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diff --git a/noao/onedspec/doc/identify.hlp b/noao/onedspec/doc/identify.hlp new file mode 100644 index 00000000..fea7086c --- /dev/null +++ b/noao/onedspec/doc/identify.hlp @@ -0,0 +1,810 @@ +.help identify Jan96 noao.onedspec +.ih +NAME +identify -- Identify features in one dimensional image vectors +.ih +SUMMARY +Features are interactively marked in one dimensional image vectors. +The features may be spectral lines when the vector is a spectrum +or profile positions when the vector is a spatial cut. A function +may be fit to the user coordinates as a function of pixel coordinates. +This is primarily used to find dispersion functions for spectra +such as arc-line calibration spectra. The profile position measurements +are generally used for geometric calibrations. +.ih +USAGE +identify images +.ih +PARAMETERS +.ls images +List of images in which to identify features and fit coordinate functions. +.le +.ls section = "middle line" +If an image is not one dimensional or specified as a one dimensional image +section then the image section given by this parameter is used. The +section defines a one dimensional vector. The image is still considered to +be two or three dimensional. It is possible to change the data vector +within the program. + +The section parameter may be specified directly as an image section or +in one of the following forms + +.nf +line|column|x|y|z first|middle|last|# [first|middle|last|#]] +first|middle|last|# [first|middle|last|#] line|column|x|y|z +.fi + +where each field can be one of the strings separated by | except for # +which is an integer number. The field in [] is a second designator +which is used with three dimensional data. See the example section for +examples of this syntax. Abbreviations are allowed though beware that 'l' +is not a sufficient abbreviation. +.le +.ls database = "database" +Database in which the feature data and coordinate functions are recorded. +.le +.ls coordlist = "linelists$idhenear.dat" +User coordinate list consisting of an list of line coordinates. A +comment line of the form "# units <units>", where <units> is one of the +understood units names, defines the units of the line list. If no units +are specified then Angstroms are assumed. Some standard line lists are +available in the directory "linelists$". The standard line lists are +described under the topic \fIlinelists\fR. +.le +.ls units = "" +The units to use if no database entry exists. The units are specified as +described in + +.nf + cl> help onedspec.package section=units +.fi + +If no units are specified and a coordinate list is used then the units of +the coordinate list are selected. If a database entry exists then the +units defined there override both this parameter and the coordinate list. +.le +.ls nsum = "10" +Number of lines, columns, or bands across the designated vector axis to be +summed when the image is a two or three dimensional spatial spectrum. +It does not apply to multispec format spectra. If the image is three +dimensional an optional second number can be specified for the higher +dimensional axis (the first number applies to the lower axis number and +the second to the higher axis number). If a second number is not specified +the first number is used for both axes. +.le +.ls match = -3. +The maximum difference for a match between the feature coordinate function +value and a coordinate in the coordinate list. Positive values +are in user coordinate units and negative values are in units of pixels. +.le +.ls maxfeatures = 50 +Maximum number of the strongest features to be selected automatically from +the coordinate list (function 'l') or from the image data (function 'y'). +.le +.ls zwidth = 100. +Width of graphs, in user coordinates, when in zoom mode (function 'z'). +.le + +The following parameters are used in determining feature positions. +.ls ftype = "emission" +Type of features to be identified. The possibly abbreviated choices are +"emission" and "absorption". +.le +.ls fwidth = 4. +Full-width at the base (in pixels) of features to be identified. +.le +.ls cradius = 5. +The maximum distance, in pixels, allowed between a feature position +and the initial estimate when defining a new feature. +.le +.ls threshold = 0. +In order for a feature center to be determined the range of pixel intensities +around the feature must exceed this threshold. +.le +.ls minsep = 2. +The minimum separation, in pixels, allowed between feature positions +when defining a new feature. +.le + +The following parameters are used to fit a function to the user coordinates. +The \fBicfit\fR package is used and further descriptions about these parameters +may be found under that package. +.ls function = "spline3" +The function to be fit to the user coordinates as a function of the pixel +coordinate. The choices are "chebyshev", "legendre", "spline1", or "spline3". +.le +.ls order = 1 +Order of the fitting function. The order is the number of polynomial terms +or number of spline pieces. +.le +.ls sample = "*" +Sample regions for fitting. This is in pixel coordinates and not the user +coordinates. +.le +.ls niterate = 0 +Number of rejection iterations. +.le +.ls low_reject = 3.0, high_reject = 3.0 +Lower and upper residual rejection in terms of the RMS of the fit. +.le +.ls grow = 0 +Distance from a rejected point in which additional points are automatically +rejected regardless of their residuals. +.le + +The following parameters control the input and output. +.ls autowrite = no +Automatically write or update the database? If "no" then when exiting the +program a query is given if the feature data and fit have been modified. +The query is answered with "yes" or "no" to save or not save the results. +If \fIautowrite\fR is "yes" exiting the program automatically updates the +database. +.le +.ls graphics = "stdgraph" +Graphics device. The default is the standard graphics device which is +generally a graphics terminal. +.le +.ls cursor = "" +Cursor input file. If a cursor file is not given then the standard graphics +cursor is read. +.le + +The following parameters are queried when the 'b' key is used. +.ls crval, cdelt +These parameters specify an approximate coordinate value and coordinate +interval per pixel when the automatic line identification +algorithm ('b' key) is used. The coordinate value is for the +pixel specified by the \fIcrpix\fR parameter in the \fBaidpars\fR +parameter set. The default value of \fIcrpix\fR is INDEF which then +refers the coordinate value to the middle of the spectrum. By default +only the magnitude of the coordinate interval is used. Either value +may be given as INDEF. In this case the search for a solution will +be slower and more likely to fail. The values may also be given as +keywords in the image header whose values are to be used. +.le +.ls aidpars = "" (parameter set) +This parameter points to a parameter set for the automatic line +identification algorithm. See \fIaidpars\fR for further information. +.le +.ih +CURSOR KEYS +.ls ? +Clear the screen and print a menu of options. +.le +.ls a +Apply next (c)enter or (d)elete operation to (a)ll features +.le +.ls b +Identify features and find a dispersion function automatically using +the coordinate line list and approximate values for the dispersion. +.le +.ls c +(C)enter the feature nearest the cursor. Used when changing the position +finding parameters or when features are defined from a previous feature list. +.le +.ls d +(D)elete the feature nearest the cursor. (D)elete all features when preceded +by the (a)ll key. This does not affect the dispersion function. +.le +.ls e +Find features from a coordinate list without doing any fitting. This is +like the 'l' key without any fitting. +.le +.ls f +(F)it a function of the pixel coordinates to the user coordinates. This enters +the interactive function fitting package. +.le +.ls g +Fit a zero point shift to the user coordinates by minimizing the difference +between the user and fitted coordinates. The coordinate function is +not changed. +.le +.ls i +(I)nitialize (delete features and coordinate fit). +.le +.ls j +Go to the preceding line, column, or band in a 2D/3D or multispec image. +.le +.ls k +Go to the next line, column, or band in a 2D/3D or multispec image. +.le +.ls l +(L)ocate features in the coordinate list. A coordinate function must be +defined or at least two features must have user coordinates from which a +coordinate function can be determined. If there are features an +initial fit is done, then features are added from the coordinate list, +and then a final fit is done. +.le +.ls m +(M)ark a new feature using the cursor position as the initial position +estimate. +.le +.ls n +Move the cursor or zoom window to the (n)ext feature (same as +). +.le +.ls o +Go to the specified line, column, or band in a 2D/3D or multispec image. +For 3D images two numbers are specified. +.le +.ls p +(P)an to the original window after (z)ooming on a feature. +.le +.ls q +(Q)uit and continue with next image. +.le +.ls r +(R)edraw the graph. +.le +.ls s +(S)hift the fit coordinates relative to the pixel coordinates. The +user specifies the desired fit coordinate at the position of the cursor +and a zero point shift to the fit coordinates is applied. If features +are defined then they are recentered and the shift is the average shift. +The shift in pixels, user coordinates, and z (fractional shift) is printed. +.le +.ls t +Reset the current feature to the position of the cursor. The feature +is \fInot\fR recentered. This is used to mark an arbitrary position. +.le +.ls u +Enter a new (u)ser coordinate for the current feature. +When (m)arking a new feature the user coordinate is also requested. +.le +.ls v +Modify the fitting weight of the current feature. The