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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
|
<!DOCTYPE doctype PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta name="generator" content=
"HTML Tidy for Mac OS X (vers 31 October 2006 - Apple Inc. build 15.18.1), see www.w3.org">
<meta http-equiv="Content-Type" content=
"text/html; charset=us-ascii">
<meta name="GENERATOR" content=
"Mozilla/4.78 [en] (X11; U; Linux 2.4.7-10 i686) [Netscape]">
<title>DS9 FAQ</title>
</head>
<body vlink="#551A8B" text="#000000" link="#0000EE" bgcolor=
"#FFFFFF" alink="#FF0000">
<h3><img alt="" src="sun.gif" width="100" height="98" align=
"middle"> SAOImageDS9 FAQ</h3>
<blockquote>
<p>This FAQ is a new, on going project, and it is far from being
complete. But as common questions on DS9 are received, the FAQ will
be updated.</p>
<p><b>Contents</b></p>
<blockquote><a href="#Copyright">Copyright</a><br>
<a href="#General">General</a><br>
<a href="#Fonts">Fonts</a><br>
<a href="faq.html#Linux">Linux</a><br>
<a href="faq.html#Windows">Windows</a><br>
<a href="#MacOSX">MacOSX</a><br>
<a href="faq.html#X11">X11</a><br>
<a href="#IRAF">IRAF</a><br>
<a href="#Coordinates">Coordinates</a><br>
<a href="#Regions">Regions</a><br>
<a href="#Printing">Printing</a><br>
<a href="#XPA">XPA</a><br>
<a href="#VO">VO</a><br></blockquote>
</blockquote>
<blockquote>
<p><b><a name="Copyright" id="Copyright"></a>Copyright</b></p>
<blockquote>
<p>DS9 is composed of approximately 20 open source packages, all of
which are distributed under their own open source license
agreements, usually GPL, LGPL, or BSD. In addition, several open
source packages have been developed here at the Smithsonian
Astrophysical Observatory, Cambridge, MA, USA and are distributed
under the terms of the GNU General Public License as published by
the Free Software Foundation. As long as you continue to adhere to
the provisions of the licenses, you are free to distribute DS9
along with your software.</p>
<p>The <a href="http://www.gnu.org/copyleft/gpl.html">GNU site</a>
contains an excellent FAQ on the the dos and donts of GPL.</p>
</blockquote>
<p><b><a name="General" id="General"></a>General</b></p>
<blockquote>
<p><b>The web browser, catalog tool, image server, and other
Analysis functions don't appear to work. Whats going
on?<br></b></p>
<p>For a number of the Analysis functions, DS9 requires temporary
disk space to download and store data. By default, this directory
is defined by the TMP or TEMP environment variable. This is usually
defined as <tt>/tmp</tt> for Linux and MacOSX users. For Windows
users, this will vary, depending on which version of Windows you
have. In any case, if the temp directory is not writable, or you
have specified an invalid directory in the preferences, these
functions will fail with a variety of error messages.<br></p>
<p><b>My system admin stripped the DS9 binary and now DS9 fails to
start with the following error message:</b></p>
<p><tt>Application initialization failed: Can't find a usable
tk.tcl in the following directories...</tt></p>
<p>DS9 is based on tcl/tk which is a scripting language which
requires many support files. To create a stand alone application,
we <i>fool</i> tcl/tk into thinking that it has a valid
installation. To do this, DS9 is really an application, along with
an zip archive attached. The first thing DS9 does is to create a
virtual file system in memory and unpack that archive into memory.
The application DS9 is already stripped of debugging symbols when
built.</p>
<p>It appears that the <tt>strip</tt> command is <i>stripping</i>
part of the archive, hence DS9 is unable to un-compress it. In
summary, don't <tt>strip</tt> the DS9 binary and everything works
fine.</p>
<p><b>When I open my FITS image, all I see is 'white'. Yet
everything, including the color bar seems to work?</b></p>
<p>New with version 2.1, is support for the DATASEC keyword. This
keyword specifies what portion of the image is valid data, for
calculating min / max and for displaying. This is very important
for images created from CCDs with over scan and bias strips. By
default, this support is enabled. However, a number of fits images
with this keyword, have invalid values. Therefor, when DS9 opens
the image, it finds no valid data to display. To correct this
problem, either disable DATASEC support, via the Scale menu, or
correct the the value of DATASEC in the fits header. You can also
change the default behavior by disabling DATASEC from the
preferences menu.<br></p>
</blockquote>
<p><b><a name="Fonts" id="Fonts"></a>Fonts</b></p>
<blockquote>
<p><b>Where is the Symbol Font? How do I enter special characters
into an entry dialog?</b></p>
<p>The concept of a separate <tt>SYMBOL</tt> font is no longer
implemented with the latest OS font and scripting support,
especially with scalable anti-alias fonts such as Xft for Linux.
