This is part one of my attempt to find an answer to my question wireframes in Mathematica.
Given a set of line segments how does one join two segments that are connected AND lie on the same line. For instance consider the line segments l1 = {(0,0), (1,1)} and l2 = {(1,1), (2,2)}. These two line segments can be combined into one line segment, namely l3 = {(0,0), (2,2)}. This is because l1 and l2 share the point (1,1) and the slope of each line segment is the same. Here is a visual:
l1 = JoinedCurve[{{{0, 2, 0}}}, {{{0, 0}, {1, 1}}}, CurveClosed -> {0}];
l2 = JoinedCurve[{{{0, 2, 0}}}, {{{1, 1}, {2, 2}}}, CurveClosed -> {0}];
Graphics[{Red, l1, Blue, l2}, Frame -> True]
One thing to notice is that in the above example l1 and l2 can be combined into one line specified by 3 points, i.e. {{0,0},{1,1},{2,2}}.
The first part of this question is: Given a set of line segments specified by 2 points, how do you reduce this set to have a set with the minimum amount of duplicate points. Consider this made up example:
lines = {
{{0,0}, {1,1}},
{{3,3}, {2,2}},
{{2,2}, {1,1}},
{{1,1}, {0.5,0.5}},
{{0,1}, {0,2}},
{{2,3}, {0,1}}
}
What I want is a function say REDUCE that gives me the following output:
R = {
{{0,0}, {1,1}, {2,2}, {3,3}},
{{1,1}, {0.5,0.5}},
{{2,1}, {0,1}, {0,2}}
}
The only duplicate we need is {1,1}. The way I did this was as follows: I put the first line in R Then I looked at the next line in lines and noticed that no end point matches an endpoint in the lines of R so I added this new line to R. The next line in lines is {{2,2},{1,1}}, the endpoint {1,1} matches the first line in R so I appended {2,2} to line in R. Now I add {{1,1}, {0.5,0.5}} to R and I also add {{0,1}, {0,2}}. Since the last line in lines has an endpoint that matches one in R I appended it and so we have {{2,1}, {0,1}, {0,2}}. Finally I look at all the lines in R and see if any of the endpoints match, in this case the line {{3,3}, {2,2}} matches the right endpoint of the first line in R so I append {3,3} thus eliminating the need for {2,2}.
This may not be the best way to do it, in the sense that it may not give you the best reduction. In any case, assuming that we have this reduction function then we can check if we need all the points to describe a line. This can be done as follows:
If we have more than 3 points describing the line, check if the first 3 points are collinear, if they are, remove the middle one and do the check on the set of the 2 endpoints and a new point. If they are not collinear then shift by one point and check the next 3 points.
The reason I'm asking this question is because I want to reduce the amount of points needed to describe a 2D figure. Try the following:
g1 = ListPlot3D[
{{0, -1, 0}, {0, 1, 0}, {-1, 0, 1}, {1, 0, 1}, {-1, 1, 1}},
Mesh -> {2, 2},
Boxed -> False,
Axes -> False,
ViewPoint -> {2, -2, 1},
ViewVertical -> {0, 0, 1}
]
The following Mathematica 8 function changes a 3D object into a list of lines (a line is a list of 2 points) that describe the wire frame of the object:
G3TOG2INFO[g_] := Module[{obj, opt},
obj = ImportString[ExportString[g, "PDF", Background -> None], "PDF"][[1]];
opt = Options[obj];
obj = Cases[obj, _JoinedCurve, \[Infinity]];
obj = Map[#[[2]][[1]] &, obj];
{obj, opt}
]
Note that in Mathematica 7 we have to substitude _JoinedCurve by _Line. Applying the function on g1 we obtain
{lines, opt} = G3TOG2INFO[g1];
Row[{Graphics[Map[Line[#] &, lines], opt], Length#lines}]
There are 90 line segments in there but we only need 12 (If I didn't make any mistake on the counting of straight lines).
So there you have the challenge. How do we manipulate lines to have minimum amount of information needed to describe the figure.
Step 1 is to find if the lines are on the same projection. This is true if the slope of the first line equals the slope of the constructed line segment from the second-last point of the first line to the second point of the second line.
I don't have Mathematica on my work machine so I can't test this out (there might be syntax errors), but something like the following should work:
(( #2[[2,2]]-#1[[-2,2]])/(#2[[2,1]]-#1[[-2,1]])) ==
(( #1[[-1,2]]-#1[[-2,2]])/(#1[[-1,1]]-#1[[-2,1]])) &
### (Transpose[{Most[lines],Rest[lines]}])
Essentialy all this does is test that "rise over run" for the first line equals "rise over run" for the joined line segment.
I am assuming that :lines: is not a list of JoinedCurve elements, but a simple list of n*2 lists of points. I am also assuming that the pairs of points defining each line segment are in a canonical order with the points in ascending order in x-direction. That is, the value of first element of the first point is lower than the first element of the second point. If not, sort them first.
Step 2 is actually joining the points. This applies the test in Step 1 and then replaces the two lines with a single joined line. You could wrap this in FixedPoint to join all the lines that are in the same projection.
If[(( #2[[2,2]]-#1[[-2,2]])/(#2[[2,1]]-#1[[-2,1]])) ==
(( #1[[-1,2]]-#1[[-2,2]])/(#1[[-1,1]]-#1[[-2,1]])), {#1[[-2]],#2[[2]]}] &
### (Transpose[{Most[lines],Rest[lines]}])
This all assumes that the pairs of lines you want to compare are adjacent in the list. If they could be any of the lines in your collection, then you first need to generate a list of all possible pairs of lines to be compared, e.g. using Tuples[listOfLines, {2}], instead of the Transpose function above.
Ok, putting this all together:
f = If[(( #2[[2,2]]-#1[[-2,2]])/(#2[[2,1]]-#1[[-2,1]])) ==
(( #1[[-1,2]]-#1[[-2,2]])/(#1[[-1,1]]-#1[[-2,1]])), {#1[[-2]],#2[[2]]}] & ;
FixedPoint[f ### #, Tuples[Sort[listOfLines],{2}] ]
I have broken out the Step 2 test-and-replace function into a named pure function so that the #s don't get confused.
In case this is still interesting, here is a different implementation:
ClearAll[collinearQ]
collinearQ[{{{x1_, y1_}, {x2_, y2_}}, {{x3_, y3_}, {x4_, y4_}}}] := (
(y1 - y2)*(x1 - x3) == (y1 - y3)*(x1 - x2)) && (y1 - y2)*(x1 - x4) ==
(y1 - y4)*(x1 - x2)
ClearAll[removeExtraPts];
removeExtraPts[{{{x1_, y1_}, {x2_, y2_}}, {{x3_, y3_}, {x4_, y4_}}}] :=
If[collinearQ[{{{x1, y1}, {x2, y2}}, {{x3, y3}, {x4, y4}}}],{First##, Last##} &#
SortBy[{{x1, y1}, {x2, y2}, {x3, y3}, {x4, y4}}, #[[1]] &],
{{{x1, y1}, {x2, y2}}, {{x3, y3}, {x4, y4}}}]
so that if lines={{{0, 0}, {1, 2}}, {{1, 1}, {2, 2}}} then it returns {{{0, 0}, {1, 2}}, {{1, 1}, {2, 2}}} while if lines2 = {{{0, 0}, {1, 2}}, {{1, 1}, {2, 2}}} then removeExtraPts[lines2] gives {{0, 0}, {2, 2}}.
