Re: [R] Surprise when mapping matrix to image
Hello, I wonder if image(t(x)[ncol(x):1, ]) can do the job correct! perhaps this does the job better: image(t(x)[,nrow(x):1]) Björn From: Prof Brian Ripley ripley_at_stats.ox.ac.uk Date: Fri 27 Aug 2004 - 06:43:50 EST On Thu, 26 Aug 2004, Glynn, Earl wrote: Start with: x - c(1:7,1) dim(x) - c(2,4) x [,1] [,2] [,3] [,4] [1,] 1 3 5 7 [2,] 2 4 6 1 2 Rows of 4 Columns. Upper-left and lower-right elements of the matrix are the same. All to this point makes good sense. It's pure convention: see below. image(x) However, this image shows 2 columns of 4 rows. The lower-left and upper-right elements are the same. This does not make sense to me. Did I miss some simple parameter to fix all of this naturally? Why would the numeric matrix of x and the image of x have such a different geometry? Did you try reading the help for image? You don't seem to understand it if you actually did. It seems you are looking for image(t(x)[ncol(x):1, ]) Easy! Mathematical conventions are just that, conventions. They differ by field of mathematics. Don't ask us why matrix rows are numbered down but graphs are numbered up the y axis, nor why x comes before y but row before column. But the matrix layout has always seemed illogical to me. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Jetzt Handykosten senken mit klarmobil - 15 Ct./Min.! Hier klicken www.klarmobil.de/index.html?pid=73025 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Surprise when mapping matrix to image
Richard A. O'Keefe [EMAIL PROTECTED] writes: How about this addition to the documentation? The x axis corresponds to the rows of the matrix (first on the left to last on the right). The y axis corresponds to the columns of the matrix (first at the bottom to last at the top). Once you know what image() is _intended_ to do with a matrix, you can figure out the transposing and reversing you need for any other view. It's knowing you need to that's the problem. Good idea, but perhaps not phrased sharply enough to catch the user's eye. How about something like this: Notice that image() interprets a matrix as a table of f(x_i, y_j), so the x axis corresponds to row number and the y axis to column number (bottom to top). and then use Brian's one-liner in the examples section? -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Surprise when mapping matrix to image
Peter Dalgaard wrote: Richard A. O'Keefe [EMAIL PROTECTED] writes: [snip] Good idea, but perhaps not phrased sharply enough to catch the user's eye. How about something like this: Notice that image() interprets a matrix as a table of f(x_i, y_j), so the x axis corresponds to row number and the y axis to column number (bottom to top). and then use Brian's one-liner in the examples section? Though I think the added text is a good idea, the addition of the example is probably 102.58 times more useful than any text that could be inserted. The examples in help files are probably the main reason that people think of R having better documentation than other programs. Like Unix man pages, for example, which would be wonderful if only they had examples so that you could figure out what the sentences mean when you understand every word. Patrick Burns Burns Statistics [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Surprise when mapping matrix to image
Patrick Burns [EMAIL PROTECTED] writes: Peter Dalgaard wrote: Richard A. O'Keefe [EMAIL PROTECTED] writes: [snip] Good idea, but perhaps not phrased sharply enough to catch the user's eye. How about something like this: Notice that image() interprets a matrix as a table of f(x_i, y_j), so the x axis corresponds to row number and the y axis to column number (bottom to top). and then use Brian's one-liner in the examples section? Though I think the added text is a good idea, the addition of the example is probably 102.58 times more useful than any text that could be inserted. The examples in help files are probably the main reason that people think of R having better documentation than other programs. Like Unix man pages, for example, which would be wonderful if only they had examples so that you could figure out what the sentences mean when you understand every word. There are limits, I think. If you put too many variations into the example section, it tends to become a grey blob of code. Anyways, I'm going to add both. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Surprise when mapping matrix to image
