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Bug #3495
openCTF matplotlib font path Error
Added by Yong Zi Tan about 9 years ago. Updated about 8 years ago.
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
| find_3.appionsub (7.86 KB) find_3.appionsub | Yong Zi Tan, 08/31/2015 09:31 PM |
Updated by Neil Voss about 9 years ago
- Related to Bug #3438: noise subtraction in ctfdisplay normalization error added
Updated by Neil Voss about 9 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 about 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 about 8 years ago
- Subject changed from CTFFind3 Error to CTF matplotlib font path Error
Updated by Neil Voss about 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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