This works for vertical lines, horizontal lines etc (there's no danger of dividing by zero).
If what you have is a list of lines, you can produce all distinct pairings between them thus:
ClearAll[permsnodupsv2]
permsnodupsv2 = Last#Last#
Reap[Do[Sow[{#[[i]], #[[j]]}], {i, 1, Length## - 1}, {j, i + 1,
Length##}]] &;
(you can do it functionally the way I described here but I find this easier to understand this version at a glance). For example,
lines = {l1, l2, l3, l4, l5, l6, l7, l8, l9};
permsnodups[lines]
(*
---> {{l1, l2}, {l1, l3}, {l1, l4}, {l1, l5}, {l1, l6}, {l1, l7}, {l1, l8},
{l1, l9}, {l2, l3}, {l2, l4}, {l2, l5}, {l2, l6}, {l2, l7},
{l2, l8}, {l2, l9}, {l3, l4}, {l3, l5}, {l3, l6}, {l3,l7},
{l3, l8}, {l3, l9}, {l4, l5}, {l4, l6}, {l4, l7}, {l4, l8},
{l4, l9}, {l5, l6}, {l5, l7}, {l5, l8}, {l5, l9}, {l6, l7},
{l6, l8}, {l6, l9}, {l7, l8}, {l7, l9}, {l8, l9}}
*)
and if l1={{pt1,pt2},{pt3,pt4}} and so on, you can simply map removeExtraPts over this, flatten the result (using something like Flatten[#,1]&, but the exact format depends on your input structure) and repeat until it stops changing (as #Verbeia said, you may use FixedPoint to make it stop once it no longer changes). This should join all the lines up.
Related
I'm looking for a fast implementation for the following, I'll call it Position2D for lack of a better term:
Position2D[ matrix, sub_matrix ]
which finds the locations of sub_matrix inside matrix and returns the upper left and lower right row/column of a match.
For example, this:
Position2D[{
{0, 1, 2, 3},
{1, 2, 3, 4},
{2, 3, 4, 5},
{3, 4, 5, 6}
}, {
{2, 3},
{3, 4}
}]
should return this:
{
{{1, 3}, {2, 4}},
{{2, 2}, {3, 3}},
{{3, 1}, {4, 2}}
}
It should be fast enough to work quickly on 3000x2000 matrices with 100x100 sub-matrices. For simplicity, it is enough to only consider integer matrices.
Algorithm
The following code is based on an efficient custom position function to find positions of (possibly overlapping) integer sequences in a large integer list. The main idea is that we can first try to eficiently find the positions where the first row of the sub-matrix is in the Flatten-ed large matrix, and then filter those, extracting full sub-matrices and comparing to the sub-matrix of interest. This will be efficient for most cases except very pathological ones (those, for which this procedure would generate a huge number of potential position candidates, while the true number of entries of the sub-matrix would be much smaller. But such cases seem rather unlikely generally, and then, further improvements to this simple scheme can be made).
For large matrices, the proposed solution will be about 15-25 times faster than the solution of #Szabolcs when a compiled version of sequence positions function is used, and 3-5 times faster for the top-level implementation of sequence positions - finding function. The actual speedup depends on matrix sizes, it is more for larger matrices. The code and benchmarks are below.
Code
A generally efficient function for finding positions of a sub-list (sequence)
These helper functions are due to Norbert Pozar and taken from this Mathgroup thread. They are used to efficiently find starting positions of an integer sequence in a larger list (see the mentioned post for details).
Clear[seqPos];
fdz[v_] := Rest#DeleteDuplicates#Prepend[v, 0];
seqPos[list_List, seq_List] :=
Fold[
fdz[#1 (1 - Unitize[list[[#1]] - #2])] + 1 &,
fdz[Range[Length[list] - Length[seq] + 1] *
(1 - Unitize[list[[;; -Length[seq]]] - seq[[1]]])] + 1,
Rest#seq
] - Length[seq];
Example of use:
In[71]:= seqPos[{1,2,3,2,3,2,3,4},{2,3,2}]
Out[71]= {2,4}
A faster position-finding function for integers
However fast seqPos might be, it is still the major bottleneck in my solution. Here is a compiled-to-C version of this, which gives another 5x performance boost to my code:
seqposC =
Compile[{{list, _Integer, 1}, {seq, _Integer, 1}},
Module[{i = 1, j = 1, res = Table[0, {Length[list]}], ctr = 0},
For[i = 1, i <= Length[list], i++,
If[list[[i]] == seq[[1]],
While[j < Length[seq] && i + j <= Length[list] &&
list[[i + j]] == seq[[j + 1]],
j++
];
If[j == Length[seq], res[[++ctr]] = i];
j = 1;
]
];
Take[res, ctr]
], CompilationTarget -> "C", RuntimeOptions -> "Speed"]
Example of use:
In[72]:= seqposC[{1, 2, 3, 2, 3, 2, 3, 4}, {2, 3, 2}]
Out[72]= {2, 4}
The benchmarks below have been redone with this function (also the code for main function is slightly modified )
Main function
This is the main function. It finds positions of the first row in a matrix, and then filters them, extracting the sub-matrices at these positions and testing against the full sub-matrix of interest:
Clear[Position2D];
Position2D[m_, what_,seqposF_:Automatic] :=
Module[{posFlat, pos2D,sp = If[seqposF === Automatic,seqposC,seqposF]},
With[{dm = Dimensions[m], dwr = Reverse#Dimensions[what]},
posFlat = sp[Flatten#m, First#what];
pos2D =
Pick[Transpose[#], Total[Clip[Reverse#dm - # - dwr + 2, {0, 1}]],2] &#
{Mod[posFlat, #, 1], IntegerPart[posFlat/#] + 1} &#Last[dm];
Transpose[{#, Transpose[Transpose[#] + dwr - 1]}] &#
Select[pos2D,
m[[Last## ;; Last## + Last#dwr - 1,
First## ;; First## + First#dwr - 1]] == what &
]
]
];
For integer lists, the faster compiled subsequence position-finding function seqposC can be used (this is a default). For generic lists, one can supply e.g. seqPos, as a third argument.
