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CTF matplotlib font path Error #3495

Open leginonbot opened 5 months ago

leginonbot commented 5 months ago

Author Name: Yong Zi Tan (Yong Zi Tan) Original Redmine Issue: 3495, https://emg.nysbc.org/redmine/issues/3495 Original Date: 2015-08-31 Original Assignee: Dmitry Lyumkis

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.

leginonbot commented 5 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-09-04T20:38:22Z

This look like it has something to do with your matplotlib install, it could not find a font to create a graph.

leginonbot commented 5 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2016-11-16T20:09:58Z

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()
leginonbot commented 5 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2016-11-16T20:13:32Z

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