JMAPs Software User Guide
$Id: build_jmaps.html,v 1.5 2010/01/19 21:01:57 nathan Exp $
OVERVIEW
Radial strips (of user-defined angular width) are cut from a sequence of running difference images (default; base-difference images can also be used) and placed chronologically to form a rectangular map of intensity as a function of time and projected radial distance.
These so-called JMaps are an alternative to using movies to perform feature tracking.
Outward motions along the strips appear as height/time tracks.
Maps are created using a modification of the technique developed by Jeffery Walters for LASCO coronagraph observations (Sheeley et al. 1999, 2008). Adam Herbst further developed the software to work with SECCHI data with support from Guillermo Stenborg.
SETBACKS
The HI images must be distorted before analysis to maintain the Sun-centered polar coordinate system whose radial coordinate is elongation angle and whose azimuthal coordinate is solar position angle.
A position angles of 150 degrees is the upper limit of suitable angles to create elongation/time maps, as the HI FOV is centered on the solar equator and has limited longitudinal visibility.
Intensity scaling must be applied by the user to produce matching contrasts in the different instruments.
Features whose path changes latitude too rapidly within the timescale (projected radial distance) of interest will not be fully captured with this method.
CREATE INPUT MOVIES
CREATE EUVI INPUT MOVIES
IDL> list = scclister()
[NOTE: select all EUVI images with 2048 x 2048 size and destination
SSR1 and specify polarity]
[NOTE: it is better to create separate
'A' and 'B' movies]
IDL> wscc_mkmovie, list.sc_a
[KATE: Four or less days of data, type movie = straight, byte scale not changed, running difference of 20 minutes to 1 hour.]
Save movie in mvi format before exiting movie window
[NOTE: be
sure to include .mvi tag in file name when saving]
[NOTE: delete
bad frames after movie is created but before saving]
[NOTE:
movies must be saved as a .mvi set of SQUARE images]
CREATE COR1 INPUT MOVIES
IDL> list = scclister()
[NOTE: select all COR1 images with 1024 x 1024 size and destination
SSR1 and select polarization type.]
[NOTE: it is better to create
separate 'A' and 'B' movies]
IDL> wscc_mkmovie, list.sc_a
[KATE: Four or less days of data, running difference of 2 frames, use every 2 files from input, average skipped frames of at least 20 minutes, bytescale [-5,5] or bytescale = [-8,8], use secchi prep color scale, linear scaling.]
[KATE: or use sharpen ratio with log scaling, but must change byte scale accordingly with this option.]
Save movie in mvi format before exiting movie window
[NOTE: be
sure to include .mvi tag in file name when saving]
[NOTE: delete
bad frames after movie is created but before saving]
[NOTE:
movies must be saved as a .mvi set of SQUARE images]
CREATE COR2 INPUT MOVIES
IDL> list = scclister()
[NOTE: select all COR2 images with 2048 x 2048 size and destination
SSR1]
[NOTE: it is better to create separate 'A' and 'B' movies]
IDL> wscc_mkmovie, list.sc_a
[KATE: Four or less days of data, running difference of 2 frames, use every 2 files from input, average skipped frames, bytescale [-2.,2], use secchi prep color scale.]
Save movie in mvi format before exiting movie window
[NOTE: be
sure to include .mvi tag in file name when saving]
[NOTE: delete
bad frames after movie is created but before saving]
[NOTE:
movies must be saved as a .mvi set of SQUARE images]
CREATE HI1 INPUT MOVIES
IDL> list = scclister()
[NOTE:
select all HI1 images with 1024 x 1024 size and destination
SSR1]
[NOTE: it is better to create separate 'A' and 'B' movies]
IDL> list = list.sc_a or IDL> list = list.sc_b
Make sure that list isn't too big for movie creation.
