## December 04, 2014

### Producing Technical Drawings In Blender

I do all my 3D design in Blender, producing models fit for 3D printing. It isn't as hard as it sounds as long as you keep to the following rules:

• Keep consistent scale. For me that means 1 Blender unit = 1 mm
• Use boolean operations on meshes, avoid editing meshes directly
• This keeps things clean, modular, and most of all, ensures the resulting mesh is manifold, aka. watertight
• Use Select Non-Manifold in edit mode to verify the correctness of the mode
• Use Recalculate Normals before exporting

Sometimes the model is a prototype, that needs to be manufactured by hand, technical drawings of a model is required, as illustrated by the following screenshot.

 Top is the model to be manufactured, bottom is a render of the model from the top in technical drawing style. In yellow are the necessary Free Style settings.
To achieve this look, you need to first set the camera to Orthographic mode, then enable Freestyle rendering in the render tab.

 In orthographic mode moving the camera towards or away from the object has no effect on its size. Orthographic Scale is what you need to change to "zoom" in and out.

 Freestyle rendering is needed.
Lastly, it is necessary to use a shadeless white material since we don't want lighting of any kind.

 A white shadeless material removes the need for lighting, and thus eliminates shading in the resulting render.

### Internal Edges

It is possible to make internal edges, such as the edge of a channel, show up in the render. This is done by changing the Visibility setting in the Freestyle Render Layer settings.

When rendering internal edges, sometimes undesirable edges will show up. These can be convinced to go away by experimenting with the Edge Type checkboxes.

 QI range allows rendering of internal edges, while Edge Types allows elimination of undesirable internal edges.

### Missing Features

Missing is the ability to add dimensions, that is something I haven't found a nice way of doing in blender, so for now it is added in post using Inkscape, or just by drawing on the printout.

Cheers,
Steve

## September 13, 2014

### Further Adventures in Python Optimisation

Previously we found that PyPy achieves the best performance gain, executing fieldfunc_py in ~6 us. At the end of that article, I mentioned that the C implementation is up to 50x faster, managing the same calculation in ~0.12 us.

The naive conclusion is that the best thing is to simply call the C function to do the heavy lifting, achieving performance somewhere between PyPy and C. But nothing in life is easy...

# Naive C Interfacing

The C code in the previous article was compiled using

gcc -O -shared -o c_fieldfunc.so -fPIC c_fieldfunc.c


The MagnetElement class was then amended to use the C function whenever possible:

class MagnetElement(object):
def __init__(self, position, size, magnetisation, fieldcalcfunc=fieldfunc_fast_py):
"""
position, and magnetisation are all expected to be numpy arrays of 3
elements each.

size is a single number, implying all elements are square
"""

self.position = position
self.size = size
self.magnetisation = magnetisation
self.moment = magnetisation * size * size * size
self._fieldcalcfunc = fieldcalcfunc

try:
import ctypes
self._fieldcalcfunc = cmodule.fieldfunc
self.fieldAt = self._cfieldAt
except OSError, ex:
pass

def _cfieldAt(self, p):
import ctypes
def voidp(x):
return ctypes.c_void_p(x.ctypes.data)
field = np.array([0,0,0], np.double)
self._fieldcalcfunc(voidp(p),
voidp(self.position),
voidp(self.moment),
voidp(field))
return field

def fieldAt(self, p):
"""
p is expected to be a numpy array of 3
"""
return self._fieldcalcfunc(p, self.position, self.moment)


This however yielded a per-run time of ~28 us!! So clearly there is significant cost in interfacing. The most obvious of these is creating a new np.array each time, and defining and calling voidp.

# A Better C Interface

Below is an improved version:

class MagnetElement(object):
def __init__(self, position, size, magnetisation, fieldcalcfunc=fieldfunc_fast_py):
"""
position, and magnetisation are all expected to be numpy arrays of 3
elements each.

size is a single number, implying all elements are square
"""

self.position = position
self.size = size
self.magnetisation = magnetisation
self.moment = magnetisation * size * size * size
self._fieldcalcfunc = fieldcalcfunc

try:
import ctypes
self._fieldcalcfunc = cmodule.fieldfunc
self.fieldAt = self._cfieldAt
self._field = np.array([0,0,0], np.double)

def voidp(x):
return ctypes.c_void_p(x.ctypes.data)
self._position_p = voidp(self.position)
self._moment_p = voidp(self.moment)
self._field_p = voidp(self._field)
except OSError, ex:
pass

def _cfieldAt(self, p):
import ctypes
self._fieldcalcfunc(ctypes.c_void_p(p.ctypes.data),
self._position_p,
self._moment_p,
self._field_p)
return self._field

def fieldAt(self, p):
"""
p is expected to be a numpy array of 3
"""
return self._fieldcalcfunc(p, self.position, self.moment)


Now we are down to ~7 us, which is about what PyPy gave us. We are still slower, and more effort is involved compared to the installing PyPy + numpy. That said, this method has the advantage that it is compatible with existing Python and numpy installations, and can be used to optimise python code that uses parts of numpy that are not yet implemented in PyPy.

