1 | Duchamp version 1.1.8 (2009/??/??) |
---|
2 | ---------------------------------- |
---|
3 | |
---|
4 | Improvements: |
---|
5 | |
---|
6 | * The FDR method involves calculating how many pixels are |
---|
7 | correlated. This previously involved multiplying the beam area by 2, |
---|
8 | implying that 2 neighbouring channels were correlated. This factor |
---|
9 | is now a user-selectable parameter, so that if you know how many |
---|
10 | spectral channels should be correlated, you can set the parameter |
---|
11 | FDRnumCorChan and the FDR calculation will be done correctly. |
---|
12 | |
---|
13 | * Screen output now has more information on the growing threshold when |
---|
14 | the cube statistics are printed. |
---|
15 | |
---|
16 | |
---|
17 | Bug fixes: |
---|
18 | |
---|
19 | * The function that grows objects had a major bug, that stopped it |
---|
20 | working when flagAdjacent=false. This has been fixed and should work |
---|
21 | fine. |
---|
22 | |
---|
23 | * All calls to uint were changed to unsigned int, as some compilers |
---|
24 | had problems recognising that they were the same thing. |
---|
25 | |
---|
26 | * src/fitsHeader.cc was missing an include statement for stdlib.h, |
---|
27 | again causing some compilers to fail. |
---|
28 | |
---|
29 | |
---|
30 | Duchamp version 1.1.7 (2009/01/16) |
---|
31 | ---------------------------------- |
---|
32 | |
---|
33 | Improvements: |
---|
34 | |
---|
35 | * The mask file that can be created with flagMask can now specify |
---|
36 | which object a given detected pixel belongs to, by taking the object |
---|
37 | ID as its value. This applies if you set flagMaskWithObjectNum=true |
---|
38 | (it defaults to false, which means each detected pixel has the value |
---|
39 | 1). Non-detected pixels still have the value 0. |
---|
40 | |
---|
41 | * The names of the output FITS files are now able to be specified |
---|
42 | directly by input parameters. These will override the default names |
---|
43 | that Duchamp provides. |
---|
44 | |
---|
45 | * The Karma annotation file now specifies a font - previously it did |
---|
46 | not and so was at the mercy of whatever was specified in other |
---|
47 | annotation files being viewed at the same time. Please let me know |
---|
48 | if the font I've chosen (lucidasans-12) is not suitable. |
---|
49 | |
---|
50 | * The default flag, used in the absence of 'E', 'S' or 'N', is now '-' |
---|
51 | rather than blank. This will ensure that each column in the results |
---|
52 | file has something in it. |
---|
53 | |
---|
54 | * The configure script is somewhat more robust to non-standard |
---|
55 | systems, particularly when the X11 libraries are in unusual |
---|
56 | places. It can also deal with the slightly different way that |
---|
57 | wcslib-4.3 installs itself. |
---|
58 | |
---|
59 | * The installation part of the Makefile was altered so that the |
---|
60 | symbolic link Duchamp that points to Duchamp-1.1.7 does not have the |
---|
61 | absolute path encoded in it. This will enable the files to be moved |
---|
62 | around at a later date. |
---|
63 | |
---|
64 | Bug Fixes: |
---|
65 | |
---|
66 | * Fixed a bug that caused problems when the flux units were less than |
---|
67 | 5 characters long (e.g. 'K') |
---|
68 | |
---|
69 | * The new velocity width values were not getting proper headers in the |
---|
70 | VOTable output. This has been remedied. |
---|
71 | |
---|
72 | * Minor improvements to help non-pgplot use |
---|
73 | |
---|
74 | * Minor fix in WCS functionality. |
---|
75 | |
---|
76 | * Minor fixes to the FitsHeader class. |
---|
77 | |
---|
78 | * Improved FITS data reading, that doesn't require a nullarray |
---|
79 | array. This will reduce memory usage. |
---|
80 | |
---|
81 | * Improved subsection parsing, particularly for non-standard WCS |
---|
82 | systems. |
---|
83 | |
---|
84 | * Improving the memory allocation of the Cube class. |
---|
85 | |
---|
86 | * Fixed a bug that meant the growthThreshold values were sometimes |
---|
87 | being lost. |
---|
88 | |
---|
89 | * Improving the way the growing and merging is done, particularly in |
---|
90 | the case of non-adjacent merging. |
---|
91 | |
---|
92 | * Fixed a scaling bug in the GaussSmooth function. |
---|
93 | |
---|
94 | Other: |
---|
95 | |
---|
96 | * Numerous changes to the code that do not affect how Duchamp itself |
---|
97 | runs, but were necessary for code development with the Duchamp |
---|