Quoting Glynn, Earl [EMAIL PROTECTED]: Prof Ripley: Thank you for your prompt reply. It's pure convention: see below. Did you try reading the help for image? You don't seem to understand it if you actually did. It seems you are looking for image(t(x)[ncol(x):1, ]) I think you guys are too close to R to understand how hard it is to use sometimes. What may be blatantly obvious to you is quite a problem especially to beginners. Some of us may be beginners to R, but we know math, science, programming, and how to solve problems with other tools and languages. I re-read the guidelines before posting fearing condemnation. Before posting I searched the online R-help Google interface with keywords image, flip, rotate. A discussion from 1998 touched on this issue but I was hoping that this was deemed a bug at some point and fixed -- or had an easy workaround, like some parameter I was missing. I read the ?image help before posting. Was the part I didn't understand buried in this note? Based on a function by Thomas Lumley [EMAIL PROTECTED] You seem to be thinking that Prof Ripley's solution had something to do with image(). It doesn't, it has to do with manipulating a matrix. image() visualizes a matrix in a particular and well-defined way. You want your matrix to be shown in a different way, and one (simple) way of doing that is to convert your matrix into a different matrix, on which calling image would give you what you want. Why would this be explained in ?image ? This is basic R. More generally, I think your frustration is caused by your expectation that a matrix object should behave like a bitmap image. It doesn't. If you want work with images, use the pixmap package. Deepayan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Surprise when mapping matrix to image
I think I'd have to respectfully disagree with both Brian and
Deepayan, as to whether it should be obvious. It is reasonable
(principle of least suprise) to expect orientation of the plot to
match the print order of the matrix. I would have expected Brian's
one-liner to be in the help page, with a notice. It's a not-so-rare
activity, being a general matrix visualization that is commonly used
in certain areas of science (whether it ought to be commonly used is a
separate question).
While heatmap might've been perhaps a better pointer, but it doesn't
seem to do the right thing, either. I.e.
myTemp - matrix(c(1,2,3,3,2,3),nrow=2)
heatmap(myTemp,Rowv=NA,Colv=NA)
doesn't look right to me (R Version 1.9.1 (2004-06-21))
I see the pixmap/bitmap issue as a bit of a red herring, in this
case.
best,
-tony
p.s. I seem to get bit by this about once a year for the last few,
hence why I'm speaking up.
Deepayan Sarkar [EMAIL PROTECTED] writes:
Quoting Glynn, Earl [EMAIL PROTECTED]:
Prof Ripley:
Thank you for your prompt reply.
It's pure convention: see below.
Did you try reading the help for image? You don't seem to
understand it
if you actually did. It seems you are looking for
image(t(x)[ncol(x):1, ])
I think you guys are too close to R to understand how hard it is to
use sometimes. What may be blatantly obvious to you is quite a problem
especially to beginners. Some of us may be beginners to R, but we know
math, science, programming, and how to solve problems with other tools
and languages.
I re-read the guidelines before posting fearing condemnation.
Before posting I searched the online R-help Google interface with
keywords image, flip, rotate. A discussion from 1998 touched on
this issue but I was hoping that this was deemed a bug at some point
and fixed -- or had an easy workaround, like some parameter I was
missing.
I read the ?image help before posting. Was the part I didn't
understand buried in this note?
Based on a function by Thomas Lumley [EMAIL PROTECTED]
You seem to be thinking that Prof Ripley's solution had something to do with
image(). It doesn't, it has to do with manipulating a matrix. image()
visualizes a matrix in a particular and well-defined way. You want your matrix
to be shown in a different way, and one (simple) way of doing that is to
convert your matrix into a different matrix, on which calling image would give
you what you want. Why would this be explained in ?image ? This is basic R.
More generally, I think your frustration is caused by your expectation that a
matrix object should behave like a bitmap image. It doesn't. If you want work
with images, use the pixmap package.
Deepayan
__
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--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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Re: [R] Surprise when mapping matrix to image
I was also surprised by the image orientation this summer and used the
easy fix of matrix manipulation. There is however another issue and that
is when you start flipping around the matrix, orders etc. and for the case
you want to have sensibly labeled axes, you may have to use the axis
commands etc. which is also easy, but accumulation of easy fixes can be
tedious so there is perhaps some argument for yet another new documentation
submission. Maybe a method for easily changing the orientation in image
could be added.
Jim
- Original Message -
From: A.J. Rossini [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, August 26, 2004 7:11 PM
Subject: Re: [R] Surprise when mapping matrix to image
I think I'd have to respectfully disagree with both Brian and
Deepayan, as to whether it should be obvious. It is reasonable
(principle of least suprise) to expect orientation of the plot to
match the print order of the matrix. I would have expected Brian's
one-liner to be in the help page, with a notice. It's a not-so-rare
activity, being a general matrix visualization that is commonly used
in certain areas of science (whether it ought to be commonly used is a
separate question).
