The specification¶
- Kliko is based on standard docker containers
- Container mush have a CMD specified, which would be the main program of the container. It should not require arguments.
- logging should be written to STDOUT and STDERR.
- We define two types of compute containers, split IO and joined IO containers.
- For split IO Input files will be mounted read only into
/input
. Output file should be written to/output
, which will be mounted by the host.- For joined IO containers input & output is the /work folder which will be mounted RW.
- parameters for the computation will be given when the container is run in the form of a file in json format called
parameters.json
in/input
- Which parameters the container will accept should be defined in a yaml file
/kliko.yml
- The
kliko.yml
file should follow the schema defined inkliko/schema.yml
.- an example parameters definition file can be found in
examples/form.yml
- fields with type file will enable supply of custom input files. these will be put in the
/input
folder.
The kliko.yml file¶
The kliko file should be in YAML format and has these required fields:
schema_version¶
The version of the kliko specification. note that this is independent of the versioning of the Kliko library.
name¶
Name of the kliko image. For example radioastro/simulator
.
description¶
A more detailed description of the image.
author¶
Who made the container.
email¶
email adres of the author.
url¶
Where to find the specific kliko project on the web.
io¶
Which IO mode to use, could be join
or split
. For split IO Input files will be mounted read only into
/input
. Output file should be written to /output
, which will be mounted by the host. For joined IO containers
input & output is the /work folder which will be mounted RW.
Sections¶
The paramaters are grouped in sections. Sections are just lists of fields.
fields¶
A section consists of a list of fields.
field¶
each field has 2 obligatory keys, a name
and a type
. Name is a short reference to the field which needs to be
unique. This will be the name for internal reference. The type defines the type
of the field and can be one of
choice
, char
, float
, file
, bool
or int
.
- Optional keys are:
initial: supply a initial (default) value for a field
max_length: define a maximum length in case of string type
choices: define a list of choices in case of a choice field. The choices should be a mapping
- label: The label used for representing the field to the end user. If no label is given the name of the field
is used.
required: Indicates if the field is required or optional
help_text: An optional help text that is presented to the end user next to the field.
An example kliko.yml file¶
Below is an example kliko file.
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name: simulator form
description: simulator form
container: skasa/simulator
author: Gijs Molenaar
email: gijsmolenaar@gmail.com
url: http://github.com/ska-sa/rodrigues/
io: split
sections:
-
name: telescope
description: Observatory
fields:
-
name: name
type: char
initial: new simulation
max_length: 200
-
name: observatory
type: choice
choices:
MeerKAT: MeerKAT
Kat-7: Kat-7
JVLA-A: JVLA-A
initial: MeerKAT
-
name: output
type: choice
choices:
Image: Image
Visibilities: Visibilities
initial: Image
label: Output type
-
name: sefd
type: float
label: SEFD
required: False
help_text: System defaults will be used if left blank
-
name: sky
description: Sky model
fields:
-
name: sky_type
type: choice
choices:
Tigger-LSM: Tigger-LSM
ASCII: ASCII
FITS: FITS
KATALOG: KATALOG
-
name: sky_model
