From fa080de7afc95aa1c19a6e6fc0e0708ced2eadc4 Mon Sep 17 00:00:00 2001
From: Joseph Hunkeler <jhunkeler@gmail.com>
Date: Wed, 8 Jul 2015 20:46:52 -0400
Subject: Initial commit

---
 noao/digiphot/daophot/doc/pexamine.hlp | 780 +++++++++++++++++++++++++++++++++
 1 file changed, 780 insertions(+)
 create mode 100644 noao/digiphot/daophot/doc/pexamine.hlp

(limited to 'noao/digiphot/daophot/doc/pexamine.hlp')

diff --git a/noao/digiphot/daophot/doc/pexamine.hlp b/noao/digiphot/daophot/doc/pexamine.hlp
new file mode 100644
index 00000000..920634bc
--- /dev/null
+++ b/noao/digiphot/daophot/doc/pexamine.hlp
@@ -0,0 +1,780 @@
+.help pexamine May00 noao.digiphot.daophot
+.ih
+NAME
+pexamine -- interactively examine or edit a photometry catalog
+.ih
+USAGE
+pexamine input output image
+.ih
+PARAMETERS
+.ls input
+The name of the input photometry catalog. Input may be either an APPHOT/DAOPHOT
+text database file or an STSDAS binary table database.
+.le
+.ls output
+The name of the edited output catalog. Output is either an APPHOT/DAOPHOT text
+database or an STSDAS binary table database depending on the file type of
+\fIinput\fR. If output = "" no output catalog is written.
+.le
+.ls image
+The name of the input image corresponding to the input photometry catalog. If
+\fIimage\fR is "" no image will be attached to PEXAMINE and some interactive
+catalog examining commands will not be available.  All the catalog editing
+commands however are still available.
+.le
+.ls deletions = ""
+The name of an optional output deletions photometry catalog. Deletions is either
+an APPHOT/DAOPHOT text database or an STSDAS binary table database depending on
+the file type of \fIinput\fR. If deletions is "" no deletions file is written.
+.le
+.ls photcolumns = "daophot"
+The list of standard photometry columns that are loaded when pexamine is run.
+The options are listed below.
+.ls "daophot"
+The standard columns for the DAOPHOT package. The current list is GROUP, ID,
+XCENTER, YCENTER, MSKY, MAG, MERR, CHI, SHARP and NITER. If any of these columns
+are multi-valued, (as in the case of magnitudes measured through more than one
+aperture), the first value is selected. The standard list may easily be
+extended at user request.
+.le
+.ls "apphot"
+The standard columns for the APPHOT package. The current list is ID, XCENTER,
+YCENTER, MSKY, MAG, and MERR. If any of these columns are multi-valued, (as in
+the case of magnitudes measured through more than one aperture), the first
+value is selected. The standard list may easily be extended at user request.
+.le
+.ls user list
+A user supplied list of standard columns. Column names are listed in full in
+either upper or lower case letters, separated by commas. If more than one value
+of a multi-valued column is requested the individual values must be listed
+separately as in the following example ID, XCENTER, YCENTER, MAG[1], MERR[1],
+MAG[2], MERR[2].
+.le
+Photcolumns can be changed interactively from within PEXAMINE at the cost
+of rereading the database. 
+.le
+.ls xcolumn = "mag" (magnitude), ycolumn = "merr" (magnitude error)
+The names of the two columns which define the default X-Y plot. Xcolumn and
+ycolumn must be listed in \fIphotcolumns\fR or \fIusercolumns\fR but may be
+changed interactively by the user. If either xcolumn or ycolumn is a
+multi-valued quantity and more than one value is listed in \fIphotcolumns\fR
+or \fIusercolumns\fR then the desired value number must be specified explicitly
+in, e.g. MAG[2] or MERR[2].
+.le
+.ls hcolumn = "mag" (magnitude)
+The name of the column which defines the default histogram plot.  Hcolumn
+must be listed in \fIphotcolumns\fR or \fIusercolumns\fR but may be changed
+interactively by the user. If hcolumn is a multi-valued quantity and more than
+one value is listed in \fIphotcolumns\fR or \fIusercolumns\fR then the desired
+value must be specified explicitly in hcolumn, e.g. MAG[2].
