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From: Ethan A M. <merritt@u.washington.edu> - 2005-10-22 18:42:20
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> this works: > plot 'file.dat' mat w image > but this doesn't anymore: > plot 'file.dat' mat u 1:2:3 w image > > Comment By: Petr Mikulik (mikulik) > Date: 2005-10-22 11:26 > >> the x and y coords are coming from the row and column indices >> of the file, right? So x is $0, but y is a problem because >> we have no pseudo-column assigned for the column. > > no, x = $1, y = $2 (autogenerated row and column index of > the matrix) Apparently that is how the program currently interprets $1 and $2. I dind't know that. It is very confusing because it is not consistent with all other plot/splot "datafile" commands. In all other cases $1 means column 1 of the file, regardless of whether it is being used as an x value. > I think we have reduced the bug to this: > This works (at least one of $1, $2 or $3 appears at least once): > splot 'file.dat' matr u ($1/100):2:3 > This works in a very strange way: > splot 'file.dat' matr u 1:2:3 > > Once this is fixed, we can extend 'help matrix ascii' to Sure, it should be fixed (although the behaviour has not changed since 3.7 so the original bug report is misleading). But I would like to provide a more logical syntax for this operation, so that this confusion isn't necessary. This is really just an axis-labelling operation, right? The "true" x and y indices of the matrix points are still integers running from 1 to however many rows/columns of data are in the file. How about if we could plot Petr's example: splot 'matrix.dat' matrix using (1+$1/100):(1+$2*10):3 as f(x) = 1 + x/100 g(y) = 1 + y*10 splot 'matrix.dat' matrix xticlabels(f(x)):yticlabels(g(y)) Would that be more natural? Alternatively, we could allow dummy variables in the using specs directly: splot 'matrix.dat' matrix using (f(x)):(g(y)):(z) Unfortunately that has no obvious meaning for non-matrix plots. > ---------------------------------------------------------------------- > > Comment By: Juergen Wieferink (wieferink) > Date: 2005-10-22 09:18 > > Message: > Logged In: YES > user_id=1090807 > > Weird. You are right. > > Using ($1):($2):3 instead of 1:2:3 works fine, though. And even > more confusing: When I try to play around with the ranges, I can > find no systematic at all... Once I only set the xrange: > > plot [0:1] "file.dat" matrix using 1:2:3 with image > > It doesn't even respect the plot borders... There is something > that really goes wrong here. > I would attach the resulting image -- if I could. > > Juergen > > > ---------------------------------------------------------------------- > > Comment By: Ethan Merritt (sfeam) > Date: 2005-10-21 23:11 > > Message: > Logged In: YES > user_id=235620 > > Huh. > Were you using the data file provided in the bug report? > > I see the problem in 3.7, 4.0 and current cvs. Well, I > don't see it as a "problem" because it does not seem like a > reasonable command in the first place. See attached png output. > file A: splot 'matrix.dat' matrix > file B: splot 'matrix.dat' matrix using 1:2:3 > > > > ---------------------------------------------------------------------- > > Comment By: Juergen Wieferink (wieferink) > Date: 2005-10-21 22:10 > > Message: > Logged In: YES > user_id=1090807 > > Ethan: > It might be confusing, but it works -- at least for me. > > > I have been using this for quite a while (I'd even say pre-4.0) in a > wide set of scripts. And it has worked fine all the time. I cannot > reproduce the problem of the OP. > > Juergen > > > ---------------------------------------------------------------------- > > Comment By: Ethan Merritt (sfeam) > Date: 2005-10-21 21:54 > > Message: > Logged In: YES > user_id=235620 > > Petr: > Your use of $1 and $2 in that example is confusing. IIn the > case of 3D matrix data, the x and y coords are coming from > the row and column indices of the file, right? So x is $0, > and y is... well y is a problem, because we don't have a > pseudo-column assigned for the column number. > > I assume your intent is more something like: > splot 'file.dat' matrix thru f(x,y,z) > > even though x and y are being autogenerated from the file > layout rather than being explicitly contained in the data. > > > ---------------------------------------------------------------------- > > Comment