Adaptive gridlines - wolfram-mathematica

I want to use gridlines to create an effect of millimeter graphing paper on a 2d graph, to show how multi-variable function depends on 1 variable. The scales of different variables differ a lot, so my naive approach (that I have used before) does not seem to work.
Example of what I have at the moment:
<< ErrorBarPlots`
Cmb[x_, y_, ex_, ey_] := {{N[x], N[y]}, ErrorBar[ex, ey]};
SetAttributes[Cmb, Listable];
ELP[x_, y_, ex_, ey_, name_] :=
ErrorListPlot[
Cmb[x, y, ex, ey],
PlotRange -> FromTo[x, y],
PlotLabel -> name,
Joined -> True, Frame -> True, GridLines -> GetGrid,
ImageSize -> {600}
]
Both FromTo (I want to leave 5% margin in the frame) and GetGrid do not work exactly as I want them to.
On some axes the variables differs many orders of 10. And I do not want, that one axis has many orders of 10 gridlines more then other. And most importantly I want the gridlines to line up with ticks.
Sample data:
ELP[
{4124961/25000000, 27573001/100000000, 9162729/25000000, 44635761/
100000000, 15737089/25000000, 829921/1562500, 4405801/4000000,
23068809/25000000, 329386201/100000000, 58079641/100000000},
{1/10, 1/5, 3/10, 2/5, 3/5, 1/2, 1/2, 1/2, 1/2, 1/2},
{2031/(250000 Sqrt[10]), 5251/(500000 Sqrt[10]), 3027/(
250000 Sqrt[10]), 6681/(500000 Sqrt[10]), 3967/(250000 Sqrt[10]),
911/(62500 Sqrt[10]), 2099/(100000 Sqrt[10]), 4803/(
250000 Sqrt[10]), 18149/(500000 Sqrt[10]), 7621/(500000 Sqrt[10])},
{1/2000, 1/1000, 3/2000, 1/500, 3/1000, 1/400, 1/400, 1/400, 1/400,
1/400},
"T2, m"
]
Would result in:
And my naive GetGrid, that works in some sence:
FromTo[x_, y_] := Module[{dx, dy},
dx = (Max[x] - Min[x])*0.1;
dy = (Max[y] - Min[y])*0.1;
{{Min[x] - dx, Max[x] + dx}, {Min[y] - dy, Max[y] + dy}}];
GetGrid[min_, max_] := Module[{step, i},
step = (max - min)/100;
Table[
{min + i*step,
If[Equal[Mod[i, 10], 0],
Directive[Gray, Thick, Opacity[0.5]],
If[Equal[Mod[i, 5], 0],
Directive[Gray, Opacity[0.5]],
Directive[LightGray, Opacity[0.5]]
]]},
{i, 1, 100}]
]
Question
How to make GridLines line up with ticks?
edit: With
GetTicks[x_, y_] := Module[{dx, dy},
dx = (Max[x] - Min[x])*0.1;
dy = (Max[y] - Min[y])*0.1;
{
Min[x] - dx + Table[i*dx*1.2, {i, 1, 9}],
Min[y] - dy + Table[i*dy*1.2, {i, 1, 9}]
}];
ELP[x_, y_, ex_, ey_, name_] :=
ErrorListPlot[
Cmb[x, y, ex, ey],
PlotRange -> FromTo[x, y],
PlotLabel -> name,
Joined -> True, Frame -> True, GridLines -> GetGrid,
FrameTicks -> GetTicks[x, y],
ImageSize -> {600},
AspectRatio -> 1
]
I can get:
And that is a lot better. But I would like to shift the grid and not the ticks.
edit: #Sjoerd C. de Vries
Your solution does what I wanted to archive and works. I also noticed, that if I take first 5 elements of sample data, then the plot will be (elements are sorted and regression line is added).
Notice the left most element is like off grid.