Most newer fonts (if not all) now have greek characters as part of
the font. The greek chars start at unicode \u0391 for 'A' and
\u03b1 for 'a'. Each OS has a tool used to build and copy a string
of characters. Then use the Edit:Paste menu of DS9 to insert the
character string.</p>
<p>Linux- Gnome: <b>gucharmap<br></b> Linux- KDE:
<b>kcharselect<br></b> MacOSX: <b>Character Viewer</b> (Select
<tt>Edit:Special Characters</tt>) Now click and drag the characters
to a terminal window. Then select the string and select
<tt>Edit:Copy</tt>.<br>
Windows: <b>Character Map</b> (from <tt>Start</tt> button, select
<tt>All Programs</tt>, <tt>Accessories</tt>, <tt>System Tools</tt>
and then <tt>Character Map</tt>)<br></p>
</blockquote>
<p><b><a name="Linux" id="Linux"></a>Linux</b></p>
<blockquote>
<p><b>My /tmp directory is mounted -noexec and bin table filtering
does not work.</b></p>
<p>Set the environment variable FILTER_TMPDIR to a directory that
is both writable and can execute.<br></p>
<p><b>I have Red Hat 7, and I'm running KDE. The magnifier keeps
going blank after a few seconds, what's going on?</b></p>
<p>The problem was in KDE. If the user has decided to hide the
panel taskbar and sets a delay time for when it appears if
the mouse is moved to the panel location, then it appears
that KDE creates mouse events that fool DS9 into thinking the
mouse is outside and it blanks the magnifier. By turning off
the hide panel, the effect goes away. The alternative is to
update to KDE2.1Beta where this method of dealing with the
hidden panel is not used and all is well, as it was for
KDE</p>
<p><b>I have FreeBSD. When I run ds9, I get the following
error:</b> <tt> <b>ELF binary type "0" not known</b></tt>
<b>Whats going on?</b></p>
<p>The solution was to use the <b><tt>brandelf</tt></b> utility on
the file to ensure that the machine understood that it was a
Linux program.</p>
<p><tt>% brandelf -t Linux (file name)<br></tt></p>
</blockquote>
<p><b><a name="Windows" id="Windows"></a>Windows</b></p>
<blockquote>
<p><b>When I do Save Image, I get the same result (and this is true
for either .gif, .jpeg, .tiff, .png and .ppm) : it saves only a
stripe at the top of my image.<br></b></p>
<p>This problem seems to be caused by running DS9 in Windows XP
compatibility mode. Please un-check the compatibility option in the
properties dialog.<br></p>
<p><b>How can I open a FITS file with an extension name?</b></p>
<p>By default, the windows port of DS9 uses the Windows standard
dialog box to open and save files. This can be a problem in that
the native Windows dialog will not allow extensions to the file
name, such as <tt>foo.fits[2]</tt>. You must use the Unix like
standard dialogs to be able to specify an extension. Select
<tt>Edit->Preferences->General:Dialogbox</tt> to change the
default standard dialog.</p>
<p><b>Every time I create an auxiliary window in ds9, such as a
Pixel Table, or Analysis Plot, it will retreat behind the main ds9
window. Then, when I bring the auxiliary window to the front and
move the mouse out of it, it automatically goes behind the main ds9
window again. What can I do to fix things so that the auxiliary
window stays on top of the ds9 window?</b></p>
<p>To fix things so that the auxiliary window stays on top of the
ds9 window, do the following:</p>
<blockquote>
<p><tt>Go to the icon task bar at the bottom of the screen.</tt>
<tt>Bring the auxiliary window to the front by clicking on its icon
in the icon task bar.</tt> <tt>While the mouse still is on the aux
window icon, press the mouse button, and keeping it pressed, move
the mouse off the task bar.</tt> <tt>Release the mouse while off
the task bar.</tt> <tt>The auxiliary window will now stay on top of
the main ds9 window.</tt></p>
</blockquote>
</blockquote>
<p><b><a name="MacOSX" id="MacOSX"></a>MacOSX</b><br></p>
<blockquote>
<p><b>I can't invoke the 'Save Image' function from the MacOSX X11