While heatmap might've been perhaps a better pointer, but it doesn't
seem to do the right thing, either. I.e.
myTemp - matrix(c(1,2,3,3,2,3),nrow=2)
heatmap(myTemp,Rowv=NA,Colv=NA)
doesn't look right to me (R Version 1.9.1 (2004-06-21))
I see the pixmap/bitmap issue as a bit of a red herring, in this
case.
best,
-tony
p.s. I seem to get bit by this about once a year for the last few,
hence why I'm speaking up.
Deepayan Sarkar [EMAIL PROTECTED] writes:
Quoting Glynn, Earl [EMAIL PROTECTED]:
Prof Ripley:
Thank you for your prompt reply.
It's pure convention: see below.
Did you try reading the help for image? You don't seem to
understand it
if you actually did. It seems you are looking for
image(t(x)[ncol(x):1, ])
I think you guys are too close to R to understand how hard it is to
use sometimes. What may be blatantly obvious to you is quite a problem
especially to beginners. Some of us may be beginners to R, but we know
math, science, programming, and how to solve problems with other tools
and languages.
I re-read the guidelines before posting fearing condemnation.
Before posting I searched the online R-help Google interface with
keywords image, flip, rotate. A discussion from 1998 touched on
this issue but I was hoping that this was deemed a bug at some point
and fixed -- or had an easy workaround, like some parameter I was
missing.
I read the ?image help before posting. Was the part I didn't
understand buried in this note?
Based on a function by Thomas Lumley [EMAIL PROTECTED]
You seem to be thinking that Prof Ripley's solution had something to do
with
image(). It doesn't, it has to do with manipulating a matrix. image()
visualizes a matrix in a particular and well-defined way. You want your
matrix
to be shown in a different way, and one (simple) way of doing that is to
convert your matrix into a different matrix, on which calling image
would give
you what you want. Why would this be explained in ?image ? This is basic
R.
More generally, I think your frustration is caused by your expectation
that a
matrix object should behave like a bitmap image. It doesn't. If you want
work
with images, use the pixmap package.
Deepayan
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
__
[EMAIL PROTECTED] mailing list
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
[EMAIL PROTECTED] mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Surprise when mapping matrix to image
I've got some simple code example at http://www.maths.lth.se/help/R/image/,
or just try:
source(http://www.maths.lth.se/help/R/image/image.R;)
Best wishes
Henrik Bengtsson
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jim Brennan
Sent: Friday, August 27, 2004 1:43 AM
To: [EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: Re: [R] Surprise when mapping matrix to image
I was also surprised by the image orientation this summer and
used the easy fix of matrix manipulation. There is however
another issue and that is when you start flipping around the
matrix, orders etc. and for the case you want to have
sensibly labeled axes, you may have to use the axis commands
etc. which is also easy, but accumulation of easy fixes can
be tedious so there is perhaps some argument for yet another
new documentation submission. Maybe a method for easily
changing the orientation in image could be added.
Jim
- Original Message -
From: A.J. Rossini [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, August 26, 2004 7:11 PM
Subject: Re: [R] Surprise when mapping matrix to image
I think I'd have to respectfully disagree with both Brian and
Deepayan, as to whether it should be obvious. It is reasonable
(principle of least suprise) to expect orientation of the plot to
match the print order of the matrix. I would have expected Brian's
one-liner to be in the help page, with a notice. It's a
not-so-rare
activity, being a general matrix visualization that is
commonly used
in certain areas of science (whether it ought to be
commonly used is a
separate question).
While heatmap might've been perhaps a better pointer, but
it doesn't
seem to do the right thing, either. I.e.
myTemp - matrix(c(1,2,3,3,2,3),nrow=2)
heatmap(myTemp,Rowv=NA,Colv=NA)
doesn't look right to me (R Version 1.9.1 (2004-06-21))
I see the pixmap/bitmap issue as a bit of a red herring, in this
case.
best,
-tony
p.s. I seem to get bit by this about once a year for the last few,
hence why I'm speaking up.
Deepayan Sarkar [EMAIL PROTECTED] writes:
Quoting Glynn, Earl [EMAIL PROTECTED]:
Prof Ripley:
Thank you for your prompt reply.
It's pure convention: see below.