By: Petr Mikulik (mikulik) > Date: 2005-10-21 21:38 > > Message: > Logged In: YES > user_id=31505 > > Thus > splot 'file.dat' matrix using ($1*2):(1+10*$2):3 > can work? Then I would like it too -- I though axes > transformations are not allowed for 'matrix'. > > When it works, it should be properly documented in 'help > matrix', the best with few examples, like above. > > > ---------------------------------------------------------------------- > > Comment By: Hans-Bernhard Broeker (broeker) > Date: 2005-10-21 21:07 > > Message: > Logged In: YES > user_id=27517 > > @Petr: no, that's not a bug, that's a very crucial feature. > I'm strictly against going back to the ancient days when > you couldn't do any parameter transformations on a data set > just because it was given as 'matrix' or 'binary'. The > difference caused by those have to be resolved for good, by > the time 'using' and friends get applied. > > ---------------------------------------------------------------------- > > Comment By: Martin Horvat (martin_horvat) > Date: 2005-10-21 18:57 > > Message: > Logged In: YES > user_id=473606 > > Greatings, > > Thanks for the comments and the explanation. It just strange > that few months ago this thing worked and all my scripts > were accordingly modified. I don't really know the > implementation of matrix data format, but the syntax "splot > 'file.dat' mat u 1:2:3 w l" seems plausible to me. But ok, > it doesn't matter, I rewrote the scripts and the programs > and so on. Now I use basic (standard) gnuplot syntax and it > works. > > Thanks guys. > > Best regards, > > Martin > > ---------------------------------------------------------------------- > > Comment By: Petr Mikulik (mikulik) > Date: 2005-10-21 18:28 > > Message: > Logged In: YES > user_id=31505 > > I think it is rather a bug that > splot 'file.dat' mat u 1:2:3 w l > passes the parser. > Gnuplot works only with > splot 'file.dat' matrix > or > splot 'file.dat' matrix using (f($1,$2,$3)) > > I think an error should be issued if nb_of_using_params >= 2. > > > > > > > > ---------------------------------------------------------------------- > > Comment By: Ethan Merritt (sfeam) > Date: 2005-10-18 04:51 > > Message: > Logged In: YES > user_id=235620 > > I am inclined to close this report, since the command being > used seems intrinsically incorrect for the data file > provided as an example. > > The data file is entirely filled with z-values, with one > entire row of values per line of the file. This is normal > for matrix data. Trying to pull x and y out of columns in > the files makes no sense at all, and will end up discarding > all but 1 z-value per line. > > The earlier procedure you remember working must have > involved a rather different layout of data in the file. > Does that make sense? > > ---------------------------------------------------------------------- > > You can respond by visiting: > https://sourceforge.net/tracker/?func=detail&atid=102055&aid=1264105&gro >up_id=2055 -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 |
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From: Ethan A M. <merritt@u.washington.edu> - 2005-10-23 19:58:01
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On Sunday 23 October 2005 12:23 am, Petr Mikulik wrote:
>
> It would be nice to organize that
> plot 'a.dat' matrix
> is equivalent to
> plot 'a.dat' matrix using 1:3
OK. That part is now in cvs.
I'm still amazed that this works.
Who knew that you could plot data rows?
I'm still confused by the documentation, and will try to
clarify it. For example, you suggest
> The z-values are read in a row at a time, i. e.,
> z11 z12 z13 z14 ...
> z21 z22 z23 z24 ...
> z31 z32 z33 z34 ...
> X- and y-indices of the matrix correspond to column and row index of the
But this is not really correct, as the use of "plot <foo> matrix"
demonstrates. "Column 3" may or may not be a Z value, depending
on what kind of graph you are describing. My current best effort
at writing a description is:
Matrix values are read in a row at a time, i. e.,
M11 M12 M13 M14 ... (i=1)
M21 M22 M23 M24 ... (i=2)
M31 M32 M33 M34 ... (i=3)
... ... ... ... Mij
The interpretation of columns in the "using" specification for
matrix data is different from the usual case. "$1" refers to the
matrix row index i, "$2" refers to the matrix column index j,
and "$3" refers to the matrix entry Mij.