version. I get an error message "An error has occurred while
creating the image. Please make sure entire image is visible on
screen."<br></b></p>
Up until MacOSX 10.8 (Mountain Lion), Apple provided their own
version of a X11 server. At first, it was based on XFree86
(X11R6.6) and available with versions up to MacOSX 10.4. Later with
MacOSX versions 10.5 to 10.7, the Apple's X11 server was based upon
X.org (X11R7.2).<br>
<br>
The Apple version of X11 server for MacOSX 10.5 to 10.7 contains a
bug which fails if you invoke certain X11 calls on a window if its
location is not at 0,0 on the screen. Hence, within DS9, if you
'Save Image' and your window is not exactly in the upper left
corner, it will fail.<br>
<br>
Again, this only affects users of MacOSX 10.5 to 10.7.<br>
<br>
Starting with MacOSX 10.8, Apple no longer provides a X11 window
server. The user must go to the XQuartz site and download/install
directly. The current version is 2.7.3.<br>
<p><b>When I invoke DS9 MacOSX Aqua from the command line, I get
weird errors such as<tt>:</tt></b></p>
<blockquote>
<p><tt>The document "foo.fits" could not be opened. SAOImage DS9
cannot open files in the "Flexible Image Transport System"
format.</tt></p>
</blockquote>
<p>When opening MacOSX Aqua from the command line, it is better to
use the <tt>OPEN</tt> application as opposed to specifying the
binary directly. The <tt>OPEN</tt> application sets up the
environment just as it is when a user double clicks.</p>
<tt># good</tt><br>
<tt>% open /Applications/SAOImage\ DS9.app foo.fits<br>
<br>
# bad<br>
% /Applications/SAOImage\ DS9.app/Contents/MacOS/ds9
bar.fits</tt><br>
<p><b>How can I open a FITS file with an extension name?</b></p>
<p>By default, DS9 MacOSX Aqua uses the MacOSX standard dialog box
to open and save files. This can be a problem in that the native
MacOSX dialog will not allow extensions to the file name, such as
<tt>foo.fits[2]</tt>. You must use the Unix like standard dialogs
to be able to specify an extension. Select
<tt>Edit->Preferences->General</tt> to change the default
standard dialog.</p>
<p><b>How do I set my PATH environment variable under MacOSX for
use with external analysis programs, such as funtools?<br></b></p>
<p>When you double click on a MacOSX application, it does not parse
any shell startup files, such as ~/.profile. Instead, the
environment is defined using a special environment file,
<tt>.MacOSX/environment.plist</tt>. This file can be created with
the MacOSX utility
<tt>/Developer/Applications/PropertyListEditor.app.</tt> For
further information, please click <a href=
"http://developer.apple.com/qa/qa2001/qa1067.html">here</a>.<br></p>
</blockquote>
<p><b><a name="X11" id="X11"></a>X11</b><br></p>
<blockquote>
<p><b>Is it possible to work in batch mode without a physical
display?<br></b></p>
<p>DS9 is written as an interactive, window client program, and as
a result, does require a window server to be available for
rendering (X11, Windows, or MacOSX).<br>
<br>
Therefore, using DS9 as a batch process can be cumbersome. We
recommend using <tt>xvfb</tt> under X11. Just set up a virtual
display buffer, reset your DISPLAY variable, then invoke DS9 with a
number of command line options or use xpa from a shell script as a
batch processor. Example:<br></p>
<p><tt>% export DISPLAY=:1</tt><tt><br></tt> <tt>% Xvfb :1 -screen
0 1024x768x16 &</tt><tt><br></tt> <tt>% ds9 -file cmap.fits
-zoom to fit -cmap b -grid skyformat degrees -grid yes -regions
../EMS-names.reg -saveimage png mytest.png -exit</tt><br></p>
<p><b>When I start DS9, I get the following error message:</b></p>
<tt>_X11TransSocketINETConnect: Can't get address for
foo.bar.edu</tt><br>
<tt>couldn't connect to display "foo.bar.edu:0.0"</tt> <br>
<p>DS9 is unable to determine a valid X11 Display server, because
of a number of reasons. Most often this is seen when you have a
laptop configured for a network, but is not physically connected.
