matplotlib-devel Mailing List for matplotlib (Page 2)

I have commited a set of changes to _transforms, collections, quiver, 
contour, and numerix as part of a move toward taking advantage of the 
efficiency of numerix arrays in place of sequences of tuples.  The 
changes are outlined very briefly in CHANGELOG and API_CHANGES.

Changes in clabel are hacks, and may make it less efficient rather than 
more, but I expect this to be temporary; I needed to simply make it work 
with the other changes.

Where breakage will occur is any place in user code that expects the 
collection segments or vertices to be lists of tuples and tries to 
append to the list, for example.  I don't know of any way to make the 
move towards use of arrays without this problem cropping up; I hope it 
is considered tolerable.

Eric

>>>>> "Edin" =3D=3D Edin Salkovi=A7 <edi...@gm...> writes:

    Edin> I finally solved the problem of automaticaly generating the
    Edin> dicts for unicode <-> TeX conversion. This is the first step
    Edin> in enabling unicode support in mathtext.

Excellent.=20


    Edin> The STIX projects is usefull after all ;) They keep a nice
    Edin> table of Unicode symbols at:
    Edin> http://www.ams.org/STIX/bnb/stix-tbl.ascii-2005-09-24

    Edin> Any comments about the script are appreciated :). Now I'll

Since you asked :-)

I may not have mentioned this but the style conventions for mpl code
are=20

  functions : lower or lower_score_separated
  variables and attributes : lower or lowerUpper
  classes : Upper or MixedUpper

Also, I am not too fond of the dict of dicts -- why not use variable
names?  Here is my version

    import pickle

    fname =3D 'stix-tbl.ascii-2005-09-24'

    uni2type1 =3D dict()
    type12uni =3D dict()
    uni2tex =3D dict()
    tex2uni =3D dict()

    for line in file(fname):
        if line[:2]!=3D' 0': continue # using continue avoids unneccesary=
 indent

        uninum =3D line[2:6].strip().lower()
        type1name =3D line[12:37].strip()
        texname =3D line[83:110].strip()

        uninum =3D int(uninum, 16)
        if type1name:
            uni2type1[uninum] =3D type1name
            type12uni[type1name] =3D uninum
        if texname:
            uni2tex[uninum] =3D texname
            tex2uni[texname] =3D uninum
    pickle.dump((uni2type1, type12uni, uni2tex, tex2uni), file('unitex.pc=
l','w'))

    # An example
    unichar =3D int('00d7', 16)
    print uni2tex.get(unichar)
    print uni2type1.get(unichar)

Also, I am a little hesitant to use pickle files for the final
mapping.  I suggest you write a script that generates the python code
contains the dictionaries you need (that is how much of _mathext_data
was generated.

Thanks,
JDH

I finally solved the problem of automaticaly generating the dicts for
unicode <-> TeX conversion. This is the first step in enabling unicode
support in mathtext.

The STIX projects is usefull after all ;) They keep a nice table of
Unicode symbols at:
http://www.ams.org/STIX/bnb/stix-tbl.ascii-2005-09-24

Any comments about the script are appreciated :). Now I'll dig a bit
deeper into the font classes to fix them to suport unicode.

'''A script for seemlesly copying the data from the stix-tbl.ascii*
file to a set
of python dicts. Dicts are then pickled to coresponding files, for
later retrieval.
Currently used table file:
http://www.ams.org/STIX/bnb/stix-tbl.ascii-2005-09-24
'''

import pickle

table_filename = 'stix-tbl.ascii-2005-09-24'
dict_names = ['uni2type1', 'type12uni', 'uni2tex', 'tex2uni']
dicts = {}
# initialize the dicts
for name in dict_names:
    dicts[name] = {}

for line in file(table_filename):
    if line[:2]==' 0':
        uni_num = eval("u'\\u"+line[2:6].strip().lower()+"'")
        type1_name = line[12:37].strip()
        tex_name = line[83:110].strip()
        if type1_name:
            dicts['uni2type1'][uni_num] = type1_name
            dicts['type12uni'][type1_name] = uni_num
        if tex_name:
            dicts['uni2tex'][uni_num] = tex_name
            dicts['tex2uni'][tex_name] = uni_num
for name in dict_names:
    pickle.dump(dicts[name], open(name + '.pcl','w'))

# An example
uni_char = u'\u00d7'
print dicts['uni2tex'][uni_char]
print dicts['uni2type1'][uni_char]
# Testing of results, testing; feel free to unquote
# _mathtext_data.py can be found in the matplolib dir
#~ from _mathtext_data import latex_to_bakoma
#~ supported = 0
#~ unsupported = 0
#~ for tex_symbol in latex_to_bakoma:
    #~ try:
        #~ print tex_symbol, dicts['tex2uni'][tex_symbol]
        #~ supported += 1
    #~ except KeyError:
        #~ unsupported += 1
        #~ pass
#~ print supported, unsupported

>>>>> "Martin" == Martin Spacek <sc...@ms...> writes:

Hey martin, thanks for all these changes.

    Martin> to inconsistent behaviour: barh() draws bars vertically
    Martin> centered on the y values (ala matlab 6.0), while bar()
    Martin> draws bars aligned according to their left edge (not ala
    Martin> matlab). I prefer the edge aligning behaviour. It's easy
    Martin> to convert from one behaviour to the other, but I had to
    Martin> duplicate all the error checking code before conversion,
    Martin> which bloated it back up.

