Summary — Project summary metadata.¶

This module defines the Summary class.

class admit.Summary.Summary[source]¶

Defines and manages the summary metadata for the ADMIT object, which is ingested by ALMA Archive and also used by data browser.

The Summary is metadata provided by the various tasks. and written to the ADMIT object and admit.xml. It is used as project information for the ALMA archive to ingest and for the data browser to display. There will be one summary object per FITS cube, which means that for flows with multiple Ingests there can be multiple Summaries. Each entry in the Summary will be a dictionary of

{ key, [ SummaryEntry ] }

where the value is a list of zero or more SummaryEntry. The summaryEntry contains the actual data value, the taskname string, the taskid integer, and string task arguments to be displayed in the web page. Each key also has a value type and description which is the same for every entry in the list. These are retrieved using getType(key) and getDescription(key). In the case where different tasks or different instances of the same task write to the same key, the new value will be appended:

{ key, [SummaryEntry task1, SummaryEntry task2,...]}

Because they are needed by the ALMA archive, the keys, value types, and description will be strictly defined ahead of time. Individual ATs will be responsible for providing the actual value data through their summary() method as a dictionary of {key, [value, taskname, taskid]}. ADMIT Summary keywords that map directly to standard FITS keywords shall have their values copied directly from the FITS header (by Ingest_AT). Below is a draft list, necessarily incomplete until we have all ATs implemented. Keywords ending in n indicate multiple keywords 1 to NAXIS (as in FITS). The table below summarizes the keys.

Key	Description	Type	Typically Provided by
FITSNAME	Pathless filename of FITS cube	string	Ingest_AT
OBJECT	Object name	string	Ingest_AT/FITS
NAXIS	Number of Axes	integer	Ingest_AT/FITS
NAXISn	size of axis n	integer	Ingest_AT/FITS
CRPIXn	Reference pixel axis n	float	Ingest_AT/FITS
CRVALn	axis value at CRPIXn	float	Ingest_AT/FITS
CTYPEn	axis type	string	Ingest_AT/FITS
CDELTn	axis increment	float	Ingest_AT/FITS
CUNITn	axis unit	string	Ingest_AT/FITS
RESTFREQ	rest frequency, Hz	float	Ingest_AT/FITS
BMAJ	beam major axis, radians	float	Ingest_AT/FITS
BMIN	beam minor axis, radians	float	Ingest_AT/FITS
BPA	beam position angle, deg	float	Ingest_AT/FITS
BUNIT	units of pixel values	string	Ingest_AT/FITS
TELESCOP	telescope name	string	Ingest_AT/FITS
OBSERVER	observer name	string	Ingest_AT/FITS
DATE-OBS	date of observation	string	Ingest_AT/FITS
DATAMAX	maximum data value	float	Ingest_AT or CubeStats_AT
DATAMIN	minimum data value	float	Ingest_AT or CubeStats_AT
DATAMEAN	mean data value	float	CubeStats_AT
DYNRANGE	dynamic range, equal to DATAMAX/CHANRMS	float	CubeStats_AT
CHANRMS	one-sigma noise in cube	float	CubeStats_AT
RMSMETHD	method and parameters used to compute RMS	list	CubeStats_AT
SPECTRA	Spectra extracted by any method	list	CubeSpectrum_AT
LINELIST	Table of parameters of identified spectral lines.	admit.util.Table	LineID_AT
LINECUBE	Info about any LineCubes produced (name, channel range, image name).	list	LineCube_AT
CUBESUM	Info about any CubeSum produced	list	CubeSum_AT
MOMENTS	Table of moments computed from the original cube.	admit.util.Table	Moment_AT
PVSLICES	Table of position-velocity slices computed from original cube.	list	PVSlice_AT
PVCORR	List of PV correlation diagrams computed from input cube.	list	PVCorr_AT
SEGMENTS	List of segments found by segment-finding algorithm	list	LineSegment_AT
SOURCES	Table of sources found by a feature-finding algorithm	admit.util.Table	SFind2D_AT
SMOOTH	Info about any smoothing done to cube.	list	Smooth_AT
OVERLAP	Overlap integral input and output images information	list	OverlapIntegral_AT
PCA	Principal component analysis information.	list of admit.util.Table	PrincipalComponent_AT
PEAKPNT	Peak Point Plot optionally produced by CubeStats_AT	list	CubeStats_AT
VELDEF	User or ASDM/source.xml derived source velocity information (value, reference frame, etc)	list	Ingest_AT?

