AIPS NRAO AIPS HELP file for LGEOM in 31DEC18



As of Wed Jan 17 16:48:46 2018


LGEOM: Task to rotate, stretch, and shift an N-dim image

INPUTS

INNAME                             Input image (name)
INCLASS                                        (class)
INSEQ           0.0      9999.0                (seq. #)
INDISK          0.0         9.0                (disk unit #)
OUTNAME                            Output image (name)
OUTCLASS                                       (class)
OUTSEQ         -1.0      9999.0                (seq #)
OUTDISK         0.0         9.0                (disk unit #)
BLC             0.0      4096.0    Bottom left corner of image
                                     0=>entire image
TRC             0.0      4096.0    Top right corner of image
                                     0=>entire image
IMSIZE          0.0      2048.0    Output image size in pixels
APARM                              (1)=del-x (pix),(2)=del-y,
                                   (3)=rotate(deg),(4)=scale,
                                   (5)=diff.scale, (6)=terp.ord,
                                   (7)=invert.flg, (8)=axes.flg,
                                   (9)=zero.flag

HELP SECTION

LGEOM
Type: Task
Use:  LGEOM will compute a linear geometric transformation (translate,
      scale, & rotate) of an input image using Everett interpolation
      (bilinear, bicubic, or biquintic).  LGEOM uses the 'scrolling
      buffer' concept of how to do geometric transformations and now
      sizes that buffer via dynamic memory.  LGEOM uses Everett
      interpolation which cannot handle blanked pixels or pixels off
      the edge.  As a consequence, even with the dynamic memory, the
      fraction of blanked pixels will grow in the output.
   =====================================================================
      We recommend use of OGEOM instead of LGEOM.  LGEOM propogates
      blanks and edges onto good areas by the width of the
      interpolation function, while OGEOM can even fill in small
      blanked regions and extrapolate a little.
   =====================================================================
Adverbs:
  INNAME.......Input map name.            Standard defaults.
  INCLASS......Input map class.           Standard defaults.
  INSEQ........First input map seq no.    0 => highest.
  INDISK.......Input map disk:            0 = any.
  OUTNAME......Output map name.           Standard defaults.
  OUTCLASS.....Output map class.          Standard defaults.
  OUTSEQ.......Output map seq no.       0 => highest unique.
  OUTDISK......Output map disk.      0 => highest with room.
  BLC..........The bottom left-hand pixel of the input image
               which becomes the bottom left corner of the
               input subimage.  The value (0,0) means (1,1).
  TRC..........The top right-hand pixel of the input image
               which becomes the top right corner of the
               subimage.  The value (0,0) means take the top
               right hand corner of the image.
  IMSIZE.......Output image size in pixels [1=columns, 2=rows]
               Default is input subimage size. Except for this
               default the output size is independent of both
               the input size and the commanded scale factor.
  APARM........Transformation parameters:
               1 & 2 = shift of image, expressed in pixels, for x & y.
                  Positive moves objects to right and up relative to
                  reference mark as they map from input image to
                  output image.
                  ** The shift applies to the scaled image; ie. if you
                  ** ask for a 4 pixel shift, they will be 4 pixels in
                  ** the output map.
               3 = rotation in degrees (positive moves objects
                  counterclockwise relative to reference mark as they
                  map from input image to output image).
               4 = scale factor (greater than one moves objects
                  outward from reference mark as they map from input
                  to output).
                  ** The scale factor is applied first. The map is
                  ** expanded about the map center (N/2+1, N/2+1).
               5 = 'differential scale'; this is an extra scale factor
                  applied to the y-axis AFTER the main transformation
                  has been done. This is useful to make spiral
                  galaxies appear face-on. Also, if it is negated the
                  result is a mirror-reflection in the y-axis.
               6 = Order of Everett interpolation formula [range 1-7:
                   1=bilinear, 3=bicubic, 5=biquintic, 7=biseptic]
                   0 => 3.
                   Higher orders will produce more accurate
                   interpolations although oddities may appear when
                   the output cell size is significantly smaller than
                   the input cell size.  See extensive discussion in
                   EXPLAIN file.
               7 = inversion flag. Causes the inverse of the specified
                  transformation to be performed.  Useful to undo
                  previous operation.
               8 = axes-only flag. Legal only if APARM(3)=0.0,
                  APARM(4)=1.0, and APARM(5)=1.0 (i.e., pure shift).
                  Transformation is applied but header axis
                  descriptions are not changed. Useful to align two or
                  more maps which have been created by a
                  Self-Calibration.
               9 = zero-flag. If > 0.0, then zeroes are used wherever
                  blanks would normally be created in the output
                  image.