+.le
+.ls xposcolumn = "xcenter", yposcolumn = "ycenter"
+The names of the two columns which define the X and Y coordinates in \fIimage\fR
+of the objects in the catalog. This information is required if the image
+display and image cursor are to be used to visually identify objects in the
+image with objects in the catalog or if plots of image data are requested.
+Xposcolumn and yposcolumn must be listed in \fIphotcolumns\fR or
+\fIusercolumns\fR but may be changed interactively by the user.
+.le
+.ls usercolumns = ""
+The list of columns loaded into memory in addition to the standard photometry
+columns \fIphotcolumns\fR. The column names are listed in full in upper or
+lower case letters and separated by commas. Usercolumns can be changed
+interactively from within PEXAMINE at the cost of rereading the database. 
+.le
+.ls first_star = 1
+The index of the first object to be read out of the catalog.
+.le
+.ls max_nstars = 5000
+The maximum number of objects that are loaded into memory at task startup time,
+beginning at object \fIfirst_star\fR. If there are more than max_nstars in the
+catalog only the first max_nstars objects are read in.
+.le
+.ls match_radius = 2.0
+The tolerance in pixels to be used for matching objects in the catalog with
+objects marked on the display with the image cursor.
+.le
+.ls use_display = yes
+Use the image display? Users without access to an image display should set
+use_display to "no".
+.le
+.ls icommands = ""
+The image display cursor. If null the standard image cursor is used whenever
+image cursor input is requested. A cursor file in the appropriate format may be
+substituted by specifying the name of the file. Also the image cursor may be
+changed to query the graphics device or the terminal by setting the environment
+variable "stdimcur" to "stdgraph" or "text" respectively.
+.ls gcommands = ""
+The graphics cursor. If null the standard graphics cursor is used whenever
+graphics cursor input is requested. A cursor file in the appropriate format may
+be substituted by specifying the name of the file.
+.le
+.ls graphics = "stdgraph"
+The default graphics device.
+.le
+
+.ih
+PLOTTING PARAMETERS
+
+PEXAMINE supports five types of plots 1) an X-Y column plot 2) a histogram
+column plot 3) a radial profile plot 4) a surface plot and 5) a contour plot.
+Each supported plot type has its own parameter set which controls the
+appearance of the plot.  The names of the five parameter sets are listed below.
+
+.nf
+    cntrplot	Parameters for the contour plot
+    histplot	Parameters for the column histogram plot
+    radplot	Parameters for radial profile plot
+    surfplot	Parameters for surface plot
+    xyplot	Parameters for the X-Y column plot	
+.fi
+
+The same  parameters dealing with graph formats occur in many of the parameter
+sets while some are specific only to one parameter set. In the summary below
+those common to more than one parameter set are shown only once. The characters
+in parenthesis are the graph key prefixes for the parameter sets in which the
+parameter occurs.
+
+.ls angh = -33., angv = 25.		(s)
+Horizontal and vertical viewing angles in degrees for surface plots.
+.le
+.ls axes = yes				(s)
+Draw axes along the edge of surface plots ?
+.le
+.ls banner = yes 			 (chrsx)
+Add a standard banner to a graph ?  The standard banner includes the IRAF user
+and host identification and the date and time.
+.le
+.ls box = yes 				(chrx)
+Draw graph box and axes ?
+.le
+.ls ceiling = INDEF			(cs)
+Ceiling data value for contour and surface plots. A value of INDEF does not
+apply a ceiling.  In contour plots a value of 0. also does not apply a ceiling.
+.le
+.ls dashpat = 528			(c)
+Dash pattern for negative contours.
+.le
+.ls fill = no (yes)			(c) (hrx)
+Fill the output viewport regardless of the device aspect ratio ?
+.le
+.ls floor = INDEF			(cs)
+Floor data value for contour and surface plots. A value of INDEF does not apply
+a floor. In contour plots a value of 0. also does not apply a floor.
+.le
+.ls grid = no				(rx)
+Draw grid lines at major tick marks ?
+.le
+.ls interval = 0.0			(c)
+Contour interval.  If 0.0, a contour interval is chosen which places 20 to 30
+contours spanning the intensity range of the image.
+.le
+.ls label= no				(c)
+Label the major contours in the contour plot ?
+.le
+.ls logx = no, logy = no		(rx) (hrx)
+Plot the x or y axis logarithmically ? The default for histogram plots is to
+plot the y axis logarithmically.