Most people prefer the center aligning behavior, at least those who
complained on the list about bar, so when I wrote barh I adopted
this.  I tried to fix bar in the process, but ended up running into
some bugs when I tested John Gill's table demo, and so left it as edge
aligned and haven't revisited it since.  So my weak preference would
be to have the two functions consistent and center aligned, but he who
does the work usually gets the biggest vote.  Maybe others can chime
in.
    Martin> And lastly... I find it odd that barh() has the width and
    Martin> bottom args (formerly x and y) in that order: barh(width,
    Martin> bottom). The general matlab convention is that the first
    Martin> argument is the positions, and the second arg is the
    Martin> values. So it would make more sense to me to have
    Martin> barh(bottom, width). That way, you could switch back and
    Martin> forth between bar() and barh() and get the expected
    Martin> behaviour without having to switch around the
    Martin> arguments. In fact, that's exactly how barh() in matlab 6
    Martin> interprets the first two arguments: arg1 is the vertical
    Martin> positions, and arg2 is the lengths of the bars at those
    Martin> positions. Same goes for matlab's bar() function. As it is
    Martin> now in matplotlib, the first and second arguments are
    Martin> interpreted differently for bar() and barh()

I was following the convention that the x arg goes first and the y
second, but I'm not wed to this.  I don't mind breaking existing code
if this order seems more natural, and since we are mostly emulating
the matlab conventions in bar and barh, it makes some sense to strive
for consistency.  Perhaps you could patch the CHANGELOG and
API_CHANGES file along with the rest which explains the changes.

JDH

Well, I seem to have really dove into this.

Here are 4 different patches against the latest svn of axes.py (rev 
2495). Note that the rest of my install is the 0.87.3 release (I had to 
copy over quiver.py to get the latest axes.py to work).

patch1 has the following changes to bar() and barh():

- fixed ignoring the rcParams['patch.facecolor'] for bar color: the 
default value for the color arg is now None, and the Patch class is left 
to handle fetching the rcparams['patch.facecolor']

- set default error bar color to None, so that errorbar() can handle 
fetching the rcParams['lines.color']

- added an edgecolor keyword arg

- left and height can now both be scalars in bar(), same goes for x and 
y in barh(). Previously, this raised a TypeError upon testing their 
lengths. Code that preventively checked for this in barh() (but not in 
bar()) has been removed.

- fixed a bug where patches would be cleared when error bars were 
plotted if rcParams['axes.hold'] was False

- it looks like the code for barh() was copied from bar(), with some of 
the args renamed. There was an error in the color checking code in 
barh() where len(left) from bar() hadn't been properly renamed to len(x)

- found one or two changes that had been made to bar() that hadn't been 
propagated to barh(), or vice versa

- rearranged the order of some code segments so that they follow the 
order of the arguments

- updated the docstrings

Hopefully I haven't introduced any new bugs.

patch2 has everything in patch1, except it removes some code duplication 
by calling bar() from within barh(). I thought this would be a good 
idea, since it's easy to make a change in bar() and forget to do the 
same in barh(). It turns out that this takes up almost as many lines of 
code as having two independent functions, but this is only due to 
inconsistent behaviour: barh() draws bars vertically centered on the y 
values (ala matlab 6.0), while bar() draws bars aligned according to 
their left edge (not ala matlab). I prefer the edge aligning behaviour. 
It's easy to convert from one behaviour to the other, but I had to 
duplicate all the error checking code before conversion, which bloated 
it back up.

So... patch3 has everything in patch2, but renames the x and y args in 
barh() to width and bottom respectively. This makes barh() draw bars 
vertically aligned to their bottom edge, consistent with bar()'s 
behaviour. Also, this makes hist(orientation='horizontal') do the same, 
which makes it consistent with hist(orientation='vertical'). Finally, it 
removes the code bloat mentioned above. However, it'll break any 
existing code that relies on x or y as named args in barh(), or code 
that expects barh() bars to be vertically centered on their y values.

And lastly... I find it odd that barh() has the width and bottom args 
(formerly x and y) in that order: barh(width, bottom). The general 
matlab convention is that the first argument is the positions, and the 
second arg is the values. So it would make more sense to me to have 
barh(bottom, width). That way, you could switch back and forth between 
bar() and barh() and get the expected behaviour without having to switch 
around the arguments. In fact, that's exactly how barh() in matlab 6 
interprets the first two arguments: arg1 is the vertical positions, and 
arg2 is the lengths of the bars at those positions. Same goes for 
matlab's bar() function. As it is now in matplotlib, the first and 
second arguments are interpreted differently for bar() and barh()

I don't know if anyone agrees with this change, but patch4 has all of 
the changes in patch3, plus the order of the width and bottom args are 
switched in barh(). This of course will break existing code that depends 
on this order. I had to modify the barh() call in 
hist(orientation='horizontal') to reflect this. I couldn't find any 
other barh() call in matplotlib. For consistency, I also switched the 
order of the yerr and xerr args, but these have default values and are 
usually passed as keyword args, so this shouldn't break (much) code.

