25 February 1988
Rob Smith
Copyright (C) 1988 Robert G. Smith Room 123, Anat-Chem Bldg. Univ. of PA Medical School Phila., PA 19104-6058 USA All Rights Reserved
In order to understand the problem of alignment, it is useful to consider a typical example. If you wanted to reconstruct a helical "spring" that had been sectioned perpendicularly to the axis of the helix, you would see only an ellipse on each section. If you simply traced each ellipse and aligned the ellipse with the ellipse on the next section, you would reconstruct an elliptical cylinder, not the original helix. This problem occurs with any obliquely cut object such as a fiber or elongated cell in a serial reconstruction.
You should have at least 3, preferably 5 fiducial marks which you draw along with your data on each section. They may be small objects which are only useable for several sections, so you may need more fiducials than 3 if some of them can't be used to align the next section. If you had only one fiducial besides your data on each section, you would accumulate a small rotational error from each section, because it's inevitably easy to misalign the angle of rotation when aligning only one small trace from section to section. Remember, you can't use your data traces to align with. So you need at least 2, and you should have at least 3 to 5 fiducials per section.
If your fiducials are related to each other in some way, for instance they're two fibers which both travel in the same oblique direction, or 3 fibers twisted around each other in a helix, their average "motion" will "bias" the reconstruction, and you will still have a problem with translational or rotational errors. So the whole 3D reconstruction process depends on using a random assortment of fiducials (or else absolute reference marks). This is the reason that you must use 3 or more fiducials; you have a better chance of using unrelated objects if you use many.
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You can make an alignment dot on the bitpad surface (or on a transparent sheet taped to the surface) which will help aligning the projector image with your traces. You make a "base link" (see the "Montage" manual, Sect. 5) on each section which corresponds with the location of the alignment dot.
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If you don't have an artist's jig, you can make an alignment jig by using tape to mark the location of two corners of your first transparent sheet. Place two pieces of tape at a right angle to make a "corner" which fits the corner of the plastic sheet; then make a second corner mark. Then you can place all the other transparent sheets on the tape marks so that their corners are aligned with the corners of the first sheet.
After you've drawn the features from the first photograph onto the transparent sheet, replace the first photograph below the sheet with the second section's photograph. Align the second photo with the first transparent sheet by carefully moving the photo around while observing how the fiducial marks drawn from the first photo align with the corresponding features from the second photo. Use all the fiducial marks (at least 3) to get a "best fit". Then tape the second photo in place to save the alignment. Replace the first transparent sheet on the artist's jig with the second transparent sheet, and draw the reconstructed features and fiducials as you did from the first photograph. Continue this process until you are finished the series.
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When you need to trace over the edge of one photograph's area, align the sheet for the next photograph area with the first by overlapping them with their holes from opposite corners placed onto one peg of the artist's jig, keeping the edges parallel, so that the second sheet is only on one peg. (Or you can just keep the sheets edge-to-edge, with the corners touching.) This keeps all of the sheets in the same relative rotation. The pictures from which you're tracing must have at least 10% overlap, and should represent neat rows of material from the sections you're photographing.
Trace some fiducial marks which overlap onto the first sheet, and then place the second, overlapping photograph so it aligns with the overlapping fiducials. When you've traced the overlapping fiducials onto both transparent sheets, you are free to move the second transparent sheet back onto both pegs on the alignment jig and move the overlapping photograph back. You can now continue tracing data onto the second sheet.
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You can make an alignment dot on the bitpad surface (or on a transparent sheet taped to the surface) which will help aligning the projector image with your traces. You make a "base link" (see below) on each section which corresponds with the location of the alignment dot.
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The first (and best) way is to use an artist's jig which is a piece of plastic about the dimensions of a ruler which has two prongs positioned to fit into the outer two holes of the transparent sheets. You tape the artist's jig to the digitizing tablet on the side away from you. Then you can lay one or more sheets onto the jig to keep them exactly aligned. The artist's jig can be made from pieces of acrylic plastic, nylon, or a similar material. Make sure that you tape the corners of the sheet opposite the holes to the tablet to prevent the sheet from moving when you are digitizing. Masking tape works nicely for this purpose. The artist's jig saves time by allowing you to position the sheets quickly.
The second way to align is to make alignment marks on the digitizing tablet which correspond to the corners of the transparent sheets. You simply lay a transparent sheet with its corners on the marks and tape it in place.
The active area of the bitpad ends at the indented line about 5 cm from the edge of the bitpad. You must keep any traces you digitize inside this area. If your traces are too large to fit inside the bitpad active area, don't worry, because there's a way of positioning your work that'll enable you to enter traces as large as you want.
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You can also give the name of an already existing file to Montage. Montage attempts to find it in the directory. If montage can't find your file, it makes a new file. If you don't remember exactly what your existing file name is, type "^C" (control-c) at this point to exit montage, and use "ls -lt" to find your file. To understand more about files and file names, see "Components" (Section 2) and the Linux Guide (section 3 of the manual).
If you have specified a new file, then montage creates it for you, zeroing it one section at a time. Montage first says:
Section size = 1024
Do you wish to change ? (Y/N)
Simply type
Zeroing Data file
Start at which section? ( for 1)
Type
Stop at which section? ( for 100 sections)
You should type in the number of sections that you
think you will use. Don't enter a large number of
sections unless you're sure: 1) there's room for the
resulting file and 2) you really need them now. For
now, you should keep the file small; you can easily add
extra sections to an existing data file later. As each
section is zeroed, montage prints dots "...." on the
screen, 50 dots to a line. To change the size of the
file later, you first compress it and then uncompress
it using the "fstor" command (Sect. 7).
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In order to save the points you enter on each section, you must give the "write mode" ("w") command before you make any links or points. You get the message "write" in red at the top of the screen when "write mode" is on. If "write mode" is not turned on, then your data will be lost when you go to the next section, or when you exit from the montage program.
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Absolute mode is the easiest to learn to use. You simply move the mouse and see the cursor move on the screen. If you press the yellow button ("1"), the cursor on the screen stops moving, allowing you to align the mouse with a different coordinate on the bitpad.
Cursor mode is useful for montages where your trace data is larger than the bitpad active area. You simply press the yellow button ("1") on the mouse whenever you want the cursor on the screen to follow your hand movements of the mouse. Whenever you let up on the 1 button, the cursor on the screen doesn't move. This allows you to move the mouse without affecting the location of the cursor on the screen. This is necessary for making montages because there has to be a way to change the relative correspondence between the screen and the bitpad coordinate systems.
Think of the graphics screen as a single window in your car on a distant planet. You can control where you point your window, and thereby what objects and stars you see in the outside world. The outside world is very large, much too large to see with one window, so you need a way to move the window. If you move the cursor off to the side of the window, the window gets "pulled" by the cursor to a new position. In absolute mode, the bitpad is like a joystick which directs the cursor (and thereby the window). In cursor mode, the bitpad is like a wheel connected to the ground outside: you can steer your car on the ground by alternately pushing the wheel (pressing the button) and lifting up your hand to get a new grip on the wheel (lifting your finger off the button). In position mode, you have more direct control of your window view.
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Another way to keep the alignment between the mouse location and the cursor on the screen is to make "alignment links", normally one per section. These serve as reference points for your traces. The alignment links are made at the same location in each section, and serve to align the cursor from one section to the next. A dot in the center of the bitpad serves as the reference point to align the mouse with the links. To make an alignment link, make the screen cursor go to (0,0) or some other location and without moving the mouse, use the "make base link" command ("0") to make a link which can be aligned with the bitpad center dot. The base link gets displayed as a "B" in the picture. You may use the keypad to enter numbers if you want. Normally the first base link on a section is entered at the location (0,0) using the "x" command.
Make a "trace link" ("2") at this point; it becomes the "current link" or "CL" on the picture. You can then make points ("1") at appropriate intervals around the outline you're entering. Don't make the last point at the position of the first point, because trace points are made in "close" mode; the first point is duplicated automatically to make the last point. This means that the first and last points of the trace link are always connected. The points in a new link aren't displayed right after you make them but you can see them when you make the next link or press "8". You can see the connections between the points using the "set line display mode" ("u"). This displays your points as connected lines, not points. Normally, you make points in a clockwise direction only. Later on, if you want to analyze your trace links for area, counter-clockwise links give negative area.
If you need to trace lines on a section which aren't closed contours, turn the "close" mode off by pressing 'c'. This mode can be used to digitize tree structures by creating new links at each branch point.
You normally make a new trace link for each profile (or "slice") you want to trace. Set the branch or cell number ("s"; see below) to a different value for each trace link. This allows your trace links to be displayed separately using the filter if needed (see Section 5: Mpict).
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Number Low inten Number High intensity 0 black 8 gray 1 blue 9 ltblue 2 green 10 ltgreen 3 cyan 11 ltcyan 4 red 12 ltred 5 magenta 13 ltmag 6 brown 14 yellow 7 white 15 brtwhtThe color numbers are used by the graphics card to display the correct color. They can be referred to later during 3D picture display by their name if you want to display only links with a certain color, or if you want to change the color of certain links only.
