User's guide - Astromatic.net
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1. Figure 9 Example of a STIFF XML metadata file displayed in the Firefox browser using the provided XSLT stylesheet 16 7 Hints for creating realistic deep sky colour images The main motivation for writing STIFF was to create vivid yet realistic images of the sky In the following we will leave aside purely aesthetic considerations to insist on a few simple basic principles that might help us reach that goal The first problem is obviously that even in the optical domain it is difficult to actually see the colours of resolved deep sky astronomical objects The colours of many HII regions and planetary nebulae can be seen through the eyepiece of large telescopes but for galaxies it is another story Their surface brightnesses are one to two orders of magnitude lower and remain mostly in the scotopic regime of the human vision The second difficulty is that the spectral response curves of astronomical imagers rarely match those of our cones Fortunately the colours of astronomical sources result essentially from a handful of well known physical phenomena the slope of a thermal or non thermal emission continuum emission absorption lines reddening and diffusion by molecules and cosmological redshift that will guide us on our way to represent multi channel data 7 1 Ordering of channels A first rule to make the physical interpretation of colours easier and consistent from a case to another will o2. 2004 remind us such problems can be circumvented by applying the addi tional non linear corrections only to the luminance part of the Red Green Blue RGB signal We simply define the luminance as _R G B Y 3 3 where R G and B are the red green and blue component values at a given pixel before any non linear transform is made to the signal By applying a gamma correction factor yy to the luminance only one will store in the output TIFF file the r g b values 1 y r x Erv a 4 1 7 g x Pr 5 B 1 7 T Sy 6 In STIFF yy is represented by the configuration parameter GAMMA_FAC which defaults to 1 0 By increasing GAMMA_FAC one can enhance low surface brightness features in the image without affecting the colours 6 3 Controlling the image dynamic range Despite the fact that as we have seen 8 bit images with a non linear intensity scale can record surface brightnesses with a dynamic range as high as 100dB it is generally preferable to restrict the intensity range in input by imposing a low and a high cut for pixel values STIFF can set these cuts semi automatically or manually for each channel colour component If one SThis definition is somewhat different from the one generally used in video when green is given much more weight 11 chooses manual mode MIN_TYPE MANUAL and MAX TYPE MANUAL the low Imin and high Imax cuts are directly set by the values of MIN_LEVEL and MAX_LEVEL respectively If MIN_T
3. a support forum The package is also directly available from the IAP anonymous FTP site at ftp ftp iap fr pub from users bertin stiff 4 3 Installation For systems that support RPM packages it is recommended to install the binary version of STIFF with the following command typed as root rpm U force nodeps stiff x x 1 y rpm where x is the version number and y the architecture i386 or x86 64 To install from the source package you must first uncompress and untar the archive gzip dc stiff x x tar gz tar xvf A new directory called stiff x x should now appear at the current position on your disk You should then just enter the directory and follow the instructions in the file called INSTALL 3Use the with tiff libdir and with tiff incdir options to specify the library and include paths if the libTIFF package has been installed at unusual locations 5 Using STIFF STIFF is run from the shell with the following syntax single channel mode stiff image c configuration file Parameter1 Value1 Parameter2 Value or in 3 channel mode stiff image_red image_green image_blue c configuration file Parameter1 Value1 Parameter2 Value2 The part enclosed within brackets is optional Any Parameter Value statement in the command line overrides the corresponding definition in the configuration file or any default value see below 5 1 The Configuration file Each time STIFF is
4. display using the libTIFF function TIFFReadTile This feature is used by e g the IIPIMAGE server Examples of results obtained on large astronomical images are shown on the AstrOmatic web site To generate a pyramidal TIFF file the IMAGE TYPE configuration parameter must be set to TIFF PYRAMID or if IMAGE_TYPE is left to AUTO the output file name must have the ptif exten sion Tile size is 256 pixels by default Although it is recommended to leave it at 256 it can be changed using the TILE_SIZE keyword PYRAMID_MINSIZE sets the minimum dimension s for the smallest image in the pyramid Shttp iipimage sourceforge net http astromatic net gallery 13 Figure 7 Depiction of a tiled four level image pyramid Orion nebula observed with the WIRCAM instrument picture credits CFHT C Marmo Terapix 6 6 Image compression Versions 2 x and above of STIFF support image compression In addition to no compression NONE the COMPRESSION_TYPE configuration parameter supports both lossless and lossy com pression schemes The supported lossless compression algorithms are LZW the default DEFLATE and ADOBE DEFLATE All three offer rather similar performance and the last two are merely there because of patent issues JPEG is a lossy compression scheme identical to that found in jpg images JPEG compression leads to much smaller files than lossless algorithms but it should be used sparingly in the as tronomical conte
