vsoch/nidmviewer

NIDM Results Viewer

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nidmviewer's Issues

'pyparsing<=1.5.7' distribution was not found error at start up of nidmviewer

This issue was reported through twitter by Jan-Bernard Marsman (‏@jbcmarsman): https://twitter.com/jbcmarsman/status/744879142148128768.

Traceback of the error on mac (MBP 2015, El Capitan):

$ nidmviewer
Traceback (most recent call last):
  File "/Users/marsman/anaconda/bin/nidmviewer", line 5, in <module>
    from pkg_resources import load_entry_point
  File "/Users/marsman/anaconda/lib/python2.7/site-packages/setuptools-19.2-py2.7.egg/pkg_resources/__init__.py", line 3138, in <module>
  File "/Users/marsman/anaconda/lib/python2.7/site-packages/setuptools-19.2-py2.7.egg/pkg_resources/__init__.py", line 3124, in _call_aside
  File "/Users/marsman/anaconda/lib/python2.7/site-packages/setuptools-19.2-py2.7.egg/pkg_resources/__init__.py", line 3151, in _initialize_master_working_set
  File "/Users/marsman/anaconda/lib/python2.7/site-packages/setuptools-19.2-py2.7.egg/pkg_resources/__init__.py", line 663, in _build_master
  File "/Users/marsman/anaconda/lib/python2.7/site-packages/setuptools-19.2-py2.7.egg/pkg_resources/__init__.py", line 676, in _build_from_requirements
  File "/Users/marsman/anaconda/lib/python2.7/site-packages/setuptools-19.2-py2.7.egg/pkg_resources/__init__.py", line 849, in resolve
pkg_resources.DistributionNotFound: The 'pyparsing<=1.5.7' distribution was not found and is required by rdfextras

More details in NIDM notes.

fields need to be read from provn file

add pandas to dependencies

python 3 support

wow, must have made this a long time ago :P

Cannot read property 'substr' of undefined

I'm getting an error with those two NIDM-Results 1.3.0 examples:
http://neurovault.org/collections/1404/fsl_ds005_sub-01.nidm
http://neurovault.org/collections/1404/fsl_ds005_group.nidm

Uncaught TypeError: Cannot read property 'substr' of undefined
papaya.volume.Volume.readURLs @ papaya.js:399
papaya.viewer.Viewer.loadOverlay @ papaya.js:648
(anonymous function) @ fsl_ds005_sub-01.nidm:205

Add tests for python 2 and python 3

To start with we could have a simple test that would download a NIDM turtle file from NeuroVault and check that the viewer runs without error with python 2 & 3.

Link to a nidm.ttl file: https://neurovault.org/collections/1425/pain_01.nidm/nidm.ttl

Display excursion set instead of unthresholded statmap

Currently the viewer is displaying the unthresholded statistical map (see https://github.com/vsoch/nidmviewer/blob/master/nidmviewer/sparql.py#L76), and then papaya does some implicit thresholding. This leads to confusion when one of the coordinates is pointing to a voxel that is inside the excursion set, but below the implicit papaya threshold.

Viewing images not in MNI space

This issue is open to discuss which behaviour should be implemented for the nidmviewer in the presence of images that are not in MNI space. See for example: http://neurovault.org/collections/1435/fsl_ds008_sub-01.nidm

One possibility would be to check in the NIDM file if the space is MNI or not and then issue a warning if images are in subject space?

@vsoch, @chrisfilo: do you have any thoughts?

"RuntimeError("'%s' is not a writable dir" error at start up

This issue was reported through twitter by Jan-Bernard Marsman (‏@jbcmarsman): https://twitter.com/jbcmarsman/status/744879142148128768.

Traceback of the error on Ubuntu (precise pengolin)