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The "nearest link" is very useful when you want to move the screen to display a different area which wasn't visible before. You simply move the cursor by alternately pressing the button and when you get near enough to a link you can press "^r" which gets the link centered in a hurry. This works in all three bitpad modes: absolute ("A"), cursor ("B"), and position ("@"). If you're in absolute mode ("A"), the screen cursor will stay in alignment as long as you don't press the yellow button and don't use any of the link move commands.
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xbio,ybio x,y coordinates of the link.
section section number.
area area number for montages.
branch branch number.
cell cell number.
color color of link on screen.
flag flag spec number (only in flag links).
type link type (base,cell,flag,trace,grain,line)
(see "types of links" below).
You can change the values in the current status with
the "set current status" ("s") command. This causes
any new links created to have the new status
incorporated into them. See "setting current status"
below.
dd displays the current link on the right.
de displays more information in the current link.
df checks for bad data in a section and erases it.
dk erases an entire section quickly.
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Montage has a limited symbolic reference capability. Inside the "s" and "t" commands (which allow you to change the current status and the current link, respectively) you can create and set variables, and use their values instead of keyboard input. For instance you could modify a series of links by defining two variables inside the ("s" or "t" commands):
xincr = 10; yincr = 20
Then you could define a macro which changes the
location of a link automatically:
b (button macro, displays current macros)
y (yes, I want to change.)
F1 (the program the F1 function key)
t (change current link command )
xbio = xbio + xincr; (increment xbio)
ybio = ybio + yincr;
(The Enter key to stop "t" )
^p (go to next section)
^r (find nearest link)
This makes it possible to run the "t" command
automatically to change the coordinates of an object
on all sections. Remember, you enter the macro
exactly as you would type it when you're
running the command yourself without a macro.
Note that in the examples shown here the commands
are on separate lines for clarity; you must not type
Another example of a useful macro is when you're
making new links with different colors and branch
numbers. It is a lot of typing to run the "s" command
and change the current status every time you want to
change a branch number.
To make it easier, try this:
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In order to create a new line, you must have the
"current link" (CL on the screen) at a link that isn't
another line link. Then each time you add another link
to the line, you must be sure the "current link" is set
to the line link that you wish to connect the new link to.
Also, you must have "write" mode ("w") set on when you
enter the link, otherwise the pointers won't be
correct.
You can travel forwards and backwards on the line
link vector with the use of the "last link" and "next
link" commands. If the pointers aren't set right, you
can figure out what the problem is with the "display
current link" ("dd" and "de") commands to enable you to
see the pointer fields. The "Lp" and "Np" link fields
tell give the link and section number for the last and
next links in the line.
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The really powerful feature about flag links is that
you can use a flag word to define the features of the
flag for one category only, and use several categories
for each flag, as you would in a relational data-base
program. Later, you can select flags for display or
analysis which match a logical relationship between the
several flag word fields. Since flags can contain an
unlimited number of flag word fields (each represented
by one integer), this is a very powerful system.
You can access the separate flag word fields through
the use of the "f0, f1, f2, etc." and "anyflag" fields
when you use the filter. "f0, f1" refer to the
contents of the first, second, etc. flag fields.
"anyflag" refers to the contents of any flag field that
matches the logical expression it's in. See the filter
example below (page 6-24) for a typical use.
Example:
The "change link status" ("t") also has the same
synt`x. It is used for changing a field of the current
link after it has already been created.
For example, to change the branch to 25 and the cell
number to 7:
Whenever you make a new file, Montage displays the
current section size, then asks you whether you want to
make a different size file. If you want to change to a
different size, you answer with a "y", then enter the
new number, which should be an even multiple of 512
(either 512, 1024, 1536, 2048, etc). When you run
"montage" with existing files, it automatically finds
the proper section size to use with that file.
The "fstor" storage program (section 6 of manual)
allows you to compress your datafile. When this is
done, each section is reduced to the exact size which
holds the points in each section; this is a variable
number. When you "uncompress" the file, each section
gets expanded to the current section size (which you
can set to less than 1024 but is normally 1024). Fstor
always asks you if you want to change the section size
before it uncompresses the file. You can also change
the section size in "fstor" with the "change section
size" command.
Another way to compress your data files for archival
storage by the use of the pack(1) and unpack(1)
commands. These use a special bit-compression scheme.
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The absolute mode allows you to enter absolute
locations of points without any need for drawing marks
on the bitpad. Once you go to a link, however, the
absolute coordinates are moved so they don't refer to
an absolute bitpad location any more. To set the
correct alignment again, you can move the bitpad mouse
to your alignment dot on the bitpad surface and press
"x" or go to the correct base link.
If you want to make a lot of base links at (0,0) the
easiest way is to make a blank file called zero.dat
which contains, say 20 sections with base links at
(0,0). Then use the "fstor" program (Sect 6) to
compress this file and save it. When you need a file
of say, 80 sections, take the zero.sto file and run
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There are two filters you can use. The first, the
general filter, controls which links the cursor will
move to with the commands "nearest link", "next link"
or "last link". This allows you to select which links
you use for alignment when making montages (see "making
montages with transparent sheets below").
The second filter is the display filter. This
filter controls which links are displayed each time a
new screen display is generated. Thus, you can greatly
simplify a large screen display by filtering out
unwanted links during display. In addition, you can
select which sections to display on the screen with the
display filter. The programs "mpict", "fstor" and
"glink" all use the same filter.
You use the filter by creating "filter specs" which
describe the form of link that you want to find. Each
filter spec describes the exact form of link by
specifying for each field (number) in the link what
range of values is acceptable. You assign an
appropriate filter spec to each filter; then the filter
automatically finds the links you want whenever you
enter a command which uses the filter.
The filter language syntax for one line is:
You may put as many filter specs on a single line as
will fit; normally this maximum is ten. To pass
through the filter, a link must statisfy all the filter
specs on one line (normally separated by semicolons);
this is a "logical and" function. The lower and upper
bounds (inclusive) allow you to specify a range of
values for any field. If you need more ambiguity in a
filter spec, you may use the "logical or" function by
using "or" between specs. You may also use left and
right parentheses to define more complicated logical
functions than exclusively "and" or "or" (see example
below).
To make it easier for you to write filter specs, the
filter accepts multiple filter specs on a line
separated by either semicolons, commas, or spaces (you
can leave out the semicolons).
You may also use the notation current - 1 (or + 1)
to describe any field in a link referred to the current
status. This can be abbreviated to "cur - 1".
Example of filter spec table:
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One hint to make this easier. If you set the value
for c to -1, then the a value is equal to the x slope
(the tangent of the y rotation), and the b value is
equal to the y slope (an x rotation). In this case,
This feature allows you to align previous sections
with your current section. To do this, set the second
filter line to "sect=cur-1". This allows you to see
the links from the previous section as dots; you can
align links on your current section with them using the
"l" (move link) command.
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When you need to trace over the edge of one area,
align the sheet for the next area with the first by
overlapping them with their holes from opposite corners
placed onto one peg of the artist's jig, keeping the
edges parallel. (Or you can just keep the sheets edge-
to-edge, with the corners touching.) This keeps all of
the sheets in the same relative rotation. The pictures
from which you're tracing must have at least 10% overlap,
and should represent neat rows of material from the
sections you're photographing.
Place the transparent sheet so that the first
montage area is within the active area of the bitpad.
Make a dot underneath the corner on a piece of tape on
the bitpad, move the sheet by the amount required to
place the next montage area in the active area of the
bitpad, and make a second dot on the bitpad. Make two
additional dots for another corner in the same manner,
to keep the sheet in correct rotation alignment. Use
these reference points to position the transparent
sheets for the different montage areas. Of course, if
you're using the peg holes for the reference points,
you don't need to make any dots on the bitpad.
If you're setting up a series of sections for
montages, you can save time by correctly making all the
alignment links in the first section. Then copy them
to all successive sections using the "next section"
("^p") command followed by the "base link" ("0")
command. If you copy area links in this manner, you
should set the "relative filter" ("fg 2") to a null
filter spec (see next paragraph) so the area number in
the current status doesn't get changed. Alternately,
you can copy all the links in a section using the
"cat" UNIX command to copy the section multiple times.
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Montage is an evolving system, and is very
easy to modify. We have tried to keep Montage as
simple as possible so it's easy for those of us who
don't have much experience with computers. At the
same time, we have added advanced features that make
Montage useful for many different types of 3-D
reconstruction. If there is a problem with the manual,
or Montage program or any of the other programs in the
Montage system, please let us know so we can fix
it.
If you think of a new feature you feel would be
really useful to others, let us know. We may be able
to change Montage to suit your needs. If you've
purchased the source code, we encourage you to make the
change yourself or get a programmer to do it for you.