5. run it looks for a configuration file If no configuration file is specified in the command line it is assumed to be called stiff conf and to reside in the current directory If no configuration file is found STIFF will use its own internal default configuration 5 1 1 Creating a configuration file STIFF can generate an ASCII dump of its internal default configuration using the d option By redirecting the standard output of STIFF to a file one creates a configuration file that can easily be modified afterward stiff d gt stiff conf A more extensive dump with less commonly used parameters can be generated by using the dd option 5 1 2 Format of the configuration file The format is ASCII There must be only one parameter set per line following the form Config parameter Value s Extra spaces or linefeeds are ignored Comments must begin with a 4 and end with a linefeed Values can be of different types strings can be enclosed between double quotes floats integers keywords or Boolean Y y or N n Some parameters accept zero or several values which must then be separated by commas Integers can be given as decimals in octal form preceded by digit 0 or in hexadecimal preceded by 0x The hexadecimal format is particularly convenient for writing multiplexed bit values such as binary masks Environment variables written as HOME or HOME are expanded It is possible to include spaces in a string
6. 1 2 a il g 1c 1999 2009 UdS CNRS Centre de Donnees astronomiques de Strasbourg 1sel 64 sre 32Mb Figure 8 STIFF colour image created with the COPY_HEADER option converted to JPEG with convert and displayed in ALADIN 6 0 with the SDSS catalogue in overlay Processing summary on 2010 01 29 at 17 03 57 Mozilla Firefox file Edit View History Bookmarks Tools Help re dee file disk2 stitf stift xml gt r Processing summary on 2010 Y O IORA has as STIFF 2 0 started on 2010 01 29 at 17 03 57 with 8 threads run time 1 h 26 min by user bertin from morpho iap fr in raid1 bertin Input image data 1 Fllename Identifier Size Background level ADU Minimum level ADU Maximum level ADU lwa_r fits w2 143 48848 48097 0 0139999 0 0128932 350 PERRAS W2 143 48848 48097 0 0076952 0 00712601 180 TS W2 143 48848 48097 0 00711048 0 00698401 40 Configuration File stiff conf l Command Line 4 home soft stiff IMAGE_TYPE TIFF PYRAMID w2_r fits w2_g fits w2_u fits PYRAMID MINSIZE 256 GANMA FAC 1 1 COLOUR_SAT 1 7 MAX TYPE MANUAL MAX LEVEL 350 180 40 MIN LEVEL 0 00001 SATUR LEVEL 10000 VMEM_DIR raid2 bertin COMPRESSION TYPE DEFLATE OUTFILE NAME w2_ugr ptif Warnings limited to the last 1000 4 Date Time Message j 2010 01 29 15 41 29 Very large TIFF file switching to BigTIFF format Done Fr OCU
7. 48dB to 100dB with 8 bits per pixel e quantization effects are reduced perceptually the perception of light intensities by the human eye is itself non linear and differences as small as 1 can be detected Storing light intensities linearly with only 256 shades of grey would bring visible banding in the darker parts of an image e the signal is often photon noise limited on astronomical images the standard deviation around the mean is proportional to the square root of the flux Hence storing the signal at the power of 1 7 gives a noise level close to constant over the pixel raster which is optimal for quantization e although CRT displays are now disappearing being progressively replaced by Liquid Crystal Displays LCDs the latters do also have a native close to 2 in the dark parts of images I x 1 cos p po however this is not the case for DLP plasma and OLED devices In practice several constraints with the display of real images perceptual contrast matching presence of ambient light signal to noise ratio limitations and colour space conversion issues have led engineers to alter the simple reverse law p I 7 and define instead a I fO lt I lt I p 2 LED INT b ELITE Equation 2 allows the transfer curve to have a finite slope close to 0 and the effective gamma to vary smoothly with brightness STIFF applies automatically a gamma correction compression to pixel values before stor ing the data t