[NOTE: while inside NRL use '.run choose' which chooses every other file and saves new list as 'listout' variable]
IDL> srem_movie, listout, /nosnow, bmin=-400, bmax=400;,/use_daily
[KATE:
recommend to use /nosnow to reduce noise in images, bmin and bmax
keyword settings, with bmin=-400 and bmax=400]
[KATE: for b also
use /use_daily]
[KATE: if HI background contains the Milky Way or
anything other problems (e.g. bright comets, particle debris, etc)
which increase the noise, use /usedate and enter a date which has a
better background]
Save
movie in mvi format before exiting movie window [NOTE: be sure to
include .mvi tag in file name when saving]
[NOTE: delete bad
frames before movie is used to create JMAP]
[NOTE: movies must be
saved as a .mvi set of SQUARE images]
CREATE HI2 INPUT MOVIES
IDL> list = scclister()
[NOTE: select all HI2 images with 1024 x 1024 size and destination
SSR1]
[NOTE: it is better to create separate 'A' and 'B' movies]
IDL> srem_movie, list.sc_a ;,box = [x_1, x_2, y_2, y_1]
[NOTE: default box is taken for background subtraction. Box=[230,450,130,400]
[NOTE: use 'box' keyword is different background subtraction needed.]
[NOTE:
'box' dimension must be within the 512 x 512 area.]
[NOTE: set
keyword box to cover area where no comets or saturating stars are
located. Box is used to create background subtraction of stars]
[NOTE: box coordinates taken as upper left corner (1) then lower right corner (2)]
Save movie in mvi format before exiting movie window
[NOTE: be sure to include .mvi tag in file name when saving]
[NOTE:
delete bad frames after movie is created but before or after
saving]
[NOTE: movies must be saved as a .mvi set of SQUARE
images]
EXTRA MOVIE NOTES
Use 'srem_movie' or 'scc_wrunmoviem, /edit' to delete bad frames before processing JMAPS.
It is best to have movies with lower contrast as you can increase the contrast manually after creation.
See secchimvi.htm for up-to-date details on MVI format and routines.
CREATE JMAPs FROM .MVI MOVIES
IDL> v2a
Individual instrument JMAPs can be combined after creation to construct a three instrument JMAP
Or you may select movies from multiple instruments to create a single set of JMAPs
Select [Instrument] of interest
Recommend starting with HI2 to define Position Angles
[Import file(s)]
Import one or more files for a single instrument.
For different instruments, go back to step 2.
Be sure that selected movies are of overlapping time frames before creating JMAPS.
Change [Angle(s)] input to be 'initial angle - final angle, frequency'
EXAMPLE: 60-140,3
creates slits every 3 degrees for position angles 60-140 degrees
Position angle (PA) measured from solar North in the counter clockwise direction
[Angle(s)] input must be consistent between JMAPs of separate instruments if you want to combine the JMAPs after separate instrument maps are created.
[Select Save File] and enter filename to which JMAPs will be saved upon completion.
Program will add _XXX before .jmp to specify angle of JMAP.
[Build jMap]
COMBINE JMAPS (IF WANTED) FROM INDIVIDUAL INSTRUMENT MAPS
IDL> wjmap_combine
Add files for the instrument time frames of interest
[NOTE: files must be added in correct order COR2 then HI1 then HI2]
Select Savefile for JMAP to be saved upon completion
Combine
Must exit widget manually as it will not close when finished
VIEW OR EDIT JMAPs FROM INDIVIDUAL INSTRUMENTS OR COMBINED JMAPs
IDL> s = findfile('/.../*.jmp')
IDL> tool2a, s
[NOTE: Use 'next' to proceed to next instrument on widget]
[KATE: Further process JMAPs to create best view of desired feature]
EUVI: chop = 2.0, smooth = 5.0
COR1: chop = 2.0, smooth = 5.0
COR2: smooth = 5.0, chop = 0.5, do not use any other options
HI1: smooth = 5.0, std dev filter = .75, chop = 2.5
HI2 smooth = 5.0, chop = 2.5, do not use any other options
Adaptions made to JMAPS are saved in newly created /edits folder with'*_t' extention.
'Draw line' allows user to get a rough idea of a features speed.
'Add map' creates a pdf output of maps.
[NOTE: maps disappear upon closing of tool2a unless they have been saved.]
To use 'crop' feature: cropping is done then click 'save file' and reopen newly saved JMAP.
'Process all' applies bottom of widget edits for box selected to all JMAPs in series.
[NOTE: for example, if chop = 2.5 is used while the HI2 insturment is selected for a particular positon angle, then 'process all' will apply the chop to all HI2 position angles in the sequence.]
[NOTE: 'process all' automatically saves edits version of JMAPS]
'Save' files
[NOTE: only final version of edits will be saved in /edits folder.]
VIEW MOVIE OF JMAP FRAMES AFTER COMPLETION
IDL> s = findfile('/.../*.jmp')
IDL> jmap2a_mov, s