Did you try reading the help for image? You don't seem to
understand it if you actually did. It seems you are
looking for
image(t(x)[ncol(x):1, ])
I think you guys are too close to R to understand how
hard it is
to use sometimes. What may be blatantly obvious to you
is quite a
problem especially to beginners. Some of us may be
beginners to R,
but we know math, science, programming, and how to solve
problems
with other tools and languages.
I re-read the guidelines before posting fearing condemnation.
Before posting I searched the online R-help Google
interface with
keywords image, flip, rotate. A discussion from
1998 touched
on this issue but I was hoping that this was deemed a
bug at some
point and fixed -- or had an easy workaround, like some
parameter I
was missing.
I read the ?image help before posting. Was the part I didn't
understand buried in this note?
Based on a function by Thomas Lumley
[EMAIL PROTECTED]
You seem to be thinking that Prof Ripley's solution had
something to
do
with
image(). It doesn't, it has to do with manipulating a matrix.
image() visualizes a matrix in a particular and well-defined way.
You want your
matrix
to be shown in a different way, and one (simple) way of
doing that
is to convert your matrix into a different matrix, on
which calling
image
would give
you what you want. Why would this be explained in ?image
? This is
basic
R.
More generally, I think your frustration is caused by your
expectation
that a
matrix object should behave like a bitmap image. It
doesn't. If you
want
work
with images, use the pixmap package.
Deepayan
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]
http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer
Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is
unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
CONFIDENTIALITY NOTICE: This e-mail message and any
attachme...{{dropped}}
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RE: [R] Surprise when mapping matrix to image
Deepayan Sarkar [EMAIL PROTECTED] wrote: You seem to be thinking that Prof Ripley's solution had something to do with image(). Glynn, Earl [EMAIL PROTECTED] could certainly be excused for thinking so, because what Prof Ripley wrote included this: Did you try reading the help for image? You don't seem to understand it if you actually did. That certainly sounds to me as though the answer should have been obvious from ?image Now, the image() function is trying to be extremely helpful and offers you lots of ways of providing the data, and that is explained in ?image. In fact a key piece of information *IS* in ?image, so it really DOES have something to do with image(): Details: The length of 'x' should be equal to the 'nrow(z)+1' or 'nrow(z)'. In the first case 'x' specifies the boundaries between the cells: in the second case 'x' specifies the midpoints of the cells. This tells us that the x direction of the image goes along the *rows* of the matrix and by implication that the y direction goes along the *columns* of the matrix, and is precisely what you need to figure out that image(t(x)) is the thing to use. One does have to be a little subtle at reading between the lines to see the relevance of details about a parameter one is not passing, but the information _is_ there and it _is_ 'something to do with image()', not something to do with matrices. The 'volcano' example from ?image also points the same way. The basic problem here is that the standard visual layout of matrices sets up such a strong expectation that it's difficult for any text to override it. I don't see anything that explicitly discusses the direction of the axes, I don't see anything explicit, but I took it that ?image would follow the usual horizontal axis increases from left to right, vertical axis increases from bottom to top convention, which means horizontal gives ROW number increasing left to right, vertical gives COLUMN number increasing bottom to top so when I do image(t(x)) I see my columns as vertical strips but they are upside down, so the last step, to image(t(x)[ncol(x):1,]) does make sense, provided you read ?image as *implying* without actually stating follows the usual graphical conventions for axes. But again, this really is a fact about image(), not about matrices. As for the claim that It doesn't, it has to do with manipulating a matrix. image() visualizes a matrix in a particular and well-defined way. Well yes, it is a particular way, and I suppose you could say that the code is defined well, but it really isn't, when you get right down to it, and *EXPLICITLY* documented way. You really have to work at it. This is NOT a criticism of R documentation. Of all the open-source programs I use, I reckon R is by far the best documented, and its on-line documentation can more than withstand comparison against most of the commercial programs I've seen. The real problem is that R is just so big and there are only so many people writing documentation for it. Given the wide range of ways that the x, y, z arguments can be passed to image(), it would actually make sense to have some kind of flip and/or mirror operations specified via an argument to image(). The source code of image is available (image.default) so it wouldn't be a lot of work for someone who wants it to produce such a thing. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Surprise when mapping matrix to image