+.le
+.ls majrx=5, minrx=5, majry=5, minry=5	(chrx)
+Maximum number of major tick marks on each axis and number of minor tick marks
+between major tick marks.
+.le
+.ls marker = "box"			(rx)
+Marker to be drawn.  Markers are "point", "box", "cross", "plus", "circle",
+"hline", "vline" or "diamond".
+.le
+.ls nbins = 512				(h)
+The number of bins in, or resolution of, histogram plots.
+.le
+.ls ncolumns = 21, nlines = 21		(cs)
+Number of columns and lines used in contour and surface plots.
+.le
+.ls ncontours = 5			(c)
+Number of contours to be drawn. If 0, the contour interval may be specified,
+otherwise 20 to 30 nicely spaced contours are drawn. A maximum of 40 contours
+can be drawn.
+.le
+.ls nhi = -1				(c)
+If -1, highs and lows are not marked. If 0, highs and lows are marked on the
+plot. If 1, the intensity of each pixel is marked on the plot.
+.le
+.ls rinner = 0, router = 8
+The inner and outer radius of the region whose radial profile is to be plotted.
+.le
+.ls round = no				(chrx)
+Extend the axes up to "nice" values ?
+.le
+.ls szmarker = 1			(rx)
+Size of mark except for points. A positive size less than 1 specifies a fraction
+of the device size. Values of 1, 2, 3, and 4 signify default sizes of increasing
+size.
+.le
+.ls ticklabels = yes			(chrx)
+Label the tick marks ?
+.le
+.ls top_closed = no			(h)
+Include z2 in the top histogram bin ? Each bin of the histogram is a subinterval
+that is half open at the top. Top_closed decides whether those pixels with
+values equal to z2 are to be counted in the histogram. If top_closed is yes,
+the top bin will be larger than the other bins.
+.le
+.ls x1 = INDEF, x2 = INDEF, y1 = INDEF, y2 = INDEF	(hrx)
+Range of graph along each axis.  If INDEF the range is determined from the data
+range. The default y1 for histogram plots is 0.
+.le
+.ls zero = 0.				(c)
+Grayscale value of the zero contour, i.e., the value of a zero point shift
+to be applied to the image data before plotting. Does not affect the values
+of the floor and ceiling parameters.
+.le
+.ls z1 = INDEF, z2 = INDEF		(h)
+Range of pixel values to be used in histogram. INDEF values default to the
+range in the region being histogramed.
+.le
+
+.ih
+DESCRIPTION
+
+PEXAMINE is a general purpose tool for interactively examining and editing
+photometry catalogs produced by the APPHOT or DAOPHOT packages. It is intended
+to aid the user in assessing the accuracy of the photometry, in diagnosing
+problems with particular catalog objects, in searching the photometry data for
+relationships between the computed quantities, and in editing the catalog
+based on those observed relationships. PEXAMINE is intended to complement the
+more batch oriented editing facilities of the PSELECT task.
+
+PEXAMINE takes the input catalog \fIinput\fR and the corresponding image
+\fIimage\fR (if defined) and produces an output catalog of selected objects
+\fIoutput\fR (if defined) and an output catalog of deleted objects
+\fIdeletions\fR (if defined). The input catalog may be either an APPHOT/DAOPHOT
+text database or an ST binary table database. The file type of the output
+catalogs \fIoutput\fR and \fIdeletions\fR is the same as that of \fIinput\fR.
+
+READING IN THE DATA
+
+PEXAMINE reads the column data specified by \fIphotcolumns\fR and
+\fIusercolumns\fR for up to \fImax_nstars\fR into memory. If there are more
+than \fImax_nstars\fR in the input catalog only the data for the first
+\fImax_nstars\fR is read. The \fIphotcolumns\fR parameter defines the list of
+standard photometry columns to be loaded. If "daophot" or "apphot" is selected
+then the standard columns are GROUP, ID, XCENTER, YCENTER, MSKY, MAG, MERR,
+CHI, SHARP and NITER and ID, XCENTER, YCENTER, MSKY, MAG and MERR respectively.
+Otherwise the user must set \fIphotcolumns\fR to his or her own preferred list
+of standard photometry columns. Non-standard columns may also be specified
+using the parameter \fIusercolumns\fR. Valid column lists contain the full
+names of the specified columns in upper or lower case letters, separated by
+commas. Either \fIphotcolumns\fR or \fIusercolumns\fR may be redefined
+interactively by the user after the task has started up, but only at the
+expense of rereading the data from \fIinput\fR.
