GREG tutorial: II. Dealing with LMV cubes Presentation by Jérôme

GREG tutorial: II. Dealing with LMV cubes
Presentation by Jérôme PETY, Sébastien BARDEAU
(IRAM/Grenoble)
Current kernel developers: Jérôme PETY, Sébastien BARDEAU, &
Stéphane GUILLOTEAU
on behalf of the GILDAS kernel developers over time
IRAM Science Software User Meeting
Apr. 6 - 8 2016, St Martin d’Hères
Table of contents
Preparing your LMV cube
I. How does it look like?
II. Rotating the spatial coordinates
III. Extracting a subcube
IV. Converting from Jy/Beam to Kelvin
V. Flagging channels close to the systemic velocity
VI. Saving the result in a safe place
Channel maps
I. Default
II. With the angular resolution
III. No header information
IV. Only blue shifted channels
V. Zooming in
VI. No cross at phase center
VII. Contour level every σ (0.5 K)
VIII. User defined contour levels
IX. Color lookup table
X. No bitmap image, only contours
XI. Contour color according to their velocity
XII. Adding the sketch of the disk and outflow
XIII. Blue-shifted and red-shifted channels
XIV. Another example
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Table of contents (cont’d)
Integrated line profiles
I. Default
II. 12CO(2-1) blue shifted channels
III. 12CO(2-1) red shifted channels
IV. 13CO(2-1) blue shifted channels
V. 13CO(2-1) red shifted channels
Overlay
I. One image + 2 different kinds of contour
II. Only contours + Sketch
III. 4 different kinds of contours
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube: I. How does it look like?
GREG> let name red/hh30-12co21
GREG> let type lmv
GREG> go view
! Interactive tool => type E to exit
GREG> go ! Replay last action,
! here: VIEW
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube: I. How does it look like?
GREG> go view
! Interactive tool => type H for help
Position-independent actions:
Press E key: EXIT loop
Press H key: HELP display
Press M key: MOVIE
Press P key: PRINT plot in "ha" subdirectory
Press Q key: QUIT loop
Press X key: EXTRACT on disk current zoomed region
Position-dependent actions:
Cursor on images:
Left clic: Display spectrum at pointed position
Right clic: Define a polygon
Press C key: COORDINATES toggled from absolute to relative and back
Press S key: SLICE definition (velocity-position)
Press K key: KILL
pointed pixel
Press U key: UNKILL pointed pixel
Press Z key: ZOOM defined spatial region
Press B key: BACK to full field of view
Press V key: Display map coordinates at current position (the associated brightness value is wrong)
Press W key: WRITE Integrated Area image
Cursor on spectra:
Left clic in Selected
Spectrum: Display selected velocity channel
Left clic in Integrated Spectrum: Define velocity range
Press C key: COORDINATES toggled from freq/velo to channels and back
Press Z key: ZOOM defined velocity region
Press B key: BACK to full velocity range
Press W key: WRITE Integrated (and current) Spectrum
Cursor outside plots:
Press B key: BACK to full velocity range AND full field of view
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube: I. How does it look like?
GREG> input view ! Minimum help + current status of input parameters
VIEW will produce a semi-interactive display of Data Cubes
The display contains 4 panels
Top Left:
Image of current plane
Top Right:
Spectrum of current pixel
Bottom left: Integrated image over current range
Bottom right: Integrated spectrum over current polygon
* Map name is controlled by character variables NAME and TYPE.
* Channels are marked according to variable MARK
[VELOCITY, FREQUENCY or CHANNEL]
* Channel range is controlled by variable RANGE (in 3rd axis internal unit)
[0 0 ==> all channels]
* Size and location of rectangular area plotted is controlled by
variables CENTER and SIZE
[SIZE[1] = SIZE[2] = 0 ==> whole map]
[X-axis limits: CENTER[1]+SIZE[1]/2 CENTER[1]-SIZE[1]/2 arcsec]
[Y-axis limits: CENTER[2]-SIZE[2]/2 CENTER[2]+SIZE[2]/2 arcsec]
* CROSS controls the size of a cross at phase center (0 ==> no cross)
* Current input values:
RANGE [ 0 0 ]
MARK [ velocity ]
SIZE [ 0 0 ]
CROSS [ 2 ]
Cube name is
CENTER [ 0 0 ]
tmp/hh30-12co21.lmv-clean
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube: II. Rotating the spatial coordinates
! Next actions will create new files
! => Do everything in a temporary directory
sic mkdir tmp
sic copy data/hh30-12co21.lmv-clean tmp/hh30-12co21.lmv-clean
let name tmp/hh30-12co21
let type lmv
! Rotate by 30 deg to bring the
! outflow axis along the vertical
! direction
! ANGLE is the desired position angle,
! not the angle of rotation...