8. IFF automatically switches the output file to BigTIFF format if the output file is likely to exceed the 2GB limit If BIGTIFF_TYPE is set to ALWAYS TIFF output files always use the BigTIFF variant regardless of file size If BIGTIFF_TYPE is set to NEVER output files stick to regular TIFF in all cases which may lead to errors if they are too large STIFF is able to manipulate input images even if their size far exceeds the machine s mem ory budget by doing memory mapping on temporary files These temporary files are used whenever the amount of memory required for processing exceeds the value of the MEM_MAX config uration parameter 1024 Mbytes by default and is less than VMEM MAX value 1048576 Mbytes by default that is 1Tbyte Temporary files are written to the directory path specified by the VMEM_DIR configuration parameter The default path for VMEM DIR is the current execution directory One should make sure that the disk system holding the VMEM_DIR path is fast and local to the processing machine 6 8 FITS header copy Setting COPY_HEADER to Y instructs STIFF to copy the first FITS image header to the output TIFF file under the ImageDescription tag The NAXIS CRPIXi CDELT and CDi j are auto matically updated to reflect geometric changes made to the image with the BINNING FLIP_TYPE or pyramidal tiling options Note that ImageMagick s convert tool propagates the header information of TIFF files written by S
9. Meaning of the MIN_LEVEL parameter QUANTILE MIN_LEVEL is taken as the lower quantile of the pixel histogram MANUAL MIN_LEVEL is directly interpreted as a pixel value GREYLEVEL MIN_LEVEL is interpreted as a grey level in the out put image a fraction of pure white 0 0 is pure black 1 0 is pure white NEGATIVE N Boolean Produces a negative image when set to Y NTHREADS O multithreaded version or 1 integer Number of threads processes to be used for parallel computations If NTHREADS is 0 the number of threads is automatically set to that of processor cores OUTFILE_NAME stiff tif string Output image file name PYRAMID_MINSIZE 256 integers 1 lt n lt 2 Minimum output image width and or height in pixels at the topmost pyramid level in TIFF PYRAMID IMAGE_TYPE mode SKY_LEVEL 0 0 floats 1 lt n lt Nima User specified sky level in SKY_TYPE MANUAL mode SKY_TYPE AUTO keywords 1 lt n lt Nima Sky level determination in each input image AUTO Sky level is automatically determined from the pixel data MANUAL Sky level is taken from the SKY LEVEL value SATUR_LEVEL 40000 0 floats 1 lt n lt Nima Input image saturation level colour is set to white if one of the images exceeds that level TILE_SIZE 256 integer Tile size in TIFF PYRAMID IMAGE_TYPE mode VERBOSE_TYPE NORMAL keyword Degree of verbosity on screen QUIET No Output besides warnings and error messages NORMAL Normal display with messages up
10. Ordering of channels 17 1 2 Colour balance colas du hand due moine dd Pe ap ap an b 17 7 3 The sky background os oa 65 ua orn woe AE aa ee a ee a 17 8 Examples 18 9 Troubleshooting 10 Acknowledgements 19 19 iii 1 What is STIFF STIFF is a program that converts scientific FITS images to the more popular TIFF format for illustration purposes The main features of STIFF are e Accurate reproduction of the original surface brightnesses and colours e Automatic or manual contrast and brightness adjustments e Automatic sky background intensity and colour balance e Adjustable colour saturation e Colour friendly gamma correction capabilities e One or three input channels gray scale or true colour output e Output with 8 or 16 bits per component e Pixel rebinning and x y flip options e Support for arbitrarily large input and output images on standard hardware BigTIFF support e Support for tiled multiresolution pyramids e Support for lossless and lossy compression methods e Multi threaded code with load balancing to take advantage of multiple cores and proces sors e XML VOTable compliant output of meta data 2 Skeptical Sam s questions Skeptical Sam doesn t have time to test software extensively but is always keen on asking agressive questions to the author to find out if a program could fit his needs S Sam I don t understand the purpose of this software The
11. STIFF V2 2 User s guide E BERTIN Institut d Astrophysique de Paris November 10 2011 Contents 1 What is STIFF 1 2 Skeptical Sam s questions 1 3 License 2 4 Installing the software 3 4 1 Software and hardware requirements 3 4 27 Obtaining TIE E wy soe oo a Gone wa A AU iS Sse A 3 AS Installationy ii dace ments Bee a aida 3 5 Using STIFF 4 5 1 The Configuration file 4 5 1 1 Creating a configuration file 4 5 1 2 Format of the configuration file 4 5 1 3 Configuration parameter list 4 6 How STIFF works 7 6 1 Overview of the software 7 6 2 Gamma corrections tia pu Panne ac wee a get A Palais a Ban ale 8 6 2 1 Gamma compensation 8 6 2 2 Colour friendly gamma corrections 10 6 3 Controlling the image dynamic range 11 6 4 Creating colour images a 12 6 5 Multi resolution pyramids 13 6 6 Image compression 14 6 7 Very large images and memory handling 14 6 8 FITS header copys 45 6 pad ein ache ee pe ow REA RUN Rance Gach fente 15 6 9 _XME outputl 2 2 one nie te nn RE ed i tie Ride amet daa 15 7 Hints for creating realistic deep sky colour images 17 7 1