@TODO: the following entries are in the summary_defs.tab file, but not documented here:

Note: Keys are stored in all lower case. All key access will change argument to lower case before accessing.

casaname, equinox, badpixel, vlsr, continuumsub, template, regrid, bdpingest

FORMATS AND EXAMPLES OF COMPLICATED SUMMARIES

RMSMETHD: [[method type, method args], input cube]

Examples:

[['metabdevmed'], foobar.im]
[['robust', 'chauvenet', 21.3, 123], foobar.im]
[['robust', 'classic', 'auto'], foobar.im]

SPECTRA: [x,y, box, axis type, display image, thumbnail image, caption, input cube]

Example:

[[ '00h47m33.159s','-25d17m17.41s',(10,-10,-20,22),'frequency','spect1.svg','spect1_thumb.svg',
   "Spectrum at Emission Peak", foobar.im],
[ +10,-20,(),'velocity','spect.svg','spect2_thumb.svg', "Pencil beam spectrum", foobar.im]]

LINELIST: [Format same as output from LineList_AT]

Example:

[['H2CS_103.0405',  103.04055,'H2CS', ...],
['NH2CHO_102.0643',102.06427, 'NH2CHO', ...]]

MOMENTS: [table of moment data ]

Columns: [Line UID, Moment value, display image, thumbnail image, caption, casa image].

If thumbnail image is not present, an empty string is given.

Example:

[['H2CS_103.0405', 0, 'foo_mom0.png', 'foo_mom0_thumb.png', 'Moment 0 of H2CS', ''],
['H2CS_103.0405', 1, 'foo_mom1.svg', '', 'Moment 1 of H2CS clipped at 3 sigma', 'foobar_mom1.im']]

PVSLICES: [pvslice type, pvslice args, display image, thumbnail image, caption, input cube, output image].

Example:

[['slice', start, end, width, 'slice1.png', 'slice1_thumb.png','pvslice of h2co','foobar.im',
   'slice.im'],
['slit', center, length, pa, width, 'slit1.png', 'slit1_thumb.png', 'pvslit of h2co','foobar.im',
   'slit.im']]

PVCORR: [display image, thumbnail image, caption, input cube, output image].

Attributes

_metadata	(dictionary of lists {key, [SummaryEntry]}.)
_datatype	(dictionary of {key, valuetype} where the keys are the as in _metadata and valuetype is defined in $ADMIT/etc/summary_defs.tab)
_description	(dictionary of {key, description} where the keys are the as in _metadata and description string is defined in $ADMIT/etc/summary_defs.tab)

Methods

`delItemsByTaskID`(taskid)	Deletes all summary entries belonging to task #`taskid`.
`get`(key)	Get the value for the input key.
`getAllTaskIDs`()	Get a list of all integer task IDs that have written to this Summary for the input key.
`getDescription`(key)	Get the description for the input key.
`getFull`(key)	Get the full entry [[value(s)], valuetype, description] for the input key.
`getItemsByTaskID`(taskid)	Return all Summary items that were produced
`getItemsByTaskname`(taskname)	Return all Summary items that were produced
`getLineTable`([index])	Get the table of spectral lines found
`getLinefluxes`([index])	Get an estimate of the line fluxes from the line list by multiplying Peak * Linewidth.
`getLinelist`([index])	Get the list of spectral lines found
`getLinenames`([index])	Get the names of spectral lines found
`getTaskID`(key)	Get the integer task ID number that produced the data for the input key.
`getTaskIDsforTaskname`(taskname)	Get the task ID(s) matching the input taskname.
`getTaskname`(key)	Get the name of the task that produced the data for the input key.
`getTasknameForTaskID`(taskid)	Get the task name matching the input taskid.
`getType`(key)	Get the value type for the input key.
`html`(outdir, flowmanager[, dotdiagram, editor])
`insert`(key, value)	Set, replace, or append the SummaryEntry value to the list for an existing input key If the key is not yet set, it will be set with the value.
`isTable`(key)	Return True if this key corresponds to an item that is natively an ADMIT table.
`makesvghtml`(image, caption, outdir)
`set`(key, value)	Set the SummaryEntry value for an existing input key
`show`([showunset])	Display the all entries [key, values, description].
`unset`(key)	Determine if the key has any data.
`write`(root)	Method to write out the summary data to XML

delItemsByTaskID(taskid)[source]¶

Deletes all summary entries belonging to task #`taskid`.