+
+PEXAMINE will fail to load a specified column if that column is not in the
+photometry database, is of a datatype other than integer or real, or adding
+that column would exceed the maximum number of columns limit currently set at
+twenty. The user can interactively examine the list of requested and loaded
+standard photometry columns, as well as list all the columns in the input after
+the task has started up.
+
+GRAPHICS AND IMAGE COMMAND MODE
+
+PEXAMINE accepts commands either from the graphics cursor \fIgcommands\fR
+(graphics command mode) or the image display cursor \fIicommands\fR if available
+(image command mode). PEXAMINE starts up in graphics command mode, but all the
+interactive commands are accessible from both modes and the user can switch
+modes at any time assuming that the \fIuse_display\fR parameter to "yes".
+
+PEXAMINE interprets the cursor position in graphics mode differently from how
+it interprets it in image command mode. In graphics command mode the cursor
+coordinates are the position of the cursor in the current plot, whereas in
+image command mode they are the x and y coordinates of the cursor in the
+displayed image. For example, if the user issues a command to PEXAMINE to
+locate the object in the catalog nearest the point in the current X-Y plot
+marked by the graphics cursor, PEXAMINE does so by searching the data for the
+object whose values of \fIxcolumn\fR and \fIycolumn\fR most closely match those
+of the current cursor position. If the user issues a command  to PEXAMINE to
+locate the object in the catalog corresponding to the object marked on the
+image display with the image cursor, PEXAMINE does so by searching the data for
+the object whose values of \fIxposcolumn\fR and \fIyposcolumn\fR most closely
+match and fall within \fImatch_radius\fR of the current cursor position.
+
+Input to PEXAMINE is through single keystroke commands or colon commands.
+Keystroke commands are simple commands that may optionally use the cursor
+position but otherwise require no arguments. The PEXAMINE keystroke commands
+fall into three categories, basic commands, data examining commands and data
+editing commands, all described in detail in the following sections. Colon
+commands take an optional argument and function differently depending on the
+presence or absence of that argument. When the argument is absent colon
+commands are used to display the current value of a parameter or list of
+parameters. When the argument is present they change their current value to
+that argument. The basic colon commands are described in detail below. 
+
+BASIC KEYSTROKE COMMANDS
+
+These keystroke commands are used to display the help page, switch from
+graphics to image command mode and quit the task.
+
+.ls ?
+Page through the help for the PEXAMINE task
+.le
+.ls :
+Execute a PEXAMINE colon command.
+.le
+.ls g
+Change to graphics command mode. Throughout PEXAMINE graphics command mode is
+the default. All PEXAMINE commands are available in graphics command mode.
+.le
+.ls i
+Change to image command mode. All the PEXAMINE commands are available in image
+command mode. However if \fIuse_display\fR is no and the image cursor has not
+been aliased to the standard input or a text file image command mode is
+disabled.
+.le
+.ls q
+Quit PEXAMINE without writing an output catalog. PEXAMINE queries the user for
+confirmation of this option.
+.le
+.ls e
+Quit PEXAMINE and write the output catalog.
+.le
+
+DATA EXAMINING COMMANDS
+
+The data examining commands fall into two categories, those that examine the
+catalog data including 'l' (catalog listing), 'o' (object listing), 'x' (Y
+column versus X column plot) and 'h' (histogram column plot) commands, and
+those which examine the image data around specific catalog objects including
+'r' (radial profile plotting), 's' (surface plotting), 'c' (contour plotting)
+and 'm' (pixel dumping). The latter group require that \fIimage\fR be defined.
+A brief summary of each data examining command is given below.
+.ls l
+Print out the name, datatype, and units for all the columns in the input
+catalog. The list command can be used to check the contents of the input
+catalog and/or determine why a particular column was not loaded.
+.le
+.ls o
+Print out the names and values of the stored columns of the object nearest the
+cursor. In graphics mode the current plot type must be X-Y. In image command
+mode the object nearest the cursor must also be no more than \fImatch-radius\fR
+pixels away from the image cursor to be found. If an object is found and the
+current plot type is X-Y the graphics cursor is moved to the position of the
+selected object in the X-Y plot.
