--- /home/sjplimp/oldpizza/src/gnu.py 2005-09-07 10:13:09.000000000 -0600
+++ /home/sjplimp/pizza/src/gnu.py 2005-09-12 16:39:05.000000000 -0600
@@ -17,9 +17,16 @@
g.plot(a) plot vector A against linear index
g.plot(a,b) plot B against A
g.plot(a,b,c,d,...) plot B against A, D against C, etc
+g.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
+
+ each plot argument can be a tuple, list, or Numeric vector
+ mplot loops over range(M,N,S) and create one plot per iteration
+ last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors
+ each plot is made from a portion of the vectors, depending on loop index i
+ Ith plot is of b[0:i] vs a[0:i], etc
+ series of plots saved as file0000.eps, file0001.eps, etc
+ if use xrange(),yrange() then plot axes will be same for all plots
- each argument can be a tuple, list, or Numeric vector
-
g("plot 'file.dat' using 2:3 with lines") execute string in GnuPlot
g.enter() enter GnuPlot shell
@@ -61,15 +68,14 @@
# History
# 8/05, Matt Jones (BYU): original version
+# 9/05, Steve Plimpton: added mplot() method
# ToDo list
# allow choice of JPG or PNG or GIF when saving ?
# can this be done from GnuPlot or have to do via ImageMagick convert ?
# way to trim EPS plot that is created ?
# hide does not work on Mac aqua
-# select does not pop window to fron on Mac aqua
-# command to allow a plot to be drawn/saved incrementally
-# e.g. 50 saved eps files that show plot growing to full data
+# select does not pop window to front on Mac aqua
# Variables
# current = index of current figure (1-N)
@@ -78,8 +84,7 @@
# Imports and external programs
-from os import popen
-import types
+import types, os
try: from DEFAULTS import PIZZA_GNUPLOT
except: PIZZA_GNUPLOT = "gnuplot"
@@ -93,7 +98,7 @@
# --------------------------------------------------------------------
def __init__(self):
- self.GNUPLOT = popen(PIZZA_GNUPLOT,'w')
+ self.GNUPLOT = os.popen(PIZZA_GNUPLOT,'w')
self.file = "tmp.gnu"
self.figures = []
self.select(1)
@@ -134,7 +139,28 @@
self.export(file,vectors[i],vectors[i+1])
self.figures[self.current-1].ncurves = len(vectors)/2
self.draw()
-
+
+ # --------------------------------------------------------------------
+ # create multiple plots from growing vectors, save to numbered files
+ # don't plot empty vector, create a [0] instead
+
+ def mplot(self,start,stop,skip,file,*vectors):
+ n = 0
+ for i in range(start,stop,skip):
+ partial_vecs = []
+ for vec in vectors:
+ if i: partial_vecs.append(vec[:i])
+ else: partial_vecs.append([0])
+ self.plot(*partial_vecs)
+
+ if n < 10: newfile = file + "000" + str(n)
+ elif n < 100: newfile = file + "00" + str(n)
+ elif n < 1000: newfile = file + "0" + str(n)
+ else: newfile = file + str(n)
+
+ self.save(newfile)
+ n += 1
+
# --------------------------------------------------------------------
# write list of equal-length vectors to filename
@@ -172,12 +198,18 @@
# --------------------------------------------------------------------
# save plot to file.eps
# final re-select will reset terminal
-
+ # do not continue until plot file is written out
+ # else script could go forward and change data file
+ # use tmp.done as semaphore to indicate plot is finished
+
def save(self,file):
self.__call__("set terminal postscript enhanced solid lw 2 color portrait")
- cmd = 'set output "' + file + '.eps"'
+ cmd = "set output '%s.eps'" % file
self.__call__(cmd)
+ if os.path.exists("tmp.done"): os.remove("tmp.done")
self.draw()
+ self.__call__("!touch tmp.done")
+ while not os.path.exists("tmp.done"): continue
self.__call__("set output")
self.select(self.current)
@@ -281,7 +313,7 @@
# draw a plot with all its settings
# just return if no files of vectors defined yet
- def draw(self):
+ def draw(self):
fig = self.figures[self.current-1]
if not fig.ncurves: return
@@ -304,7 +336,7 @@
self.__call__(cmd)
else: self.__call__("set xr [*:*]")
if fig.ylimit:
- cmd = 'set yr [' + str(fig.xlimit[0]) + ':' + str(fig.xlimit[1]) + ']'
+ cmd = 'set yr [' + str(fig.ylimit[0]) + ':' + str(fig.ylimit[1]) + ']'
self.__call__(cmd)
else: self.__call__("set yr [*:*]")
--- /home/sjplimp/oldpizza/src/matlab.py 2005-09-07 10:13:09.000000000 -0600
+++ /home/sjplimp/pizza/src/matlab.py 2005-09-12 15:04:36.000000000 -0600
@@ -17,9 +17,16 @@
m.plot(a) plot vector A against linear index
m.plot(a,b) plot B against A
m.plot(a,b,c,d,...) plot B against A, D against C, etc
+m.mplot(M,N,S,"file",a,b,...) multiple plots saved to file0000.eps, etc
+
+ each plot argument can be a tuple, list, or Numeric vector
+ mplot loops over range(M,N,S) and create one plot per iteration
+ last args are same as list of vectors for plot(), e.g. 1, 2, 4 vectors
+ each plot is made from a portion of the vectors, depending on loop index i
+ Ith plot is of b[0:i] vs a[0:i], etc
+ series of plots saved as file0000.eps, file0001.eps, etc
+ if use xrange(),yrange() then plot axes will be same for all plots
- each argument can be a tuple, list, or Numeric vector
-
m("c = a + b") execute string in MatLab
m.enter() enter MatLab shell
@@ -75,8 +82,6 @@
# allow choice of JPG or PNG or GIF when saving via "saveas" command
# have vec/array import/export functions to pass variables between
# Pizza.py and MatLab and have them named in MatLab
-# command to allow a plot to be drawn/saved incrementally
-# e.g. 50 saved eps files that show plot growing to full data
# Variables
# current = index of current figure (1-N)
@@ -88,8 +93,7 @@
# Imports and external programs
-from os import popen
-import types
+import types, os
try: from DEFAULTS import PIZZA_MATLAB
except: PIZZA_MATLAB = "matlab -nosplash -nodesktop -nojvm"
@@ -101,7 +105,7 @@
# --------------------------------------------------------------------
def __init__(self):
- self.MATLAB = popen(PIZZA_MATLAB,'w')
+ self.MATLAB = os.popen(PIZZA_MATLAB,'w')
self.file = "tmp.matlab"
self.figures = []
self.select(1)
@@ -142,7 +146,28 @@
self.export(file,vectors[i],vectors[i+1])
self.figures[self.current-1].ncurves = len(vectors)/2
self.draw()
-
+
+ # --------------------------------------------------------------------
+ # create multiple plots from growing vectors, save to numbered files
+ # don't plot empty vector, create a [0] instead
+
+ def mplot(self,start,stop,skip,file,*vectors):
+ n = 0
+ for i in range(start,stop,skip):
+ partial_vecs = []
+ for vec in vectors:
+ if i: partial_vecs.append(vec[:i])
+ else: partial_vecs.append([0])
+ self.plot(*partial_vecs)
+
+ if n < 10: newfile = file + "000" + str(n)
+ elif n < 100: newfile = file + "00" + str(n)
+ elif n < 1000: newfile = file + "0" + str(n)
+ else: newfile = file + str(n)
+
+ self.save(newfile)
+ n += 1
+
# --------------------------------------------------------------------
# write list of equal-length vectors to filename
@@ -177,10 +202,16 @@
# --------------------------------------------------------------------
# save plot to file.eps
+ # do not continue until plot file is written out
+ # else script could go forward and change data file
+ # use tmp.done as semaphore to indicate plot is finished
def save(self,file):
+ if os.path.exists("tmp.done"): os.remove("tmp.done")
cmd = "saveas(gcf,'%s.eps','psc2')" % file
self.__call__(cmd)
+ self.__call__("!touch tmp.done")
+ while not os.path.exists("tmp.done"): continue
# --------------------------------------------------------------------
# restore default attributes by creating a new fig object
--- /home/sjplimp/oldpizza/scripts/logview.py 2005-09-07 10:13:10.000000000 -0600
+++ /home/sjplimp/pizza/scripts/logview.py 2005-09-12 15:51:06.000000000 -0600
@@ -25,7 +25,7 @@
style = argv[1]
files = ' '.join(argv[2:])
-lg = logview(files)
+lg = log(files)
exec "plot = %s()" % style
p = plotview(lg,plot)
--- /home/sjplimp/oldpizza/src/image.py 2005-09-07 10:13:09.000000000 -0600
+++ /home/sjplimp/pizza/src/image.py 2005-09-12 17:49:31.000000000 -0600