You need to set the DISPLAY environment variable to :0.0</p>
<blockquote><tt>$ xhost +</tt><br>
<tt>$ set DISPLAY=:0.0</tt><br>
<tt>$ export DISPLAY</tt><br></blockquote>
<p><b>Under Solaris, when I start DS9, my twm window manager
crashes!</b></p>
<p>TWM distributed with X11R5 had a major bug, that was corrected
around 1996. DS9 will trigger this bug, and will cause TWM to
crash. If you are running Solaris, and have X11R5 installed, be
sure that /usr/openwin/bin is in your path before X11R5/bin. This
will insure that you are running the correct version of TWM .</p>
<p><b>When I run ds9 with the tvtwm window manager, sometimes the
open file dialog box does not appear?</b></p>
<p>If you are running tvtwm, and you are currently viewing a
virtual screen other than the first, when you open a file, the
dialog box will appear in the first virtual screen, not your
current. This is a bug with tvtwm and not ds9.</p>
</blockquote>
</blockquote>
<blockquote>
<p><b><a name="IRAF" id="IRAF"></a>IRAF</b></p>
</blockquote>
<blockquote>
<blockquote>
<p><b>I can't use more than 9 frames with the IMEXAMINE
task?</b><br></p>
<p>The task <tt>IMEXAMINE</tt> can not be used with frame numbers
greater than 9.</p>
<p><b>Can I display from IRAF to DS9 running under Windows or
MacOSX?</b></p>
<p>Yes, DS9 for Windows and MacOSX is also a fully functional IRAF
display server. To direct image output from IRAF to DS9 running
under Windows or MacOSX, use the IMTDEV environment variable. For
example, if the machine is named 'foo.bar.edu', define IMTDEV to
the follow value before entering IRAF.</p>
<blockquote><tt>$ setenv IMTDEV inet:5137:foo.bar.edu</tt><br>
<tt>$ cl</tt><br>
<tt>cl> display dev$pix</tt><br></blockquote>
<p><b>I'm having problems with</b> <b>mscred task</b>
<b>msczero?</b></p>
DS9 now supports IRAF's new IIS image display protocol. However,
there is one minor problem with the <b>mscred</b> task
<b>msczero.</b> Before using <b>msczero</b>, issue the following
command in the cl:<br>
<br>
<tt>cl> set disable_wcs_maps=""<br>
cl> flpr</tt><br>
<p><b>I find that there is a frustrating delay in performing
operations on images displayed from IRAF - there's a wait of a
second or two before an image is (re)displayed, whereas
<i>saoimage</i> reacts virtually instantly for the same type of
operation. This makes running imexamine on a batch of images a
pain, and using the mouse to change color gamma/bias to desired
values basically impossible.</b></p>
<p>DS9 and <i>saoimage</i> are similar in speed when working with
IRAF. In fact, DS9 uses the same code to interface with IRAF
as saoimage and ximtool. The only difference is that DS9 is
double buffered, whereas, <i>saoimage</i> and <i>ximtool</i>
only use a single buffer. So with <i>saoimage</i> and
<i>ximtool</i>, you see incremental progress, where DS9 will
render the image all at one time. However, the overall time
to finish rendering should almost be the same.</p>
<p>DS9 runs in both 8 bit and 24 bit environments, but
<i>saoimage</i> is restricted to 8 bit. If you are running DS9 and
<i>saoimage</i> at the same time, then you must be in 8 bit mode.