weights are +integers with the lowest weight being the default of 1. +.le +.ls w +(W)indow the graph. A window prompt is given and a number of windowing +options may be given. For more help type '?' to the window prompt or +see help under \fIgtools\fR. +.le +.ls x +Find a zero point shift for the current dispersion function. This is used +by starting with the dispersion solution and features from a different +spectrum. The mean shift in user coordinates, mean shift in pixels, and +the fractional shift in user coordinates is printed. +.le +.ls y +Up to \fImaxfeatures\fR emission peaks are found automatically (in order of +peak intensity) and, if a dispersion solution is defined, the peaks are +identified from the coordinate list. +.le +.ls z +(Z)oom on the feature nearest the cursor. The width of the zoom window +is determined by the parameter \fIzwidth\fR. +.le +.ls . +Move the cursor or zoom window to the feature nearest the cursor. +.le +.ls 4 + +Move the cursor or zoom window to the (n)ext feature. +.le +.ls 4 - +Move the cursor or zoom window to the previous feature. +.le + +Parameters are shown or set with the following "colon commands", which may be +abbreviated. To show the value of a parameter type the parameter name alone +and to set a new value follow the parameter name by the value. +.ls :show file +Show the values of all the parameters. If a file name is given then the +output is appended to that file. If no file is given then the terminal +is cleared and the output is sent to the terminal. +.le +.ls :features file +Print the feature list and the fit rms. If a file name is given then the +output is appended to that file. If no file is given then the terminal +is cleared and the output is sent to the terminal. +.le +.ls :coordlist file +Set or show the coordinate list file. +.le +.ls :cradius value +Set or show the centering radius in pixels. +.le +.ls :threshold value +Set or show the detection threshold for centering. +.le +.ls :database name +Set or show the database for recording feature records. +.le +.ls :ftype value +Set or show the feature type (emission or absorption). +.le +.ls :fwidth value +Set or show the feature width in pixels. +.le +.ls :image imagename +Set a new image or show the current image. +.le +.ls :labels value +Set or show the feature label type (none, index, pixel, coord, user, or both). +None produces no labeling, index labels the features sequentially in order +of pixel position, pixel labels the features by their pixel coordinates, +coord labels the features by their user coordinates (such as wavelength), +user labels the features by the user or line list supplied string, and +both labels the features by both the user coordinates and user strings. +.le +.ls :match value +Set or show the coordinate list matching distance. +.le +.ls :maxfeatures value +Set or show the maximum number of features automatically found. +.le +.ls :minsep value +Set or show the minimum separation allowed between features. +.le +.ls :read name ap +Read a record from the database. The record name defaults to the image name +and, for 1D spectra, the aperture number defaults to aperture of +the current image. +.le +.ls :write name ap +Write a record to the database. The record name defaults to the image name +and, for 1D spectra, the aperture number defaults to aperture of +the current image. +.le +.ls :add name ap +Add features from a database record. The record name defaults to the image name +and, for 1D spectra, the aperture number defaults to aperture of +the current image. Only the features are added to any existing list +of features. The dispersion function is not read. +.le +.ls :zwidth value +Set or show the zoom width in user units. +.le +.ls :/help +Print additional help for formatting graphs. See help under "gtools". +.le +.ih +DESCRIPTION +Features in the input images are identified interactively and assigned +user coordinates. A "coordinate function" mapping pixel coordinates to +user coordinates may be determined from the identified features. A +user coordinate list may be defined to automatically identify additional +features. This task is used to measure positions of features, +determine dispersion solutions for spectra, and to identify features in +two and three dimensional images for mapping a two or three dimensional +coordinate transformation. Because of this dual use the terms vector +and feature are used rather than spectrum and spectral line. + +Each image in the input list is considered in turn. If the image is +not one dimensional or a one dimensional section of an image +then the image section given by the parameter +\fIsection\fR is used. This parameter may be specified in several ways as +described in the PARAMETERS and EXAMPLES sections. The image section is used +to select a starting vector and image axis. + +If the image is not one dimensional or in multispec format then the number +of lines, columns, or bands given by the parameter \fInsum\fR are summed. +The one dimensional image vector is graphed. The initial feature list and +coordinate function are read from the database if an entry exists. The +features are marked on the graph. The image coordinates are in pixels +unless a coordinate function is defined, in which case they are in user +coordinate units. The pixel coordinate, coordinate function value, and +user coordinate for the current feature are printed. + +The graphics cursor is used to select features and perform various +functions. A menu of the keystroke options and functions is printed +with the key '?'