type: file
required: False
-
name: katalog_id
type: choice
label: KATALOG
required: False
initial: nvss6deg
choices:
nvss6deg: nvss6deg
scubed1deg: scubed1deg
3c147_field: 3c147_field
3c147_field_no_core: 3c147_field_no_core
-
name: radius
type: float
label: Radius
initial: 0.5
required: False
help_text: Radius of degrees
-
name: fluxrange
type: char
label: Flux range
initial: 0.001-1
max_length: 32
help_text: Flux range in Jy
-
name: ms_dec
type: char
label: Declination
initial: -30d0m0s
help_text: in dms
-
name: ms_ra
type: char
label: Right ascension
initial: 0h0m0s
help_text: in hms
max_length: 32
-
name: add_noise
type: bool
initial: True
required: False
-
name: vis_noise_std
type: float
label: Visibility noise std
initial: 0
help_text: Generates from SEFD if 0
-
name: observation
description: Observation setup
fields:
-
name: ms_synthesis
type: float
label: Synthesis time
initial: 0.25
help_text: in hours
-
name: ms_dtime
type: int
label: Integration time
initial: 10
help_text: in seconds
-
name: ms_freq0
type: float
label: Start frequency
initial: 700
help_text: in MHz
-
name: ms_dfreq
type: float
label: Channel width
initial: 50e3
help_text: in kHz
-
name: ms_nchan
type: int
label: Channels
initial: 1
help_text: Number of frequency channels
-
name: imaging
description: imaging settings
fields:
-
name: use_default_im
type: bool
label: Use default imaging settings
initial: True
required: False
-
name: imager
type: choice
label: Imager
initial: LW
choices:
LWIMAGER: LWIMAGER
WSCLEAN: WSCLEAN
CASA: CASA
-
name: im_npix
type: int
label: Image size
initial: 512
help_text: in pixels
-
name: im_cellsize
type: float
label: Pixel size
help_text: in arcseconds
initial: 1
-
name: im_weight
type: choice
label: uv-Weighting
choices:
Natural: Natural
Uniform: Uniform
Briggs: Briggs
initial: N
-
name: im_robust
type: float
label: Robust
initial: 0
help_text: Briggs robust parameter
-
name: im_weight_fov
type: float
label: Weight FoV
help_text: in arcminutes
required: False
-
name: im_wprojplanes
type: int
label: w-Projection planes
initial: 0
-
name: im_mode
type: choice
label: Imaging mode
choices:
channel: channel
mfs: mfs
velocity: velocity
frequency: frequency
initial: channel
-
name: channelise
type: int
label: Image channelise
initial: 0
help_text: 0 means average all, 1 per channel, etc.
-
name: im_stokes
type: char
label: Stokes
initial: I
max_length: 4
-
name: lwimager
description: LWIMAGER deconvolution settings
fields:
-
name: lwimager
type: bool
label: Deconvolve with me!
required: False
-
name: lwimager_niter
type: int
label: NITER
initial: 1000
-
name: lwimager_gain
type: float
label: Loop gain
initial: 0.1
-
name: lwimager_threshold
type: float
label: Clean Threshold
initial: 0
help_text: In Jy
-
name: lwimager_sigmalevel
type: float
label: Clean sigma level
initial: 0
help_text: In sigma above noise
-
name: lwimager_operation
type: choice
label: Clean algorithm
choices:
csclean: csclean
hogbom: hogbom
clark: clark
multiscale: multiscale
initial: csclean
-
name: lwimager_cyclefactor
type: float
label: Cycle factor
initial: 1.5
-
name: lwimager_cyclespeedup
type: float
label: Cycle speed up
initial: -1
-
name: lwimager_stoppointmode
type: float
label: Stop point mode
initial: -1
-
name: lwimager_nscales
type: int
label: Scales for MS clean
initial: 4
-
name: lwimager_uservector
type: char
label: Clean scales
required: False
help_text: Comma seperated scales in pixels
max_length: 64
-
name: wsclean
description: WSCLEAN deconvolution settings
fields:
-
name: wsclean
type: bool
label: Deconvolve with me!