+.le
+.ls x
+Plot the data in \fIycolumn\fR versus the data in \fIxcolumn\fR excluding any
+already deleted points and identifying objects marked for deletion with a
+cross. X-Y plotting is undefined if \fIxcolumn\fR or \fIycolumn\fR is undefined.
+.le
+.ls h
+Plot the histogram of the data in \fIhcolumn\fR excluding any already deleted
+points and those marked for deletion. Histogram plotting is disabled if
+\fIhcolumn\fR is undefined.
+.le
+.ls r
+Plot the radial profile of the object nearest the cursor including only pixels
+within a distance of \fIrinner\fR and \fIrouter\fR of the object center. Radial
+profile plotting is disabled if \fIimage\fR or \fIxposcolumn\fR or
+\fIyposcolumn\fR is undefined.
+.le
+.ls s
+Plot the surface plot of the object nearest the cursor including only pixels
+within an image section \fIncols\fR by \fInlines\fR around the object center.
+Surface plotting is disabled if \fIimage\fR or \fIxposcolumn\fR or
+\fIyposcolumn\fR is undefined.
+.le
+.ls c
+Plot the contour plot of the object nearest the cursor including only pixels
+within an image section \fIncols\fR by \fInlines\fR around the object center.
+Contour plotting is disabled if \fIimage\fR or \fIxposcolumn\fR or
+\fIyposcolumn\fR is undefined.
+.le
+.ls m
+Dump the pixel values of a grid of 10 by 10 pixels around the object nearest
+the cursor. Pixel value dumping is disabled if \fIimage\fR or \fIxposcolumn\fR
+or \fIyposcolumn\fR is undefined.
+.le
+.ls p
+Replot the current graph.
+.le
+
+DATA EDITING COMMANDS
+
+Data points can be deleted from the catalog in either graphics command mode or
+image command mode. In graphics command mode the graphics cursor and either the
+X-Y or histogram plot is used to delete points. In image command mode the image
+cursor and the displayed image are used to delete points. A data point has three
+possible states good, marked for deletion and deleted. Any one of the keystroke
+commands 'd' (delete point), '(' (delete points with x less than x cursor),
+')' (delete points with x greater than x cursor, '^' (delete points with y > y
+cursor), 'v' (delete points with y < y cursor) or 'b' (delete points in a box)
+can be used to mark points for deletion. The 'f' key is used to actually delete
+the points and replot the data. In between marking the points for deletion and
+actually deleting the marked points the 't' (toggle) key can be used to undelete
+the last set marked. The full list of the data editing keystroke commands is
+given below.
+
+.ls z
+Undelete not just unmark all the data points replot.
+.le
+.ls f
+Delete points marked for deletion and replot. Points marked for deletion but
+not actually deleted will be written to the output catalog and not written to
+the deletions catalog.
+.le
+.ls d
+Mark the point nearest the cursor for deletion.
+.le
+.ls u
+Undelete the marked point nearest the cursor.
+.le
+.ls (
+Mark all points with x values less than the x value of the cursor for deletion.
+In graphics command mode points can only be marked for deletion if the current
+plot type is "xyplot" or "histplot". In image command mode \fIxposcolumn\fR and
+\fIyposcolumn\fR must be defined before points can be marked for deletion.
+.le
+.ls )
+Mark all points with x values greater than the x value of the cursor for
+deletion.  In graphics command mode points can only be marked for deletion if
+the current plot type is "xyplot" or "histplot". In image command mode
+\fIxposcolumn\fR and \fIyposcolumn\fR must be defined before points can be
+marked for deletion.
+.le
+.ls v
+Mark all points with y values less than the y value of the cursor for deletion.
+In graphics command mode points can only be marked for deletion if the current
+plot type is "xyplot". In image command mode \fIxposcolumn\fR and
+\fIyposcolumn\fR must be defined before points can be marked for deletion.
+.le
+.ls ^
+Mark all points with y values greater than the y value of the cursor for
+deletion.  In graphics command mode points can only be marked for deletion if
+the current plot type is "xyplot". In image command mode \fIxposcolumn\fR and
+\fIyposcolumn\fR must be defined before points can be marked for deletion.
+.le
+.ls b
+Mark all points within a box whose lower left and upper right hand corners are
+marked by the cursor for deletion. In graphics mode points can only be marked
+for deletion if the current plot type is "xyplot". In image command mode
+\fIxposcolumn\fR and \fIyposcolumn\fR must be defined before points can be
+marked for deletion.