12. TIFF while converting to JPEG format The resulting JPEG colour images can be loaded in the Aladin visualisation software Fernique et al 2009 which will automatically take advantage of the World Coordinate System information copied from the original FITS header if present Fig 8 6 9 XML output An XML file providing a processing summary and various statistics in VOTable format is written if the WRITE_XML switch is set to Y the default The XML_NAME parameter can be used to change the default file name stiff xml The XML file can be displayed with any recent web browser the XSLT stylesheet installed together with STIFF will automatically translate it into a dynamic user friendly web page Fig 9 For more advanced usages e g access from a remote web server alternative XSLT translation URLs may be specified using the XSL_URL configuration parameter nttp www awaresystems be imaging tiff bigtiff html nttp www imagemagick org nttp aladin u strasbg fr 13See http www astromatic net 2009 10 05 understanding astromatic metadata files for more details and hints on how to use XML metadata files 15 Aladin v6 0 File Edit Image Catalog Overlay Tool View Interop Heip a ES gt Zoom 2x 44 sf mis Search Oye z mi ci SDSS m_SDSS zs RAJ2000 DEJ2000 ObsDate O 1 3 J141831 0 08151 18 210 16 743 16 027 15 675 15 392 214 629305 52 894367 2003 188
13. YPE and or MAX_TYPE are set to QUANTILE MIN_LEVEL and or MAX_LEVEL are interpreted as quantiles between 0 0 and 1 0 of the histogram of pixel values This is the default for MAX_TYPE There is a third mode specific to MIN_TYPE called GREYLEVEL In that mode the lower cut Imin is automatically adjusted to have the sky background reach a given apparent grey level Pgrey specified by MIN_LEVEL as a fraction of full white in the TIFF image This is the default mode for MIN_TYPE with a default MIN_LEVEL of Pgrey 0 001 a very dark grey The gamma correction factor is taken into account Perey Imax z Imin Hence y I sky Derey Imax Des Petey 8 Imin Note that the default Perey 0 001 corresponds roughly to the decimal 8 bit pixel value 11 for a power law gamma of 2 2 3 for an sRGB gamma correction and only 1 for a Rec 709 gamma correction The sky background intensity x is estimated automatically from the input image s by STIFF when SKY_TYPE is set to AUTO which is the default Note that this estimation is rather crude it is the median of the histogram of pixel values Therefore it is sometimes better to switch to manual grey level mode SKY_TYPE MANUAL for which the sky background level is directly read from SKY_LEVEL 6 4 Creating colour images STIFF can generate a composite RGB TIFF image from 3 co aligned FITS images obtained in different channels The 3 images must have the same number of pixels in each di
14. be displayed in a totally dark environment e g for the big screen Note that when GAMMA_TYPE is set to REC 709 the intensity mapping follows the Rec BT 709 coding black at 16 and reference white at 235 for an 8 bit output Figure 4 Deep sky colour images generated by STIFF using three different GAMMA_TYPEs From left to right POWER LAW SRGB and REC 709 6 2 2 Colour friendly gamma corrections In some cases one may want to enhance or reduce the contribution of low surface brightnesses to the final image without saturating brighter regions For this a non linear transformation has to be applied and modifying the gamma correction is the easiest way to achieve this Increasing or decreasing y will compress or expand the contrast scale respectively Although this works 10 fine with monochromatic images it affects colours on multi channel images Fig 5 shows using a simulation the effect of increasing y to enhance the extended wings of a galaxy profile here as no background light is present the consequence is only a desaturation of the colours When several components of various colours are superimposed significant shifts in colour can occur Figure 5 A simulated colour image of an early type galaxy converted in TIFF by STIFF Left original gamma of 2 2 Middle using a gamma of 3 3 affects the colour saturation Right applying a gamma correction factor of 1 5 to luminance only preserves colour rendition As Lupton et al