@@ -23,14 +23,26 @@
i.view("*.png *.gif") display thumbnails of matching images
view arg is same as constructor arg
+
+i.convert("image*.svg","new*.png") each SVG file to PNG
+i.convert("image*.svg","new*.jpg","-quality 50") 3rd arg is switch
+i.convert("image*.png","movie.mpg") all PNGs to MPG movie
+i.convert("image*.png","movie.mpg","-resize 128x128") 3rd arg is switch
+i.montage("","image*.png","plot*.png","two*.png") image + plot = two
+i.montage("-geometry 512x512","i*.png","new.png") 1st arg is switch
+
+ convert with 2 wildcard args loops over 1st set of files to make 2nd set
+ convert with not all wildcard args will issue single convert command
+ montage with all wildcard args loops over 1st set of files,
+ combines with one file from other sets, to make last set of files
+ montage with not all wildcard args will issue single montage command
"""
# History
# 8/05, Matt Jones (BYU): original version
+# 9/05, Steve Plimpton: added convert() and montage() methods
# ToDo list
-# i.convert("image*gif","-crop 100x200","tmp*png")
-# i.join("image*png","plot*gif","","new*png")
# Variables
@@ -42,6 +54,11 @@
import Pmw
import Image,ImageTk
+try: from DEFAULTS import PIZZA_CONVERT
+except: PIZZA_CONVERT = "convert"
+try: from DEFAULTS import PIZZA_MONTAGE
+except: PIZZA_MONTAGE = "montage"
+
# Class definition
class image:
@@ -111,6 +128,73 @@
if len(files) % ncolumns != 0: rowframe.pack(side=TOP)
scroll.pack(side=LEFT)
+ # --------------------------------------------------------------------
+ # wrapper on ImageMagick convert command
+
+ def convert(self,file1,file2,switch=""):
+ if file1.find('*') < 0 or file2.find('*') < 0:
+ cmd = "%s %s %s %s" % (PIZZA_CONVERT,switch,file1,file2)
+ commands.getoutput(cmd)
+ return
+
+ index = file1.index('*')
+ pre1 = file1[:index]
+ post1 = file1[index+1:]
+ index = file2.index('*')
+ pre2 = file2[:index]
+ post2 = file2[index+1:]
+ expr = "%s(.*)%s" % (pre1,post1)
+
+ filelist = glob.glob(file1)
+ for file1 in filelist:
+ middle = re.search(expr,file1).group(1)
+ file2 = "%s%s%s" % (pre2,middle,post2)
+ cmd = "%s %s %s %s" % (PIZZA_CONVERT,switch,file1,file2)
+ print middle,
+ sys.stdout.flush()
+ commands.getoutput(cmd)
+ print
+
+ # --------------------------------------------------------------------
+ # wrapper on ImageMagick montage command
+
+ def montage(self,switch,*fileargs):
+ nsets = len(fileargs)
+ if nsets < 2: raise StandardError,"montage requires 2 or more file args"
+
+ for i in range(nsets):
+ if fileargs[i].find('*') < 0:
+ cmd = "%s %s" % (PIZZA_MONTAGE,switch)
+ for j in range(nsets): cmd += " %s" % fileargs[j]
+ commands.getoutput(cmd)
+ return
+
+ nfiles = len(glob.glob(fileargs[0]))
+ filesets = []
+ for i in range(nsets-1):
+ filesets.append(glob.glob(fileargs[i]))
+ if len(filesets[-1]) != nfiles:
+ raise StandardError,"each montage arg must represent equal # of files"
+
+ index = fileargs[0].index('*')
+ pre1 = fileargs[0][:index]
+ post1 = fileargs[0][index+1:]
+ index = fileargs[-1].index('*')
+ preN = fileargs[-1][:index]
+ postN = fileargs[-1][index+1:]
+ expr = "%s(.*)%s" % (pre1,post1)
+
+ for i in range(nfiles):
+ cmd = "%s %s" % (PIZZA_MONTAGE,switch)
+ for j in range(nsets-1): cmd += " %s" % filesets[j][i]
+ middle = re.search(expr,filesets[0][i]).group(1)
+ fileN = "%s%s%s" % (preN,middle,postN)
+ cmd += " %s" % fileN
+ commands.getoutput(cmd)
+ print middle,
+ sys.stdout.flush()
+ print
+
# --------------------------------------------------------------------
# thumbnail class
--- /home/sjplimp/oldpizza/src/DEFAULTS.py 2005-09-07 10:13:09.000000000 -0600
+++ /home/sjplimp/pizza/src/DEFAULTS.py 2005-09-09 17:46:22.000000000 -0600
@@ -39,11 +39,17 @@
# --------------
+# ImageMagick programs to manipulate image files
# DISPLAY = program to view GIF, PNG, SVG files
# tools that use it: rasmol, raster, svg
+# CONVERT = program to convert one image format to another