The patches are numbered in increasing order of preference. They look 
rather big (and I'm not sure if my file compare util is bug-free). If 
there seem to be problems with them, I can provide the full axes.py file 
that corresponds to each patch.

Cheers,

Martin

John Hunter wrote:
>>>>>>"Eric" == Eric Firing <ef...@ha...> writes:
> 
> 
>     Eric> Based on a quick look, I think it would be easy to make
>     Eric> LineCollection and PolyCollection accept a numerix array in
>     Eric> place of [(x,y), (x,y), ...] for each line segment or
>     Eric> polygon; specifically, this could replaced by an N x 2
>     Eric> array, where the first column would be x and the second
>     Eric> would be y.  Backwards compatibility could be maintained
>     Eric> easily.  This would eliminate quite a bit of useless
>     Eric> conversion back and forth among lists, tuples, and arrays.
>     Eric> As it is, each sequence of sequences is converted to a pair
>     Eric> of arrays in backend_bases, and typically it started out as
>     Eric> either a 2-D numerix array or a pair of 1-D arrays in the
>     Eric> code that is calling the collection constructor.
> 
> I think this is a useful enhancement.  I would think that representing
> each segment as (x,y) where x and y are 1D arrays, might be slightly
> more natural than using an Nx2 but others may disagree.

John,

I have been working on this and I can probably commit something in the 
next few days.  I have been pursuing the Nx2 representation for the 
following reasons:

1) It is highly compatible with the present sequence of tuples, so that 
the two representations can coexist peacefully:

a = [(1,2), (3,4), (5,6)]  # present style
aa = numerix.array(a)      # new style

In most places, a and aa work the same with no change to the code.  The 
exception is where code does something like "a.append(b)".  This occurs 
in the contour labelling code.  I haven't fixed it yet, but I don't see 
any fundamental problem in doing so.

2) The Nx2 representation streamlines code because it involves one 2-D 
object, "XY", in place of two 1-D objects, X and Y.  This also 
eliminates the need to check that the lengths of X and Y match. 
Logically, X and Y must go together, so why not keep them glued together 
in a single array?

Because of the compatibility, there is very little code that actually 
has to be changed to support the numerix array.  There is a potential 
for breakage of user code, however.  This is a concern.  I don't know of 
any way of eliminating it entirely while retaining the efficiency 
benefits of using numerix arrays when possible.  One thing that might 
help is to have the transform seq_xy_tups method handle both input 
forms, and return the form corresponding to the input.  I can do this; I 
now have a transform method that handles both "a" and "aa", but 
presently it returns a numerix array in either case.

The optimization you describe below sounds good, but I want to finish 
stage 1, above, first.

Eric
> 
> How often does it come up that we want a homogeneous line collection,
> ie a bunch of lines segments with the same properties (color,
> linewidth...)?  The most expensive part of the agg line collection
> renderer is probably the multiple calls to render_scanlines, which is
> necessary every time we change the linewidth or color.  
> 
> If all of the lines in a collection shared the same properties, we
> could draw the entire path with a combination of lineto/moveto, and
> just stroke and render it once (agg has an upper limit on path length
> though, since at some point I added the following to draw_lines
> 
>     if ((i%10000)==0) {
>       //draw the path in chunks
>       _render_lines_path(path, gc);
>       path.remove_all();
>       path.move_to(thisx, thisy);
>     }
> 
> Ie I render it every 10000 points.  
> 
> Actually, as I type this I realize the case of homogeneous lines (and
> polys) can be handled by the backend method "draw_path".  One
> possibility is for the LineCollection to detect the homogeneous case
> len(linewidths)==1 and len(colors)==1 and call out to draw_path
> instead of draw_line_collection (the same could be done for a regular
> poly collection).  Some extra extension code would probably be
> necessary to build the path efficiently from numerix arrays, and to
> handle the "chunking" problem to avoid extra long paths, but for
> certain special cases (scatters and quiver w/o color mapping) it would
> probably be a big win.  The downside is that not all backend implement
> draw_paths, but the Collection front-end could detect this and fall
> back on the old approach if draw_paths is not implemented.
> 
> JDH

>>>>> "Martin" == Martin Spacek <sc...@ms...> writes:


    Martin> Don't know if this is the best way, but here's a solution:

    Martin> def bar(self, left, height, width=0.8, bottom=0,
    Martin> color=matplotlib.rcParams['patch.facecolor'], yerr=None,
    Martin> xerr=None, ecolor=matplotlib.rcParams['patch.edgecolor'],
    Martin> capsize=3 ):

Hey Martin, 

We don't put the rc defaults in the function declaration because these
are evaluated only once, at module load time, which prevents users
from being able to change the defaults after the module is loaded.  So
we use this idiom

def somefunc(edgecolor=None):
   if edgecolor is None: edgecolor = rcParams['patch.edgecolor']

If you'd like to submit a patch for bar and barh, that'd be great.