+.le
+.ls t
+Toggle between marking points for deletion or undeletion. The default is to
+mark points for deletion.
+.le
+
+BASIC COLON COMMANDS
+
+All the PEXAMINE parameters can be changed interactively with colon commands,
+including those which determine which data is read in, which data is plotted
+and the parameters of each plot. A brief description of the basic commands is
+given here. The full list is given in the following section.
+
+.ls :photcolumns [col1,col2,...]
+Show or set the list of requested standard photometry columns and the list
+of loaded photometry columns. If the user supplies a new list of columns the
+data will be reread from disk.
+.le
+.ls :usercolumns [col1,col2,...]
+Show or set the list of requested user columns and the list of loaded user
+columns. If the user supplies a new list of columns the data will be reread
+from disk.
+.le
+.ls :xcolumn [colname]
+Show or set the name of the column to be plotted along the x axis of the X-Y
+plot.
+.le
+.ls :ycolumn [colname]
+Show or set the name of the column to be plotted along the y axis of the X-Y
+plot.
+.le
+.ls :hcolumn [colname]
+Show or set the name of the column to be whose histogram is to be plotted.
+.le
+.ls :eparam [cntrplot/histplot/radplot/surfplot/xyplot]
+Review or edit the list of parameters for the various plot types.
+.le
+.ls :unlearn [cntrplot/histplot/radplot/surfplot/xyplot]
+Return the list of parameters for the various plot types to their default
+values.
+.le
+.ls :x y key cmd
+Execute any defined keystroke "key" supplying the appropriate x and y value in
+place of the cursor position. In graphics command mode the x and y position are
+assumed to be the position in the current graph. In image command mode the x
+and y position are assumed to be the x and y coordinate in the image display.
+.le
+
+.ih
+COMMANDS
+
+.nf
+	PEXAMINE Interactive Cursor Keystroke Commands
+
+                   Basic Commands
+
+?	Print help for the PEXAMINE task
+:	PEXAMINE colon commands
+g	Activate the graphics cursor
+i	Activate the image cursor
+e	Exit PEXAMINE and save the edited catalog
+q	Quit PEXAMINE and discard the edited catalog
+
+		   Data Examining Commands
+
+l	List the name, datatype and units for all columns in the catalog 	
+o	Print out the names and values of the stored columns for the
+	    object nearest the cursor
+x	Replot the current y column versus the current x column
+h	Replot the current histogram
+r	Plot the radial profile of the object nearest the cursor
+s	Plot the surface of the object nearest the cursor
+c	Plot the contour plot of the object nearest the cursor
+m	Print the data values of the object nearest the cursor
+p	Replot the current graph
+
+                   Data Editing Commands
+
+z	Reinitialize the data by removing all deletions and replot
+d	Mark the point nearest the cursor for deletion
+u	Undelete the marked point nearest the cursor
+t	Toggle between marking points for deletion or undeletion
+(	Mark points with X < X (cursor) for deletion or undeletion
+)	Mark points with X > X (cursor) for deletion or undeletion
+v	Mark points with Y < Y (cursor) for deletion or undeletion
+^	Mark points with Y > Y (cursor) for deletion or undeletion
+b	Mark points inside a box for deletion or undeletion
+f	Actually delete the marked points and replot
+
+
+	      PEXAMINE Interactive Colon Commands
+
+:xcolumn	  [name]	     Show/set the X-Y plot X axis quantity
+:ycolumn	  [name]	     Show/set the X-Y plot Y axis quantity
+:hcolumn	  [name]	     Show/set the histogram plot quantity  
+:photcolumns	  [col1,col2,...]    Show/set the list of photometry columns
+:usercolumns	  [col1,col2,...]    Show/set the list of user columns
+:delete		  [yes/no]	     Delete or undelete points
+:eparam		  [x/h/r/s/c]	     Edit/unlearn the specified plot pset
+    or
+:unlearn
+
+
+	     PEXAMINE Interactive X-Y Plotting Commands
+
+:x1	    [value]	  Left  world x-coord if not autoscaling
+:x2 	    [value]	  Right world x-coord if not autoscaling
+:y1         [value]	  Lower world y-coord if not autoscaling
+:y2         [value]	  Upper world y-coord if not autoscaling
+:szmarker   [value]	  Marker size
+:marker [point|box|plus|cross|circle|diamond|hline|vline]    Marker type
+:logx       [yes/no]	  Log scale the x axis?