required: False
-
name: wsclean_niter
type: int
label: NITER
initial: 1000
-
name: wsclean_gain
type: float
label: Minor loop gain
initial: 0.1
-
name: wsclean_mgain
type: float
label: Major loop gain
initial: 0.9
-
name: wsclean_threshold
type: float
label: Clean Threshold
initial: 0
help_text: In Jy
-
name: wsclean_sigmalevel
type: float
label: Clean sigma level
initial: 0
help_text: In sigma above noise
-
name: wsclean_joinpolarizations
type: bool
label: Join polarizations
required: False
-
name: wsclean_joinchannels
type: bool
label: Join channels
required: False
-
name: wsclean_multiscale
type: bool
label: Multiscale clean
required: False
-
name: wsclean_multiscale_dash_threshold_dash_bias
type: float
label: Multi scale threshold bias
initial: 0.7
-
name: wsclean_multiscale_dash_scale_dash_bias
type: float
label: Multi scale bias
initial: 0.6
-
name: wsclean_cleanborder
type: float
label: Clean border
initial: 5
help_text: In percentage of image width/height
-
name: wsclean_smallpsf
type: bool
label: Small PSF
required: False
help_text: Resize the psf to speed up minor clean iterations
-
name: wsclean_nonegative
type: bool
label: No negative
required: False
help_text: Do not allow negative components during cleaning
-
name: wsclean_stopnegative
type: bool
label: Stop on negative
required: False
-
name: wsclean_beamsize
type: char
label: Restoring beam size
required: False
help_text: In arcseconds
max_length: 32
-
name: casa
description: CASA deconvolution settings
fields:
-
name: casa
type: bool
label: Deconvolve with me!
required: False
-
name: casa_niter
type: int
label: NITER
initial: 1000
-
name: casa_threshold
type: float
label: Threshold
initial: 0
-
name: casa_sigmalevel
type: float
label: Clean sigma level
initial: 0
help_text: In sigma above noise
-
name: casa_gain
type: float
label: Loop Gain
initial: 0.1
help_text: Clean Loop gain
-
name: casa_psfmode
type: choice
label: PSF mode
initial: clark
choices:
clark: clark
clarkstokes: clarkstokes
hogbom: hogbom
-
name: casa_imagermode
type: choice
label: Imager mode
required: False
choices:
csclean: csclean
mosiac: mosiac
initial: csclean
-
name: casa_gridmode
type: choice
label: Grid mode
required: False
choices:
widefield: widefield
aprojection: aprojection
initial: widefield
help_text: A-projection only works JVLA
-
name: casa_nterms
type: int
label: NTERMS
initial: 1
help_text: See CASA clean task
-
name: casa_reffreq
type: float
label: MFS ref Frequency
required: False
help_text: in MHz
-
name: casa_multiscale
type: char
label: Multiscale
required: False
help_text: Deconvolution scales in pixels
max_length: 200
-
name: casa_negcomponent
type: float
label: Negative Components
initial: -1
help_text: See CASA clean task
-
name: casa_smallscalebias
type: float
label: Small scale bias
initial: 0.6
help_text: See CASA clean task
-
name: casa_restoringbeam
type: char
label: Restoring beam
required: False
max_length: 32
-
name: casa_cyclefactor
type: float
label: Cycle factor
initial: 1.5
-
name: casa_cyclespeedup
type: int
label: Cycle speed up
initial: -1
-
name: moresane
description: MORESANE deconvolution settings
fields:
-
name: moresane
type: bool
label: Deconvolve with me!
