else:
data_min = data[data.nonzero()].min()
return [data_min, data_max]
print 'getting range'
ranges = np.array([get_range(pfile) for pfile in pfiles])
dmin = ranges.min()
dmax = ranges.max()
print 'min=%.4f; max=%.4f' % (dmin, dmax)
###
###
# Surface Viz
for i, pfile in enumerate(pfiles):
print pfile
oprefix = path.join(odir,
"C4_fstats_global_easythresh_surface_scan%i" % (i + 1))
sw = SurfWrap(name=factor,
infile=pfile,
cbar="red-yellow",
outprefix=oprefix)
sw.min = dmin
sw.max = dmax
sw.run(compilation="box")
sw.montage(compilation="stick")
###
]
# Output prefixes
obase = "/home2/data/Projects/CWAS/figures"
odir = path.join(obase, "fig_03")
if not path.exists(odir): os.mkdir(odir)
###
###
# Get scan overlays
# Scan 1
i = 0
print pfiles[i]
sw1 = SurfWrap()
sw1.set_overlay("overlap", pfiles[i], "red-yellow")
scan1_lh = io.read_scalar_data(sw1.overlay_surf['lh'])
scan1_rh = io.read_scalar_data(sw1.overlay_surf['rh'])
# Scan 2
i = 1
print pfiles[i]
sw2 = SurfWrap()
sw2.set_overlay("overlap", pfiles[i], "red-yellow")
scan2_lh = io.read_scalar_data(sw2.overlay_surf['lh'])
scan2_rh = io.read_scalar_data(sw2.overlay_surf['rh'])
###
###
# Output prefixes
obase = "/home2/data/Projects/CWAS/figures"
odir = path.join(obase, "fig_03")
if not path.exists(odir): os.mkdir(odir)
###
###
# Get scan overlays
# Scan 1
i = 0
print pfiles[i]
sw1 = SurfWrap()
sw1.set_overlay("overlap", pfiles[i], "red-yellow")
scan1_lh = io.read_scalar_data(sw1.overlay_surf['lh'])
scan1_rh = io.read_scalar_data(sw1.overlay_surf['rh'])
# Scan 2
i = 1
print pfiles[i]
sw2 = SurfWrap()
sw2.set_overlay("overlap", pfiles[i], "red-yellow")
scan2_lh = io.read_scalar_data(sw2.overlay_surf['lh'])
scan2_rh = io.read_scalar_data(sw2.overlay_surf['rh'])
###
data_max = data.max()
if data_max == 0:
data_min = data_max
else:
data_min = data[data.nonzero()].min()
return [data_min, data_max]
print "getting range"
ranges = np.array([get_range(pfile) for pfile in pfiles])
dmin = ranges[ranges != 0].min()
dmax = ranges[ranges != 0].max()
print "min=%.4f; max=%.4f" % (dmin, dmax)
###
###
# Surface Viz
for i, pfile in enumerate(pfiles):
print pfile
oprefix = path.join(odir, "C2_global_perms_surface_scan%i" % (i + 1))
sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow", outprefix=oprefix)
sw.min = dmin
sw.max = dmax
sw.run(compilation="box")
sw.montage(compilation="stick")
###
from os import path
from surfwrap import SurfWrap
obase = "/home2/data/Projects/CWAS/adhd200_rerun/cwas"
comparisons = ["adhdc_vs_adhdi", "tdc_vs_adhdc", "tdc_vs_adhdi"]
# GLOBAL!
preproc = "global"
for comparison in comparisons:
print "group comparison: %s" % comparison
# Input pfile
distdir = path.join(obase, "%s_rois_random_k3200" % preproc)
mdmrdir = path.join(distdir, "%s_gender+age+iq+mean_FD.mdmr" % comparison)
pfile = path.join(mdmrdir, "log_pvals_%s.nii.gz" % comparison)
# Output oprefix
odir = path.join(mdmrdir, "images")
if not path.exists(odir): os.mkdir(odir)
oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", ""))
# Surface Viz
sw = SurfWrap(name=comparison, infile=pfile, cbar="red-yellow", outprefix=oprefix)
sw.min = 1.3
sw.run()
# import pysurfer
# pysurfer = reload(pysurfer)
# SurfWrap = pysurfer.SurfWrap
# Input Directory
indir = path.join(basedir, "%s_%s" % (strategy, kstr))
# Input Measure Files
infiles = [path.join(indir, "%s.nii.gz" % measure) for measure in measures]
if not path.exists(infiles[0]):
raise Exception("infiles %s doesn't exist" % infiles[0])
# Output prefixes
obase = "/home2/data/Projects/CWAS/figures"
odir = path.join(obase, "fig_02")
if not path.exists(odir): os.mkdir(odir)
###
###
# Surface Viz
for i, infile in enumerate(infiles):
print "%i: %s" % (i, infile)
oprefix = path.join(odir, "A_surface_%s" % measures[i])
sw = SurfWrap(name=measures[i],