How it works
We will use a simple example to dissect the code and explain its inner workings. This defines our test matrix and sub-matrix:
m = {{0, 1, 2, 3}, {1, 2, 3, 4}, {2, 3, 4, 5}};
what = {{2, 3}, {3, 4}};
This computes the dimensions of the above (it is more convenient to work with reversed dimensions for a sub-matrix):
In[78]:=
dm=Dimensions[m]
dwr=Reverse#Dimensions[what]
Out[78]= {3,4}
Out[79]= {2,2}
This finds a list of starting positions of the first row ({2,3} here) in the Flattened main matrix. These positions are at the same time "flat" candidate positions of the top left corner of the sub-matrix:
In[77]:= posFlat = seqPos[Flatten#m, First#what]
Out[77]= {3, 6, 9}
This will reconstruct the 2D "candidate" positions of the top left corner of a sub-matrix in a full matrix, using the dimensions of the main matrix:
In[83]:= posInterm = Transpose#{Mod[posFlat,#,1],IntegerPart[posFlat/#]+1}&#Last[dm]
Out[83]= {{3,1},{2,2},{1,3}}
We can then try using Select to filter them out, extracting the full sub-matrix and comparing to what, but we'll run into a problem here:
In[84]:=
Select[posInterm,
m[[Last##;;Last##+Last#dwr-1,First##;;First##+First#dwr-1]]==what&]
During evaluation of In[84]:= Part::take: Cannot take positions 3 through 4
in {{0,1,2,3},{1,2,3,4},{2,3,4,5}}. >>
Out[84]= {{3,1},{2,2}}
Apart from the error message, the result is correct. The error message itself is due to the fact that for the last position ({1,3}) in the list, the bottom right corner of the sub-matrix will be outside the main matrix. We could of course use Quiet to simply ignore the error messages, but that's a bad style. So, we will first filter those cases out, and this is what the line Pick[Transpose[#], Total[Clip[Reverse#dm - # - dwr + 2, {0, 1}]], 2] &# is for. Specifically, consider
In[90]:=
Reverse#dm - # - dwr + 2 &#{Mod[posFlat, #, 1],IntegerPart[posFlat/#] + 1} &#Last[dm]
Out[90]= {{1,2,3},{2,1,0}}
The coordinates of the top left corners should stay within a difference of dimensions of matrix and a sub-matrix. The above sub-lists were made of x and y coordiantes of top - left corners. I added 2 to make all valid results strictly positive. We have to pick only coordiantes at those positions in Transpose#{Mod[posFlat, #, 1], IntegerPart[posFlat/#] + 1} &#Last[dm] ( which is posInterm), at which both sub-lists above have strictly positive numbers. I used Total[Clip[...,{0,1}]] to recast it into picking only at those positions at which this second list has 2 (Clip converts all positive integers to 1, and Total sums numbers in 2 sublists. The only way to get 2 is when numbers in both sublists are positive).
So, we have:
In[92]:=
pos2D=Pick[Transpose[#],Total[Clip[Reverse#dm-#-dwr+2,{0,1}]],2]&#
{Mod[posFlat,#,1],IntegerPart[posFlat/#]+1}&#Last[dm]
Out[92]= {{3,1},{2,2}}
After the list of 2D positions has been filtered, so that no structurally invalid positions are present, we can use Select to extract the full sub-matrices and test against the sub-matrix of interest:
In[93]:=
finalPos =
Select[pos2D,m[[Last##;;Last##+Last#dwr-1,First##;;First##+First#dwr-1]]==what&]
Out[93]= {{3,1},{2,2}}
In this case, both positions are genuine. The final thing to do is to reconstruct the positions of the bottom - right corners of the submatrix and add them to the top-left corner positions. This is done by this line:
In[94]:= Transpose[{#,Transpose[Transpose[#]+dwr-1]}]&#finalPos
Out[94]= {{{3,1},{4,2}},{{2,2},{3,3}}}
I could have used Map, but for a large list of positions, the above code would be more efficient.
Example and benchmarks
The original example:
In[216]:= Position2D[{{0,1,2,3},{1,2,3,4},{2,3,4,5},{3,4,5,6}},{{2,3},{3,4}}]
Out[216]= {{{3,1},{4,2}},{{2,2},{3,3}},{{1,3},{2,4}}}
Note that my index conventions are reversed w.r.t. #Szabolcs' solution.
Benchmarks for large matrices and sub-matrices
Here is a power test:
nmat = 1000;
(* generate a large random matrix and a sub-matrix *)
largeTestMat = RandomInteger[100, {2000, 3000}];
what = RandomInteger[10, {100, 100}];
(* generate upper left random positions where to insert the submatrix *)
rposx = RandomInteger[{1,Last#Dimensions[largeTestMat] - Last#Dimensions[what] + 1}, nmat];
rposy = RandomInteger[{1,First#Dimensions[largeTestMat] - First#Dimensions[what] + 1},nmat];
(* insert the submatrix nmat times *)
With[{dwr = Reverse#Dimensions[what]},
Do[largeTestMat[[Last#p ;; Last#p + Last#dwr - 1,
First#p ;; First#p + First#dwr - 1]] = what,
{p,Transpose[{rposx, rposy}]}]]
Now, we test:
In[358]:= (ps1 = position2D[largeTestMat,what])//Short//Timing
Out[358]= {1.39,{{{1,2461},{100,2560}},<<151>>,{{1900,42},{1999,141}}}}
In[359]:= (ps2 = Position2D[largeTestMat,what])//Short//Timing
Out[359]= {0.062,{{{2461,1},{2560,100}},<<151>>,{{42,1900},{141,1999}}}}
(the actual number of sub-matrices is smaller than the number we try to generate, since many of them overlap and "destroy" the previously inserted ones - this is so because the sub-matrix size is a sizable fraction of the matrix size in our benchmark).
To compare, we should reverse the x-y indices in one of the solutions (level 3), and sort both lists, since positions may have been obtained in different order:
In[360]:= Sort#ps1===Sort[Reverse[ps2,{3}]]
Out[360]= True
I do not exclude a possibility that further optimizations are possible.
This is my implementation:
position2D[m_, k_] :=
Module[{di, dj, extractSubmatrix, pos},
{di, dj} = Dimensions[k] - 1;
extractSubmatrix[{i_, j_}] := m[[i ;; i + di, j ;; j + dj]];
pos = Position[ListCorrelate[k, m], ListCorrelate[k, k][[1, 1]]];
pos = Select[pos, extractSubmatrix[#] == k &];
{#, # + {di, dj}} & /# pos
]
It uses ListCorrelate to get a list of potential positions, then filters those that actually match. It's probably faster on packed real matrices.
As per Leonid's suggestion here's my solution. I know it isn't very efficient (it's about 600 times slower than Leonid's when I timed it) but it's very short, rememberable, and a nice illustration of a rarely used function, PartitionMap. It's from the Developer package, so it needs a Needs["Developer`"] call first.
Given that, Position2D can be defined as:
Position2D[m_, k_] := Position[PartitionMap[k == # &, m, Dimensions[k], {1, 1}], True]
This only gives the upper-left coordinates. I feel the lower-right coordinates are really redundant, since the dimensions of the sub-matrix are known, but if the need arises one can add those to the output by prepending {#, Dimensions[k] + # - {1, 1}} & /# to the above definition.