Example:
set view map
splot <foo> matrix using ($1 * 5.):2:(sqrt($3))
This example will plot the value sqrt(Mij) at the coordinates
x=5i, y=j for each entry i,j represented in the matrix.
Does this description seem OK to you?
> ***
>
> Proposal for 'help matrix', please modify:
>
> Datafile can be in an ascii or binary matrix format. The `matrix` flag
> indicates that the file is ascii, the `binary` or `matrix binary` stands
> for a binary format. For details, see `matrix ascii` or `matrix binary`.
>
> Basic usage in `splot`:
> splot 'a.dat' matrix
> splot 'a.gpbin' {matrix} binary
> Advanced usage in `splot`:
> splot 'a.dat' matrix using 1:2:3
> splot 'a.gpbin' {matrix} binary using 1:2:3
> allows to manipulate the axes coordinates and the z-data.
>
> Usage in `plot`:
> plot `a.dat` matrix using 1:3
> plot 'a.gpbin' {matrix} binary using 1:3
> will plot rows of the matrix, while using 2:3 will plot matrix columns,
> and 1:2 point coordinates. Applying the `every` option you can specify
> explicit rows and columns.
>
> Example -- rescale axes for an ascii matrix:
> splot `a.dat` matrix using (1+$1):(1+$2*10):3
>
> Example -- plot the 3rd row of an ascii matrix:
> plot 'a.dat' matrix using 1:3 every 1:999:1:2
> (rows are enumerated from 0, thus 2 instead of 3).
>
> ***
>
> Proposal for 'help matrix ascii', please modify:
>
> The `matrix` flag in
> {s}plot 'a.dat' matrix
> indicates that the ASCII data are stored in matrix format.
>
> The z-values are read in a row at a time, i. e.,
> z11 z12 z13 z14 ...
> z21 z22 z23 z24 ...
> z31 z32 z33 z34 ...
> and so forth.
>
> X- and y-indices of the matrix correspond to column and row index of the
> matrix, starting from 0. You can rescale or transform the axes as usual
> for a data file with three columns (x=$1, y=$2, z=$3), for example
> splot 'a.dat' matrix using (1+$1/100):(1+$2*10):3
>
> A blank line or comment line ends the matrix, and starts a new
> surface mesh. You can select among the meshes inside a file by the
> `index` option to the `splot` command, as usual.
>
>
> ---
> PM
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
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From: <mi...@ph...> - 2005-10-24 05:38:37
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> I'm still confused by the documentation, and will try to
> clarify it. For example, you suggest
>
>> X- and y-indices of the matrix correspond to column and row index of the
>
> But this is not really correct, as the use of "plot <foo> matrix"
> demonstrates. "Column 3" may or may not be a Z value, depending
> on what kind of graph you are describing.
I would keep the x, y and z for both plot and splot cases, and add that
the default using for plot is
plot 'a.dat' matrix using 1:3
and not using 1:2 which makes no good sense for matrices.
> Matrix values are read in a row at a time, i. e.,
> M11 M12 M13 M14 ... (i=1)
> M21 M22 M23 M24 ... (i=2)
> M31 M32 M33 M34 ... (i=3)
> ... ... ... ... Mij
>
> The interpretation of columns in the "using" specification for
> matrix data is different from the usual case. "$1" refers to the
> matrix row index i, "$2" refers to the matrix column index j,
> and "$3" refers to the matrix entry Mij.
Indexing starts from 0. Further, x is the column index j, y is row index i.
> Does this description seem OK to you?
Please combine it with my longer description with example for both 'help
matrix' and 'help matrix ascii'.
