Commit 3a2a0e5d authored by Taylor Hanayik's avatar Taylor Hanayik
Browse files

switch to venv from conda, and add devpath for sourcing

parent 0479059a
export PYTHONPATH=$PYTHONPATH:./fsl
#!/bin/bash
conda-build condaRecipes
\ No newline at end of file
conda build -c conda-forge condaRecipes
\ No newline at end of file
if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonLink.sh ]; then
$FSLDIR/etc/fslconf/requestFSLpythonLink.sh Bet_gui
$FSLDIR/etc/fslconf/requestFSLpythonLink.sh Bet_gui Flirt_gui
fi
if [ -e ${FSLDIR}/etc/fslconf/requestFSLpythonUnlink.sh ]; then
$FSLDIR/etc/fslconf/requestFSLpythonUnlink.sh Bet_gui
$FSLDIR/etc/fslconf/requestFSLpythonUnlink.sh Bet_gui Flirt_gui
fi
#!/usr/bin/env pythonw
#!/usr/bin/env python
import wx
import sys
......
#!/usr/bin/env pythonw
#!/usr/bin/env python
import wx
import sys
......
#!/usr/bin/env pythonw
import wx
import sys
from fslgui.gui import BetGui
import argparse
parser = argparse.ArgumentParser(description="FSL's brain extraction tool")
parser.add_argument(
'-input',
default="",
type=str,
required=False,
help="an input image file"
)
parser.add_argument(
"-output",
default="",
required=False,
type=str,
help="the output name for the brain extracted image(s)"
)
parser.add_argument(
"-o",
action='store_false',
required=False,
help="generate brain surface outline overlaid onto original image"
)
parser.add_argument(
"-m",
action='store_false',
required=False,
help="generate binary brain mask"
)
parser.add_argument(
"-s",
action='store_false',
required=False,
help="generate approximate skull image"
)
parser.add_argument(
"-n",
action='store_false',
required=False,
help="do not save segmented brain image"
)
parser.add_argument(
"-f",
default=0.5,
type=float,
required=False,
help="do not save segmented brain image"
)
def main():
args = parser.parse_args()
# get an app instance
app = wx.App()
# get our wx.Frame (this bet window will not be embedded in a panel)
# betview = BetView(
# parent=None,
# in_img=args.input,
# out_img=args.output,
# o_opt=args.o,
# m_opt=args.m,
# s_opt=args.s,
# n_opt=args.n,
# f_opt=args.f) # parent=None will return a wx.Frame
# betview.window.Show()
frame = wx.Frame(None, size=(800, 600))
sizer = wx.BoxSizer(wx.VERTICAL)
controller = BetGui(frame, "BET")
sizer.Add(controller.view, proportion=1, flag=wx.EXPAND | wx.ALL, border=5)
frame.SetSizer(sizer)
frame.Centre()
frame.Show()
app.MainLoop()
if __name__ == "__main__":
sys.exit(main())
......@@ -3,12 +3,12 @@ from os import listdir
from os.path import isfile, join
# list scripts
scripts = [join('./fslgui/scripts', f) for f in listdir('./fslgui/scripts') if isfile(join('./fslgui/scripts', f))]
scripts = [join('./fsl/gui/scripts', f) for f in listdir('./fsl/gui/scripts') if isfile(join('./fsl/gui/scripts', f))]
with open('requirements.txt', 'rt') as f:
install_requires = [l.strip() for l in f.readlines()]
setup(name='fslgui',
version='0.0.1',
version='0.0.2',
description='fslgui',
author='Taylor Hanayik',
install_requires=install_requires,
......
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