You should not see any delay in changing the color
bias/contrast between the two.</p>
<p>However, if you are running DS9 in 24 bit mode, then you will
see slower performance in changing the bias/contrast, as
compared to 8 bit mode. Instead of changing a color look up
table, as in 8 bit mode, DS9 has to update every pixel on the
screen. If your cpu speed is slow, you can select the
Edit:Preferences:True Colorbar to tell DS9 not to update the entire
screen, only a part of the screen. This should only be needed
if your machine is slower than 200 MHz. Again <i>saoimage</i>
does not even run in 24 bit mode, so there are no
comparisons.</p>
<p><b>I try to display an image from IRAF and I get the following
error message:</b></p>
<p><tt>Cannot open device (node!imtool,,512,512)</tt></p>
<p>DS9 works the same way as <tt>ximtool,</tt> <tt>saoimage,</tt>
and <tt>saotng.</tt> No special scripts should be needed. If
you have one of the above currently working, DS9 should work
<i>out of the box</i>.</p>
<p>IRAF can use one of three methods to communicate with DS9: fifo,
socket, and unix domain name. The DS9 defaults are:</p>
<blockquote><tt>fifo /dev/imt1</tt><br>
<tt>port 5137</tt><br>
<tt>unix /tmp/.IMT%d</tt></blockquote>
<p>If your IRAF configuration is set up different (i.e., a
different port number, or via a fifo), you need to tell DS9
how to communicate with iraf. DS9 uses the same command line
options as XIMTOOL:</p>
<blockquote><tt>-fifo</tt><br>
<tt>-fifo_only</tt><br>
<tt>-inet_only</tt><br>
<tt>-port</tt><br>
<tt>-port_only</tt><br>
<tt>-unix</tt><br>
<tt>-unix_only</tt></blockquote>
</blockquote>
</blockquote>
<blockquote>
<blockquote>
<p><b>I try to display an image, I see something, but it's
corrupted and I get multiple error messages from DS9...</b></p>
<p>An IRAF image server (<i>ximtool</i>, <i>saoimage</i>, DS9,
etc...) uses a configuration file to specify the number of
available buffers and their sizes. What actually passes from
IRAF is not the buffer size, but an index number into this
file.</p>
<p>So when an image server starts (DS9), it will attempt to locate
this file as $HOME/.imtoolrc and /usr/local/lib/imtoolrc. If
not found, it will look for shell environment variables
IMTOOLRC and imtoolrc, that contains the name of the configuration
file.</p>
<p>If no configuration file is found, DS9 will assume the following
default configuration:</p>
<blockquote><tt> 1 2 512 512 #
imt1|imt512</tt><br>
<tt> 2 2 800 800 #
imt2|imt800</tt><br>
<tt> 3 2 1024 1024 # imt3|imt1024</tt><br>
<tt> 4 1 1600 1600 # imt4|imt1600</tt><br>
<tt> 5 1 2048 2048 # imt5|imt2048</tt><br>
<tt> 6 1 4096 4096 # imt6|imt4096</tt><br>
<tt> 7 1 8192 8192 # imt7|imt8192</tt><br>
<tt> 8 1 1024 4096 # imt8|imt1x4</tt><br>
<tt> 9 2 1144 880 # imt9|imtfs full screen
(1152x900 minus frame)</tt><br>
<tt>10 2 1144 764 # imt10|imtfs35 full screen at
35mm film aspect ratio</tt><br>
<tt>11 2 128 128 # imt11|imt128</tt><br>
<tt>12 2 256 256 # imt12|imt256</tt><br>
<tt>13 2 128 1056 # imt13|imttall128 tall &
narrow for spectro.</tt><br>
<tt>14 2 256 1056 # imt14|imttall256 tall &
wider for spectro.</tt><br>
<tt>15 2 1056 128 # imt15|imtwide128 wide &
thin for spectro.</tt><br>
<tt>16 2 1056 256 # imt16|imtwide256 wide &
fatter for spectro.</tt><br>
<tt>17 2 1008 648 # imt17|imtssy Solitaire fmt w/
imtool border</tt><br>
<tt>18 2 1024 680 # imt18|imtssn Solitaire fmt
w/out imtool border</tt><br>
<tt>19 1 4096 1024 # imt19|imt4x1</tt><br></blockquote>
<p>If on the other hand, IRAF assumes a different buffer size, the
image will appear corrupted and DS9 may issue a number of error
messages.</p>
<p>Another problem is that this file must be in sync with
dev$graphcap. If your system administrator has made changes
to graphcap, they must also be implemented in imtoolrc.</p>
<p>Here is a note from NOAO:</p>
<blockquote>
<p><tt>The messages means that there is no /usr/local/lib/imtoolrc
file</tt> <tt>on the machine. This is created as a symlink to
dev$imtoolrc by the</tt> <tt>iraf install script but only if the
/usr/local/lib dir already exists on the</tt> <tt>machine. The fix
is the create the dir and rerun the install script or</tt> <tt>else
make the link by hand. Users can also just copy
dev$imtoolrc</tt> <tt>to $HOME/.imtoolrc and restart the server to