We would appreciate a copy of your changes so we can
evaluate and add them for use by others.
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You may not actually see anything on the screen the first
time you display a picture with the "run" command because the
"xcent, ycent, zcent" center location can't be set until after the
picture is drawn. Just run it a second time and the picture
should be centered on the screen so it just fits in. The x,y,zcent
and mag parameters are set automatically (when auto=1) so
you don't have to worry about getting it centered.
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If you want to make several pictures display at once, you can
use the command "save !
You can also use the commands "save filename" or "save !
filename" to create corfiles. If the corfile is not explicitly given
or has not been defined by the "corfile = name" command, then
the default file name "data.cor" is used for both the "save" and
"save !" commands.
To load the parameters from a corfile you have already made,
give the command "load filename
After you save a corfile, you can edit it with "vi" or "joe" and
add extra "run", "include" and "erase" lines. To make your
corfile easier to understand, you can put comments in wherever
you want by putting a "#" at the beginning of the line. This
causes "mpict" to ignore that line.
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Flag sizes range from a tiny dot (1) to one-half the
size of the full picture (15). Pen colors 1 to 4 are
the pen numbers on the HP plotter, and colors 5 to 8
are a second round of colors used after pens 1 to 4.
Shapes are:
The filter line:
The filter line:
You can include your "flag.def" file that you
defined for the "montage" program into your corfile to
allow you to make use of the flag definitions.
For example, if your flag.def file had:
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The syntax is:
For printouts of flags, "Symbol" means any one of:
triangle, square, circle, cross, asterisk, or char
(see the flags description above).
"size" ranges from 1 to 9, giving symbols the size of
a small dot to one half the whole picture.
"fill" can be set on (=1) or off (=0) and will produce trace links
or flags filled with color.
The filterspec is everything on the line after the options.
It has syntax exactly like the filter in "montage" and "fstor"
(see "filter" in section 4: Montage manual.)
You may run the filter very simply like: filter cell 5
Or you may make up to one hundred filters each with a unique
number (0-99). These will appear in the corfile just as
they do on the screen.
To turn off a filter, type "filter (num)" with the rest of the
line blank.
You may include your flag definition file in a corfile so
flags can be described by character strings instead of numbers.
You can abbreviate the above label commands to single chars;
only the first character in each command is used. Multiple
commands per line are allowed, separated by spaces.
For example:
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After you get familiar with the corfile commands,
you may use "vi" to edit corfiles, adding "run",
"erase" and "include" commands to draw large pictures
composed of many individual corfiles. You can make
your corfiles easier to understand by using comment
lines. You enter comments by placing a "#" at the
beginning of a line; this causes mpict to ignore that
line.
You can run mpict with several different switch
options on the command line:
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For instance, the command "draw9" (in "/usr/bin/draw9")
contains:
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The posit program allows you to merge several
pictures and send the resulting picture to be hidden,
displayed or drawn on the plotter. This process
simplifies complicated illustrations because all the
individual pictures can be generated and hidden
separately, and this need only be done once. Composing
the illustration is thereby easier because only the
locations of the individual pictures has to be defined.
Example 1:
Example 2:
If you have several picture files to make, hide and
position, you can run them most easily by using the -f
options with mpict, hide and posit. For example, by running
An alternate way is to use the command "makehid11 file1... filen"
and then to use posit afterwards (see page 6-20).
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You might want to repeat this sequence of commands
several times to get the positions of the pictures and
labels right. Instead of retyping the whole command
sequence, you can simply put it into a text file using
"vi" or "ice" and have the shell run this file for you.
This allows you to copy the file and easily make
changes without removing your original copy if you want
to go back to it.
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When you run fstor, get the help table with "h":
You can also run fstor with command line switches.
When you are familiar with Linux, this is the faster
way. The Linux version of fstor has the following
switches (see Section 3 for a description of command
line switches):
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The glink help table:
For instance, you could enter the following command
line:
You can use column and var (supplied with
Montage) to get the standard deviation of selected
data. column prints out a selected column from the
standard input or a text file, and var prints the
mean, variance, and standard deviation of a list of
numbers. For instance:
The column command (used above) is merely a
shell file (executable text file: chmod(1)) invoking
awk(1):
Use the editor to make the command "garea":
The command "grad":
As you can see, "awk" is very powerful and easy to
use. See "The awk Programming Language" chapter in the
Linux Support Tools Guide, or The AWK Programming Language by Aho,
Kernighan and Weinberger (available
in paperback) for information and examples on how to
use awk(1).
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Command line switches for hide are:
The usual way to run the "hide" programs is to run a
shell command file (See Sect 3) which contains a
command line invoking the "hide" program. A typical
hide command is:
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The drawpic command is a convenient way to run the
"hpflt -c | hplot" ("ibmflt -c | iplot") combination
because these individual commands are all put into a
command file for you, set up to use either standard
input or a list of files. The command 8by11 draws
pictures on standard 8 1/2 x 11 inch paper in the same
way as drawpic but at a smaller mag. See section 5 for
a description of picture command files.
If you want to include more command line switches,
you can add them before the file name:
When you have defined more than 4 pens in a picture,
you can use the "drawpic -w" switch to stop the plotter
after each pen is used. This allows you to change the
paper or the pen for each separately defined pen.
Another way to insert more pens is to wait until the
first four pens have been used, you stop the plotter by
pressing the plotter "Enter" button, and then change
the first four pens (1 - 4) to their corresponding
colors the second set (5 - 8). After the pens are
changed, press the plotter "Enter" button again to
resume plotting.
The "drawpic", "vid" and "posit" commands are
designed to use many of the same command line switches
so they can be used nearly identically in command
files.
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Vid command line switches are:
Posit command line switches:
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If you want to have control over the scale of the
plot (so that it isn't always drawn as a square which
fills the page) you can use the "-m" and "-M" switches
for the y-axis, and you can include some dummy extra
points to extend the x-axis, one for each end.
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b (button macro command)
y (yes, I want to change)
You can use macros for any sequence of keys that you
could type yourself at normal speed. You will notice
that when you exit Montage and run it again, the macros
get erased and your must re-enter them. One way to
eliminate this problem is to avoid exiting Montage by
using the "!" command (see below) to run UNIX commands
from within Montage. You can then return back to
Montage with your macros intact. Another way:reading commands from a file
If you have made some long macros, you will find
that you lose the macro definitions when you exit from
Montage. You can put your macros into a text file and
read them automatically into Montage using the "r"
command. For instance you can make a file "macros"
using "vi" or "ice" which contains:
by
This "macros" file could be read in from the disk
drive whenever you run the "r" command:
r
Please enter the file to be read: macros
Then your three macros for F2, F3 and F4 would be
read in automatically. You can also read in one file
from within another file's "r" command (recursively),
so you can read several files at once, and accomplish
quite complicated actions.
Types of links
There are commands to make five types of links:
Type Enter Use
0) Base 0 for alignment
2) Trace 2 for tracing cells.
3) Flag 3 to mark synapses, etc.
4) Grain 4 for marking grains.
5) line 5 for marking fibers which pass through sections.
Any one of these types of links may be used for
alignment of transparent sheets. The base, trace, and
grain links all simply display their single characters
in the screen display. The flag link displays "F"
followed by the flag name. The line link gives a "L 4
5" display on the screen where the "4 5" are typical
cell and branch numbers.Line links
Line links are used for defining lines which go
through many sections. The line can go from one
section both forward and backward. It is useful for
defining the path which a fiber moves through tissue.
Line links are difficult to enter correctly, because
each line link has a pointer to both the line link
immediately before and after it. This gives an order
to the links in a line vector, and allows the line to
go through tissue any direction, forward or backward. Grain links
Grain links are exactly like trace links, except
that their points are not displayed as a connected
polygon. You can use them for displaying point
information, such as individual grains on an
autoradiogram.
Flag links
Flag links are used to make a point stand out by
displaying it as one or several words. You use the "g"
command to define the current flag specification, and
you can enter a list of numbers or words. This list is
displayed on the bottom left of the screen, and this
definition will appear in any flag links made. In
order for the flag words to appear correctly, you must
create a file called "flag.def" which contains all the
definitions you are using. Montage reads the
"flag.def" file each time you run it as a command, and
translates each word into a number, to be used as an
"index" in the symbol table. Later, you can use the
same flag word definitions when you run the picture
program "mict" and the definition file "flag.def" will
allow the picture program to respond correctly.Flag link definitions
Flag links display their name or number on the
screen. You can make a definition table for all your
flag types which associates each flag type with a name.
The definition table is put in a separate "flag.def"
file which gets read each time you run the montage
program. You make the definition file using an editor
such as "vi" or "ice" just as you would any other text
file. The syntax for the flag definition file is:
For example, a typical file might be:
----------------------------------------------
# Flag definition file
#
#
flat = 20
round = 21
"large square" = 22
#
# end of file
----------------------------------------------
Once you have set the flag definition table, you can
then enter any flag into the "current flag
specification" at the bottom of the screen with the
"make flag spec" ("g") command. You can enter as many
names or numbers, separated by spaces, as you like;
these will all appear in the current flag spec. When
you create a flag link, the flag spec. names and
numbers will appear in the screen display along with
the marking "F". Thus, you can see the name of all
your flags right on the screen where you place them.
