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Message #06698
[Branch ~yade-dev/yade/trunk] Rev 2647: 1. Fix State.rot() mistake (was returning displacement instead)
------------------------------------------------------------
revno: 2647
committer: Václav Šmilauer <eu@xxxxxxxx>
branch nick: yade
timestamp: Wed 2011-01-12 13:01:03 +0100
message:
1. Fix State.rot() mistake (was returning displacement instead)
2. Add qt.SnapshoeEngine.plot for adding snapshot name to plot.imgData automatically
3. Add plot.savePlotSequence for making movies with plots
4. Rename utils.makeVideo bps to kbps (is really kb/s, not b/s)
5. Rename OpenGLRenderer.displayGhosts to ghosts (shorter, sufficient -- sorry, Bruno)
modified:
core/State.hpp
gui/qt4/GLViewer.cpp
gui/qt4/GLViewer.hpp
pkg/common/OpenGLRenderer.cpp
pkg/common/OpenGLRenderer.hpp
py/plot.py
py/utils.py
--
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=== modified file 'core/State.hpp'
--- core/State.hpp 2011-01-09 16:34:50 +0000
+++ core/State.hpp 2011-01-12 12:01:03 +0000
@@ -71,7 +71,7 @@
.add_property("pos",&State::pos_get,&State::pos_set,"Current position.")
.add_property("ori",&State::ori_get,&State::ori_set,"Current orientation.")
.def("displ",&State::displ,"Displacement from :yref:`reference position<State.refPos>` (:yref:`pos<State.pos>` - :yref:`refPos<State.refPos>`")
- .def("rot",&State::displ,"Rotation from :yref:`reference orientation<State.refPos>` (as rotation vector)")
+ .def("rot",&State::rot,"Rotation from :yref:`reference orientation<State.refPos>` (as rotation vector)")
);
REGISTER_INDEX_COUNTER(State);
DECLARE_LOGGER;
=== modified file 'gui/qt4/GLViewer.cpp'
--- gui/qt4/GLViewer.cpp 2010-12-26 15:42:43 +0000
+++ gui/qt4/GLViewer.cpp 2011-01-12 12:01:03 +0000
@@ -24,6 +24,8 @@
#include<iomanip>
#include<boost/algorithm/string/case_conv.hpp>
#include<yade/lib/serialization/ObjectIO.hpp>
+#include<yade/lib/pyutil/gil.hpp>
+
#include<QtGui/qevent.h>
@@ -69,6 +71,7 @@
}
snapshots.push_back(fss.str());
usleep((long)(msecSleep*1000));
+ if(!plot.empty()){ pyRunString("import yade.plot; yade.plot.addImgData("+plot+"='"+fss.str()+"')"); }
}
=== modified file 'gui/qt4/GLViewer.hpp'
--- gui/qt4/GLViewer.hpp 2010-12-21 12:19:50 +0000
+++ gui/qt4/GLViewer.hpp 2011-01-12 12:01:03 +0000
@@ -30,6 +30,7 @@
((vector<string>,snapshots,,,"Files that have been created so far"))
((int,msecSleep,0,,"number of msec to sleep after snapshot (to prevent 3d hw problems) [ms]"))
((Real,deadTimeout,3,,"Timeout for 3d operations (opening new view, saving snapshot); after timing out, throw exception (or only report error if *ignoreErrors*) and make myself :yref:`dead<Engine.dead>`. [s]"))
+ ((string,plot,,,"Name of field in :yref:`yade.plot.imgData` to which taken snapshots will be appended automatically."))
);
DECLARE_LOGGER;
};
=== modified file 'pkg/common/OpenGLRenderer.cpp'
--- pkg/common/OpenGLRenderer.cpp 2011-01-11 14:47:55 +0000
+++ pkg/common/OpenGLRenderer.cpp 2011-01-12 12:01:03 +0000
@@ -379,7 +379,7 @@
}
// if the body goes over the cell margin, draw it in positions where the bbox overlaps with the cell in wire
// precondition: pos is inside the cell.
