## Re: [Matplotlib-users] plotting a circle in log space

 Re: [Matplotlib-users] plotting a circle in log space From: Michael Droettboom - 2009-01-26 14:41:08 ```Support for handling NaNs in curves is now on the branch and trunk. While this solves the infinite recursion problem, it still may be better in your specific case to use a CirclePolygon. All my fix does is remove an entire bezier curve when any of its elements are non-finite -- so we're talking an entire eighth-wedge at least here. By using CirclePolygon, the amount of removal could be much less. Mike Michael Droettboom wrote: > At one point in history, the Agg backend would not do NaN removal on > paths with curves -- but it looks like that's been inadvertently lost, > probably in all the shuffling wrt simplification that went on, since > simplification has similar restrictions. So at present, we have > problems because it's passing curves with too few points to Agg, since > it removes points with NaNs, but not necessarily the entire curve > segment. In any case, even passing the vertices as-is (without NaNs > removed) to Agg still results in an infinite loop. > > The "real" fix, IMO, is to make the NaN-handling code aware of curves, > which requires doing a look-ahead. That is -- if a curve segment has > any NaNs at all, remove the entire curve segment. I've thought about > this for a bit, but now here's some impetus to finally implement it. :) > > Mike > > John Hunter wrote: > >> On Fri, Jan 23, 2009 at 2:06 PM, Michael Hearne wrote: >> >> >>> I have discovered, from the mailing list, the easy way to draw a circle >>> in linear space: >>> ...snip >>> cx = 700 >>> cy = 700 >>> r = 1000 >>> >>> xmin = cx - r >>> xmax = cx + r >>> ymin = cy - r >>> ymax = cy + r >>> >>> cir = Circle( (cx,cx), radius=r,facecolor='w',edgecolor='b') >>> a = gca() >>> a.add_patch(cir) >>> >>> axis([xmin,xmax,ymin,ymax]) >>> axis('equal') >>> >>> How can I plot a circle in log space? >>> >>> >> The problem is that your circle has negative vertices since cx-r<0 and >> cy-r<0. When this happens, mpl is transforming the vertices with log >> coordinates and getting nans, as it should. The problem is that these >> nan vertices are getting passed to the agg backend, and when the >> vertex type is curve4, as it is for a circle, agg gets stuck in an >> infinite recursion in the spline code. I suspect this is because the >> recursion expects the comparison operator on the vertices to be well >> behaved, but it is not in the presence of nans. The function in >> question is agg_curve.cpp curve4_div::recursive_bezier. There is a >> "maximum recursion limit" in that function, but for some reason I >> don't understand, it is not breaking out of the function. >> >> I committed a simple "fix" to the branch and the trunk to simply drop >> any patch where any of the vertices are nans >> >> if not np.isnan(tpath.vertices).any(): >> renderer.draw_path(gc, tpath, affine, rgbFace) >> >> We might be able to do better than this -- is there a well defined way >> to deal with patches where any of the transformed vertices are nans? >> For simple polygons (no splines vertices), we could plot the polygon >> with all the nan containing vertices removed, though in some cases >> this could be a strange object -- this appears to be what was >> happening by default with CirclePolygon with negative vertices but I >> think this was mostly fortuitous that agg dealt with the nans >> gracefully in this case. But for patches containing curve vertices, >> this seems like a bad idea, since simply dropping vertices from a >> spline curve is not defined. >> >> I'm including below some sample code that shows the bug on Agg >> >> JDH >> >> import matplotlib >> matplotlib.use('Agg') >> >> import matplotlib.pyplot as plt >> import matplotlib.patches as patches >> cx = 700 >> cy = 700 >> r = 1000 >> >> fig = plt.figure() >> ax = fig.add_subplot(111) >> >> #cir = patches.CirclePolygon( (cx,cy), radius=r,facecolor='w',edgecolor='b') >> cir = patches.Circle( (cx,cy), radius=r,facecolor='w',edgecolor='b') >> ax.add_patch(cir) >> ax.set_yscale('log') >> fig.savefig('test') >> plt.show() >> >> > > -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA ```

