# CRUSH

Author: Attila Kovacs <attila[AT]sigmyne.com>  
Last updated: 12 July 2019


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#### Table of Contents

1. __Getting Started__
    - 1.1. Installation
    - 1.2. (optional) Java Runtime Configuration
    - 1.3. CRUSH Pipeline Configuration
    - 1.4. The Tools of the CRUSH Suite
    - 1.5 Quick Start
    - 1.6 A Brief Description of What CRUSH Does and How...
    - 1.7 Command-line Options and Scripting Support
    - 1.8 Making Sense of the Console Output
    - 1.9 Examples

2. __Advanced Topics__
    - 2.1 Pointing Corrections
    - 2.2 Pixelization and Smoothing
    - 2.3 Recovery of Extended Emission
    - 2.4 Filtering corrections, transfer functions, etc.
    - 2.5 Image Processing Post-Reduction
    - 2.6 Reducing Very Large Datasets (to do...)

3. __Advanced Configuration__
    - 3.1 Commands
    - 3.2 Pipeline Configuration
    - 3.3 Source (Map) Configuration
    - 3.4 Scan Configuration
    - 3.5 Instrument Configuration
    - 3.6 Advanced startup environment and Java configuration

4. __Correlated Signals__ 
    - 4.1 Modes and Modalities
    - 4.2 Removing Correlated Signals
    - 4.3 User-defined Modalities

5. __Custom Logging Support__
    - 5.1 Log Files and Versioning
    - 5.2 Decimal Formatting of Values
    - 5.3 Loggable Quantities

6. __Supported Cameras__

7. __Future Developments (A Wish List...)__
    - 7.1 Support for Heterodyne Receivers and Interferometry
    - 7.2 Interactive Reductions
    - 7.3 Distributed and GPU Computing
    - 7.4 Graphical User-Interface (GUI)

8. __Further information__


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## 1. Getting Started

CRUSH-2 is a reduction and imaging package for various astronomical imaging
arrays. Version 2 provides a unified platform for reducing data from
virtually any fast-sampling scanning camera. 



### 1.1. Installation

#### Install Java (if not already installed)
   
  Download Java, e.g. from www.java.com. If you have Java already, check that 
  it is version 1.8.0 (a.k.a. Java 8) or later, by typing:

    > java -version

  Note, that The GNU java a.k.a. gij (default on some older RedHat and Fedora
  systems) is painfully slow and unreliable, and will not always run CRUSH
  correctly. If you need Java, you can download the latest JRE from
  
   https://java.com


#### Download CRUSH

  You can get the latest version of CRUSH from:

   http://www.sigmyne.com/crush 

  Linux users can grab one of the distribution packages to install CRUSH via
  a package manager. Packages are provided for both RPM-based distributions 
  (like Fedora, Redhat, CentOS, or SUSE), and Debian-based distributions (e.g.
  Ubuntu, Mint). Both will install CRUSH in `/usr/share/crush`. Note, if you 
  use one of these packages you will need root privileges (e.g. via `sudo`) on
  the machine. Unprivileged users should install using the tarball.

  For all others, CRUSH is distributed as a gzipped tarball (or as a zip 
  archive). Simply unpack it in the directory, where you want the crush to 
  reside. 

  
#### A. Installation from tarball (POSIX/UNIX, incl. Mac OS X)

  Unpack the tarball in the desired location (e.g. under `~/astrotools/`):

	> cd ~/astrotools
	> tar xzf crush-2.xx-x.tar.gz

  Verify that CRUSH works:

	> cd crush
	> ./crush

  You should see a brief information screen on how to use CRUSH.



#### B. Installation via Linux packages
  
  Use the package manager on your system to install. E.g., on RPM-based 
  systems (Fedora, RHEL, CentOS, SUSE) you may type:

	> sudo yum localinstall --nogpg crush-<version>-noarch.rpm

  On Debian based systems (e.g. Ubuntu, Mint) the same is achieved by:

	> sudo apt-get install crush-<version>.deb

  Or, you may simply double click the package icon from a file browser. 



#### C. Windows Installation
   
  Please refer to `README.windows`, which may be found in the 
  `Install\windows\` subdirectory of the distribution, or online under the 
  'Documents' tab.

 

### 1.2. (optional) Java Configuration


 CRUSH ships with a default Java configuration. On Windows and the most 
 common POSIX platforms (Linux, Mac OS X, BSD, and Solaris), it will 
 automatically attempt to set an optimal configuration. On other platforms, 
 it comes with fail-safe default values (default java, 32-bit mode and 1GB 
 of RAM use).

 You can override the defaults by placing your settings in arbitrary files 
 under /etc/crush2/startup or `~/.crush2/startup` (for the equivalent 
 configuration under Windows, please refer to `README.windows`)

 (Any settings in the user's home under `.crush2/startup` will overrride the 
 system-wide values in `/etc/crush2/startup` or `C:\Program Data\startup`. 
 If multiple config files exist in the same location, these will be parsed in 
 non-specific order). 

 E.g., placing the following lines in `~/.crush2/startup/java.conf` overrides 
 all available runtime configuration settings:

    JAVA="/usr/java/latest/bin/java"
    USEMB="4000"
    JVM="-server"
    EXTRAOPTS="-Djava.awt.headless=true"

 upon startup CRUSH will find and apply these settings, so it will use
 `/usr/java/latest/bin/java` to run CRUSH with 4GB of RAM, using the HotSpot 
 `server` VM, and in headless mode (without display, mouse or keyboard).

 Below is a guide to the variables that you can override to set your own
 Java runtime configuration:

    JAVA       Set to the location of the Java executable you want to use. 
               E.g. "java" to use the default Java, or
               `/usr/java/latest/bin/java` to use the latest from Oracle or 
               OpenJDK.

    USEMB      Set to the maximum amount of RAM (in MB) available to 
               CRUSH. E.g. "4000" for 4GB. On a 32-bit OS, or with a 32-bit
               Java installation no more than 2GB of RAM may be accesssed. In
               practice, the maximum 32-bit OS/Java values range from around 
               "1000" (32-bit Windows / Java) to "1900" (32-bit Linux / Java).  

    JVM        Usually set to `-server` for Oracle or OpenJDK. If using IBM's 
               Java, set it to "" (empty string). On ARM platforms, you 
               probably get better performance using `-jamvm` or `-avian`. To 
               see what VM options are available on your platform, run 
               `java -help`. The VM options are listed near the top of the 
               resulting help screen. 

    EXTRAOPTS  Any other non-standard options you may want to pass to the Java 
               VM should go here. 
	

 You can also specify environment variables, and add shell scripts (bash),
 since these configuation files are in fact sourced as bash scripts before
 launching Java / CRUSH. For example you can add:

```bash
 CRUSH_NO_UPDATE_CHECK="1"
 CRUSH_NO_VM_CHECK="1" 
	  
 echo "Will try to parse my own configuration now... "

 if [ -f \~/mycrushconfig.sh ] ; then
   echo -n "OK"
   source \~/mycrushconfig.sh
 else
   echo -n "Not found"
 fi
```

 The above will disable update checking (not recommended!) and VM checking
 (also not recommended!) and will source the contents of 
 `~/mycrushconfig.sh` if and when such a file exists.



### 1.3.  CRUSH Pipeline Configuration

 The preferred way of creating user-specific configurations for CRUSH is to
 place your personalized configuration files inside a `.crush2/` 
 configuration directory within your home. This way, your personalized 
 configurations will survive future updates to CRUSH.

 You can create/edit your default configuration by editing `default.cfg`
 (either in the installation folder or `~/.crush2`, or in the appropriate
 instrument subdirectory within it. 
 As an example a user configuration for LABOCA data can be placed into 
 `~/.crush2/laboca/default.cfg`, with the a content:
	
	datapath \~/data
	outpath \~/images
	project T-79.F-0002-2006

 This tells crush that when reducing LABOCA data it should look for raw data 
 files in `~/data`, write all output to `~/images`, and specifies the default
 project to be `T-79.F-0002-2006`
 
 The tilde character `~` is used as a shorthand for the home directory 
 (similarly to UNIX shell syntax). In your configuration you can also refer 
 to environment variables or other settings (see more about it further below).

 Of course, you can create any number of configurations, name them as you 
 like place them where you like (practical if you have many data locations, 
 projects etc.). You can easily invoke configuration files as needed via

	> crush [...] -config=<path-to-myconfig> [...]




### 1.4. The Tools of the CRUSH Suite

 CRUSH provides a collection of other useful tools. Here's a short description
 of what is there and what they are used for. Each tool, when run without
 options (or with the -help option) will provide you a list of available
 options on the console.

    crush       The principal reduction tool.

    imagetool   A tool for manipulating images. Can also deal with 
                images produced by BoA (and to some degree other 
                images also).

    show        A simple display program for the FITS files, with 
                various useful functions for simple analysis and image
                manipulation capabilities.

    coadd       Add FITS images together. Use as a last resort tool as
                it is always better to reduced scans together.

    difftool    Allows to look at the difference between two images.
		(used to be named 'difference')

    histogram   Write a histogram of the pixel distribution of an 
                image plane. (e.g. `flux`, `rms`, `s2n`, `weight`, or 
                `time`).
	
    detect      A source extraction tool for maps. You should make
                sure that the noise is close enuogh to Gaussian (e.g. 
                with `histogram`) before relying on this. 

    esorename	 Rename ESO archive files to their original names.




### 1.5. Quick Start

 To reduce data, simply specify the instrument (E.g. `sharc2`, `laboca`...) 
 and the scan numbers/ids (or names of the scan files or directories) to 
 crush. (You may have to add `./` before `crush` if the current directory 
 `.` is not in your path.) E.g.,

	> crush laboca 10059

 will reduce LABOCA scan 10059 with the default reduction parameters.
 (Try `crush -help` to see a full list of the supported instrument names.)

 After the instrument name, you can specify additional options. Some of these
 apply to the reduction as a whole while others will affect the scan 
 processing for those scan numbers that are listed *after* the option flag. 

 If you are new to CRUSH (or used version 1.xx before), you should be able
 to start working with it by the time you get to the end of this page.
 Nevertheless, I recommend that you read on through the entire Sections 
 1--2 (Getting Started & Basic Configuration), and you will become a
 truly well-versed user. :-)

 Once you get the hang of it, and feel like you need more tweaking ability,
 feel free to read on yet further to see what other fine tuning capabilities
 exist...

 Here are some quick tips:

 * Reduce as many scans together as you can. E.g.
		
        > crush laboca 10657-10663 10781 11233-11235 [...]

 * You can specify opacities, pointings, scaling etc, for each
   of the set of scans listed (See section for Scan-specific options). 
   E.g.,

        > crush laboca -tau=0.32 10657-10663 10781 -tau=0.18 11233 [...]

   will use a zenith tau value of 0.32 for 10657-10663 and 10781, and
   0.18 for the last scan (11233).