+:logy       [yes/no]      Log scale the y axis?
+:box        [yes/no]      Draw box around periphery of window?
+:ticklabels [yes/no]	  Label tick marks?
+:grid       [yes/no]	  Draw grid lines at major tick marks? 
+:majrx      [value]	  Number of major divisions along x axis
+:minrx      [value]	  Number of minor divisions along x axis
+:majry      [value]	  Number of major divisions along y axis
+:minry      [value]	  Number of minor divisions along y axis
+:round      [yes/no]      Round axes to nice values?
+:fill       [yes/no]      Fill viewport vs enforce unity aspect ratio?
+
+
+	PEXAMINE Interactive Histogram Plotting Commands
+
+:nbins	    [value]	  Number of bins in the histogram
+:z1	    [value]	  Minimum histogram intensity
+:z2	    [value]	  Maximum histogram intensity
+:top_closed [y/n]	  Include z in the top bin?
+:x1	    [value]	  Left  world x-coord if not autoscaling
+:x2	    [value]	  Right world x-coord if not autoscaling
+:y1         [value]	  Lower world y-coord if not autoscaling
+:y2         [value]	  Upper world y-coord if not autoscaling
+:logy       [yes/no]      Log scale the y axis?
+:box        [yes/no]      Draw box around periphery of window?
+:ticklabels [yes/no]	  Label tick marks?
+:majrx      [value]	  Number of major divisions along x axis
+:minrx      [value]	  Number of minor divisions along x axis
+:majry      [value]	  Number of major divisions along y axis
+:minry      [value]	  Number of minor divisions along y axis
+:round      [yes/no]      Round axes to nice values?
+:fill       [yes/no]      Fill viewport vs enforce unity aspect ratio?
+
+	PEXAMINE Interactive Radial Profile Plotting Commands
+
+:rinner	    [value]	  Inner radius of the region to be plotted
+:router	    [value]	  Outer radius of the region to be plotted
+:x1	    [value]	  Left  world x-coord if not autoscaling
+:x2 	    [value]	  Right world x-coord if not autoscaling
+:y1         [value]	  Lower world y-coord if not autoscaling
+:y2         [value]	  Upper world y-coord if not autoscaling
+:szmarker   [value]	  Marker size
+:marker [point|box|plus|cross|circle|diamond|hline|vline]    Marker type
+:logx       [yes/no]	  Log scale the x axis?
+:logy       [yes/no]      Log scale the y axis?
+:box        [yes/no]      Draw box around periphery of window?
+:ticklabels [yes/no]	  Label tick marks?
+:grid       [yes/no]	  Draw grid lines at major tick marks? 
+:majrx      [value]	  Number of major divisions along x axis
+:minrx      [value]	  Number of minor divisions along x axis
+:majry      [value]	  Number of major divisions along y axis
+:minry      [value]	  Number of minor divisions along y axis
+:round      [yes/no]      Round axes to nice values?
+:fill       [yes/no]      Fill viewport vs enforce unity aspect ratio?
+
+
+	PEXAMINE Interactive Surface Plotting Commands
+
+:ncolumns   [value]	  Number of columns to be plotted
+:nlines	    [value]	  Number of lines to be plotted
+:axes	    [yes/no]	  Draw axes?
+:angh	    [value]	  Horizontal viewing angle
+:angv	    [value]	  Vertical viewing angle
+:floor	    [value]	  Minimum value to be plotted
+:ceiling    [value]	  Maximum value to be plotted
+
+
+	PEXAMINE Interactive Contour Plotting Commands
+
+:ncolumns   [value]	  Number of columns to be plotted
+:nlines	    [value]	  Number of lines to be plotted
+:floor	    [value]	  Minimum value to be plotted
+:ceiling    [value]	  Maximum value to be plotted
+:zero	    [value]       Grayscale value of zero contour
+:ncontours  [value]	  Number of contours to be drawn
+:interval   [value]       Contour interval
+:nhi	    [value]       Hi/low marking option
+:dashpat    [value]       Bit pattern for generating dashed lines
+:label      [yes/no]      Label major contours with their values?
+:box        [yes/no]      Draw box around periphery of window?
+:ticklabels [yes/no]	  Label tick marks?