15. bviously be to let the red component represent the largest effective wavelengths and the blue one the shortest wavelengths 7 2 Colour balance Away from nebular and HII regions the light from point sources and galaxies is largely dom inated by continuum emission in the near optical domain Despite the fact that the spectral responses of the observation filters do not match those of our cones we might want at least to have the colours of regular unreddened stars to fall roughly on the blackbody track in a CIE diagram Fig 10 That is from red orange to white blue in particular green stars or galax ies are seldom observed Experience shows that this is quite easy to achieve for contiguous broadband filters in the optical near IR after adjusting 2 of the 3 MAX_LEVELs 7 3 The sky background Although this is not realistic it is strongly advised to use a dark neutral grey colour for the sky background actually the real night sky from the ground or in orbit around the earth is redder than the sun in the visible see Leinert et al 1998 This is what automatically done with the MIN_TYPE GREYLEVEL option the default A dark grey sky does not affect too much the perception of object colours and prevents the faintest objets from disappearing in a completely black background The intensity of the dark grey is set by default to MIN_ LEVEL 0 001 that is 0 1 of full white a good value for a high contrast display screen For print outs one
16. by enclosing the string in double quotes 5 1 3 Configuration parameter list Here is a list of all the parameters known to STIFF Please refer to next section for a detailed description of their meaning Advanced parameters are indicated with an asterisk They must be used with caution and may be re scoped or removed in future versions BIGTIFF_TYPE NONE keyword BigTIFF support policy AUTO Automatically switch to BigTIFF format for very large files if the TIFF library supports it NEVER Never use BigTIFF format and stick to basic TIFF in all cases ALWAYS Always use BigTIFF if the TIFF library offers BigTIFF support even for small files BINNING 1 integers 1 lt n lt 2 Pixel binning factor for both axes or along each axis BITS_PER_CHANNEL 8 integer 8 or 16 Number of bits per channel in the output image COMPRESSION_QUALITY 90 integer Quality factor between 0 and 100 for lossy compression algorithms Smaller numbers lead to a smaller file size but more prominent compression artifacts COMPRESSION_TYPE LZW keyword Image compression algorithm used in the TIFF file NONE No compression LZW Lempel Ziv Welsh lossless algorithm JPEG JPEG lossy algorithm DEFLATE Deflate lossless algorithm ADOBE DEFLATE Adobe deflate lossless algorithm COLOUR_SAT 1 0 float Colour saturation factor COPY_HEADER N Boolean when set to Y a copy of the first FITS image header replaces the content of the ImageDescription tag i
17. dated in real time using ASCII escapes sequences FULL Everything VMEM_DIR string Path of the directory where temporary files are written VMEM_MAX 1048576 integer Maximum amount of virtual memory disk space in the VMEM_DIR directory that can be used for processing WRITE_XML Y Boolean If true Y an XML summary file will be written after completing the processing XML_NAME stiff xml string File name for the XML output of STIFF XSL_URL string URL of an XSL style sheet for the XML output of STIFF This URL will appear in the href attribute of the style sheet tag 6 How STIFF works 6 1 Overview of the software Basically the action of STIFF can be summarized as reading one monochromatic case or three colour case one for each of the primary colours respectively red green and blue input FITS images and saving a grayscale or colour TIFF image to disk The work is done in two passes through the data 1 Input images are examined a histogram of pixel values is constructed from which statistics are derived for the automatic determination of the low and high cuts in dynamic range 2 The images are actually processed and converted to TIFF format The global layout of STIFF is presented in Fig 2 Let us now describe in details the processing of STIFF and how to control it Figure 2 Global Layout of STIFF 6 2 Gamma corrections 6 2 1 Gamma compensation The true light intensity I or more formally ra
18. diant emittance radiated or reflected by a properly adjusted display device is related to the pixel value p stored in the computer s frame buffer through the power law I p 1 where y is what we will call the gamma This operation is sometimes called gamma ex pansion The display gamma is nowadays generally assumed to have an average value of 2 2 although in practice it may roughly vary from 1 7 to 2 5 A reverse transform sometimes called gamma compression must therefore be applied before writing an image in GIF JPEG PNG or TIFF format This also applies to other electronic image and video storage formats including analog ones like Laserdiscs and VHS video tapes The reason behind this non linear relation between light intensity and voltage comes from the times when Cathode Ray Tubes CRTs were ruling the world of electronic imaging CRT screens have a natural response function I x p which has to be at least partially compensated for before being transmitted or stored This non linear transformation has many advantages More information on the issues related to gamma corrections can be found on the web see e g http www cgsd com papers gamma html http www normankoren com makingfineprints1A html http www poynton com GammaFAQ html or http www marcelpatek com gamma html e the recordable intensity range between the darkest and the brightest parts of an image is effectively increased from
