with __init__.py

__init__.py

@@ -0,0 +1,56 @@
+'''BatchBrain
+a Python batch processing interface for neuroimaging analysis. Basically a
+fancy wrapper around functionality from NiPype (nipy.sourceforge.net). We
+assume that you have a fully functional NiPype install (including
+interfaces for SPM/FSL/etc).
+2012 J Carlin'''
+
+__version__ = 'alpha'
+# TODO:
+# move code out of __init__.py 
+# implement parallel support
+import sys
+import os
+import platform
+
+# Could also write outputs to a file...
+output = sys.stdout.write
+output('Welcome to BatchBrain.\nInitialising...\n')
+
+# Initialise FSL
+arch = platform.architecture()[0]
+cp = os.environ['PATH']
+# Check if fsl is already added
+fslver = 'fsl-4.1.8'
+
+
+# Note that the 64bit switching here will only work if your Python
+# install is also 64bit
+if fslver in cp:
+	sys.stdout.write('FSL already on path\n')
+else:
+	sys.stdout.write('Adding FSL to system path...\n')
+	if arch == '32bit':
+		sys.stdout.write('Adding 32bit FSL...\n')
+		fsldir = '/imaging/local/software/fsl/fsl32/fsl-4.1.8/fsl'
+	elif arch == '64bit':
+		sys.stdout.write('Adding 64bit FSL...\n')
+		fsldir = '/imaging/local/software/fsl/fsl64/fsl-4.1.8/fsl'
+	else:
+		raise Exception('Unknown system architecture: %s' % arch)
+	os.environ['PATH'] = os.path.join(fsldir,'bin:') + cp
+	os.environ['FSLDIR'] = fsldir
+	os.environ['FSLOUTPUTTYPE'] = 'NIFTI'
+
+# Add dti_motion script to path
+bbdir = '/home/jc01/code/UtilityScripts/Python/batchbrain:'
+os.environ['PATH'] = bbdir + os.environ['PATH']
+
+import batchbrain.base
+import batchbrain.data
+import batchbrain.processes
+import batchbrain.runners
+
+sys.stdout.write('Initialisation done.\n')
+
+# TODO - parallelisation initialisation and settings here