required: False
-
name: moresane_scalecount
type: int
label: Scale count
required: False
help_text: See MORESANE help
-
name: moresane_subregion
type: int
label: Sub region
required: False
help_text: Inner region to deconvolve in pixels
-
name: moresane_startscale
type: int
label: Start scale
initial: 1
-
name: moresane_stopscale
type: int
label: Stop scale
initial: 20
-
name: moresane_sigmalevel
type: float
label: Threshold level
initial: 3
help_text: in sigma above noise
-
name: moresane_loopgain
type: float
label: Loop gain
initial: 0.1
-
name: moresane_tolerance
type: float
label: Tolerance
initial: .75
-
name: moresane_accuracy
type: float
label: Accuracy
initial: 1e-6
-
name: moresane_majorloopmiter
type: int
label: Major loop iterations
initial: 100
-
name: moresane_minorloopmiter
type: int
label: Minor loop iterations
initial: 50
-
name: moresane_convmode
type: choice
label: Convolution mode
initial: circular
choices:
circular: circular
linear: linear
-
name: moresane_enforcepositivity
type: bool
label: Enforce Positivity
required: False
-
name: moresane_edgesupression
type: bool
label: Edge Suppression
required: False
-
name: moresane_edgeoffset
type: int
label: Edge offset
initial: 0
-
name: moresane_mfs
type: bool
label: MFS map
required: False
help_text: Comes with an spi map
-
name: moresane_spi_dash_sigmalevel
type: float
label: spi threshold level
initial: 10
help_text: In sigma above noise
|
Loading a Kliko container with the previous kliko file is loaded up in RODRIGUES will result in the form below:
Processing this form will result in the following parameters.json file which is presented to the Kliko container on runtime:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 | {
"wsclean_threshold": 0.0,
"im_stokes": "I",
"casa_smallscalebias": 0.6,
"casa_threshold": 0.0,
"sky_model": null,
"casa_niter": 1000,
"wsclean_sigmalevel": 0.0,
"im_cellsize": 1.0,
"im_robust": 0.0,
"moresane_scalecount": null,
"casa_reffreq": null,
"casa_multiscale": "",
"lwimager_threshold": 0.0,
"casa_cyclefactor": 1.5,
"wsclean_cleanborder": 5.0,
"lwimager_nscales": 4,
"im_npix": 512,
"casa_cyclespeedup": -1,
"moresane_edgesupression": false,
"im_weight": "initial",
"wsclean_beamsize": "",
"radius": 0.5,
"wsclean_gain": 0.1,
"im_weight_fov": null,
"im_wprojplanes": 0,
"ms_ra": "0h0m0s",
"moresane_accuracy": 1e-06,
"ms_freq0": 700.0,
"lwimager_cyclefactor": 1.5,
"wsclean_multiscale_dash_threshold_dash_bias": 0.7,
"lwimager_niter": 1000,
"moresane_spi_dash_sigmalevel": 10.0,
"ms_nchan": 1,
"wsclean_niter": 1000,
"im_mode": "channel",
"moresane_majorloopmiter": 100,
"casa_gridmode": "widefield",
"fluxrange": "0.001-1",
"moresane_mfs": false,
"name": "new simulation",
"channelise": 0,
"moresane_subregion": null,
"lwimager_operation": "csclean",
"wsclean_multiscale": false,
"casa_psfmode": "clark",
"moresane_tolerance": 0.75,
"lwimager": false,
"lwimager_uservector": "",
"lwimager_stoppointmode": -1.0,
"casa_sigmalevel": 0.0,
"sefd": null,
"lwimager_gain": 0.1,
"moresane_edgeoffset": 0,
"moresane_loopgain": 0.1,
"katalog_id": "nvss6deg",
"wsclean_joinpolarizations": false,
"ms_dfreq": 50000.0,
"output": "Image",
"wsclean": false,
"wsclean_nonegative": false,
"wsclean_stopnegative": false,
"moresane_convmode": "circular",
"ms_synthesis": 0.25,
"casa_negcomponent": -1.0,
"casa_imagermode": "csclean",
"ms_dec": "-30d0m0s",
"moresane_minorloopmiter": 50,
"use_default_im": true,
"casa_nterms": 1,
"ms_dtime": 10,
"moresane_enforcepositivity": false,
"moresane": false,
"add_noise": true,
"wsclean_multiscale_dash_scale_dash_bias": 0.6,
"moresane_sigmalevel": 3.0,
"moresane_stopscale": 20,
"casa_restoringbeam": "",
"casa": false,
"wsclean_mgain": 0.9,
"wsclean_joinchannels": false,
"imager": "CASA",
"vis_noise_std": 0.0,
"moresane_startscale": 1,
"lwimager_cyclespeedup": -1.0,
"lwimager_sigmalevel": 0.0,
"observatory": "MeerKAT",
"wsclean_smallpsf": false,
"sky_type": "Tigger-LSM",
"casa_gain": 0.1
}
|