F input amacrine 7
You can include your flag definition file in your
corfiles when you use "picture" to make 3D pictures of
your data. This allows you to use the same flag
definitions to describe to the filter which flags to
display in your picture. To create or change the
"flag.def" file when you're running Montage, you can
make use of the "!" system command (see below) to run
the editor ("vi" or "ice"; see Sect 7) from inside
Montage. This allows you to run any Linux command line
while you're running Montage; you can even run Montage
inside itself to look at a different data file! setting current status
The current status is the information which you
incorporate into a link when you first create it. To
change the current status, you simply enter the "set
current status" ("s") command. Then you may enter as
many changes as you like, separated with semicolons
";". Each status change has: 1) the link field you're
changing; this can be abbreviated. 2) The new value
for the field. 3) If another field change is on the
same line, you must have a semicolon ";". You end your
entry with a blank line.
br 25; ce 7
would do the trick!size of sections
Montage allows you to make data files of different
sizes. You can change the section size whenever you
make a new data file. Normally, you use the largest
size possible, but you can use a smaller size if you're
running out of room on the working disk. The data
files normally have a section size of 1024.
zero x,y position
Normally, montage starts out with the cursor set at
location 0,0 and you can make your first base link
there to keep an absolute reference point from which to
make all your other base links (if you don't have
multiple areas). However, in absolute mode ("A"), your
first link will be at the absolute coordinate of the
bitpad cursor, which will not usually be 0,0. If you
want your base links to start out at 0,0 (this is nice
but not necessary), then use the "x" command which
causes the current bitpad position to be 0,0 and shows
that location on the screen (as if you went to a link
there).
cat z20.sto z20.sto >x40.sto
cat x40.sto x40.sto >file.sto
fstor -n file.sto xxx.sto -r xxx.sto file.dat
to make the file. It will have 80 blank sections, each
with a copy of the original link. "fstor -n file1 file2"
means renumber the sections in the file.The Linux system command "!"
You can run any Linux command when you're running
Montage by entering a "!" in front of the line.
Montage responds to your "!" by resetting the screen
back to text mode so you can see your command
operating normally. After your one-line command stops
running, Montage says: Type
Filter
The montage program has a very powerful filter
system which allows you to select links with any
combination of field values (branch, area, color, cell
number, etc). The purpose of the filter is to give you
a way to describe different parts of your drawings so
you can separate them later. If you'll ever need to
display parts of your drawings separately, or in a
different color on the plotter, you need the filter.
Think of the filter as a seive through which to pass
your datafile.link fields
The filter can look for any combination of the
following fields:
type the link type (base,cell,ftype,trace,grain)
xbio,ybio the x,y coordinates of the link.
section the section number.
area the area number for montages.
branch the branch number.
cell the cell number.
color link color.
flag the first flag spec number (only in flag links).
f1,f2,f3, etc. other flag spec numbers in flag links.
anyflag any flag spec in a flag link.
To make it easier for you to create and use the
filter specs, there is a table with space for eight
filter specs to be defined for use in the filters. A
simple numbering scheme, in which each filter spec line
is given a number, allows you to refer to this spec by
its number when you use it for either filter. Thus,
any filter spec may be used for either filter. In
practice, you define new filter specs as you need them,
and add them to the filter spec table.
1) Link field, which can be abbreviated.
2) Equals "=" sign.
3) Lower bound for field.
4) Comma "," (optional, use with upper bound.)
5) Upper bound for field (optional).
6) If more filter specs. are on the same line, you
separate them with a space or semicolon ";".
Example of filter syntax:
typ = flag; flag = 4,7; branch = 5
This example would filter for a flag type link whose
flag value was either 4, 5, 6 or 7, and whose branch
was 5.
filter spec table:
1) typ = base; (link type must be 0)
2) typ = trace,grain; (link type 2,3,4)
3)
4)
5) typ = 2; (cel = 1) or (cel = 3); (trace link on cell 1 or 3)
6) f1=dark; anyflag=bipolar; (any dark bipolar)
7) typ = ftype,grain; (link type 3 and 4)
8) sec = cur - 1; typ = trace; (any trace link on previous section)
reference numbers:
g 2 (link type 2,3,4)
r 1 (link type 0)
d 7 (Flag,grain links on current section, and
any trace links on previous section)
To change the filter, use the "filter" ("f")
command, then type "g", "r", "d" to change any of the
filters to a different filter spec; or to change filter
specs, type "f". Then enter the number of the filter
spec. you want to change, and enter the filter spec.
use of filter by other programs
The "fstor", "glink" and "mpict" programs all use
the same filter language, with the same syntax as
described above. Corfiles for "mpict" can have up to
100 filter spec lines, each with its own pen number and
hide status.
Surgery with filter
Another feature of the filter is the ability to do
surgery by selecting only links above or below a plane
located in three-space. Planes are defined by the
syntax:
above xloc yloc zloc a b c
below xloc yloc zloc a b c
The (xloc,yloc,zloc) define a point in original x,y bio
coordinates which the plane passes through. The
(a b c) define the solid angle at which the plane
passes through the point for the equation:
a(x-xloc) + b(y-yloc) + c(z-zloc) = 0
It is sometimes difficult to find the proper
locations for the planes because they can't be seen,
only their effect on the display can be seen. For
starters, define the (xloc,yloc,zloc) point to be the
center of the cell, so that no matter which angle you
choose for the plane, you will be able to see where it
cuts through the material. The values for a,b, and c
be determined empirically or intuitively by noting
that a,b,c affect the x,y or z slope of the plane,
respectively. The values for a,b,c should not all be
zero at once, since this selects for all points.
Setting one of a,b or c to zero makes the plane have no
slope in that direction. Increasing one of a,b or c
makes that coordinate affect the slope more. Once you
get the slope right, you can move the intersection
point very easily.
z-z0 = tan(yrot)(x-x0) + tan(xrot)(y-y0)
for example
above 0 0 0 2 3 -1
selects for points above a plane with a slope of 2 in
the x direction (a y rotation), and 3 in the y direction (an x
rotation). A similar equation holds for setting either a or b to
equal -1. display filter: additional sections use to align
sections
Normally, the display filter can accept links for
display from the current section only. However, it has
a special feature not found in the other filter
functions which allows display of other sections in
addition to the current section. The Display filter
function will use additional filter spec lines each of
which may display links from one other section. The
display filter continues to use all succeeding filter
spec lines until a blank line or the end of the filter
table. Only the first section displayed will have
trace links displayed as lines. The other sections are
displayed as dots only. For instance, if filter specs
6, 7 and 8 are set, you can use all three specs for
display by setting the display filter to 6. Filter
specs 7 and 8 will then also display on the screen, but
will have only dots, no lines.
First page of the main menu:
^2 = Next section (rfilt) ^p = Last section (rfilt) Nov 87
^a = Next link (gfilt) ^w = Last link (gfilt)
^b = Current link ^r = Nearest link (gfilt)
^c = Go to cursor ^s = Nearest link, don't move (gfilt)
^d = Next point ^t = Last point
^h = Next frame ^x = Last frame
0 = Make base link P = Erase link
1 = Make point Q = Erase point
2 = Make trace link
3 = Make flag link
4 = Make grain link @ = position mode
5 = Make line link A = absolute mode (default)
7 = Close slice B = cursor mode
8 = Redisplay for abs mode
Second page of the main menu:
b = make Button macro
c = Close trace link (off/on)
d = link display menu: link params (on/off)
f = change Filter
g = make flag spec
h = Help table
i = display symbol defs.
j = Jump to section
k = make screen upside down
l = move Link mode
m = change Magnification
n = short screen display
q = exit program
r = read commands from file
s = Set current status
t = Change link status
u = Set line display mode
w = write mode (on/off)
x = stage to zero pos
y = link display (on/off)
X,q = exit program
z = change screen size
! = run Linux system command!