Don't use FrameTicks but shift the grid correctly. This is a first approach. Dinner waits.
getGrid[min_, max_] :=
Module[{step, i},
Print[{min, max}];
step = 1/100;
Table[
{
Floor[min, 0.1] + i*step,
If[Equal[Mod[i, 10], 0], Directive[Gray, Thick, Opacity[0.5]],
If[Equal[Mod[i, 5], 0], Directive[Gray, Opacity[0.5]],
Directive[LightGray, Opacity[0.5]]
]
]
},
{i, 1, (Ceiling[max, 0.1] - Floor[min, 0.1])/step // Round}
]
]
Use an AspectRatio that's appropriate for the grid (probably the ratio of x and y ranges)
After-dinner update
To make it more robust for different value ranges (per your comment) I generate the ticks that would be chosen by ListPlot and base my steps on that:
getGrid[min_, max_] :=
Module[{step, i,j},
i = Cases[(Ticks /.
AbsoluteOptions[ListPlot[{{min, min}, {max, max}}],
Ticks])[[1]], {a_, ___, {_, AbsoluteThickness[0.25`]}} :> a];
step = i[[2]] - i[[1]];
Table[
{
i[[1]] + j*step/10,
If[Equal[Mod[j, 10], 0], Directive[Gray, Thick, Opacity[0.5]],
If[Equal[Mod[j, 5], 0], Directive[Gray, Opacity[0.5]],
Directive[LightGray, Opacity[0.5]]
]
]
},
{j, 0, 10 Length[i]}
]
]
and getting the aspect ratio which yields a square raster
getAspect[{{minX_, maxX_}, {minY_, maxY_}}] :=
Module[{stepx, stepy, i, rx, ry},
i = (Ticks /.AbsoluteOptions[ListPlot[{{minX, minY}, {maxX, maxY}}], Ticks]);
rx = Cases[i[[1]], {a_, ___, {_, AbsoluteThickness[0.25`]}} :> a];
stepx = rx[[2]] - rx[[1]];
ry = Cases[i[[2]], {a_, ___, {_, AbsoluteThickness[0.25`]}} :> a];
stepy = ry[[2]] - ry[[1]];
((maxY - minY)/stepy)/((maxX - minX)/stepx)
]
Test
ELP[x_, y_, ex_, ey_, name_] :=
ErrorListPlot[Cmb[x, y, ex, ey], PlotLabel -> name, Joined -> True,
Frame -> True, GridLines -> getGrid, ImageSize -> {600},
PlotRangePadding -> 0, AspectRatio -> getAspect[FromTo[x, y]],
PlotRange -> FromTo[x, y]]
ELP[{4124961/25000000, 27573001/100000000, 9162729/25000000,
44635761/100000000, 15737089/25000000, 829921/1562500,
4405801/4000000, 23068809/25000000, 329386201/100000000,
58079641/100000000}, {1/10, 1/5, 3/10, 2/5, 3/5, 1/2, 1/2, 1/2, 1/2,
1/2}, {2031/(250000 Sqrt[10]), 5251/(500000 Sqrt[10]),
3027/(250000 Sqrt[10]), 1/100000 6681/(500000 Sqrt[10]),
3967/(250000 Sqrt[10]), 911/(62500 Sqrt[10]),
2099/(100000 Sqrt[10]), 4803/(250000 Sqrt[10]),
18149/(500000 Sqrt[10]), 7621/(500000 Sqrt[10])}, {1/2000, 1/1000,
3/2000, 1/500, 3/1000, 1/400, 1/400, 1/400, 1/400, 1/400}, "T2, m"]
Here I divide the y-values by 20 and multiplied the x-values by 10000 to show the grid is still good:
Final update (I hope)
This uses FindDivisions as suggested by belisarius. However, I used the three level line structure standard for milimeter paper as requested by Margus:
getGrid[x_, y_] :=
FindDivisions[{x, y}, {10, 2, 5}] /. {r_, s_, t_} :>
Join[
{#, Directive[Gray, Thick, Opacity[0.5]]} & /# r,
{#, Directive[Gray, Opacity[0.5]]} & /# Union[Flatten[s]],
{#, Directive[LightGray, Opacity[0.5]]} & /# Union[Flatten[t]]
]
and
getAspect[{{minX_, maxX_}, {minY_, maxY_}}] :=
Module[{stepx, stepy},
stepx = (#[[2]] - #[[1]]) &#FindDivisions[{minX, maxX}, 10];
stepy = (#[[2]] - #[[1]]) &#FindDivisions[{minY, maxY}, 10];
((maxY - minY)/stepy)/((maxX - minX)/stepx)
]
WARNING!!!
I just noticed that if you have this in MMA:
and you copy it to SO (just ctrl-c ctrl-v), you get this:
(maxY - minY)/stepy/(maxX - minX)/stepx
which is not mathematically equivalent. It should be this:
((maxY - minY)*stepx)/((maxX - minX)*stepy)
I corrected this in the code above, but it has been posted wrong for half a day while working correctly on my computer. Thought that it would be good to mention this.

I think FindDivisions[ ] is what you're after:
FindDivisions[{xmin,xmax},n]
finds a list of about n "nice" numbers that divide the interval around xmin to xmax into equally spaced parts.
getTicks[x_, y_] := Flatten#FindDivisions[#, {10}] & /# FromTo[x, y]
getGrid [x_,y_] := FindDivisions[{x,y},{10,5}]/.
{r__,{s__}}:>Join##{s,{#,{Gray,Thick}}&/#r}

If you use the same function for FrameTicks and Gridlines, they'll line up.
See FrameTicks, and GridLines. I think you'll need ImageMargins for the border.