let angle -30
go rot
go view
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube: III. Extracting a subcube
@ tools/extract-tools.sic
let name tmp/hh30-12co21-rot-30deg
let type lmv
let center 0
let size 20
! Velocity range in km/s
let range -0.2 15
@ extract-do
! Reset plotting parameters to
! their default values
let center 0
let size 0
let range 0
go view
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube:
IV. Converting from Jy/Beam to Kelvin
@ tools/brightness-tools.sic
let name tmp/hh30-12co21-rot-30deg-ext
let type lmv
@ jy2k
go view
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube:
V. Flagging channels close to the systemic velocity
begin procedure 12co21-flag-cloud-channels
define image in ’name’"."’type’ read
define image out ’name’"-flag."’type’ real /like in
let out% in%
let out in
for ichan 14 to 25
let out[ichan] 0.
next ichan
delete /var in out
let name ’name’"-flag"
header ’name’"."’type’ /extrema
end procedure 12co21-flag-cloud-channels
!
let name tmp/hh30-12co21-rot-30deg-ext-tmb
@ 12co21-flag-cloud-channels
go view
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Preparing your LMV cube:
VI. Saving the result in a safe place
! We like this result => Let’s save it
sic mkdir red
sic rename ’name’"."’type’ "red/hh30-12co21.lmv"
let name red/hh30-12co21
let type lmv
go view
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: I. Default
let name red/hh30-12co21
let type lmv
go bit
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: II. With the angular resolution
let name red/hh30-12co21
let type lmv
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: III. No header information
let name red/hh30-12co21
let type lmv
let do_header no
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: IV. Only blue shifted channels
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: V. Zooming in
let name red/hh30-12co21
let type lmv
let do_header no
! Field size in arcsec
let size 9.5 11.5
! Field center offset in arcsec
let center 0 4
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: VI. No cross at phase center
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
let size 9.5 11.5
let center 0 4
let cross 0 ! Cross size in arcsec
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: VII. Contour level every σ (0.5 K)
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
let size 9.5 11.5
let center 0 4
let cross 0
! Contour level spacing in current
! brightness unit
let spacing 0.5
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: VIII. User defined contour levels
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
let size 9.5 11.5
let center 0 4
let cross 0
define real noise
let noise 0.5
! Exponential levels
levels 2*noise 4*noise 8*noise 16*noise
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: IX. Color lookup table
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
let size 9.5 11.5
let center 0 4
let cross 0
define real noise
let noise 0.5
levels 2*noise 4*noise 8*noise 16*noise
go nice
wedge /level ! With current contour levels
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: X. No bitmap image, only contours
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
let size 9.5 11.5
let center 0 4
let cross 0
define real noise
let noise 0.5
levels 2*noise 4*noise 8*noise 16*noise
let do_nice yes
! Beam
let do_contour yes ! Contours
let do_bit no
! No bitmap image
! "go bit", "go nice" are wrappers
! around "go lmv"
go lmv
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: XI. Contour color according to their velocity
let name red/hh30-12co21
let type lmv
let do_header no
let first 2
let last 13
let size 9.5 11.5
let center 0 4
let cross 0
define real noise
let noise 0.5
levels 2*noise 4*noise 8*noise 16*noise
let do_nice yes
let do_contour yes
let do_bit no
let do_vsys yes
let vsys 7.3 ! km/s
go lmv
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: XII. Adding the sketch of the disk and outflow
begin procedure 12co21-sketch-one-panel
define real disk jet angle cos sin
pen 0 /dash 3
let disk 3*sec
draw relo +disk 0 /user
draw line -disk 0 /user
!
let jet 15*sec
draw relo 0 +jet /user
draw line 0 -jet /user /clip
!
pen 0 /dash 1
let angle 30*pi/180
let cos cos(angle)
let sin sin(angle)
draw relo jet*sin jet*cos /user
draw line -jet*sin -jet*cos /user /clip
draw relo jet*sin jet*cos /user
draw line -jet*sin -jet*cos /user /clip
let cos cos(-angle)
let sin sin(-angle)
draw relo jet*sin jet*cos /user
draw line -jet*sin -jet*cos /user /clip
end procedure 12co21-sketch-one-panel
GREG tutorial: II. Dealing with LMV cubes
let name red/hh30-12co21
let type lmv
...
let first 2
let last 13
go lmv
@ 12co21-sketch-all-panels
J. Pety & S. Bardeau 2016
Channel maps: XIII. Blue-shifted and red-shifted channels
let name red/hh30-12co21
let type lmv
let do_header no
let size 9.5 11.5
let center 0 4
let cross 0
define real noise
let noise 0.5
levels 2*noise 4*noise 8*noise 16*noise
let do_nice yes
let do_contour yes
let do_bit no
let do_vsys yes
let vsys 7.3 ! km/s
!