How about something like
Position2D[bigMat_?MatrixQ, smallMat_?MatrixQ] :=
Module[{pos, sdim = Dimensions[smallMat] - 1},
pos = Position[bigMat, smallMat[[1, 1]]];
Quiet[Select[pos, (MatchQ[
bigMat[[Sequence##Thread[Span[#, # + sdim]]]], smallMat] &)],
Part::take]]
which will return the top left-hand positions of the submatrices.
Example:
Position2D[{{0, 1, 2, 3}, {1, 2, 3, 4}, {2, 3, 4, 5}, {3, 5, 5, 6}},
{{2, 3}, {3, _}}]
(* Returns: {{1, 3}, {2, 2}, {3, 1}} *)
And to search a 1000x1000 matrix, it takes about 2 seconds on my old machine
SeedRandom[1]
big = RandomInteger[{0, 10}, {1000, 1000}];
Position2D[big, {{1, 1, _}, {1, 1, 1}}] // Timing
(* {1.88012, {{155, 91}, {295, 709}, {685, 661},
{818, 568}, {924, 45}, {981, 613}}} *)
When I type the following
lis = {1, 2};
pos = Position[lis, 1];
result = Extract[lis, pos]
the result is always a list.
{1}
another example
lis = {{1}, {2}};
pos = Position[lis, {1}];
result = Extract[lis, pos]
{{1}}
Mathematica always adds an extra {} in the result. What would be the best way to remove this extra {}, other than applying Flatten[result,1] each time? And is there a case where removing these extra {} can cause a problem?
You probably realise this, but Position and Extract return lists because the requested values may be found in more than one position. So in general, removing the outer brackets doesn't make sense.
If you are sure the result is a singleton list, using Flatten would destroy information if the element is itself a list. For example,
Position[{{1}},1]
gives a list whose sole element is a list. So in this case, using Extract would make more sense.
Even so, there are many situations where Mathematica treats {x} very differently to x, as in
Position[1,1]
Position[{1},1]
which have very different results. So whether you can remove the outer braces from a one-member list depends on what you plan to do with it.
If I understood your question correctly, you are asking why
lis = {{1}, {2}};
pos = Position[lis, {1}];
result = Extract[lis, pos]
returns
{{1}}
rather than
{1}
The answer is, I think, simple: Position[lis,{1}] gives the position at which {1}, not 1 appears in lis; when you then go and look at that position using Extract, you do indeed get {1} which is then wrapped in a list (which is exactly what happened in the first case, when you looked for 1 and obtained {1} as a result; just replace 1 by {1}, because that is now what you are asking for.
To see this more clearly, try
lis = {f[1], f[2]};
pos = Position[lis, f[1]];
result = Extract[lis, pos]
which gives
{f[1]}
The point here is that List in {1} (which is the same as List[1] if you check look at the FullForm) before was just a head, like f here. Should mathematica have remove f here? If not, then why should it have removed the innermost List earlier?
And finally, if you really want to remove the inner {} in your second example, try
lis = {{1}, {2, {1}}};
pos = Position[lis, {1}];
result = Extract[lis, pos, #[[1]] &]
giving
{1, 1}
EDIT: I am becoming puzzled with some of the answers here. If I do
lis = {{1}, {2, {1, 2, {1}}}};
pos = Position[lis, 1];
result = Extract[lis, pos]
then I get
{1, 1, 1}
in result. I only get the extra brackets when I actually obtain the positions of {1} in pos instead of the positions of 1 (and then when I look at those positions, I find {1}). Or am I missing something in your question?
Short answer: You should probably use First#Position[...]
Long answer:
Lets separate the question to 2 parts:
Why do you have the extra {} in the result for Position?
i.e. why:
lis = {1, 2};
Position[lis, 1]
returns {{1}}?
This is in order to work consistently with n-dimensional list, that may have the requested values in more than one position. For example:
lis = {{1, 2, 3}, {1, 5, 6}, {1, 2, 1}};
Position[lis, 1]
returns {{1, 1}, {2, 1}, {3, 1}, {3, 3}}
which is a list of the coordinates the result is found in.
So in your case:
lis = {1, 2};
Position[lis, 1]
return {{1}}, as in: we found your requested value one time, in the coordinate-set {1}.
Now, a lot of times Mathematica assume that there might be a list of solutions (for example, in Solve), but the user know that he expect only one. A suitable code to this in your case will be First#Position[...]. this will return the first (and, assumebly, only) element in the list of positions --
So, if you are sure that the element you are searching for exist only once in the list and want to know where, use this way.
Why do you have the extra {} in the result for Extract?
Extract can work in two different ways.
If I'm doing Extract[{{a, b, c}, {d, e, f}, {g, e, h}}, {1, 2}]
I will get b, so extract with a 1 dimensional list of is just choosing and returning this element. In fact, Extract[lis, {1, 2}] is equal to lis[[1, 2]]
If I'm doing Extract[{{a, b, c}, {d, e, f}, {g, e, h}}, {{1, 2}, {3, 4}}]
I will get {b, h}, so extract with a 2 dimensional list is choosing and returning a list of elements.
In your case(s), you are doing Extract[lis, {{1}}], as in: give me a list containing only the element lis[[1]]. The result is always this element in a list, which is the extra {}
Does Mathematica support hidden line removal for wire frame images? If this isn't the case, has anybody here ever come across a way to do it? Lets start with this:
Plot3D[Sin[x+y^2], {x, -3, 3}, {y, -2, 2}, Boxed -> False]
To create a wire frame we can do:
Plot3D[Sin[x+y^2], {x, -3, 3}, {y, -2, 2}, Boxed -> False, PlotStyle -> None]
One thing we can do to achieve the effect is to color the all the surfaces white. This however, is undesirable. The reason is because if we export this hidden line wire frame model to pdf we will have all of those white polygons that Mathematica uses to render the image. I want to be able to obtain a wire frame with hidden line removal in pdf and/or eps format.
UPDATE:
I have posted a solution to this problem. The problem is that the code runs very slow. In its current state it is unable to generate the wireframe for the image in this question. Feel free to play with my code. I added a link to it at the end of my post. You can also find the code in this link
Here I present a solution. First I will show how to use the function that generates the wire frame, then I will proceed to explain in detail the rest of the functions that compose the algorithm.
wireFrame
wireFrame[g_] := Module[{figInfo, opt, pts},
{figInfo, opt} = G3ToG2Info[g];
pts = getHiddenLines[figInfo];
Graphics[Map[setPoints[#] &, getFrame[figInfo, pts]], opt]
]
The input of this function is a Graphics3D object preferably with no axes.
fig = ListPlot3D[
{{0, -1, 0}, {0, 1, 0}, {-1, 0, 1}, {1, 0, 1}, {-1, 1, 1}},
Mesh -> {10, 10},
Boxed -> False,
Axes -> False,
ViewPoint -> {2, -2, 1},
ViewVertical -> {0, 0, 1},
MeshStyle -> Directive[RGBColor[0, 0.5, 0, 0.5]],
BoundaryStyle -> Directive[RGBColor[1, 0.5, 0, 0.5]]
]
Now we apply the function wireFrame.
wireFrame[fig]
As you can see wireFrame obtained most of the lines and its colors. There is a green line that was not included in the wireframe. This is most likely due to my threshold settings.