98 | libraries (primarily as a part of the ASKAP code development). |
---|
99 | |
---|
100 | |
---|
101 | Duchamp version 1.1.6 (2008/09/08) |
---|
102 | ---------------------------------- |
---|
103 | |
---|
104 | New features: |
---|
105 | |
---|
106 | * The velocity widths can now be quoted in two additional ways: the |
---|
107 | full width at 50% of the peak flux (ie. the FWHM) and the full width |
---|
108 | at 20% of the peak flux (w_50 and w_20 respectively). The w_50 |
---|
109 | parameter is now quoted in the results printed to the screen |
---|
110 | (instead of w_VEL), but all three are written to the results file. |
---|
111 | |
---|
112 | * The facility now exists to bypass the searching step and go straight |
---|
113 | to the output stage using a list of previously detected objects. The |
---|
114 | list is extracted from a previously-created log file. The user can |
---|
115 | change the way the spectra are plotted (e.g. choose to plot |
---|
116 | integrated rather than peak spectra), and select a subset of the |
---|
117 | detected objects to be printed to individual postscript files. Use |
---|
118 | the input parameter usePrevious (set to true) to use this facility, |
---|
119 | and provide a list of objects using the objectList parameter |
---|
120 | (eg. 1,2,4,7-10,15) |
---|
121 | |
---|
122 | * A new parameter "growthThreshold" has been created, that goes with |
---|
123 | "threshold". If you manually specify a threshold, and you wish to |
---|
124 | grow detections, you need to manually specify a growthThreshold (in |
---|
125 | flux units). |
---|
126 | |
---|
127 | Bug fixes: |
---|
128 | |
---|
129 | * Cubes that do not have a spectral axis (such as Stokes cubes) were |
---|
130 | causing memory leaks and crashing, due to some assumptions of the |
---|
131 | existence of the spectral axis. These bugs have been fixed, so that |
---|
132 | Duchamp will run on such cubes, although the WCS transforms may not |
---|
133 | always work appropriately. Please let me know via bug reports of |
---|
134 | difficulties you encounter! |
---|
135 | |
---|
136 | * The growing function has had a few bugs fixed and is now more |
---|
137 | efficient. |
---|
138 | |
---|
139 | * The FDR method was previously overriding any manually-specified |
---|
140 | threshold. This has been fixed so that if the user specifies |
---|
141 | threshold=X, then the FDR method is not called. |
---|
142 | |
---|
143 | * Some undefined things were happening with textual output when no |
---|
144 | objects were detected. This has been fixed. |
---|
145 | |
---|
146 | * Memory leaks caused by FITS WCS irregularities have been fixed |
---|
147 | (specifically, if a FITS header had NAXIS=2 but more than two WCS |
---|
148 | axes were defined). |
---|
149 | |
---|
150 | |
---|
151 | |
---|
152 | Duchamp version 1.1.5 (2008/03/20) |
---|
153 | ---------------------------------- |
---|
154 | |
---|
155 | Bug fixes: |
---|
156 | * A major bug was discovered in the calculation of integrated |
---|
157 | fluxes. The flux was incorrectly being weighted by the spatial size |
---|
158 | of the detection, resulting in a (often considerable) overestimation |
---|
159 | of the integrated flux. This has been corrected. |
---|
160 | |
---|
161 | * The beam size calculation was also incorrect, being out by a factor |
---|
162 | of 1/ln(2). |
---|
163 | |
---|
164 | * The "make install" command previously failed to work properly if the |
---|
165 | library had not been created. This has been fixed so that the |
---|
166 | installation works even if there is no library file. |
---|
167 | |
---|
168 | New Features: |
---|
169 | * You can now provide a new flux unit string, so that the pixel fluxes |
---|
170 | will be converted to these new fluxes before any calculations are |
---|
171 | done. This is done with the newFluxUnits input parameter. The new |
---|
172 | units should be directly convertible from the old ones (given by the |
---|
173 | BUNIT header -- e.g. if BUNIT = Jy/beam, you can give newFluxUnits |
---|
174 | as mJy/beam, but not mJy). |
---|
175 | |
---|
176 | * You can now specify the precision used in the output files for flux, |
---|
177 | velocity and S/N ratio columns, via new input parameters precFlux, |
---|
178 | precVel and precSNR. These will apply to the VOTable output as well |
---|
179 | as the text table and information on the spectral plots. |
---|
180 | |
---|
181 | * The Karma annotation files previously provided just a circle at the |