Thanks,
JDH

I've noticed that the rcparams settings for patch.facecolor and
patch.endcolor is ignored by bar() and barh() (and therefore hist()),
always displaying as blue and black, respectively. Is this intentional? 
I'm running matplotlib 0.87.3

The culprit:

def bar(self, left, height, width=0.8, bottom=0,
         color='b', yerr=None, xerr=None, ecolor='k', capsize=3
         ):

Don't know if this is the best way, but here's a solution:

def bar(self, left, height, width=0.8, bottom=0,
         color=matplotlib.rcParams['patch.facecolor'],
         yerr=None, xerr=None,
         ecolor=matplotlib.rcParams['patch.edgecolor'], capsize=3
         ):

Similar situation for barh()

Cheers,

Martin

Hi - this is my first post to such a list, so bear with me.=20

=20

I've just installed mpl3d and have had success with the examples shown =
at
http://www.scipy.org/Cookbook/Matplotlib/mplot3D

=20

We currently don't have numpy installed and using the older Numeric, so =
I
used the following instead:

=20

N =3D 100

x =3D zeros((N,N),Float)

y =3D zeros((N,N),Float)

z =3D zeros((N,N),Float)

u =3D arange(0,2*pi,2.*pi/N)

v =3D arange(0,2*pi,2.*pi/N)

=20

for i in range(N):

    for j in range(N):

        x[i,j] =3D cos(u[i])*sin(v[j])

        y[i,j] =3D sin(u[i])*sin(v[j])

        z[i,j] =3D cos(v[j])

=20

fig=3Dp.figure()

ax =3D p3.Axes3D(fig)

ax.plot_surface(x,y,z)

ax.set_xlabel('X')

ax.set_ylabel('Y')

ax.set_zlabel('Z')

fig.add_axes(ax)

p.show()

p.savefig('surfacetest')

p.close()

=20

which worked a treat (apart from the figure not closing on the first =
instance
...).

=20

However, if I change N to 10, I get the following error message:

=20

Traceback (most recent call last):

  File "test.py", line 47, in ?

    ax.plot_surface(x,y,z)

  File "c:\Python24\lib\site-packages\mpl3d\mplot3d.py, line 921, in
plot_surface

    norm =3D normalize(min(shade),max(shade))

ValueError: min() arg is an empty sequence

=20

It seems that if the number of columns or rows is less than 20 than =
rstride
and cstride =3D 0. This means that the boxes required to make the =
polygons in
the surface plot won't be constructed. However, you can get a 3D plot if =
you
use plot_wireframe or plot3D instead with N =3D 10 (but these plots =
aren't
quite as nice as the surface plot would be).

=20

Is there a minimum size of the arrays which plot_surface will work on? =
Is
there a workaround for smaller examples? I'm looking at plotting a =
(smallish)
number of time series solutions as a surface.

=20

Cheers, Jane.

=20

Dr Jane Sexton

Risk Research Group

Geospatial and Earth Monitoring Division

Geoscience Australia

Hi Edin,

Edin Salković wrote:
> Hi all,
> 
<snip>
> Also, if anyone has some good online sources about parsing etc. on the
> net, I vwould realy appreciate it.

Everything that David Mertz wrote about text processing in his excellent 
"Charming Python" articles:
<http://gnosis.cx/publish/tech_index_cp.html>

and "Building Recursive Descent Parsers with Python":
http://www.onlamp.com/pub/a/python/2006/01/26/pyparsing.html

If you were after a book on the subject, Mertz's book "Text Processing 
in Python" <http://gnosis.cx/TPiP/> would be an obvious choice or you 
could pick up any book about writing compilers.

Gary R.

On 6/15/06, John Hunter <jdh...@ac...> wrote:
> How often does it come up that we want a homogeneous line collection,
> ie a bunch of lines segments with the same properties (color,
> linewidth...)?

Hi,
for b&w PS publication quality plotting, this must be a common thing to draw;
contour lines, vectors, xy plots, the axes, tick marks, even fonts
can all be constructed from disjoint line segments, no?
if matplotlib could pass numerix arrays more or less directly to gtk it could
perhaps also become the speed king of plotting packages :)

Helge

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>>>>> "Edin" =3D=3D Edin Salkovi=A7 <edi...@gm...> writes:

    Edin> Hi all, Is it that the code in the mathtext module looks
    Edin> ugly or is it just me not understanding it?  Also, if anyone
    Edin> has some good online sources about parsing etc. on the net,
    Edin> I vwould realy appreciate it.


It's probably you not understanding it :-) In my opinion, the code is
pretty nice and modular, with a few exceptions, but I'm biased.
Parsers can be a little hard to understand at first.  You might start
by trying to understand pyparsing

  http://pyparsing.wikispaces.com

and work through some of the basic examples there.  Once you have your
head wrapped around that, it will get easier.

    Edin> Considering the foowing code (picked on random, from
    Edin> mathtext.py)

    Edin> I don't understand, for example, what does the statement:

    Edin> expression.parseString( s )

    Edin> do?

    Edin> "expression" is defined globaly, and is called (that is -
    Edin> its method) only once in the above definition of the
    Edin> function, but I don't understand - what does that particular
    Edin> line do?!?

It's not defined globally, but at module level.  There is only one
expression that represents a TeX math expression (at least as far as
mathtext is concerned) so it is right that there is only one of them
at module level.  It's like saying "a name is a first name followed by
an optional middle initial followed by a last name".  You only need to
define this one, and then you set handlers to handle the different
components.