 [Matplotlib-users] plotting a circle in log space From: Michael Hearne - 2009-01-23 20:06:29 ```I have discovered, from the mailing list, the easy way to draw a circle in linear space: cx = 700 cy = 700 r = 1000 xmin = cx - r xmax = cx + r ymin = cy - r ymax = cy + r cir = Circle( (cx,cx), radius=r,facecolor='w',edgecolor='b') a = gca() a.add_patch(cir) axis([xmin,xmax,ymin,ymax]) axis('equal') However, when trying to overplot a circle on an existing log/log plot, I get a circle section: e = [70,1,1,12,7,185,6,3,0,1015,6,222,500,0,661,105,0,8706,0,23,131,0,0,0,6,22,1,4,0] o = [180,2,0,15,13,3,0,0,0,20,6,2000,9748,0,38,100,0,20023,0,2,0,0,0,0,1,0,0,0,1] f1 = figure() loglog(o,e,'b.') hold('on') cx = 700 cy = 700 r = 1000 xmin = cx - r xmax = cx + r ymin = cy - r ymax = cy + r cir = Circle( (cx,cx), radius=r,facecolor='w',edgecolor='b') a = gca() a.add_patch(cir) axis([xmin,xmax,ymin,ymax]) axis('equal') How can I plot a circle in log space? As an additional aside, I've discovered that even if I define the points that make up a circle (in linear space), I cannot plot a smooth line through them using the plot() function: def pol2cart(th,r): x = r*cos(th) y = r*sin(th) return (x,y) def drawCircle(cx,cy,radius,np,style): theta = linspace(0,2*pi,np) rho = ones((1,np))*radius x,y = pol2cart(theta,rho) x = x + cx y = y + cy plot(x,y,style) cx = 700 cy = 700 r = 1000 drawCircle(cx,cy,r,1000,'b') When I look at the resulting plot, I see empty axes. If I change the plot style to 'b.', then I see the circle. Is this a bug or an undocumented feature? Thanks, Mike Hearne ```
 Re: [Matplotlib-users] plotting a circle in log space From: John Hunter - 2009-01-24 18:14:25 ```On Fri, Jan 23, 2009 at 2:06 PM, Michael Hearne wrote: > I have discovered, from the mailing list, the easy way to draw a circle > in linear space: > ...snip > cx = 700 > cy = 700 > r = 1000 > > xmin = cx - r > xmax = cx + r > ymin = cy - r > ymax = cy + r > > cir = Circle( (cx,cx), radius=r,facecolor='w',edgecolor='b') > a = gca() > a.add_patch(cir) > > axis([xmin,xmax,ymin,ymax]) > axis('equal') > > How can I plot a circle in log space? The problem is that your circle has negative vertices since cx-r<0 and cy-r<0. When this happens, mpl is transforming the vertices with log coordinates and getting nans, as it should. The problem is that these nan vertices are getting passed to the agg backend, and when the vertex type is curve4, as it is for a circle, agg gets stuck in an infinite recursion in the spline code. I suspect this is because the recursion expects the comparison operator on the vertices to be well behaved, but it is not in the presence of nans. The function in question is agg_curve.cpp curve4_div::recursive_bezier. There is a "maximum recursion limit" in that function, but for some reason I don't understand, it is not breaking out of the function. I committed a simple "fix" to the branch and the trunk to simply drop any patch where any of the vertices are nans if not np.isnan(tpath.vertices).any(): renderer.draw_path(gc, tpath, affine, rgbFace) We might be able to do better than this -- is there a well defined way to deal with patches where any of the transformed vertices are nans? For simple polygons (no splines vertices), we could plot the polygon with all the nan containing vertices removed, though in some cases this could be a strange object -- this appears to be what was happening by default with CirclePolygon with negative vertices but I think this was mostly fortuitous that agg dealt with the nans gracefully in this case. But for patches containing curve vertices, this seems like a bad idea, since simply dropping vertices from a spline curve is not defined. I'm including below some sample code that shows the bug on Agg JDH import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import matplotlib.patches as patches cx = 700 cy = 700 r = 1000 fig = plt.figure() ax = fig.add_subplot(111) #cir = patches.CirclePolygon( (cx,cy), radius=r,facecolor='w',edgecolor='b') cir = patches.Circle( (cx,cy), radius=r,facecolor='w',edgecolor='b') ax.add_patch(cir) ax.set_yscale('log') fig.savefig('test') plt.show() ```
 Re: [Matplotlib-users] plotting a circle in log space From: Michael Droettboom - 2009-01-26 13:02:25 ```At one point in history, the Agg backend would not do NaN removal on paths with curves -- but it looks like that's been inadvertently lost, probably in all the shuffling wrt simplification that went on, since simplification has similar restrictions. So at present, we have problems because it's passing curves with too few points to Agg, since it removes points with NaNs, but not necessarily the entire curve segment. In any case, even passing the vertices as-is (without NaNs removed) to Agg still results in an infinite loop. The "real" fix, IMO, is to make the NaN-handling code aware of curves, which requires doing a look-ahead. That is -- if a curve segment has any NaNs at all, remove the entire curve segment. I've thought about this for a bit, but now here's some impetus to finally implement it. :) Mike John Hunter wrote: > On Fri, Jan 23, 2009 at 2:06 PM, Michael Hearne wrote: > >> I have discovered, from the mailing list, the easy way to draw a circle >> in linear space: >> ...snip >> cx = 700 >> cy = 700 >> r = 1000 >> >> xmin = cx - r >> xmax = cx + r >> ymin = cy - r >> ymax = cy + r >> >> cir = Circle( (cx,cx), radius=r,facecolor='w',edgecolor='b') >> a = gca() >> a.add_patch(cir) >> >> axis([xmin,xmax,ymin,ymax]) >> axis('equal') >> >> How can I plot a circle in log space? >> > > The problem is that your circle has negative vertices since cx-r<0 and > cy-r<0. When this happens, mpl is transforming the vertices with log > coordinates and getting nans, as it should. The problem is that these > nan vertices are getting passed to the agg backend, and when the > vertex type is curve4, as it is for a circle, agg gets stuck in an > infinite recursion in the spline code. I suspect this is because the > recursion expects the comparison operator on the vertices to be well > behaved, but it is not in the presence of nans. The function in > question is agg_curve.cpp curve4_div::recursive_bezier. There is a > "maximum recursion limit" in that function, but for some reason I > don't understand, it is not breaking out of the function. > > I committed a simple "fix" to the branch and the trunk to simply drop > any patch where any of the vertices are nans > > if not np.isnan(tpath.vertices).any(): > renderer.draw_path(gc, tpath, affine, rgbFace) > > We might be able to do better than this -- is there a well defined way > to deal with patches where any of the transformed vertices are nans? > For simple polygons (no splines vertices), we could plot the polygon > with all the nan containing vertices removed, though in some cases > this could be a strange object -- this appears to be what was > happening by default with CirclePolygon with negative vertices but I > think this was mostly fortuitous that agg dealt with the nans > gracefully in this case. But for patches containing curve vertices, > this seems like a bad idea, since simply dropping vertices from a > spline curve is not defined. > > I'm including below some sample code that shows the bug on Agg > > JDH > > import matplotlib > matplotlib.use('Agg') > > import matplotlib.pyplot as plt > import matplotlib.patches as patches > cx = 700 > cy = 700 > r = 1000 > > fig = plt.figure() > ax = fig.add_subplot(111) > > #cir = patches.CirclePolygon( (cx,cy), radius=r,facecolor='w',edgecolor='b') > cir = patches.Circle( (cx,cy), radius=r,facecolor='w',edgecolor='b') > ax.add_patch(cir) > ax.set_yscale('log') > fig.savefig('test') > plt.show() > -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA ```
 Re: [Matplotlib-users] plotting a circle in log space From: Michael Droettboom - 2009-01-26 14:41:08 ```Support for handling NaNs in curves is now on the branch and trunk. While this solves the infinite recursion problem, it still may be better in your specific case to use a CirclePolygon. All my fix does is remove an entire bezier curve when any of its elements are non-finite -- so we're talking an entire eighth-wedge at least here. By using CirclePolygon, the amount of removal could be much less. Mike Michael Droettboom wrote: > At one point in history, the Agg backend would not do NaN removal on > paths with curves -- but it looks like that's been inadvertently lost, > probably in all the shuffling wrt simplification that went on, since > simplification has similar restrictions. So at present, we have > problems because it's passing curves with too few points to Agg, since > it removes points with NaNs, but not necessarily the entire curve > segment. In any case, even passing the vertices as-is (without NaNs > removed) to Agg still results in an infinite loop. > > The "real" fix, IMO, is to make the NaN-handling code aware of curves, > which requires doing a look-ahead. That is -- if a curve segment has > any NaNs at all, remove the entire curve segment. I've thought about > this for a bit, but now here's some impetus to finally implement it. :) > > Mike > > John Hunter wrote: > >> On Fri, Jan 23, 2009 at 2:06 PM, Michael Hearne wrote: >> >> >>> I have discovered, from the mailing list, the easy way to draw a circle >>> in linear space: >>> ...snip >>> cx = 700 >>> cy = 700 >>> r = 1000 >>> >>> xmin = cx - r >>> xmax = cx + r >>> ymin = cy - r >>> ymax = cy + r >>> >>> cir = Circle( (cx,cx), radius=r,facecolor='w',edgecolor='b') >>> a = gca() >>> a.add_patch(cir) >>> >>> axis([xmin,xmax,ymin,ymax]) >>> axis('equal') >>> >>> How can I plot a circle in log space? >>> >>> >> The problem is that your circle has negative vertices since cx-r<0 and >> cy-r<0. When this happens, mpl is transforming the vertices with log >> coordinates and getting nans, as it should. The problem is that these >> nan vertices are getting passed to the agg backend, and when the >> vertex type is curve4, as it is for a circle, agg gets stuck in an >> infinite recursion in the spline code. I suspect this is because the >> recursion expects the comparison operator on the vertices to be well >> behaved, but it is not in the presence of nans. The function in >> question is agg_curve.cpp curve4_div::recursive_bezier. There