19. een developed on Unix machines GNU Linux and should compile on any POSIX compliant system provided that the following libraries packages have been installed e LIBTIFF V3 6 and above http www libtiff org e LIBJPEG V6 0 and above http www ijg org e ZLIB V1 2 and above http www zlib net All these libraries generally come installed with regular Linux distributions Users requiring BigTIFF support for very large images larger than about 1 Gpixel however will need to upgrade to LIBTIFF version 4 0 in beta stage as of January 2010 Note that a 64 bit system is required for processing images as large in STIFF The software is run in ANSI text mode from a shell The amount of memory required depends mostly on the size of the input images in most cases physical memory requirements are well below 100 megabytes A large fraction of the program is parallelised and will take advantage of multiple processor cores Performance is also heavily dependent on the sequential disk read write speed it is recommended to operate STIFF with files located on a fast storage system such as a local RAID array and avoid network based file systems 4 2 Obtaining STIFF The easiest way to obtain STIFF is to download it from the official AstrOmatic web site http astromatic net software stiff There can be found the latest versions of the package as standard tar gz and binary RPM archives documentation development reposito ries and
20. handled automatically by software that supports advanced colour management The sRGB correction may however be useful for illustration purposes when the image is to be displayed on a dark background or when the sky pixel values are very noisy Rec BT 709 is to be reserved for http www itu int rec R REC BT 709 E I T T I T T T T T I T T T T T a TTIT T T Tru T T rrr T T TTTTTT 250 H 1 y 0 45 power law 4 1 1 y 0 45 power law _ gRGB Fo sRGB 1 200 L Rec 709 a x L ds A J Rec 709 0 1 F 150 H a E J 5 F F 2 o J C fav Fry trie TT LES Es L 4 x F IL J 4 a E 4 100 H E F J A e Y E 274 0 01 H 7 4 a To E J E J J C Al 50 e 7 4 Pele bees 1 L F ae J L O 0 005 0 01 4 aa F I 3 0 001 4 O Pr E 1 C L L L L L L L L L L L L L L E nul L L rl L Lil L L toil J 0 0 2 0 4 0 6 0 8 1 0 001 0 01 0 1 1 I I Figure 3 Three types of gamma compression performed by STIFF Left encoded pixel values for an 8 bit image vs relative original image intensity black curve continuous GAMMA_TYPE POWER LAW red short dashes GAMMA TYPE SRGB green long dashes GAMMA TYPE REC 709 Note the important difference at low intensities insert Right Comparison between the end to end transfer curves assuming a 2 2 display gamma and a minimum black level at 0 1 of full white movies intended to
21. iguration parameter s Note that this does not prevent pixels with values exceeding Fmax in one channel or more to appear shifted in colour in the output image for instance the core of some bright orange star may appear slightly yellowish Figure 6 A three channel deep sky image converted to TIFF RGB by STIFF with 4 different values of COLOUR_SAT From left to right 0 0 1 0 2 0 and 4 0 Note the CCD saturation artifacts on top of bright stars 6 5 Multi resolution pyramids Some astronomical wide field images are both very large and extremely detailed to the point that a regular display will not do justice to them unless they get printed on posters with gigantic proportions One way to improve the visual experience with a very detailed image is to allow the user to navigate quickly through it as in web applications like GOOGLE MAPSTM These web applications require images to be stored in tiles at multiple resolutions like a pyramid of tiled images Fig 7 The TIFF format allows the raster of pixels to be organised in tiles and several images to be stored in a single file This makes it the ideal format to store a large image at multiple resolutions STIFF offers the possibility to generate automatically in the same TIFF file different versions of the image rebinned at octave intervals and organised in tiles of arbitrary size The position of each tile is indexed in the TIFF header so that it can be accessed directly for
22. m num 1 f close 9 Troubleshooting I have trouble to properly adjust the contrast and brightness of large mosaic images in MIN_TYPE QUANTILE mode Because of memory constraints for large frames the quantile is not computed on all the pixels at once The quantile algorithm in STIFF may be confused if in addition a large fraction of pixels is set to constant values because of gaps image margins or overscans Currently the best solution is then to return to MIN_TYPE MANUAL mode 10 Acknowledgements Many thanks to the TERAPIX crew for early testing to Henry Joy McCracken for proof reading an early version of this documentation to Jean Mouette at IAP for checks on his calibrated monitor to Rodolfo Barba for suggesting the header copy mechanism and Emmanuel Pietriga for help with debugging the Mac OS X version References 1 Bertin E 1999 SExtractor 2 1 User s manual AP 2 Fernique P Boch T Bonnarel F 2009 Astronomical Data Analysis Software and Systems XVII ASP Conference Series 411 559 3 Leinert C et al 1998 A ApS 127 1 4 Lupton R et al 2004 PASP 116 133 5 Stokes M Anderson M Chandrasekar S Motta R 1996 http www color org SsRGB xalter 19