 * If you suspect that you are missing extended emission (see section
   on the Recovery of Extended Structures), then you can specify the
   'extended' option, which will better preserve large scale structures
   albeit at the price of more noise. E.g.

        > crush laboca -extended 10657-10663

 * If your source is faint (meaning S/N `<` 10 in a single scan), then
   you may try using the `faint` option. E.g.

        > crush laboca -faint 10657-10663

   or,

        > crush laboca -faint -extended 10657-10663

   to also try preserve extended structures (see above).

 * For finer control of how much large scale structures are retained
   you can use the `sourcesize` option, providing a typical source 
   scale (in arcsecs) that you'd like to see preserved. Then CRUSH will
   optimize its settings to do the best it can to get clean maps while 
   keeping structures up to the specified scales more or less intact. 
   E.g.

        > crush [...] -sourcesize=45.0 10657-10663
  
   Will optimize reduction for <\~ 45 arcsec sources.

 * Finally, if your sources are not only faint, but also point-like, 
   you should try the `deep` option. This will use the most aggressive
   filtering to yield the cleanest looking maps possible.
   E.g.,

        > crush laboca -deep 10657-10663

   With just these few tips you should be able to achieve a decent job in
   getting the results you seek. CRUSH can also help you reduce 
   pointing/calibration, skydip, and pixelmap scans. E.g.:

 * To reduce a laboca pointing/calibration scan 11564:

        > crush laboca -point 11564

   At the end of the reduction CRUSH will suggest pointing corrections
   and provide detailed information on the source (such as peak and
   integrated fluxes, FWHM and elongation). Once you determine the
   appropriate pointing corrections for your science scans, you
   can apply these via the `pointing=x,y` option. E.g.:

        > crush laboca -pointing=3.2,-0.6 12069

 * You can also reduce skydips, for determining in-band atmospheric
   opacities. E.g.:

        > crush hawc+ -skydip 26648
	  
 * Finally, you can derive pixel position information from appropriate
   scans, which are designed to ensure the source is moved over every
   detector, in a fully sampled manner. To reduce such beam-maps:

        > crush gismo -pixelmap 5707

   CRUSH will write rcp files as output, containing pixel positions
   source and sky gains in a standard 5 column APEX RCP format. 
   You can feed the pixel position information to reduce other scans 
   via the `rcp` option.

   
 There are a lot more fine-tuning possibilities for the more adventurous. If 
 interested, you can find documentation further below, as well as in the 
 README files inside the instrument sub-directories. For a complete list of 
 crush options, please refer to the GLOSSARY.


   

### 1.6. A Brief Description of What CRUSH Does and How...

 CRUSH is a pipeline reduction that is principally meant to remove
 correlated signals (correlated noise) in the time-streams to arrive
 at clean & independent bolometer signals, which are then used to make
 a source model (usually an image).

 As such it is not an interactive reduction software (e.g. as opposed to 
 e.g. BoA). The term 'scripting' in CRUSH mainly means defining configuration 
 options (in the command line or through configuration files) which are 
 parsed in the order they are read.

 During the reduction CRUSH aims to arrive at a consistent set of
 solutions for various correlated signals, the corresponding gains and
 the pixel weights, as well as tries to identify and flag problematic data.

 This means a series of reduction steps, which are iterated a few times
 until the required self-consistent solutions are arrived at. 
   
 To learn more about the details please refer to Kovacs, A., "CRUSH: 
 fast and scalable data reduction for imaging arrays," Proc. SPIE 7020, 45, 
 (2008). If that does not satisfy your curiousity, then you can find yet
 more explanation in Kovacs, A., PhD thesis, Caltech (2006).




### 1.7. Command-line Options and Scripting Support

 Configuration of CRUSH is available either through command line 
 options or via scripting. You have seen scripting already in the form
 of 'default.cfg', which stores the default configuration values (Sec. 1.1). 

 The syntax is designed so that it accomodates both scripting and
 command-line (bash) use alike. Thus, white spaces are optional and curved 
 brackets are avoided (unless these are placed in quotes).

 For a complete guide on using the configuration engine, please read
 README.syntax. Below we provide only a very basic overview, and describe
 only what is specific to CRUSH, beyond the cofiguration engine in general.


#### Basic Rules
 
  When defining settings, keys can be separated from their values either by
  `=`, `:` or empty spaces (or even a combination of these).

  Command line options start with a dash `-` in front. Thus, what may look
  like:
	
	key1 value1
	key2 value2, value3

  in a configuration script, will end up as

	> crush [...] -key1=value1 -key2=value2,value3 [...] 

  on the command line. Otherwise, they two ways of configuring are generally 
  equivalent to one-another. One exception to this rule is reading scans,
  which is done via the `read` key in a script, but on command line you can
  simply list the scan number (or ranges or lists or names). I.e., 

	[...]
	read 10056                # in script

	> crush [...] 10056       # on the command line.

  In the next section you'll find a description of the scripting keywords.
  Now that you know how to use them also as command line options, you
  can choose scripting or command-line, or mix-and-match them to your
  liking and convenience...
 
  Key/value pairs are parsed in the order they are specified. Thus, each
  specification may override previously defined values. 

  Lines that start with `#` designate comments that are ignored by the 
  parser.
 

 
#### Dynamic Conditionals
 
 Some conditions are interpreted dynamically. For example CRUSH, can 
 activate settings based on observation date (or MJD) or serial number, on 
 a scan-by-scan basis, such as:

	mjd.[54555-54869] rcp {$CRUSH}/laboca/laboca-3.rcp
 
 which loads the pixel positions (RCP) `laboca-3.rcp` inside the `laboca`
 subfolder in the crush installation for scans taken in the MJD range
 54555 to 54869. Similarly,

	date.[2007.02.28-2009.10.13] instrument.gain -1250.0

 or

	serial.[14203-15652] flag 112-154,173

 are examples of setting activated based on dates or scan serial numbers.

 You may also specify conditional settings based on the
 source names under the `object` branch. E.g.:

	object.[Jupiter] bright

 will invoke the `bright` configuration for Jupiter. The check for the
 source name is case insensitive, and matches all source names that begin
 with the specified sequence of characters. Thus, the SHARC-2 configuration
 line:

	object.[PNT_] point

 will perform a pointing fit at the end of the reduction for all sources
 whose catalog names begin with `PNT_` (e.g. `PNT_3C345`).

 These examples also demonstrates that conditionals can be branched just
 like options. (In the above cases, the conditions effectively reside in the
 `mjd`, `date` or `serial` branches). Other commonly used conditionals of
 this type are iteration based settings:

	> crush [...] -iteration.[last-1]whiten=2.0 [...]

 will activate the noise whitening in the iteration before the last one.

   
#### Startup Configuration
   
  At launch, crush will parse `config/default.cfg` to establish a default 
  configuration set. All configurations files are first parsed from the 
  files in the `config/` directory inside crush, then additional options or 
  overriders  are read also from the appropriate instrument subdirectories, 
  if exist.
 
  After that, crush will check if these configuration files also exists 
  under the inside the `~/.crush2` directory of the user. If so, they will be
  used to override again. See more on this in the next section under the
  `config` option. In this way, the `~/.crush` directory can be used as
  a convenient way to create user specific setting and/or overrides to
  global defaults.





### 1.8. Making sense of the console output
 
 Don't ignore the console output. It contains a lot of information, which
 may be useful for diagnosing your reduction, and troubleshooting if things
 don't go as expected. 

 In the beginning of the console output, you will see information from each
 scan as it is being read, followed by output from the preprocessing steps
 (such as downsampling, scan statistics, velocity clipping, opacity used,
 pointing corrections applied etc.). This part is verbose enough that it 
 should be eszsentially self-explanatory.

 Once all the scans are loaded, and the source model (usually a map) has been
 created to accomidate the dataset, CRUSH will enter the iterated pipeline
 reduction. It may look cryptic at first, as it captures a lot of information
 in very little console space. Below is a short guide to figure out what
 it all means. Understanding it will help you diagnose and troubleshoot all
 sorts of issues that might affect the reduction of your dataset. So, don't
 be shy, dive in!


##### An example line from the console output

 Let's begin with a concrete example. Here is a section from the console 
 output from the reduction of LABOCA scan 11564 (from 2007): 

    $ Round 4: 
    $
    $  [11564] D(128) C245 W(8.44E-2)245 dN(0)245 B245 c245 Map(8.44E-2) 
    $  [Source] {check} (smooth) (clip:4.0) (blank:10.0) (sync) 

 Each _phrase_ (separated by spaces around it) represents a short summary of
 a pipeline step. The leading characters identify the step, often followed by 
 some quantitative capure (or figure-of-merit) summarizing what the step
 accomplished.
	
 Here is how the above section is interpreted: 

   In the 4th iteration, the following steps are performed on scan 11564: 

    D(128)        1/f filtering (on 128 frame timescale)

    C245          removing the correlated noise from the array with 
                  245 pixels surviving the gain range criterion.

    W(8.44E0-2)   Deriving pixel weights with the `rms` method. The
                  average sensitivity of the array is estimated to be
                  84.4 mJy sqrt(s).

    dN(0)245      Despiking via the `neighbours` method, with 0 frames
                  flagged as spiky, and 245 pixels surviving the
                  flagging of pixels with too many spikes.

    B245          Decorrelating on amplifier boxes, with 245 pixels 
                  having acceptable gains to the correlated signals.

    c245          Decorrelating on electronic cables, with 245 pixels
                  showing acceptable gain response to these signals.

    Map(8.44E-2)  Mapping scan, with estimated point source NEFD of
                  84.4 mJy sqry(s).

   Then, at the end of the iteration a composite source model is created. This
   is further processed as:

    {check}       Remove invalid data from the scan maps (before adding
                  to composite).

    (smooth)      smooth composite by the desired amount.

    (clip:4.0)    Discard map points below an S/N of 4.0 from composite.

    (blank:10.0)  Do not use bolometer data in other steps, which are
                  collected over the map points with S/N > 10, thus
                  reducing the bias that bright sources can cause in the
                  reduction steps.

    (sync)        Synchronize the composite model back to the time-stream
                  data.

 Once the reduction is done, various files, including the source map, are
 written. This is appropriately echoed on the console output.


   
#### Console Output Reference Guide

  Below is a reference guide for interpreting the console output for your 
  particular reduction:
  

##### Quantities inside the brackets:

    [nnnnn|m]:  processing scan nnnnn, subscan m from the list

    (#.##E#)    The effective point-source NEFD (usually after 
                weighting or at the mapping step)
                shown in the effective mapping units times sqrt(s).

    []          bracketed models are solved via median estimators

    (#)         Indicates the time resolution of the given step as
                the number of downsampled frames, when this is not
                the default full resolution.