EXPLAIN SECTION

Explanation of various details of LGEOM
(DCW, 11 October 1984)

On the Interpretation of the "Shift Factors":

First we need to describe how LGEOM maps the input image onto
the output with the shifts set to zero. LGEOM defines the
transformation so that the center of the input window maps onto
the center of the output image. The input center is computed as
(0.5*(BLC(1)+TRC(1)),0.5*(BLC(2)+TRC(2)). The output center is
considered to be (0.5*(1+IMSIZE(1)),0.5*(1+IMSIZE(2)). Please
note that if IMSIZE is given as (0,0) it defaults to
((TRC(1)-BLC(1)+1),(TRC(2)-BLC(2)+1)). These computations are
done in floating point in units of pixels. So, for example, if
we have 1) input image 800-square, 2) BLC and TRC both zeroes,
3) IMSIZE set to 1000-square, 4) the shifts and rotate all
zero, and 5) the scale set to unity, then the pixel coordinate
(400.5,400.5) in the input will map to (500.5,500.5) in the
output. It follows that pixel (400,400) will map to (500,500),
and there will be a blank or zero border area in the outer part
of the output image. But if the scale is set to 2 only the
inner 500-square region of the input will appear in the output
(see the discussion in the next section) and pixel (400,400)
will actually be at (499.5,499.5) in the output (because
500.5+2.0*(400.0-400.5) is 499.5).

Now we can discuss the effect of the shift factors. In the
example of the previous paragraph (400.5,400.5) mapped to
(500.5,500.5) in the output image with shifts set to zero. In
fact, the shifts are added to the output center position. So if
we have shifts APARM(1) and APARM(2) equal to (0.15,-1.2), then
(400.5,400.5) in the input will map to (500.65,499.3) in the
output. Scale and rotate occur relative to this "reference
mark" in the output image as implied by the formula shown at
the end of the previous paragraph.


More about the concept of the "Reference Mark":

In the previous section we explained that the image value at
the center of the input window maps to the center of the output
window plus the offsets. This point in the image we call the
reference mark. Scale and rotation occur about it. The terms
"to the right relative to the reference mark",
"counterclockwise relative...", and "outward from reference
mark", all refer to the appearance of the image on a standard
AIPS television display in which location (1,1) of the display
is in the lower left corner.


On the Relation of Input Image Size to Output Image Size:

The adverb IMSIZE specifies the dimensions of the output image.
If it is set to zero then the default applies and the output
image is the same size as the input. But if it is nonzero it
means EXACTLY what it says: the output will have dimensions
specified by IMSIZE regardless of what the dimensions of the
input image or the geometric transformation parameters happen
to be. Suppose the input image is 800-square and BLC and TRC
are zero (i.e., all of the image). If IMSIZE is 100-square then
the output is 100-square. This is true no matter what the scale
factor APARM(4) happens to be. So, if APARM(4)=2 the output
will be a 100-square blown-up image of a 50-square region from
somewhere (controlled by APARM(1) and APARM(2)) in the input
image. If APARM(4)=0.5 the output (100-square) will be a
decimated image of a 200-square region in the input. On the
other hand, if IMSIZE is bigger than the input, say
1000-square, the result is that the input maps to the output
controlled by the APARMs and regions which are outside the
input image will be blank in the output. E.g., rotate the
800-square by 10 degrees into a 1000-square output or blow it
up with scale factor of 2 into a 1600-square output. Note that
the portion of the input which is used is delimited by BLC and
TRC completely independently of IMSIZE and the APARMs (see the
discussion of the shift factors above).