---|
182 | spatial location of the detected object. You now have the option to |
---|
183 | draw a border around the detected pixels (in a similar manner to the |
---|
184 | PGPLOT moment maps). Karma does not do this perfectly, so the lines |
---|
185 | may not line up exactly with the pixel borders, so the option |
---|
186 | remains to keep using the circles. This is controlled by the |
---|
187 | parameter "annotationType", with possible options being "borders" |
---|
188 | (the default) or "circles". |
---|
189 | |
---|
190 | * There is a new function getMetadata() that loads the header and WCS |
---|
191 | data, but no pixel information. This is only of interest if you are |
---|
192 | doing code development with the Duchamp library -- it does not |
---|
193 | affect the running of Duchamp itself. |
---|
194 | |
---|
195 | Duchamp version 1.1.4 (2008/02/15) |
---|
196 | ---------------------------------- |
---|
197 | |
---|
198 | Most of the changes incorporated in this update result from ASKAP code |
---|
199 | development (that makes use of some of the Duchamp functionality), |
---|
200 | but do not actually affect the way Duchamp runs (other than, in a |
---|
201 | couple of cases, making it a bit faster). Changes that are |
---|
202 | relevant for regular users of Duchamp are as follows: |
---|
203 | |
---|
204 | * A new option has been made available (thanks to Mary Putman et al |
---|
205 | for the suggestion!) to save the spectra of all detected objects in |
---|
206 | a text file. This has the form of one column for the spectral |
---|
207 | coordinates and one column of fluxes for each object. This is |
---|
208 | enabled by the input parameters flagTextSpectra and spectraTextFile. |
---|
209 | |
---|
210 | * Slight changes to the output include he formatting of the way the |
---|
211 | detected objects are written to the log file. This meant the |
---|
212 | verification files were also updated. Also the cube statistics are |
---|
213 | not printed to the results file if a user threshold is specified (as |
---|
214 | they are not calculated!). |
---|
215 | |
---|
216 | * The determination of beam size has been made more reliable, as has |
---|
217 | the BUNIT determination. |
---|
218 | |
---|
219 | * Fixed a bug that meant source merging was not done for 2D images |
---|
220 | (not usually a problem, as the source-finding takes care of this, |
---|
221 | but came up in parallelisation development). |
---|
222 | |
---|
223 | Duchamp version 1.1.3 (2008/01/08) |
---|
224 | ---------------------------------- |
---|
225 | |
---|
226 | A minor update that just improves the build process. The location of |
---|
227 | the wcslib include files was not specified correctly, so that some |
---|
228 | machines were unable to find them. The configure script has been fixed |
---|
229 | so that the compilation should work in all cases. |
---|
230 | |
---|
231 | Some minor changes have also been made to the code in the PixelMap |
---|
232 | directory, and to param.cc, to fix warnings or errors that may appear |
---|
233 | in compilation. |
---|
234 | |
---|
235 | However, there are no changes to the actual workings of the code in |
---|
236 | this minor version, so if you have a working version of Duchamp 1.1.2 |
---|
237 | there is probably no reason to update. |
---|
238 | |
---|
239 | Duchamp version 1.1.2 (2007/12/07) |
---|
240 | ---------------------------------- |
---|
241 | |
---|
242 | Compilation: |
---|
243 | |
---|
244 | * The compilation had problems working correctly when the cfitsio and |
---|
245 | wcs libraries were not in standard locations. The configure script |
---|
246 | has been tweaked to make sure the libraries are found. |
---|
247 | |
---|
248 | * Problems with compiling in the absence of pgplot have been fixed, |
---|
249 | and it should now compile fine. |
---|
250 | |
---|
251 | * Improved the configure script for use with Mac OS X and gfortran. |
---|
252 | |
---|
253 | |
---|
254 | Bugfixing: |
---|
255 | |
---|
256 | * A major problem with the text-based output was fixed. The widths of |
---|
257 | the columns were not being calculated correctly, and were running |
---|
258 | together. This should no longer be the case. |
---|
259 | |
---|
260 | * There was a bug in the way Duchamp interpreted spectral axes, |
---|
261 | particularly AIPS types such as FELO-HEL, leading to incorrect |
---|
262 | scaling of the velocity axis. This has been fixed, so that |
---|