is a >> "maximum recursion limit" in that function, but for some reason I >> don't understand, it is not breaking out of the function. >> >> I committed a simple "fix" to the branch and the trunk to simply drop >> any patch where any of the vertices are nans >> >> if not np.isnan(tpath.vertices).any(): >> renderer.draw_path(gc, tpath, affine, rgbFace) >> >> We might be able to do better than this -- is there a well defined way >> to deal with patches where any of the transformed vertices are nans? >> For simple polygons (no splines vertices), we could plot the polygon >> with all the nan containing vertices removed, though in some cases >> this could be a strange object -- this appears to be what was >> happening by default with CirclePolygon with negative vertices but I >> think this was mostly fortuitous that agg dealt with the nans >> gracefully in this case. But for patches containing curve vertices, >> this seems like a bad idea, since simply dropping vertices from a >> spline curve is not defined. >> >> I'm including below some sample code that shows the bug on Agg >> >> JDH >> >> import matplotlib >> matplotlib.use('Agg') >> >> import matplotlib.pyplot as plt >> import matplotlib.patches as patches >> cx = 700 >> cy = 700 >> r = 1000 >> >> fig = plt.figure() >> ax = fig.add_subplot(111) >> >> #cir = patches.CirclePolygon( (cx,cy), radius=r,facecolor='w',edgecolor='b') >> cir = patches.Circle( (cx,cy), radius=r,facecolor='w',edgecolor='b') >> ax.add_patch(cir) >> ax.set_yscale('log') >> fig.savefig('test') >> plt.show() >> >> > > -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA ```
 Re: [Matplotlib-users] plotting a circle in log space From: John Hunter - 2009-01-26 14:55:17 ```On Mon, Jan 26, 2009 at 8:40 AM, Michael Droettboom wrote: > Support for handling NaNs in curves is now on the branch and trunk. > > While this solves the infinite recursion problem, it still may be better in > your specific case to use a CirclePolygon. All my fix does is remove an > entire bezier curve when any of its elements are non-finite -- so we're > talking an entire eighth-wedge at least here. By using CirclePolygon, the > amount of removal could be much less. While I think it's great that you fixed this with a scapel rather than my blunt hammer of simply dropping the patch, I wonder if we should be expecting the backends to handle nans. The general philosophy has been to keep them as simple as possible, and nan handling is definitely not simple. Most likely we would pay a price in efficiency by moving the nan handling to the frontend, but would we be better off passing a nan-filtered path to the backend? JDH ```
 Re: [Matplotlib-users] plotting a circle in log space From: Michael Droettboom - 2009-01-26 15:18:45 ```John Hunter wrote: > On Mon, Jan 26, 2009 at 8:40 AM, Michael Droettboom wrote: > >> Support for handling NaNs in curves is now on the branch and trunk. >> >> While this solves the infinite recursion problem, it still may be better in >> your specific case to use a CirclePolygon. All my fix does is remove an >> entire bezier curve when any of its elements are non-finite -- so we're >> talking an entire eighth-wedge at least here. By using CirclePolygon, the >> amount of removal could be much less. >> > > While I think it's great that you fixed this with a scapel rather than > my blunt hammer of simply dropping the patch, I wonder if we should be > expecting the backends to handle nans. The general philosophy has > been to keep them as simple as possible, and nan handling is > definitely not simple. Most likely we would pay a price in efficiency > by moving the nan handling to the frontend, but would we be better off > passing a nan-filtered path to the backend? > I don't see this as a backend/frontend issue -- I see it as a C++/Python one. This recent change was in C++ (in PathIterator), which is generic and not specific to Agg, other than some conventions. For the Python backends, this is handled by Path.iter_vertices. This separation of NaN-handling (in C++ and in Path.iter_vertices) has been there for ages. In fact, the non-C++ backends have supported NaNs on curves for a long time (though with a small corner-case bug that's now fixed). The Cocoa backend should probably use the common NaN-handling and simplification code, but that may require using Objective-C++, rather than just Objective-C. Alternatively, we could rewrite the NaN-handling/simplification code to use pure C, with a little shim to make it work in the highly-templatized C++ Agg world. We could (as we do now for simplification) call out to C++ for NaN-handling as well, but I would be wary of doing the opposite. Mike -- Michael Droettboom Science Software Branch Operations and Engineering Division Space Telescope Science Institute Operated by AURA for NASA ```