- if(b->bound && scene->isPeriodic && displayGhosts){
+ if(b->bound && scene->isPeriodic && ghosts){
const Vector3r& cellSize(scene->cell->getSize());
pos=scene->cell->unshearPt(pos); // remove the shear component
// traverse all periodic cells around the body, to see if any of them touches
=== modified file 'pkg/common/OpenGLRenderer.hpp'
--- pkg/common/OpenGLRenderer.hpp 2011-01-11 14:47:55 +0000
+++ pkg/common/OpenGLRenderer.hpp 2011-01-12 12:01:03 +0000
@@ -104,7 +104,7 @@
((bool,intrWire,false,,"If rendering interactions, use only wires to represent them."))
((bool,intrGeom,false,,"Render :yref:`Interaction::geom` objects."))
((bool,intrPhys,false,,"Render :yref:`Interaction::phys` objects"))
- ((bool,displayGhosts,true,,"Render objects crossing periodic cell edges by cloning them in multiple places (periodic simulations only)."))
+ ((bool,ghosts,true,,"Render objects crossing periodic cell edges by cloning them in multiple places (periodic simulations only)."))
#ifdef YADE_SUBDOMAINS
((int,subDomMask,0,,"If non-zero, render shape only of particles that are inside respective domains - -they are counted from the left, i.e. 5 (binary 101) will show subdomains 1 and 3. If zero, render everything."))
#endif
=== modified file 'py/plot.py'
--- py/plot.py 2011-01-09 16:34:50 +0000
+++ py/plot.py 2011-01-12 12:01:03 +0000
@@ -6,12 +6,19 @@
"""
## all exported names
-__all__=['data','plots','labels','live','liveInterval','autozoom','plot','reset','resetData','splitData','reverse','addData','saveGnuplot','saveDataTxt']
+__all__=['data','plots','labels','live','liveInterval','autozoom','plot','reset','resetData','splitData','reverse','addData','saveGnuplot','saveDataTxt','savePlotSequence']
# multi-threaded support for Tk
# safe to import even if Tk will not be used
import mtTkinter as Tkinter
+try:
+ import Image
+except:
+ raise ImportError("PIL (python-imaging package) must be installed to use yade.plot")
+
+
+
import matplotlib,os,time,math,itertools
# running in batch
@@ -36,8 +43,10 @@
data={}
"Global dictionary containing all data values, common for all plots, in the form {'name':[value,...],...}. Data should be added using plot.addData function. All [value,...] columns have the same length, they are padded with NaN if unspecified."
+imgData={}
+"Dictionary containing lists of strings, which have the meaning of images corresponding to respective :yref:`yade.plot.data` rows. See :yref:`yade.plot.plots` on how to plot images."
plots={} # dictionary x-name -> (yspec,...), where yspec is either y-name or (y-name,'line-specification')
-"dictionary x-name -> (yspec,...), where yspec is either y-name or (y-name,'line-specification')"
+"dictionary x-name -> (yspec,...), where yspec is either y-name or (y-name,'line-specification'). If ``(yspec,...)`` is ``None``, then the plot has meaning of image, which will be taken from respective field of :yref:`yade.plot.imgData`."
labels={}
"Dictionary converting names in data to human-readable names (TeX names, for instance); if a variable is not specified, it is left untranslated."
xylabels={}
@@ -58,11 +67,14 @@
"Linewidth (in points) to make *x* and *y* axes better visible; not activated if non-positive."
current=-1
"Point that is being tracked with a scatter point. -1 is for the last point, set to *nan* to disable."