263 | non-standard types are now dealt with appropriately and the velocity |
---|
264 | scaling should be accurate. |
---|
265 | |
---|
266 | * Another bug meant the beam correction was always applied to the |
---|
267 | integrated spectra, regardless of whether the flux units involved |
---|
268 | the beam (e.g. Jy/beam). This has been fixed. Note that the values |
---|
269 | of the integrated flux presented in the results table were always |
---|
270 | calculated correctly. |
---|
271 | |
---|
272 | * Other minor changes to improve the speed and efficiency, especially |
---|
273 | of the merging code. |
---|
274 | |
---|
275 | New user parameters: |
---|
276 | |
---|
277 | * There is now the possibility to save a FITS file that contains a |
---|
278 | mask array, indicating where the detected objects are. This is |
---|
279 | governed by the flagOutputMask parameter. |
---|
280 | |
---|
281 | * The header information that is printed at the start of the results |
---|
282 | file -- that is, the list of parameters, the statistics of the cube, |
---|
283 | and the number of detections -- can now be written to a separate |
---|
284 | file. Set the flagSeparateHeader parameter to true or 1 and it will |
---|
285 | go to the file indicated by the headerFile parameter (the default is |
---|
286 | duchamp-Results.hdr). |
---|
287 | |
---|
288 | * A "scaleMax" parameter has been added, so that the wavelet |
---|
289 | reconstruction can include only a specified range of scales (for |
---|
290 | instance, if one wants to search just for narrow features such as |
---|
291 | absorption lines). |
---|
292 | |
---|
293 | * A "flagRobustStats" parameter has been added. This allows the user |
---|
294 | to elect to use robust statistics (median and median absolute |
---|
295 | deviation from the median) to estimate the noise parameters. If set |
---|
296 | to false, the mean and standard deviation will be used. The default |
---|
297 | value is true. |
---|
298 | |
---|
299 | New Feature: |
---|
300 | |
---|
301 | * When Duchamp is run on a 2D image (i.e. with no spectral output), it |
---|
302 | now produces a postscript file that shows information each |
---|
303 | individual source plus the image cutout of the source. This is |
---|
304 | similar to the spectral output file, but without the spectra. The |
---|
305 | filename is given by the spectraFile parameter. |
---|
306 | |
---|
307 | * Ability to save a FITS file containing a mask array, with pixel |
---|
308 | values of 1 for pixels in a detected object, and 0 elsewhere. |
---|
309 | |
---|
310 | |
---|
311 | Duchamp version 1.1.1 (2007/07/20) |
---|
312 | ------------------------------------ |
---|
313 | |
---|
314 | Minor update to the release, with just a few changes: |
---|
315 | |
---|
316 | * The verification script was generating diffs due to differences in |
---|
317 | the precision of some calculations when done on different machines. |
---|
318 | One of these was the integrated flux, and this has been corrected so |
---|
319 | that the same value should appear on all machines. |
---|
320 | The verification script has also changed so that just the number of |
---|
321 | sources and their positions are tested, as well as the |
---|
322 | logfiles. This should avoid the reporting of spurious differences. |
---|
323 | |
---|
324 | * The grey-scale used in the image cutouts (in the spectral plots) has |
---|
325 | been inverted. This makes it consistent with the scale used in the |
---|
326 | maps, and hopefully easier to see when printing. |
---|
327 | |
---|
328 | * The configure/make system has been altered to make it easier to |
---|
329 | install, and to specify different external libraries. In particular, |
---|
330 | it is now not necessary to have PGPLOT installed on your system to |
---|
331 | run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, |
---|
332 | just without any graphical output. Some source code needed to be |
---|
333 | restructured to make this work. Please read the README file, or the |
---|
334 | Installation appendix in the User's Guide, for complete details. |
---|
335 | |
---|
336 | * The time of completion is now written to the log file, so that the |
---|
337 | user can have some idea of how long the program took. |
---|
338 | |
---|
339 | |
---|
340 | Duchamp version 1.1 (2007/05/17) |
---|
341 | ------------------------------------ |
---|
342 | |
---|
343 | Changes made since the last numbered release: |
---|
344 | |
---|
345 | EFFICIENCY OF EXECUTION: |