+# MONTAGE = program to stitch 2 images together
+# tools that use it: image
# default = display
#PIZZA_DISPLAY = "/usr/bin/display"
+#PIZZA_CONVERT = "/usr/bin/convert"
+#PIZZA_MONTAGE = "/usr/bin/montage"
# --------------
--- /home/sjplimp/oldpizza/examples/test_image.py 2005-09-07 10:13:10.000000000 -0600
+++ /home/sjplimp/pizza/examples/test_image.py 2005-09-12 18:00:04.000000000 -0600
@@ -2,6 +2,8 @@
# requires files/bucky*.png
i = image("files/bucky*.png")
-i.view("files/bucky*.png")
+i.convert("files/bucky*.png","tmp*.gif")
+i.montage("","files/bucky*.png","tmp*.gif","tmpnew*.png")
+i.view("")
print "all done ... type CTRL-D to exit Pizza.py"
--- /home/sjplimp/oldpizza/examples/test_gnu.py 2005-09-07 10:13:10.000000000 -0600
+++ /home/sjplimp/pizza/examples/test_gnu.py 2005-09-12 15:46:22.000000000 -0600
@@ -11,6 +11,7 @@
g.plot(a)
g.plot(a,b)
g.plot(a,b,b,a)
+g.mplot(0,10,2,"tmp",a,b)
g.export("tmp.gnu",a,b)
--- /home/sjplimp/oldpizza/examples/test_matlab.py 2005-09-07 10:13:10.000000000 -0600
+++ /home/sjplimp/pizza/examples/test_matlab.py 2005-09-12 15:46:15.000000000 -0600
@@ -9,6 +9,7 @@
m.plot(a)
m.plot(a,b)
m.plot(a,b,b,a)
+m.mplot(0,10,2,"tmp",a,b)
m("3*400 - 50")
--- /home/sjplimp/oldpizza/doc/image.txt 2005-09-07 10:13:10.000000000 -0600
+++ /home/sjplimp/pizza/doc/image.txt 2005-09-12 17:24:55.000000000 -0600
@@ -14,19 +14,39 @@
[Description:]
-The image tool displays a palette of thumbnail-size images for a set
-of files. Each thumbnail can be clicked on to view the full-size
-image. Clicking on the full-size image removes it.
-
-The image constructor creates the GUI for a set of files. The view()
-method does the same thing for a new set of files.
+The image tool can be used to display image files or convert them to
+other formats via the ImageMagick tools (or alternate tools if
+specified in the DEFAULTS.py file).
+
+The image constructor creates a GUI to view a set of image files as a
+palette of thumbnail-size images. Each thumbnail can be clicked on to
+view the full-size image. Clicking on the full-size image removes it.
+The view() method does the same operation for a new set of files.
+
+The convert() method invokes the ImageMagick "convert" command to
+convert an image file to a different format. If both arguments have a
+wildcard character, one conversion is done for each file in the 1st
+argument to create a file in the 2nd argument, e.g. "convert
+image0012.svg new0012.png". If either argument has no wildcard, one
+"convert" command is issued using both arguments. This form can be
+used to create a movie file, e.g. "convert *.png ligand.mpg".
+
+The montage() method invokes the ImageMagick "montage" command to
+combine 2 image files to create a 3rd. If all 3 arguments have a
+wildcard character, one montage is created for each file in the 1st
+argument, paired with one file in the 2nd argument, e.g. "montage
+image0012.svg plot0012.eps combine0012.png". For this to work, the
+1st arguments must each expand to the same number of files. If any of
+the 3 arguments does not have a wildcard, one "montage" command is
+issued using all 3 arguements.
Image files can be in any format (PNG, GIF, JPG, etc) recognized by
-the Python Image Library (PIL) installed in your Python. Various
-Pizza.py visualization tools (raster, deja, rasmol, etc) create such
-image files. If a particular image format fails to load, your PIL
-installation was linked without support for that format. Rebuild PIL,
-and follow the install instructions included in its top directory.
+the Python Image Library (PIL) installed in your Python or by
+ImageMagick. Various Pizza.py visualization tools (raster, deja,
+rasmol, etc) create such image files. If a particular image format
+fails to load, your PIL installation was linked without support for
+that format. Rebuild PIL, and follow the install instructions
+included in its top directory.
