From c4dca51588b113ba8f7b02f706b062821848c8ad Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Fri, 15 Feb 2013 18:40:02 -0500 Subject: [PATCH 1/1] Animation examples with mencoder and convert --- .gitignore | 3 + COPYING | 674 ++++++++++++++++++++++++++++++++++++++++++++++++++ Makefile | 55 ++++ README | 53 ++++ life.py | 87 +++++++ plot_image.py | 306 +++++++++++++++++++++++ 6 files changed, 1178 insertions(+) create mode 100644 .gitignore create mode 100644 COPYING create mode 100644 Makefile create mode 100644 README create mode 100755 life.py create mode 100755 plot_image.py diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..0f8465d --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +data +*.avi +*.gif diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..8b849ab --- /dev/null +++ b/Makefile @@ -0,0 +1,55 @@ +# Copyright (C) 2012-2013 W. Trevor King +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + +RUN_PROGRAM = life.py +PYTHON = python2.7 +MOVIES = movie.avi movie.gif +HEIGHT = 40 +WIDTH = 40 +N = 80 +FRAMES = $(patsubst %,data/frame-%.png,$(shell seq -f '%05g' $(N))) + +.PHONY: all clean + +all: $(MOVIES) + +clean: + rm -rf $(MOVIES) data + +data: + mkdir "$@" + +# For details on .PRECIOUS, see: +# http://www.gnu.org/software/make/manual/html_node/Special-Targets.html#index-g_t_002ePRECIOUS-223 +.PRECIOUS: data/frame-%.dat data/frame-%.png + +# Create all the frames with a single program run +data/frame-%.dat: $(RUN_PROGRAM) | data + cd data && $(PYTHON) ../$(RUN_PROGRAM) -h $(HEIGHT) -w $(WIDTH) -n $(N) + +# Pattern rule to turn ASCII frame data into a PNG +data/frame-%.png: data/frame-%.dat plot_image.py + $(PYTHON) plot_image.py -i "$<" -o "$@" -s "$(WIDTH),$(HEIGHT)" -f + +# target: movie.avi - generate a movie from PNG frames +# For details on the mencoder invocation, see +# http://www.mplayerhq.hu/DOCS/HTML/en/menc-feat-enc-images.html +movie.avi: $(FRAMES) + mencoder mf://data/*.png -mf w=$(WIDTH):h=$(HEIGHT):fps=10:type=png -ovc copy -oac copy -o "$@" + +# target: movie.gif - generate a movie-map animated GIF +# Using `convert` from the ImageMagick suite. +movie.gif: $(FRAMES) + convert $^ "$@" diff --git a/README b/README new file mode 100644 index 0000000..0919b63 --- /dev/null +++ b/README @@ -0,0 +1,53 @@ +Poisson diffusion +================= + +This package provides an example of simple packaging for a C or C++ +program. This will give you an idea of what I expect when you submit +homework assignments. + +Building +======== + +This package contains a simple C or C++ program that can be compiled +using the `GNU Compiler Collection`_. We record the commands you need +to build the software in the ``Makefile``, which is interpreted by +`GNU Make`_ to build the software. + +Compile the program ``poisson`` generate an AVI movie with:: + + $ make + +Generate an animated GIF with:: + + $ ./make heat.gif + +Run ``make help`` to get a list of other targets defined in the +``Makefile``. + +reStructuredText +================ + +If you're wondering why I keep using backticks and underscores in this +``README``, it's because I've writing `reStructuredText`_. +reStructedText is a markup syntax that is easy to read, and also easy +to convert to other formats. However, you can write your ``README`` +using any syntax you like, so long as it is easy to understand. + +License +======= + +This example package is released under the GNU GPLv3+. See +``COPYING`` for details. It's a good idea to distribute your code +under an explicit license so your users will know how they are allowed +to use it. + +Contact +======= + +W. Trevor King +wking@drexel.edu + + +.. _GNU Compiler Collection: http://www.gnu.org/software/gcc/ +.. _GNU Make: http://www.gnu.org/software/make/ +.. _reStructuredText: http://docutils.sourceforge.net/rst.html diff --git a/life.py b/life.py new file mode 100755 index 0000000..be89fd8 --- /dev/null +++ b/life.py @@ -0,0 +1,87 @@ +#!