also workaround it. Note</tt> <tt>that an existing .imtoolrc might
define old frame buffer configs which</tt> <tt>might confuse
things, so if the system file exists check for a private</tt>
<tt>copy screwing things up.</tt></p>
</blockquote>
</blockquote>
</blockquote>
<blockquote>
<blockquote>
<p><b>Where do I find this .imtoolrc file?</b></p>
<p>Again, here a note from NOAO concerning this issue:</p>
<blockquote>
<p><tt>In a smooth installation the imtoolrc file is installed as
a</tt> <tt>/usr/local/lib/imtoolrc symlink pointing to the
dev$imtoolrc file in the</tt> <tt>iraf system. This is
normally what's used but XImtool (and DS9?) also</tt> <tt>allow a
$HOME/.imtoolrc and IMTOOLRC environment variable defining the</tt>
<tt>path as fallbacks. There are several practical problems
with this: for</tt> <tt>some reason (I'm trying to fix)
the imtoolrc link won't be created if</tt> <tt>the /usr/local/lib
directory doesn't exist when the install script is</tt> <tt>run on
the machine, even though it's run as root and the file can be</tt>
<tt>directory easily. On PC-IRAF systems there is also a typo
in the install</tt> <tt>script (extra logical or at line 515) which
causes it to exit before</tt> <tt>the display setup is run (i.e. no
/dev fifos or imtoolrc). If users don't</tt> <tt>catch this or see
it in the README file they'll think everything went</tt> <tt>fine.
Lastly, the local iraf admin might not have run the install
script</tt> <tt>on the local iraf NFS client machine at
all.</tt></p>
</blockquote>
</blockquote>
</blockquote>
<blockquote>
<blockquote>
<p><b>When I display an image from IRAF, the SCALE menu option is
not active, Why?</b></p>
<p>When you display an image from IRAF into DS9, IRAF actually does
the color scale distribution. In Display, use the ztrans and
z1,z2 parameters to set the upper/lower bounds and distribution.
You can also use the zscale parameter to auto determine z1,z2.Here
are the DISPLAY parameters in question:</p>
<blockquote><tt>ztrans=[linear|log|none|user]</tt><br>
<tt>z1=min</tt><br>
<tt>z2=max</tt><br>
<tt>zscale=[yes|no]</tt></blockquote>
<p>What actually is sent from IRAF to DS9 is one byte per pixel,
values 0-200, which already has applied both the upper and
lower clipping bounds and the distribution. So this is why, the
SCALE menu is disabled in DS9 when it receives a image from
IRAF.</p>
</blockquote>
</blockquote>
<blockquote>
<p><b><a name="Coordinates" id=
"Coordinates"></a>Coordinates</b></p>
</blockquote>
<blockquote>
<blockquote>
<p><b>Why don't I see PHYSICAL/WCS/WCSA...WCSZ coordinates
displayed when I load my image?</b></p>
<p>DS9 supports the following coordinate systems:</p>
<blockquote><tt>WCS Sky coords
(fk4,fk5,icrs,galactic,ecliptic)<br></tt> <tt>WCS Linear
coords<br></tt> <tt>Image (also known as Logical)<br></tt>
<tt>Physical (also known as CCD)<br>
Detector<br>
Amplifier </tt><br></blockquote>
<p>DS9 uses the following FITS keywords in the header to define a
coordinate system: </p>
</blockquote>
<center>
<table nosave="" width="75%" cellpadding="4" border="1">
<tbody>
<tr>
<td><b>Coordinate System</b></td>
<td><b>Keyword Values</b></td>
</tr>
<tr nosave="">
<td nosave=""><tt>WCS / WCSA...WCSZ</tt></td>
<td><tt>CRVAL,CRPIX,CRDELT,CD... (for images)<br>
TCRVL,TCRPX,TCDLT,... (for tables)</tt></td>
</tr>
<tr>
<td><tt>Image</tt></td>
<td><tt>none required</tt></td>
</tr>
<tr>
<td><tt>Physical</tt></td>
<td><tt>WCSNAMEP='PHYSICAL' or LTMx_x/LTVx</tt></td>
</tr>
<tr>
<td valign="top"><tt>Detector</tt><br></td>
<td valign="top"><tt>DTMx_x/DTVx</tt><br></td>
</tr>
<tr>
<td valign="top"><tt>Amplifier</tt><br></td>
<td valign="top"><tt>ATMx_x/ATVx</tt><br></td>
</tr>
</tbody>
</table>
</center>
<blockquote>
<p>If the required keywords are not present, values for those
coordinates are not displayed.</p>
<p>Note: For PHYSICAL, DS9 will first look for an alternative WCS
with WCSNAMEx='PHYSICAL'. If not found, DS9 will then look for the
LTMx_x LTVx keywords.</p>
</blockquote>
</blockquote>
<blockquote>
<p><b><a name="Regions" id="Regions"></a>Regions</b></p>
<blockquote>
<p><b>How do I indicate distance on my printed
images?</b> </p>
<p>You have two choices, the RULER region and the LINE region. The
ruler region is mainly used for interactive measurements. For
printed output, use the LINE region to create a distance indicator.