##### Reduction-step Shorthands (alphabetically)

    a          Decorrelating amplifier boards (e.g. LABOCA,GISMO).

    am         Remove correlated telescope acceleration (magnitude)

    ax         Remove correlated telescope x acceleration

    ay         Remove correlated telescope y acceleration

    B          Decorrelating electronic boxes (e.g. LABOCA).

    C          Solving for correlated noise and pixel gains
               The time resolution (in frames) is shown in brackets
               if not full resolution, followed by the number of 
               unflagged pixels if gains are solved and a gain range
               is defined for flagging.

    c          Decorrelating electronic cables (e.g. LABOCA)	
               or geometric columns (e.g. GISMO)

    cx         Remove correlated chopper x position

    cy         Remove correlated chopper y position

    D          Solving for pixel drifts (1/f filtering).

    dA(#)      despiking absolute deviations.	
               In brackets it shows the percentage # of frames
               flagged in the data as spiky by any method.

    dG(#)      like above but proceeds gradually.

    dN(#)      despiking using neighbouring samples in the timeseries.

    dM(#)      despiking at multiple resolutions (up to the 1/f
               filter timescale).

    E          Remove correlated SAE error signal (GISMO)	

    G          Estimating atmospheric gradients accross the FOV.

    J          De-jumping frames (e.g. for GISMO). Followed by two
               colon (:) separated numbers: the first, the number of
               de-jumped blocks that were re-levelled and kept; and
               the number of blocks flagged.

    m          Decorrelating on multiplexers (e.g. GISMO, SCUBA-2)

    Mf         Filtering principal telescope motion.

    O          Solving for pixel offsets

    p          Decorrelating on (virtual) amplifier pins (e.g. GISMO)

    Q          Decorrelating wafers (e.g. ASZCA).

    r          Decorrelating on geometric rows (e.g. SHARC-2, GISMO)

    t          Solving for the twisting of band cables (e.g. LABOCA).

    tx         Remove correlated telescope x position

    ty         Remove correlated telescope y position

    tW         Estimating time weights.

    W          Estimating pixel weights.

    w          Estimating pixel weights using the 'differential'
               method.

    wh(x.xx)  Noise whitening. The average source throughput factor
              from the whitening is shown.	

##### Source model-specific:

     
    Map         Calculating source map from scan. The effective point
                source NEV/NEFD of the instrument is shown in the 
                brackets (e.g. as Jy sqrt(s)).

    [C1\~#.##]  Filtering corrections are applied directly and are
                #.## on average.

    [C2=#.##]   Faint structures are corrected for filtering after
                the mapping via an average correction factor #.##.

    [Source]    Solving for source map.

    {check}     Discarding invalid map data.

    {despike}   despiking scan maps before adding to composite.

    {filter}    Spatial large-scale structure (LSS) filtering of the 
                scan maps.

    (level)     Zero levelling to map median.

    (smooth)    Smoothing map.

    (filter)    Spatial filtering of the composite map.

    (noiseclip) Clip out the excessively noisy parts of the map.

    (filter)    Filtering large scale structures (i.e. sky-noise).

    (exposureclip)  Clipping under-exposed map points.

    (blank)    Blank excessively bright points from noise models.

    (sync)     Removing the source model from the time-stream.





### 1.9. Examples

 Reduce scans 12065-12069 and 12072 with zenith tau of 0.18:

	> crush laboca -tau=0.18 12065-12069 12072

 Reduce scans 10562 and 10645 together, with the first scan observed at a
 zenith tau of 0.21, and the second at tau of 0.35 with.

	> crush laboca -tau=0.21 10562 -tau=0.35 10645

 Say you realize that the pointing was off by -5.4" in AZ, and 2.4" in EL
 for the second scan. Then:

	> crush laboca -tau=0.21 10562 -tau=0.35 -pointing=-5.4,2.4 10645

 Say scan 10049 is a scan of a bright source (e.g. Saturn) and the default
 reduction ends up clipping much of it. Then,

	> crush laboca -bright 10049

 If the source still gets nipped from the resulting map, you can try 
 disabling pixel weigting altogether (this is the likely culprit) by:
	
	> crush laboca -bright -blacklist=weighting 10049

 Perhaps you suspect there is missing extended emission (large-scale 
 structure) in scan 10550. You can try to recover more by:

	> crush laboca -extended 10550.

 Try reduce some faint source (scan 10057):

	> crush laboca -faint 10057

 Maybe your faint source has extended structure that you want to try recover
 better, and willing to pay some noise penalty for it. Then try:

	> crush laboca -faint -extended 10057.

 You can also fine-tune, what is the largest source-scale (more-or-less) 
 that you are interested in. Then the reduction will adjust its parameters
 accordingly. Say you expect your source to be a blob around 1' in diameter,
 then you can try:

	> crush laboca -faint -sourcesize=60.0 10057.

 You can also play with the blanking clipping methods above, if there is
 annoying negative dips remaining around your brighter peaks. Note, that
 you porbably want to stick with -extended, or else such dips may be the
 result of the aggressive filtering settings applied to your specific
 source size (via `sourcesize`).

 As mentioned before, command-line options and scripting are equivalent
 ways of configuring the reduction. Thus, the running the script `test.cfg`:

	faint
	extended
	tau 0.18
	pointing -3.2,4.8
	read 12065-12069
	pointing 2.3,-0.5
	read 12072
	blank 10.0
	clip 3.0
	iteration.[last-1] forget clip

 via 

	> crush laboca -config=test.cfg	

 is equivalent to the command line:

	> crush laboca -faint -extended -tau=0.18 \
	  	-pointing=-3.2,4.8 12065-12069 \
		-pointing=2.3,-0.5 12072 \ 
		-blank=10.0 -clip=3.0 -iteration.[last-1]forget:clip  


 Finally, suppose you want to reduce a dataset on a very faint point source, 
 such as a distance galaxy, or a faint core, with a set of scans:

	> crush laboca -deep 23165-23169 

 And, perhaps you want to comprate the result to a random jackknife, which
 you can obtain with:

	> crush labova -deep -jackknife 23165-23169
   



----------------------------------------------------------------------------

## 2. Advanced Topics



### 2.1. Pointing Corrections

 Reducing the data with the correct pointing can be crucial (esp. when 
 attempting to detect/calibrate faint point sources). At times the pointing
 may be badly determined at the time of observation. Luckily, getting the 
 exact pointing offset wrong at the time of the observation has no serious 
 consequences as long as the source still falls on the array, and as long as 
 the exact pointing can be determined later. If you, at the time of the data 
 reduction, have a better guess of what the pointing was at the time the
 data was taken (e.g. by fitting a model to the night's pointing data), you 
 can specify the pointing offsets that you believe were more characteristic
 to the data, by using the `-pointing` option *before* listing the scans 
 that should be reduced with the given corrections. E.g.,

	> crush [...] -pointing=12.5,-7.3 <scans>

 Will instruct minicrush that the _true_ pointing was at dAZ=12.5 and 
 dEL=-7.3 arcsec each (i.e. it works just like pcorr on APECS).

 Some instruments, like SHARC-2, may allow specifying the aggregated pointing
 offsets (e.g. `fazo` and `fzao`) instead of the differential corrections 
 supplied by `pointing`.


#### Obtaining Corrections

  Good practice demands that you regularly observe pointing/calibration 
  sources near your science targets, from which you can derive appropriate
  corrections. CRUSH provides the means for a analyzing pointing/calibration
  data effectively, using the `point` option:

	> crush [...] -point [...]

  At the end of the reduction, CRUSH will analyze the map, and suggest
  appropriate pointing corrections (to use with `-pointing`, or other
  instrument-specific options), and provide calibration information as well
  as some basic measures of source extent and shape.



#### After Reduction (a poor alternative)
   
  You can also make pointing changes after the reduction (alas, now in 
  RA/DEC). You can read off the apparent source position from each separately 
  reduced scan (e.g. by using `show` and placing the cursor above the apparent
  source center/peak). Then you can use `imagetool` to adjust the pointing. 
  E.g.:

	> imagetool [...] -origin=3.0,-4.5 ... 

 The above moves the map origin by 3" in RA and -4.5" in DEC. 

 Then, other crush tools (like `coadd`, `imagetool` etc.) will use these images 
 with the proper alignment. Clearly, this method of adjusting the pointing is
 only practical if your source is clearly detected in the map.




### 2.2. Pixelization and Smoothing

 There seem to be many misconceptions about the _correct_ choice of 
 pixelization and about the (mal)effects of smoothing. This section aims to 
 offer a balanced account on choosing an appropriate mapping grid and on the 
 pros and cons of applying smoothing to your maps.

#### Pixelization (i.e. choosing the 'right' grid)

  **Misconception**: You should always _Nyquist_ sample your map, with 2 
  pixels per beam FWHM, to ensure ideal representation.

  There is more than one thing wrong with the above idea. First, there is no
  'Nyquist' sampling of Gaussian beams. The Nyquist sampling theorem applies 
  only to data, which has a natural cutoff frequency (the Nyquist frequency), 
  above which there is no information present. Then, and only then, will 
  sampled data (at a frequency strictly larger[!] than twice the Nyquist 
  cutoff) preserve all information about the signals. 

  Two pixels per beam is almost certainly too few for the case of Gaussian 
  beams. Gaussian beams have no true frequency cutoff -- the signal spreads
  across the spectrum, with information present at all frequencies, even if it
  is increasingly tapered at the higher frequencies. By choosing a sampling 
  (i.e. pixel size in your map) the information above your sampling rate will 
  be aliased into the sampled band, corrupting your pixelized data. 

  Thus, you can choose a practical cutoff frequency (i.e. pixelization) based
  on the level of information loss and corruption you are willing to tolerate.
  At 2.5 pixels pear FWHM, you retain \~95% of the underlying information, and 
  corrupt it by the remaining 5%. With more pixels per beam, you get more 
  accurate maps. (The 2-pixels per beam, that many understand to be the 
  Nyquist  sampled, is certainly too few by most standards of accuracy!)

  Thus, the CRUSH default is to use around 5-pixels per FWHM, representing a 
  compromise between completeness (\~99%) with minimal corruption (`<`1%) and a 
  senseless increase of map pixels (i.e. number of model parameters).


#### Smoothing
   
  **Misconception**: You should not smooth your maps, because it does 
  something _unnatural_ to your _raw_ image.

  The first problem with this view is that there is no _natural_ or _raw_ image
  to start with, because there is no _natural_ pixelization (see above). 
  Secondly, by choosing a map pixel size, you effectively apply smoothing -- 
  only that your smoothing kernel is a square pixel, with an abrupt edge, 
  rather than a controlled (and directionless) taper of choice. 