Related

Coloring plot in Mathematica according to labels

I have a dataset with labels which I would like to plot with points colored according to their label. Is there a simple way how to get current line numer inside plot, so that I can determine which category does the point belong to?
I understood that x,y,z are the coordinates of plotted data, but it doesn't help for the external labels.
This is quite ugly and it works just on sorted dataset with regular distribution.
data = Import["http://ftp.ics.uci.edu/pub/machine-learning-databases/iris/iris.data"];
data = Drop[data, -1]; (*there one extra line at the end*)
inData = data[[All, 1 ;; 4]];
labels = data[[All, 5]];
ListPlot3D[inData,
ColorFunction ->
Function[{x, y, z},
If[y < 0.33, RGBColor[1, 1, 0.],
If[y < 0.66, RGBColor[1, 0, 0.], RGBColor[1, 0, 1]]
]
]
]
Expected result:
Suppose that points is the lists of coordinates and labels a list of the corresponding labels so for example
points = Flatten[Table[{i, j, Sin[i j]},
{i, 0, Pi, Pi/20}, {j, 0, Pi, Pi/10}], 1];
labels = RandomChoice[{"label a", "label b", "label c"}, Length[points]];
Each label corresponds to a colour which I'm writing as a list of rules, e.g.
rules = {"label a" -> RGBColor[1, 1, 0],
"label b" -> RGBColor[1, 0, 0], "label c" -> RGBColor[1, 0, 1]};
Then the points can be plotted in the colour corresponding to their label as follows
ListPointPlot3D[Pick[points, labels, #] & /# Union[labels],
PlotStyle -> Union[labels] /. rules]
Edit
To colour individual points in a ListPlot3D you can use VertexColors, for example
ListPlot3D[points, VertexColors -> labels /. rules, Mesh -> False]
For Example:
(* Build the labeled structure and take a random permutation*)
f[x_, y_] = Sqrt[100 - x x - y y];
l = RandomSample#Flatten[{Table[{{"Lower", {x, y, f[x, y] - 5}},
{"Upper", {x, y, 5 - f[x, y]}}},
{x, -5, 5, .1}, {y, -5, 5, .1}]}, 3];
(*Plot*)
Graphics3D[
Riffle[l[[All, 1]] /. {"Lower" -> Red, "Upper" -> Green},
Point /# l[[All, 2]]], Axes -> True]

Can we generate "foveated Image" in Mathematica

"Foveated imaging is a digital image processing technique in which the image resolution, or amount of detail, varies across the image according to one or more "fixation points." A fixation point indicates the highest resolution region of the image and corresponds to the center of the eye's retina, the fovea."
I want to use such image to illustrate humans visual acuity, The bellow diagram shows the relative acuity of the left human eye (horizontal section) in degrees from the fovea (Wikipedia) :
Is there a way to create a foveated image in Mathematica using its image processing capabilities ?
Something along the following lines may work for you. The filtering details should be adjusted to your tastes.
lena = ExampleData[{"TestImage", "Lena"}]
ImageDimensions[lena]
==> {512, 512}
mask = DensityPlot[-Exp[-(x^2 + y^2)/5], {x, -4, 4}, {y, -4, 4},
Axes -> None, Frame -> None, Method -> {"ShrinkWrap" -> True},
ColorFunction -> GrayLevel, ImageSize -> 512]
Show[ImageFilter[Mean[Flatten[#]] &, lena, 20, Masking -> mask], ImageSize -> 512]
Following on Sjoerd's answer, you can Fold[] a radius-dependent blur as follows.
A model for the acuity (very rough model):
Clear[acuity];
acuity[distance_, x_, y_, blindspotradius_] :=
With[{\[Theta] = ArcTan[distance, Sqrt[x^2 + y^2]]},
Clip[(Chop#Exp[-Abs[\[Theta]]/(15. Degree)] - .05)/.95,
{0,1}] (1. - Boole[(x + 100.)^2 + y^2 <= blindspotradius^2])]
Plot3D[acuity[250., x, y, 25], {x, -256, 256}, {y, -256, 256},
PlotRange -> All, PlotPoints -> 40, ExclusionsStyle -> Automatic]
The example image:
size = 100;
lena = ImageResize[ExampleData[{"TestImage", "Lena"}], size];
Manipulate[
ImageResize[
Fold[Function[{ima, r},
ImageFilter[(Mean[Flatten[#]] &), ima,
7*(1 - acuity[size*5, r, 0, 0]),
Masking -> Graphics[Disk[p/2, r],
PlotRange -> {{0, size}, {0, size}}]
]],
lena, Range[10, size, 5]],
200],
{{p, {size, size}}, Locator}]
Some examples:
WaveletMapIndexed can give a spatially-varying blur, as shown in the Mathematica documentation (WaveletMapIndexed->Examples->Applications->Image Processing). Here is an implementation of a foveatedBlur, using a compiled version of the acuity function from the other answer:
Clear[foveatedBlur];
foveatedBlur[image_, d_, cx_, cy_, blindspotradius_] :=
Module[{sx, sy},
{sy, sx} = ImageDimensions#image;
InverseWaveletTransform#WaveletMapIndexed[ImageMultiply[#,
Image[acuityC[d, sx, sy, -cy + sy/2, cx - sx/2, blindspotradius]]] &,
StationaryWaveletTransform[image, Automatic, 6], {___, 1 | 2 | 3 | 4 | 5 | 6}]]
where the compiled acuity is
Clear[acuityC];
acuityC = Compile[{{distance, _Real}, {sx, _Integer}, {sy, _Integer}, {x0, _Real},
{y0, _Real}, {blindspotradius, _Real}},
Table[With[{\[Theta] = ArcTan[distance, Sqrt[(x - x0)^2 + (y - y0)^2]]},
(Exp[-Abs[\[Theta]]/(15 Degree)] - .05)/.95
*(1. - Boole[(x - x0)^2 + (y - y0 + 0.25 sy)^2 <= blindspotradius^2])],
{x, Floor[-sx/2], Floor[sx/2 - 1]}, {y, Floor[-sy/2], Floor[sy/2 - 1]}]];
The distance parameter sets the rate of falloff of the acuity. Focusing point {cx,cy}, and blind-spot radius are self-explanatory. Here is an example using Manipulate, looking right at Lena's right eye:
size = 256;
lena = ImageResize[ExampleData[{"TestImage", "Lena"}], size];
Manipulate[foveatedBlur[lena, d, p[[1]], p[[2]], 20], {{d, 250}, 50,
500}, {{p, ImageDimensions#lena/2}, Locator, Appearance -> None}]
See the blind spot?