Parameters:

taskid : int

ID of task for which to delete summary information.

Returns:

None

get(key)[source]¶

Get the value for the input key.

Parameters:

key : str

Key to retrieve, case insensitive.

getAllTaskIDs()[source]¶

Get a list of all integer task IDs that have written to this Summary for the input key.

Parameters:

None

Returns:

Sorted list of zero or more integer task ids that produced data for the Summary.

If no tasks ids, the list is empty because you have empty Summary!

getDescription(key)[source]¶

Get the description for the input key.

Parameters:

key : str

Key to retrieve, case insensitive.

Returns:

String description for the key

getFull(key)[source]¶

Get the full entry [[value(s)], valuetype, description] for the input key.

Parameters:

key : str

Key to retrieve, case insensitive.

getItemsByTaskID(taskid)[source]¶

Return all Summary items that were produced by the given taskid, as dict of SummaryEntrys

Parameters:

taskid : int

Task ID to look up

Returns:

Return a dictionary of all SummaryEntrys that were produced

by the given task, with keys as in Summary or an empty

dictionary if there is no match for the input taskid.

Notes

The values in the returned dictionary may be single SummaryEntry instances or a list of entries; in general, caller code needs to check this explicitly for every key...

getItemsByTaskname(taskname)[source]¶

Return all Summary items that were produced by the given task, as dict of SummaryEntrys

Parameters:

taskname : str

Task name to look up, case-insensitive

Returns:

Return a dictionary of all SummaryEntrys that were produced

by the given task, with keys as in Summary or an empty

dictionary if there is no match for the input taskid.

Notes

The values in the returned dictionary may be single SummaryEntry instances or a list of entries; in general, caller code needs to check this explicitly for every key...

getLineTable(index=0)[source]¶

Get the table of spectral lines found

Parameters:

None

Returns:

An admit.Table with spectral line entries or empty Table if

no lines were found

getLinefluxes(index=0)[source]¶

Get an estimate of the line fluxes from the line list by multiplying Peak * Linewidth.

Parameters:

None

Returns:

A dictionary of ‘image filename’:flux for all non-blended spectral lines in the line list,

or an empty dictionary if no line list is available or linecubes were not created.

getLinelist(index=0)[source]¶

Get the list of spectral lines found

Parameters:

None

Returns:

A Python list with spectral line entries or empty list if

no lines were found

getLinenames(index=0)[source]¶

Get the names of spectral lines found

Parameters:

None

Returns:

A list of string spectral line names or empty list if

no lines were found

getTaskID(key)[source]¶

Get the integer task ID number that produced the data for the input key.

Parameters:

key : str

Key to retrieve, case insensitive.

Returns:

List of zero or more integer taskids that produced data for the

input key. If no tasks did, the list is empty.

getTaskIDsforTaskname(taskname)[source]¶

Get the task ID(s) matching the input taskname.

Parameters:

taskname : str

Task name to look up

Returns:

List of taskids matching the taskname. Empty list if none.

getTaskname(key)[source]¶

Get the name of the task that produced the data for the input key.

Parameters:

key : str

Key to retrieve, case insensitive.

Returns:

List of zero or more string task names that produced data for the

input key. If no tasks did, the list is empty.

getTasknameForTaskID(taskid)[source]¶

Get the task name matching the input taskid.

Parameters:

taskid : int

Task ID to look up

Returns:

String task name or empty string if no match

getType(key)[source]¶

Get the value type for the input key.

Parameters:

key : str

Key to retrieve, case insensitive.

Returns:

String indicating underlying data type, e.g., ‘float’, ‘table’

html(outdir, flowmanager, dotdiagram='', editor=True)[source]¶

insert(key, value)[source]¶

Set, replace, or append the SummaryEntry value to the list for an existing input key If the key is not yet set, it will be set with the value. If the key is set, the taskid(s) will be checked and the value will replace the existing value(s) if the keys match. If the taskids do not match the input value(s) will be appended to the existing value.

