Enable logging so users can download a script to run what they just did in the GUI.

Hi,

could you direct me on how to invoke allen.py trying to match the allen data to a parcellation different from the one Dr. Whitaker used in her papers.

Need some unit tests for the GUI.

With new versions of numpy, using subclass matrix raises a Warning. Thus, necessary to find an alternative to nx.to_numpy_matrix() that exists in histograms and bct modules.

New methods of preprocessing produce voxelwise p-values to determine the confidence of edge connection strengths. This possibility should be implemented. It would involve:

1. input file of p-values in the same shape as the association matrix
2. Specifying global thresholding based on p-values rather than strength

Potential challenge - it may not be possible to construct a minimum spanning tree in these networks.

When I ran "python guiTest.py":

ERROR: test_highlights (main.TestSequenceFunctions)
test the ability to highlight some part of a brain

Traceback (most recent call last):
File "guiTest.py", line 32, in setUp
self.app = gui.runGui()
File "/home/Tianjie/maybrain-master/bin/gui/mayBrainGUI.py", line 539, in runGui
ex = mayBrainGUI()
File "/home/Tianjie/maybrain-master/bin/gui/mayBrainGUI.py", line 37, in init
self.plot = mb.plotObj() # start plot object
AttributeError: 'module' object has no attribute 'plotObj'

======================================================================
ERROR: test_loadData (main.TestSequenceFunctions)
test inputting of basic data

Traceback (most recent call last):
File "guiTest.py", line 32, in setUp
self.app = gui.runGui()
File "/home/Tianjie/maybrain-master/bin/gui/mayBrainGUI.py", line 539, in runGui
ex = mayBrainGUI()
File "/home/Tianjie/maybrain-master/bin/gui/mayBrainGUI.py", line 37, in init
self.plot = mb.plotObj() # start plot object
AttributeError: 'module' object has no attribute 'plotObj'

Ran 2 tests in 0.595s

FAILED (errors=2)

Can we make the node labels for plotting the actual node names rather than an index? I don't want to update this before you do a merge with the master.

Trying to get this running for a work colleague.

On copying the maybrain/maybrain folder to site-packages and then trying to run test/basicTests.py

$ python basicTests.py Traceback (most recent call last): File "basicTests.py", line 17, in <module> from maybrain import recipes File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/maybrain/recipes.py", line 12, in <module> from plot import plotObj ImportError: No module named plot

Surely this should be mbplot?

Regardless of this, running basicTests.py results in the following error:

`$ python basicTests.py
red
red
green
blue
green
green
green
green
green
green
('x', 'gt', 0.5, 'x1', 'node')
('colour', 'eq', 'green', 'green', 'edge')
{'colour': 'green', 'weight': 0.60080034391699999}
('green', 'eq', 'green', True)
{'colour': 'green', 'weight': 0.203602458588}
('green', 'eq', 'green', True)
{'colour': 'green', 'weight': 0.16390494700200001}
('green', 'eq', 'green', True)
{'colour': 'green', 'weight': 0.84379894778099995}
('green', 'eq', 'green', True)
{'colour': 'green', 'weight': 0.242747996199}
('green', 'eq', 'green', True)
{'colour': 'green', 'weight': 0.63727884848299998}
('green', 'eq', 'green', True)

..E.

ERROR: test_loadAndPlot (main.TestSequenceFunctions)

load, threhsold and plot

Traceback (most recent call last):
File "basicTests.py", line 56, in test_loadAndPlot
br, plt = recipes.loadAndPlot(self.fnameAdj, self.fnameCo, 0.5, opacity = 0.2)
File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/maybrain/recipes.py", line 50, in loadAndPlot
plt = plotObj()
File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/maybrain/plot.py", line 41, in init
self.startMayavi()
File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/maybrain/plot.py", line 55, in startMayavi
self.mfig = mlab.figure(bgcolor = (1., 1., 1.,), fgcolor = (0., 0., 0.), engine = self.engine, size=(1500, 1500))
File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/mayavi/tools/figure.py", line 68, in figure
engine.new_scene(name=name, size=size)
File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/apptools/scripting/recordable.py", line 45, in _wrapper
result = func(_args, *_kw)
File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/mayavi/core/engine.py", line 452, in new_scene
viewer = self.scene_factory(**factory_kwargs)
File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/mayavi/core/ui/mayavi_scene.py", line 86, in viewer_factory
viewer = MayaviViewer()
File "/opt/rh/python27/root/usr/lib64/python2.7/site-packages/tvtk/tools/ivtk.py", line 382, in init
super(IVTK, self).init(**traits)
File "/opt/rh/python27/root/usr/lib/python2.7/site-packages/pyface/toolkit.py", line 124, in init
raise NotImplementedError("the %s pyface backend doesn't implement %s" % (ETSConfig.toolkit, oname))
NotImplementedError: the null pyface backend doesn't implement ApplicationWindow