The display menu:
Display Menu
d = display current link on screen
e = display more information about current link
f = fix section
k = kill section, clear to all zeroes
any other key = return to display
Making montages with transparent sheets
When you trace pictures on the bitpad, there is a
problem because the bitpad active area can only fit one
8" x 10" print. You make montages whenever you want to
trace features which lie on more than one photograph. A
montage is a large picture composed of smaller
pictures. The drawings from each photograph must
therefore be traced separately on the bitpad. To allow
the drawings from each separate "montage area"
(photograph on same section) to be merged into one
picture properly, you use a special method of aligning
the transparent sheets when you trace from the photographs.
using alignment links to create the montage
When you're tracing from montages of transparent sheets,
you first make the alignments for different "montage
areas" by making extra alignment links (normally base
links) which are created with the screen cursor moved
from the first alignment link by an amount equivalent
to the offset between your transparent sheets. Thus, each
montage area should have its own alignment link which
corresponds to the location of the same bitpad dot, but
which represents a different area of the picture. Each
area alignment link has a unique number in its "area"
link field. When you're tracing from transparent sheets,
you can select for that area by using the "general
filter" for any of the "move to link commands"
("^a","^q","^r","^t"). Whenever you move to a link,
the current status (defines the data to be entered into
the fields of a new link) area field is set from the
current link, so any new links are put inside the new
area.reference points
To create the extra alignment links, you need two
reference points defined by the transparent sheet you're
working from. The distance between the reference
points represents the distance between adjacent montage
areas. The reference points may be the artist jig peg
holes, or you may use a corner of the sheet to define
them.making montage areas
Montage areas are defined by alignment links; the
"area" number in each link defines which area. To make
a new area alignment link, you first set the "area"
number in the current status ("s"). Go to the first
alignment link with the "nearest link" ("^r") command,
move the mouse (with the button down in absolute mode;
in cursor mode) to the first reference point, move the
mouse (with the button up in absolute mode; down in
cursor mode) the proper distance to the second
reference point, and make the new alignment (base "0")
link. This alignment link defines a new montage area by
changing the alignment between the bitpad coordinate
system and the picture on the screen.tracing transparent sheets using areas
Once all the alignment links are in place, you can
easily switch from one area to another by going to the
alignment link which defines that area. Whenever you
go to a link, the current status gets set from the
nearest link defined by the relative filter. This
automatically sets the correct area number in the
current status, so that you make all trace links which
use that alignment link have the same area number. You
can easily change the relative filter to define which
links are used to set the current status. This is
necessary when you're first making the alignment links:
you don't want any previous alignment links on a new
section to change your area number when you're copying
area alignment links from an old section (see above).tracing montage overlaps
Sometimes, you find that trace points overlap
between two montage areas. In this case, you need to
add new trace points to an already existing trace link
from a different montage area. To do this, first
position the new transparent sheet on the bitpad
reference point (see "reference points" above). Next,
go to the alignment link for the new sheet and move the
mouse to the center bitpad dot, as you normally would
to align the mouse with the cursor; then move the
cursor near to the old trace link in the other montage
area. Use the "nearest link, don't move" ("^s")
command to establish the old trace link as the current
link; this doesn't change the cursor position. With
the "next point" ("^d") command, move the "CP" marker
to the point just before (clockwise) the new ones
you're going to add. Then add points to the trace link
with the "make point" ("1") command.coping with slow displays
When you're tracing cells with many points, you will
find that the picture display is very slow. This is
due to the small but real time it takes the computer to
calculate and display the position of each point. You
can alleviate this somewhat by keeping the bitpad
button pressed (in cursor mode); then no new picture
display occurs. You can also use the "short screen
display" ("n") command to eliminate most of the numbers
on the current status display. You can use the display
filter to select only nearby links for display; set the
display filter to
xbio = cur -200, cur+200; ybio = cur -200, cur+200".
Montage switches
To run montage with different graphics boards, you
enter a command switch on the command line right after
the "montage". The switches are:
-b Linux standard driver, as in plot(1G): "setenv GTERM epc"
-e Enhanced Graphics Adapter (EGA)
-g Video Graphics Adapter (VGA) default
-h Hercules board
-c change calibration for bitpad with 200 points/inch
-x X Windows driver
Some final words from experience
There are several ways to use Montage without
going through the transparent sheet step, so 3-D
reconstruction is available for many kinds of material.
The standard transparent sheet tracing technique is
often preferable because it gives a permanent record of
how a cell was aligned and traced which can be checked
by a second person. When studies must be occasionally
re-checked after several months or a year, this factor
is sometimes more important than the extra amount of
time it takes to separately align and trace from
photographs onto transparent sheets.
Mpict User's Manual
mpict interactive
To run mpict on the video terminal, type "picture picture display
The picture displays when you give the "run" command. You
can stop the picture during the display by typing one "^C"
(control-C). To stop the program, type two "^C's" or type the
command "quit" or "q", followed by a blank line.
save and load corfiles
When you've got your picture to look exactly right, set the
"corfile" with the line "corfile = myfile.cor". Then give the
command "save
flags
Flag links in your picture can be displayed in a
variety of sizes, shapes, and in eight colors. To
define a flag for display, give the command:
filter [num] [pen num] shape [size num] flag num
where:
"filter num" is the filter number, from 0 to 99;
"pen num" is the pen number for the plotter;
"shape [char]" is the symbol type printed at the flag;
"size num" is the symbol size;
"flag num" is the link flag number.
There are 100 filters available for displaying
links. Each category of flag described in a filter
line will be displayed with the pen color and symbol
shape defined in the filter line. The pen color and
symbol size do not need to be put on the line; if
they're left out, the default pen color defined by the
pen parameter in the corfile controls the color and the
size is set to 4. If the symbol is "char", a following
single character defines the shape to be a standard
alphabetical character. To erase a flag display, type
"flag number" and leave the rest of the line blank.
char single char following symbol name: "char x"
triangle
square
circle
cross (plus symbol)
asterisk
For example, the filter line:
filter 1 pen 2 circle size 8 flag 24
defines flag 24 to be displayed as a circle of
size 8 (fairly large) drawn with pen 2.
filter char R size 4 flag=10 f2=12
defines flag (10,12) to be drawn as an "R" of size
4 (small) drawn with the default pen. This filter line
defines filter 0 by default because no filter number
appears.
filter tri anyflag=23
draws a triangle for a flag having a 23 in any of
its flag fields.
bipolar = 25
amacrine = 26
You could make use of these definitions by including
the flag.def file into your corfile and defining a flag
filter like:
blue = 4
include flag.def
filter pen blue square size 3 anyflag=bipolar f2=7
This draws a small square using the blue (4th) pen
for any flag with a 25 in any of its flag fields and a
7 in field 2.
Display parameters (set = 1 to turn on; set = 0
to turn off)
xrot,yrot,zrot Sets rotation of picture: xrot first, zrot last.
xcent,ycent,zcent Sets the center of rotation for the cell (set by auto)
Three-dimensional point in bitpad coordinates.
mag Sets the overall magnification of the picture (set by auto)
auto Normally set to 1. This makes mag, xcent, ycent, and zcent
be changed the next time you run the picture. This
automatically keeps your picture the largest size possible
and centers it for you. If you turn "auto" off (0), you
can change the mag to match the mag of other pictures.
Always turned off in corfiles (automatically).
xtran,ytran Sets location of picture on screen (normally 0.5,0.5).
incr section increment (initially set to 1)
finc flag section increment; 0 means finc = "incr" above (set to 1)
pen Default plotter pen number (default 1).
zdist Distance between sections (default 5)
line Sets number of microns for calibration line.
calib Sets proportion of (x,y) to z values for points, and length of
calibration line (number of microns per cm on bitpad).
xline,yline Sets location of calibration line (default .95 .1);
fill If set=1 produces slices filled with color. Can be
overridden by the value of fill in a filter spec.
hide Sets default hidden line status. Draws a picture on the
plotter with hidden line removal; set "hide 1".
This causes the flags to be displayed
before the cell data, so the flags will not be hidden.
The hidden-line memory is reinitialized after
each "run" command.
clear Clears the screen of text before the picture gets displayed.
If you are running the program from a graphics terminal with
the same screen for both graphics and text, set "clear=1".
If not set, the previous picture stays.
notext Causes screen to wait after picture is drawn before
returning to text mode for paramater display.
silent The "silent = 1" command prevents printout of the parameters
when running mpict from a corfile. You can set this in
the corfile, or you can run mpict with the extra switch "-s"
which accomplishes the same thing (e.g. "mpict -s ....")
filter
Use this command to display only
selected links.
filter [n] [pen[=]n][;] [hide[=]n][;] [fill=n][;] [symbol] [size[=]n] filterspec
Everything inside square brackets "[]" above is optional;
that is, the equals signs "=" and ";" semicolons may be
left out. The pen and hide commands are also optional;
if they are left out, the default pen and hide settings
take over.label
Use this command to draw lines and write of text in
your picture. The syntax is:
label [num] label commands (rest of line)
The "label commands" are:
charwidth x set character width to "x".
erase erase screen
move x y move pen to (x,y)
draw x y draw to (x,y)
line x1 y1 x2 y2 draw line segment from (x1,y1) to (x2,y2)
text x y "text" write "text" starting at (x,y). '"' is the
delimiter char, which can be any character;
there must be matching char at end.
pen num change pen to "num".
size x change picture size to a square "x" on a side
include "name" include command file "name" at this point.
flag shape size draw flag like the filter
The picture labels are drawn on a square picture which extends
from 0 to 1.0 in both X and Y. This, however, may be
changed with the "size" command.
c .02 p 3 t .2 .8 /Cell 8: bipolar/
p 1 t .2 .75 " Corfile zzz"
says character width = .02, pen number 3, text starting
at .2 .8., followed by more text drawn with pen 1.
flag tri 9 says make a flag which is a triangle of size 9
The above label commands are exactly the same as
those for the "labels" command. The only difference is
that you can enter the label commands into a corfile
and the label will be drawn on your picture immediately
after the picture is done. See page 6-15 for more details
on drawing labels.
reverse
Causes the sections in a data file to be displayed in
reverse; this has the effect that the cell is drawn as its
mirror image.
erase
This command resets all corfile values, including the
flags,
filters, and labels. The "erase" command is automatically
inserted into the beginning of a saved corfile. You may,
however, delete this line with the editor or add further
"erases" if you wish. You can also give the commands:
erase flags Erases only the flag defs in corfile
erase filter Erases only the filter lines in corfile
erase label Erases only the label lines in corfile
derase This command turns on/off the "erase" which
is normally put at the start of a
saved corfile. Default is on (derase = 1).
include name This command causes corfile "name" to be
loaded immediately into the display paramater
tables. Previous values not set in the corfile are
not changed in the tables, unless the "erase" command
is in the included file.