The expression assigns subexpressions to handlers.  The statement
below says that an expression is one or more of a space, font element,
an accent, a symbol, a subscript, etc...

expression =3D OneOrMore(
    space ^ font ^ accent ^ symbol ^ subscript ^ superscript ^ subsupersc=
ript ^ group ^ composite  ).setParseAction(handler.expression).setName("e=
xpression")

A subscript, for example, is a symbol group followed by an underscore
followed by a symbol group

subscript << Group( Optional(symgroup) + Literal('_') + symgroup  )

and the handler is defined as

subscript =3D Forward().setParseAction(handler.subscript).setName("subscr=
ipt")

which means that the function handler.subscript will be called every
time the pattern is matched.  The tokens will be the first symbol
group, the underscore, and the second symbol group.  Here is the
implementation of that function

    def subscript(self, s, loc, toks):
        assert(len(toks)=3D=3D1)
        #print 'subsup', toks
        if len(toks[0])=3D=3D2:
            under, next =3D toks[0]
            prev =3D SpaceElement(0)
        else:
            prev, under, next =3D toks[0]           =20

        if self.is_overunder(prev):
            prev.neighbors['below'] =3D next
        else:
            prev.neighbors['subscript'] =3D next

        return loc, [prev]

This grabs the tokens and assigns them to the names "prev" and "next".
Every element in the TeX expression is a special case of an Element,
and every Element has a dictionary mapping surrounding elements to
relative locations, either above or below or right or superscript or
subscript.  The rest of this function takes the "next" element, and
assigns it either below (eg for \Sum_\0) or subscript (eg for x_0) and
the layout engine will then take this big tree and lay it out.  See
for example the "set_origin" function?


    Edin> ------ Regarding the unicode s
upport in mathtext, mathtext
    Edin> currently uses the folowing dictionary for getting the glyph
    Edin> info out of the font files:

    Edin> latex_to_bakoma =3D {

    Edin>     r'\oint' : ('cmex10', 45), r'\bigodot' : ('cmex10', 50),
    Edin> r'\bigoplus' : ('cmex10', 55), r'\bigotimes' : ('cmex10',
    Edin> 59), r'\sum' : ('cmex10', 51), r'\prod' : ('cmex10', 24),
    Edin> ...
    Edin> }

    Edin> I managed to build the following dictionary(little more left
    Edin> to be done): tex_to_unicode =3D { r'\S' : u'\u00a7', r'\P' :
    Edin> u'\u00b6', r'\Gamma' : u'\u0393', r'\Delta' : u'\u0394',
    Edin> r'\Theta' : u'\u0398', r'\Lambda' : u'\u039b', r'\Xi' :
    Edin> u'\u039e', r'\Pi' : u'\u03a0', r'\Sigma' : u'\u03a3',

    Edin> unicode_to_tex is straight forward.  Am I on the right
    Edin> track? What should I do next?

Yes, this looks like the right approach.  Once you have this
dictionary mostly working, you will need to try and make it work with
a set of unicode fonts.  So instead of having the tex symbol point to
a file name and glyph index, you will need to parse a set of unicode
fonts to see which unicode symbols they provide and build a mapping
from unicode name -> file, glyph index.  Then when you encounter a tex
symbol, you can use your tex_to_unicode dict combined with your
unicode -> filename, glyphindex dict to get the desired glyph.


    Edin> I also noticed that some TeX commands (commands in the sense
    Edin> that they can have arguments enclosed in brackets {}) are
    Edin> defined as only symbols: \sqrt alone, for example, displays
    Edin> just the begining of the square root:=BA, and \sqrt{123}
    Edin> triggers an error.

We don't have support for \sqrt{123} because we would need to do
something a little fancier (draw the horizontal line over 123).  This
is doable and would be nice.  To implement it, one approach would be
add some basic drawing functionality to the freetype module, eg to
tell freetype to draw a line on it's bitmap.  Another approach would
simply be to grab the bitmap to freetype and pass it off to agg and
use the agg renderer to decorate it.  This is probably preferable.

But I think this is a lower priority right now.

JDH

>>>>> "Eric" == Eric Firing <ef...@ha...> writes:

    Eric> Based on a quick look, I think it would be easy to make
    Eric> LineCollection and PolyCollection accept a numerix array in
    Eric> place of [(x,y), (x,y), ...] for each line segment or
    Eric> polygon; specifically, this could replaced by an N x 2
    Eric> array, where the first column would be x and the second
    Eric> would be y.  Backwards compatibility could be maintained
    Eric> easily.  This would eliminate quite a bit of useless
    Eric> conversion back and forth among lists, tuples, and arrays.
    Eric> As it is, each sequence of sequences is converted to a pair
    Eric> of arrays in backend_bases, and typically it started out as
    Eric> either a 2-D numerix array or a pair of 1-D arrays in the
    Eric> code that is calling the collection constructor.

I think this is a useful enhancement.  I would think that representing
each segment as (x,y) where x and y are 1D arrays, might be slightly
more natural than using an Nx2 but others may disagree.

How often does it come up that we want a homogeneous line collection,
ie a bunch of lines segments with the same properties (color,
linewidth...)?  The most expensive part of the agg line collection
renderer is probably the multiple calls to render_scanlines, which is
necessary every time we change the linewidth or color.  

