Input/Output, Plotting Data and Displaying Images
Commands used for inputting and outputting data are listed below.
The term "plotting" is used to refer to line plots of the data array.
Plotting is generally used for spectroscopic data consisting of one or
two lines scans, or for individual line scans (line cuts) from
topographic or other sorts of data.
A variety of specialized plotting routines exist for plotting
multiple spectra on a single page.
The term "displaying" is used to refer to a grey-scale or color display of the
image array (the former outputs a PGM file, and the latter a PPM file, which
is then displayed).
AUto/1
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic printing of data, with one datafile per page. Works for line plots or images.
AUto/2
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic printing of data, with two datafiles per page. Works for line plots or images.
AUto/3
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic printing of data, with three datafiles per page. Works only for images.
AUto/4
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic printing of data, with four datafiles per page. Works only for images.
AUto/10
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic printing of data, with ten datafiles per page. Works only for line plots.
AUto/a
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic viewing of all types of files. Useful for quick viewing of all data from a given day. (Also, can maximize DOS window to view filenumber of given data set).
AUto/i
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic viewing of image files. Only displays constant-current image files, but the starting and ending filenumbers can also include other data types. Useful for quick viewing of all images from a given day. (Also, can maximize DOS window to view filenumber of given image).
AUto/c
arguments: filename (without extension) (string)
starting filenumber (integer)
ending filenumber (integer)
Automatic viewing of conductance files only. Useful for quick viewing of all spectra from a given day. Only displays conductance files, but the starting and ending filenumbers can also include other data types.
Display Color
arguments: lookup table (integer)
Outputs file img.PPM which shows the image array in a color representation using
lookup table (1=gray, 2=black-body, 3=rainbow, 4=VP), and displays that. For the
black-body lookup table, the use is prompted for a further parameter b that determines
the amount of blue in the spectrum. With b=0 the colors range from red to yellow, with
b=0.5 the colors are more brownish to yellow, and with b=1 a gray scale results.
DIsplay
arguments: none
Outputs file img.PGM which shows the image array in a grey-scale representation,
and displays that.
DIsplay/r
arguments: none
Displays the image array in a grey-scale representation, with reverse order of the rows (useful for determining regions, for some image display routines).
GEt/i
arguments: number of regions (integer)
min, max columns (integers) | repeat number of regions times
min, max rows (integers) |
Get an I(V) curve from a multiple I(V) data set. The acquired curves from the specified regions are all averaged together to form the result.
GEt/io
arguments: number of regions (integer)
min, max columns (integers) | repeat number of regions times
min, max rows (integers) |
Get an I(V) curve in old format.
GEt/d
arguments: number of regions (integer)
min, max columns (integers) | repeat number of regions times
min, max rows (integers) |
Get an dI/dV curve from a multiple dI/dV data set. The acquired curves from the specified regions are all averaged together to form the result.
GEt/do
arguments: number of regions (integer)
min, max columns (integers) | repeat number of regions times
min, max rows (integers) |
Get an dI/dV curve in old format.
INput
arguments: filename (string)
Inputs specified file into the raw data array. If the size of the
array to be input is greater than 512x512, then one must follow the
INput command with the SEgment command, described below.
INput/g
arguments: filename (string)
Inputs a "general" list of (x,y) pairs, in ASCII free format.
INput/i
arguments: filename (string)
Inputs specified file as described above. The 'i' option (short for
interdigitate) inputs only the EVEN rows of the data, with the ODD
rows being unchanged from their previous values in the data array.
This allows a subsequent hysterisis correction for data which
has been acquired in a scan up/down manner.
INput/o
arguments: filename (string)
Inputs data in old format.
INput/p
arguments: filename (string)
nx,ny (integers)
Inputs pgm file into the raw data array.
The pgm file must have the header (top 3 or 4 lines) stripped off,
and the nx,ny values must be supplied as parameters to the routine.
INput/s
arguments: filename (string)
Inputs specified file as described above. The 's' option sums the
current data file into the data array (i.e. useful for averaging
a number of data files together).
INput/t
arguments: filename (string)
Inputs specified file as described above. The 't' option performs a
correction on related to the 'topo-16' option on the PSI software. If
a 2^16 bit boundary is crossed, the data is corrected for that.
INput/z
arguments: filename (string)
Inputs text file consisting of sequence of z-values for an image, as extracted
from an Integra AFM data file. The image width (assumed equal to the height) is
extracted from the header at the top of the file, and the number of columns
(assumed equal the number of rows) is deduced from the total number of
data points.
