Python SurfWrap.min Examples

Example #1

File: save_C4_fstats_global_pysurfer_easythresh.py Project: czarrar/cwas-paper

    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")

###

Example #2

File: save_x_cwas+global_overlay_pysurfer_easythresh.py Project: czarrar/cwas-paper

# Overlap
overlap_lh = scan1_lh[:] * scan2_lh[:]
overlap_rh = scan1_rh[:] * scan2_rh[:]

###

###
# Plot overlap

import code

sw0 = SurfWrap()
sw0.set_underlay()
sw0.set_options()
sw0.min = 0
sw0.max = 2
sw0.sign = "pos"
oprefix = path.join(odir, "E_global_easythresh_surface_overlap")
sw0.set_output(oprefix)

scan1_surfs = {"lh": scan1_lh, "rh": scan1_rh}
scan2_surfs = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs = {"lh": overlap_lh, "rh": overlap_rh}

#code.interact(local=locals())

for hemi in sw0.hemis:
    print "visualize %s" % hemi

    # Bring up the beauty (the underlay)

Example #3

File: save_C4_fstats_global_pysurfer_easythresh.py Project: czarrar/cwas-paper

    data = img.get_data()
    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.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")

###

Example #4

File: save_C2_cwas_global_pysurfer_perms.py Project: czarrar/cwas-paper

    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")

###

Example #5

    data = img.get_data()
    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, "B_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")

###

Example #6

scan2_lh[scan2_lh>dmin] = 2
scan2_rh[scan2_rh>dmin] = 2

# Overlap
overlap_lh = scan1_lh[:] * scan2_lh[:]
overlap_rh = scan1_rh[:] * scan2_rh[:]

###

###
# Plot overlap

sw0 = SurfWrap()
sw0.set_underlay()
sw0.set_options()
sw0.min = 1; sw0.max = 2; sw0.sign = "pos"
oprefix = path.join(odir, "D_perms_surface_overlap")
sw0.set_output(oprefix)

scan1_surfs     = {"lh": scan1_lh, "rh": scan1_rh}
scan2_surfs     = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs   = {"lh": overlap_lh, "rh": overlap_rh}

for hemi in sw0.hemis:
    print "visualize %s" % hemi
    
    # Bring up the beauty (the underlay)
    brain = Brain(sw0.subject_id, hemi, sw0.surf, \
                  config_opts=sw0.config_opts, \
                  subjects_dir=sw0.subjects_dir)
    

Example #7

File: 10_pysurfer.py Project: czarrar/cwas-paper

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

Example #8

File: C_surface_glm_vs_mdmr_meangcor.py Project: czarrar/cwas-paper

    # 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])
        #sw0.set_output(oprefix)
        #
        #brain = Brain(sw0.subject_id, hemi, sw0.surf, \

Example #9

File: B_surface_glm_vs_mdmr_top_percentiles.py Project: czarrar/cwas-paper

    # 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])
        #sw0.set_output(oprefix)

Example #10

File: 10_pysurfer.py Project: czarrar/cwas-paper

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

Example #11

File: save_x_cwas+global_overlay_pysurfer_easythresh.py Project: czarrar/cwas-paper

# Overlap
overlap_lh = scan1_lh[:] * scan2_lh[:]
overlap_rh = scan1_rh[:] * scan2_rh[:]

###

###
# Plot overlap

import code

sw0 = SurfWrap()
sw0.set_underlay()
sw0.set_options()
sw0.min = 0
sw0.max = 2
sw0.sign = "pos"
oprefix = path.join(odir, "E_global_easythresh_surface_overlap")
sw0.set_output(oprefix)

scan1_surfs = {"lh": scan1_lh, "rh": scan1_rh}
scan2_surfs = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs = {"lh": overlap_lh, "rh": overlap_rh}

# code.interact(local=locals())

for hemi in sw0.hemis:
    print "visualize %s" % hemi

    # Bring up the beauty (the underlay)