. The cursor keys and their functions are defined in +the CURSOR KEYS section and described further below. The standard +cursor mode keys are also available to window and redraw the graph and +to produce hardcopy "snaps". + +There are a number of ways of defining features. They fall into +two categories; interactively defining features with the cursor +and using automatic algorithms. + +The 'm' key is the principle interactive feature marking method. Typing +'m' near the position of a feature applies a feature centering algorithm +(see \fBcenter1d\fR) and, if a center is found, the feature is entered in +the feature list and marked on the spectrum. If the new position is within +a distance given by the parameter \fIminsep\fR of a previous feature it is +considered to be the same feature and replaces the old feature. Normally +the position of a new feature will be exactly the same as the original +feature. The coordinate list is searched for a match between the +coordinate function value (when defined) and a user coordinate in the +list. If a match is found it becomes the default user coordinate which the +user may override. The new feature is marked on the graph and it becomes +the current feature. The redefinition of a feature which is within the +minimum separation may be used to set the user coordinate from the +coordinate list. The 't' key allows setting the position of a feature to +other than that found by the centering algorithm. + +The principle automatic feature identification algorithm is executed +with the 'b' key. The user is queried for an approximate coordinate +value and coordinate interval per pixel. The coordinate value +is for the center of the spectrum by default though this may be changed +with the \fBaidpars\fR parameters. Only the magnitude of the +coordinate interval per pixel is used by default though this also +may be changed. Either value may be given as INDEF to do an unconstrained +search, however, this will be much slower and more likely to fail. +The algorithm searches for matches between the strong lines in the +spectrum and lines in the coordinate list. The algorithm is described +in the documentation for \fBaidpars\fR. + +The 'b' key works with no predefined dispersion solution or features. If +two or more features are identified, with 'm', spanning the range of the +data or if a coordinate function is defined, from a previous solution, then +the 'e', 'l', and 'y' keys may be used to identify additional features from +a coordinate list. The 'e' key only adds features at the coordinates of +the line lists if the centering algorithm finds a feature at that +wavelength (as described below). The 'y' key works in reverse by finding +the prominent features using a peak finding algorithm and then looking in +the coordinate list for entries near the estimated position. Up to a +maximum number of features (\fImaxfeatures\fR) will be selected. If there +are more peaks only the strongest are kept. In either of these cases there +is no automatic fitting and refitting of the dispersion function. + +The 'l' key combines automatic fits with locating lines from the coordinate +list. If two or more features are defined an initial fit is made. Then +for each coordinate value in the coordinate list the pixel coordinate is +determined and a search for a feature at that point is made. If a feature +is found (based on the parameters \fIftype, fwidth\fR, \fIcradius\fR, and +\fBthreshold\fR) its user coordinate value based on the coordinate function +is determined. If the coordinate function value matches the user +coordinate from the coordinate list within the error limit set by the +parameter \fImatch\fR then the new feature is entered in the feature list. +Up to a maximum number of features, set by the parameter \fImaxfeatures\fR, +may be defined in this way. A new user coordinate function is fit to all +the located features. Finally, the graph is redrawn in user coordinates +with the additional features found from the coordinate list marked. + +A minimum of two features must be defined for the 'l' key algorithm to +work. However, three or more features are preferable to determine changes +in the dispersion as a function of position. + +The 'f' key fits a function of the pixel