/usr/bin/env python +# Copyright (C) 2013 W. Trevor King +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + +"Conway's Game of Life" + +import math as _math + +import numpy as _numpy + + +class Life (object): + def __init__(self, height=20, width=20): + self.board = _numpy.zeros((height, width), dtype=bool) + + def step(self): + # Any live cell with fewer than two live neighbours dies. + neighbors = self.get_neighbors() + self.board *= neighbors >= 2 + # Any live cell with two or three live neighbours lives. + self.board *= (neighbors >= 2) * (neighbors <= 3) + # Any live cell with more than three live neighbours dies. + self.board *= neighbors <= 3 + # Any dead cell with exactly three live neighbours is born. + self.board += (self.board == False) * (neighbors == 3) + + def get_neighbors(self): + neighbors = 0 * self.board + neighbors[:-1,:] += self.board[1:,:] + neighbors[1:,:] += self.board[:-1,:] + neighbors[:,:-1] += self.board[:,1:] + neighbors[:,1:] += self.board[:,:-1] + neighbors[:-1,:-1] += self.board[1:,1:] + neighbors[1:,1:] += self.board[:-1,:-1] + neighbors[:-1,1:] += self.board[1:,:-1] + neighbors[1:,:-1] += self.board[:-1,1:] + return neighbors + + def __str__(self): + return '\n'.join( + [' '.join(str(x) for x in row) for row in 1*self.board]) + + +if __name__ == '__main__': + import argparse as _argparse + + parser = _argparse.ArgumentParser(description=__doc__, add_help=False) + parser.add_argument( + '-H', '--help', action='help', + help='show this help message and exit') + parser.add_argument( + '-h', '--height', type=int, default=200) + parser.add_argument( + '-w', '--width', type=int, default=100) + parser.add_argument( + '-n', '--steps', type=int, default=80) + + args = parser.parse_args() + + life = Life(height=args.height, width=args.width) + b = life.board[:,:] + b[1:3,1:3] = True # block + b = life.board[:,7:] + b[2,1] = b[1,2:4] = b[3,2:4] = b[2,4] = True # beehive + b = life.board[7:,:] + b[2,1:4] = True # blinker + b = life.board[7:,7:] + b[2,2:5] = b[3,1:4] = True # toad + b = life.board[20:,20:] + b[1,1] = b[1,4] = b[3,1] = b[4,2:5] = b[2:5,5] = True # LWSS + for i in range(args.steps): + with open('frame-{0:05d}.dat'.format(i+1), 'w') as f: + f.write(str(life)) + f.write('\n') + life.step() diff --git a/plot_image.py b/plot_image.py new file mode 100755 index 0000000..fffab70 --- /dev/null +++ b/plot_image.py @@ -0,0 +1,306 @@ +#!/usr/bin/env python + +"""Generate an image from ASCII data. + +Step 1: make this file executable:: + + chmod +x plot_image.py + +Step 2: pipe data into python script:: + + ./gen_data | ./plot_image.py -s nx,ny -c nc -t 'image title' + +Data should be one ASCII float per line, in the following order:: + + z[x1,y1] + z[x2,y1] + ... + z[xN,y1] + z[x1,y2] + ... + z[xN,y2] + ... + z[xN,yN] + +where `x` increases from `x1` to `xN` and `y` increases from `y1` +through `yN`. + +You can use the `--xyz` option to read an alternative data format, +which is:: + + x1 y1 z[x1,y1] + x2 y2 z[x1,y1] + ... + +If you use this method, the ordering of lines in the data file is +irrelevant, and `Nx` and `Ny` are extracted from the data file itself. +However, you still need to use a rectangular grid (i.e. for every +`xi`, you need to have entries for every `yi`). + +For usage info, run:: + + ./plot_image.py --help + +When run with interactive output (i.e. no `-o ...