infile=infile,
cbar="spectral-cb",
outprefix=oprefix)
sw.run(compilation="box")
sw.montage(compilation="stick")
print ''
###
rh_glm_perc += (rh_glm > p) * 1
# Overlap top 15% between mdmr and glm
lh_overlap = (lh_cwas_perc>0)*1 + (lh_glm_perc>0)*2
rh_overlap = (rh_cwas_perc>0)*1 + (rh_glm_perc>0)*2
###
###
# Plot top percentiles
print "plot percentiles"
sw0 = SurfWrap(hemis=['lh'])
sw0.set_underlay()
sw0.set_options()
sw0.min = 1; sw0.max = 3; sw0.sign = "pos"
oprefix = op.join(figdir, "B_surface_percentiles")
sw0.set_output(oprefix)
cwas_perc_surfs = {"lh": lh_cwas_perc}
glm_perc_surfs = {"lh": lh_glm_perc}
overlap_surfs = {"lh": lh_overlap}
for hemi in sw0.hemis:
print "visualize %s" % hemi
## MDMR
#oprefix = op.join(figdir, "B_%s_percentiles_mdmr" % scans[i])
# Input Directory
indir = path.join(basedir, "%s_%s" % (strategy, kstr))
# Input Measure Files
infiles = [ path.join(indir, "%s.nii.gz" % measure) for measure in measures ]
if not path.exists(infiles[0]):
raise Exception("infiles %s doesn't exist" % infiles[0])
# Output prefixes
obase = "/home2/data/Projects/CWAS/figures"
odir = path.join(obase, "fig_02")
if not path.exists(odir): os.mkdir(odir)
###
###
# Surface Viz
for i,infile in enumerate(infiles):
print "%i: %s" % (i,infile)
oprefix = path.join(odir, "A_surface_%s" % measures[i])
sw = SurfWrap(name=measures[i], infile=infile, cbar="spectral-cb",
outprefix=oprefix)
sw.run(compilation="box")
sw.montage(compilation="stick")
print ''
###
obase = "/home2/data/Projects/CWAS/adhd200_rerun/cwas"
comparisons = ["adhdc_vs_adhdi", "tdc_vs_adhdc", "tdc_vs_adhdi"]
# GLOBAL!
preproc = "global"
for comparison in comparisons:
print "group comparison: %s" % comparison
# Input pfile
distdir = path.join(obase, "%s_rois_random_k3200" % preproc)
mdmrdir = path.join(distdir, "%s_gender+age+iq+mean_FD.mdmr" % comparison)
pfile = path.join(mdmrdir, "log_pvals_%s.nii.gz" % comparison)
# Output oprefix
odir = path.join(mdmrdir, "images")
if not path.exists(odir): os.mkdir(odir)
oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", ""))
# Surface Viz
sw = SurfWrap(name=comparison,
infile=pfile,
cbar="red-yellow",
outprefix=oprefix)
sw.min = 1.3
sw.run()
# import pysurfer
# pysurfer = reload(pysurfer)
# SurfWrap = pysurfer.SurfWrap
if name == "vox2vox":
dirname = "%s_k%s_to_k%s" % (strategy, k, k)
elif name == "roi2vox":
dirname = "%s_rois_random_k%04i" % (strategy, k)
elif name == "roi2roi":
dirname = "%s_only_rois_random_k%04i" % (strategy, k)
else:
raise Exception("whoops")
distdir = path.join(basedir, scan, dirname)
# Input pfile
mdmrdir = path.join(distdir, mname)
pfile = path.join(mdmrdir, cname, "clust_logp_%s.nii.gz" % factor)
# Output oprefix
odir = path.join(mdmrdir, cname, "images")
if not path.exists(odir): os.mkdir(odir)
oprefix = path.join(odir,
path.basename(pfile).replace(".nii.gz", ""))
# Surface Viz
sw = SurfWrap(name=factor,
infile=pfile,
cbar="red-yellow",
outprefix=oprefix)
sw.run(compilation="box")
# import pysurfer
# pysurfer = reload(pysurfer)
# SurfWrap = pysurfer.SurfWrap
dirname = "%s_k%s_to_k%s" % (strategy, k, k)
elif name == "roi2vox":
dirname = "%s_rois_random_k%04i" % (strategy, k)
elif name == "roi2roi":
dirname = "%s_only_rois_random_k%04i" % (strategy, k)
else:
raise Exception("whoops")
distdir = path.join(basedir, scan, dirname)
# Input pfile
mdmrdir = path.join(distdir, mname)
pfile = path.join(mdmrdir, cname, "clust_logp_%s.nii.gz" % factor)
# Output oprefix
odir = path.join(mdmrdir, cname, "images")
if not path.exists(odir): os.mkdir(odir)
oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", ""))
# Surface Viz
sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow",
outprefix=oprefix)
sw.run(compilation="box")
# import pysurfer
# pysurfer = reload(pysurfer)
# SurfWrap = pysurfer.SurfWrap