  (To convice yourself that a map pixels apply smoothing, consider the mapping 
  process: each pixel will represent an average of the emission from the area 
  it covers. Thus, the pixel values are essentially samples of a moving 
  integral under the pixel shape -- i.e. samples of the emission convolved 
  [smoothed] by the pixel shape.)

  However, smoothing (including coarse pixelization!) does have a real 
  downside, in that it degrades the effective resolution of the image. Consider
  smoothing by Gaussian kernels. Then, the image resolution (imageFWHM) 
  increases with the smoothing width (`smoothFWHM`) as

	imageFWHM^2 = beamFWHM^2 + smoothFWHM^2

  from the instrument resolution (`beamFWHM`). However, you can smooth a fair 
  bit before the degradation of resolution becomes a problem or even really
  noticeable. If you use sub-beam smoothing with `smoothFWHM < beamFWHM`, then 
  the relative widening is roughly

	dW / W0 ~ 0.5 * (smoothFWHM / beamFWHM)^2

  Thus, smoothing by half a beam, degrades resolution by \~12% only... At the 
  same time, smoothing can bring many benefits:

 * Improves image appearance and S/N by rejecting pixelization noise. It is
   better to use a finer grid and smooth the image by the desired amount,
   than to pixelize coarsely -- not only for visual appearance but also
   for the preservation of information.

 * Smoothing can help avoid pathological solutions during the iterations, 
   by linking nearby pixel values together.

 * Beam-smoothing is the optimal (Wiener) filtering for determining point 
   source fluxes in a white noise background. I.e., smoothing by the 
   beam produces the highest signal-to-noise measurement of point sources.

 * Beam-smoothing is mathematically equivalent to fitting fixed-width beams
   at every pixel position. The beam-smoothed flux value in each pixel
   represents the amplitude of a beam fitted at that position using 
   chi-squared minimization. Thus, beam smoothed images are the bread-and-
   butter of point source extraction (e.g. the `detect` tool of CRUSH).

  Given the pros and the con for smoothing, the different reduction modes 
  (_default_, `faint` or `deep`) of CRUSH make different compromises. The 
  default reduction aims to provide maps with maximal resolution (i.e. no 
  smoothing), although a some smoothing is used during the iterations to aid
  convergence to a robust solution. `faint` mode reductions smooth by 2/3 
  beams (resulting in \~22% degradation of resolution), to provide better 
  signal-to-noise at a moderate loss of spatial resolution. 
  Finally, `deep` reductions yield beam smoothed images, which are ideal for 
  point source extraction, even if some spatial details are sacrificed.

  You can change/override these default settings. The smoothing during 
  reduction is  controlled by the `smooth` setting, which can take both a 
  Gaussian FWHM (in arcsec) as its arguments as well as the preset values 
  `minimal`, `halfbeam`, `2/3beam` and `beam`. The smoothing of the final map 
  can be controlled by 'final:smooth' (the `final` stands as a shorthand 
  conditional for the last iteration). Thus,

	> crush [...] -smooth=halfbeam -final:smooth=minimal [...]

  smoothes by half a beam during the iterations, and only slightly for the 
  output image, while

	> crush [...] -forget=smooth -final:forget=smooth [...]

  disables smoothing both during reduction and at the end. The table below
  summarizes the effect of the preset smoothing values, indicating both the
  degradation of resolution (relative to the telescope beam) and the relative
  peak S/N on point sources:


   
   **Table 1.** _Smoothing properties_

   _smooth_       | widening     |	rel. S/N
   ---------------|--------------|--------------
   minimal        |      6%      |      0.33
   halfbeam       |      12%     |      0.50
   2/3beam        | 	 22%     |      0.67
   beam           |      41%     |      1.00






### 2.3. Recovery of Extended Emission

 As a general rule, ground based instruments (in the mm and submm) are only 
 sensitive to structures smaller than the Field-of-View (FoV) of the 
 instrument. All scales larger than the FoV will be strongly degenerate with 
 the bright correlated atmosphere (a.k.a. sky noise), and will be very 
 difficult, if not outright impossible, to measure accurately. In a sense, 
 this is analogous to the limitations of interferometric imaging, or the 
 diffraction-limited resolution of finite apertures. 

 However, there is a some room for pushing this limit, just like it is 
 possible to obtain some limited amount of super-resolution (beyond the 
 diffraction limit) using deconvolution. The limits to recovery of scales 
 over the FoV is similar to those of obtaining super-resolution beyond the 
 diffraction limit. Both these methods

 1. yield imperfect answers, because the relevant spatial scales are 
    poorly measured in the first place.

 2. are only feasible for high signal-to-noise structures.

 3. can, at best, go beyond by a factor of a few beyond the fundamental 
    limit.

 You can usually choose to recover more extended emission if you are willing 
 to put up with more noise on those larger scales. This trade-off works 
 backwards too -- i.e., you can get cleaner maps if you are willing to filter
 them more.

 As a general principle, structures that are bright (`>>` 5-sigma) can be fully
 recovered to up to a few times the field-of-view (FOV) of the bolometer 
 array. However, the fainter the structure, the more it will be affected by 
 filtering.

 Generally, the fainter the reduction mode, the more filtering of faint
 structures results, and the more limited the possibility of recovering 
 extended structures becomes. The table below is a rough guide of what 
 maximum scales you may expect for such faint feaures, and also, how noise is
 expected to increase on the large scales as these are added in `extended` 
 mode:


   **Table 2.** _Maximum faint structure scales for S/N `<`\~ 5_
	
   option              | Max. sensitive scale        | Noise power scaling 
   --------------------|-----------------------------|--------------------
   _default_ / `bright`|          FOV/2              |  \~L^2
   `+ extended`        |           FOV               |  \~L^2
   `faint` / `deep`    | `2*sourceSize` or `2*beam`  |   \~L
   `+ extended`        |          FOV/2              |   \~L


 Iterating longer, will generally help recover more of the not-too-faint 
 large-scale emission (along with the large-scale noise!). Thus,

   	> crush -extended -rounds=50 [...] 

 will generally recover more extended emission than just the default

   	> crush -extended [...]

 (which iterates 10 times). In general, you may expect to recover significant
 (`>`5 sigma) emission up to scales L as:

	L ~= FoV + sqrt(N v T)

 in terms the number of iteration N, limiting Field-of-View (FoV), scanning 
 velocity v and correlated noise stability time-scale T. Unfortunately, the 
 correlated noise stability of most ground-based instruments is on the order 
 of a second or less due to a highly variable atmosphere. At the same time, 
 the noise rms on the large scales will increase assymptotically as:

	rms ~ sqrt(N)

 for large numbers of iterations.





### 2.4. Filtering corrections, transfer functions, etc.

 Most reduction steps (decorrelation, 1/f drift removal, spectral filtering) 
 will impact different spatial frequencies of the source structure 
 differently. In general, the low spatial frequency components are most 
 affected (suppressed). E.g. decorrelating the full array will reject 
 scales larger than the field-of-view, while 1/f filtering will result in
 1/f spatial filtering of the map due to the scanning motion, which more
 or less directly maps temporal frequencies into spatial frequencies.

 The approach of CRUSH is to apply appropriate point-source corrections
 (rescaling) such that point sources in the map yield the same fluxes no
 matter how (i.e. with what options exactly) the source was reduced. 
 While the corrections will be readily sufficient for a large fraction of 
 the science cases in this simple form, there are two notable exceptions
 to this rule: (i) extended emission, and (ii) small, fast maps reduced
 in `deep` mode (when the source is scanned over the same detector more than
 once over the `stability` timescale). 

 The better approach for these cases is to measure a transfer function, or 
 otherwise check the reduction of a similar simulated source.


#### Transfer functions and simulated sources

  The `sources` option provides a means for inserting test sources into
  CRUSH maps, while one of the `jackknife` options can be used to remove
  any real emission beforehand but retaining the signal and noise structure
  of the data otherwise (which is important in order to get a representative
  measure of the transfer function). E.g.

	> crush [...] -jackknife.alternate -sources=test.mask ...

  will apply an alternating jackknife to the input scans, and insert sources
  specified in the mask file `test.mask` (See `example.mask` on the format
  of mask files, and the GLOSSARY for more on jackknifing options).

  To measure transfer functions (i.e. complete spatial characterization of
  the point-source response) you would want to insert a single beam-sized 
  point source. Alternatively, you can insert one or more Gaussian-shaped 
  source(s) with a range of FWHMs to create a simulated source structure that
  resembles the structure you expect your source(s) to have.

  Make sure your test source is bright enough to see with high S/N, but not
  too bright to trigger unintended flagging, or despiking. In general, a S/N
  between 100 and 1000 should be fine for default reductions, and 100 to 300 
  for `faint` or `deep` modes.

  Additionally, in `faint` or `deep` modes, you may want to disable some 
  features which may affect your relatively bright test sources differently
  than your much fainter real science target(s). Thus, the following are
  recommended for reducing `faint` and `deep` test sources:

	> crush [...] -blacklist=clip,blank,source.filter.blank

  Note also that the spatial filtering (transfer function) will be varying
  with location on the map (since the scanning speed and directions will
  themselves be non-uniform over the map). Therefore, it is strongly 
  recommended that test sources are inserted near the same locations as the
  real sources in the field.
    



### 2.5. Image processing post-reduction

 CRUSH also provides `imagetool` for post-processing images after reduction. 
 The typical usage of imagetool is:

	> imagetool -name=<output.fits> [options] <input.fits>

 which processes `<input.fits>` with the given options, and writes the result 
 to `<output.fits>`. 

 With imagetool, you can apply the desired level of smoothing (`-smooth`), or
 spatial filtering (`-extFilter`), specify circular regions to be skipped by 
 the filter (`-mask=<filename>`). You can adjust the clipping of noisy map 
 edges by relative exposure (`-minExp`) or by relative noise (`-maxNoise`).
 You can also crop a rectangular region (`-crop=dx1,dy1,dx2,dy2`). There are 
 many more image operations. See the imagetool manual (in your UNIX shell, or
 online) or simply run `imagetool` without an argument:

	> imagetool

 One of the useful options allows to toggle between the noise estimate from 
 the detector time-streams (`-noise=data`) and from the image itself 
 (`-noise=image`) using a robust estimator. For example, after spatial 
 filtering, you probably want to re-estimate the map noise:
   
	> imagetool [...] -extFilter=45.0 -noise=image <input.fits>

 The built-in image display tool `show` also takes all processing options
 of imagetool, but rather than writing the result, it will display it in
 an interactive window. See the manual page of `show` (either inside your
 UNIX shell, or online), or run `show` without an argument.



    
### 2.6. Reducing Very Large Datasets

 Coming soon...


---------------------------------------------------------------------------



## 3. Advanced Configuration


In this section, you can find information on the most useful configuration
options. A complete list of available settings can be found in the
text file GLOSSARY, located in the CRUSH installation directory.