Several of the above picture commands make use of
the "standard graphics screen". This is defined to be
a square with its lower left corner at the point (0,0)
and its upper right corner at (1.0, 1.0). The
(xtran,ytran) and (xline,yline) params as well as all
of the (x,y) label commands use this standard screen,
so their values should normally range from 0 to 1.
system commands from within mpict
You can run any UNIX system command by typing a "!"
at the beginning of the line followed by any one line
UNIX command. This is useful for looking at your
directory while running "mpict" or "picture".
mpict non-interactive
You may also run mpict in a non-interactive mode
directly from a corfile you've already made. All the
parameters in the corfile get read in, just as if you
typed them in from the keyboard. You can type
"mpict
mpict -f make ".m" output files from multiple ".cor" input files
mpict -m use the secondary monochrome screen to display text
mpict -s don't write any text onto the screen; useful for batch processing
some useful picture commands
There are several commands you can use to run mpict
automatically from corfiles. They are executable text
files ("command files"), so you can print them out or
copy them for your own use if you like. The "$argv" in
some of the files means that the command will work on
one or many files equally well. See next section for
details on the "vid", "hide" and "hpflt" programs.
These commands are in the "/usr/bin" directory:
picture This is the normal way to interactively
draw pictures, but can also be run
from a corfile or the standard input.
Pictures on screen are not drawn with
hidden lines removed.
"mpict | vid -i"
picthide This is like "picture" except that it
will remove hidden lines if the "hide"
parameter is set. Not normally used.
"mpict | hide9 -i | vid -i"
drawpic This draws from a list of files to the plotter,
or it can draw from the standard input.
For the IBM Color Plotter, drawpic contains the
"ibmflt" line. The "-c" option for hpflt (ibmflt)
sorts pens by color. You may use any switch options
for hpflt (ibmflt) on the command line;
the third example below and pages 6-6, 6-7.
"hpflt -c $argv | hplot" for HP 7221A plotter
"ibmflt -c $argv | iplot" for IBM Color plotter
Examples of drawpic usage:
drawpic < file1.plt
drawpic file1.m file2.m file3.h file4.plt
drawpic -w -m 2.5 -x 4500 -y 4500 file1.h -m 1.5 -x 7500 file2.h
dopic9, dopic11: These draw pictures from one or many
corfiles at once, using hide9 or hide11.
Remember, hide9 runs 16 times faster than
hide11, and hide10 4 times faster.
"mpict -s $argv | hide9 -i"
makehid9, makehid11: These take one or many corfiles and
produce corresponding ".h" files
for later display or plotting.
#
foreach i ($argv)
mpict -s <$i | hide11 -i >$i:r.h
end
Shell commands
You can combine any valid command lines in Linux to
make more elaborate commands which can be put into
command files using the vi editor, and then make
them executable using the command "chmod +x file". These
commands can then be run at low priority by the "nice"
prefix command.
#
nice +20 dopic9 $argv | drawpic
The "#" in the first line of the file makes this
command run under the "C-shell" program (see the CSH
chapter in the Linux Introductory manual). This command
line is be equivalent to:
nice +20 mpict -s (command args) | hide9 -i | hpflt -c | hplot
When the command runs, the "$argv" in the "draw9"
command gets replaced by any switches or file names you
type on the line after "draw" (see the Linux csh manual
for more details). The "nice" command only runs the
first command in the line at low priority. The "draw9"
command runs:
"mpict -s file | hide9 -i"
at low priority because these commands are inside
"dopic9". This command is also found in the directory
"/usr/bin" for your use. You can use it like:
draw9 file1 or draw9 < file1
Or more elaborately:
draw9 file1 file2 ... filen
Still more elaborately:
draw `cat filelist`
Where "file1 ... filen" are corfiles to be plotted,
or "filelist" is a file which contains a list of
corfiles to be plotted. The "`"s (reverse quotes)
around "cat filelist" in the last example cause the
C-shell to run the command "cat filelist" first; the
result of this (its standard output) is given as a list
to "draw". You can draw pictures on the screen or
with:
dopic9 corfiles | vid
Composing illustrations: posit
Once you've drawn several pictures to your
satisfaction, with rotations and details like flags and
pen colors set correctly, you can compose illustrations
by combining several pictures into one on the plotter.
This is useful where you need to take existing pictures
and adjust their relative positions on a page. You can
position the individual pictures from corfiles and then
hide them all at once to create distance perspective
where one picture overlaps another. posit -f -x 1000 -y 7000 file1.h -x 4000 -5000 file2
This creates file1.p and file2.p with (x,y) offsets
from existing ".h" files which had already been hidden.
posit -f -x 1000 -y 2500 file1.m -x 1500 -y 2000 file2.m
hide11 -f -h file1.p file2.p
This creates file1.h and file2.h with (x,y) offsets
from corresponding ".m" (mpict) files and then hides
the second picture behind the first using the "-h"
option for hide on the ".p" output files. Pen colors
are preserved.
mpict -f ab*.cor
you can make lots of pictures from many cor files all
at once. Each corfile must have a different name, but
if the names have some of their characters in common,
you can use the "?" and "*" wildcards to refer to them
selectively. The "datfiles" referred to inside the
corfiles may be any valid data file, and in particular
may be the same data file. This is a good way of
generating several views of one cell from one command
line, without needing to type lots of file names.
transparency
You can create quite subtle overlay and transparency
effects with judicious use of the hide11 and posit
commands. You can merge two pictures, each with its
hidden lines removed, by drawing one on top of the
other with a different pen, to give the impression of
transparency. By running the output of posit through
hide11, you can cause the first pictures in an
illustration to be in front of those added later.
Normally, however you get better results if you run
hide on pictures not previously hidden, so you should
posit all you pictures before you run them though
hide11. For example:
posit -f -x 1000 -y 3000 file1.m -x 2000 -y 4500 file2.m
hide -f file*.p
drawpic file*.h
Another way to achieve the same transparency effect
is to make a ".cor" file which draws several pictures
using filters from one file, separated by "runs". For
example you could use the ice or vi editor to make the
following corfile "file1.cor":
xrot 0
yrot 10
zrot 0
.
.
hide 1
.
.
datfile file1.dat
corfile file1.cor
filter 1 pen 5 cell=4
run
filter 1 pen 3 cell=8
run
filter 1 pen 6 cell=12
run
This "file1.cor" corfile draws three cells with
different pens, all on the same picture. When the
picture is run through the hide filter, the cells all
have their internal hidden lines removed but will be
"transparent" to each other. You can position them
with "xtran" and "ytran" in the corfile. To create
this picture, use the following commands:
mpict -s file1.cor | hide11 >file1.h
or
makehid11 file1.cor makes same ".h" file
drawpic file1.h draws the picture on plotter
vid file1.h draws the picture on the screen
Summary of file types
In the UNIX system, file names can be anything you
want, but the "C-Shell" has an easy way to deal with
names that have ".something" at the end of the file
name ($var:r cuts off ".something"; see the csh manual
for details). This makes it useful to have the
".something" stand for a file type, and in this manual
we have standardized the following file types:
program
which creates
file Picture vi mpict -s hide posit
------------------------------------------------------------------------------
file type .cor .cor .m .h .p
------------------------------------------------------------------------------
purpose To store To modify to make to remove to position
parameters labels, picture hid lines a picture
filters
------------------------------------------------------------------------------
Making higher level commands
If want to compose an illustration which requires a
set of pictures individually placed, with labels to go
with them, you might run commands like:
makehid ab*.cor
posit -f -x 2000 -y 3300 ab1.cor
posit -f -x 4500 -y 3800 ab2.cor
posit -f -x 6700 -y 2000 ab3.cor
drawpic ab*.p
labels << eof | drawpic -x 6000
t .2 .3 "Washington"
t .4 .35 "Lincoln"
t .65 .2 "Trudeau"
eof
In this example, the "<< eof" after labels is a csh
command which says take all the text up to the word
"eof" in the shell file as the standard input to
"labels". See the csh manual for more details. You
can achieve the same result with the command:
labels < labelfile | drawpic
where labelfile contains the same sequence of
labels as above. Which is easier for you?
