def processLCC():
global lccOutputFileName
global inputRoi_raw
global inputRoi_xml
global inputFiber_dat
global bigGraphOutputFileName
lcc.process_single_brain(inputRoi_xml, inputRoi_raw, bigGraphOutputFileName, lccOutputFileName)
def processData(fiber_fn,
roi_xml_fn,
roi_raw_fn,
graphs,
graphInvariants,
graphsize,
run=False):
'''
Run graph building and other related scripts
@param fiber_fn: fiber tract file
@param roi_xml_fn: region of interest xml file
@param roi_raw_fn: region of interest raw file
@param graphs: Dir where biggraphs & smallgraphs are saved
@param graphInvariants: Dir where graph invariants are saved
@param graphsize: the size of the graph 'big' or 'small'
@param run: Whether or not to run processor intensive jobs. Default is - false so nothing is actually run
'''
if (run):
import mrcap.svd as svd
import mrcap.lcc as lcc
print "Imported svd and lcc modules..."
baseName = getFiberID(fiber_fn) #VERY TEMPORARY
smGrfn = os.path.join(graphs, (baseName + 'smgr.mat'))
bgGrfn = os.path.join(graphs, (baseName + 'bggr.mat'))
if (run):
if (graphsize == 'small'):
''' Run gengraph SMALL & save output '''
print("Running Small gengraph....")
gengraph.genGraph(fiber_fn,
smGrfn,
roi_xml_fn,
roi_raw_fn,
bigGraph=False)
elif (graphsize == 'big'):
''' Run gengrah BIG & save output '''
print("\nRunning Big gengraph....")
gengraph.genGraph(fiber_fn,
bgGrfn,
roi_xml_fn,
roi_raw_fn,
bigGraph=True)
else:
print '[ERROR]: Graphsize Unkwown' # should never happen
''' Run LCC '''
lccfn = os.path.join(graphInvariants, "LCC", (baseName + 'concomp.npy'))
if (run):
'''Should be big but we'll do small for now'''
if (graphsize == 'big'):
print "Running biggraph Largest connected component..."
lcc.process_single_brain(bgGrfn, lccfn)
if (graphsize == 'small'):
print "Running smallgraph Largest connected component..."
lcc.process_single_brain(smGrfn, lccfn)
''' Run Embed - SVD '''
SVDfn = os.path.join(graphInvariants, "SVD", (baseName + 'embed.npy'))
print("Running SVD....")
if (run):
if (graphsize == 'big'):
print "Running SVD on biggraph"
svd.embed_graph(lccfn, bgGrfn, SVDfn)
if (graphsize == 'small'):
print "Running SVD on smallgraph"
svd.embed_graph(lccfn, smGrfn, SVDfn)
print "Completed generating - graph, lcc & svd"
return [smGrfn, bgGrfn, lccfn, SVDfn]
def processData(fiber_fn, roi_xml_fn, roi_raw_fn,graphs, graphInvariants, graphsize, run = False):
'''
Run graph building and other related scripts
@param fiber_fn: fiber tract file
@param roi_xml_fn: region of interest xml file
@param roi_raw_fn: region of interest raw file
@param graphs: Dir where biggraphs & smallgraphs are saved
@param graphInvariants: Dir where graph invariants are saved
@param graphsize: the size of the graph 'big' or 'small'
@param run: Whether or not to run processor intensive jobs. Default is - false so nothing is actually run
'''
if (run):
import mrcap.svd as svd
import mrcap.lcc as lcc
print "Imported svd and lcc modules..."
baseName = getFiberID(fiber_fn) #VERY TEMPORARY
smGrfn = os.path.join(graphs, (baseName +'smgr.mat'))
bgGrfn = os.path.join(graphs, (baseName +'bggr.mat'))
if (run):
if (graphsize == 'small'):
''' Run gengraph SMALL & save output '''
print("Running Small gengraph....")
gengraph.genGraph(fiber_fn, smGrfn, roi_xml_fn, roi_raw_fn, bigGraph=False)
elif(graphsize == 'big'):
''' Run gengrah BIG & save output '''
print("\nRunning Big gengraph....")
gengraph.genGraph(fiber_fn, bgGrfn, roi_xml_fn, roi_raw_fn, bigGraph=True)
else:
print '[ERROR]: Graphsize Unkwown' # should never happen
''' Run LCC '''
lccfn = os.path.join(graphInvariants,"LCC", (baseName + 'concomp.npy'))
if (run):
'''Should be big but we'll do small for now'''
if (graphsize == 'big'):
print "Running biggraph Largest connected component..."
lcc.process_single_brain(bgGrfn, lccfn)
if (graphsize == 'small'):
print "Running smallgraph Largest connected component..."
lcc.process_single_brain(smGrfn, lccfn)
''' Run Embed - SVD '''
SVDfn = os.path.join(graphInvariants,"SVD" ,(baseName + 'embed.npy'))
print("Running SVD....")
if (run):
if (graphsize == 'big'):
print "Running SVD on biggraph"
svd.embed_graph(lccfn, bgGrfn, SVDfn)
if (graphsize == 'small'):
print "Running SVD on smallgraph"
svd.embed_graph(lccfn, smGrfn, SVDfn)
print "Completed generating - graph, lcc & svd"
return [ smGrfn, bgGrfn, lccfn, SVDfn ]