---
PM
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From: Ethan A M. <merritt@u.washington.edu> - 2005-10-24 07:02:06
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On Sunday 23 October 2005 10:38 pm, mi...@ph... wrote: > > "Column 3" may or may not be a Z value, depending > > on what kind of graph you are describing. > > I would keep the x, y and z for both plot and splot cases, and add that > the default using for plot is > plot 'a.dat' matrix using 1:3 > and not using 1:2 which makes no good sense for matrices. Sorry, I must be really dense today. I am just not understanding your way of naming things. In a 2D plot we are plotting y = f(x). x is taken from the first using spec. y is taken from the second using spec. There is no z. So when you say "plot 'a.dat' matrix using 1:3" you are asking for x from column 1 and y from column 3. How can it be correct to document column 3 as being z in this case? > > Matrix values are read in a row at a time, i. e., > > M11 M12 M13 M14 ... (i=1) > > M21 M22 M23 M24 ... (i=2) > > M31 M32 M33 M34 ... (i=3) > > ... ... ... ... Mij > > > > The interpretation of columns in the "using" specification for > > matrix data is different from the usual case. "$1" refers to the > > matrix row index i, "$2" refers to the matrix column index j, > > and "$3" refers to the matrix entry Mij. > > Indexing starts from 0. Oops. Yes. > Further, x is the column index j, y is row index i. Yeah, I'm not doing so well in describing this either. And on top of that we may be suffering from a difference in naming conventions. I am now uncertain whether the term "row index" means the same thing to you that it does to me. And even if it does, there are people in the world that use a different convention so maybe it is better not to use the terms at all. I agree that the x value of the plot is taken from the index j. But neither i nor j is "y" in the sense of a 2D graph coordinate. The y value is take from Mij. If there are multiple lines in the data file, then i will be counting out successive plots in the 2D graph. So it is neither "x" nor "y", but rather it is "plot number". Maybe we need to write totally separate sections for the 2D case and the 3D case. Anyhow, I don't seem to be having much luck at writing this section. I'll hand it back to you. Or maybe somebody else wants to take a stab at it? -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 |
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From: Petr M. <mi...@ph...> - 2005-10-24 17:19:35
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>> I would keep the x, y and z for both plot and splot cases, and add that >> the default using for plot is >> plot 'a.dat' matrix using 1:3 >> and not using 1:2 which makes no good sense for matrices. > > Sorry, I must be really dense today. > I am just not understanding your way of naming things. > > In a 2D plot we are plotting y = f(x). > x is taken from the first using spec. > y is taken from the second using spec. > There is no z. > > So when you say "plot 'a.dat' matrix using 1:3" > you are asking for x from column 1 and y from column 3. > How can it be correct to document column 3 as being z > in this case? I consider matrix as a 3D object, and I draw its section in 2D. See 'help binary general' and 'help binary general examples' -- it's the same thing, just binary not ascii, and also plot as (x,y,z) via "plot" in 2D. > Maybe we need to write totally separate sections for the 2D case > and the 3D case. I tried that in my proposal text for the two help sections, with examples. > section. I'll hand it back to you. > Or maybe somebody else wants to take a stab at it? At the moment I stay with the proposed text. --- PM |
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From: Hans-Bernhard B. <br...@ph...> - 2005-10-24 13:48:45
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Ethan A Merritt wrote: > On Saturday 22 October 2005 02:55 pm, Petr Mikulik wrote: > > >>>> x = $1, y = $2 (autogenerated row and column index of the matrix) That's indeed at least slightly strange. It boils down to two questions, which are strongly inter-connected: 1) Why not use existing pseudo-column numbers 0 and -1, instead of 1 and 2? 2) Should 1 2 3 4 5 6 7 8 9 read as 'matrix' be equivalent to a file 1 2 3 4 5 6 7 8 9 read by the ordinary routines, or to 0 0 1 1 0 2 2 0 3 0 1 4 1 1 5 2 1 6 0 2 7 1 2 8 2 2 9 The current implementation seems to be implying the latter format, which in turn makes column numbers 1, 2 a suitable choice. It effectively gives x values $1 = $0, and y vales $2 = column(-1). > You don't find it confusing that in 2D plots you need to say > plot 'data' matrix using ($1):($3) Well, given the current documentation (as in: lack of) what 'matrix' actually means in terms of column numbers, any expectations would be wrong by default. Thus my suggestion is: we make up our mind about the answers to the above questions, and add to 'help matrix' accordingly. |
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From: Petr M. <mi...@ph...> - 2005-10-24 17:15:16
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>>>>> x = $1, y = $2 (autogenerated row and column index of the matrix) > > That's indeed at least slightly strange. It boils down to two questions, > which are strongly inter-connected: > > 1) Why not use existing pseudo-column numbers 0 and -1, instead of 1 and 2? I think $1, $2 and $3 is logic for this matrix case. > 2) Should > > 1 2 3 > 4 5 6 > 7 8 9 > > read by the ordinary routines, or to > > 0 0 1 > 1 0 2 > 2 0 3 yes, to this one, as it now works -- just the docs is missing >> You don't find it confusing that in 2D plots you need to say >> plot 'data' matrix using ($1):($3) No, because you "plot" (in 2D) a 3D object (matrix with axes). That's the same as for "plot ... with image". > Thus my suggestion is: we make up our mind about the answers to the above > questions, and add to 'help matrix' accordingly. That's what I meant when sending proposal for the new text of 'help matrix' and 'help matrix ascii'. Please update it if you like. --- PM |
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From: Petr M. <mi...@ph...> - 2005-10-22 21:55:32
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>> no, x = $1, y = $2 (autogenerated row and column index of
>> the matrix)
>
> Apparently that is how the program currently interprets
> $1 and $2. I dind't know that.
