import os
# %% General----------------------
gl.backcolor(255, 255, 255)
# %% background image ----------------------
gl.loadimage('mni152')
# %% overlay ----------------------
FILESPATH = 'D:\\GD_UNICAMP\\IC_NeuroFisica\\Projetos\\fMRI_TLE_2020\\Seed_based_analysis'
os.chdir(FILESPATH)
#networks_names=['DMN','SMOTOR','VISUAL','AUDIT','DAN']
networks_names = ['DAN_R', 'DAN_L']
netfile_sufx = ['_Group1X', '_Group2L', '_Group3R', '_Group4N']
for net in networks_names:
SEEDFILENAME = net + '_seed'
for sufx in netfile_sufx:
FILENAME = net + sufx
gl.overlaycloseall()
gl.overlayload(FILENAME)
gl.overlayload(SEEDFILENAME)
gl.colorname(2, "3blue")
gl.azimuthelevation(0, 90)
gl.savebmp(FILESPATH + '\\' + FILENAME)
networks_names=['DMN','SMOTOR','VISUAL','AUDIT','ECN_L','ECN_R']
netfile_sufx= ['_Group1X','_Group2L','_Group3R','_Group4N']
for net in networks_names:
savefolder=FILESPATH + '\\' + net + '\\'
for i in netfile_sufx:
FILENAME=net+i
SEEDFILENAME=net+"_seed"
gl.overlaycloseall()
gl.overlayload(FILENAME)
gl.overlayload(SEEDFILENAME)
gl.colorname (2,"3blue")
#gl.opacity(1,50)
# changing view ----------------------
gl.azimuthelevation(140,20)
ktime= 1
ksteps= 72
for x in range(0, ksteps):
gl.azimuthelevation(140+(x*5),20)
gl.wait(ktime)
if x < 10:
gl.savebmp(savefolder + FILENAME + '_0' + str(x)+'.png')
else:
gl.savebmp(savefolder + FILENAME + '_' + str(x)+'.png')
import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152Right.mz3')
gl.overlayload('motor_4t95mesh.mz3')
gl.overlaycolorname(1, 'red')
gl.shaderxray(0.9, 0.5)
gl.azimuthelevation(110, 15)
gl.shadername('MatCap')
gl.shadermatcap('Cortex')
gl.meshcurv()
gl.overlaytranslucent(2, 1)
import gl
gl.resetdefaults()
kframesperrotation = 180
gl.meshcolor(210, 148, 148)
gl.meshload('BrainMesh_ICBM152Left.mz3')
gl.edgeload('LPBA40.edge')
gl.clipazimuthelevation(0.3, 0, 130)
gl.nodesize(6, 1)
gl.edgesize(3, 1)
gl.nodehemisphere(-1)
gl.azimuthelevation(250, 35)
gl.edgecolor('actc', 1)
gl.nodecolor('red', 1)
gl.nodethresh(1.0, 1.0)
gl.edgethresh(0.5, 1.0)
for i in range(1, kframesperrotation * 5):
s = 0.5 + (i + 0.0) / 72
if (s <= 1):
gl.cameradistance(s)
if ((i % kframesperrotation) == 0):
rot = (i / kframesperrotation)
if rot == 1:
gl.shadername('metal')
elif rot == 2:
gl.shadername('wireframe')
elif rot == 3:
gl.shadername('toon')
gl.shaderambientocclusion(0)
else:
gl.shadername('wire')
gl.shaderforbackgroundonly(1)
import gl
gl.resetdefaults()
gl.azimuthelevation(70, 15)
gl.meshload('BrainMesh_ICBM152Right.mz3')
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(1, 2, 12)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(2, -1, -2)
gl.colorbarvisible(1)
gl.overlaytransparencyonbackground(25)
gl.meshcurv()
import gl
gl.resetdefaults()
gl.meshload('BrainMesh_ICBM152.rh.mz3')
gl.meshcurv()
gl.overlayminmax(1, -1, 1)
