options, this statements count as a logical “or” statements.

Parameters:

kwargs (Keyword Arguments or unpacked dictionary) – item_name_option : value

Return type:

bool

Notes

If a header item has a “-” character on its name, use two underscores to represent it.

Examples

NAME_BEGIN_ICASE_NOT = “WASP” (False if string starts with wasp) NAXIS1_GT_EQUAL = 20 (True if NAXIS1 >= 20)

setheader(**kwargs)

Set header values from kwargs. They can be specified as tuple to add comments as in pyfits.

Parameters:

**kwargs (Keyword argument or unpacked dict) –

Examples

setheader(item1 = data1, item2 = data2) setheader(**{"item1" : data1, "item2" : data2})

Return type:

True if header was edited properly

Notes

Setting a header value to None will remove said item from the header

getheaderval(*args, single_in_list=False, **kwargs)

Get header value for each of the fields specified in args.

Parameters:

• single_in_list (bool) – returns a 1 element list if given one element.

• args (list, tuple) – One string per argument, or a list as a single argument: getheaderval(field1,field2,…) or getheaderval([field1,field2,…]). In addition to return headers from the file, it can return “basename” and “dirname” from the filename itself if available.

• cast (function, optional) – Function to use for casting each element of the result.

• hdu (int, optional) – HDU to read.

Returns:

• list – If multiple values are found

• string – If only one result was found

reader(*args, skip_calib=False, hdud=None, hdu=None, verbose=True, **kwargs)

Read astro data and return it calibrated if provided

TODO: Respond to different exposure times or filters

Parameters:

• hdu (int, optional) – hdu slot to be read

• hdud (int, optional) – hdu slot to be read

• skip_calib (bool, optional) – If True returns data without calibration

has_calib()

Checks if a bias or flat has been associated with this file

Return type:

bool

read_headers(*args, **kwargs)

Reads header from the file

Parameters:

hdu (int, optional) – Specific hdu slot to be read

writer(data, *args, **kwargs)

Writes given data to file

basename()

Obtains the file basename

Return type:

str

property shape

stats(*args, **kwargs)

Calculates statistical data from the file, a request can include header keywords to be included in the response.

Parameters:

• *args (str) – Statistic to be extracted, Possible values are: min, max, mean, mean3sclip, std and median

• **kwargs (str) – Options available: verbose_heading and extra_headers

Returns:

List containing the requested data

Return type:

list

jd_from_ut(target='jd', source='date-obs')

Add jd in header’s cache to keyword ‘target’ using ut on keyword ‘source’

Parameters:

• target (str) – Target keyword for JD storage

• source (str or list) – Input value in UT format, if a tuple is given it will join the values obtained from both keywords following the UT format (day+T+time)

merger(start=1, end=None)

Merges multiple ImageHDU objects into a single composite image , saves the new ImageHDU into a new hdu slot.

Parameters:

• start (int, optional) – HDU slot from which the algorithm starts concatenating images

• end (int, optional) – Last HDU to be merged, if None will continue until the end of the HDUList

spplot(axes=None, title=None, xtitle=None, ytitle=None, *args, **kwargs)

Plots spectral data contained on this file

class procastro.AstroCalib(mbias=None, mflat=None, exptime_keyword='exptime', mbias_header=None, mflat_header=None, filter_keyword='filter', auto_trim=None)

Bases: object

Object to hold calibration frames.

Since several AstroFiles might use the same calibration frames, one AstroCalib object might be shared by more than one AstroFile. For instance, all the files initialized through AstroDir share a single calibration object.

has_bias

Type:

bool

has_flat

Type:

bool

Parameters:

• mbias (dict indexed by exposure time, array or AstroFile) – Master Bias

• mflat (dict indexed by filter name, array or AstroFile) – Master Flat

• exptime_keyword (str, optional) – Header item name containing the exposure time of te frames

• mbias_header (astropy.io.fits.Header, optional) – Header of the master bias

• mflat_header (astropy.io.fits.Header, optional) – Header of the master bias

• filter_keyword (str, optional) –

• auto_trim (str) – Header field name which is used to cut a portion of the data. This field should contain the dimensions of the section to be cut. (i.e. TRIMSEC = ‘[1:1992,1:1708]’)

add_bias(mbias, mbias_header=None)

Add Master Bias to Calib object.

Parameters:

• mbias (dict indexed by exposure time, array_like or AstroFile) – Master bias to be included

• mbias_header (astropy.io.fits.Header) – Header to be included

Raises:

ValueError – If the bias type is invalid

add_flat(mflat, mflat_header=None)

Add master flat to Calib object

Parameters:

• mflat (dict indexed by filter name, array_like, AstroFile) – Master flat to be included

• mflat_header (astropy.io.fits.Header, optional) – Master flat header

Raises:

ValueError – If the bias type is invalid

reduce(data, exptime=None, ffilter=None, data_trim=None, verbose=True)

Process given “data” using the bias and flat contained in this instance

Parameters:

• data (array_like) – Data to be reduced

• exptime (int, optional) – Exposure time for bias

• ffilter (str, optional) – Filter used by the flat

• header (astropy.io.fits.Header, optional) –

Returns:

Reduced data

Return type:

array_like

Subpackages

• procastro.astro package
  • Subpackages
  • Submodules
  • procastro.astro.astro module
  • procastro.astro.moon module
  • Module contents
• procastro.obsrv package
  • Subpackages
  • Submodules
  • procastro.obsrv.nightly module
  • procastro.obsrv.obscalc module
  • procastro.obsrv.obsrv module
  • Module contents
• procastro.photography package
  • Submodules
  • procastro.photography.orchestrator module
  • procastro.photography.plotting module
  • procastro.photography.rawinfo module
  • Module contents
• procastro.timeseries package
  • Subpackages
  • Submodules
  • procastro.timeseries.photometry module
  • Module contents