> It is very confusing because it is not consistent with all other
> plot/splot "datafile" commands. In all other cases $1 means
> column 1 of the file, regardless of whether it is being used as
> an x value.
It's not confusing, because you specify the "matrix" keyword. Same for
(the new) "binary" stuff.
> But I would like to provide a more logical syntax for this
> operation, so that this confusion isn't necessary.
> splot 'matrix.dat' matrix using (1+$1/100):(1+$2*10):3
> as
> f(x) = 1 + x/100
> g(y) = 1 + y*10
> splot 'matrix.dat' matrix xticlabels(f(x)):yticlabels(g(y))
>
> Would that be more natural?
>
> Alternatively, we could allow dummy variables in the using specs
> directly:
> splot 'matrix.dat' matrix using (f(x)):(g(y)):(z)
> Unfortunately that has no obvious meaning for non-matrix plots.
I would stay with my proposal
splot 'matrix.dat' matrix using (1+$1/100):(1+$2*10):3
For me, it's easy to understand, and consistent with "binary".
---
PM
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From: Ethan A M. <merritt@u.washington.edu> - 2005-10-22 23:48:39
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On Saturday 22 October 2005 02:55 pm, Petr Mikulik wrote: >>> x = $1, y = $2 (autogenerated row and column index of the matrix) >> It is very confusing because it is not consistent with all other >> plot/splot "datafile" commands. In all other cases $1 means >> column 1 of the file, regardless of whether it is being used as >> an x value. > It's not confusing, because you specify the "matrix" keyword. Same for > (the new) "binary" stuff. You don't find it confusing that in 2D plots you need to say plot 'data' matrix using ($1):($3) Why ($3)? -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 |
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From: Petr M. <mi...@ph...> - 2005-10-23 07:23:14
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> You don't find it confusing that in 2D plots you need to say
> plot 'data' matrix using ($1):($3)
>
> Why ($3)?
I never know I can use
plot ... matrix
I'm still learning gnuplot :-))
It would be nice to organize that
plot 'a.dat' matrix
is equivalent to
plot 'a.dat' matrix using 1:3
***
Proposal for 'help matrix', please modify:
Datafile can be in an ascii or binary matrix format. The `matrix` flag
indicates that the file is ascii, the `binary` or `matrix binary` stands for
a binary format. For details, see `matrix ascii` or `matrix binary`.
Basic usage in `splot`:
splot 'a.dat' matrix
splot 'a.gpbin' {matrix} binary
Advanced usage in `splot`:
splot 'a.dat' matrix using 1:2:3
splot 'a.gpbin' {matrix} binary using 1:2:3
allows to manipulate the axes coordinates and the z-data.
Usage in `plot`:
plot `a.dat` matrix using 1:3
plot 'a.gpbin' {matrix} binary using 1:3
will plot rows of the matrix, while using 2:3 will plot matrix columns, and
1:2 point coordinates. Applying the `every` option you can specify explicit
rows and columns.
Example -- rescale axes for an ascii matrix:
splot `a.dat` matrix using (1+$1):(1+$2*10):3
Example -- plot the 3rd row of an ascii matrix:
plot 'a.dat' matrix using 1:3 every 1:999:1:2
(rows are enumerated from 0, thus 2 instead of 3).