coordinates to the user +coordinates. The type of function, order and other fitting parameters +are initially set with the parameters \fIfunction, order, sample, +niterate, low_reject, high_reject\fR and \fIgrow\fR.. The value of the +function for a particular pixel coordinate is called the function +coordinate and each feature in the feature list has a function +coordinate value. The fitted function also is used to convert pixel +coordinates to user coordinates in the graph. The fitting is done +within the interactive curve fitting package which has its own set of +interactive commands. For further information on this package see the +help material under \fBicfit\fR. + +If a zero point shift is desired without changing the coordinate function +the user may specify the coordinate of a point in the spectrum with +the 's' key from which a shift is determined. The 'g' key also +determines a shift by minimizing the difference between the user +coordinates and the fitted coordinates. This is used when a previously +determined coordinate function is applied to a new spectrum having +fewer or poorer lines and only a zero point shift can reasonably be +determined. Note that the zero point shift is in user coordinates. +This is only an approximate correction for shifts in the raw spectra +since these shifts are in pixels and the coordinate function should +also be appropriately shifted. + +One a set of features is defined one may select features for various +operations. To select feature as the current feature the keys '.', 'n', +'+', and '-' are used. The '.' selects the feature nearest the cursor, the +'n' and '+' select the next feature, and the '-' selects the previous +feature relative to the current feature in the feature list as ordered by +pixel coordinate. These keys are useful when redefining the user +coordinate with the 'u' key, changing the fitting weight of a feature with +'v', and when examining features in zoom mode. + +Features may be deleted with the key 'd'. All features are deleted +when the 'a' key immediately precedes the delete key. Deleting the +features does not delete the coordinate function. Features deleted in the +curve fitting package also are removed from the feature list upon +exiting the curve fitting package. + +It is common to transfer the feature identifications and coordinate function +from one image to another. When a new image without a database entry +is examined, such as when going to the next image in the input list, +changing image lines or columns with 'j', 'k' and 'o', or selecting +a new image with the ":image" command, the current feature list and coordinate +function are kept. Alternatively, a database record from a different +image may be read with the ":read" command. When transferring feature +identifications between images the feature coordinates will not agree exactly +with the new image feature positions and several options are available to +reregister the feature positions. The key 'c' centers the feature nearest +the cursor using the current position as the starting point. When preceded +with the 'a' key all the features are recentered (the user must refit +the coordinate function if desired). As an aside, the recentering +function is also useful when the parameters governing the feature +centering algorithm are changed. An additional options is the ":add" +command to add features from a database record. This does not overwrite +previous features (or the fitting functions) as does ":read". + +The (c)entering function is applicable when the shift between the current +and true feature positions is small. Larger shifts may be determined +automatically with the 's' or 'x' keys. + +A zero point shift is specified interactively with the 's' key by using the +cursor to indicate the coordinate of a point in the spectrum. If there are +no features then the shift is exactly as marked by the cursor. If there +are features the specified shift is applied, the features are recentered, +and the mean shift for all the features is determined. + +The 'x' key uses the automatic line identification algorithm (see +\fBaidpars\fR) with the constraint that the dispersion is nearly the +same and the is primarily a shift in the coordinate zero point. If +features are defined, normally by inheritance from another spectrum, then a +first pass is done to identify those features in the spectrum. Since this +only works when the shifts are significantly less than the dispersion range +of the spectrum (i.e. a significant number of features are in common) a +second pass using the full coordinate line list is performed if a shift +based on the features is not found. After a shift is found any features +remaining from the original list are recentered and a mean shift is +computed. + +In addition to the single keystroke commands there are commands initiated +by the key ':' (colon commands). As with the keystroke