LGEOM and N-dimensional Cubes:

LGEOM does geometric transformations on the first two axes of
the input image (i.e., on two dimensional images, simple
matricies). If the input image has dimensionality greater than
two, LGEOM will perform its operations on the successive planes
of the "cube" one by one, as selected by BLC and TRC. For
example, if the input is a cube of 32 channel maps which are
512-square (512x512x32), and BLC and TRC are zeroes, then the
whole cube will be transformed by doing the geometric operation
32 times: once for each separate 512-square plane. A subset of
the planes can be processed by setting BLC(3) and TRC(3)
appropriately. If the cube were transposed to, for example,
32x512x512, then LGEOM would operate on 512 planes which are
32x512. This would be a rotation of inhomogenous coordinates
(such as velocity and RA), a poorly defined operation, but
LGEOM will cheerfully perform it anyway. A rotation about more
than one axis could be performed by the sequence of tasks
LGEOM, TRANS, and LGEOM, possibly followed by another TRANS to
bring the desired axes back to the front of the cube. The
resulting cube would have rotation angles specified for more
than one axis. NOTE: rotation is really only defined well for
angular axis combinations like RA and Dec. AIPS generally
expects to find only ONE rotation angle in a header, and to
find that rotation angle attached to the "Dec-like" axis. The
moral is: if you want cursor settings and contour map axis
labels to come out right  in AIPS, it will probably be best to
stick to fairly sensible things like rotating spiral galaxies
so that their major axes are parallel with the first axis of
the cube. Transposing the resulting velocity cube and rotating
the major-axis/velocity plane so that the gradient of velocity
along the major axis is mostly cancelled will be computed by
LGEOM, but AIPS will probably be totally confused by the
presence of TWO rotation angles in the header.


A Discussion of Blanking in LGEOM:

Output pixels are computed as a weighted sum of the input
pixels in the neighborhood of the computed location in the
input (the interpolation weights depend on the fraction of the
pixel spacing). If one of the input pixel values in the sum is
blanked, i.e., indefinite in value, then the whole sum, i.e.
the output pixel, is blanked. If APARM(9) is true, then instead
of blank a zero is delivered as the output pixel value. As a
result, if an isolated pixel in the input is blank it will
produce blanks (or zeroes) in a region in the output image the
same size as the interpolating kernel (4x4 pixels for bicubic,
8x8 for biseptic). This is not nice, but all suggested cures
considered so far have other difficulties.

There is a special case implemented for the edges of the input
image. Here LGEOM "reflects" the pixels near the boundary out
into the terra incognita and uses them for interpolation. This
means that pixel 1 is copied into the pixel 0 position, pixel 2
is copied into pixel -1, etc. The effect of this algorithm,
implemented on all four edges, is that first derivatives of the
interpolant are zero at all boundaries. NOTE: "Boundary" in
this case also means the window defined by BLC and TRC.

If the output image is larger than the transformation of the
input window then the extra area will be blanked (or zeroed).


Regarding the Everett Interpolation Formula:

This program computes where in the input image each output
pixel appears. This location is generally at some arbitrary
fractional pixel position in x and y, surrounded by four input
pixels. The program then interpolates in the pixel values
surrounding the position. For APARM(6)=1  it uses linear
interpolation, first in in x (twice) and then in y. This is
called "bilinear" interpolation, and is the default choice.

If APARM(6)=3 two pixels on each side in x and y are used,
sixteen pixels total. A cubic polynomial is fitted through the
four pixels in each of the four rows in x, and evaluated at the
computed x-position. Then a cubic is put through those four
values (in y) and evaluated. This is "bicubic" interpolation.
For APARM(6)=5 we use a 6x6 array, 36 pixels total; this is
"biquintic" interpolation. For APARM(6)=7, we have 8x8, 64 pixels,
"biseptic" interpolation.