vi presidents make the file
chmod +x presidents make it executable
presidents run it
cp presidents pres2 copy it
vi pres2 make new version
pres2 run new version
You can replace the drawpic in the above example
with a variable like plot so that you can first run the
command with "vid" to plot on the screen and then run
it on the plotter with "drawpic". Vid and drawpic are
designed to use the same switch arguments, to make this
possible. You can set numeric variables with the "@"
command (see the csh manual). You set string (char)
variables in the csh language with the "set" command:
set plot = "abc"
$plot ab*.p use "$" to invoke variable
labels < labelfile | $plot -x 6000
You can set a variable from the command line which
invokes the command using the standard csh notation:
set plot = $argv[1]
$plot ab*.p var is first arg after command
labels < labelfile | $plot -x 6000
Then run the command with different values for the
variable:
president vid
president drawpic
There are numerous possibilities for this type of
command-making. The csh has many of the control
statements which exist in the "C" language, including
the "for" and "if" statements. Use your imagination,
and read the "csh" manual.
fstor
"fstor" allows you to store data files into
compressed form and retrieve them from compressed form
into data files, optionally using the filter to select
which data to copy. You can compress files to make
them fit on a floppy disk by using the "store" command.
You can get them back into the original data file with
the "retrieve" command. You can also copy files with
the filter. Normally, you use fstor for making backup
copies of your data files. You can also break a large
file into smaller files using fstor to copy only
selected ranges of sections.
c copy file using filter
f change filter (see section 4: montage manual)
h help table
l change section length (see section 4: montage manual)
n renumber sections in file; useful after merging files
r retrieve file from storage using filter
s store file in compressed form using filter
v verify file (take out garbage, make all trace
links clockwise, fix section numbers)
z change from format (old UNIX system) to
current .dat file format
X exit from program
The "fstor" filter command uses the same filter as
described in the montage manual (section 5 of this
manual). However, a special feature of the fstor
filter table is that the filter continues from one
filter spec to the next as long as the next filter spec
has been defined. A link will be selected if it fits
any of the filter specs on different lines. This gives
you more space to define filters.
-C copy from stdin to stdout
-D reverse copy from stdin to stdout
-N renumber from stdin to stdout
-R retrieve from storage from stdin to stdout
-S store from stdin to stdout
-a num calib for "above", "below" in filter (um per cm)
-b use following number as start section
-q use following number as stop section
-l num change section length to num
-c copy from immediately following filename to next
-d reverse copy file from following filename to next
-n renumber from immediately following filename to next
-r retrieve from immediately following filename to next
-s store from immediately following filename to next
-t num section thickness in um for "above","below" in filter
-v verify from immediately following filename to next
Examples:
fstor -l 512 -r file1.sto file1.dat Retrieve a data file
fstor -s file2.dat file2.sto make a .sto file
fstor -b 10 -q 120 -R
For archival storage, you may want to further compress your
files using the gzip(1) and gunzip(1) commands supplied with
Linux. These commands use a data-compression technique
which makes use of the fact that some 8-bit bytes are more
common in a file than others. This works well for text files and
some binary data files (".dat" or ".sto" files) because they don't
contain an equal distribution of all bit patterns.
gzip alpha.dat gzip is Linux's compression prog.
gunzip alpha.dat.gz
glink
Glink prints out links in a data file. It can display the
number and type of links and the number of points, or it can
print the area, grain density and perimeter of links. You can
select which links to display using the filter. See next page for
more "glink" examples.
a find area, perim (print section totals and grand total)
c change Calibration (microns per centimeter)
d display links (print section totals of number
of links and points, and grand total)
f change Filter (see section 4: montage manual)
l change section length (see section 5: montage manual)
s section thickness (microns)
t display indiv trace and areas and perims when
used with "a" mode above
q exit program
The Linux version of glink can be run from the standard
input to the standard output with the use of the following
switches (see the Section 3 for a description of command line
switches):
-A area and perimeter
-D display number and type of links
-F flag links only
-Z display all link fields (for debugging)
-a area of following filename, output to following filename
-d number and type of links from following filename
-b use following number as start section
-c num calib for "above","below" in filter
-f make ".g" files from data files
-g read flag defs from "flag.def"
-q use following number as stop section
-s section thickness (microns)
-t display indiv trace areas and perims with totals
For example:
glink -D file.dat
This command causes glink to display the number of
links in "file.dat" on the screen. If you want to put
the output into a file, you could use:
glink -D file.dat >file.g
You can run glink on several data files at once,
using the "-f" command-line switch. For instance:
glink -f -A file1.dat file2.dat file3.sto
This analyzes the data files for area and perimeter
and makes "file1.g", "file2.g", "file3.g" from the data files.
Using glink intelligently
Glink analyzes your data and prints large reports.
However glink's reports may not be formatted exactly as
you would like them. UNIX makes it easy to get the
report you want by filtering (selectively printing) and
sorting, using standard tools. You can filter and sort
the output from Glink with grep(1) and sort(1) to
organize your data for printouts. For more powerful
list processing you can use awk(1) to reformat, move
columns around, and make totals of columns. See the
Linux User's Guide for more on awk(1).
glink -F file.dat | grep amacrine | sort +3 >file.srt
to get a total of all "amacrine" flags in a data file,
sorted by their flag numbers (column 3 of glink output).
glink -t -A -b 4 -q 9 datafile | grep ' a ' | column 3 | var
gives the standard deviation of all trace links on
sections 4 through 9 of "datafile". The "grep ' a '"
filters out only the individual trace areas printed
by the glink "-t" switch. You could make it easier to
use this sequence of commands by inventing your own
command called gvar:
glink -t -A -b $1 -q $2 $3 | grep ' a ' | column 3 | var
Then you could invent another command to
automatically graph this data in a histogram, which you
could name histo:
gvar $1 $1 $2 | bins -w 20 | graph -M 40 | drawpic
This command "histo" allows you to gather data from any selected set
of sections, make a histogram
with "bins" (see below), and plot the data using
"graph" (see below) and "drawpic".
awk "{print \$$1}" $2
Everything inside the "{ }" brackets is the awk
command. The \$$1 passes the column number to awk from
the shell command, in this case "column". The $2 means
pass the second argument from column to awk as a file
name. This means you can use the column command on a
file name without a pipe to its standard input:
column 4 file5.g
To find the approximate radius of traced polygons,
you might use the formula:
radius = (perim / (2*pi) + sqrt( area / pi)) / 2
It's easy to do this kind of processing with the
following commands. First make the glink file which
contains the areas and perims of individual polygons.
glink -t -A -b $1 -q $2 $3 > $3.g
Next process the separate "a" and "p" lines together
and compute the formula:
awk ' $1 == "p" { printf ("%g ", $3) }
$1 == "a" { printf ("%g\n",$3) }' |\
awk ' { print ($1/(2*3.1416) + sqrt($2/3.1416)) / 2; }
You could then run the commands:
garea 1 2 file.sto
grad < file.sto.g
and you get a list of radii of individual traces.
hide
The hide program erases lines in a three-dimensional
drawing which should not be seen because they're
hidden. You can pipe the picture data from the picture
program through one of the hide programs. There are
three hide programs, called "hide9", "hide10", and
"hide11". They are exactly the same except that the
resolution of the picture is different. "hide9" gives
a resolution of 512 x 512; "hide10" gives 1024 x 1024,
and "hide11" gives 2048 x 2048. "hide9" runs 16 times
faster than "hide11", and "hide10" runs four times
faster. Use "hide9" for rough copies and the video
screen, and use "hide10" for testing pens on the
plotter. Use "hide11" for final illustrations only
because it runs much slower.
-i run hide in non-interruptable mode
-f make all input files into corresponding
".h" output files
-h make picture hidden even when hide not set
-j make picture non-hidden even when hide set
For instance, to make a picture on the video
screen with hidden line removal, enter "mpict | hide9 -i | vid -i".
This is the same as the command "picthid9".
makehid11 *.cor makes ".h" files from ".cor" files
You can use the "-f" option in the mpict and hide
programs to automatically create files for you. Mpict
makes ".m" files and hide makes ".h" files. This is
especially helpful when you are making composite
illustrations out of picture files you have already
made.
mpict -f -s *.cor makes ".m" files from ".cor"
hide11 -f *.m makes ".h" files from ".m" files
hpflt and hplot, ibmflt and iplot
You use "hpflt" (or "ibmflt") to convert the picture
data coming from mpict or hide into plotting data
suitable for the HP 7221A (or IBM color) plotter.