commands there are +a number of standard graphics features available beginning with ":." +(type ":.help" for these commands). The identify colon commands +allow the task parameter values to be listed and to be reset +within the task. A parameter is listed by typing its name. The colon command +":show" lists all the parameters. A parameter value is reset by +typing the parameter name followed by the new value; for example +":match 10". Other colon commands display the feature list (:features), +control reading and writing records to the database (:read and :write), +and set the graph display format. + +The feature identification process for an image is completed by typing +'q' to quit. Attempting to quit an image without explicitly +recording changes in the feature database produces a warning message +unless the \fIautowrite\fR parameter is set. If this parameter is +not set a prompt is given asking whether to save the results otherwise +the results are automatically saved. Also +the reference spectrum keyword REFSPEC is added to the image header at +this time. This is used by \fBrefspectra\fR and \fBdispcor\fR. +As an immediate exit the 'I' interrupt key may be used. This does not save +the feature information and may leave the graphics in a confused state. +.ih +DATABASE RECORDS +The database specified by the parameter \fIdatabase\fR is a directory of +simple text files. The text files have names beginning with 'id' followed +by the entry name, usually the name of the image. The database text files +consist of a number of records. A record begins with a line starting with the +keyword "begin". The rest of the line is the record identifier. Records +read and written by \fBidentify\fR have "identify" as the first word of the +identifier. Following this is a name which may be specified following the +":read" or ":write" commands. If no name is specified then the image name +is used. For 1D spectra the database entry includes the aperture number +and so to read a solution from a aperture different than the current image +and aperture number must be specified. For 2D/3D images the entry name +has the 1D image section which is what is specified to read the entry. +The lines following the record identifier contain +the feature information and dispersion function coefficients. + +The dispersion function is saved in the database as a series of +coefficients. The section containing the coefficients starts with the +keyword "coefficients" and the number of coefficients. + +The first four coefficients define the type of function, the order +or number of spline pieces, and the range of the independent variable +(the line or column coordinate along the dispersion). The first +coefficient is the function type code with values: + +.nf + Code Type + 1 Chebyshev polynomial + 2 Legendre polynomial + 3 Cubic spline + 4 Linear spline +.fi + +The second coefficient is the order (actually the number of terms) of +the polynomial or the number of pieces in the spline. + +The next two coefficients are the range of the independent variable over +which the function is defined. These values are used to normalize the +input variable to the range -1 to 1 in the polynomial functions. If the +independent variable is x and the normalized variable is n, then + +.nf + n = (2 * x - (xmax + xmin)) / (xmax - xmin) +.fi + +where xmin and xmax are the two coefficients. + +The spline functions divide the range into the specified number of +pieces. A spline coordinate s and the nearest integer below s, +denoted as j, are defined by + +.nf + s = (x - xmin) / (xmax - xmin) * npieces + j = integer part of s +.fi + +where npieces are the number of pieces. + +The remaining coefficients are those for the appropriate function. +The number of coefficients is either the same as the function order +for the polynomials, npieces+1 for the linear spline, or npieces + 3 +for the cubic spline. + +1. Chebyshev Polynomial + +The polynomial can be expressed as the sum + +.nf + y = sum from i=1 to order {c_i * z_i} +.fi + +where the c_i are the coefficients and the z_i are defined +interactively as: + +.nf + z_1 = 1 + z_2 = n + z_i = 2 * n * z_{i-1} - z_{i-2} +.fi + +2. Legendre Polynomial + +The polynomial can be expressed as the sum + +.nf + y = sum from i=1 to order {c_i * z_i} +.fi + +where the c_i are the coefficients and the z_i are defined +interactively as: + +.nf + z_1 = 1 + z_2 = n + z_i = ((2*i-3) * n * z_{i-1} - (i-2) * z_{i-2}) / (i-1) +.fi + +3. Linear Spline + +The linear spline is evaluated as + +.nf + y = c_j * a + c_{j+1} * b +.fi + +where j is as defined earlier and a and b are fractional difference +between s and the nearest integers above and below + +.nf + a = (j + 1) - s + b = s - j +.fi + +4. Cubic Spline + +The cubic spline is evaluated as + +.nf + y = sum from i=0 to 3 {c_{i+j} * z_i} +.fi + +where j is as defined earlier. The term z_i are computed from +a and