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)