In the line region dialog, there is a read-only entry that
indicates the length in pixels, degrees, arcmin, or arcsec. Edit to
the desired distance and enter the desired label, including ' or ",
in the region text labile entry. You have the option of arrows at
each end of the line.</p>
</blockquote>
</blockquote>
<blockquote>
<p><b><a name="Printing" id="Printing"></a>Printing</b></p>
<blockquote>
<p><b>I can make some wonderful color images in DS9 and save them
as postscript files that look great, but often when I print them
they appear washed out or very different than they do on the
screen. My question then is what, if anything, can I do about
this?</b></p>
<p>The problem is that you create an image on a display, which is
the product of RGB colors (red, green, and blue) and print
the image on a printer, which is the product of CMYK colors
(cyan, yellow, magenta, and black). Furthermore, every
monitor is different in how it will display a certain color, and
every printing technology is different in how well it will
reproduce that color. And finally, the translation between
RGB and CMYK is not symmetric, i.e. its not possible to
translate some colors back and forth.</p>
<p>It's possible to calibrate your monitor and your printer, to
create a translation matrix, to correct for problems outlined
above (in the Macintosh world, this is what ColorSync does).
The idea is to <i>apply</i> a gamma correction to the output of
DS9, so that it will print much more in line with what you
expect. To do this you'd need special software and hardware,
and its only valid for your monitor and your printer.</p>
<p>In summary, its not worth it. Especially in the case of
publication, such as ApJ, where you have no idea on what
printing technology will be used to reproduce your image. So
the only control you have is to calibrate your monitor and to
hope for the best.</p>
<p>However, there are some <i>rules of thumb</i> that might help.
First, printers have a very hard time with <i>blues</i> and
<i>purples</i>, as they tend to be washed out. Either avoid these
colors, or over compensate these colors. </p>
<p>ApJ has a good idea in that you send in both an electronic
version and a hard copy of your color image. That way, they can
manually adjust the printers to try to match your output.</p>
<p><i>NOTE: Even though ApJ requests images in CMYK, we recommend
RGB. From personal experience, if you send RGB, the printed results
will be closer to the original.</i></p>
<p><b>We used DS9 to generate 300 dpi CMYK eps figures, as per the
ApJ specifications, but the color scheme on our proofs is
wrong. In the proofs, the violet is washed out and looks
similar to the black, and the blue is not nearly as
intense.</b></p>
<p>There are two issues here: first, color printers are
notorious for failure to reproduce blues and purples correctly.