b, as defined earlier, as follows + +.nf + z_0 = a**3 + z_1 = 1 + 3 * a * (1 + a * b) + z_2 = 1 + 3 * b * (1 + a * b) + z_3 = b**3 +.fi +.ih +EXAMPLES +1. Because this task is interactive and has many possible applications +it is difficult to provide actual examples. Instead some uses of the task +are described. + +.ls o +For defining distortions in the slit dimension as a function of +wavelength the positions of objects are marked at some wavelength. +The task \fBreidentify\fR is then used to trace the features to other +wavelengths. +.le +.ls o +For determining dispersion solutions in a one dimensional +spectrum an arc calibration is used. Three emission features are marked +and the (l)ocate key is used to find additional features from a +coordinate list of arc lines. The dispersion solution is fit interactively +and badly determined or misidentified lines are deleted. The +solution may be written to the database or transferred to the object +spectrum by reading the object image and deleting all the features. +Deleting the features does not delete the coordinate function. +.le +.ls o +For determining a two or three dimensional coordinate transformation a +dispersion solution is determined at one slit position in a long slit arc +spectrum or one spatial position in a Fabry-Perot spectrum as in the +previous example. The features are then traced to other positions with the +task \fBreidentify\fR. +.le + +2. For images which are two or three dimensional it is necessary to +specify the image axis for the data vector and the number of pixels at each +point across the vector direction to sum. One way specify a vector is to +use an image section to define a vector. For example, to select column +20: + +.nf + cl> identify obj[20,*] +.fi + +The alternative is to use the section parameter. Below are some examples +of the section parameter syntax for an image "im2d" which is 100x200 +and "im3d" which is 100x200x50. On the left is the section string syntax +and on the right is the image section + +.nf + Section parameter | Image section | Description + ------------------|---------------------|--------------------- + first line | im2d[*,1] | First image line + middle column | im2d[50,*] | Middle image column + last z | im3d[100,200,*] | Last image z vector + middle last y | im3d[50,*,50] | Image y vector + line 20 | im2d[*,20] | Line 20 + column 20 | im2d[20,*] | Column 20 + x 20 | im2d[*,20] | Line 20 + y 20 | im2d[20,*] | Column 20 + y 20 30 | im2d[20,*,30] | Column 20 + z 20 30 | im3d[20,30,*] | Image z vector + x middle | im3d[*,100,25] | Middle of image + y middle | im3d[50,*,25] | Middle of image + z middle | im3d[50,100,*] | Middle of image +.fi + +The most common usage should be "middle line", "middle column" or "middle z". + +The summing factors apply to the axes across the specified vector. For +3D images there may be one or two values. The following shows which axes +are summed, the second and third columns, when the vector axis is that shown +in the first column. + +.nf + Vector axis | Sum axis in 2D | Sum axes in 3D + ------------------|---------------------|-------------------- + 1 | 2 | 2 3 + 2 | 1 | 1 3 + 3 | - | 1 2 +.fi + +.ih +REVISIONS +.ls IDENTIFY V2.11 +The dispersion units are now determined from a user parameter, +the coordinate list, or the database entry. + +A new key, 'e', has been added to add features from a line list without +doing any fits. This is like the 'l' but without the automatic +fitting before and after adding new features. + +A new key, 'b', has been added to apply an automatic line identification +algorithm. + +The 'x' key has been changed to use the automatic line identification +algorithm. The allows finding much larger shifts. + +The match parameter may now be specified either in user coordinates or +in pixels. The default is now 3 pixels. + +The default threshold value has been changed to 0. +.le +.ls IDENTIFY V2.10.3 +The section and nsum parameter syntax was extended to apply to 3D +images. The previous values and defaults may still be used. + +The 'v' key was added to allow assigning weights to features. +.le +.ls IDENTIFY V2.10 +The principle revision is to allow multiple aperture images and long slit +spectra to be treated as a unit. New keystrokes allow jumping or scrolling +within multiple spectra in a single image. For aperture spectra the +database entries are referenced by image name and aperture number and not +with image sections. Thus, IDENTIFY solutions are not tied to specific +image lines in this case. There is a new autowrite parameter which may +be set to eliminate the save to database query upon exiting. The new +colon command "add" may be used to add features based on some other +spectrum or arc type and then apply the fit to the combined set of features. +.le +.ih +SEE ALSO +autoidentify, reidentify, aidpars, center1d, linelists, fitcoords, icfit, +gtools +.endhelp |