Python SurfWrap.montage Exemples

Exemple #1

Fichier : save_x_cwas+global_overlay_pysurfer_easythresh.py Projet : czarrar/cwas-paper

        # Refresh
        brain.show_view("lat")
        brain.hide_colorbar()

    # Save the beauts
    brain.save_imageset("%s_%s" % (sw0.outprefix, hemi),
                        sw0.views,
                        'jpg',
                        colorbar=None)

    # End a great journey, till another life
    brain.close()

sw0.cropify()
sw0.montage("box")
sw0.montage("stick")

####
## Setup
#
## 3dcalc -a /home2/data/Projects/CWAS/nki/cwas/short/compcor_kvoxs_smoothed_to_kvoxs_smoothed/iq_age+sex+meanFD.mdmr/cluster_correct_v05_c05/clust_logp_FSIQ.nii.gz -b /home2/data/Projects/CWAS/nki/cwas/medium/compcor_kvoxs_smoothed_to_kvoxs_smoothed/iq_age+sex+meanFD.mdmr/cluster_correct_v05_c05/clust_logp_FSIQ.nii.gz -expr 'step(a)+(2*step(b))' -prefix /home2/data/Projects/CWAS/figures/fig_03/C_overlap.nii.gz
#
#basedir = "/home2/data/Projects/CWAS"
#
#figdir = path.join(basedir, "figures/fig_03")
#pfile = path.join(figdir, "C_overlap.nii.gz")
#
## Output prefixes
#odir = path.join(basedir, "figures", "fig_03")
#if not path.exists(odir): os.mkdir(odir)

Exemple #2

Fichier : save_C2_cwas_global_pysurfer_perms.py Projet : 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")

###

Exemple #3

Fichier : save_C4_fstats_global_pysurfer_easythresh.py Projet : 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")

###

Exemple #4

Fichier : save_B2_cwas_iq_overlap_perms.py Projet : czarrar/cwas-paper

        lut[:,0:3] = [230,171,2]
        tmp.pos_bar.lut.table = lut
    
        # Refresh
        brain.show_view("lat")
        brain.hide_colorbar()
    
    # Save the beauts
    brain.save_imageset("%s_%s" % (sw0.outprefix, hemi), sw0.views, 
                        'jpg', colorbar=None)
    
    # End a great journey, till another life
    brain.close()

sw0.cropify()
sw0.montage("box")
sw0.montage("stick")



####
## Setup
#
## 3dcalc -a /home2/data/Projects/CWAS/nki/cwas/short/compcor_kvoxs_smoothed_to_kvoxs_smoothed/iq_age+sex+meanFD.mdmr/cluster_correct_v05_c05/clust_logp_FSIQ.nii.gz -b /home2/data/Projects/CWAS/nki/cwas/medium/compcor_kvoxs_smoothed_to_kvoxs_smoothed/iq_age+sex+meanFD.mdmr/cluster_correct_v05_c05/clust_logp_FSIQ.nii.gz -expr 'step(a)+(2*step(b))' -prefix /home2/data/Projects/CWAS/figures/fig_03/C_overlap.nii.gz
#
#basedir = "/home2/data/Projects/CWAS"
#
#figdir = path.join(basedir, "figures/fig_03")
#pfile = path.join(figdir, "C_overlap.nii.gz")
#
## Output prefixes