gl.overlaycolorname(1, 'surface')
gl.overlayinvert(1, 1)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlaycolorname(2, 'kelvin')
gl.overlayminmax(2, 2, 7)
gl.overlayload('scalp.mz3')
gl.overlaycolorname(3, 'gold')
gl.shaderxray(1.0, 0.9)
gl.meshoverlayorder(1)
gl.colorbarvisible(0)
gl.shaderambientocclusion(0.05)
gl.azimuthelevation(90, 15)
gl.clipazimuthelevation(0.5, 0, 90)
#open overlay: sub 291, 2 sites
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/291sph_bin.nii.gz')
gl.minmax(11, 0, 14)
gl.colorname(11, "NIH")
#open overlay: sub 300, 5 sites
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/300sph_bin.nii.gz')
gl.minmax(12, 0, 14)
gl.colorname(12, "NIH")
#open overlay: sub 301, 1 site
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/301sph_bin.nii.gz')
gl.minmax(13, 0, 14)
gl.colorname(13, "NIH")
#open overlay: sub 321, 6 sites
gl.overlayload(
'/Users/mflounders/Desktop/cnds/multiplied_BLA/321sph_bin.nii.gz')
gl.minmax(14, 0, 14)
gl.colorname(14, "NIH")
#shader settings
gl.shadername('Standard')
#set perspective1
gl.azimuthelevation(132, 30)
#set perspective2
gl.azimuthelevation(110, 11)
import gl
gl.resetdefaults()
gl.loadimage('CT_Philips')
gl.colorname(0, 'CT_Kidneys')
gl.shadername('Tomography')
gl.azimuthelevation(150, 10)
gl.clipazimuthelevation(0.25, 180, 60)
import gl
gl.resetdefaults()
ktime = 30
ksteps = 72
gl.resetdefaults()
gl.loadimage('CT_Abdo')
#adjust contrast to show bones
gl.minmax(0, -1024, 640)
for x in range(1, ksteps):
gl.azimuthelevation(160 + (x * 5), 30)
gl.wait(ktime)
#adjust color scheme to show kidneys
gl.colorname(0, 'CT_Kidneys')
gl.shadername('Tomography')
#gl.shaderadjust('brighten', 1.2)
for x in range(1, ksteps):
gl.azimuthelevation(160 + (x * 5), 30)
gl.wait(ktime)
import gl
gl.resetdefaults()
gl.meshload('mni152_2009.mz3')
gl.overlayload('motor_4t95mesh.mz3')
gl.clipazimuthelevation(0.37, 0, 140)
gl.shaderambientocclusion(0.5)
gl.azimuthelevation(90, 20)
gl.shaderxray(1.0, 0.3)
if j == 1:
if i < 3:
gl.cutout(0.5, 0.5, 0.5, 0, 0, 1)
else:
gl.cutout(0.38, 0.5, 0.2, 0, 0, 1)
# help(gl.colorname)
gl.shadername('overlaysurface')
#im_list = []
for iRot in range(nRot):
print(iRot)
Rot = iRot * (360 / nRot)
print(Rot)
gl.azimuthelevation(round(Rot), 20)
filepath = output_path + '/imagenew' + '_' + str(
round(Rot)).rjust(3, '0')
gl.savebmp(filepath)
#im = PIL.Image.open(filepath)
#im_list.append(im)
#print('saving '+output_gif_path)
#im_list[0].save(output_gif_path, save_all=True, append_images=images[1:], optimize=False, duration=40, loop=0)
#files = glob.glob(os.path.join(output_path, '*'))
#os.listdir(output_path)
#files = [f"{folder}/{file}" for file in os.listdir(output_path)]
##images = [imageio.imread(file) for file in files]
##imageio.mimwrite(os.path.join(analysis_path, 'movie.gif'), images, fps=20)