From: Richard A. O'Keefe [snip] Given the wide range of ways that the x, y, z arguments can be passed to image(), it would actually make sense to have some kind of flip and/or mirror operations specified via an argument to image(). The source code of image is available (image.default) so it wouldn't be a lot of work for someone who wants it to produce such a thing. I'd suggest adding an `as.matrix' argument to image.default. Best, Andy __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Surprise when mapping matrix to image
Quoting Richard A. O'Keefe [EMAIL PROTECTED]: Deepayan Sarkar [EMAIL PROTECTED] wrote: You seem to be thinking that Prof Ripley's solution had something to do with image(). Glynn, Earl [EMAIL PROTECTED] could certainly be excused for thinking so, because what Prof Ripley wrote included this: Did you try reading the help for image? You don't seem to understand it if you actually did. That certainly sounds to me as though the answer should have been obvious from ?image I agree with you that the issues are related, but your (edited) quoting is misleading. I interpret Prof Ripley's comment as implying that reading ?image would tell the user what happens when he calls image(x). This is distinct from how to manipulate a matrix, which is what t(x)[ncol(x):1, ] is doing. It doesn't seem obvious to me that this information should be in ?image, and I still don't see how Prof Ripley's comment suggested that it was. Anything but the most trivial use of S involves combining different ideas. One can hardly expect all possible interactions to be documented. Of course, documentation can always use improvements (and the rest of your comments on ?image are all valid), and it would be nice to anticipate frequently faced problems and offer solutions preemptively, but that's a different issue. Deepayan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Surprise when mapping matrix to image
Deepayan Sarkar [EMAIL PROTECTED] wrote: I agree with you that the issues are related, but your (edited) quoting is misleading. My quotes were selective but not otherwise edited. I interpret Prof Ripley's comment as implying that reading ?image would tell the user what happens when he calls image(x). And that's how I interpreted it too. This is distinct from how to manipulate a matrix, which is what t(x)[ncol(x):1, ] is doing. It doesn't seem obvious to me that this information should be in ?image, Nobody whatsoever has suggested that the matrix manipulation code *SHOULD* be in ?image. Nobody. Not me. Not anyone else. The original poster's problem was not how do I manipulate a matrix but why is the image the wrong way around. and I still don't see how Prof Ripley's comment suggested that it was. It didn't. NOBODY has made any such suggestion. One can hardly expect all possible interactions to be documented. Nobody has suggested that either. All I was saying is this: (1) The original poster's problem was a problem about image(), NOT a problem about matrix manipulation. (2) We have no reason whatsoever to assert, hint, believe, or opine that the original poster was any less competent at matrix manipulation per se than anyone else reading this mail list. He didn't have a matrix problem. (3) The problem basically is precisely where Prof Ripley located it: a clash between (a) an extremely strong cultural expectation that the elements of a matrix will be presented with rows running from 1 at top to m at bottom and columns running from 1 at left to n at right, and (b) an extremely strong cultural expectation that the vertical axis of a plot runs from low at the bottom to high at the top, and (c) the fact that image() maps the row axis of a matrix to the horizontal axis of a plot and the column axis of a matrix to the vertical axis of a plot. Expectations (a) and (b) are not only part of general computing, they are strongly supported by R itself. As for (c), it doesn't seem to me that it _had_ to be that way. (4) Point (c) is a sufficiently strange quirk of image() that it is a stumbling block waiting to trip people up. I've stumbled over it myself, which is how come I knew where to look in ?image. That makes it *essential* that it should be documented. (5) And it *IS* documented. It really is an image() problem, not a matrix problem, and the essential part of it *IS* documented. Pointing out that a obvious nasty interaction *is* documented is hardly a demand that all possible interactions should be documented. How about this addition to the documentation? The x axis corresponds to the rows of the matrix (first on the left to last on the right). The y axis corresponds to the columns of the matrix (first at the bottom to last at the top). Once you know what image() is _intended_ to do with a matrix, you can figure out the transposing and reversing you need for any other view. It's knowing you need to that's the problem. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Surprise when mapping matrix to image
Richard A. O'Keefe [EMAIL PROTECTED] writes:
Once you know what image() is _intended_ to do with a matrix,
you can figure out the transposing and reversing you need for any
other view. It's knowing you need to that's the problem.