Configuration options here are listed as scripting keys i.e., without a 
preceding dash. However, you can use the same options in the command line by 
adding the dash. (Also, `=` can be replaced by space(s) in scripting...) 


### 3.1. Commands

 There are a handful of keywords that are treated as commands by crush. (The
 difference being that commands are interpreted and acted on right away, whereas 
 typical configuration keys are stored settings that are interpreted later as 
 necessary.) The commands are:
   

   	config=<filename>	Load the configuration file filename. 
				The file is looked for in the locations in the
				following order:

					1. ./
					
					2. ./<instrument>/

					3. ~/.crush2/

					4. ~/.crush2/<instrument>/

				Whenever a matching file is found its contents
				are parsed. Because of the ordering, it is 
				convenient to create overriding configurations.
				Thus instrument specific settings can be used 
				to override default settings, and user specific
				settings placed in '~/.crush2' can override
				shipped defaults. Whenever a configuration is
				parsed, there is a note of it on the console
				output so that one always knows which files 
				were read and in what order.
				E.g. when using
				
				   > crush laboca -faint 12066

				the following configuration files will be
				loaded in order (provided they exist):

				   <crush>/config/default.cfg
				   <crush>/config/laboca/default.cfg
				   ~/.crush2/default.cfg
				   ~/.crush2/laboca/default.cfg
				  
				   <crush>/config/faint.cfg
				   <crush>/config/laboca/faint.cfg
				   ~/.crush2/faint.cfg
				   ~/.crush2/laboca/faint.cfg
				   
				Each successively loaded file may override
				the options set before it.
				When a matching configuration file is not found
				in any of the standard locations (above), CRUSH
				will make one last attempt to interpret the
				argument as a regular pathname. This allows
				users to store and invoke configuration files
				anywhere on the filesystem.
				
	forget=<option>...	Forget the priorly set values for <option>
				as if it were never defined. E.g. 
		     		
					forget=outpath

				will unset the 'outpath' option.
				You can specify more than one options as a
				comma-separated list. E.g.
	
					forget=outpath,project
				
				With unset both the 'outpath' and 'project' 
				options.
				Additionally, the arguments 'conditions' and
				'blacklist' can be used to clear the 
				conditional or blacklisted settings 
				respectively	

	recall=<option>		Undoes 'forget', and reinstates the <option>
				to its old value.	

	remove=<option>		Similar to 'forget', but removes the entire
				branch. Thus '-remove=despike' unsets:

					despike
					despike.level
					despike.method
					despike.flagfraction
					...

	replace=<option>	Undoes the 'remove' option, reinstating the
				<option> tree to its prior state.

	blacklist=<option>...	Similar to 'forget', except it will not
				set options even if they are then specified
				at a later time. This is useful for altogether
				removing settings from the configuration.

	whitelist=<option>...	Remove <option> from the blacklist, allowing
				it to be set again if desired. Whitelisting
				an option will not reinstate it to its prior
				value. After whitelisting, you must explicitly
				set it again, or 'recall' or 'replace' it
				to its prior state.

	poll			Whenever unsure what options are set at any
	poll=<option>		given stage, you can poll the settings.
				Without an additional argument it will list
				all options to the standard output. When
				an argument is specified it will list
				all configuration settings that start with
				the specified string. E.g.

					> crush [...] -poll=iter
	
				will list all iteration based options that 
				are set including all the [...] options set
				prior to '-poll' in the command line.


	list.divisions		List all pixels divisions, which can be
				decorrelated for the instrument.

	list.response		List all response modalities for the
				instrument (to known signals, such as
				telescope movement, or temperature data).


### 3.2. Pipeline Configuration

#### a. Source types. 

  The default reduction (see `default.cfg`) is optimized 
  for mapping compact (up to the field-of-view or smaller) sources in the S/N
  range of \~10-1000. These options are useful if your source does not match
  these criteria.


	bright		Use for bright sources (S/N > ~1000). This setting
			entirely bypasses all filtering to produce a very
			faithful map. The drawback is more noise, but
			that should not be an issue for such a bright guy :-)
			Will invoke 'bright.cfg'.

	faint		Use with faint sources (S/N < ~30) when the
			source is faint but still visible in a single scan. 
			This setting applies some more aggressive filtering of 
			the timestreams, and extended structures. It invokes 
			'faint.cfg'.

	deep		Use for very faint sources which are not at all 
			detected in single scans, or if you think
			there is too much residual noise (baselines) in your 
			map to your liking. This setting results in the most 
			agressive filtering. Will load the configuration from
			'deep.cfg'. The output map is optimally filtered
			(smoothed) for point sources.

	extended	Try to better preserve extended structures. This
			setting can be used alone or in combination with
			the above brightness options. See also '-sourcesize=X' 
			below. With the fainter settings the recovery of 
			extended structures becomes increasingly more 
			difficult. For bright structures recovery up to FOV 
			(or beyond!) should be possible, while for faint 
			structures \~1/4 FOV - FOV scales are maximally 
			obtainable (see more on this in the section below.)
  
	source.type=<type>	By default, crush will try to make a map from
				the data. However, some istruments may take
			data that is analyzed differently. For example, you 
			may want to use crush to reduce pixel maps (to
			determine the positions of your pixels on sky), or
			skydips (to derive appropriate opacities), or do
			point source photometry. Presently, the following
			source types are supported accross the board:
		
			   map 		Make a map of the source (default)

			   skydip	Reduced skydips, and determine 
					opacities by fitting a model to it.

			   pixelmap	Create individual maps for every
					pixel, and use it to determine their
					location in the field of view.
			
			Note, that you may also just use 'skydip' and 
			'pixelmap' shorthands to the same effect. E.g.

			  > crush [...] -skydip [...]

	sourcesize=X	This option can be used instead of 'extended' in 
			conjunction with 'faint' or 'deep' to specify the 
			typical size of sources (FWHM in arcsec) that are 
			expected. The reduction then allows filtering 
			structures that are much larger than the specified 
			source-size...
			If 'sourcesize' or 'extended' is not specified, then 
			point-like compact sources are assumed.	


#### b. Other commonly used pipeline settings:

  (in typical order of importance to users...)


	outpath=<path>	Set the directory into which output files (e.g. maps) 
			will be written. Can use '\~' for home directory and 
			environment variables in {}'s. Thus,

			   outpath=\~/images

			and

			   outpath={$HOME}/images

			are equivalent

	
	rounds=N	Iterate N times. You may want to increase the number
			of default iterations either to recover more extended
			emission (e.g. when 'extended' is set), or to go
			deeper (esp. when the 'faint' or 'deep' options are
			used).


	iteration.[N]	Use as a condition to delay settings until the Nth
			iteration. E.g.

			   iteration.[3] smooth halfbeam

			or 

			   > crush [...] -iteration.[3]smooth=halfbeam [...]
			 
			to specify half-beam smoothing starting from the 3rd
			iteration.
			
	iteration.[last]    Specify settings that should be interpreted only
			    at the beginning of the last iteration.

	final:key=value	    A shorthand for the above :-).
	
	iteration.[last-N]  Activate settings N iterations before the last
			    one.

	iteration.[xx%]	    Activate settings as a percentage of the total
			    number of iterations (as set by 'rounds'). E.g.
			
				iteration.[50%] forget clip

			    can be used to disable the S/N clipping of the
			    source map half way through the reduction.

			Because of the flexible syntax, the same iteration
			can be referred to in different ways. Consider
			a reduction with 10 rounds. Then,

				iteration.[5] smooth 5.0
				iteration.[50%] smooth 10.0
				iteration.[last-5] smooth beam

			can all be used to define what happens in the 5th
			iteration. CRUSH will parse these conditionals in 
			the above order: first the explicit iteration settings
			then those relative to the reduction length, and
			finally the settings relative to the end of the
			reduction. Thus, in the above example the beam 
			smoothing will always override the other two settings.

	idle=N		Instruct crush NOT to use N number of CPUs of the 
			machine. By default crush will try to use all 
			processors in your machine for maximum performance. 
			This option allows to modify this behavior according 
			to need. Note, that at least 1 CPU will always be used 
			by crush, independent of this setting.
			The number of actual parallel threads will be the 
			smaller of the allowed number of CPUs and the number 
			of scans processed.




### 3.3. Source (Map) Configuration
	
	altaz		Shorthand for 'system=horizontal' to reduce in Alt/Az.
			It is also aliased to 'horizontal'.

	grid=X		set the map pixelization to X arcsec. Pixelization
			smaller than 2/5 beam is recommended. The default is
			\~1/5 beam pixelization.

	name=		Specify the output image file name, relative to the
			directory specified by 'outpath'. When not given
			minicrush will chose a file name based on the source
			name and scan number(s), which is either

				<sourcename>.<scanno>.fits

			or
	
				<sourcename>.<firstscan>-<lastscan>.fits

			For mapping. Other source model types (e.g. skydips
			or pixel maps) may have different default naming 
			conventions.

	pixelmap	Reduce pixel map data. Instead of making a single map
			from all pixels, separate maps are created for each
			pixel (Note, this can chew up some memory if you have
			a lot of pixels). At the end of the reduction CRUSH
			determines the actual pixel offsets in the focal plane.
			This option is equivalent to 'source.type=pixelmap'.
	
	pixelmap.writemaps	Pixel maps (above) normally only produce the
				pixel position information. Use this option
			if you want CRUSH to write individual pixel maps as
			well, so you can peek at these yourself.

	projection=	Choose a map projection to use. The following 
			projections are supported:

				SFL  --  Sanson-Flamsteed
				SIN  --  Slant Orthographic
				TAN  --  Gnomonic
				ZEA  --  Zenithal Equal Area
				SFL  --  Sanson-Flamsteed
				MER  --  Mercator
				CAR  --  Plate-Carree
				AIT  --  Hammer-Aitoff
				GLS  --  Global Sinusoidal
				STG  --  Stereographic
				ARC  --  Zenithal Equidistant

	skydip		Reduce skydip data, instead of trying to make an 
			impossibly large map out of it :-). This option is
			equivalent to specifying 'source.type=skydip'.

	smooth=X	Smooth the map by X arcsec FWHM beam. Smoothing
			helps improve visual appearance, but is also useful
			during reduction to create more redundancy in the data
			in the intermediate reduction steps. Also, smoothing
			by the beam is optimal for point source extaction from
			deep fields. Therefore, beam smoothing is default in
			with the 'deep' option (see 'deep.cfg').
			Typically you want to use some smoothing during 
			reduction, and you may want to turn it off in the 
			final map. Thus, you may have something like:

			  smooth=9.0			# 9" smoothing at first
			  iteration.[2]smooth=12.0 	# smooth more later
			  iteration.[last]forget=smooth # no smoothing at last

			Other than specifying explicit values, you can use
			the predefined values: 'minimal', 'halfbeam', '2/3beam'
			or 'beam'. See more on smoothing in the advanced
			configuration section.

	source.filter   Filter extended structures. By default the filter will
			skip over map pixels that are above the 'blanking' S/N 
			level (>6 by default). Thus any structure above this 
			significance level will remain unfiltered.
			Filtering is useful to get deeper in the map when 
			retaining the very faint extended structures is not 
			an issue. Thus filtering above 5 times the source size
			(see 'sourcesize') is default when the filter is used.
			See the advanced configuration section for further
			details on fine tuning the large-scale structure 
			filter.	

	source.fixedgains	Specifies to use the fixed source gains 
			        (e.g. from an RCP file -- see 'rcp' key).
			Normally, crush calculates source gains based on the 
			correlated noise response and the specified point
			source couplings (e.g. as derived from the two gain
			columns of RCP files.)

	system=<type>	Select the coordinate system for mapping. The default
			is 'equatorial'. Other possibilities are 'horizontal'
			'ecliptic', 'galactic' or 'supergalactic'. Each of 
			these values is additionally aliased to simple keys. 
			Thus, you may use:
			
			   > crush -galactic [...]
			   
			as a shorthand for '-system=galactic'.
			       
	unit=xxx	Set the output to units xxx. You can use either the
			instrumental units (e.g. 'V/beam' or 'counts/beam') or
			the more typical 'Jy/beam' (default), as well as their
			common multiples (e.g. 'uJy/beam', or 'nV/beam').	