# Summary

• C interfacing needs to be done carefully to gain maximum benefit
• Not quite as easy as using PyPy, but more compatible

While we achieved performance similar to PyPy using C interfacing in this one function, PyPy is going to give faster performance across the entire program, while Python+C will only speed up this one function. In my particular case, Python+C is over all ~2x as slow as PyPy.

Cheers,
Steve

Recently I found myself looking at the following piece of code and trying to optimise it:

from __future__ import division

import numpy as np

MagneticPermeability = 4*np.pi*1e-7
MagneticPermeabilityOver4Pi = MagneticPermeability / (4*np.pi)

def fieldfunc_py(p, q, moment):
r = p - q
rmag = np.sqrt(r.dot(r))

rdash3 = rmag**3
rdash5 = rmag**5

rminus5term = r * moment.dot(r) * 3 / rdash5
rminus3term = moment / rdash3

field = (rminus5term - rminus3term) * MagneticPermeabilityOver4Pi
return field


This, I have been told, computes the field at p due to a magnetic di-pole at q.

To profile this code I wrote the following function:

def profile(fieldfunc, dtype=np.double):
def V(*args):
return np.array(args, dtype)

q = V(0, 0, 0)
moment = V(1, 0, 0)
p = V(10,10,10)

def f():
fieldfunc(p, q, moment)

# force the JIT or whatever to run
f()

from timeit import Timer
t = Timer(f)
runs = 100000
print fieldfunc.__name__,'per run', t.timeit(number=runs)*1e6/runs, 'us'


This yields a per-run time of ~22 us.

# Optimise Python/Numpy

The first optimisation then is to write a better optimised version:

def fieldfunc_fast_py(p, q, moment):
r = p - q
rmag2 = np.dot(r, r)

rdash3 = rmag2**1.5
rdash5 = rmag2**2.5

rminus5term = r * np.dot(moment, r) * 3 / rdash5
rminus3term = moment / rdash3

field = (rminus5term - rminus3term) * MagneticPermeabilityOver4Pi
return field


The main difference is using np.dot() and avoiding np.sqrt(). Using ** is faster than using square root and multiplication. These changes gets us down to ~18 us or so, so slight improvement.

# numba

Numba offers JIT compilation of python into native code, and is pretty easy to use and compatible with numpy. To use it the profile function was called as:

profile(jit(fieldfunc_py))
profile(jit(fieldfunc_fast_py))


Using jit without type arguments causes numba to infer the type. This yields per-run time of ~22 us for fieldfunc_py and ~18 us for fieldfunc_fast_py. There is no noticable speed up, in fact per-run times increased slightly. This is possibly due to the fact that the code is already pretty well optimised, and the extra overhead of interfacing between compiled code and the python runtime.

# PyPy

PyPy is an altnerative implementation of Python that also uses JIT, but does it for the entire program. It is a little harder to use because it needs its own version of numpy, which is only partially implemented. For our needs this will suffice.

With PyPy, we see significant improvement. fieldfunc_py's per-run time went down to ~6 us, and fieldfunc_fast_py's per-run time went down to ~6 us also. This is a huge improvement.

# Data Type Matters

The diligent reader may have noticed that profile accepts dtype as a keyword arguments. This was used to test the effects of using np.float32 vs np.float64. The following code was written:

for dtype in np.float32, np.float64:
print 'With', dtype
profile(fieldfunc_py, dtype)
profile(fieldfunc_fast_py, dtype)

try:
from numba import jit
print '==> Using numba jit'
profile(jit(fieldfunc_py))
profile(jit(fieldfunc_fast_py))
except:
pass


This yielded the following output using CPython:

With <type 'numpy.float32'>
fieldfunc_py per run 30.8365797997 us
fieldfunc_fast_py per run 27.7728509903 us
==> Using numba jit
fieldfunc_py per run 22.2719597816 us
fieldfunc_fast_py per run 18.1778311729 us

With <type 'numpy.float64'>
fieldfunc_py per run 21.8909192085 us
fieldfunc_fast_py per run 17.5257897377 us
==> Using numba jit
fieldfunc_py per run 22.4718093872 us
fieldfunc_fast_py per run 18.2463383675 us


Choice of data type has a significant effect, and it counter-intuitive: the larger data type is faster. Interestingly the same isn't true for PyPy, which outputted:

With <type 'numpy.float32'>
fieldfunc_py per run 6.29536867142 us
fieldfunc_fast_py per run 6.067070961 us

With <type 'numpy.float64'>
fieldfunc_py per run 6.28163099289 us
fieldfunc_fast_py per run 6.17563962936 us


Which is essentially the same.