Second, not all colors in RGB space can be reproduced
correctly in CMYK space, blues being the prime example. Below is an
excerpt from an industry pamphlet:</p>
<blockquote>
<p><tt>Be aware that it is possible to see colors in RGB that you
can't make with CMYK. They are said to be "out of the CMYK color
gamut". What happens is that the RGB-to-CMYK translator just gets
as close as possible to the appearance of the original and that's
as good as it can be. It's something that everyone in the industry
puts up with. So it's best to select any colors you use for fonts
or other design elements in your layout using CMYK definitions
instead of RGB. That way, you will have a better idea of how they
will appear in your printed piece. Here's a common example: many
programs translate the 100% Blue in RGB into a somewhat
purple-looking color in CMYK. We recommend a CMYK value of
100-65-0-0 to get a nice clean blue.<font size=
"-1"><br></font></tt></p>
</blockquote>
<p>For this reason, you may wish to use the RGB color space or
colormaps without deep blues and purples, such as <tt>BB</tt> or
<tt>Heat.</tt></p>
</blockquote>
</blockquote>
<blockquote>
<p><b><a name="XPA" id="XPA"></a>XPA</b></p>
<blockquote>
<p><b>How can I use XPA to display from a client machine to DS9 on
a server machine?<br></b></p>
<p>Assuming you have direct IP reachability between the machines
(i.e. one host can successfully connect() to the other), XPA does
allow you to have an XPA-enabled server like DS9 on one machine and
a client on another. To make this work, you need to do two things
(let's assume DS9 is running on a machine called "server_host" and
you want to send xpa commands from "client_host"):<br></p>
<ol>
<li>The XPA server program (i.e. DS9) must allow the client host to
send XPA commands. Access can be permitted in one of two ways:<br>
<ol style="list-style-type: lower-alpha;">
<li>Send the XPA server an acl request by running xpaset on the
same host on which the server is running (i.e. on the
server_host):<br>
<br>
<span style="font-family: monospace;">% xpaset -p ds9 -acl
client_host +<br>
<br></span></li>
<li>For more permanent access, add permissions in ~acls.xpa:<br>
<br>
<span style="font-family: monospace;">% cat >
~/acls.xpa</span><br style="font-family: monospace;">
<span style="font-family: monospace;">DS9:ds9 client_host
+<br></span><br>
You can check the acls for an XPA server using xpaget:<br>
<br>
<span style="font-family: monospace;">% xpaget ds9
-acl<br></span><br></li>
</ol>
</li>
<li>On the client side, the client needs to communicate with the
xpansname server program on the server machine to find the XPA
server communication info. This also can be done in two ways:<br>
<ol style="list-style-type: lower-alpha;">
<li>use the -i [host] switch to override <span style=
"font-family: monospace;">XPA_NSINET</span> for this execution (The
default port is 14285):<br>
<span style="font-family: monospace;"><br>
% xpaget -i 'server_host:14285<span style=
"font-family: monospace;">' ds9</span></span><br>
<br></li>
<li>Set the <span style="font-family: monospace;">XPA_NSINET</span>
variable for more permanent selection of xpans on the server
host:<br>
<br>
<span style="font-family: monospace;">% setenv XPA_NSINET
'server_host:14285'</span><br></li>
</ol>
</li>
</ol>
<p>Once these two setup steps are performed, you should be able to
send commands to DS9 and receive data from DS9. You can look at the
<a href="http://hea-www.harvard.edu/saord/xpa/acl.html">xpaacl man
page</a> for more information.</p>
<p><b>I have a laptop, that most of the time, is connected to a
network. DS9 runs fine. However, when I'm not connected to a
network and I start DS9, it hangs. What's going on?</b></p>
<p> DS9 uses XPA for interprocess communication. When DS9
starts, XPA initializes itself. XPA uses either IP sockets or UNIX
sockets, based if your machine is configured to connect to the
internet. In the case where your machine is configured for the
internet, but you are not currently connected, XPA gets very
confused. So, you can define a shell variable, XPA_METHOD, that
tells XPA which method to use.</p>
<p>The following is from the XPA documentation:</p>
<blockquote>
<p><tt>Determines the socket connection method used by this session
of XPA. The choices are: inet (to use INET or Internet-based
sockets) and local (unix) (to use UNIX sockets). The default is
INET. Using the inet method will allow access from other machines
(subject to access controls) but using local will not. Local is
most useful for private access and when the machine in question is
not connected to the Internet</tt></p>
</blockquote>
<p>More information is available on XPA shell variables at:
<a href="http://hea-www.harvard.edu/RD/xpa/env.html">The XPA
Environment</a><br></p>
</blockquote>
</blockquote>
<blockquote>
<p><b><a name="VO" id="VO"></a>VO</b></p>
<blockquote>
<p><b>I can't connect to any of the virtual observatories. What do
I do now?</b></p>
<p>The DS9 help facility now contains a tutorial on how to
configure DS9 to by pass network firewalls. See <a href=
"ref/vo.html">Virtual Observatory Reference</a> for more
information.</p>
</blockquote>
</blockquote>
</body>
</html>
|