### 3.4. Scan Configuration

 Some options relate to the scans, helping to configure and handle them
 These options are specified *before* the list or range of scans to
 which they apply, and remain valid for all scans read after, or until
 an overriding option is placed. E.g.

	> ./crush -option1=x 10218-10532 12425 -option2=y 11411 \
	          -option1=z 10496

 will set option1 to 'x' for all scans but the last one, which will have
 this option set to 'z'. And the last two scans will have option2
 set to 'y'.

 A detailed listing of all scan specific options can be found in the 
 'GLOSSARY'. Here are a few of the most commonly used ones (in alphabetical
 order).


	pointing=dx,dy	  Specify incremental pointing offsets x,y in the
			  system of the telescope mount (I.e., azimuth and
			  elevation for horizontal mounts. (Note, this option
			  works like pcorr in APECS). 

	datapath=<dir>	  Start looking for raw data in directory <dir>. Some
			  instruments may also interpret it as a root directory
			  in which data may reside some specific hierarchy. E.g.
			  in <dir>/<project> for APEX bolometers. Thus, if an
			  APEX instrument defines:
				
				datapath /homes/data
				project T-79.F-0002-2007

			  then crush will try to find data first in
			  '/homes/data', then in '/homes/data/T-79.F-0002-2007'
			  This provides a convenient way for accessing
			  hierarchically stored data. See the instrument-
			  specific usage of 'datapath' in the GLOSSARY.
 
	jackknife	  Jackkniving is a useful technique to produce accurate
			  noise maps from large datasets. When the option is 
			  used the scan signals are randomly inverted, s.t. the
			  source signals in large datasets will tend to cancel 
			  out, leaving one with pure noise maps.

	project=<id>      Some instruments (e.g. APEX bolometers) may require 
			  a project ID to be set in order to locate scans by 
			  serial number. Use capitalized form when defining 
			  APEX projects. E.g.,

                              project  T-79.F-0002-2007

	read <filename>	  Read the scan data from <filename>, which can be 
			  either a fully specified path, or relative to
			  'datapath'. (On the command line it is sufficient
			  to list the filename without a preceding dash.)

	read scanNo	  Read scan number scanNo (scripting only).
			  in command line mode, ommit '-read='.

	read from-to	  Read the range of scan numbers between from and to.
	     		  (inclusive). On the command line, you can omit 
			  '-read=' and simply list the scan range.

	read X Y [...]    You can combine scan numbers and different ranges
			  in a space-spearated list...
			
	read...		  As mentioned, the 'read' keys only apply to scripts.
			  Thus, 

				read 10755-10762             # in script

			  and

				> ./crush [...] 10755-10762  # command line

			  are equvivalent.
				
	scale=X		  Scale the fluxes by X. With this option you can apply
			  calibration corrections to your data.

	scale=<filename>  Alternatively, scan specific scaling can be defined
			  by an appropriate calibration file, which among 
			  other things, contains the ISO time-stamp and	
			  the corresponding calibration values for each scan.
			  The filename may contain references to environment
			  variables enclosed in {} brackets. E.g.:

			    scale={$HOME]}/laboca/scaling.dat

	scramble	  Another technique for generating noise maps, which 
			  can be used also for small datasets, for which
			  jackknifing cannot be used. This approach scrambles
			  the pixel positions, such that the source signals
			  will be smeared out in the maps.

	tau=X		  Specify a zenith tau value to use. When not used
			  minicrush will try to interpolate from
			  <instrument>/<instrument>-taus.master.dat if possible
			  or use 0.0 as default.

	tau=<filename>	  Alternatively, tau can also specify a file-name with 
			  lookup information (usually containing tau
			  values from the radiometer or from the skydips).
			  Tau values will be interpolated for each scan,
			  as long as the scan falls inside the interpolator's
			  range. Otherwise, tau of 0.0 will be used. The 
			  filename may contain references to environmnent 
			  variables enclosed in {} brackets. E.g.:

			    tau={$HOME}/laboca/tau.dat



### 3.5. Instrument Configuration

 There are various instrument configuration files. These reside in the
 corresponding instrument subdirectories inside the main crush directory.
 Some types of files are commonly used among many or all instruments, while 
 others may be strongly instrument specific. 

 In most cases the instrument configurations should be set correctly, and 
 you probably can leave these settings alone. However, here you will find
 some of the most common instrument configuration options that you may, at 
 times, want to adjust to your preference. 

 A more complete list of the available instrument-specific configuration
 options can be found in the GLOSSARY.


#### Generic Instrument Parameters


	pixeldata=<filename>	Specifies a pixel data file, providing initial
				gains, weights and flags for the detectors,
			and possible other information as well depending on the
			specific instrument. Such files can be produced via the
			'write.pixeldata' option (in addition to which you
			may want to specify 'forget=pixeldata' s.t. flags are
			determined without prior bias).

	rcp		Specify pixel positions (and optionally point-source
			and sky-noise gains). These are standard IRAM
			or APEX RCP files containing the information in ASCII
			columns. RCP files can be produced by the 'pixelmap' 
			option, from scans, which move a bright point source 
			over all pixels.

	rcp.gains	Use gains from the RCP files. Otherwise gains may 
			come from the 'pixeldata' file, or assume default
			values, such as 'uniform'.

	rcp.center=x,y	Define the center RCP position at x,y in arcseconds.
			Centering takes place immediately after the parsing
			of RCP data.

	rcp.rotate=X	Rotate the RCP positions by X degrees (counter 
			clockwise). Rotations take place after centering (if
			specified).

	rcp.zoom=X	Zoom (rescale) the RCP position data by the scaling
			factor X. Rescaling takes place after the centering
			(if defined).	

	stability=X	Specify the instrument 1/f stability time-scale in
			seconds. This is used for determining optimal 1/f
			filtering of the time-streams in the reduction.



### 3.6. Advanced startup environment and Java configuration

 We have seen before how to configure the startup environment and Java by
 placing configuration snipplets inside the directory `~/.crush2/startup/`. 
 However, what if you want certain settings to apply to just a specific 
 program within the crush suite (e.g. to `crush` or `show`) only, but not 
 to all of them? That too is possible, by (creating and) editing a file
 under the corresponding `~/.crush2/startup/<progname>` directory. E.g.:

	~/.crush2/startup/crush/myconfig.conf

 will source the bash snippled contained in `myconfig.conf` for reductions
 (`crush` executable) only. As with other startup scripts, the name of the
 file itself is irrelevant, and all files will be parsed inside the 
 program's startup directory (albeit in unspecified order!).

 Inside this file you can set up environment variables, and add shell 
 (bash) scripts. E.g., the `crush` startup configuration file may contain 
 the lines:

	CRUSH_NO_UPDATE_CHECK="1"
	EXTRAOPTS="$EXTRAOPTS -Djava.awt.headless=true"

 (The first disables update checking, the second adds headless mode to the
 list of extra Java options already defined).



--------------------------------------------------------------------------
  

## 4. Correlated Signals


The removal of correlated signals, atmospheric or instrumental, is really the
heart of CRUSH. In its most generic form the decorrelation is a two-step
process: the first step finds and removes the correlated signals, assuming
some initial detector gains to it, after which the gains are estimated during 
the second step based on the individual detector responses to the bolometer
signals. (For details, see the CRUSH paper: Kovacs 2008, Proc. SPIE, 7020, 45.)
Flagging of non-responsive pixels, based on outlying gains (i.e. responses to
the correlated signals) may be part of the second step of the decorrelation.



### 4.1. Modes and Modalities

 For each instrument, crush defines a set of _modalities_ (i.e. a set of
 correlated modes) on which decorrelation may be performed. Each mode in a
 _modality_ affects a _group_ of pixels. Thus, the collection of pixel groups
 with related modes constitutes a _division_. For example, SHARC-2 has 12 
 detector rows (each with 32 pixels). The dividing of pixels into 12 groups,
 each representing a detector row, is a pixel _division_. Pixels in a given 
 row respond to the same correlated _mode_, and so there are 12 row-related 
 modes, which are bunched together in a _modality_.

 Some of the modalities (and pixel divisions) are common to all (or most)
 instruments. These are:

   `<modality name>` |	Description
   ----------------|-------------------------------------------------------
   `all`	   |	All channels, regardless of their state
   `live`	   |	All channels that aren't dead.
   `detectors`	   |	All detectors (e.g. excluding resistors etc.)
   `obs-channels`  |	All observing detectors (e.g. that see sky).
   `gradients`	   |	A focal plane gradients of 'observing' detectors.
   `blinds`	   |	Blind detectors (if exist)
   `telescope-x`   |	Telescope position in the _x_ direction (e.g. AZ)
   `telescope-y`   |	Telescope poistion in the _y_ direction (e.g. EL)
   `accel-<dir>`   |	Acceleration in some direction (see below).
   `chopper-<dir>` |	Chopper motion in some direction (see below).
  


 Above, the motion-related modalities may have the following directionalities:



   `<dir>`  |  Description
   ---------|-------------------------------
   `x`      |  _x_ direction.	
   `y`      |  _y_ direction.
   `x^2`    |  square of the _x_ coordinate.
   `y^2`    |  square of the _y_ coordinate.
   `|x|`    |  _x_ magnitude.
   `|y|`    |  _y_ magnitude.
   `mag`    |  vector magnitude.
   `norm`   |  square of vector magnitude.