# How Fast Can It Be Done?

The final question is, how fast can this be done? Here is a naive C implementation:

#include <math.h>
#include <stdio.h>

typedef double dtype;

dtype vdot(dtype *u, dtype *v) {
return u[0]*v[0] + u[1]*v[1] + u[2]*v[2];
}

/**
* Computes w=u+v
*/
void vadd(dtype *u, dtype *v, dtype *w) {
w[0] = u[0] + v[0];
w[1] = u[1] + v[1];
w[2] = u[2] + v[2];
}

/**
* Computes w=u-v
*/
void vsub(dtype *u, dtype *v, dtype *w) {
w[0] = u[0] - v[0];
w[1] = u[1] - v[1];
w[2] = u[2] - v[2];
}
/**
* Computes w = x*u, returns w
*/
void vmult(dtype x, dtype *u, dtype *w) {
w[0] = x*u[0];
w[1] = x*u[1];
w[2] = x*u[2];
}

#define MagneticPermeability          (4*M_PI*1e-7f)
#define MagneticPermeabilityOver4Pi   (MagneticPermeability/(4*M_PI))

void vprint(dtype *v) {
printf("(%e, %e, %e)\n", v[0], v[1], v[2]);
}

void fieldfunc(dtype *p, dtype *q, dtype *moment, dtype *out) {
dtype r[3];
vsub(p, q, r);
dtype rmag2 = vdot(r,r);

dtype rdash3 = pow(rmag2, 1.5);
dtype rdash5 = pow(rmag2, 2.5);

dtype t5[3];
vmult(vdot(moment, r), r, t5);
vmult(3/rdash5, t5, t5);

dtype t3[3];
vmult(1/rdash3, moment, t3);

vsub(t5, t3, out);
vmult(MagneticPermeabilityOver4Pi, out, out);
}

int main(int argc, char **argv) {
dtype q[] = {0, 0, 0};
dtype p[] = {10, 10, 10};
dtype moment[] = {1, 0, 0};
dtype field[3];

fieldfunc(p, q, moment, field);
vprint(field);

int x;
for (x = 0; x < 1000000; ++x) {
fieldfunc(p, q, moment, field);
}

return 0;
}


timing was done as follows:

\$ gcc -o c_bench c_bench.c -lm && time ./c_bench
(0.000000e+00, 1.924501e-11, 1.924501e-11)

real    0m0.116s
user    0m0.114s
sys     0m0.001s


Because we do 1 million iterations, per-run time is ~0.12 us, or around 50 times faster.

# Summary

• Most gain/effort comes from using PyPy
• In this particular case, numba did not yield signficant speed up
• C is still much faster

Cheers,
Steve

## August 30, 2014

### Play Child of Light in English on PS Vita

If you want to play Child of Light on PS Vita, you will not only need to download the online update, you will also need to set your system language to English (US). If you have it set as English (UK) then you will continue seeing the game in Japanese.

I know right?

## August 27, 2014

### From Lyx/Latex to Word

This is sort of a placeholder post. Busy meeting a deadline, but this should help future Steve and anyone else when you need to turn your Lyx document into a Word document while keeping the format mostly sane. Broken, but sane.
1. Export as Latex (plain).
2. Run
• latex <name of tex file, with or without extension>

3. Run
• bibtex <filename>

4. Run
• latex <filename>

5. Run
• latex <filename>

6. Try to run
• htlatex <filename> "html,0,charset=utf-8" "" -dhtml/
• html: format to output
• 0: normally chapters go into their own page, putting 0 here forces everything into a single page
• charset=utf-8: let us be civilised
• -dhtml/: puts the output files in a html sub-directory. Note that you can't have a space between -d and the html/

7. If the above fails with something like 'illegal storage address', and you get a warning about text4ht.env not been found, then you need to find where it is in your TeX installation, and:
• export TEX4HTENV and try again
• Copy text4ht.env into your working directory
• This approach also lets you affect locally some export parameters. More on this later...

8. Open the html to verify correctness. You might object to the poor graphics quality. In this case copy text4ht.env into the working directory if you haven't done so, and then modify it so it uses a high density when converting images.
• See this tex.stackexchange.com answer for more details
• In my case, since dvipng was been used, I replaced all instances of
• -D 96
• with
• -D 300

9. It also helps if you
• These look like <!-- xxx -->
• centre aligned image divs
• remove <hr/> instances

10. These changes will make the import into Libre/OpenOffice go easier

11. Open the html file in Libre/OpenOffice

12. File > Export > ODT

13. Close html file

14. Open exported ODT

18. Verify that the ODT file is now much larger!

19. File > Save As > Word 97 (doc)

Phew! To help future visitors, a simple python script to fix up the html as I have described is included at the end of this post. You will need lxml and cssselector installed. Cheers, Steve
#!/usr/bin/env python

from lxml.html import parse, HtmlComment
from lxml import etree

def main(*args):
if len(args) == 0:
return 1

doc = parse(args[0]).getroot()

body = doc.cssselect('body')[0]

# replace <hr/> with <br/> to make doc conversion easier
for hr in body.cssselect('hr'):
p = hr.getparent()
p.remove(hr)

br = etree.Element('br')
p.append(br)

# remove comments because for some reason libreoffice opens up
for node in doc.getiterator():
if isinstance(node, HtmlComment):
node.getparent().remove(node)

# centre align all figures
for div in doc.cssselect('div.figure'):
div.attrib['style']='text-align:center'

print etree.tostring(doc, method='html', encoding='utf-8')
if __name__ == '__main__':
import sys
sys.exit(main(*sys.argv[1:]))