! Top panel
let first 2
let last 13
go lmv
@ 12co21-sketch-all-panels
!
! Bottom panel
let first 26
let last 37
go lmv
@ 12co21-sketch-all-panels
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Channel maps: XIV. Another example
let name data/hh30-13co21-rot-30deg
let type lmv
let do_header no
let do_bit no
let do_contour yes
let do_vsys yes
let vsys 7.3
let first 5
let last 16
let spacing 0.68 ! K = 3 sigma
let center 0
let size 10
let cross 1
go lmv
let do_vsys no
@ go-pause 13co21-channel-maps
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Integrated line profile: I. Default ⇒ Full velocity range
let name red/hh30-12co21
let type lmv
go area
! Name set to red/hh30-12co21-area-1-39
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Integrated line profile: II. 12CO(2-1) blue shifted channels
! Required because NAME was automatically
! changed by GO AREA
let name red/hh30-12co21
let type lmv
let first 2
let last 13
go area
! Name set to red/hh30-12co21-area-2-13
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Integrated line profile: III. 12CO(2-1) red shifted channels
! Required because NAME was automatically
! changed by GO AREA
let name red/hh30-12co21
let type lmv
let first 26
let last 37
go area
! Name set to red/hh30-12co21-area-26-37
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Integrated line profile: IV. 13CO(2-1) blue shifted channels
let name red/hh30-13co21-rot-30deg
let type lmv
let first 12
let last 17
go area
! Name set to red/hh30-13co21-rot-30deg-area-12-17
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Integrated line profile: V. 13CO(2-1) red shifted channels
let name red/hh30-13co21-rot-30deg
let type lmv
let first 5
let last 10
go area
! Name set to red/hh30-13co21-rot-30deg-area-5-10
go nice
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Overlay: I. One image + 2 different kinds of contour
let do_rcoord yes
let do_nice no
let do_header no
!
let mark "none"
let cross 0
let size 6 10
let center 0 2.5
!
lut heat
let nimages 3
let nreference 1
let names[1] "data/hh30-hst-rot-30deg"
let names[2] "red/hh30-12co21-area-1-39"
let names[3] "data/hh30-cont1mm-rot-30deg"
let types[1] "gdf"
let types[2] "lmv"
let types[3] "lmv-clean"
let spacings[1:3] 1e6 4 1e-3
let pens[1] 0 7
let pens[2] 7 7
let pens[3] 0 7
go over
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Overlay: II. Only contours + Sketch
let size 7.5 11.5
let center 0 3
let do_contour yes
let do_bit no
!
pen 1 /col 0 /weight 1 /dash 1
pen 2 /col 1 /weight 1 /dash 2
pen 3 /col 3 /weight 1 /dash 3
pen 0
let nimages 3
let nreference 1
let names[1] "data/hh30-cont1mm-rot-30deg"
let names[2] "red/hh30-12co21-area-2-13"
let names[3] "red/hh30-12co21-area-26-37"
let types[1] "lmv-clean"
let types[2] "lmv"
let types[3] "lmv"
let spacings[1:3] 1e-3 2 2
let pens[1] 1 7
let pens[2] 2 7
let pens[3] 3 7
go over
@ 12co21-sketch-one-panel
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016
Overlay: IV. 4 different kinds of contours
pen 1 /col 0 /weight 1 /dash 4
pen 2 /col 1 /weight 1 /dash 2
pen 3 /col 3 /weight 1 /dash 3
pen 4 /col 0 /weight 1 /dash 1
pen 0
let nimages 4
let nreference 1
let names[1] "red/hh30-12co21-area-1-39"
let names[2] "red/hh30-13co21-rot-30deg-area-5-10"
let names[3] "red/hh30-13co21-rot-30deg-area-12-17"
let names[4] "data/hh30-cont1mm-rot-30deg"
let types[1] "lmv"
let types[2] "lmv"
let types[3] "lmv"
let types[4] "lmv-clean"
let spacings[1:4] 4 0.6 0.6 1e-3
let pens[1] 1 7
let pens[2] 2 7
let pens[3] 3 7
let pens[4] 4 7
go over
GREG tutorial: II. Dealing with LMV cubes
J. Pety & S. Bardeau 2016