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--- public:user_software:documentation:makesourcedb [2022-04-29 11:46] – [Format string] Add OrientationIsAbsolute Tammo Jan Dijkema
+++ public:user_software:documentation:makesourcedb [2022-10-21 14:25] (current) – Fix non logarithmic si definition Tammo Jan Dijkema
@@ Line 36: / Line 36: @@
 </code>
-tells that the lines in the input file contain source name, ra, and dec. It also tells that the values on each line are separated by commas.
+tells that the lines in the input file contain source name, ra, and dec. It also tells that the values on each line are separated by commas. A field name can consist of alphanumeric characters, underscores and colons. A colon cannot be the first character. All other characters (including whitespace) can be used as separator. A colon can also be used as field separator as long as it is surrounded by whitespace in the format string (to distinguish it from a colon in a field name).
-A field name can consist of alphanumeric characters, underscores and colons. A colon cannot be the first character.
-All other characters (including whitespace) can be used as separator. A colon can also be used as field separator as long as it is surrounded by whitespace in the format string (to distinguish it from a colon in a field name).
 A few special options are available in the format string.
@@ Line 65: / Line 63: @@
 </code>
-means that the third field is skipped.  Note that the name ''dummy''  has to be used if whitespace is used as separator like:
+means that the third field is skipped. Note that the name ''dummy''  has to be used if whitespace is used as separator like:
 <code>
@@ Line 75: / Line 73: @@
   * Directly in the program ''format''  keyword.
-  * As a format line in the input file (before the first value line) or optionally in a separate text file. Such a format line has to start with ''format=''  (whitespace is allowed).  For backward compatibility the format line can also be given as a special comment line like ''#(…)=format'', where … is the format string. Whitespace can be used.
+  * As a format line in the input file (before the first value line) or optionally in a separate text file. Such a format line has to start with ''format=''  (whitespace is allowed). For backward compatibility the format line can also be given as a special comment line like ''#(…)=format'', where … is the format string. Whitespace can be used.
 === Field types ===
-makesourcedb distinguishes two types of fields: standard fields and other fields.  The standard fields have a predefined (case-insensitive) name. However, the name is case-sensitive in the sense that the name given in the table below is used as the parameter name in the parm table.  The following standard fields are known:
+makesourcedb distinguishes two types of fields: standard fields and other fields. The standard fields have a predefined (case-insensitive) name. However, the name is case-sensitive in the sense that the name given in the table below is used as the parameter name in the parm table. The following standard fields are known:
 ^Field^Type^Unit^Default^Description|
@@ Line 93: / Line 91: @@
 |MinorAxis|double|arcsec|1|FWHM of minor axis for a Gaussian source|
 |Orientation|double|deg|1|Orientation of the major axis in degrees North over East|
-|OrientationIsAbsolute|boolean| |false| |
+|OrientationIsAbsolute|boolean| |false|Whether the Orientation is absolute (w.r.t. declination axis) or relative (w.r.t. m axis in not-specified field). See the note below.|
 |IShapelet|string| | |Name of the ASCII file defining the shapelet coefficients and scale of the I flux in the 'Sarod' format. Note that field ''I'' gives the total flux, while ''IShapelet'' defines the shape.|
-|QShapelet|string| |_ckgedit_QUOT__ckgedit> | Idem for Q flux. An empty name means that no Q flux is present. Note that the Q (and U) flux can still be given using RotationMeasure. | UShapelet | string | _ckgedit_QUOT__ckgedit>|Idem for U flux.|
+|QShapelet|string| | |Idem for Q flux. An empty name means that no Q flux is present. Note that the Q (and U) flux can still be given using RotationMeasure.|
-|VShapelet|string| |""|Idem for V flux.|
+|UShapelet|string| | |Idem for U flux.|
+|VShapelet|string| | |Idem for V flux.|
 |SpectralIndex|doubles| |[]|Spectral index. Multiple values can be given enclosed in square brackets and separated by commas. The n-th value defines the n-th order term. \\ Note that the old way of specifying the spectral index (using SpectralIndexDegree and SpectralIndex:i) is not supported anymore. If used, an error is given.|
+|LogarithmicSI|bool| true |Determines the meaning of the spectral index. See Logarithmic SI below|
 |ReferenceFrequency|double|Hz| |Reference frequency (in Hz) for the spectral index|
 |RotationMeasure|double|rad/m<nowiki>^</nowiki>2| |Rotation measure for the polarized flux Q and U|
 |PolarizationAngle|double|rad|0|Polarization angle (in radians) for the polarized flux|
 |PolarizedFraction|double| |0|Fraction of I that is polarized|
-|ReferenceWavelength|double|m|c/ReferenceFrequency|Reference wavelength (in m) if RM is specified using Q and U|
+|ReferenceWavelength|double|m||Reference wavelength (in m) if RM is specified using Q and U|
 |Category|integer| |2|Source category (must be 1, 2, or 3)|
 |Patch|string| | |Patch name|
@@ Line 117: / Line 117: @@
 Note that the polarized flux can be given directly (as Q and U) or by means of the rotation measure, polarization angle, and polarized fraction. An error is given if both are given for the same source.
+=== Logarithmic Spectral Index ===
+If ''LogarithmicSI'' is ''true'' (the default), the source intensity 'I' is computed as
+''I = I0 * (v/v0) ^ (c0 + c1 * log10(v/v0) + c2 * log10(v/v0)^2 + ...)'', where 'v' is the frequency and 'v0' is the reference frequency.
+If ''LogarithmicSI'' is ''false'', the spectral index is interpreted in a way compatible with wsclean, namely as
+''I = I0 + c0 * (v/v0 - 1) + c1 * (v /v0 - 1)^2 + c2 * (v/v0 -1)^3 + ...''
+This definition is also described in the [[https://wsclean.readthedocs.io/en/latest/component_list.html|WSClean documentation]].
 === Using Rotation Measure ===
@@ Line 130: / Line 141: @@
 A source is attached to a patch if its input line contains a patch name. A line defining that patch should have been processed before this line. \\ If no patch name is given for a source (as is usually the case), the source forms a patch in itself and the source name is used as the patch name (with an optional prefix/suffix). In this way BBS can always deal with patches.
+=== Orientation of Gaussian sources ===
+Until 2022, the orientation of Gaussian sources has been interpreted somewhat wrong. It was interpreted (both by DP3 and pybdsf) as the angle with respect to the m axis of a certain image. The correct (implicit) definition is the orientation w.r.t. the declination axis. For fields far away from the NCP, and/or sources not too far from the field center, these two definitions are almost identical.
+In DP3 v5.3 a fix was implemented to take the projection effects into account properly. This fix is only called when OrientationIsAbsolute is true. A script will be added to LSMTool to convert from 'relative' orientation to absolute ones (this script needs the phase center of the original image as an input).