---|
346 | |
---|
347 | * Major change to the way detections are stored. They are now recorded |
---|
348 | via run-length encoding in the x-y plane, and stored as collections |
---|
349 | of channel-maps. This improves the memory usage and the speed of |
---|
350 | execution (particularly for routines such as the merging |
---|
351 | routines). The memory usage has also been improved by changing the |
---|
352 | way the list of detected objects is stored. |
---|
353 | |
---|
354 | SMOOTHING: |
---|
355 | |
---|
356 | * Addition of ability to spatially smooth the cube before |
---|
357 | searching. This is done with a Gaussian kernel, the size and shape |
---|
358 | of which can be specified by the user, using the parameters kernMaj |
---|
359 | & kernMin (which are the FWHM for the major & minor axes -- if |
---|
360 | kernMin is not given it is assumed to match kernMaj) and kernPA (the |
---|
361 | position angle of the major axis). There is a new parameter |
---|
362 | smoothType that distinguishes this method from the spectral (Hanning) |
---|
363 | smoothing already in use. |
---|
364 | |
---|
365 | DETECTIONS: |
---|
366 | |
---|
367 | * Changed the way detection is done -- now only search in 2D images, |
---|
368 | keeping all detections (ie. no minimum-pixel requirement). This |
---|
369 | should be the same as doing both the 1D and 2D searches with the |
---|
370 | minimum pixel requirement in, but simpler. The rejection is done at |
---|
371 | the end after all the merging and growing has been done. This leads |
---|
372 | to a larger number of intermediate detections (ie. the number |
---|
373 | before merging), which may increase the run-time slightly, although |
---|
374 | this is offset by the changes to the efficiency (see above). |
---|
375 | |
---|
376 | * Increased the range over which objects can be grown to match the |
---|
377 | threshSpatial & threshVelocity parameters, as well as rejecting new |
---|
378 | pixels based on the BLANK and MW tests. |
---|
379 | |
---|
380 | INPUTS: |
---|
381 | |
---|
382 | * There has been a subtle change in the way BLANK pixels are dealt |
---|
383 | with. To enable trimming of BLANK pixels, users should use the new |
---|
384 | parameter flagTrim. The parameters flagBlankPix and blankPixVal are |
---|
385 | no longer accessible via the parameter file -- warning messages are |
---|
386 | given if they are provided in the parameter file. |
---|
387 | |
---|
388 | * Added ability to specify a statsec, so that the statistics are only |
---|
389 | calculated from a given subsection of the cube, rather than the full |
---|
390 | cube. |
---|
391 | |
---|
392 | * The subsections can also specify the ability to remove a border of n |
---|
393 | pixels from the edges of an axis (ie. n from the start and from the |
---|
394 | end) -- as requested in Trac ticket #5. |
---|
395 | |
---|
396 | * Changed the default value of the reconDim parameter from 3 to 1, and |
---|
397 | the default value of the flagATrous parameter to false. |
---|
398 | |
---|
399 | OUTPUTS: |
---|
400 | |
---|
401 | * The output now includes three different estimates of the "centre" of |
---|
402 | the detection: peak location, centroid (flux-weighted), or average. |
---|
403 | |
---|
404 | * Some slight improvements to the user feedback during execution. |
---|
405 | |
---|
406 | * Spectral output now includes the baseline, if one was fitted. The |
---|
407 | format of the plot headers is slightly changed, to stop information |
---|
408 | falling off the edge of the page. |
---|
409 | |
---|
410 | * Added command-line option -x to directly disable the PGPLOT X-window |
---|
411 | map plotting. This overrides the setting of flagXOutput in the |
---|
412 | parameter file. |
---|
413 | |
---|
414 | * Fallback spectral units (in case the FITS header fails to record |
---|
415 | them) changed to SPC, but code has been fixed so that any problem |
---|
416 | should be caught before this becomes an issue. |
---|
417 | |
---|
418 | BUGFIXES: |
---|
419 | |
---|
420 | * Fixed bug (Trac ticket #4) that meant the velocity units were not |
---|
421 | correctly dealt with. Duchamp should be more robust for different |
---|
422 | velocity axis setups now. |
---|
423 | |
---|
424 | * Fixed bug (ticket #9) with the VOTable output, where the tags were |
---|
425 | not closing. |
---|
426 | |
---|
427 | * Fixed a bug that meant the integrated fluxes were not calculated |
---|