"hplot" ("iplot") does the actual data transmission to
the plotter. Switches for hpflt (ibmflt) are:
-c sort output by pen color (waits until end to draw)
-i non-interrupt mode
-m Use following number as mag, default 1.0
-p Use following number as plotter pen number.
This overrides any pens defined in the picture file.
-r Rotate picture sideways 90o
-s Use following number as speed for plotter,
up to 30. Default is 4 cm/sec.
-x Use following number as x offset (default 7500)
This is the center of the picture, calibrated in
thousandths of an inch. One cm = 400 units.
-y Use following number as y offset (default 5000)
Calibrated as "-x" above.
-w Wait after using each pen, to allow paper to be changed
-z Save individual pen files after exit; use with "-c" above
To use the plotter, first read "running the plotter"
below. Pipe the your picture data into "hpflt"
("ibmflt"), and then into "hplot" ("iplot"). The
"drawpic" command combines these two into one command
that is easier to use. For instance, to make a picture
defined by the corfile "cell.cor" you could type:
mpict cell.cor | hide10 | hpflt | hplot
or mpict cell.cor | hide10 | drawpic
When you run the plotting programs this way, you may
find that they run too slow, causing the plotter pen to
leak on the paper. You can save the results of the
hidden line routine in a temporary file by typing:
mpict -s cell.cor | hide10 > cell.h
or makehid10 cell.cor
then later: drawpic cell.h
This will draw the picture faster, because the slow
hide10 program does not run when the picture is being
plotted. Use the makehid or dopic commands described
in section 5 to create plot files (".m",".p", or ".h").
drawpic -w -p 2 -m 1.5 -x 5600 -y 4600 file.plt
The drawpic ("hpflt -c" switch) command sorts
all the pen draw commands according to the color of the
current pen used. This is a more efficient use of
plotter time, because each pen is only used once. This
makes the plotting process go faster, although the
plotting is delayed by up to a minute because of the
need to sort all the plotter commands.
vid
You use "vid" to display graphics data that
comes from "nc" or "plotmod".
-a make "postscript" file on stdout: "vid -a > file"
-c make color "postscript" file on stdout: "vid -c > file"
-l make "postscript" raster file on stdout.
-e use Enhanced Graphics Adapter
-h use monochrome Hercules board
-t use Tektronix 4014 type display terminal
-X use X-windows for graphics display
-d name define name of X-windows screen to display on
-k invert screen (upside down)
-m n use "n" as mag, default 1.0
-p n use "n" as color (16 colors)
-r rotate picture sideways 90 deg
-w n use "n" as size of X-window.
-x n use "n" as x offset (default 8192)
This defines center of picture.
-y n use "n" as y offset (default 8192)
This defines center of picture.
-v don't erase screen when first starting video graphics mode.
Example: nc -t file1 | vid (="neurc file1")
nc -t file2 | vid -v (don't erase screen)
Vid normally erases the screen when you first run
it, but you can tell it not to with the "-v" switch
listed above. Vid normally doesn't erase its picture
when it is finished displaying. To get back to text
mode you use the "t" (or "textmod") command. This
doesn't erase the graphics screen, so you can run vid
several times with as many text commands in between as
you want. For instance:
vid file1 (make first picture on screen)
t
ls -l
cd otherdir
vid -v file2 (superimpose 2nd picture on first)
textmod
This command changes the video screen back to text mode.
Command line switches are:
-e EGA driver.
-h Hercules driver.
-v Change from text mode back to video
(restore a previous picture)
"textmod" is normally run (aliased) to run as the command "t".
posit
Posit allows you to set the position of subpictures
in an illustration consisting of several picture files.
Posit has the same command switches as "vid" and
"hpflt", but it doesn't display the files; it merely
puts them on the standard output or into output files
of extension ".p".
-i non-interrupt mode
-f make ".p" output files from input
-m Use following number as mag, default 1.0
-p Use following number as plotter pen number.
This overrides any pens defined in the picture file.
-x Use following number as x offset (default 5000)
This is the center of the picture, calibrated in
thousandths of an inch. One cm = 400 units
-y Use following number as y offset (default 5000)
Calibrated as "-x" above.
Example 1:
posit -f -x 1000 -y 7000 file1.h -x 4000 y -6000 file2.h
This creates file1.p and file2.p with (x,y) offsets
from existing ".h" files which had already been hidden.
Example 2:
posit -f -x 100 -y 250 file1.m -x 150 -y 200 file2.m
hide11 -f -h file1.p file2.p
This creates file1.h and file2.h with (x,y) offsets
from corresponding ".m" (mpict) files and then hides
the second picture behind the first using the "-h"
option for hide on the ".p" output files. Pen colors
are preserved.
Batch proccessing using mpict, hide, hpflt, posit, fstor, glink
These programs may all be run with their standard
inputs redirected to files. You can also run them like
"hpflt file" without the "<" symbol for the standard
input redirection. Multiple input files are also
allowed on the command line, as in "hpflt file1 file2".
This allows batch processing of your files into one
output file. Mpict and hide can be run with the "-f"
switch to automatically create output files
corresponding to input files with the ".m" and ".h"
extensions added onto the input file names.
graph
Graph is described in the Ampex Plotting Package
Manual. It is similar to the standard "graph" command
that comes with most UNIX systems. It takes pairs of
numbers separated by spaces from the standard input as
the X and Y values of a graph. Successive points are
connected by straight lines. You can display the graph
by piping to either "vid" for the video screen or
"hpflt" for the plotter. The maximum and minimum
dimensions for the graph axes are normally determined
automatically from the data on the input stream. There
are many useful switch options for this program,
described in the manual. Graph switch options:
-c char char is point label
-C char char is point label; no connecting lines
-f filename "filename" is a file containing a list
of points; filename "-" means standard input;
maximum of 8 filenames allowed.
-g num num is grid style; 0-> solid grid; 1-> dotted grid;
2-> no grid but solid maxima; 3-> no grid(default)
-l "label" label for x axis
-L "label" label for y axis
-m val min for y axis
-M val max for y axis
-p num num is pen/dash style when doing multiple graphs
with the -f switch:
0-> dashes only (default);
1-> pen changes and dashes;
2-> pen changes only
-t num num is the tic style of x-axis:
0 -> many tics, few numbers (default);
1 -> few tics, few numbers;
2 -> many tics, many numbers;
3 -> few tics, many numbers
-T num num is the tic style of y-axis:
0 -> many tics, few numbers (default);
1 -> few tics, few numbers;
2 -> many tics, many numbers;
3 -> few tics, many numbers;
-o make x axis logarighmic (bug in axis labeling)
-O make y axis logarighmic (bug in axis labeling)
-v num point label char size, 1=small, 7=large;
-w num x axis char size for label, 1=small, 7=large;
-W num y axis char size for label, 1=small, 7=large;
You can run graph interactively by typing "graph | vid"
and then entering a set of points, one x,y point pair
per line (x and y separated by spaces not commas), and
a CTRL-D to stop entering data and display the graph.
You can also make a text file with an editor and run
"graph < file | vid" which causes graph to get its
input from the file instead of the keyboard.
using graph intelligently
If you want to draw several (up to 8) lines on a
graph, you can use the "-f" switch to include several
files as input data. Put a "-f" before each file like
this:
graph -f file1 -f file2 -f file3
and the first one will be a solid line, the second
will be a dotted line, and the third will be a dashed
line. If you want colors, use the "-p" switch.
For instance:
0 0 extends left side to 0
data points
10 0 extends right side to 10
You can use the "grp" comand to run graph
automatically on several file names:
grp file1 file2 file3 | vid
"grp" is a C-shell command file which contains
something like:
#
set pen = 1
#set axis =
set axis = "-T 3 -t 0"
set min =
#set min = "-m -.1"
set max =
#set max = "-M 1.2"
if ($#argv == 1) then
graph -p $pen $axis $min $max -f $1
else if ($#argv == 2) then
graph -p $pen $axis $min $max -f $1 -f $2
( and so on up to 8: "-f 1 ... -f $8" )
endif
bins
Bins generates a histogram from a sequence of
numbers at the standard input. The histogram is output
as a sequence of X,Y number pairs, suitable for input
to "graph" above.
Bins switch options:
-h make two points per bin for histogram graph
-n cause bins to be not centered on binwidths
-o num num = offset value for array
-w num num = bin width
The switch option "-w" uses the following number in
the command line as the bin width. For example, given
a file of numbers "sample" you could type:
bins -w 5 -h < sample | graph | vid
to see the histogram of "sample" displayed on the
screen, with a bin width of 5.
spline
Spline is a nice addition to the graph command. It
takes a sequence of X,Y number pairs and generates a
smooth curve from them, suitable for input to graph.
For example, you could type:
spline < list | graph | vid
to see "list" displayed as a smooth curve instead of with
straight lines.
var
Var takes a sequence of numbers, one num