LIst
arguments: min, max rows (0,0 for header) (integers)
min, max columns (integers)
Produces a listing of values from the data array on the monitor.
If the min, max rows = (0,0), then the contents of the data
array header (20 integers) are listed.
MOdify/h
arguments: index (0=exit) (integer)
Modifies contents of the header value at index location. These
header values contain calibration information which accompanies the input
file of raw data. NOTE: when the data is input, this header information
is converted into various parameter values associated with the data.
Subsequent modification of the header values using this command will NOT
produce changes in those parameters values. Rather, it is necessary to
first output the file, then input it again so that the header information
is processed.
Multiple Plot/1
arguments: ...
Plot multiple spectra, one atop the other, using normalized conductance format.
Multiple Plot/2
arguments: ...
Plot multiple spectra, one atop the other, using measured conductance on linear scale.
Multiple Plot/3
arguments: ...
Plot multiple spectra, one atop the other, using conductance normalized to constant-z,
on log scale.
Multiple Plot/4
arguments: ...
Plot multiple spectra, one atop the other, using measured conductance on log scale.
OUt
arguments: filename (string)
Outputs the data array into a data file, using the same format used for
the input data files. NOTE: this command should be used only rarely, if
ever, since the input data files are stored as 16-bit integers, not as
real numbers. Thus, after some manipulations on the data by the IM
program, the resulting data array may not conveniently be expressed as
16-bit integers.
OUt/uim
arguments: xmin, xmax pixels (integers)
ymin, ymax pixels (integers)
Outputs the specified portion of the image array into a file named "img.uim",
using uim format, which can later be input into the VP plotting program.
OUt/vp
arguments: filename (string)
Outputs the data array as columns of real numbers, suitable to be read
into a general purpose plotting program such as VP.
PLot options: /1 /2 /g /c /a
optional argument: z offset (-1 for recommended value) (real)
Plots the data, row by row, in a series of line plots. The precise
appearance of the plot depends on the type of data array.
The argument z offset is not used for spectra or for any data type
consisting of a single line scan. For data sets with multiple line scans
this argument refers to the spacing between consecutive lines of the plot.
If the /g option is used, the y-axis will be logarithmic.
If the /c option is used, the x-axis will be expressed in "channel number"
(i.e. column number) rather than in whatever units would normally be used.
Note that the magnitude of the y-scale is determined simply by the minimum
and maximum data values. Thus, to change the y-scale, one must put limits
on these values, which can be done with the MOdify/z command
(described in
Cutting, Scaling, and Rearranging). Similary, to modify the x-scale one
must simply CUt a portion of the data array.
This routine can be used to put two plots, one above the other, on a single
page. In that case, the first data set is input with the /1 option, and
the second data set is input with the /2 option. The /2 option also
causes the resultant page, with both graphs, to be displayed on the monitor.
If the /a option (auto mode) is used, the graph is displayed, and execution of
the IM program is halted until the display is completed. This is useful if one
wants to print out the graph using the PRint command following the
PL command as part of a batch file, since without this option the
printing will often occur before the graph has actually been displayed.
Plot Multiple options: /0 /1 /2 /3 /4 /5 /6 /7 /8 /9 /o
arguments: none
Plots multiple (ten) graphs on a single page.
Data for each graphs is input using the /0, /1, ... /9 options.
Then, the command should to executed with the /o (output) option, and
the resultant page will be displayed on the monitor.
NOTE: this routine is intended mainly for automatic processing of data
files to produce hardcopy. In this case, the display on the monitor is
erased immediately after it appears (to avoid building up too many
windows on the monitor).
PRInt
arguments: none
Prints out the data array as a graph or image.
If the array consists of image-type data then the most recently
rendered image is output. Otherwise, the most recently constructed
graph is output.
SEgment
arguments: min,max columns (integers)
min,max rows (integers)
bin size (integer)
Specifies which segment of the data will be input into the raw data
array. The data is put into bins of size bin size before being
put into the array (e.g. bin size of 2 for a 1024x1024 data set will
produce a 512x512 data array with each value being an average of 2x2
values from the original data set).
SLice
arguments: ...
Takes a slice (CITS image, at specified range of voltages) from a
multiple I(V) data set.
XV
arguments: none
Displays the image array in a grey-scale presentation, using the xv
program for the display.