Regarding the Numerical Accuracy of Interpolation:

The accuracy of interpolation increases with the order of the
polynomial, but of course so does the cost of computation. As
the polynomial order increases the interpolating function
approaches ever more closely to the sinc function, the perfect
bandlimited interpolator, as a limit. Bicubic is good enough
for many ordinary purposes. Biquintic will probably be good
enough even for high dynamic range data like optical CCD
imagery and self-calibrated VLA maps. The point is, if we want
very accurate results we want the "noise" of interpolation
errors to be less than the observational noise in the data at
all spatial frequencies of interest.

The interpolation is done by computing a set of interpolating
weights which are a function of the fractional pixel position
where the answer is desired. The answer is then computed by
multiplying the weights by the data. This is a convolution. It
follows that an interpolator of a given order has a
corresponding transfer function. I.e., in the terminology of
aperture synthesis, it acts somewhat like a peculiar, probably
"bumpy" taper function in the u-v plane. This function is
always going to be less than unity in the neighborhood of the
Nyquist frequency of the map. The size of this "neighborhood"
where the transfer function is significantly different from
unity is smaller for higher order polynomials. It follows that
maps which are well sampled, say three or four pixels per beam,
are easier to interpolate accurately.


How to Evaluate the Numerical Errors of Interpolation:

DCW is not aware of any proper quantitative treatment of the
interpolation accuracy issues anywhere in the literature of
image processing. This situation is not as bad as it seems
because for critical work there are two simple tests which can
be used to estimate the interpolation error:

Test1: compute a small change, reverse it, then difference input
and output. E.g., rotate the input image by 1 degree, then
rotate the output image back by 1 degree. Use COMB to subtract
the second output from the input. The difference is all
interpolation noise. If that noise level (due to TWO
interpolations) is small enough to suit you then you know that
the noise of the first answer, the rotated image, is even lower
(only one interpolation). Actually, this test is excessively
conservative because the transfer function of interpolation is
SQUARED by the double calculation (NOTE: any multiple
application of interpolation to data will square, cube, etc.,
the transfer function of data. Mostly one loses high spatial
frequencies in the data, but errors creep into the lower
spatial frequencies, too.)

Test2: compute a small change with one order of interpolation,
compute again with increased order, then difference the two
results. E.g., rotate the input image by 1 degree using
APARM(6)=3 (bicubic), then perform the operation again with
APARM(6)=5 (biquintic). Use COMB to subtract the the first
answer from the second. The difference is an estimate of the
error of bicubic interpolation for your image. An even more
accurate estimate of the error would be obtained by using
APARM(6)=7 (biseptic) for the second computation. Although this
test does not inspire the degree of conviction which Test1 can
by reproducing the input image, it more than makes up for this
by giving an estimate of the interpolation error of a SINGLE
operation.

NOTE: in performing tests such as are suggested above it will
make sense to use BLC and TRC to select a small region of the
input image (say, 100-square) which contains interesting
structure whose details need to be preserved. This will save
time and make it reasonable to perform both Test1 and Test2,
and to use biseptic interpolation for Test2. For example, one
could perform Test1 using biseptic interpolation in order to be
convinced that it's results are accurate. Then perform Test2
for bicubic and/or biquintic and compare them to the biseptic
computation.


Regarding Timing:

In a trial on a completely unloaded 4Mb VAX780, LGEOM needed
3.38 minutes real time to rotate a 512-square integer image by
43 degrees using bilinear interpolation, producing a 750-square
integer output image.