Parameters:

key : str

Key to insert, case insensitive. Key must already exist.

value : SummaryEntry or list of SummaryEntry

Entry to insert

Returns:

None

isTable(key)[source]¶

Return True if this key corresponds to an item that is: natively an ADMIT table.

Parameters:

key : str

Key to set, case insensitive. Key must already exist.

Returns:

boolean

True if this key corresponds to an item that is natively an ADMIT table, False otherwise

makesvghtml(image, caption, outdir)[source]¶

set(key, value)[source]¶

Set the SummaryEntry value for an existing input key

Parameters:

key : str

Key to set, case insensitive. Key must already exist.

value : SummaryEntry or list of SummaryEntry

Entry to set

Returns:

None

show(showunset=False)[source]¶

Display the all entries [key, values, description].

Parameters:

showunset : boolean

If True, show unset values in addition to set values. Default: False

Returns:

None

unset(key)[source]¶

Determine if the key has any data.

Parameters:

key : str

Key to retrieve, case insensitive.

Returns:

boolean

True if the value for the key has not been set, False otherwise.

write(root)[source]¶

Method to write out the summary data to XML

Parameters:	root : cElementTree node to attach to
Returns:	None

class admit.Summary.SummaryEntry(value=[], taskname='', taskid=-1, taskargs='')[source]¶

Defines a single ‘row’ of a Summary data entry. A Summary key can refer to a list of SummaryEntry. This class makes management of complicated data entries easier. It was getting tough to slice and unzip all those lists!

Attributes

`taskargs`	The arguments of the task to display in the data browser web page.
`taskid`	The integer task ID that created this SummaryEntry
`taskname`	The name of the task that created this SummaryEntry
`value`	The underlying data value

Methods

`getTaskArgs`()	Get the arguments of the task to display in the data browser web page.
`getTaskID`()	Get the ID of the task that created this SummaryEntry.
`getTaskname`()	Get the name of the task that created this SummaryEntry.
`getValue`()	Get the underlying data value from this SummaryEntry.
`setTaskArgs`(args)	Set any arguments of the task that should be displayed in the data browser web page.
`setTaskID`(taskid)	Set the ID of the task that created this SummaryEntry.
`setTaskname`(name)	Set the name of the task that created this SummaryEntry.
`unset`()	Find out if this SummaryEntry instance has data or not.
`write`(root)	Method to write out the SummaryEntry data to XML

getTaskArgs()[source]¶

Get the arguments of the task to display in the data browser web page.

Parameters:

None

Returns:

str

The string task arguments

getTaskID()[source]¶

Get the ID of the task that created this SummaryEntry.

Parameters:

None

Returns:

int

The integer task ID that produced the data value

getTaskname()[source]¶

Get the name of the task that created this SummaryEntry.

Parameters:

None

Returns:

str

The string task name that produced the data value

getValue()[source]¶

Get the underlying data value from this SummaryEntry. Value will be list containing zero or more items.

Parameters:

None

Returns:

list

A (possibly empty) list of SummaryEntry.

setTaskArgs(args)[source]¶

Set any arguments of the task that should be displayed in the data browser web page.

Parameters:

args : str

The task args that produced the data value

Returns:

None

setTaskID(taskid)[source]¶

Set the ID of the task that created this SummaryEntry.

Parameters:

taskid : int

The task id number that produced the data value

Returns:

None

setTaskname(name)[source]¶

Set the name of the task that created this SummaryEntry.

Parameters:

name : str

The task name that produced the data value

Returns:

None

taskargs¶: The arguments of the task to display in the data browser web page.

taskid¶: The integer task ID that created this SummaryEntry

taskname¶: The name of the task that created this SummaryEntry

unset()[source]¶

Find out if this SummaryEntry instance has data or not.

Parameters:

None

Returns:

bool

True if this SummaryEntry has no data set

value¶: The underlying data value

write(root)[source]¶

Method to write out the SummaryEntry data to XML

Parameters:	root : cElementTree node to attach to
Returns:	None