An efficient data structure or method to manage plotting data that grow with time

I'd like to ask if the following way I manage plotting result of simulation is efficient use of Mathematica and if there is a more 'functional' way to do it. (may be using Sow, Reap and such).
The problem is basic one. Suppose you want to simulate a physical process, say a pendulum, and want to plot the time-series of the solution (i.e. time vs. angle) as it runs (or any other type of result).
To be able to show the plot, one needs to keep the data points as it runs.
The following is a simple example, that plots the solution, but only the current point, and not the full time-series:
Manipulate[
sol = First#NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4, y'[0] == 0},
y, {t, time, time + 1}];
With[{angle = y /. sol},
(
ListPlot[{{time, angle[time]}}, AxesLabel -> {"time", "angle"},
PlotRange -> {{0, max}, {-Pi, Pi}}]
)
],
{{time, 0, "run"}, 0, max, Dynamic#delT, ControlType -> Trigger},
{{delT, 0.1, "delT"}, 0.1, 1, 0.1, Appearance -> "Labeled"},
TrackedSymbols :> {time},
Initialization :> (max = 10)
]
The above is not interesting, as one only sees a point moving, and not the full solution path.
The way currently I handle this, is allocate, using Table[], a buffer large enough to hold the largest possible time-series size that can be generated.
The issue is that the time-step can change, and the smaller it is, the more data will be generated.
But since I know the smallest possible time-step (which is 0.1 seconds in this example), and I know the total time to run (which is 10 seconds here), then I know how much to allocate.
I also need an 'index' to keep track of the buffer. Using this method, here is a way to do it:
Manipulate[
If[time == 0, index = 0];
sol = First#NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4,y'[0] == 0},
y, {t, time, time + 1}];
With[{angle = y /. sol},
(
index += 1;
buffer[[index]] = {time, angle[time]};
ListPlot[buffer[[1 ;; index]], Joined -> True, AxesLabel -> {"time", "angle"},
PlotRange -> {{0, 10}, {-Pi, Pi}}]
)
],
{{time, 0, "run"}, 0, 10, Dynamic#delT, AnimationRate -> 1, ControlType -> Trigger},
{{delT, 0.1, "delT"}, 0.1, 1, 0.1, Appearance -> "Labeled"},
{{buffer, Table[{0, 0}, {(max + 1)*10}]}, None},
{{index, 0}, None},
TrackedSymbols :> {time},
Initialization :> (max = 10)
]
For reference, when I do something like the above in Matlab, it has a nice facility for plotting, called 'hold on'. So that one can plot a point, then say 'hold on' which means that the next plot will not erase what is already on the plot, but will add it.
I did not find something like this in Mathematica, i.e. update a current plot on the fly.
I also did not want to use Append[] and AppendTo[] to build the buffer as it runs, as that will be slow and not efficient.
My question: Is there a more efficient, Mathematica way (which can be faster and more elegent) to do a typical task such as the above, other than what I am doing?
thanks,
UPDATE:
On the question on why not solving the ODE all at once.
Yes, it is possible, but it simplifies things alot to do it in pieces, also for performance reasons.
Here is an example with ode with initial conditions:
Manipulate[
If[time == 0, index = 0];
sol = First#
NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == y0,
y'[0] == yder0}, y, {t, time, time + 1}];
With[{angle = (y /. sol)[time]},
(
index += 1;
buffer[[index]] = {time, angle};
ListPlot[buffer[[1 ;; index]], Joined -> True,
AxesLabel -> {"time", "angle"},
PlotRange -> {{0, 10}, {-Pi, Pi}}])],
{{time, 0, "run"}, 0, 10, Dynamic#delT, AnimationRate -> 1,
ControlType -> Trigger}, {{delT, 0.1, "delT"}, 0.1, 1, 0.1,
Appearance -> "Labeled"},
{{y0, Pi/4, "y(0)"}, -Pi, Pi, Pi/100, Appearance -> "Labeled"},
{{yder0, 0, "y'(0)"}, -1, 1, .1, Appearance -> "Labeled"},
{{buffer, Table[{0, 0}, {(max + 1)*10}]}, None},
{{index, 0}, None},
TrackedSymbols :> {time},
Initialization :> (max = 10)
]
Now, in one were to solve the system once before, then they need to watch out if the IC changes. This can be done, but need extra logic and I have done this before many times, but it does complicate things a bit. I wrote a small note on this here.