This is a much better statement of my point, and precisely why it
keeps (though only occassionally) burning me.
best,
-tony
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
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[R] Surprise when mapping matrix to image
Start with:
x - c(1:7,1)
dim(x) - c(2,4)
x
[,1] [,2] [,3] [,4]
[1,]1357
[2,]2461
2 Rows of 4 Columns. Upper-left and lower-right elements of the matrix
are the same.
All to this point makes good sense.
image(x)
However, this image shows 2 columns of 4 rows. The lower-left and
upper-right elements are the same. This does not make sense to me.
Did I miss some simple parameter to fix all of this naturally? Why
would the numeric matrix of x and the image of x have such a
different geometry?
I'd love to use R for some simple image processing, but I don't want to
spend my time fixing all my images.
Because Image Pro Plus wasn't doing a calculation the way we wanted, I
dumped 16-bit pixel data into Excel and used Excel to create CSVs. All
of this went much faster than figuring out the surprise that R didn't
display the images correctly. Did I miss something simple?
I really don't want to do this:
ReadImageMatrix - function(filename)
{
x - as.matrix(read.csv(filename,header=FALSE))
x - t(x)
return( x[,ncol(x):1] )
}
oldpar - par(mfrow=c(2,2))
x - ReadImageMatrix(1n.csv)
image(x, col=gray((0:255)/255), main=1N, axes=FALSE)
y - ReadImageMatrix(2n.csv)
image(y, col=gray((0:255)/255), main=2N, axes=FALSE)
z - ReadImageMatrix(3n.csv)
image(z, col=gray((0:255)/255), main=3N, axes=FALSE)
par(oldpar)
efg
--
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
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Re: [R] Surprise when mapping matrix to image
On Thu, 26 Aug 2004, Glynn, Earl wrote: Start with: x - c(1:7,1) dim(x) - c(2,4) x [,1] [,2] [,3] [,4] [1,]1357 [2,]2461 2 Rows of 4 Columns. Upper-left and lower-right elements of the matrix are the same. All to this point makes good sense. It's pure convention: see below. image(x) However, this image shows 2 columns of 4 rows. The lower-left and upper-right elements are the same. This does not make sense to me. Did I miss some simple parameter to fix all of this naturally? Why would the numeric matrix of x and the image of x have such a different geometry? Did you try reading the help for image? You don't seem to understand it if you actually did. It seems you are looking for image(t(x)[ncol(x):1, ]) Easy! Mathematical conventions are just that, conventions. They differ by field of mathematics. Don't ask us why matrix rows are numbered down but graphs are numbered up the y axis, nor why x comes before y but row before column. But the matrix layout has always seemed illogical to me. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Surprise when mapping matrix to image
Prof Ripley: Thank you for your prompt reply. It's pure convention: see below. Did you try reading the help for image? You don't seem to understand it if you actually did. It seems you are looking for image(t(x)[ncol(x):1, ]) I think you guys are too close to R to understand how hard it is to use sometimes. What may be blatantly obvious to you is quite a problem especially to beginners. Some of us may be beginners to R, but we know math, science, programming, and how to solve problems with other tools and languages. I re-read the guidelines before posting fearing condemnation. Before posting I searched the online R-help Google interface with keywords image, flip, rotate. A discussion from 1998 touched on this issue but I was hoping that this was deemed a bug at some point and fixed -- or had an easy workaround, like some parameter I was missing. I read the ?image help before posting. Was the part I didn't understand buried in this note? Based on a function by Thomas Lumley [EMAIL PROTECTED] I asked the question because I did not find the answer under ?image. Please quote the portion that I missed that you think explains this. I was tempted to post the whole ?image section here to prove my point. There is no entry on that page with transpose, t(, or ncol the way you explained above. I'm not sure what you think I missed, but I did my homework on this problem before posting. Easy! Mathematical conventions are just that, conventions. They differ by field of mathematics. Don't ask us why matrix rows are numbered down but graphs are numbered up the y axis, nor why x comes before y but row before column. But the matrix layout has always seemed illogical to me. My 30+ years of software experience says this is a design flaw. A good design would reconcile the differences between conventions. Coordinate transformations are not that hard, but I wouldn't burden the end-user with them needlessly. I'll go back to lurking in the daily R-Helps and not ask any more questions until I've read all the old R-help messages. I'm working on December 1998 right now and reading forward. Perhaps by next year I'll will have read all the old R-help postings and I'll dare ask another question then. efg __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