Traceback (most recent call last):
  File "/usr/local/bin/nidmviewer", line 9, in <module>
    load_entry_point('nidmviewer==0.1.3', 'console_scripts', 'nidmviewer')()
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 337, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2279, in load_entry_point
    return ep.load()
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 1989, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/usr/local/lib/python2.7/dist-packages/nidmviewer/scripts.py", line 9, in <module>
    from nidmviewer.viewer import generate
  File "/usr/local/lib/python2.7/dist-packages/nidmviewer/viewer.py", line 7, in <module>
    from nidmviewer.templates import get_template, add_string, save_template, remove_resources
  File "/usr/local/lib/python2.7/dist-packages/nidmviewer/templates.py", line 8, in <module>
    import pandas
  File "/usr/local/lib/python2.7/dist-packages/pandas/__init__.py", line 41, in <module>
    from pandas.core.api import *
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/api.py", line 9, in <module>
    from pandas.core.groupby import Grouper
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/groupby.py", line 15, in <module>
    from pandas.core.frame import DataFrame
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/frame.py", line 38, in <module>
    from pandas.core.series import Series
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/series.py", line 2524, in <module>
    import pandas.tools.plotting as _gfx
  File "/usr/local/lib/python2.7/dist-packages/pandas/tools/plotting.py", line 26, in <module>
    import pandas.tseries.converter as conv
  File "/usr/local/lib/python2.7/dist-packages/pandas/tseries/converter.py", line 7, in <module>
    import matplotlib.units as units
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 774, in <module>
    rcParams = rc_params()
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 692, in rc_params
    fname = matplotlib_fname()
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 604, in matplotlib_fname
    fname = os.path.join(get_configdir(), 'matplotlibrc')
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 253, in wrapper
    ret = func(*args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 475, in _get_configdir
    raise RuntimeError("'%s' is not a writable dir; you must set %s/.matplotlib to be a writable dir.  You can also set environment variable MPLCONFIGDIR to any writable directory where you want matplotlib data stored "% (h, h))
RuntimeError: '/home/marsman' is not a writable dir; you must set /home/marsman/.matplotlib to be a writable dir.  You can also set environment variable MPLCONFIGDIR to any writable directory where you want matplotlib data stored
marsman@nicserver:/data/local_dir2/marsman$ nidmviewer
Traceback (most recent call last):
  File "/usr/local/bin/nidmviewer", line 9, in <module>
    load_entry_point('nidmviewer==0.1.3', 'console_scripts', 'nidmviewer')()
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 337, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2279, in load_entry_point
    return ep.load()
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 1989, in load
    entry = __import__(self.module_name, globals(),globals(), ['__name__'])
  File "/usr/local/lib/python2.7/dist-packages/nidmviewer/scripts.py", line 9, in <module>
    from nidmviewer.viewer import generate
  File "/usr/local/lib/python2.7/dist-packages/nidmviewer/viewer.py", line 7, in <module>
    from nidmviewer.templates import get_template, add_string, save_template, remove_resources
  File "/usr/local/lib/python2.7/dist-packages/nidmviewer/templates.py", line 8, in <module>
    import pandas
  File "/usr/local/lib/python2.7/dist-packages/pandas/__init__.py", line 41, in <module>
    from pandas.core.api import *
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/api.py", line 9, in <module>
    from pandas.core.groupby import Grouper
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/groupby.py", line 15, in <module>
    from pandas.core.frame import DataFrame
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/frame.py", line 38, in <module>
    from pandas.core.series import Series
  File "/usr/local/lib/python2.7/dist-packages/pandas/core/series.py", line 2524, in <module>
    import pandas.tools.plotting as _gfx
  File "/usr/local/lib/python2.7/dist-packages/pandas/tools/plotting.py", line 26, in <module>
    import pandas.tseries.converter as conv
  File "/usr/local/lib/python2.7/dist-packages/pandas/tseries/converter.py", line 7, in <module>
    import matplotlib.units as units
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 774, in <module>
    rcParams = rc_params()
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 692, in rc_params
    fname = matplotlib_fname()
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 604, in matplotlib_fname
    fname = os.path.join(get_configdir(), 'matplotlibrc')
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 253, in wrapper
    ret = func(*args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/__init__.py", line 475, in _get_configdir
    raise RuntimeError("'%s' is not a writable dir; you must set %s/.matplotlib to be a writable dir.  You can also set environment variable MPLCONFIGDIR to any writable directory where you want matplotlib data stored "% (h, h))
RuntimeError: '/home/marsman' is not a writable dir; you must set /home/marsman/.matplotlib to be a writable dir.  You can also set environment variable MPLCONFIGDIR to any writable directory where you want matplotlib data stored

More details in NIDM notes.

convert all queries to sparql

ideally in the future they will come from some kind of REST API, as we discussed!

table of coordinates should change based on image selected

NeuroVault/NeuroVault#354 (comment)

Use statistic label as a title for each brain map

Currently the "BRAIN" button in the nidmviewer displays a temporary file name:

Could we use the label of the corresponding statistic map to have something more meaningful? I can update the query accordingly if that's useful. Let me know!