Ran 4 tests in 0.005s

Python 2.7
apptools (4.4.0)
Babel (0.9.6)
cmp (2.1.0b0)
configobj (5.0.6)
cycler (0.10.0)
decorator (4.0.6)
docutils (0.11)
Easy-Lausanne (0.5)
functools32 (3.2.3-2)
Jinja2 (2.6)
MarkupSafe (0.11)
matplotlib (2.0.0b4-2053.g440adff)
mayavi (4.5.0)
mpmath (0.19)
networkx (1.11)
nibabel (2.0.2)
nipy (0.4.0)
nipype (0.7.0.gd2cbeaa-dev)
nose (1.3.0)
numpy (1.11.1)
pip (8.1.2)
pyface (5.1.0)
Pygments (2.1.3)
pyparsing (2.1.9)
python-dateutil (2.5.3)
pytz (2016.6.1)
scipy (0.17.0)
setuptools (27.2.0)
simplejson (3.2.0)
six (1.10.0)
Sphinx (1.1.3)
SQLAlchemy (0.7.9)
subprocess32 (3.2.7)
sympy (1.0)
traits (4.5.0)
traitsui (5.1.0)
virtualenv (13.1.0)
Werkzeug (0.8.3)
wheel (0.24.0)

Hi,
When I install the module, there is an error: package directory 'maybrain/test' does not exist. Is there anything wrong?

Hi, I have run allen.py to match the AHBA genetic data to MNI coordinate. I used the data in the test folder. But it returns some wrong:
I have modified the scripts from the other issue:
from maybrain import allen
from os import path
from glob import glob
import time
start_time=time.time()
nodesToExclude=[]
diags = ['AD308']
for d in diags:
a = allen.multisubj('3d_grid_adj.txt',
nodesToExclude=nodesToExclude,
allen_dir="D:\\WorkingSoftware\\Maybrain\\maybrain-master",
symmetrise=True,
subj_list= ['9861'],
imaging_spatial_file="3d_grid_coords.txt",
delim="\t",
convert_mni=True)
print("comparison")
a.comparison()
print("writeXmatrix")
a.xmatrix(out_file="Xmatrix.csv")
`
Firstly, it returns the wrong message :"allen_data\9861\Probe.csv" not exist. It seems the allen.py has lost 'self' in line 560 and 588. I have addressed the problem after add 'self' in line 561 and 588 before 'allen_dir'.
But I have met the other problem when saving the Xmatrix.csv. The script firstly returns the wrong message: type error: a bytes-like object is required, not 'str'. This seems a problem of python 3, I have addressed the problem by removing the 'r' in line 567. But the script returns wrong message: ValueError: zero-size array to reduction operation maximum which has no identity. Could you provide some examples of the modified allen.py to coordinate matching?

Right now, pylint is ignoring the following warnings/conventions (on top of the default ones):
too-many-arguments
too-many-locals
too-many-branches
wildcard-import
too-many-instance-attributes
too-few-public-methods
too-many-instance-attributes
global-statement
inconsistent-return-statements

Maybe some of those can be corrected and incorporated back in pylint analysis after changing accordingly in maybrain's code. This way we can conform more to PEP style rules without loosing readability .

Also, two variables added to good-names might be removed if corrected, from the utils package:
highlights
__number_of_highlights

Finally, the following modules are being ignored by pylint:
allen.py
braineac.py
mayavi_wrapper.py
degeneration.py
modularity.py

This might be an issue for people who generate their spatial information files in windows and some mac programmes. The brainObj.importSpatialInfo function can't manage files with line breaks ^M