23. may prefer a slightly higher value since many printers have a tendancy to bury low surface brightnesses in dark backgrounds 17 Figure 10 CIE chromaticity diagram source Wikimedia Commons The dark line is the track followed by a blackbody with increasing temperature from right to left 8 Examples Example 1 The following command was used to generate one of the colour image pyramids which can be seen at http astromatic net gallery stiff IMAGE TYPE TIFF PYRAMID di_i fits di_r fits di_g fits GAMMA FAC 1 1 COLOUR_SAT 2 2 MAX_TYPE MANUAL MAX_LEVEL 550 350 160 MIN_LEVEL 0 00001 SATUR_LEVEL 10000 COMPRESSION TYPE DEFLATE OUTFILE NAME di gri ptif Example 2 The following Python script generates a small 64x64 pixel TIFF image of each detection at the coordinates read in columns 1 and 2 of the ASCII file whose filename is given as second argument usr bin env python import sys re os if len sys argv lt 2 print Syntax sys argv 0 lt image gt lt catalog gt sys exit sys argv 1 cat sys argv 2 f open cat num 1 for line in f readlines if line 0 col float split for split in re split st line 0 1 alpha col 0 delta col 1 os system swarp VERBOSE TYPE QUIET RESAMPLE N IMAGE_SIZE 64 CENTER_TYPE MANUAL CENTER 10f ima 18 alpha 10f delta ima os system stiff VERBOSE_ TYPE QUIET coadd fits OUTFILE_NAME obj_ 06d tif nu
24. mension If the data are properly astrometered but not aligned you might want to pass them through SWarp first Without further processing the colours obtained from images observed with broadband optical filters often look dull and disappointing STIFF offers the possibility to increase the colour saturation of images while maintaining their luminance and global white balance To this aim we introduce an additional parameter that linearly replaces each R G B input triplet with R G B such that R G a R G 9 G B a G B 10 R G B R G B 11 from which we obtain 2R G B R p ii E 12 2G R B 15 Thttp astromatic net software swarp 12 a is represented in STIFF by the COLOUR_SAT configuration parameter COLOUR_SAT acts exactly like the saturation knob of a colour TV if COLOUR_SAT is set to 0 the 3 channels are combined to form a black and white greyscale image a COLOUR SAT of 1 0 the default lets the input colour saturation unaffected while a COLOUR_SAT above 1 0 exaggerates the colours Fig 6 shows the impact of various COLOUR_SAT settings on a deep sky colour image For images observed in contiguous channels a COLOUR_SAT of 2 0 generally gives best results To avoid funny looking artifacts showing up with high COLOUR_SATs for very bright objets a per channel clipping is applied to saturated pixels prior to exaggerating the colours the saturation level is defined by the SATUR_LEVEL conf
25. n the output TIFF file COPYRIGHT AstrOmatic net string Copyright author string to include in the output TIFF image header Copyright tag DESCRIPTION STIFF image string Description string to include in the output TIFF image header ImageDescription tag FLIP_TYPE NONE keyword Flip the image NONE No flipping X about the X axis Y about the Y axis XY about both the X and Y axes GAMMA 2 2 float Image gamma exponent of the display intensity transfer curve for POWER LAW GAMMA_TYPEs GAMMA_FAC 1 0 float gamma correction factor for the luminance image component GAMMA_TYPE POWER LAW keyword Gamma correction POWER LAW pure power law SRGB SRGB standard gamma correction REC 709 ITU R recommendation BT 709 HDTV stan dard gamma correction IMAGE TYPE TIFF keyword Output image format AUTO based on filename extension TIFF TIFF image format scanline TIFF pyramid TIFF pyramid tiled MAX LEVEL 0 995 floats 1 lt Nn lt Nima Upper end of image dynamic range see MAX_TYPE MAX_TYPE QUANTILE keywords 1 lt n lt Nima Meaning of the MAX LEVEL parameter QUANTILE MAX_LEVEL is taken as the upper quantile of the pixel histogram MANUAL MAX LEVEL is directly interpreted as a pixel value MEM_MAX 1024 integer Maximum amount of physical memory that can be used for processing MIN_LEVEL 0 001 floats 1 lt n lt Nima Lower end of image dynamic range see MIN TYPE MIN_TYPE GREYLEVEL keywords 1 lt n lt Nima