428 | properly -- no allowance was made for the number of spatial |
---|
429 | pixels. This should also work properly for 2D images now as well. |
---|
430 | |
---|
431 | * Fixed minor bug in calculating the flux threshold from the p-value |
---|
432 | threshold when the FDR method is used. This did not affect the |
---|
433 | actual thresholding, merely the quoted flux threshold in the results |
---|
434 | file. Also, the MW channels are kept out of the p-value threshold |
---|
435 | determination if they are being flagged. |
---|
436 | |
---|
437 | |
---|
438 | |
---|
439 | Duchamp version 1.0.7 (2006/11/22) |
---|
440 | ---------------------------------- |
---|
441 | |
---|
442 | One new feature, and some improvements and bug-fixes. |
---|
443 | |
---|
444 | * The user can now elect to Hanning-smooth the spectral direction of |
---|
445 | the cube before the searching is done. This can be done instead of the |
---|
446 | wavelet reconstruction (although if both are selected, the |
---|
447 | reconstruction takes precendence). This functionality is switched on |
---|
448 | and off by the flagSmooth parameter, and the width of the Hanning |
---|
449 | kernel is governed by the hanningWidth parameter. |
---|
450 | |
---|
451 | * The smoothed array can also be written to a FITS file and read in at |
---|
452 | the start in the same manner as the reconstructed array. |
---|
453 | |
---|
454 | * Several improvements have been made to the memory |
---|
455 | management. Several memory leaks were fixed, and the memory usage of |
---|
456 | Duchamp is considerably less, which will be a help for running it on |
---|
457 | large cubes. The speed of some routines has also been improved, by |
---|
458 | removing unnecessarily repetitive loops. |
---|
459 | |
---|
460 | * The sorting routines have been changed, and should now be slightly quicker |
---|
461 | (and a bit more robust). |
---|
462 | |
---|
463 | * Enabled the scale bar (plotted on the 0th moment map in the spectral |
---|
464 | output file) to be able to deal with much finer spatial scales (as |
---|
465 | may be expected from VLBI data). |
---|
466 | |
---|
467 | * Other minor changes to code and presentation. |
---|
468 | |
---|
469 | |
---|
470 | Duchamp version 1.0.6 (2006/11/01) |
---|
471 | ---------------------------------- |
---|
472 | |
---|
473 | Some incremental improvements and changes to the code: |
---|
474 | |
---|
475 | * The statistics used for the detection are now calculated once for |
---|
476 | the entire cube, rather than being calculated separately for each |
---|
477 | channel map and spectrum. This results in a uniform threshold value |
---|
478 | across the entire cube. The way the statistics calculations are |
---|
479 | implemented in the code was changed, using a new statistics class. |
---|
480 | |
---|
481 | * This means we can report a peak signal-to-noise value for each |
---|
482 | detection. This is given in the text-based output, as well as in the |
---|
483 | summary information above the spectral output for each source. |
---|
484 | |
---|
485 | * The user can now elect not to have the moment map displayed in a |
---|
486 | PGPlot window, through the use of the new flagXOutput |
---|
487 | parameter. This should help in cases of running Duchamp on a dumb |
---|
488 | terminal (with no X-display capabilities), or as part of a batch |
---|
489 | script where the continual popping-up of the PGPlot window might |
---|
490 | become annoying. |
---|
491 | |
---|
492 | * There are different Flags reported for the case of an object lying on |
---|
493 | the spatial edge and spectral edge of the cube (E and S respectively). |
---|
494 | |
---|
495 | * A few minor bug fixes: |
---|
496 | - When providing a subsection, any axes with the range given by * |
---|
497 | had the pixel values offset incorrectly. This has been fixed. |
---|
498 | - Negative searches now correctly invert the reconstructed array |
---|
499 | when it is read in from a file. |
---|
500 | |
---|
501 | * Other minor changes to the code, to improve memory handling and |
---|
502 | remove redundant arrays and variables. |
---|
503 | |
---|
504 | |
---|
505 | Duchamp version 1.0.5 (2006/09/06) |
---|
506 | ---------------------------------- |
---|
507 | |
---|
508 | Since version 1.0, there have been a range of mostly minor |
---|
509 | changes. These are generally bug-fixes, thanks to feedback from a |
---|
510 | number of users, as well as a few extra features. |
---|
511 | |
---|