Also, I noticed that I can get much better speed by solving the system for smaller time segments as time marches on, than the whole thing at once. NDSolve call overhead is very small. But when the time duration to NDsolve for is large, problems can result when one ask for higher accuracy from NDSolve, as in options AccuracyGoal ->, PrecisionGoal ->, which I could not when time interval is very large.
Overall, the overhead of calling NDSolve for smaller segments seems to much less compare to the advantages it makes in simplifing the logic, and speed (may be more accurate, but I have not checked on this more). I know it seems a bit strange to keep calling NDSolve, but after trying both methods (all at once, but add logic to check for other control variables) vs. this method, I am now leaning towards this one.
UPDATE 2
I compared the following 4 methods for 2 test cases:
tangle[j][j] method (Belisarius)
AppendTo (suggested by Sjoerd)
Dynamic linked list (Leonid) (with and without SetAttributes[linkedList, HoldAllComplete])
preallocate buffer (Nasser)
The way I did this, is by running it over 2 cases, one for 10,000 points, and the second for 20,000 points. I did leave the Plot[[] command there, but do not display it on the screen, this is to eliminate any overhead of the actual rendering.
I used Timing[] around a Do loop which iterate over the core logic which called NDSolve and iterate over the time span using delT increments as above. No Manipulate was used.
I used Quit[] before each run.
For Leonid method, I changed the Column[] he had by the Do loop. I verified at the end, but plotting the data using his getData[] method, that the result is ok.
All the code I used is below. I made a table which shows the results for the 10,000 points and 20,000. Timing is per seconds:
result = Grid[{
{Text[Style["method", Bold]],
Text[Style["number of elements", Bold]], SpanFromLeft},
{"", 10000, 20000},
{"", SpanFromLeft},
{"buffer", 129, 571},
{"AppendTo", 128, 574},
{"tangle[j][j]", 612, 2459},
{"linkedList with SetAttribute", 25, 81},
{"linkedList w/o SetAttribute", 27, 90}}
]
Clearly, unless I did something wrong, but code is below for anyone to verify, Leonid method wins easily here. I was also surprised that AppendTo did just as well as the buffer method which pre-allocated data.
Here are the slightly modified code I used to generate the above results.
buffer method
delT = 0.01; max = 100; index = 0;
buffer = Table[{0, 0}, {(max + 1)*1/delT}];
Timing[
Do[
sol = First#
NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4,
y'[0] == 0}, y, {t, time, time + 1}];
With[{angle = y /. sol},
(index += 1;
buffer[[index]] = {time, angle[time]};
foo =
ListPlot[buffer[[1 ;; index]], Joined -> True,
AxesLabel -> {"time", "angle"},
PlotRange -> {{0, 10}, {-Pi, Pi}}]
)
], {time, 0, max, delT}
]
]
AppendTo method
Clear[y, t];
delT = 0.01; max = 200;
buffer = {{0, 0}}; (*just a hack to get ball rolling, would not do this in real code*)
Timing[
Do[
sol = First#
NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4,
y'[0] == 0}, y, {t, time, time + 1}];
With[{angle = y /. sol},
(AppendTo[buffer, {time, angle[time]}];
foo =
ListPlot[buffer, Joined -> True, AxesLabel -> {"time", "angle"},
PlotRange -> {{0, 10}, {-Pi, Pi}}]
)
], {time, 0, max, delT}
]
]
tangle[j][j] method
Clear[y, t];
delT = 0.01; max = 200;
Timing[
Do[
sol = First#
NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4,
y'[0] == 0}, y, {t, time, time + 1}];
tangle[time] = y /. sol;
foo = ListPlot[
Table[{j, tangle[j][j]}, {j, .1, max, delT}],
AxesLabel -> {"time", "angle"},
PlotRange -> {{0, max}, {-Pi, Pi}}
]
, {time, 0, max, delT}
]
]
dynamic linked list method
Timing[
max = 200;
ClearAll[linkedList, toLinkedList, fromLinkedList, addToList, pop,
emptyList];
SetAttributes[linkedList, HoldAllComplete];
toLinkedList[data_List] := Fold[linkedList, linkedList[], data];
fromLinkedList[ll_linkedList] :=
List ## Flatten[ll, Infinity, linkedList];
addToList[ll_, value_] := linkedList[ll, value];
pop[ll_] := Last#ll;
emptyList[] := linkedList[];
Clear[getData];
Module[{ll = emptyList[], time = 0, restart, plot, y},
getData[] := fromLinkedList[ll];
plot[] := Graphics[
{
Hue[0.67`, 0.6`, 0.6`],
Line[fromLinkedList[ll]]
},
AspectRatio -> 1/GoldenRatio,
Axes -> True,
AxesLabel -> {"time", "angle"},
PlotRange -> {{0, 10}, {-Pi, Pi}},
PlotRangeClipping -> True
];
DynamicModule[{sol, angle, llaux, delT = 0.01},
restart[] := (time = 0; llaux = emptyList[]);
llaux = ll;