If all of the lines in a collection shared the same properties, we
could draw the entire path with a combination of lineto/moveto, and
just stroke and render it once (agg has an upper limit on path length
though, since at some point I added the following to draw_lines

    if ((i%10000)==0) {
      //draw the path in chunks
      _render_lines_path(path, gc);
      path.remove_all();
      path.move_to(thisx, thisy);
    }

Ie I render it every 10000 points.  

Actually, as I type this I realize the case of homogeneous lines (and
polys) can be handled by the backend method "draw_path".  One
possibility is for the LineCollection to detect the homogeneous case
len(linewidths)==1 and len(colors)==1 and call out to draw_path
instead of draw_line_collection (the same could be done for a regular
poly collection).  Some extra extension code would probably be
necessary to build the path efficiently from numerix arrays, and to
handle the "chunking" problem to avoid extra long paths, but for
certain special cases (scatters and quiver w/o color mapping) it would
probably be a big win.  The downside is that not all backend implement
draw_paths, but the Collection front-end could detect this and fall
back on the old approach if draw_paths is not implemented.

JDH

Hello,

I use matplotlib 0.87.3 on win32 with wxpython.

 From the command line, the numeric package is set correctly : numpy 
(read from matplotlibrc) and all woks fine.

I try to use matplotlib from pyxpcom (the connector between xpcom and 
python in the mozilla world), it seems matplotlib doesn't read 
matplotlibrc since it  looks for numeric package which is not installed.

I don't undestand, is there a reason the matplotlibrc file is not read, 
interpreted ?

thanks a lot,

Cyril.

Eric Firing wrote:
> Jordan,
>
> I understand what you wrote.  I am a bit worried about the amount of 
> complexity it would add to the collection code, however, and it seems 
> like it would be useful only in quite special situations--and in those 
> situations, there may be reasonable alternatives.  For example, the ps 
> backend uses nan as a flag or separator to skip drawing a line 
> segment; if all backends did this, then it would provide a more 
> general way to accomplish what you want to do.
>
> I will keep your idea in mind, but I want to start off with a much 
> simpler change.
I would tend to agree that nan entries would be a better idea than what 
I was talking about.  I'll think about trying to modify the backend 
codes to support this behaviour, if they don't already.

Jordan

I have one suggestion, slightly off-topic, and I'm not sure how useful 
it would be: you might think about making LineCollection accept a 3-D 
numerix array.  This came up for me while I was looking at turning the 
quiver arrows into line segments.  As I understand it (and as the 
documentation says) LineCollection takes a set of a lines which are 
composed of continuous line segments, like:

segments = ( line0, line1, line2 )
linen = ( (x0,y0), (x1,y1), (x2, y2) )

I'd like an extra level of organization, like so:

linegroups = ( group0, group1, group2)
groupi = ( line0, line1, line2 )
linen = ( (x0,y0), (x1,y1), (x2, y2) )

Where "linegroups" would be the input to LineCollection.  I assume it's 
fairly obvious how this turns into a rank 3 array.

The reason for this is that it allows for the drawing of non-continuous 
lines.  This came up with the quiver arrow stuff because, as it stands, 
drawing a line-based arrow requires you to back-track over a previous 
line at least once.  This created some rendering problems, where the 
back-tracked line was darker than the others, at least on the agg 
backend.  This can be fixed by backtracking along every line in the 
arrow, so you are essentially drawing the arrow twice, but that seems 
inefficient.  It is possible to draw 3 seperate line segments for each 
arrow, but then the colormapping no longer works; each line segment gets 
a different color, and the arrows look like a mess.

As I said, I don't know how useful this would be; it only comes up when 
drawing non-closed line segments that need to be addressed as a single 
object.  Does what I wrote make sense?

Jordan

Eric Firing wrote:
> Based on a quick look, I think it would be easy to make LineCollection 
> and PolyCollection accept a numerix array in place of [(x,y), (x,y), 
> ...] for each line segment or polygon; specifically, this could replaced 
> by an N x 2 array, where the first column would be x and the second 
> would be y.  Backwards compatibility could be maintained easily.  This 
> would eliminate quite a bit of useless conversion back and forth among 
> lists, tuples, and arrays.  As it is, each sequence of sequences is 
> converted to a pair of arrays in backend_bases, and typically it started 
> out as either a 2-D numerix array or a pair of 1-D arrays in the code 
> that is calling the collection constructor.
>
> Using a single 2-D array makes it easier to determine whether one is 
> dealing with 'old-style' inputs or 'new-style' inputs, but it might 
> still be reasonable to allow [X, Y] instead or in addition, where X and 
> Y are 1-D numerix arrays.
>
> Any objections or alternative suggestions?
>
> Eric
>
>
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>   

Based on a quick look, I think it would be easy to make LineCollection 
and PolyCollection accept a numerix array in place of [(x,y), (x,y), 
...] for each line segment or polygon; specifically, this could replaced 
by an N x 2 array, where the first column would be x and the second 
would be y.  Backwards compatibility could be maintained easily.  This 
would eliminate quite a bit of useless conversion back and forth among 
lists, tuples, and arrays.  As it is, each sequence of sequences is 
converted to a pair of arrays in backend_bases, and typically it started 
out as either a 2-D numerix array or a pair of 1-D arrays in the code 
that is calling the collection constructor.

Using a single 2-D array makes it easier to determine whether one is 
dealing with 'old-style' inputs or 'new-style' inputs, but it might 
still be reasonable to allow [X, Y] instead or in addition, where X and 
Y are 1-D numerix arrays.

