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gallantlab / pycortex

Pycortex is a python-based toolkit for surface visualization of fMRI data
https://gallantlab.github.io/pycortex
BSD 2-Clause "Simplified" License
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glrework-merged config file #207

Closed marklescroart closed 7 years ago

marklescroart commented 7 years ago

The glrework-merged branch has new requirements for the config file that are not in the old config files for master branch. The correct way to handle this will be to update the defaults.cfg file in pycortex, and to have pycortex look for missing options in a user's config file in that defaults config file (and then update the user's config file with the missing defaults). I believe this is already done on the master branch, but didn't get merged here.

In the meantime, before this change is implemented, here is a sample config file that should work with glrework-merged:

[basic] default_cmap = RdBu_r default_cmap2d = RdBu_covar fsl_prefix = fsl5.0- filestore = ~/pycortex_store/ # THIS WILL BE USER SPECIFIC

[mayavi_aligner] line_width = 1 point_size = 2 outline_color = white outline_rep = wireframe opacity = 0 colormap = gray

[paths_default] stroke = white fill = none display = inline filter = url(#dropshadow) stroke-width = 3 stroke-opacity = 1 fill-opacity = 0 stroke-dashoffset = None stroke-dasharray = None

[labels_default] font-family = Helvetica, sans-serif font-size = 18pt font-weight = bold font-style = italic fill = white fill-opacity = 1 text-anchor = middle filter = url(#dropshadow)

[rois_paths] stroke = white fill = none display = inline filter = url(#dropshadow) stroke-width = 2 stroke-opacity = 1 fill-opacity = 0 stroke-dashoffset = None stroke-dasharray = None

[rois_labels] font-family = Helvetica, sans-serif font-size = 14pt font-weight = bold font-style = italic fill = white fill-opacity = 1 text-anchor = middle filter = url(#dropshadow)

[sulci_paths] stroke = white fill = none display = inline filter = url(#dropshadow) stroke-width = 2 stroke-opacity = 1 fill-opacity = 0 stroke-dashoffset = None stroke-dasharray = 1,5 stroke-linecape = round

[sulci_labels] font-family = Helvetica, sans-serif font-size = 12pt font-weight = font-style = fill = white fill-opacity = 1 text-anchor = middle filter = url(#dropshadow)

[overlay_paths] stroke = white fill = none display = inline filter = url(#dropshadow) stroke-width = 2 stroke-opacity = 1 fill-opacity = 0 stroke-dashoffset = None stroke-dasharray = None

[overlay_text] font-family = Helvetica, sans-serif font-size = 14pt font-weight = bold font-style = italic fill = white fill-opacity = 1 text-anchor = middle filter = url(#dropshadow)

[curvature] max = .6 min = -.6 threshold = False

[webgl_viewopts] voxlines = false voxline_color = #FFFFFF voxline_width = 0.01 specularity = 1.0 curvalpha = 1.0 curvscale = 0.0 curvlim = 0.25 overlayscale = 1

[webgl] layers = rois,

eickenberg commented 7 years ago

as of the latest updates of the docs the file also seems to need curvature->contrast:

Unexpected failing examples:
/pycortex/examples/quickstart/plot_retinotopy_flatmap.py failed leaving traceback:
Traceback (most recent call last):
  File "/anaconda/envs/python27/lib/python2.7/site-packages/sphinx_gallery/gen_rst.py", line 475, in execute_code_block
    exec(code_block, example_globals)
  File "<string>", line 13, in <module>
  File "/software/pycortex/cortex/quickflat.py", line 542, in make_figure
    curv_im = add_curvature(fig, dataview, extents)
  File "/pycortex/cortex/quickflat.py", line 74, in add_curvature
    contrast = float(config.get('curvature', 'contrast'))
  File "/anaconda/envs/python27/lib/python2.7/ConfigParser.py", line 618, in get
    raise NoOptionError(option, section)
NoOptionError: No option 'contrast' in section: 'curvature'
alexhuth commented 7 years ago

@marklescroart is in the midst of fixing this right now