Before I proceed to explain the details of the functions G3ToG2Info, getHiddenLines, getFrame and setPoints I will show you why wire frames with hidden line removal can be useful.
The image shown above is a screenshot of a pdf file generated by using the technique described in rasters in 3D graphics combined with the wire frame generated here. This can be advantageous in various ways. There is no need to keep the information for the triangles to show a colorful surface. Instead we show a raster image of the surface. All of the lines are very smooth, with the exception of the boundaries of the raster plot not covered by lines. We also have a reduction of file size. In this case the pdf file size reduced from 1.9mb to 78kb using the combination of the raster plot and the wire frame. It takes less time to display in the pdf viewer and the image quality is great.
Mathematica does a pretty good job at exporting 3D images to pdf files. When we import the pdf files we obtain a Graphics object composed of line segments and triangles. In some cases this objects overlap and thus we have hidden lines. To make a wire frame model with no surfaces we first need to remove this overlap and then remove the polygons. I will start by describing how to obtain the information from a Graphics3D image.
G3ToG2Info
getPoints[obj_] := Switch[Head[obj],
Polygon, obj[[1]],
JoinedCurve, obj[[2]][[1]],
RGBColor, {Table[obj[[i]], {i, 1, 3}]}
];
setPoints[obj_] := Switch[Length#obj,
3, Polygon[obj],
2, Line[obj],
1, RGBColor[obj[[1]]]
];
G3ToG2Info[g_] := Module[{obj, opt},
obj = ImportString[ExportString[g, "PDF", Background -> None], "PDF"][[1]];
opt = Options[obj];
obj = Flatten[First[obj /. Style[expr_, opts___] :> {opts, expr}], 2];
obj = Cases[obj, _Polygon | _JoinedCurve | _RGBColor, Infinity];
obj = Map[getPoints[#] &, obj];
{obj, opt}
]
This code is for Mathematica 8 in version 7 you would replace JoinedCurve in the function getPoints by Line. The function getPoints assumes that you are giving a primitive Graphics object. It will see what type of object it recieves and then extract the information it needs from it. If it is a polygon it gets a list of 3 points, for a line it obtains a list of 2 points and if it is a color then it gets a list of a single list containing 3 points. This has been done like this in order to maintain consistency with the lists.
The function setPoints does the reverse of getPoints. You input a list of points and it will determine if it should return a polygon, a line or a color.
To obtain a list of triangles, lines and colors we use G3ToG2Info. This function will use
ExportString and ImportString to obtain a Graphics object from the Graphics3D version. This info is store in obj. There is some clean up that we need to perform, first we get the options of the obj. This part is necessary because it may contain the PlotRange of the image. Then we obtain all the Polygon, JoinedCurve and RGBColor objects as described in obtaining graphics primitives and directives. Finally we apply the function getPoints on all of these objects to get a list of triangles, lines and colors. This part covers the line {figInfo, opt} = G3ToG2Info[g].
getHiddenLines
We want to be able to know what part of a line will not be displayed. To do this we need to know point of intersection between two line segments. The algorithm I'm using to find the intersection can be found here.
lineInt[L_, M_, EPS_: 10^-6] := Module[
{x21, y21, x43, y43, x13, y13, numL, numM, den},
{x21, y21} = L[[2]] - L[[1]];
{x43, y43} = M[[2]] - M[[1]];
{x13, y13} = L[[1]] - M[[1]];
den = y43*x21 - x43*y21;
If[den*den < EPS, Return[-Infinity]];
numL = (x43*y13 - y43*x13)/den;
numM = (x21*y13 - y21*x13)/den;
If[numM < 0 || numM > 1, Return[-Infinity], Return[numL]];
]
lineInt assumes that the line L and M do not coincide. It will return -Infinity if the lines are parallel or if the line containing the segment L does not cross the line segment M. If the line containing L intersects the line segment M then it returns a scalar. Suppose this scalar is u, then the point of intersection is L[[1]] + u (L[[2]]-L[[1]]). Notice that it is perfectly fine for u to be any real number. You can play with this manipulate function to test how lineInt works.
Manipulate[
Grid[{{
Graphics[{
Line[{p1, p2}, VertexColors -> {Red, Red}],
Line[{p3, p4}]
},
PlotRange -> 3, Axes -> True],
lineInt[{p1, p2}, {p3, p4}]
}}],
{{p1, {-1, 1}}, Locator, Appearance -> "L1"},
{{p2, {2, 1}}, Locator, Appearance -> "L2"},
{{p3, {1, -1}}, Locator, Appearance -> "M1"},
{{p4, {1, 2}}, Locator, Appearance -> "M2"}
]
Now that we know how to far we have to travel from L[[1]] to the line segment M we can find out what portion of a line segment lies within a triangle.
lineInTri[L_, T_] := Module[{res},
If[Length#DeleteDuplicates[Flatten[{T, L}, 1], SquaredEuclideanDistance[#1, #2] < 10^-6 &] == 3, Return[{}]];
res = Sort[Map[lineInt[L, #] &, {{T[[1]], T[[2]]}, {T[[2]], T[[3]]}, {T[[3]], T[[1]]} }]];
If[res[[3]] == Infinity || res == {-Infinity, -Infinity, -Infinity}, Return[{}]];
res = DeleteDuplicates[Cases[res, _Real | _Integer | _Rational], Chop[#1 - #2] == 0 &];
If[Length#res == 1, Return[{}]];
If[(Chop[res[[1]]] == 0 && res[[2]] > 1) || (Chop[res[[2]] - 1] == 0 && res[[1]] < 0), Return[{0, 1}]];
If[(Chop[res[[2]]] == 0 && res[[1]] < 0) || (Chop[res[[1]] - 1] == 0 && res[[2]] > 1), Return[{}]];
res = {Max[res[[1]], 0], Min[res[[2]], 1]};
If[res[[1]] > 1 || res[[1]] < 0 || res[[2]] > 1 || res[[2]] < 0, Return[{}], Return[res]];
]
This function returns the the portion of the line L that needs to be deleted. For instance, if it returns {.5, 1} this means that you will delete 50 percent of the line, starting from half the segment to the ending point of the segment. If L = {A, B} and the function returns {u, v} then this means that the line segment {A+(B-A)u, A+(B-A)v} is the section of the line that its contained in the triangle T.
When implementing lineInTri you need to be careful that the line L is not one of the edges of T, if this is the case then the line does not lie inside the triangle. This is where rounding erros can be bad. When Mathematica exports the image sometimes a line lies on the edge of the triangle but these coordinates differ by some amount. It is up to us to decide how close the line lies on the edge, otherwise the function will see that the line lies almost completely inside the triangle. This is the reason of the first line in the function. To see if a line lies on an edge of a triangle we can list all the points of the triangle and the line, and delete all the duplicates. You need to specify what a duplicate is in this case. In the end, if we end up with a list of 3 points this means that a line lies on an edge. The next part is a little complicated. What we do is check for the intersection of the line L with each edge of the triangle T and store this the results in a list. Next we sort the list and find out what section, if any, of the line lies in the triangle. Try to make sense out of it by playing with this, some of the tests include checking if an endpoint of the line is a vertex of the triangle, if the line is completely inside the triangle, partly inside or completely outside.