sol :=
First#NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4,
y'[0] == 0}, y, {t, time, time + 1}];
angle := y /. sol;
ll := With[{res =
If[llaux === emptyList[] || pop[llaux][[1]] != time,
addToList[llaux, {time, angle[time]}],
(*else*)llaux]
},
llaux = res
];
Do[
time += delT;
plot[]
, {i, 0, max, delT}
]
]
]
]
thanks for everyone help.
I don't know how to get what you want with Manipulate, but I seem to have managed getting something close with a custom Dynamic. The following code will: use linked lists to be reasonably efficient, stop / resume your plot with a button, and have the data collected so far available on demand at any given time:
ClearAll[linkedList, toLinkedList, fromLinkedList, addToList, pop, emptyList];
SetAttributes[linkedList, HoldAllComplete];
toLinkedList[data_List] := Fold[linkedList, linkedList[], data];
fromLinkedList[ll_linkedList] := List ## Flatten[ll, Infinity, linkedList];
addToList[ll_, value_] := linkedList[ll, value];
pop[ll_] := Last#ll;
emptyList[] := linkedList[];
Clear[getData];
Module[{ll = emptyList[], time = 0, restart, plot, y},
getData[] := fromLinkedList[ll];
plot[] :=
Graphics[{Hue[0.67`, 0.6`, 0.6`], Line[fromLinkedList[ll]]},
AspectRatio -> 1/GoldenRatio, Axes -> True,
AxesLabel -> {"time", "angle"}, PlotRange -> {{0, 10}, {-Pi, Pi}},
PlotRangeClipping -> True];
DynamicModule[{sol, angle, llaux, delT = 0.1},
restart[] := (time = 0; llaux = emptyList[]);
llaux = ll;
sol := First#
NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0, y[0] == Pi/4, y'[0] == 0},
y, {t, time, time + 1}];
angle := y /. sol;
ll := With[{res =
If[llaux === emptyList[] || pop[llaux][[1]] != time,
addToList[llaux, {time, angle[time]}],
(* else *)
llaux]},
llaux = res];
Column[{
Row[{Dynamic#delT, Slider[Dynamic[delT], {0.1, 1., 0.1}]}],
Dynamic[time, {None, Automatic, None}],
Row[{
Trigger[Dynamic[time], {0, 10, Dynamic#delT},
AppearanceElements -> { "PlayPauseButton"}],
Button[Style["Restart", Small], restart[]]
}],
Dynamic[plot[]]
}, Frame -> True]
]
]
Linked lists here replace your buffer and you don't need to pre-allocate and to know in advance how many data points you will have. The plot[] is a custom low-level plotting function, although we probably could just as well use ListPlot. You use the "Play" button to both stop and resume plotting, and you use the custom "Restart" button to reset the parameters.
You can call getData[] at any given time to get a list of data accumulated so far, like so:
In[218]:= getData[]
Out[218]= {{0,0.785398},{0.2,0.771383},{0.3,0.754062},{0.4,0.730105},{0.5,0.699755},
{0.6,0.663304},{0.7,0.621093},{0.8,0.573517},{0.9,0.521021},{1.,0.464099},
{1.1,0.403294},{1.2,0.339193},{1.3,0.272424}}
I just wonder why you want to solve the DE in pieces. It can be solved for the whole interval at once. There is also no need to place the NDSolve in the Manipulate then. It doesn't need to be solved time and again when the body of the Manipulateis triggered. Plot itself is sufficiently fast to plot the growing graph at each time step. The following code does what you want without the need for any storage.
sol = First#
NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]]==0,y[0] == Pi/4,y'[0] == 0}, y, {t, 0, 10}];
eps = 0.000001;
Manipulate[
With[{angle = y /. sol},
Plot[angle[t], {t, 0, time + eps},
AxesLabel -> {"time", "angle"},
PlotRange -> {{0, max}, {-Pi, Pi}}
]
],
{{time, 0, "run"}, 0, max,Dynamic#delT, ControlType -> Trigger},
{{delT, 0.1, "delT"}, 0.1, 1, 0.1, Appearance -> "Labeled"}, TrackedSymbols :> {time},
Initialization :> (max = 10)
]
BTW: AppendTo may be vilified as slow, but it is not that slow. On a typical list suitable for plotting it takes less than a milisecond, so it shouldn't slow plotting at all.
Not memory efficient at all, but its virtue is that it only needs a slight modification of your first code:
Clear[tangle];
Manipulate[
sol = First#NDSolve[{y''[t] + 0.1 y'[t] + Sin[y[t]] == 0,
y[0] == Pi/4,
y'[0] == 0},
y, {t, time, time + 1}];
(tangle[time] = y /. sol;
ListPlot[Table[{j, tangle[j][j]}, {j, .1, max, delT}],
AxesLabel -> {"time", "angle"},
PlotRange -> {{0, max}, {-Pi, Pi}}]),
{{time, 0, "run"}, 0, max, Dynamic#delT, ControlType -> Trigger},
{{delT, 0.1, "delT"}, 0.1, 1, 0.1, Appearance -> "Labeled"},
TrackedSymbols :> {time},
Initialization :> {(max = 10); i = 0}]