[Usage:]
@@ -43,10 +63,24 @@
view arg is same as constructor arg :pre
+i.convert("image*.svg","new*.png") each SVG file to PNG
+i.convert("image*.svg","new*.jpg","-quality 50") 3rd arg is switch
+i.convert("image*.png","movie.mpg") all PNGs to MPG movie
+i.convert("image*.png","movie.mpg","-resize 128x128") 3rd arg is switch
+i.montage("","image*.png","plot*.png","two*.png") image + plot = two
+i.montage("-geometry 512x512","i*.png","new.png") 1st arg is switch :pre
+
+ convert with 2 wildcard args loops over 1st set of files to make 2nd set
+ convert with not all wildcard args will issue single convert command
+ montage with all wildcard args loops over 1st set of files,
+ combines with one file from other sets, to make last set of files
+ montage with not all wildcard args will issue single montage command :pre
+
[Related tools:]
"raster"_raster.html, "rasmol"_rasmol.html, "animate"_animate.html
[Prerequisites:]
-Python Tkinter, Pmw, and PIL packages.
+Python Tkinter, Pmw, and PIL packages. ImageMagick convert and
+montage commands or equivalent.
--- /home/sjplimp/oldpizza/doc/image.html 2005-09-07 10:13:10.000000000 -0600
+++ /home/sjplimp/pizza/doc/image.html 2005-09-13 09:17:16.000000000 -0600
@@ -17,19 +17,39 @@
Description:
-The image tool displays a palette of thumbnail-size images for a set
-of files. Each thumbnail can be clicked on to view the full-size
-image. Clicking on the full-size image removes it.
-
-The image constructor creates the GUI for a set of files. The view()
-method does the same thing for a new set of files.
+
The image tool can be used to display image files or convert them to
+other formats via the ImageMagick tools (or alternate tools if
+specified in the DEFAULTS.py file).
+
+The image constructor creates a GUI to view a set of image files as a
+palette of thumbnail-size images. Each thumbnail can be clicked on to
+view the full-size image. Clicking on the full-size image removes it.
+The view() method does the same operation for a new set of files.
+
+The convert() method invokes the ImageMagick "convert" command to
+convert an image file to a different format. If both arguments have a
+wildcard character, one conversion is done for each file in the 1st
+argument to create a file in the 2nd argument, e.g. "convert
+image0012.svg new0012.png". If either argument has no wildcard, one
+"convert" command is issued using both arguments. This form can be
+used to create a movie file, e.g. "convert *.png ligand.mpg".
+
+The montage() method invokes the ImageMagick "montage" command to
+combine 2 image files to create a 3rd. If all 3 arguments have a
+wildcard character, one montage is created for each file in the 1st
+argument, paired with one file in the 2nd argument, e.g. "montage
+image0012.svg plot0012.eps combine0012.png". For this to work, the
+1st arguments must each expand to the same number of files. If any of
+the 3 arguments does not have a wildcard, one "montage" command is
+issued using all 3 arguements.
Image files can be in any format (PNG, GIF, JPG, etc) recognized by
-the Python Image Library (PIL) installed in your Python. Various
-Pizza.py visualization tools (raster, deja, rasmol, etc) create such
-image files. If a particular image format fails to load, your PIL
-installation was linked without support for that format. Rebuild PIL,
-and follow the install instructions included in its top directory.
+the Python Image Library (PIL) installed in your Python or by
+ImageMagick. Various Pizza.py visualization tools (raster, deja,
+rasmol, etc) create such image files. If a particular image format
+fails to load, your PIL installation was linked without support for
+that format. Rebuild PIL, and follow the install instructions
+included in its top directory.
Usage:
@@ -46,12 +66,26 @@
view arg is same as constructor arg
+i.convert("image*.svg","new*.png") each SVG file to PNG
+i.convert("image*.svg","new*.jpg","-quality 50") 3rd arg is switch
+i.convert("image*.png","movie.mpg") all PNGs to MPG movie
+i.convert("image*.png","movie.mpg","-resize 128x128") 3rd arg is switch
+i.montage("","image*.png","plot*.png","two*.png") image + plot = two
+i.montage("-geometry 512x512","i*.png","new.png") 1st arg is switch
+
+ convert with 2 wildcard args loops over 1st set of files to make 2nd set
+ convert with not all wildcard args will issue single convert command
+ montage with all wildcard args loops over 1st set of files,
+ combines with one file from other sets, to make last set of files
+ montage with not all wildcard args will issue single montage command
+
Related tools:
raster, rasmol, animate
Prerequisites:
-Python Tkinter, Pmw, and PIL packages.
+
Python Tkinter, Pmw, and PIL packages. ImageMagick convert and
+montage commands or equivalent.