### 4.2. Removing Correlated Signals

 The decorrelation step is invoked by:

	correlated.<modality-name>

 For example, a decorrelation of the signals induced by the chopper 
 displacement in x (e.g. SHARC-2) is invoked by:

	correlated.chopper-x

 (Of course, the same keyword must also appear in the pipeline 'ordering', 
 for the step to actually take place during the reduction process -- 
 otherwise crush will not know when to correlated.the chopper signals.)

 You can fine-tune how CRUSH deals with each correlated mode. For example, 
 the following lines:

	correlated.obs-channels.resolution 1.0
	correlated.obs-channels.gainrange 0.3--3.0

 Specifies that atmospheric signals, which appear in all observing channels, 
 should be correlated. only every second (vs. the default every available 
 frame), and that any channel that exhibits a response outside of 0.3--3.0 
 times the 'average' response of the array, should be flagged, and ignored 
 in the reduction afterwards.



### 4.3. User-defined Modalities

 In addition to the most common modalities listed above, each instruments 
 defines its specific ones (e.g. `rows` for SHARC-2 from the example above). 
 See the README files in the instrument sub-directories of crush for a full 
 list of  predefined instrument specific modalities. You can also define your 
 own pixel groups, divisions and modalities using the `group` and `division` 
 keywords. Here is an example:

	group.my-group-1 10,13,20-25
	group.my-group-2 40-56,78,80-82
	division.my-division my-group-1 my-group-2

 The first two lines defines two pixel groups (`my-group-1` and `my-group-2`) 
 from pixel indexes and ranges, while the last line creates a division 
 (`my-division`) from these pixel groupings. CRUSH will also create a 
 correlated modality with the same name as the division. So, given the 
 definitions above you can correlated.on `my-division` by:

	correlated.my-division



## 5. Custom Logging Support

CRUSH (as of version 2.03 really) provides a poweful scan/reduction logging
capability via the `log` and `obslog` keys. 

`log` writes the log entries for each scan *after* the reduction, whereas 
`obslog` does not reduce data at all, only logs the scans immediately after 
reading them. While both logging functions work identically, some of the 
values are generated during reduction, and therefore may not be available to
`obslog`.




### 5.1. Log Files and Versioning

 You can specify the log files to use with the `log.file` and `obslog.file`
 keys (the default is to use `<instrument>.log` and `<instrument>.obs.log` in 
 the `outpath` directory). Equivalently, you can also set the filename 
 directly as an optional argument to `log` and `obslog`:

	> crush [...] -log=myLog.log [...]

 You can specify the quantities, and the formatting in which they will appear,
 using the `log.format` and `obslog.format` keys. Below you will find more
 information on how to set the number formatting of quantities and a list
 of values available for the logging.
   
 A log file always has a fixed format, the one which was used when creating 
 it. Therefore, a conflict may arise if the same log file is specified for 
 use with a different format. The policy for resolving such conflicts can be
 set via the `log.conflict` and `obslog.conflict` keys, which can have one
 of the following values:

	overwrite   Overwrites the previous log file, with a new one in the
		    newly specified format

	version	    Tries to find a sub-version of the same log file (with .1,
		    .2, .3 ... extension added) in the new format, or create
		    the next available sub-version.

 The default behaviour is to assume versioning, in order to preserve 
 information in case of conflicts.




### 5.2. Decimal Formatting of Values

 Many of the quantities you can log are floating point values, and you have
 the possibility of controlling how these will appear in your log files. 
 Simply put one of the formatting directives in brackets after the value
 to specifts its format. 

 E.g. the keys `RA` or `RAh` will write the right-ascention coordinate either
 as radians or as hours, with the default floating point formats. However,
 `RA(h:2)` will write the value in human-readable `hh:mm:ss.ss` format, 
 whereas `RAh(f3)` will express it as `hh.hhh`.

 You can choose from the following formats to express various quantities.
 Be careful, because not all formats are appropriate to all types of data.
 (For example, you should not try to format angles expressed in degrees with
 the DMS formatting capabilities of the `a` angle formats. Use these only
 with angles expressed in radians!)


	d0...d9		Integer format with 0...9 digits. E.g. 'd3' will write
			Pi (3.1415...) as 003.

	e0...e9		Exponential format with 0...9 decimals. E.g. e4 will
			write Pi as 3.1415E0.

	f0...f9		Floating point format with 0...9 decimals. E.g. f3 will
			write Pi as 3.141.

	s0...s9		Human readable format with 0...9 significant figures 
			(floating point or exponential format,
			whichever is more compact).

	a:0...a:3
	as0...as3
	al0...al3	Angle format with 0...3 decimals on the seconds. E.g.
			'a:1' produces angles in ddd:mm:ss.s format. Use only
			with values expressed as radians (not in degrees!).
			As such, 'a:1' will format Pi as '180:00:00.0'. The
			difference between the 'a:', 'as', and 'al' formats is
			the separators used between degrees, minutes and seconds
			(colons, symbols, and letters respectively).

	h:0...h:3
	hs0...hs3
	hl0...hl3	Hour-angle format (e.g. for RA coordinate) with 0...3
			decimals on the seconds. E.g. 'h:2' formats angles in
			'hh:mm:ss.ss' format. Use only with values expressed
			as radians (not in degrees!). As such 'h:2' will format
			Pi as '12:00:00.0'. The difference between the 'h:', 
			'hs', and 'hl' formats is the separators used between 
			hours, minutes and seconds (colons, symbols, and 
			letters respectively).

			E.g. Pi will be:

				h:1	12:00:00.0
				hs1	12h00'00.0"
				hl1	12h00m00.0s

	t:0...t:3
	ts0...ts3
	tf0...tf3	Time format with 0...3 decimals on the seconds. E.g.
			't:1' formats time in 'hh:mm:ss.s' format. Use only
			on time values expressed in seconds! The difference 
			between the 't:', 'ts', and 'tl' formats is the 
			separators used between hours, minutes and seconds 
			(colons, symbols, and letters respectively).


	

### 5.3. Loggable Quantities

 Currently, CRUSH offers the following quantities for logging. Directives
 starting with '?' will log the values of configuration keys. Other 
 quantitites reflect the various internals of the scan or instrument state.
 More quantities will be added to this list in the future, especially 
 values that are specific to certain instruments only. Keep an eye out for
 changes/addititions :-).


    ?<keyword>       The value of the configuration <keyword>. If the
                     configuration option is not defined '---' is written.
                     If the keyword is set without a value, then '<true>'
                     is written.

    AZ               Azymuth coordinate (in radians). E.g. 'AZ(a:1)'
                     produces ddd:mm:ss.s formatted output. See also 'AZd' 
                     and 'EL'.

    AZd              Azymuth coordinate in degrees. E.g. 'AZd(f2)'
                     produces output in ddd.dd format. See also 'AZ' and 
                     'ELd'

    channels         Number of channels processed in the reduction. See
                     also 'okchannels' and 'maxchannels'.

    chopeff          Chopper efficiency.

    chopfreq         Chopper frequency (in Hz).

    chopthrow        Chopper throw (2x amplitude).

    creator          Software that created the data file (as stored by
                     the FITS CREATOR keyword).

    date             Date (and time) of the observation. E.g. 
                     'date(yyyy-MM-dd)'. The format follows the rules for 
                     Java's SimpleDateFormat class.
			
    DEC              Declination coordinate (in radians). E.g. 'DEC(a:0)'
                     produces the declination in ddd:mm:ss format. See also
                     'RA' and 'DECd'.

    DECd             Declination coordinate (in degrees). E.g. 'DECd(f1)'
                     produces output in ddd.d format. See also 'RAh' and
                     'DEC'.

    descriptor       A descriptor string for the scan (e.g. the scan number
                     or file name used to invoke the scan).

    dir              Scanning direction. E.g. 'HO', 'EQ', 'EC', 'GL', 'SG'.

    EL               Elevation coordinate (in radians). 
	
    ELd              Elevation coordinate (in degrees).

    epoch            Full coordinate epoch, e.g. (J2000.0).

    epochY           E.g. epochY(f1) -> 2000.0

    frames           Number of unflagged frames in the scan.

    FWHM             Mean beam FWHM of the instrument (in 'sizeunit').

    gain             Instrument gain.

    generation       Source model generation.

    hipass           Highpass filtering timescale (in seconds)

    humidity         Ambient humidity (if recorded).

    id               Scan identifier (e.g. scan number)

    integrations     Number of integrations (subscans) contained in the 
                     scan.

    LST              Local Sidereal Time (in seconds). E.g. use 'LST(t:1)'
                     to format is as 'hh:mm:ss.s'.

    LSTh             LST in hours.

    maxchannels      Maximum number of channels the instrument can have
                     (effectively the number of channels stored in the
                     data file).

    maxFWHM          Smallest beam of the instrument (in sizeunit).

    minFWHM          Largest beam of the instrument (in sizeunit).

    MJD              Modified Julian Date of the scan.

    mount            The focus in which the instrument is mounted.

    NEFD             Average Noise Equivalent Flux Density (Jy sqrt[s]) as a
                     measure of the array sensitivity.

    object           Name of observed object.

    observer         Name(s) of the observer(s).

    obshours         Effective on-source time (in hours).

    obsmins          Effective on-source time (in minutes).

    obstime          Effective on-source time (in seconds).

    okchannels       Number of good (unflagged) channels.

    PA               Mean parallactic angle (in radians).

    PAd              Mean parallactic angle in degrees.

    pnt.angle        Source elongation angle on map (degrees).

    pnt.asymX        Asymmetry in telescope X (%). 

    pnt.asymY        Asymmetry in telescope Y (%). `

    pnt.AZ           Azymuth pointing (arcsec).

    pnt.EL           Elevation pointing (arcsec).

    pnt.DEC          Declination pointing (arcsec).

    pnt.dasymX       Asymmetry uncertainty in telescope X (%).

    pnt.dasymY       Asymmetry uncertainty in telescope Y (%). `

    pnt.dangle       Source elongation angle error (deg).

    pnt.dAZ          Azymuth pointing residual (if available).

    pnt.dDEC         Pointing residual in the declination dir (if available).
	
    pnt.dEL          Elevation pointing residual (if available).

    pnt.delong       Source elongation error (%).

    pnt.delongX      Source elongation error in telescope X direction (%).

    pnt.dNasX        Pointing residual in the Nasmyth X dir (if available).

    pnt.dNasY        Pointing residual in the Nasmyth Y dir (if available).

    pnt.dRA          Pointing residual in the RA direction (if available).

    pnt.dX           Pointing residual in native X direction.

    pnt.dY           Pointing residual in native Y direction.

    pnt.elong        Source elongation (%).

    pnt.elongX       Source elongation in telescope X direction (%).

    pnt.RA           RA pointing (arcsec).

    pnt.X            Aggregated X pointing correction (including applied
                     corrections and sometimes the pointing model too).

    pnt.Y            Aggregated Y pointing correction (including applied
                     corrections and sometimes the pointing model too).

    pressure         Ambient pressure (if recorded) in hPa.

    project          Project name (if defined)

    ptfilter         The point-source flux filtering throughput of the 
                     reduction.