Any objections or alternative suggestions?

Eric

I'm making an errorbar plot with assymetric errorbars. The docstring says:

xerr and yerr may be any of:
        a rank-0, Nx1 Numpy array  - symmetric errorbars +/- value
        an N-element list or tuple - symmetric errorbars +/- value
        a rank-1, Nx2 Numpy array  - asymmetric errorbars -column1/+column2

I think that last line should read:
	a 2xN Numpy array  - asymmetric errorbars -row1/+row2


Darren

How about 'plots'?  (i.e., a bunch of plot commands)

Perhaps this could also be the function that loops through multiple =20
lines.  For example in matlab you can do

plot (x, y)
plot (x', y')

to plot out a grid -- the columns (or is it the rows..) are looped =20
through inside the plot command.  Is this the sort of thing you have =20
in mind for the new 'parplot' command?

-Rob

On Jun 14, 2006, at 1:06 AM, Ga=EBl Varoquaux wrote:

> On Tue, Jun 13, 2006 at 05:33:57PM +0200, Ga=EBl Varoquaux wrote:
>>     I find that "parplot" is not a great name for such a function, =20=

>> but I
>> cannot think of a better one. Maybe the list will have better ideas.
>
>     Talking to a friend we came up with a name like "pathcolor", or
> "pathplot".
>
> 	Ga=EBl
>
>
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel

-----
Rob Hetland, Assistant Professor
Dept of Oceanography, Texas A&M University
p: 979-458-0096, f: 979-845-6331
e: he...@ta..., w: http://pong.tamu.edu

On Tue, Jun 13, 2006 at 05:33:57PM +0200, Ga=EBl Varoquaux wrote:
>     I find that "parplot" is not a great name for such a function, but =
I
> cannot think of a better one. Maybe the list will have better ideas.

    Talking to a friend we came up with a name like "pathcolor", or
"pathplot".

	Ga=EBl

Robert,

Thanks for the feedback.  Comments are below.  I think I addressed some 
items over the weekend, so the version in svn should work better than 
the one you tested, assuming you tested the original one I sent out as a 
diff.

Robert Hetland wrote:
> 
> Eric-
> 
> I had a chance to play around with the new quiver this morning.  Here  
> are some thoughts:
> 
> 1. I read that somebody thought it was a bit slow, but this is not my  
> experience.  I tried to quiver my model data (128x128 with masking),  
> and it rendered in a few seconds.  I tried to look at images with  more 
> arrows, but I could not actually see the arrows with so many  points.  
> In my experience you can't put more than about O(100000)  (i.e., about 
> 100x100) arrows on a figure and have it make any sense  anyways.
> 
> 2.  It seems to handle masking fine.  I gave it masked arrays and  
> arrays with nans (it complained a bit about the masked array, but  
> rendered anyways).  This is key for me.
> 

Interesting.  I did nothing to explicitly deal with masked arrays or 
nans, so how well this works may be backend-dependent and/or platform 
dependent.  If this turns out to be a problem, I can put in more 
explicit handling of masks and nans, but it is likely to add overhead.

Question: should handling of masks apply to all input arrays, or is it 
enough to have it apply to U, V, and C?  It doesn't matter so much for 
Quiver, but it is one of the differences between pcolor and 
pcolormesh--support of masked X, Y complicates the former and might be 
hard to add to the latter.  I hope it is unnecessary.

> 3.  It handles colors nicely, but there is no apparent way to set the  
> color limits. Perhaps adding vmin and vmax as kwargs (matching  pcolor) 
> would make some sense.

This brings up a more general design question: when should functionality 
like this be added via kwargs versus other mechanisms?  It would be nice 
to have more uniformity among classes and functions, so that the general 
strategy could be documented once for a whole bunch of functions, 
instead of being repeated, with variations, for each.  This would go 
along with better factoring out of chunks of functionality.  In the 
absence of a big push, all this is going to have to happen piecemeal if 
at all, and complicated by the demands of backwards compatibility.

Returning to the specific question, however, I left vmin and vmax out to 
keep things simple, with the idea that there are other standard ways of 
setting them: via an explicit norm kwarg, via the clim  method of any 
scalar mappable (which the Quiver is, since it inherits from 
PolyCollection), and via the pylab clim command.  If there is a 
consensus that scalar mappables should uniformly support the vmin and 
vmax kwargs directly, then I don't mind adding that.  I can see the 
argument for uniformity, given that this is common among scalar 
mappables.  Probably it could be factored out by inclusion in 
ScalarMappable.__init__.


> 
> 4.  I *really* like how the arrows get gray (and don't try to render  at 
> a whole pixel) when they get small.  I agree with the other person  that 
> it might be nice to have a  small dot to indicate zero  velocity.  No 
> dot should be rendered *ever* for values masked or  NaNed, however.
> 

The graying is a function of the backend--specifically, whether 
rendering is antialiased.

The optional dot (actually a hexagon) for arrows below a threshold size 
is in svn, one of the changes I made over the weekend.

