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Bug #3495
openCTF matplotlib font path Error
Start date:
08/31/2015
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:
Description
CTFFind3 crashes before finishing a micrograph - the log file is attached. This was run at the Salk server, and we have updated to the latest version of myami. Thank you.
Files
Updated by Neil Voss almost 10 years ago
- Related to Bug #3438: noise subtraction in ctfdisplay normalization error added
Updated by Neil Voss almost 10 years ago
- Assignee changed from Neil Voss to Dmitry Lyumkis
This look like it has something to do with your matplotlib install, it could not find a font to create a graph.
Updated by Neil Voss over 8 years ago
perhaps relevant code in apCtf/ctfdisplay.py:
#########
## setup font to add text
#########
fontpath = "/usr/share/fonts/liberation/LiberationSans-Regular.ttf"
from PIL import ImageFont
if os.path.isfile(fontpath):
fontsize = int(math.ceil( 48/2. * min(powerspec.shape)/float(maxsize))*2)
font = ImageFont.truetype(fontpath, fontsize)
else:
font = ImageFont.load_default()
Updated by Neil Voss over 8 years ago
- Subject changed from CTFFind3 Error to CTF matplotlib font path Error
Updated by Neil Voss over 8 years ago
Easier to read Traceback
Traceback (most recent call last):
File "/data2/log-l/progs/myami/appion/bin/ctfestimate.py", line 449, in <module>
imgLoop.run()
File "/data2/log-l/progs/myami/appion/appionlib/appionLoop2.py", line 93, in run
self.loopCommitToDatabase(imgdata)
File "/data2/log-l/progs/myami/appion/appionlib/appionLoop2.py", line 143, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/data2/log-l/progs/myami/appion/bin/ctfestimate.py", line 349, in commitToDatabase
ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
File "/data2/log-l/progs/myami/appion/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
File "/data2/log-l/progs/myami/appion/appionlib/apCtf/ctfinsert.py", line 83, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
File "/data2/log-l/progs/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1266, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
File "/data2/log-l/progs/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1148, in CTFpowerspec
normpowerspec = self.normalizeCtf(powerspec, twod=twod)
File "/data2/log-l/progs/myami/appion/appionlib/apCtf/ctfdisplay.py", line 622, in normalizeCtf
pyplot.savefig(self.plotsfile, format="png", dpi=300, orientation='landscape', pad_inches=0.0)
File "/usr/lib64/python2.6/site-packages/matplotlib/pyplot.py", line 356, in savefig
return fig.savefig(*args, **kwargs)
File "/usr/lib64/python2.6/site-packages/matplotlib/figure.py", line 1032, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/usr/lib64/python2.6/site-packages/matplotlib/backend_bases.py", line 1476, in print_figure
**kwargs)
File "/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", line 358, in print_png
FigureCanvasAgg.draw(self)
File "/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", line 314, in draw
self.figure.draw(self.renderer)
File "/usr/lib64/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *kl)
File "/usr/lib64/python2.6/site-packages/matplotlib/figure.py", line 773, in draw
for a in self.axes: a.draw(renderer)
File "/usr/lib64/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *kl)
File "/usr/lib64/python2.6/site-packages/matplotlib/axes.py", line 1735, in draw
a.draw(renderer)
File "/usr/lib64/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *kl)
File "/usr/lib64/python2.6/site-packages/matplotlib/axis.py", line 742, in draw
tick.draw(renderer)
File "/usr/lib64/python2.6/site-packages/matplotlib/artist.py", line 46, in draw_wrapper
draw(artist, renderer, *kl)
File "/usr/lib64/python2.6/site-packages/matplotlib/axis.py", line 196, in draw
self.label1.draw(renderer)
File "/usr/lib64/python2.6/site-packages/matplotlib/text.py", line 515, in draw
bbox, info = self._get_layout(renderer)
File "/usr/lib64/python2.6/site-packages/matplotlib/text.py", line 279, in _get_layout
clean_line, self._fontproperties, ismath=ismath)
File "/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_agg.py", line 156, in get_text_width_height_descent
self.mathtext_parser.parse(s, self.dpi, prop)
File "/usr/lib64/python2.6/site-packages/matplotlib/mathtext.py", line 2797, in parse
font_output = fontset_class(prop, backend)
File "/usr/lib64/python2.6/site-packages/matplotlib/mathtext.py", line 658, in __init__
self._stix_fallback = StixFonts(*args, **kwargs)
File "/usr/lib64/python2.6/site-packages/matplotlib/mathtext.py", line 900, in __init__
fullpath = findfont(name)
File "/usr/lib64/python2.6/site-packages/matplotlib/font_manager.py", line 1306, in findfont
if not os.path.exists(font):
File "/usr/lib64/python2.6/genericpath.py", line 18, in exists
st = os.stat(path)
TypeError: coercing to Unicode: need string or buffer, dict found
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