Manipulate[
Grid[{{
Graphics[{
RGBColor[0, .5, 0, .5], Polygon[{p3, p4, p5}],
Line[{p1, p2}, VertexColors -> {Red, Red}]
},
PlotRange -> 3, Axes -> True],
lineInTri[{p1, p2}, {p3, p4, p5}]
}}],
{{p1, {-1, -2}}, Locator, Appearance -> "L1"},
{{p2, {0, 0}}, Locator, Appearance -> "L2"},
{{p3, {-2, -2}}, Locator, Appearance -> "T1"},
{{p4, {2, -2}}, Locator, Appearance -> "T2"},
{{p5, {-1, 1}}, Locator, Appearance -> "T3"}
]
lineInTri will be used to see what portion of the line will not be drawn. This line will most likely be covered by many triangles. For this reason, we need to keep a list of all the portions of each line that will not be drawn. These lists will not have an order. All we know is that this lists are one dimensional segments. Each one consisting of numbers in the [0,1] interval. I'm not aware of a union function for one dimensional segments so here is my implementation.
union[obj_] := Module[{p, tmp, dummy, newp, EPS = 10^-3},
p = Sort[obj];
tmp = p[[1]];
If[tmp[[1]] < EPS, tmp[[1]] = 0];
{dummy, newp} = Reap[
Do[
If[(p[[i, 1]] - tmp[[2]]) > EPS && (tmp[[2]] - tmp[[1]]) > EPS,
Sow[tmp]; tmp = p[[i]],
tmp[[2]] = Max[p[[i, 2]], tmp[[2]]]
];
, {i, 2, Length#p}
];
If[1 - tmp[[2]] < EPS, tmp[[2]] = 1];
If[(tmp[[2]] - tmp[[1]]) > EPS, Sow[tmp]];
];
If[Length#newp == 0, {}, newp[[1]]]
]
This function would be shorter but here I have included some if statements to check if a number is close to zero or one. If one number is EPS apart from zero then we make this number zero, the same applies for one. Another aspect that I'm covering here is that if there is a relatively small portion of the segment to be displayed then it is most likely that it needs to be deleted. For instance if we have {{0,.5}, {.500000000001}} this means that we need to draw {{.5, .500000000001}}. But this segment is very small to be even noticed specially in a large line segment, for all we know those two numbers are the same. All of this things need to be taken into account when implementing union.
Now we are ready to see what needs to be deleted from a line segment. The next requires the list of objects generated from G3ToG2Info, an object from this list and an index.
getSections[L_, obj_, start_ ] := Module[{dummy, p, seg},
{dummy, p} = Reap[
Do[
If[Length#obj[[i]] == 3,
seg = lineInTri[L, obj[[i]]];
If[Length#seg != 0, Sow[seg]];
]
, {i, start, Length#obj}
]
];
If[Length#p == 0, Return[{}], Return[union[First#p]]];
]
getSections returns a list containing the portions that need to be deleted from L. We know that obj is the list of triangles, lines and colors, we know that objects in the list with a higher index will be drawn on top of ones with lower index. For this reason we need the index start. This is the index we will start looking for triangles in obj. Once we find a triangle we will obtain the portion of the segment that lies in the triangle using the function lineInTri. At the end we will end up with a list of sections which we can combine by using union.
Finally, we get to getHiddenLines. All this requires is to look at each object in the list returned by G3ToG2Info and apply the function getSections. getHiddenLines will return a list of lists. Each element is a list of sections that need to be deleted.
getHiddenLines[obj_] := Module[{pts},
pts = Table[{}, {Length#obj}];
Do[
If[Length#obj[[j]] == 2,
pts[[j]] = getSections[obj[[j]], obj, j + 1]
];
, {j, Length#obj}
];
Return[pts];
]
getFrame
If you have manage to understand the concepts up to here I'm sure you know what will be done next. If we have the list of triangles, lines and colors and the sections of the lines that need to be deleted we need to draw only the colors and the sections of the lines that are visible. First we make a complement function, this will tell us exactly what to draw.
complement[obj_] := Module[{dummy, p},
{dummy, p} = Reap[
If[obj[[1, 1]] != 0, Sow[{0, obj[[1, 1]]}]];
Do[
Sow[{obj[[i - 1, 2]], obj[[i, 1]]}]
, {i, 2, Length#obj}
];
If[obj[[-1, 2]] != 1, Sow[{obj[[-1, 2]], 1}]];
];
If[Length#p == 0, {}, Flatten# First#p]
]
Now the getFrame function
getFrame[obj_, pts_] := Module[{dummy, lines, L, u, d},
{dummy, lines} = Reap[
Do[
L = obj[[i]];
If[Length#L == 2,
If[Length#pts[[i]] == 0, Sow[L]; Continue[]];
u = complement[pts[[i]]];
If[Length#u > 0,
Do[
d = L[[2]] - L[[1]];
Sow[{L[[1]] + u[[j - 1]] d, L[[1]] + u[[j]] d}]
, {j, 2, Length#u, 2 }]
];
];
If[Length#L == 1, Sow[L]];
, {i, Length#obj}]
];
First#lines
]
Final words
I'm somewhat happy with the results of the algorithm. What I do not like is the execution speed. I have written this as I would in C/C++/java using loops. I tried my best to use Reap and Sow to create growing lists instead of using the function Append. Regardless of all of this I still had to use loops. It should be noted that the wire frame picture posted here took 63 seconds to generate. I tried doing a wire frame for the picture in the question but this 3D object contains about 32000 objects. It was taking about 13 seconds to compute the portions that need to be displayed for a line. If we assume that we have 32000 lines and it takes 13 seconds to do all the computations that will be about 116 hours of computational time.
I'm sure this time can be reduced if we use the function Compile on all of the routines and maybe finding a way not to use the Do loops. Can I get some help here Stack Overflow?
For your convinience I have uploaded the code to the web. You can find it here. If you can apply a modified version of this code to the plot in the question and show the wire frame I will mark your solution as the answer to this post.
Best,
J Manuel Lopez
This isn't right, but somewhat interesting:
Plot3D[Sin[x + y^2], {x, -3, 3}, {y, -2, 2}, Boxed -> False,
PlotStyle -> {EdgeForm[None], FaceForm[Red, None]}, Mesh -> False]
With a FaceForm of None, the polygon isn't rendered. I'm not sure there's a way to do this with the Mesh lines.
When plotting a function using Plot, I would like to obtain the set of data points plotted by the Plot command.