512 | Here is a summary of the changes since version 1.0: |
---|
513 | |
---|
514 | USER INTERFACE: |
---|
515 | |
---|
516 | * The user is now able to enter the value of flag parameters in the |
---|
517 | parameter file as strings, as well as integers (so one can enter |
---|
518 | true or 1 to give the same result). |
---|
519 | |
---|
520 | GRAPHICAL OUTPUT: |
---|
521 | |
---|
522 | * Added a new function that draws the edge of the blank region on the |
---|
523 | maps and image cutouts. There is a new flag parameter -- |
---|
524 | drawBlankEdges -- that controls the use of this function (the |
---|
525 | default is true). |
---|
526 | Also, the edge of the field is plotted on the image cutouts as a |
---|
527 | yellow line. This distinguishes it from the purple blank pixel |
---|
528 | dividing line. |
---|
529 | |
---|
530 | * The size of the tick mark in the image cutout (indicating the |
---|
531 | spatial scale of the image) is now adaptable, so that it shows the |
---|
532 | scale that best fits the image (ranging from 1 arcsec to 15 |
---|
533 | degrees). (This is a change from the previous standard length of 15 |
---|
534 | arcmin.) |
---|
535 | |
---|
536 | * The zoomed spectrum had its flux scale determined by all points in |
---|
537 | the zoom box,including those flagged by the Milky Way (MW) |
---|
538 | range. This has been fixed so that any MW channels will not affect |
---|
539 | the flux scaling, potentially improving the appearance of objects |
---|
540 | detected close in velocity to strong MW emission or absorption. |
---|
541 | |
---|
542 | * Improved Karma Annotation file output, so that files without good |
---|
543 | WCS are dealt with appropriately. |
---|
544 | |
---|
545 | TEXT-BASED OUTPUT: |
---|
546 | |
---|
547 | * The position resolution in the IAU-format names has been increased, |
---|
548 | so that distinct objects close to one another are more readily |
---|
549 | distinguished. Overlapping sources at different velocities may |
---|
550 | still have the same name, but this is a more general problem. |
---|
551 | |
---|
552 | * The presentation of the results in tabular format has been improved, |
---|
553 | so that the precision of faint sources is sufficient to show their |
---|
554 | flux, for instance, is not 0. This also applies to the information |
---|
555 | presented above the spectral plots. |
---|
556 | |
---|
557 | * Improved error and warning reporting, so that the formatting and |
---|
558 | presentation of information is clearer. |
---|
559 | |
---|
560 | FITS I/O RELATED: |
---|
561 | |
---|
562 | * The previous version was did not deal well with 4 (or greater) |
---|
563 | dimensions in the FITS file -- the memory allocation was badly done, |
---|
564 | and the axes needed to be in a particular order. This has been |
---|
565 | fixed, so that the FITS I/O routines can now handle any sized FITS |
---|
566 | file, with axes in any order (as long as there are two spatial and one |
---|
567 | spectral axes). |
---|
568 | |
---|
569 | * When the FITS file does not have a rest frequency defined, there is |
---|
570 | no way to transform the frequency axis into velocity. In this case, |
---|
571 | the spectral axis is left as frequency, and put into units of MHz. |
---|
572 | |
---|
573 | * If the beam size is not indicated by the FITS header (through the |
---|
574 | BMAJ and BMIN keywords), the user can manually specify the size |
---|
575 | through the parameter file (using parameter beamSize). |
---|
576 | |
---|
577 | * The FITS I/O routines make use of the command fits_file_exists. This |
---|
578 | was introduced into the CFITSIO package from version 2.5, so Duchamp |
---|
579 | will only work with this version or higher. Version 3+ is preferred. |
---|
580 | |
---|
581 | OTHER BUG-FIXING: |
---|
582 | |
---|
583 | * Several bugs related to the blank-pixels were dealt with. |
---|
584 | The correct values were not propagating through correctly, meaning |
---|
585 | that the default values were being used. Also, there was the |
---|
586 | potential for blank pixels to be detected when the FDR method was |
---|
587 | used. Finally, the image cutout displays occasionally did not |
---|
588 | obscure the blank pixels. All these problems should be fixed now. |
---|
589 | |
---|
590 | * The FDR setup routine was occasionally failing with a segmentation |
---|
591 | fault, due to it accessing unallocated memory. This has been fixed. |
---|
592 | |
---|