26. nt details on the rightmost image On the left image on the contrary most of the faint stuff is missed This is because the aforementioned standard software ignores the non linear behaviour of your display Figure 1 The same 3 R G and B deep sky images processed by a regular FITS image converter left and STIFF right using the same intensity cuts S Sam Well within many image viewers you are generally afforded a choice of non linear transformations to apply in order to make the faint stuff stand out more clearly in the images Author Sure but with the limited selection of choices you are given colours will not be accurately rendered and some manual tweaking will be necessary The purpose of STIFF is to produce beautiful pictures in an automatic and consistent way 3 License STIFF is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version STIFF is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MER CHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Pub lic License for more details You should have received a copy of the GNU General Public License along with STIFF If not see http www gnu org licenses 4 Installing the software 4 1 Software and hardware requirements STIFF has b
27. o TIFF The GAMMA_ TYPE configuration parameter lets the user choose between three types of gamma corrections a pure power law with a user selected y and b 0 POWER LAW the default the sRGB standard gamma correction with y 2 4 a 12 92 b 0 055 and J 0 00304 SRGB and the ITU R rec BT 709 gamma correction with y 2 22 a 4 5 b 0 099 and J 0 018 REC 709 In pure power law mode y may be modified by using the GAMMA configuration parameter The defaut value is 2 2 It is usually not recommended to change it especially for colour images use GAMMA_FAC instead see 6 2 2 The sRGB correction Stokes et al 1996 has been optimized for displays in the office environment and is the default standard for images displayed on the web The ITU R rec BT 709 is the standard for HDTV media The three types of gamma compensation are shown in Fig 3 as well as the end to end transfer curves in viewing conditions typical of a computer LCD monitor watched in a dark environment Figure 4 shows images generated by STIFF using the three different GAMMA_TYPEs The sRGB curve and even more notably the Rec 709 curve have both a tendency to bury much of the dark tones of the image into a black background It is advised to stick to the pure power law transfer curve for scientific or general use as STIFF images currently lack the TIFF metadata with the proper transformation tables that would make sRGB and rec BT 709 corrections
28. re seem to be already a lot of convenient FITS viewers and batch converters available out there Author Yes but most of them do not do the best job at converting FITS image data to 8 bits It is often said that 8 bit images stored in JPEG PNG or TIFF files are unable to cope with the high dynamic range of 16 bits CCD images from the professional astronomy world This is not entirely true actually perceptually they even offer a larger contrast because in these 8 bit file formats the intensities are implicitely stored in a non linear way But strangely most current FITS image viewers and converters seem to ignore this fact which leads to an inconsistent translation of the FITS image content by simply rescaling linearly input pixel values A first consequence is that the people working on astronomical images usually have to apply narrow intensity cuts or square root or logarithmic intensity transformations to actually see something on their deep sky images A less obvious consequence is that colours obtained by combining images processed this way are not consistent across such a large range of surface brightnesses lhttp fits gsfc nasa gov e g http wuw awaresystems be imaging tiff html The picture below shows the same 3 FITS images passed through a standard FITS image converter and STIFF The same cuts in surface brightness were applied If your display or printer is properly calibrated you should be able to distinguish most of the fai
29. xt deep sky astronomical images generally exhibit a low signal to noise ratio per pixel Noise which is generally close to white does not compress very well and eats up precious bits in the output code which may lead to obvious artifacts The level of JPEG com pression can be adjusted with the COMPRESSION_QUALITY configuration parameter in quality percentage the higher the parameter the more faithful to the original the result at the price of a larger file size The default for COMPRESSION QUALITY is 90 which would be considered a fairly high value for everyday images but which appears to be the right compromise for most astronomical images 6 7 Very large images and memory handling On 64 bit systems STIFF can manage images with very large sizes up to a few terapixels both in input and output The original TIFF format has itself a file size limit of 2 to 4 Gbytes which is roughly equivalent to a 1 Gpixel image To handle larger output images STIFF must rely on 14 the BigTIFF modification to the TIFF format BigTIFF is implemented in version 4 0 of the LIBTIFF library which is only available in beta form but otherwise perfectly functional as of January 2010 Note that the binary version of the STIFF package comes linked with LIBTIFF v4 0 The BIGTIFF_TYPE configuration parameter sets the policy regarding BigTIFF usage STIFF must have been linked with LIBTIFF version 4 0 or above In AUTO mode the default ST
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