def genGraph(infname, outfname, roixmlname = None, roirawname = None, bigGraph = False , numfibers=0): # Edit
"""
infname - file name of _fiber.dat file
outfname - Dir+fileName of output .mat file
roixmlname - file name of _roi.xml file
roirawname - file name of _roi.raw file
bigGraph - boolean True or False on whether to process a bigraph=True or smallgraph=False
numfibers - the number of fibers
"""
"""Generate a sparse graph from an MRI studio file and write it as a Matlab file"""
# Disa Edit - Determine size of graph to be processed i.e pick a fibergraph module to import
if bigGraph:
from fibergraph import FiberGraph
else:
from fibergraph_sm import FiberGraph
# Disa Edit - if these filenames are undefined then,
# assume that there are ROI files in ../roi
if not(roixmlname and roirawname):
[ inpathname, inbasename ] = os.path.split ( infname )
inbasename = str(inbasename).rpartition ( "_" )[0]
roifp = os.path.normpath ( inpathname + '/../roi/' + inbasename )
roixmlname = roifp + '_roi.xml'
roirawname = roifp + '_roi.raw'
# # Assume that there are mask files in ../mask
# maskfp = os.path.normpath ( inpathname + '/../mask/' + inbasename )
# maskxmlname = maskfp + '_mask.xml'
# maskrawname = maskfp + '_mask.raw'
# Get the ROIs
try:
roix = roi.ROIXML( roixmlname ) # Create object of type ROIXML
rois = roi.ROIData ( roirawname, roix.getShape() )
except:
print "ROI files not found at: ", roixmlname, roirawname
sys.exit (-1)
# Get the mask
# try:
# maskx = mask.MaskXML( maskxmlname )
# masks = mask.MaskData ( maskrawname, maskx.getShape() )
# except:
# print "Mask files not found at: ", maskxmlname, maskrawname
# sys.exit (-1)
# Create fiber reader
reader = FiberReader( infname )
# Create the graph object
# get dims from reader
# fbrgraph = FiberGraph ( reader.shape, rois, masks )
fbrgraph = FiberGraph ( reader.shape, rois, None )
print "Parsing MRI studio file {0}".format ( infname )
# Print the high-level fiber information
print(reader)
count = 0
# iterate over all fibers
for fiber in reader:
count += 1
# add the contribution of this fiber to the
fbrgraph.add(fiber)
if numfibers > 0 and count >= numfibers:
break
if count % 10000 == 0:
print ("Processed {0} fibers".format(count) )
print "Deleting the reader"
del reader
print "Completing the graph"
# Done adding edges
fbrgraph.complete()
print "Saving matlab file"
# Save a version of this graph to file
fbrgraph.saveToMatlab ( "fibergraph", outfname )
# Load a version of this graph from
# fbrgraph.loadFromMatlab ( "fibergraph", outfname )
del fbrgraph
return
def genGraph(infname,
outfname,
roixmlname=None,
roirawname=None,
bigGraph=False,
numfibers=0): # Edit
"""
infname - file name of _fiber.dat file
outfname - Dir+fileName of output .mat file
roixmlname - file name of _roi.xml file
roirawname - file name of _roi.raw file
bigGraph - boolean True or False on whether to process a bigraph=True or smallgraph=False
numfibers - the number of fibers
"""
"""Generate a sparse graph from an MRI studio file and write it as a Matlab file"""
# Disa Edit - Determine size of graph to be processed i.e pick a fibergraph module to import
if bigGraph:
from fibergraph import FiberGraph
else:
from fibergraph_sm import FiberGraph
# Disa Edit - if these filenames are undefined then,
# assume that there are ROI files in ../roi
if not (roixmlname and roirawname):
[inpathname, inbasename] = os.path.split(infname)
inbasename = str(inbasename).rpartition("_")[0]