> 5. It's a bit of a pain to find values of scale and width that work  
> well, and quiver doesn't seem to make very good choices by default.   I 
> don't think this is a big deal, but rather simply the price of the  
> added functionality.  Making some more intelligent default choices  
> might not be a bad idea, though.  In particular, smaller arrows when  
> there are more arrows to be rendered would be a good place to start.
> 

I changed the autoscaling so that both the length scale and the shaft 
width (and therefore the head size, which scales with shaft width) vary 
with the square root of the number of arrows, but with limits to prevent 
arrows from getting too large and fat or too small and thin.  So I think 
you will find the svn version much improved in this regard.



> Some ideas for future work:
> 
> 1. I'm pretty happy with the polygons, but it would be nice to have  
> line collections instead.  This would also facilitate my next idea:
> 

Not "line collections instead", but "in addition": the functionality and 
appearance are very different with polygons than with lines.  I think I 
can add a line alternative with only a little extra code, but I won't 
even look at it again until this weekend, at the very earliest.

> 2. I would love to have a 'curly vector' tool.  However, I'm not sure  
> how much to put into the curly_quiver package, and how much work must  
> be done by the user.  I think that at a minimum, it would be nice to  
> give curly lines (i.e., an additional dimension to u and v)that have  
> arrows on the end of them, and leave it to the user to define what  
> those lines are somehow.  If these lines could change color along  their 
> track, then it would be the best thing ever made!

You can make curly lines with mapped colors using a LineCollection 
(recent change: it now inherits from ScalarMappable).  Curly_quiver 
sounds like quite a different animal, though, and potentially much more 
difficult to do well; I don't think there would be much overlap with the 
present code in quiver, or with the code even after I add the line version.

Eric

With the latest svn matplotlib and numpy 0.9.8 I'm now getting:

Python 2.4.3 (#1, Mar 30 2006, 13:31:07)
[GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
 >>> import pylab
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/Users/jsw/lib/python/pylab.py", line 1, in ?
    from matplotlib.pylab import *
  File "/Users/jsw/lib/python/matplotlib/pylab.py", line 196, in ?
    import cm
  File "/Users/jsw/lib/python/matplotlib/cm.py", line 5, in ?
    import colors
  File "/Users/jsw/lib/python/matplotlib/colors.py", line 33, in ?
    from numerix import array, arange, take, put, Float, Int, where, \
  File "/Users/jsw/lib/python/matplotlib/numerix/__init__.py", line 66, in ?
    import numpy.oldnumeric as numpy
ImportError: No module named oldnumeric

With numpy 0.9.8 I can do

from numpy.core import oldnumeric

but not

from numpy import oldnumeric.


I suppose this is a consequence of Travis's numerix commits yesterday - 
is the latest numpy svn now required?


-Jeff

-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
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On Tue, Jun 13, 2006 at 09:21:44AM -0500, John Hunter wrote:
> I'm not at all opposed to making a helper function like scatter to plot
> parametric lines with colormaps, but I don't think "plot" is the right
> vehicle, since it returns a Line2d, not a LineCollection, and since it
> is already heavily overloaded.  parplot? =20

    I think having a helper function is a good idea. Not only does it
help the newcomer, but it also allows the oldtimer to write shorter and
more readable code.

    I find that "parplot" is not a great name for such a function, but I
cannot think of a better one. Maybe the list will have better ideas.

    Ga=EBl

Eric-

I had a chance to play around with the new quiver this morning.  Here  
are some thoughts:

1. I read that somebody thought it was a bit slow, but this is not my  
experience.  I tried to quiver my model data (128x128 with masking),  
and it rendered in a few seconds.  I tried to look at images with  
more arrows, but I could not actually see the arrows with so many  
points.  In my experience you can't put more than about O(100000)  
(i.e., about 100x100) arrows on a figure and have it make any sense  
anyways.

2.  It seems to handle masking fine.  I gave it masked arrays and  
arrays with nans (it complained a bit about the masked array, but  
rendered anyways).  This is key for me.

3.  It handles colors nicely, but there is no apparent way to set the  
color limits. Perhaps adding vmin and vmax as kwargs (matching  
pcolor) would make some sense.

4.  I *really* like how the arrows get gray (and don't try to render  
at a whole pixel) when they get small.  I agree with the other person  
that it might be nice to have a  small dot to indicate zero  
velocity.  No dot should be rendered *ever* for values masked or  
NaNed, however.

5. It's a bit of a pain to find values of scale and width that work  
well, and quiver doesn't seem to make very good choices by default.   
I don't think this is a big deal, but rather simply the price of the  
added functionality.  Making some more intelligent default choices  
might not be a bad idea, though.  In particular, smaller arrows when  
there are more arrows to be rendered would be a good place to start.

Some ideas for future work:

1. I'm pretty happy with the polygons, but it would be nice to have  
line collections instead.  This would also facilitate my next idea:

2. I would love to have a 'curly vector' tool.  However, I'm not sure  
how much to put into the curly_quiver package, and how much work must  
be done by the user.  I think that at a minimum, it would be nice to  
give curly lines (i.e., an additional dimension to u and v)that have  
arrows on the end of them, and leave it to the user to define what  
those lines are somehow.  If these lines could change color along  
their track, then it would be the best thing ever made!

-Rob.

-----
Rob Hetland, Assistant Professor
Dept of Oceanography, Texas A&M University
p: 979-458-0096, f: 979-845-6331
e: he...@ta..., w: http://pong.tamu.edu