593 | * Fixed bugs that affected the way 2D images (rather than 3D cubes) |
---|
594 | were dealt with. The minChannels test failed when minChannels=0. |
---|
595 | |
---|
596 | * If there is no beam information in the FITS header, the user can now |
---|
597 | enter a beam size as a parameter. |
---|
598 | |
---|
599 | * Other minor fixes to the code, to improve its structure and |
---|
600 | robustness. |
---|
601 | |
---|
602 | |
---|
603 | Duchamp version 1.0 (2006/06/30) |
---|
604 | -------------------------------- |
---|
605 | |
---|
606 | The first full release version. |
---|
607 | |
---|
608 | Several major changes compared to previous version: |
---|
609 | |
---|
610 | * Incorporated a FitsHeader class, to keep track of header information |
---|
611 | (including WCS) from the FITS file. All units-related calculations |
---|
612 | are done with this class, such as conversion to velocity, and |
---|
613 | pixel-to-WCS conversion. The main advantage of this is improved |
---|
614 | speed of execution, more adaptable to different units, and improved |
---|
615 | code (easier for me!). |
---|
616 | |
---|
617 | * Able to select the dimensionality of the reconstruction, rather than |
---|
618 | just doing it in 3-D. |
---|
619 | |
---|
620 | * Robust text output, so that the columns are sized correctly given |
---|
621 | the data being written, and the relevant units (derived from the |
---|
622 | FITS header) are included in the output table. |
---|
623 | |
---|
624 | * Improved the way the reconstructed image is saved and read back in, |
---|
625 | with a better naming scheme and a better set of new FITS header |
---|
626 | keywords. The MW headers are now not written. |
---|
627 | |
---|
628 | Other, more minor changes include: |
---|
629 | |
---|
630 | * MW channels now not set to 0, but just ignored for searching |
---|
631 | purposes (and for the scaling of the spectral output -- they are |
---|
632 | plotted though and highlighted with a hashed box). |
---|
633 | |
---|
634 | * The scale bar in the moment map in the spectral output file has its |
---|
635 | length indicated. |
---|
636 | |
---|
637 | * Improved VOTable output, with more information about the way Duchamp |
---|
638 | was run. |
---|
639 | |
---|
640 | * Made sure all statistics calculations in the reconstruction are |
---|
641 | based on robust (ie. median) methods. |
---|
642 | |
---|
643 | Also moved to an autoconf based configure/make compilation, for ease of use. |
---|
644 | |
---|
645 | |
---|
646 | Duchamp version 0.9.2 (2006/06/27) |
---|
647 | -------------------------------- |
---|
648 | |
---|
649 | * Added the use of warning flags for detections: for either edge |
---|
650 | location or negative enclosed flux. |
---|
651 | |
---|
652 | * A new command line option added so that the user can specify a FITS |
---|
653 | file to be searched with the default parameters, rather than giving |
---|
654 | a full parameter file. |
---|
655 | |
---|
656 | * The scale bar on the moment cutout now works in general case, using |
---|
657 | an iterative process to get to the correct length. |
---|
658 | |
---|
659 | * RA axes are now done correctly on the full-scale maps. |
---|
660 | |
---|
661 | * Various coding fixes, improving the readability of the code, |
---|
662 | particularly regarding the declaration of temporary variables. |
---|
663 | |
---|
664 | * Changed the way the time of execution is called : now using time.h |
---|
665 | functions, rather than a system call. |
---|
666 | |
---|
667 | * Changed output in Detection/outputDetection.cc for the pixel |
---|
668 | information of detected objects (the info printed above the spectral |
---|
669 | plots) -- now print out number of voxels in object, and have |
---|
670 | improved the formatting a little. |
---|
671 | |
---|
672 | * Improved the functionality of saving the FITS file containing the |
---|
673 | reconstructed array. Added ability to save and read back in the MW |
---|
674 | parameters when saving a reconstructed cube (if a reconstructed cube |
---|
675 | has different MW range to that being considered, it would cause |
---|
676 | problems). ReadRecon now just returns a FAILURE and will reconstruct |
---|
677 | the cube anew. |
---|
678 | |
---|
679 | * Changed default value of flagGrowth to 0. |
---|
680 | |
---|
681 | |
---|
682 | |
---|
683 | Duchamp version 0.9 (2006/05/05) |
---|
684 | -------------------------------- |
---|
685 | |
---|
686 | First public release version. |
---|