roifp = os.path.normpath(inpathname + '/../roi/' + inbasename)
roixmlname = roifp + '_roi.xml'
roirawname = roifp + '_roi.raw'
# # Assume that there are mask files in ../mask
# maskfp = os.path.normpath ( inpathname + '/../mask/' + inbasename )
# maskxmlname = maskfp + '_mask.xml'
# maskrawname = maskfp + '_mask.raw'
# Get the ROIs
try:
roix = roi.ROIXML(roixmlname) # Create object of type ROIXML
rois = roi.ROIData(roirawname, roix.getShape())
except:
print "ROI files not found at: ", roixmlname, roirawname
sys.exit(-1)
# Get the mask
# try:
# maskx = mask.MaskXML( maskxmlname )
# masks = mask.MaskData ( maskrawname, maskx.getShape() )
# except:
# print "Mask files not found at: ", maskxmlname, maskrawname
# sys.exit (-1)
# Create fiber reader
reader = FiberReader(infname)
# Create the graph object
# get dims from reader
# fbrgraph = FiberGraph ( reader.shape, rois, masks )
fbrgraph = FiberGraph(reader.shape, rois, None)
print "Parsing MRI studio file {0}".format(infname)
# Print the high-level fiber information
print(reader)
count = 0
# iterate over all fibers
for fiber in reader:
count += 1
# add the contribution of this fiber to the
fbrgraph.add(fiber)
if numfibers > 0 and count >= numfibers:
break
if count % 10000 == 0:
print("Processed {0} fibers".format(count))
print "Deleting the reader"
del reader
print "Completing the graph"
# Done adding edges
fbrgraph.complete()
print "Saving matlab file"
# Save a version of this graph to file
fbrgraph.saveToMatlab("fibergraph", outfname)
# Load a version of this graph from
# fbrgraph.loadFromMatlab ( "fibergraph", outfname )
del fbrgraph
return
def genGraph( infname, outfname, numfibers=0 ):
"""Generate a sparse graph from an MRI studio file and write it as a Matlab file"""
# Assume that there are ROI files in ../roi
[ inpathname, inbasename ] = os.path.split ( infname )
inbasename = str(inbasename).rpartition ( "_" )[0]
roifp = os.path.normpath ( inpathname + '/../roi/' + inbasename )
roixmlname = roifp + '_roi.xml'
roirawname = roifp + '_roi.raw'
# # Assume that there are mask files in ../mask
# maskfp = os.path.normpath ( inpathname + '/../mask/' + inbasename )
# maskxmlname = maskfp + '_mask.xml'
# maskrawname = maskfp + '_mask.raw'
# Get the ROIs
try:
roix = roi.ROIXML( roixmlname )
rois = roi.ROIData ( roirawname, roix.getShape() )
except:
print "ROI files not found at: ", roixmlname, roirawname
sys.exit (-1)
# Get the mask
# try:
# maskx = mask.MaskXML( maskxmlname )
# masks = mask.MaskData ( maskrawname, maskx.getShape() )
# except:
# print "Mask files not found at: ", maskxmlname, maskrawname
# sys.exit (-1)
# Create fiber reader
reader = FiberReader( infname )
# Create the graph object
# get dims from reader
# fbrgraph = FiberGraph ( reader.shape, rois, masks )
fbrgraph = FiberGraph ( reader.shape, rois, None )
print "Parsing MRI studio file {0}".format ( infname )
# Print the high-level fiber information
print(reader)
count = 0
# iterate over all fibers
for fiber in reader:
count += 1
# add the contribution of this fiber to the
fbrgraph.add(fiber)
if numfibers > 0 and count >= numfibers:
break
if count % 10000 == 0:
print ("Processed {0} fibers".format(count) )
print "Deleting the reader"
del reader
print "Completing the graph"
# Done adding edges
fbrgraph.complete()
print "Saving matlab file"
# Save a version of this graph to file
fbrgraph.saveToMatlab ( "fibergraph", outfname )
# Load a version of this graph from
# fbrgraph.loadFromMatlab ( "fibergraph", outfname )
del fbrgraph
return