+#take3dSnapshots=False
+#"If true, take snapshot of the 3d view using :yref:`yade.qt.SnapshotEngine` every time :yref:`yade.plot.addData` is called"
+#snapshotEngine=None
def reset():
"Reset all plot-related variables (data, plots, labels)"
global data, plots, labels # plotLines
- data={}; plots={}; # plotLines={};
+ data={}; plots={}; imgData={} # plotLines={};
pylab.close('all')
def resetData():
@@ -101,15 +113,45 @@
import numpy
if len(data)>0: numSamples=len(data[data.keys()[0]])
else: numSamples=0
- #reduceData(numSamples)
+ # align with imgData, if there is more of them than data
+ if len(imgData)>0 and numSamples==0: numSamples=max(numSamples,len(imgData[imgData.keys()[0]]))
d=(d_in[0] if len(d_in)>0 else {})
d.update(**kw)
for name in d:
- if not name in data.keys():
- data[name]=[nan for i in range(numSamples)] #numpy.array([nan for i in range(numSamples)])
+ if not name in data.keys(): data[name]=[]
for name in data:
- if name in d: data[name].append(d[name]) #numpy.append(data[name],[d[name]],1)
- else: data[name].append(nan)
+ data[name]+=(numSamples-len(data[name]))*[nan]
+ data[name].append(d[name] if name in d else nan)
+ #print [(k,len(data[k])) for k in data.keys()]
+ #numpy.array([nan for i in range(numSamples)])
+ #numpy.append(data[name],[d[name]],1)
+
+def addImgData(**kw):
+ for k in kw:
+ if k not in imgData: imgData[k]=[]
+ # align imgData with data
+ if len(data.keys())>0 and len(imgData.keys())>0:
+ nData,nImgData=len(data[data.keys()[0]]),len(imgData[imgData.keys()[0]])
+ #if nImgData>nData-1: raise RuntimeError("imgData is already the same length as data?")
+ if nImgData<nData-1: # repeat last value
+ for k in imgData.keys():
+ lastValue=imgData[k][-1] if len(imgData[k])>0 else None
+ imgData[k]+=(nData-len(imgData[k])-1)*[lastValue]
+ elif nData<nImgData:
+ for k in data.keys():
+ lastValue=data[k][-1] if len(data[k])>0 else nan
+ data[k]+=(nImgData-nData)*[lastValue] # add one more, because we will append to imgData below
+ # add values from kw
+ newLen=(len(imgData[imgData.keys()[0]]) if imgData else 0)+1 # current length plus 1
+ for k in kw:
+ if k in imgData and len(imgData[k])>0: imgData[k]+=(newLen-len(imgData[k])-1)*[imgData[k][-1]]+[kw[k]] # repeat last element as necessary
+ else: imgData[k]=(newLen-1)*[None]+[kw[k]] # repeat None if no previous value
+ # align values which were not in kw by repeating the last value
+ for k in imgData:
+ if len(imgData[k])<newLen: imgData[k]+=(newLen-len(imgData[k]))*[imgData[k][-1]]
+ assert(len(set([len(i) for i in imgData.values()]))<=1) # no data or all having the same value
+
+
# not public functions
def addPointTypeSpecifier(o):
@@ -129,26 +171,36 @@
class LineRef:
"""Holds reference to plot line and to original data arrays (which change during the simulation),
and updates the actual line using those data upon request."""
- def __init__(self,line,scatter,xdata,ydata):
- self.line,self.scatter,self.xdata,self.ydata=line,scatter,xdata,ydata
+ def __init__(self,line,scatter,xdata,ydata,dataName=None):
+ self.line,self.scatter,self.xdata,self.ydata,self.dataName=line,scatter,xdata,ydata,dataName
def update(self):
- import numpy
- self.line.set_xdata(self.xdata)
- self.line.set_ydata(self.ydata)
- try:
- x,y=[self.xdata[current]],[self.ydata[current]]
- except IndexError: x,y=0,0
- # this could be written in a nicer way, very likely
- try:
- pt=numpy.ndarray((2,),buffer=numpy.array([x,y]))
- if self.scatter: self.scatter.set_offsets(pt)
- except TypeError: pass # this happens at i386 with empty data, saying TypeError: buffer is too small for requested array
+ if isinstance(self.line,matplotlib.image.AxesImage):
+ # image name
+ try:
+ if len(self.xdata)==0 and self.dataName: self.xdata=imgData[self.dataName] # empty list reference an empty singleton, not the list we want; adjust here
+ if self.xdata[current]==None: img=Image.new('RGBA',(1,1),(0,0,0,0))
+ else: img=Image.open(self.xdata[current])
+ self.line.set_data(img)
+ except IndexError: pass