    RA               Right-ascention coordinate (in radians). E.g. use
                     'RA(h:2)' to format as 'hh:mm:ss.ss'.

    RAd              Right-ascention coordinate (in degrees).

    RAh              Righ-ascention coordinate (in hours).

    rate             Sampling rate of the data (Hz). See also 'sampling'

    resolution       Instrument resolution (i.e. FWHM of the main beam).
                     in 'sizeunit'.
	
    rmsspeed         RMS fluctuation of the scanning speed (arcsec/s).

    sampling         Sampling interval (seconds). The inverse of 'rate'.

    scale            Scaling factor applied to the scan. 

    scanspeed        Average scanning speed (arcsec/s).

    serial           Serial number of the scan.

    sizeunit         Size unit for measuring resolutions. E.g. 'arcsec'. 

    src.a            Major axis (arcsec) of the source ellipse.

    src.angle        Orientation of the source ellipse (deg).
	
    src.b            Minor axis (arcsec) of the source ellipse.

    src.da           Uncertainty of the minor axis (arcsec).
	
    src.dangle       Uncertainty of the orientation (deg).

    src.db           Uncertainty of the major axis (deg).

    src.dFWHM        Uncertainty of the source FWHM (arcsec).

    src.dint         Uncertainty of the integrated source flux (Jy). 

    src.dpeak        Uncertainty of the peah source flux (Jy/beam).

    src.FWHM         Source FWHM (arcsec).

    src.int          Integrated source flux (Jy) insize and adaptive
                     aperture.

    src.peak         Peak source flux (Jy/beam).

    stat1f           A measure of the 1/f noise averaged over the array.
                     The configurations options '1overf.freq' and 
                     '1overf.ref' define the frequencies for the 1/f
                     measurement and white-noise reference respectively.

    Tamb             Ambient temperature (if recorded) in degrees C.

    tau              The in-band, line-of-sight opacity value.

    tau.<id>         The zenith tau value for <id>. E.g. 'tau.225GHz' or
                     'tau.PWV' if these are defined by appropriate scaling
                     relations.

    UT               UT in seconds. E.g. use 'UT(t:1)' to format is as 
                    'hh:mm:ss.s'.

    UTh             UT in hours.

    weight          The relative weight of the scan, based on the actual
                    noise of the map it generates.

    winddir         Wind direction (if recorded) in degrees.

    windpk          Peak wind speed (if recorded) in m/s.
	
    windspeed       Wind speed (if recorded) im m/s.

    zenithtau       In-band opacity at zenith.


#### Source model specific log entries

    map.beams        Number of (smoothed) beams in the map.

    map.contentType  Type of data stored in the map.

    map.creator      Creator's name or description.
	
    map.depth        Weighted average depth of the map in map units.

    map.max          Maximum value in map units.

    map.min          Minimum value in map units.

    map.name         Name of map data (e.g. object's name)

    map.points       Number of pixels in the map.

    map.rms          Typical RMS of the map in map units.

    map.size         Size of the map in pixels e.g. '121x432'.

    map.sizeX        Map size in the 'x' direction (pixels).

    map.sizeY        Map size in the 'y' direction (pixels).

    map.system       Coordinate system id, e.g. 'HO', 'EQ', 'GL' etc.

    map.unit         Name of map unit, e.g. 'Jy/beam'.

    phot.flux        Photometric flux in Jy/beam (e.g. for LABOCA).

    phot.dflux       Uncertainty in the photometric flux (Jy/beam).

    skydip.kelvin    Data units that corresponf to a 1K load on the detectors.
                     (for skydip data, if and when fitted.)

    skydip.dkelvin   Uncertainty in data units per kelvin conversion.

    skydip.tau       Tau value derived (or assumed) from skydip data
   
    skydip.dtau      Tau uncertainty from skydip data

    skydip.tsky      Derived (or assumed) sky temperature in K.

    skydip.dtsky     Sky temperature uncertanity (K).

    smooth           Smoothing applied, in the default size unit of
                     the instrument (e.g. in arcsecs).




#### Telescope specific log entries

   APEX: see the `crush/Documentation/README.apex.


#### Instrument specific log entries

   See the `crush/Documentation/README.<instrument>`, for each `<instrument>`.
  
	
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## 6. Supported Cameras

Currently, CRUSH supports the following instruments (in alphabetical order):

   
    GISMO        (2mm) Goddard-IRAM Superconducting 2-Millimeter Observer
                 www.iram.es/IRAMES/mainWiki/GoddardIramSuperconductingTwo\
                 Millimeter

    LABOCA       (870um) Large APEX Bolometer Camera
                 www.apex-telescope.org/bolometer/laboca

    PolKa        (polarimetry) Polarimeter for LABOCA
                 www.mpifr-bonn.mpg.de/staff/gsiringo/laboca/laboca\
                 _polarimeter.html

    SABOCA       (350um) Submillimeter APEX Bolometer Camera
                 www.apex-telescope.org/bolometer/saboca

    SCUBA-2      (450um, 850um) Submillimetre Common User Bolometer Array 2
                 www.roe.ac.uk/ukatc/projects/scubatwo

    SHARC-2      (350um, 450um, 850um) The second-generation Submillimeter 
                 High-Angular Resolution Camera
                 Caltech, Pasadena, CA
                 www.submm.caltech.edu:/~sharc

    SOFIA/HAWC+  (53um, 62um, 89um, 155um, 216um)
                 High-resolution Airborne Wide-angle Camera


The following instruments have legacy support only (supported by CRUSH 2.4x
and earlier releases):


    ASZCa        (2mm) APEX SZ Camera, from Berkeley, CA
                 bolo.berkeley.edu/apexsz/instrument.html

    MAKO         (350um) KID technology demonstration camera for the CSO.

    MAKO-2       (350um, 850um) Second-generation KID technology demonstration
                 camera for the CSO with dual-pol pixel response, and dual-band 
                 imaging capability.

    MUSTANG-2    (3mm) Large focal plane array for the 100m Greenbank Telescope.
                 www.gb.nrao.edu/mustang/

    p-ArTeMiS    (200um, 350um, 450um) 3-color camera for APEX (prototype)
                 www.apex-telescope.org/instruments/pi/artemis

    SHARC        (350um, 450um) Submillimeter High-Angular Resolution Camera
                 Caltech, Pasadena, CA
                 http://www.submm.caltech.edu/cso/sharc/cso_sharc.html




Further support for instruments is possible. If interested to use CRUSH for
your bolometer array, please contact Attila Kovacs 
`<attila[AT]sigmyne.com>`.

In principle, it is possible to extend CRUSH support for other types of scanning
instruments, like heterodyne receiver arrays, or single-pixel receivers that
scan in frequency space, or for the reduction of line-surveys from double
side-band (DSB) receivers. Such new features may appear in future releases, 
especially upon specific request and/or arrangement...


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## 7. Future Developments (A Wish List...)


There are a number of plans for new features in CRUSH. Some may come in the
near future, others perhaps later, depending on the resources available for
implementation. Nonetheless, the following avenues of feature enrichment are
being considered. 


### 7.1. Support for Heterodyne Receivers and Interferometry

 CRUSH was born as a bolometer array reduction package. However, there is no
 reason why many of its principles could not be applied to other types of 
 instruments (astronomical or otherwise), especially those, which are affected
 by correlated signals. Besides, CRUSH also provides powerful tools for other
 analysis steps, like weighting, despiking, spectral filtering, and mapping.

 Two obvious extensions would be heterodyne receivers (and receiver arrays) 
 and the use of CRUSH for interferometry (e.g. ALMA) since it is well-suited
 to deal with immense data volumes also.


### 7.2. Interactive Reductions

 At present CRUSH offers only a reduction pipeline. This is ideal for
 crunching large volumes of data in a more-or-less automated fashion, and 
 for making reduction painless. It is also ideal for most users, who might 
 not wish to learn about the intricacies of each and every reduction step. 
 However, in some cases having more control may be beneficial.

 Many astronomers are used to interactive reduction packages (e.g. GILDAS
 AIPS, BoA etc.). CRUSH should eventually offer such a capability also. This
 would allow step-by-step reductions, together with varous plotting 
 capabilities to look at data at every stage. Such a capability would be
 very useful in the process of building pipelines for new instruments

 It should be relatively simple to provide this feature. The current 
 configuration languange of CRUSH can be easily adapted for more interactive
 use. Even more detailed control may be possible though a standard scripting
 language like JavaScript or Rhino. The main job would be to supply the
 essential plotting capabilities, but that too may come sooner than later...


### 7.3. Distributed and GPU Computing

 The reduction paradigm of CRUSH is massively parallelizable. CRUSH can
 already make good use of any number of processing cores within a computer.
 It should be quite staighforward to extend implementation over several
 computing nodes and super-computers, allowing orders of magnitude increases
 in data reduction speeds and data volumes.

 Another way of improving speeds may come from the use of Graphical (GPU)
 Computing. Today's grahics chips provide computing power well in excess of
 that offered by the CPUs. This can be harnessed with programming tools
 like CUDA or OpenCL. GPU computing is still in its infancy, and thus
 its languange specifications are likely very fluid. But technical
 details aside, GPUs clearly offer a way for boosting the number crunching
 performace of CRUSH. 


### 7.4. Graphical User-Interface (GUI)

 The addition of a Graphical User Interface (GUI) to CRUSH would make 
 configurations more transparent and intuitive. It would allow users, who do 
 not use CRUSH often, to avoid learning the complexities of command-line
 options and scripting support, and instead click their way through the
 essential configuration settings.

 GUIs may also aid the more expert users, in providing a way to look at 
 details, such as monitoring quantities, signals or maps during the reduction.


-----------------------------------------------------------------------------

## 8. Further information


CRUSH-2 is the next-generation data reduction package, inheriting its DNA from
the pioneering SHARC-2 specific version (crush-1.xx) and from the APEX specific
minicrush implementation. It is a much more capable package than either of its
predecessors. However, because the output FITS images are backward compatible 
with the  older versions (for the most part), parts of the original CRUSH 
package can still be useful for manipulating images post reduction.

Mainly, the crush-1.xx distribution provides tools for displaying (`show`), 
minupulating (`imagetool`), and coadding (`coadd`) or differencing 
images (`difftool`), and  producing histogram (`histogram`) from them.

Downloading the CRUSH package(s), and further information on the FITS images
is available at:

  http://www.sigmyne.com/crush

I hope you'll find this helpful and may you end up with beautiful images!!!


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Copyright (C)2019 -- Attila Kovacs 