For instance, how can I obtain the list of points {t,f} Plot uses in the following simple example?
f = Sin[t]
Plot[f, {t, 0, 10}]
I tried using a method of appending values to a list, shown on page 4 of Numerical1.ps (Numerical Computation in Mathematica) by Jerry B. Keiper, http://library.wolfram.com/infocenter/Conferences/4687/ as follows:
f = Sin[t]
flist={}
Plot[f, {t, 0, 10}, AppendTo[flist,{t,f[t]}]]
but generate error messages no matter what I try.
Any suggestions would be greatly appreciated.
f = Sin[t];
plot = Plot[f, {t, 0, 10}]
One way to extract points is as follows:
points = Cases[
Cases[InputForm[plot], Line[___],
Infinity], {_?NumericQ, _?NumericQ}, Infinity];
ListPlot to 'take a look'
ListPlot[points]
giving the following:
EDIT
Brett Champion has pointed out that InputForm is superfluous.
ListPlot#Cases[
Cases[plot, Line[___], Infinity], {_?NumericQ, _?NumericQ},
Infinity]
will work.
It is also possible to paste in the plot graphic, and this is sometimes useful. If,say, I create a ListPlot of external data and then mislay the data file (so that I only have access to the generated graphic), I may regenerate the data by selecting the graphic cell bracket,copy and paste:
ListPlot#Transpose[{Range[10], 4 Range[10]}]
points = Cases[
Cases[** Paste_Grphic _Here **, Point[___],
Infinity], {_?NumericQ, _?NumericQ}, Infinity]
Edit 2.
I should also have cross-referenced and acknowledged this very nice answer by Yaroslav Bulatov.
Edit 3
Brett Champion has not only pointed out that FullForm is superfluous, but that in cases where a GraphicsComplex is generated, applying Normal will convert the complex into primitives. This can be very useful.
For example:
lp = ListPlot[Transpose[{Range[10], Range[10]}],
Filling -> Bottom]; Cases[
Cases[Normal#lp, Point[___],
Infinity], {_?NumericQ, _?NumericQ}, Infinity]
gives (correctly)
{{1., 1.}, {2., 2.}, {3., 3.}, {4., 4.}, {5., 5.}, {6., 6.}, {7.,
7.}, {8., 8.}, {9., 9.}, {10., 10.}}
Thanks to Brett Champion.
Finally, a neater way of using the general approach given in this answer, which I found here
The OP problem, in terms of a ListPlot, may be obtained as follows:
ListPlot#Cases[g, x_Line :> First#x, Infinity]
Edit 4
Even simpler
ListPlot#Cases[plot, Line[{x__}] -> x, Infinity]
or
ListPlot#Cases[** Paste_Grphic _Here **, Line[{x__}] -> x, Infinity]
or
ListPlot#plot[[1, 1, 3, 2, 1]]
This evaluates to True
plot[[1, 1, 3, 2, 1]] == Cases[plot, Line[{x__}] -> x, Infinity]
One way is to use EvaluationMonitor option with Reap and Sow, for example
In[4]:=
(points = Reap[Plot[Sin[x],{x,0,4Pi},EvaluationMonitor:>Sow[{x,Sin[x]}]]][[2,1]])//Short
Out[4]//Short= {{2.56457*10^-7,2.56457*10^-7},<<699>>,{12.5621,-<<21>>}}
In addition to the methods mentioned in Leonid's answer and my follow-up comment, to track plotting progress of slow functions in real time to see what's happening you could do the following (using the example of this recent question):
(* CPU intensive function *)
LogNormalStableCDF[{alpha_, beta_, gamma_, sigma_, delta_}, x_] :=
Block[{u},
NExpectation[
CDF[StableDistribution[alpha, beta, gamma, sigma], (x - delta)/u],
u \[Distributed] LogNormalDistribution[Log[gamma], sigma]]]
(* real time tracking of plot process *)
res = {};
ListLinePlot[res // Sort, Mesh -> All] // Dynamic
Plot[(AppendTo[res, {x, #}]; #) &#
LogNormalStableCDF[{1.5, 1, 1, 0.5, 1}, x], {x, -4, 6},
PlotRange -> All, PlotPoints -> 10, MaxRecursion -> 4]
etc.
Here is a very efficient way to get all the data points:
{plot, {points}} = Reap # Plot[Last#Sow#{x, Sin[x]}, {x, 0, 4 Pi}]
Based on the answer of Sjoerd C. de Vries, I've now written the following code which automates a plot preview (tested on Mathematica 8):
pairs[x_, y_List]:={x, #}& /# y
pairs[x_, y_]:={x, y}
condtranspose[x:{{_List ..}..}]:=Transpose # x
condtranspose[x_]:=x
Protect[SaveData]
MonitorPlot[f_, range_, options: OptionsPattern[]]:=
Module[{data={}, plot},
Module[{tmp=#},
If[FilterRules[{options},SaveData]!={},
ReleaseHold[Hold[SaveData=condtranspose[data]]/.FilterRules[{options},SaveData]];tmp]]&#
Monitor[Plot[(data=Union[data, {pairs[range[[1]], #]}]; #)& # f, range,
Evaluate[FilterRules[{options}, Options[Plot]]]],
plot=ListLinePlot[condtranspose[data], Mesh->All,
FilterRules[{options}, Options[ListLinePlot]]];
Show[plot, Module[{yrange=Options[plot, PlotRange][[1,2,2]]},
Graphics[Line[{{range[[1]], yrange[[1]]}, {range[[1]], yrange[[2]]}}]]]]]]
SetAttributes[MonitorPlot, HoldAll]
In addition to showing the progress of the plot, it also marks the x position where it currently calculates.
The main problem is that for multiple plots, Mathematica applies the same plot style for all curves in the final plot (interestingly, it doesn't on the temporary plots).
To get the data produced into the variable dest, use the option SaveData:>dest
Just another way, possibly implementation dependent:
ListPlot#Flatten[
Plot[Tan#t, {t, 0, 10}] /. Graphics[{{___, {_, y__}}}, ___] -> {y} /. Line -> List
, 2]
Just look into structure of plot (for different type of plots there would be a little bit different structure) and use something like that:
plt = Plot[Sin[x], {x, 0, 1}];
lstpoint = plt[[1, 1, 3, 2, 1]];
Is there any way of abstracting the vertex order that GraphPlot applies to VertexCoordinate Rules from the (FullForm or InputForm) of the graphic produced by GraphPlot? I do not want to use the GraphUtilities function VertexList. I am also aware of GraphCoordinates, but both of these functions work with the graph, NOT the graphics output of GraphPlot.
For example,
gr1 = {1 -> 2, 2 -> 3, 3 -> 4, 4 -> 5, 5 -> 6, 6 -> 1};
gp1 = GraphPlot[gr1, Method -> "CircularEmbedding",
VertexLabeling -> True];
Last#(gp1 /. Graphics[Annotation[x___], ___] :> {x})
gives the following list of six coordinate pairs:
VertexCoordinateRules -> {{2., 0.866025}, {1.5, 1.73205}, {0.5,
1.73205}, {0., 0.866025}, {0.5, 1.3469*10^-10}, {1.5, 0.}}
How do I know which rule applies to which vertex, and can I be certain that this is
the same as that given by VertexList[gr1]?