+ else:
+ # regular data
+ import numpy
+ self.line.set_xdata(self.xdata)
+ self.line.set_ydata(self.ydata)
+ try:
+ x,y=[self.xdata[current]],[self.ydata[current]]
+ except IndexError: x,y=0,0
+ # this could be written in a nicer way, very likely
+ try:
+ pt=numpy.ndarray((2,),buffer=numpy.array([x,y]))
+ if self.scatter: self.scatter.set_offsets(pt)
+ except TypeError: pass # this happens at i386 with empty data, saying TypeError: buffer is too small for requested array
currLineRefs=[]
liveTimeStamp=0 # timestamp when live update was started, so that the old thread knows to stop if that changes
nan=float('nan')
-def createPlots(subPlots=True):
+def createPlots(subPlots=True,scatterSize=20,wider=False):
global currLineRefs
figs=set([l.line.get_axes().get_figure() for l in currLineRefs]) # get all current figures
for f in figs: pylab.close(f) # close those
@@ -157,11 +209,20 @@
if subPlots:
# compute number of rows and colums for plots we have
subCols=int(round(math.sqrt(len(plots)))); subRows=int(math.ceil(len(plots)*1./subCols))
- #print 'subplot',subCols,subRows
+ if wider: subRows,subCols=subCols,subRows
for nPlot,p in enumerate(plots.keys()):
pStrip=p.strip()
if not subPlots: pylab.figure()
else: pylab.subplot(subRows,subCols,nPlot)
+ if plots[p]==None: # image plot
+ if not pStrip in imgData.keys(): imgData[pStrip]=[]
+ # fake (empty) image if no data yet
+ if len(imgData[pStrip])==0 or imgData[pStrip][-1]==None: img=Image.new('RGBA',(1,1),(0,0,0,0))
+ else: img=Image.open(imgData[pStrip][-1])
+ img=pylab.imshow(img,origin='lower')
+ currLineRefs.append(LineRef(img,None,imgData[pStrip],None,pStrip))
+ pylab.gca().set_axis_off()
+ continue
plots_p=[addPointTypeSpecifier(o) for o in tuplifyYAxis(plots[p])]
plots_p_y1,plots_p_y2=[],[]; y1=True
missing=set() # missing data columns
@@ -204,7 +265,7 @@
# use (0,0) if there are no data yet
scatterPt=[0,0] if len(data[pStrip])==0 else (data[pStrip][current],data[d[0]][current])
# if current value is NaN, use zero instead
- scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,color=line.get_color())
+ scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color())
currLineRefs.append(LineRef(line,scatter,data[pStrip],data[d[0]]))
axes=line.get_axes()
labelLoc=(legendLoc[0 if isY1 else 1] if y2Exists>0 else 'best')
@@ -258,7 +319,8 @@
ax.yadeYNames.add(new)
if new in data.keys() and id(data[new]) in linesData: continue # do not add when reloaded and the old lines are already there
print 'yade.plot: creating new line for',new
- if not new in data.keys(): data[new]=[] # create data entry if necessary
+ if not new in data.keys(): data[new]=len(data[ax.yadeXName])*[nan] # create data entry if necessary
+ #print 'data',len(data[ax.yadeXName]),len(data[new]),data[ax.yadeXName],data[new]
line,=ax.plot(data[ax.yadeXName],data[new],label=xlateLabel(new)) # no line specifier
scatterPt=(0 if len(data[ax.yadeXName])==0 or math.isnan(data[ax.yadeXName][current]) else data[ax.yadeXName][current]),(0 if len(data[new])==0 or math.isnan(data[new][current]) else data[new][current])
scatter=ax.scatter(scatterPt[0],scatterPt[1],color=line.get_color())
@@ -279,6 +341,64 @@
except RuntimeError: pass # happens here too
time.sleep(liveInterval)
+def savePlotSequence(fileBase,stride=1,imgRatio=(5,7),title=None,titleFrames=20,lastFrames=30):
+ '''Save sequence of plots, each plot corresponding to one line in history. It is especially meant to be used for :yref:`yade.utils.makeVideo`.
+
+ :param stride: only consider every stride-th line of history (default creates one frame per each line)
+ :param title: Create title frame, where lines of title are separated with newlines (``\\n``) and optional subtitle is separated from title by double newline.
+ :param int titleFrames: Create this number of frames with title (by repeating its filename), determines how long the title will stand in the movie.
+ :param int lastFrames: Repeat the last frame this number of times, so that the movie does not end abruptly.