Extract contours from ContourPlot in Mathematica

I have a function f(x,y) of two variables, of which I need to know the location of the curves at which it crosses zero. ContourPlot does that very efficiently (that is: it uses clever multi-grid methods, not just a brute force fine-grained scan) but just gives me a plot. I would like to have a set of values {x,y} (with some specified resolution) or perhaps some interpolating function which allows me to get access to the location of these contours.
Have thought of extracting this from the FullForm of ContourPlot but this seems to be a bit of a hack. Any better way to do this?
If you end up extracting points from ContourPlot, this is one easy way to do it:
points = Cases[
Normal#ContourPlot[Sin[x] Sin[y] == 1/2, {x, -3, 3}, {y, -3, 3}],
Line[pts_] -> pts,
Infinity
]
Join ## points (* if you don't want disjoint components to be separate *)
EDIT
It appears that ContourPlot does not produce very precise contours. They're of course meant for plotting and are good enough for that, but the points don't lie precisely on the contours:
In[78]:= Take[Join ## points /. {x_, y_} -> Sin[x] Sin[y] - 1/2, 10]
Out[78]= {0.000163608, 0.0000781187, 0.000522698, 0.000516078,
0.000282781, 0.000659909, 0.000626086, 0.0000917416, 0.000470424,
0.0000545409}
We can try to come up with our own method to trace the contour, but it's a lot of trouble to do it in a general way. Here's a concept that works for smoothly varying functions that have smooth contours:
Start from some point (pt0), and find the intersection with the contour along the gradient of f.
Now we have a point on the contour. Move along the tangent of the contour by a fixed step (resolution), then repeat from step 1.
Here's a basic implementation that only works with functions that can be differentiated symbolically:
rot90[{x_, y_}] := {y, -x}
step[f_, pt : {x_, y_}, pt0 : {x0_, y0_}, resolution_] :=
Module[
{grad, grad0, t, contourPoint},
grad = D[f, {pt}];
grad0 = grad /. Thread[pt -> pt0];
contourPoint =
grad0 t + pt0 /. First#FindRoot[f /. Thread[pt -> grad0 t + pt0], {t, 0}];
Sow[contourPoint];
grad = grad /. Thread[pt -> contourPoint];
contourPoint + rot90[grad] resolution
]
result = Reap[
NestList[step[Sin[x] Sin[y] - 1/2, {x, y}, #, .5] &, {1, 1}, 20]
];
ListPlot[{result[[1]], result[[-1, 1]]}, PlotStyle -> {Red, Black},
Joined -> True, AspectRatio -> Automatic, PlotMarkers -> Automatic]
The red points are the "starting points", while the black points are the trace of the contour.
EDIT 2
Perhaps it's an easier and better solution to use a similar technique to make the points that we get from ContourPlot more precise. Start from the initial point, then move along the gradient until we intersect the contour.
Note that this implementation will also work with functions that can't be differentiated symbolically. Just define the function as f[x_?NumericQ, y_?NumericQ] := ... if this is the case.
f[x_, y_] := Sin[x] Sin[y] - 1/2
refine[f_, pt0 : {x_, y_}] :=
Module[{grad, t},
grad = N[{Derivative[1, 0][f][x, y], Derivative[0, 1][f][x, y]}];
pt0 + grad*t /. FindRoot[f ## (pt0 + grad*t), {t, 0}]
]
points = Join ## Cases[
Normal#ContourPlot[f[x, y] == 0, {x, -3, 3}, {y, -3, 3}],
Line[pts_] -> pts,
Infinity
]
refine[f, #] & /# points
A slight variation for extracting points from ContourPlot (possibly due to David Park):
pts = Cases[
ContourPlot[Cos[x] + Cos[y] == 1/2, {x, 0, 4 Pi}, {y, 0, 4 Pi}],
x_GraphicsComplex :> First#x, Infinity];
or (as a list of {x,y} points)
ptsXY = Cases[
Cases[ContourPlot[
Cos[x] + Cos[y] == 1/2, {x, 0, 4 Pi}, {y, 0, 4 Pi}],
x_GraphicsComplex :> First#x, Infinity], {x_, y_}, Infinity];
Edit
As discussed here, an article by Paul Abbott in the Mathematica Journal (Finding Roots in an Interval) gives the following two alternative methods for obtaining a list of {x,y} values from ContourPlot, including (!)
ContourPlot[...][[1, 1]]
For the above example
ptsXY2 = ContourPlot[
Cos[x] + Cos[y] == 1/2, {x, 0, 4 Pi}, {y, 0, 4 Pi}][[1, 1]];
and
ptsXY3 = Cases[
Normal#ContourPlot[
Cos[x] + Cos[y] == 1/2, {x, 0, 4 Pi}, {y, 0, 4 Pi}],
Line[{x__}] :> x, Infinity];
where
ptsXY2 == ptsXY == ptsXY3