For example
Needs["GraphUtilities`"];
gr2 = SparseArray#
Map[# -> 1 &, EdgeList[{2 -> 3, 3 -> 4, 4 -> 5, 5 -> 6}]];
VertexList[gr2]
gives {1, 2, 3, 4, 5}
But ....
gp2 = GraphPlot[gr2, VertexLabeling -> True,
VertexCoordinateRules ->
Thread[VertexList[gr1] ->
Last#(gp1 /. Graphics[Annotation[x___], ___] :> {x})[[2]]]];
Last#(gp2 /. Graphics[Annotation[x___], ___] :> {x})
gives SIX coordinate sets:
VertexCoordinateRules -> {{2., 0.866025}, {1.5, 1.73205}, {0.5,
1.73205}, {0., 0.866025}, {0.5, 1.3469*10^-10}, {1.5, 0.}}
How can I abstract the correct VertexList for VertexCoordinateRules for gr2, for example?
(I am aware that I can correct things by taking the VertexList after generating gr2 as follows, for example)
VertexList#
SparseArray[
Map[# -> 1 &, EdgeList[{2 -> 3, 3 -> 4, 4 -> 5, 5 -> 6}]], {6, 6}]
{1, 2, 3, 4, 5, 6}
but the information I need appears to be present in the GraphPlot graphic: how can I obtain it?
(The reason I convert the graph to an adjacency matrix it that, as pointed out by Carl Woll of Wolfram, it allows me to include an 'orphan' node, as in gp2)
With vertex labeling, one way is to get coordinates of the labels. Notice that output of GraphPlot is in GraphicsComplex where coordinates of coordinate aliases are as first label, you can get it as
points = Cases[gp1, GraphicsComplex[points_, __] :> points, Infinity] // First
Looking at FullForm you'll see that labels are in text objects, extract them as
labels = Cases[gp1, Text[___], Infinity]
The actual label seems to be two levels deep so you get
actualLabels = labels[[All, 1, 1]];
Coordinate alias is the second parameter so you get them as
coordAliases = labels[[All, 2]]
Actual coordinates were specified in GraphicsComplex, so we get them as
actualCoords = points[[coordAliases]]
There a 1-1 correspondence between list of coordinates and list of labels, so you can use Thread to return them as list of "label"->coordinate pairs.
here's a function that this all together
getLabelCoordinateMap[gp1_] :=
Module[{points, labels, actualLabels, coordAliases, actualCoords},
points =
Cases[gp1, GraphicsComplex[points_, __] :> points, Infinity] //
First;
labels = Cases[gp1, Text[___], Infinity];
actualLabels = labels[[All, 1, 1]];
coordAliases = labels[[All, 2]];
actualCoords = points[[coordAliases]];
Thread[actualLabels -> actualCoords]
];
getLabelCoordinateMap[gp1]
Not that this only works on labelled GraphPlot. For ones without labels you could try to extract from other graphics objects, but you may get different results depending on what objects you extract the mapping from because there seems to be a bug which sometimes assigns line endpoints and vertex labels to different vertices. I've reported it. The way to work around the bug is to either always use explicit vertex->coordinate specification for VertexCoordinateList, or always use "adjacency matrix" representation. Here's an example of discrepancy
graphName = {"Grid", {3, 3}};
gp1 = GraphPlot[Rule ### GraphData[graphName, "EdgeIndices"],
VertexCoordinateRules -> GraphData[graphName, "VertexCoordinates"],
VertexLabeling -> True]
gp2 = GraphPlot[GraphData[graphName, "AdjacencyMatrix"],
VertexCoordinateRules -> GraphData[graphName, "VertexCoordinates"],
VertexLabeling -> True]
BTW, as an aside, here are the utility functions I use for converting between adjacency matrix and edge rule representation
edges2mat[edges_] := Module[{a, nodes, mat, n},
(* custom flatten to allow edges be lists *)
nodes = Sequence ### edges // Union // Sort;
nodeMap = (# -> (Position[nodes, #] // Flatten // First)) & /#
nodes;
n = Length[nodes];
mat = (({#1, #2} -> 1) & ### (edges /. nodeMap)) //
SparseArray[#, {n, n}] &
];
mat2edges[mat_List] := Rule ### Position[mat, 1];
mat2edges[mat_SparseArray] :=
Rule ### (ArrayRules[mat][[All, 1]] // Most)
If you execute FullForm[gp1] you'll get a bunch of output which I won't post here. Near the start of the output you'll find a GraphicsComplex[]. This is, essentially, a list of points and then a list of uses of those points. So, for your graphic gp1 the beginning of the GraphicsComplex is:
GraphicsComplex[
List[List[2., 0.866025], List[1.5, 1.73205], List[0.5, 1.73205],
List[0., 0.866025], List[0.5, 1.3469*10^-10], List[1.5, 0.]],
List[List[RGBColor[0.5, 0., 0.],
Line[List[List[1, 2], List[2, 3], List[3, 4], List[4, 5],
List[5, 6], List[6, 1]]]],
The first outermost list defines the positions of 6 points. The second outermost list defines a bunch of lines between those points, using the numbers of the points within the first list. It's probably easier to understand if you play around with this.
EDIT: In response to OP's comment, if I execute:
FullForm[GraphPlot[{3 -> 4, 4 -> 5, 5 -> 6, 6 -> 3}]]
I get
Graphics[Annotation[GraphicsComplex[List[List[0.`,0.9997532360813222`],
List[0.9993931236462025`,1.0258160108662504`],List[1.0286626995939243`,
0.026431169015735057`],List[0.02872413637035287`,0.`]],List[List[RGBColor[0.5`,0.`,0.`],
Line[List[List[1,2],List[2,3],List[3,4],List[4,1]]]],List[RGBColor[0,0,0.7`],
Tooltip[Point[1],3],Tooltip[Point[2],4],Tooltip[Point[3],5],Tooltip[Point[4],6]]],
List[]],Rule[VertexCoordinateRules,List[List[0.`,0.9997532360813222`],
List[0.9993931236462025`,1.0258160108662504`],
List[1.0286626995939243`,0.026431169015735057`],List[0.02872413637035287`,0.`]]]],
Rule[FrameTicks,None],Rule[PlotRange,All],Rule[PlotRangePadding,Scaled[0.1`]],
Rule[AspectRatio,Automatic]]
The list of vertex positions is the first list inside the GraphicsComplex. Later in the FullForm you can see the list where Mathematica adds tooltips to label the vertices with the identifiers you supplied in the original edge list. Since what you are now looking at is the code describing a graphic there's only an indirect relationship between your vertices and what will be plotted; the information is all there but not entirely straightforward to unpack.
p2 = Normal#gp1 // Cases[#, Line[points__] :> points, Infinity] &;
p3 = Flatten[p2, 1];
ListLinePlot[p3[[All, 1 ;; 2]]]
V12.0.0