+ :return: List of filenames with consecutive frames.
+ '''
+ createPlots(subPlots=True,scatterSize=60,wider=True)
+ sqrtFigs=math.sqrt(len(plots))
+ pylab.gcf().set_size_inches(8*sqrtFigs,5*sqrtFigs) # better readable
+ pylab.subplots_adjust(left=.05,right=.95,bottom=.05,top=.95) # make it more compact
+ if len(plots)==1 and plots[plots.keys()[0]]==None: # only pure snapshot is there
+ pylab.gcf().set_size_inches(5,5)
+ pylab.subplots_adjust(left=0,right=1,bottom=0,top=1)
+ #if not data.keys(): raise ValueError("plot.data is empty.")
+ pltLen=max(len(data[data.keys()[0]]) if data else 0,len(imgData[imgData.keys()[0]]) if imgData else 0)
+ if pltLen==0: raise ValueError("Both plot.data and plot.imgData are empty.")
+ global current, currLineRefs
+ ret=[]
+ print 'Saving %d plot frames, it can take a while...'%(pltLen)
+ for i,n in enumerate(range(0,pltLen,stride)):
+ current=n
+ for l in currLineRefs: l.update()
+ out=fileBase+'-%03d.png'%i
+ pylab.gcf().savefig(out)
+ ret.append(out)
+ if len(ret)==0: raise RuntimeError("No images created?!")
+ if title:
+ titleImgName=fileBase+'-title.png'
+ createTitleFrame(titleImgName,Image.open(ret[-1]).size,title)
+ ret=titleFrames*[titleImgName]+ret
+ if lastFrames>1: ret+=(lastFrames-1)*[ret[-1]]
+ return ret
+
+def createTitleFrame(out,size,title):
+ 'create figure with title and save to file; a figure object must be opened to get the right size'
+ pylab.clf(); fig=pylab.gcf()
+ #insize=fig.get_size_inches(); size=insize[1]*fig.get_dpi(),insize[0]*fig.get_dpi() # this gives wrong dimensions...
+ #fig.set_facecolor('blue'); fig.patch.set_color('blue'); fig.patch.set_facecolor('blue'); fig.patch.set_alpha(None)
+ title,subtitle=title.split('\n\n')
+ lines=[(t,True) for t in title.split('\n')]+([(t,False) for t in subtitle.split('\n')] if subtitle else [])
+ nLines=len(lines); fontSizes=size[1]/10.,size[1]/16.
+ import matplotlib.mathtext
+ def writeLine(text,vertPos,fontsize):
+ rgba,depth=matplotlib.mathtext.MathTextParser('Bitmap').to_rgba(text,fontsize=fontsize,dpi=fig.get_dpi(),color='blue')
+ textsize=rgba.shape[1],rgba.shape[0]
+ if textsize[0]>size[0]:
+ rgba,depth=matplotlib.mathtext.MathTextParser('Bitmap').to_rgba(text,fontsize=fontsize*size[0]/textsize[0],dpi=fig.get_dpi(),color='blue')
+ textsize=rgba.shape[1],rgba.shape[0]
+ fig.figimage(rgba.astype(float)/255.,xo=(size[0]-textsize[0])/2.,yo=vertPos-depth)
+ ht=size[1]; y0=ht-2*fontSizes[0]; yStep=(ht-2.5*fontSizes[0])/len(lines)
+ for i,(l,isTitle) in enumerate(lines):
+ writeLine(l,y0-i*yStep,fontSizes[0 if isTitle else 1])
+ fig.savefig(out)
+
+
def plot(noShow=False,subPlots=True):
"""Do the actual plot, which is either shown on screen (and nothing is returned: if *noShow* is ``False``) or, if *noShow* is ``True``, returned as matplotlib's Figure object or list of them.
@@ -298,13 +418,17 @@
"""
createPlots(subPlots=subPlots)
global currLineRefs
+ figs=set([l.line.get_axes().get_figure() for l in currLineRefs])
+ if not hasattr(list(figs)[0],'show') and not noShow:
+ import warnings
+ warnings.warn('plot.plot not showing figure (matplotlib using headless backend?)')