` option), the +interactive figure is displayed using `pylab.show`, which means that +you'll have to kill `plot_image.py` using ^C or similar [1]_. + +For other ideas, see the Matplotlib website [2]_. + +.. [1] http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show +.. [2] http://matplotlib.sourceforge.net/ +""" + +import optparse +import sys + +import matplotlib +import matplotlib.image +import numpy + +# Depending on your Matplotlib configuration, you may need to adjust +# your backend. Do this before importing pylab or matplotlib.backends. +#matplotlib.use('Agg') # select backend that doesn't require X Windows +#matplotlib.use('GTKAgg') # select backend that supports pylab.show() + +import pylab + + +_DOC = __doc__ + + +def read_data_1d(stream, nx, ny): + """Read in data, one entry per line. + + >>> from StringIO import StringIO + >>> s = StringIO('\\n'.join(map(str, range(10)))+'\\n') + >>> X,Y,Z = read_data_1d(s, 5, 2) + >>> X + array([[0, 1, 2, 3, 4, 5], + [0, 1, 2, 3, 4, 5], + [0, 1, 2, 3, 4, 5]]) + >>> Y + array([[0, 0, 0, 0, 0, 0], + [1, 1, 1, 1, 1, 1], + [2, 2, 2, 2, 2, 2]]) + >>> Z + array([[ 0., 1., 2., 3., 4.], + [ 5., 6., 7., 8., 9.]]) + """ + X,Y = pylab.meshgrid(range(nx+1), range(ny+1)) + Z = numpy.loadtxt(stream) + assert Z.size == nx*ny, 'Z.size = %d != %d = %dx%d' % ( + Z.size, nx*ny, nx, ny) + Z = Z.reshape([x-1 for x in X.shape]) + return (X,Y,Z) + +def read_data_3d(stream): + """Read in data, one `(x, y, z)` tuple per line. + + >>> from StringIO import StringIO + >>> lines = [] + >>> for x in range(5): + ... for y in range(2): + ... lines.append('\t'.join(map(str, [x, y, x+y*5]))) + >>> s = StringIO('\\n'.join(lines)+'\\n') + >>> X,Y,Z = read_data_3d(s) + >>> X + array([[ 0., 1., 2., 3., 4., 5.], + [ 0., 1., 2., 3., 4., 5.], + [ 0., 1., 2., 3., 4., 5.]]) + >>> Y + array([[ 0., 0., 0., 0., 0., 0.], + [ 1., 1., 1., 1., 1., 1.], + [ 2., 2., 2., 2., 2., 2.]]) + >>> Z + array([[ 0., 1., 2., 3., 4.], + [ 5., 6., 7., 8., 9.]]) + """ + XYZ = numpy.loadtxt(stream) + assert len(XYZ.shape) == 2 and XYZ.shape[1] == 3, XYZ.shape + Xs = numpy.array(sorted(set(XYZ[:,0]))) + Ys = numpy.array(sorted(set(XYZ[:,1]))) + Z = numpy.ndarray((len(Ys), len(Xs)), dtype=float) + xyz = {} # dict of z values keyed by (x,y) tuples + for i in range(XYZ.shape[0]): + xyz[(XYZ[i,0], XYZ[i,1])] = XYZ[i,2] + for i,x in enumerate(Xs): + for j,y in enumerate(Ys): + Z[j,i] = xyz[x,y] + # add dummy row/column for pcolor + dx = Xs[-1] - Xs[-2] + dy = Ys[-1] - Ys[-2] + Xs = numpy.append(Xs, Xs[-1] + dx) + Ys = numpy.append(Ys, Ys[-1] + dy) + X,Y = pylab.meshgrid(Xs, Ys) + return (X,Y,Z) + +def plot(X, Y, Z, full=False, title=None, contours=None, interpolation=None, + cmap=None): + """Plot Z over the mesh X, Y. + + >>> X, Y = pylab.meshgrid(range(6), range(2)) + >>> Z = X[:-1,:-1]**2 + Y[:-1,:-1] + >>> plot(X, Y, Z) # doctest: +ELLIPSIS + + """ + X_min = X[0,0] + X_max = X[-1,-1] + Y_min = Y[0,0] + Y_max = Y[-1,-1] + + fig = pylab.figure() + if full: + axes = fig.add_axes([0, 0, 1, 1]) + else: + axes = fig.add_subplot(1, 1, 1) + if title: + axes.set_title(title) + axes.set_axis_off() + + if contours: + cset = axes.contour(X[:-1,:-1], Y[:-1,:-1], Z, contours, cmap=cmap) + # [:-1,:-1] to strip dummy last row & column from X&Y. + axes.clabel(cset, inline=1, fmt='%1.1f', fontsize=10) + else: + # pcolor() is much slower than imshow. + #plot = axes.pcolor(X, Y, Z, cmap=cmap, edgecolors='none') + #axes.autoscale_view(tight=True) + plot = axes.imshow(Z, aspect='auto', interpolation=interpolation, + origin='lower', cmap=cmap, + extent=(X_min, X_max, Y_min, Y_max)) + if not full: + fig.colorbar(plot) + return fig + + +def get_possible_interpolations(): + try: # Matplotlib v1.0.1 + return sorted(matplotlib.image.AxesImage._interpd.keys()) + except AttributeError: + try: # Matplotlib v0.91.2 + return sorted(matplotlib.image.AxesImage(None)._interpd.keys()) + except AttributeError: + # give up ;) + pass + return ['nearest'] + +def test(): + import doctest + results = doctest.testmod() + return results.failed + + +def main(argv=None): + """Read in data and plot it. + + >>> from tempfile import NamedTemporaryFile + >>> i = NamedTemporaryFile(prefix='tmp-input', suffix='.dat') + >>> i.write('\\n'.join([str(x) for x in range(10)])+'\\n') + >>> i.flush() + >>> o = NamedTemporaryFile(prefix='tmp-output', suffix='.png') + >>> main(['-i', i.name, '-s', '5,2', '-o', o.name, '-m', 'binary']) + Plot_image + Title: Some like it hot + Image size: 5 2 + False color + X range: 0 4 (6 steps) + Y range: 0 1 (3 steps) + Z range: 0.0 9.0 + >>> img = o.read() + >>> img.startswith('\\x89PNG') + True + >>> i.close() + >>> o.close() + """ + if argv == None: + argv = sys.argv[1:] + + usage = '%prog [options]' + epilog = _DOC + p = optparse.OptionParser(usage=usage, epilog=epilog) + p.format_epilog = lambda formatter: epilog+'\n' + + p.add_option('-i', '--input', dest='input', metavar='FILE', + help='If set, read data from FILE rather than stdin.') + p.add_option('-o', '--output', dest='output', metavar='FILE', + help=('If set, save the figure to FILE rather than ' + 'displaying it immediately')) + p.add_option('-s', '--size', dest='size', default='%d,%d' % (16, 16), + help='Data size (columns,rows; default: %default)') + p.add_option('-3', '--xyz', dest='xyz', default=False, action='store_true', + help=('If set, read (x,y,z) tuples from the input data rather' + 'then reading `z` and calculating `x` and `y` from ' + '`--size`.')) + p.add_option('-c', '--contours', dest='contours', type='int', + help=('Number of contour lines (if not set, draw false color ' + 'instead of contour lines; default: %default)')) + p.add_option('-f', '--full-figure', dest='full', action='store_true', + help=('Set axes to fill the figure (i.e. no title or color ' + 'bar')) + p.add_option('-t', '--title', dest='title', default='Some like it hot', + help='Title (%default)') + p.add_option('--test', dest='test', action='store_true', + help='Run internal tests and exit.') + interpolations = get_possible_interpolations() + p.add_option('--interpolation', dest='interpolation', default='nearest', + help=('Interpolation scheme (for false color images) from %s ' + '(%%default)') % ', '.join(interpolations)) + maps=[m for m in pylab.cm.datad if not m.endswith("_r")] + maps.sort() + p.add_option('-m', '--color-map', dest='cmap', default='jet', + help='Select color map from %s (%%default)' % ', '.join(maps)) + + options,args = p.parse_args(argv) + + if options.test: + sys.exit(test()) + + nx,ny = [int(x) for x in options.size.split(',')] + try: + cmap = getattr(pylab.cm, options.cmap) + except AttributeError: + raise Exception('no color map named %s in %s' + % (options.cmap, ', '.join(maps))) + + print('Plot_image') + print('Title: {0}'.format(options.title)) + if not options.xyz: + print('Image size: {0} {1}'.format(nx, ny)) + if options.contours: + print('# countour lines: {0}'.format(options.contours)) + else: + print('False color') + if options.input: + fin = open(options.input, 'r') + else: + fin = sys.stdin + + if options.xyz: + X,Y,Z = read_data_3d(fin) + else: + X,Y,Z = read_data_1d(fin, nx, ny) + + if options.input: + fin.close() + + Z_min = numpy.min(Z.flat) + Z_max = numpy.max(Z.flat) + print('X range: {0} {1} ({2} steps)'.format( + X[0,0], X[0,-2], X.shape[1])) + print('Y range: {0} {1} ({2} steps)'.format( + Y[0,0], Y[-2,0], Y.shape[0])) + print('Z range: {0} {1}'.format(Z_min, Z_max)) + + fig = plot(X, Y, Z, full=options.full, title=options.title, + contours=options.contours, interpolation=options.interpolation, + cmap=cmap) + + if options.output: + fig.savefig(options.output) + else: + pylab.show() + + +if __name__ == '__main__': + main() -- 2.26.2