Plotting arrows at the edges of a curve

Inspired by this question at ask.sagemath, what is the best way of adding arrows to the end of curves produced by Plot, ContourPlot, etc...? These are the types of plots seen in high school, indicating the curve continues off the end of the page.
After some searching, I could not find a built-in way or up-to-date package to do this. (There is ArrowExtended, but it's quite old).
The solution given in the ask.sagemath question relies on the knowledge of the function and its endpoints and (maybe) the ability to take derivatives. Its translation into Mathematica is
f[x_] := Cos[12 x^2]; xmin = -1; xmax = 1; small = .01;
Plot[f[x],{x,xmin,xmax}, PlotLabel -> y==f[x], AxesLabel->{x,y},
Epilog->{Blue,
Arrow[{{xmin,f[xmin]},{xmin-small,f[xmin-small]}}],
Arrow[{{xmax,f[xmax]},{xmax+small,f[xmax+small]}}]
}]
An alternative method is to simply replace the Line[] objects generate by Plot[] with Arrow[]. For example
Plot[{x^2, Sin[10 x], UnitStep[x]}, {x, -1, 1},
PlotStyle -> {Red, Green, {Thick, Blue}},
(*AxesStyle -> Arrowheads[.03],*) PlotRange -> All] /.
Line[x__] :> Sequence[Arrowheads[{-.04, .04}], Arrow[x]]
But this has the problem that any discontinuities in the lines generate arrow heads where you don't want them (this can often be fixed by the option Exclusions -> None). More importantly, this approach is hopeless with CountourPlots. Eg try
ContourPlot[x^2 + y^3 == 1, {x, -2, 2}, {y, -2, 1}] /.
Line[x__] :> Sequence[Arrowheads[{-.04, .04}], Arrow[x]]
(the problems in the above case can be fixed by the rule, e.g., {a___, l1_Line, l2_Line, b___} :> {a, Line[Join[l2[[1]], l1[[1]]]], b} or by using appropriate single headed arrows.).
As you can see, neither of the above (quick hacks) are particularly robust or flexible. Does anyone know an approach that is?
The following seems to work, by sorting the segments first:
f[x_] := {E^-x^2, Sin[10 x], Sign[x], Tan[x], UnitBox[x],
IntegerPart[x], Gamma[x],
Piecewise[{{x^2, x < 0}, {x, x > 0}}], {x, x^2}};
arrowPlot[f_] :=
Plot[{#}, {x, -2, 2}, Axes -> False, Frame -> True, PlotRangePadding -> .2] /.
{Hue[qq__], a___, x___Line} :> {Hue[qq], a, SortBy[{x}, #[[1, 1, 1]] &]} /.
{a___,{Line[x___], d___, Line[z__]}} :>
List[Arrowheads[{-.06, 0}], a, Arrow[x], {d},
Arrowheads[{0, .06}], Arrow[z]] /.
{a___,{Line[x__]}}:> List[Arrowheads[{-.06, 0.06}], a, Arrow[x]] & /# f[x];
arrowPlot[f]
Inspired by both Alexey's comment and belisarius's answers, here's my attempt.
makeArrowPlot[g_Graphics, ah_: 0.06, dx_: 1*^-6, dy_: 1*^-6] :=
Module[{pr = PlotRange /. Options[g, PlotRange], gg, lhs, rhs},
gg = g /. GraphicsComplex -> (Normal[GraphicsComplex[##]] &);
lhs := Or##Flatten[{Thread[Abs[#[[1, 1, 1]] - pr[[1]]] < dx],
Thread[Abs[#[[1, 1, 2]] - pr[[2]]] < dy]}]&;
rhs := Or##Flatten[{Thread[Abs[#[[1, -1, 1]] - pr[[1]]] < dx],
Thread[Abs[#[[1, -1, 2]] - pr[[2]]] < dy]}]&;
gg = gg /. x_Line?(lhs[#]&&rhs[#]&) :> {Arrowheads[{-ah, ah}], Arrow##x};
gg = gg /. x_Line?lhs :> {Arrowheads[{-ah, 0}], Arrow##x};
gg = gg /. x_Line?rhs :> {Arrowheads[{0, ah}], Arrow##x};
gg
]
We can test this on some functions
Plot[{x^2, IntegerPart[x], Tan[x]}, {x, -3, 3}, PlotStyle -> Thick]//makeArrowPlot
And on some contour plots
ContourPlot[{x^2 + y^2 == 1, x^2 + y^2 == 6, x^3 + y^3 == {1, -1}},
{x, -2, 2}, {y, -2, 2}] // makeArrowPlot
One place where this fails is where you have horizontal or vertical lines on the edge of the plot;
Plot[IntegerPart[x],{x,-2.5,2.5}]//makeArrowPlot[#,.03]&
This can be fixed by options such as PlotRange->{-2.1,2.1} or Exclusions->None.
Finally, it would be nice to add an option so that each "curve" can arrow heads only on their boundaries. This would give plots like those in Belisarius's answer (it would also avoid the problem mentioned above). But this is a matter of taste.
The following construct has the advantage of not messing with the internal structure of the Graphics structure, and is more general than the one suggested in ask.sagemath, as it manage PlotRange and infinities better.
f[x_] = Gamma[x]
{plot, evals} =
Reap[Plot[f[x], {x, -2, 2}, Axes -> False, Frame -> True,
PlotRangePadding -> .2, EvaluationMonitor :> Sow[{x, f[x]}]]];
{{minX, maxX}, {minY, maxY}} = Options[plot, PlotRange] /. {_ -> y_} -> y;
ev = Select[evals[[1]], minX <= #[[1]] <= maxX && minY <= #[[2]] <= maxY &];
seq = SortBy[ev, #[[1]] &];
arr = {Arrow[{seq[[2]], seq[[1]]}], Arrow[{seq[[-2]], seq[[-1]]}]};
Show[plot, Graphics[{Red, arr}]]
Edit
As a function:
arrowPlot[f_, interval_] := Module[{plot, evals, within, seq, arr},
within[p_, r_] :=
r[[1, 1]] <= p[[1]] <= r[[1, 2]] &&
r[[2, 1]] <= p[[2]] <= r[[2, 2]];
{plot, evals} = Reap[
Plot[f[x], Evaluate#{x, interval /. List -> Sequence},
Axes -> False,
Frame -> True,
PlotRangePadding -> .2,
EvaluationMonitor :> Sow[{x, f[x]}]]];
seq = SortBy[Select[evals[[1]],
within[#,
Options[plot, PlotRange] /. {_ -> y_} -> y] &], #[[1]] &];
arr = {Arrow[{seq[[2]], seq[[1]]}], Arrow[{seq[[-2]], seq[[-1]]}]};
Show[plot, Graphics[{Red, arr}]]
];
arrowPlot[Gamma, {-3, 4}]
Still thinking what is better for ListPlot & al.

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