+:majrx      [value]	  Number of major divisions along x axis
+:minrx      [value]	  Number of minor divisions along x axis
+:majry      [value]	  Number of major divisions along y axis
+:minry      [value]	  Number of minor divisions along y axis
+:round      [yes/no]      Round axes to nice values?
+:fill       [yes/no]      Fill viewport vs enforce unity aspect ratio?
+.fi
+
+.ih
+EXAMPLES
+
+1. Examine and edit an APPHOT aperture photometry catalog and a DAOPHOT
+allstar catalog without either attaching the associated image or using the
+image display.
+
+.nf
+    pt> pexamine ypix.mag.1 ypix.mag.ed use_display-
+
+	... a plot of magnitude error versus magnitude appears on
+	    the screen and the graphics cursor comes up ready to accept
+	    commands
+
+	... the user sees a generally smooth trend of increasing
+	    magnitude error with increasing magnitude except for a
+	    single deviant point at the bright end of the plot
+
+	... the user decides to remove the deviant point using the
+	    'd' keystroke command to mark the point and the 'f'
+	    keystroke command to actually delete and replot the graph
+
+	... after examining the plot further the user decides to delete
+	    all objects for which the magnitude error is > 0.1 magnitudes
+	    using the '^' keystroke command, followed by the 'f'
+	    keystroke command to actually replot and delete the data.
+
+	... after deciding that this new plot is satisfactory the user
+	    issues the 'e' keystroke command to exit pexamine and save
+	    the good data in m92.mag.ed
+
+    pt> pexamine ypix.als.1 ypix.als.ed use_display-
+
+	... a plot of magnitude error versus magnitude appears on the
+	    screen and the graphics cursor comes up ready to accept
+	    commands
+
+	... after looking at the plot the user decides that what they
+	    really want to see is a plot of the goodness of fit parameter
+	    chi versus magnitude
+
+	... the user issues the colon command :ycol chi followed by 'p'
+	    keystroke command to replot the data
+
+	... the user sees a generally smooth trend of increasing
+	    chi with increasing magnitude 
+
+	... after examining the plot further the user decides to delete
+	    all objects for which the chi value  > 2.0  and the
+	    magnitude is > 25 using the '^' key and ')' keystroke
+	    commands followed by 'f' to save the deletions and replot
+	    the data
+
+	... after deciding that this new plot is satisfactory the user
+	    issues the 'e' keystroke command to exit pexamine and save
+	    the good data in m92.als.ed
+.fi
+
+2. Examine and edit a DAOPHOT allstar catalog using the subtracted image, the
+original image and the image display.
+
+.nf
+	pt> display ypix.sub.1 1
+
+	    ... display the subtracted image
+
+	pt> pexamine ypix.als.1 ypix.als.ed dev$ypix xcol=mag ycol=chi
+
+	... a plot of the goodness of fit versus magnitude appears
+	    on the terminal and the graphics cursor comes up ready to
+	    accept commands
+
+	... the user notices some very anomalous chi values and decides
+	    to see if these correspond to objects which have poor
+	    subtraction on the displayed image
+
+	... the user switches to image command mode by tapping the 'i'
+	    key, moves to the first poorly subtracted object and taps
+	    the 'o' key
+
+	... a list of the values of the loaded columns including chi
+	    appears in the text window , the program switches to graphics
+	    mode and places the graphics cursor on the corresponding
+	    point in the X-Y plot
+
+	... the point in question indeed has a very high chi value
+	    and the user decides to try and investigate the reason for the
+	    anomalous value
+
+	... the user taps the 'r' key to get a radial profile of the
+	    object in the original image
+
+	... after carefully examining the profile it appears that the
+	    object's profile is too broad and that it is not a star
+
+	... the user switches back to the X-Y plot with the 'x' key,
+	    marks the point with the 'd' key and saves the deletions
+	    and replots with the 'f' key.
+
+	... the user goes back to image command mode with the 'i' key
+	    and begins investigating the next object
+
+	... finally after examining the image and making all the changes
+	    the user decides to quit and save the changes with the 'e' key
+
+.fi
+
+.ih
+TIME REQUIREMENTS
+
+.ih
+BUGS
+
+INDEF valued points cannot be accessed by PEXAMINE. INDEF valued points should
+be removed from the input catalog with PSELECT prior to entering PEXAMINE.
+
+.ih
+SEE ALSO
+ptools.pselect, ptools.txselect,ptools.tselect
+
+.endhelp
-- 
cgit 