Another trial computed a 500-square image scaled up by 1.5 and
rotated by -65 degrees out of the middle of an 816-by-800 input
image using biquintic interpolation (APARM(6)=5). The trial ran
in a moderately loaded VAX which had 3.75 MB at the time. The
peak virtual space used by LGEOM was about 8000 pages (4 MB),
and the peak working set was 1024 pages (0.5 MB), which are the
values to be expected for this problem. The typical page fault
rate was 5-20 per second depending on the fraction of the CPU
which LGEOM was receiving. Total CPU time was about 10.5
minutes and real time was about 33 minutes.


Relation to other Tasks:

LGEOM is a upgraded version of the old program GEOM, which
remains in 15OCT84 release purely for compatibility reasons.

Program PGEOM is a clone of LGEOM and uses its technology to
produce a "rho-theta" transformation of an image, i.e., a
transformation from rectangular to polar geometry. This is a
useful tool for analyzing or filtering images of circularly
symmetric objects. see HELP PGEOM.


Comments on the use of Virtual Memory in LGEOM:

LGEOM is notable in the AIPS project as being the first program
developed in Charlottesville and officially sanctioned which
makes explicit use of virtual memory. It was released for
15JAN84 after an extensive review and performance trials which
demonstrated that it is unlikely to cause "thrashing" in NRAO's
VAXes. So far the Charlottesville programmers have received no
reports of such trouble with LGEOM. Probably this is because,
in practice, LGEOM really uses virtual memory only for worst
case problems (for small images or small rotation angles LGEOM
utilizes ONLY the amount of space which it really needs).

The operation of virtual memory is complicated. The following
discussion gives DCW's theory of its operation under VMS on
VAXes (behavior of other operating systems and CPUs is likely
to differ in various ways): LGEOM has a working array
dimensioned as R4(700000). This is 2.8 megabytes. VMS will
create a scratch file of about this size to hold an image of
the job. The space is divided into "pages" (512 bytes in VMS).
If there is not enough PHYSICAL memory to hold the array and
the rest of the program and data, pieces of it (i.e., pages)
will be in the scratch file. As the DO-loops of LGEOM cycle
over the array VMS may be obliged to swap some portions between
memory and disk. If this page cycling and the resulting disk
I/O traffic occur repetitively and excessively we say that the
job (and the VAX) are "thrashing", a very unpleasant state of
affairs which tends to drag down the whole system.

At any one moment LGEOM is accessing some trajectory in the
matrix. It can be shown that in the worst cases LGEOM needs a
physical memory of about NROWS pages. For an 800-square image
this will be about 800 pages, or 800*512 bytes (410 KB). With
various overheads we can say that LGEOM will need to have about
0.5 megabyte of physical memory to run properly. Obviously not
all VAXes will be able to give LGEOM this much memory at all
times, and so we should not be surprised if LGEOM displays some
thrashing behavior in some environments at some times. In
practice VMS often has some extra memory and pages which are to
be swapped to disk in fact stay in memory somewhere (not in
LGEOM's space) and the actual flush to disk is delayed. If
LGEOM asks for the page to come back VMS just fiddles with the
page tables and doesn't have to wait for the disk to come
around. But this page table fiddling does cost some CPU time.
The availability of this extra memory will depend on loading
and on the total physical memory of a particular VAX.  If the
pages are actually flushed to disk, CPU times for LGEOM will be
about the same but the wall-clock times can change
dramatically!  The fact that execution timing for LGEOM may
vary from site to site and from day to day is a major criticism
of the virtual memory technique.

Of all computing problems known to DCW, LGEOM and its clones
(e.g., PGEOM) are the ones for which the case for virtual
memory is strongest, because virtual memory vastly simplifies
the logic of the implementation. The position taken by DCW on
this situation is: virtual memory in LGEOM is a temporary
expedient which allows us to have a working program while
putting off having to design a software emulation of the effect
of virtual memory in the program. Ultimately we will be obliged
to do the design job because not all computers will have the
appropriate virtual memory facilities (and sufficient PHYSICAL
memory), and because we want LGEOM and friends to be portable
to all machines that the rest of AIPS can run on.

AIPS