***
Proposal for 'help matrix ascii', please modify:
The `matrix` flag in
{s}plot 'a.dat' matrix
indicates that the ASCII data are stored in matrix format.
The z-values are read in a row at a time, i. e.,
z11 z12 z13 z14 ...
z21 z22 z23 z24 ...
z31 z32 z33 z34 ...
and so forth.
X- and y-indices of the matrix correspond to column and row index of the
matrix, starting from 0. You can rescale or transform the axes as usual for
a data file with three columns (x=$1, y=$2, z=$3), for example
splot 'a.dat' matrix using (1+$1/100):(1+$2*10):3
A blank line or comment line ends the matrix, and starts a new
surface mesh. You can select among the meshes inside a file by the
`index` option to the `splot` command, as usual.
---
PM
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From: Petr M. <mi...@ph...> - 2005-10-22 22:03:09
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I think I've tracked the bug down; it seems to be in datafile.c: df_readbinary(double v[], int max). Use this script: set grid set ticslevel 0.3 set auto fix set xlabel "xxxx" set ylabel "yyyy" splot 'a.dat' matrix u 1:2:3 set table replot with this a.dat: 11 12 13 14 15 21 22 23 24 25 ==> it produces: #IsoCurve 0, 5 points #x y z type 0 1 21 i 1 1 22 i 2 1 23 i 3 1 0 i 4 1 0 i #IsoCurve 1, 5 points #x y z type 0 0 11 i 1 0 12 i 2 0 13 i 3 0 0 i 4 0 0 i Thus, it reads only 3 columns, not the full line. It looks that df_readbinary() is used also for reading the ascii matrix file. However, I couldn't found where is the problem. Who else can find the problem? --- PM |
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From: Ethan A M. <merritt@u.washington.edu> - 2005-10-22 22:17:24
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On Saturday 22 October 2005 03:02 pm, Petr Mikulik wrote: > I think I've tracked the bug down; it seems to be in datafile.c: > df_readbinary(double v[], int max). Remember that this bug was already present in version 4.0, and in version 3.7 for that matter. The earlier versions did not use df_readbinary for input of ascii matrix data. > Who else can find the problem? I have had no luck so far. My prime suspect is get_3ddata() in plot3d.c, but I have not found it there either. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 |
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From: Ethan A M. <merritt@u.washington.edu> - 2005-10-23 04:27:05
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On Saturday 22 October 2005 03:02 pm, Petr Mikulik wrote:
> I think I've tracked the bug down
Found it. Bleah. It really has been there since forever.
It's in df_tokenise(), and it is specific to ascii matrix data.
Here is the fix:
--- gnuplot/src/datafile.c 2005-10-21 22:50:13.000000000 -0700
+++ gnuplot-cvs/src/datafile.c 2005-10-22 21:10:08.276728128 -0700
@@ -1145,6 +1146,7 @@
if (df_matrix) { duplication=TRUE; break; }
df_matrix = TRUE;
#endif
+ fast_columns = 0;
continue;
}
Corey Satten's monster optimization test skips all columns past the
first three unless some test has previously cleared the fast_columns
flag. Examples of things that clear the flag are parentheses in the
using spec and the presence of the "binary" flag. The optimization
test is also skipped if there are no using specs at all.
Ascii matrix data is not covered by any of these exceptions, so
df_tokenise() only parses the first 3 columns.
Amazing that no one has complained in all the time since 3.7 came
out.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
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From: Juergen W. <wie...@fr...> - 2005-10-23 08:46:48
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On Saturday 22 October 2005 20:42 Ethan A Merritt wrote: > How about if we could plot Petr's example: > splot 'matrix.dat' matrix using (1+$1/100):(1+$2*10):3 > as > f(x) = 1 + x/100 > g(y) = 1 + y*10 > splot 'matrix.dat' matrix xticlabels(f(x)):yticlabels(g(y)) > > Would that be more natural? With this, I would expect one label for each row and each column. I think it would be more natural to introduce some set format x function f(x) where f(x) is a string valued expression with a dummy variable "x". But in the case of matrix, I prefer Petr's example. Juergen |