+ noShow=True
if not noShow:
if not yade.runtime.hasDisplay: return # would error out with some backends, such as Agg used in batches
if live:
import thread
thread.start_new_thread(liveUpdate,(time.time(),))
# pylab.show() # this blocks for some reason; call show on figures directly
- figs=set([l.line.get_axes().get_figure() for l in currLineRefs])
for f in figs:
f.show()
# should have fixed https://bugs.launchpad.net/yade/+bug/606220, but does not work apparently
@@ -394,6 +518,7 @@
i=0
for p in plots:
pStrip=p.strip()
+ if plots[pStrip]==None: continue ## this plot is image plot, which is not applicable to gnuplot
plots_p=[addPointTypeSpecifier(o) for o in tuplifyYAxis(plots[p])]
if term in ['wxt','x11']: fPlot.write("set term %s %d persist\n"%(term,i))
else: fPlot.write("set term %s; set output '%s.%d.%s'\n"%(term,baseNameNoPath,i,extension))
=== modified file 'py/utils.py'
--- py/utils.py 2010-12-26 15:42:43 +0000
+++ py/utils.py 2011-01-12 12:01:03 +0000
@@ -519,28 +519,30 @@
_deprecatedUtilsFunction('utils.encodeVideoFromFrames','utils.makeVideo')
return makeVideo(*args,**kw)
-def makeVideo(frameSpec,out,renameNotOverwrite=True,fps=24,bps=2400):
+def makeVideo(frameSpec,out,renameNotOverwrite=True,fps=24,kbps=6000,bps=None):
"""Create a video from external image files using `mencoder <http://www.mplayerhq.hu>`__. Two-pass encoding using the default mencoder codec (mpeg4) is performed, running multi-threaded with number of threads equal to number of OpenMP threads allocated for Yade.
:param frameSpec: wildcard | sequence of filenames. If list or tuple, filenames to be encoded in given order; otherwise wildcard understood by mencoder's mf:// URI option (shell wildcards such as ``/tmp/snap-*.png`` or and printf-style pattern like ``/tmp/snap-%05d.png``)
:param str out: file to save video into
:param bool renameNotOverwrite: if True, existing same-named video file will have -*number* appended; will be overwritten otherwise.
:param int fps: Frames per second (``-mf fps=…``)
- :param int bps: Bitrate (``-lavcopts vbitrate=…``)
+ :param int kbps: Bitrate (``-lavcopts vbitrate=…``) in kb/s
"""
- import os,os.path,subprocess
+ import os,os.path,subprocess,warnings
+ if bps!=None:
+ warnings.warn('plot.makeVideo: bps is deprecated, use kbps instead (the significance is the same, but the name is more precise)',stacklevel=2,category=DeprecationWarning)
+ kbps=bps
if renameNotOverwrite and os.path.exists(out):
i=0
while(os.path.exists(out+"~%d"%i)): i+=1
os.rename(out,out+"~%d"%i); print "Output file `%s' already existed, old file renamed to `%s'"%(out,out+"~%d"%i)
if isinstance(frameSpec,list) or isinstance(frameSpec,tuple): frameSpec=','.join(frameSpec)
for passNo in (1,2):
- cmd=['mencoder','mf://%s'%frameSpec,'-mf','fps=%d'%int(fps),'-ovc','lavc','-lavcopts','vbitrate=%d:vpass=%d:threads=%d:%s'%(int(bps),passNo,O.numThreads,'turbo' if passNo==1 else ''),'-o',('/dev/null' if passNo==1 else out)]
+ cmd=['mencoder','mf://%s'%frameSpec,'-mf','fps=%d'%int(fps),'-ovc','lavc','-lavcopts','vbitrate=%d:vpass=%d:threads=%d:%s'%(int(kbps),passNo,O.numThreads,'turbo' if passNo==1 else ''),'-o',('/dev/null' if passNo==1 else out)]
print 'Pass %d:'%passNo,' '.join(cmd)
ret=subprocess.call(cmd)
if ret!=0: raise RuntimeError("Error when running mencoder.")
-
def replaceCollider(colliderEngine):
"""Replaces collider (Collider) engine with the engine supplied. Raises error if no collider is in engines."""
colliderIdx=-1
