Merge pull request #42 from pnlbwh/many-upgrades

Many upgrades

Author: tashrifbillah

environment.yml

@@ -161,19 +161,19 @@ def template_masking(refMaskPath, targetMaskPath, templatePath, siteName):
     ref = load(refMaskPath)
     target = load(targetMaskPath)
 
-    templateMask = applymask(ref.get_data(), target.get_data())
+    templateMask = applymask(ref.get_fdata(), target.get_fdata())
 
     if not isfile(pjoin(templatePath, 'templateMask.nii.gz')):
         save_nifti(pjoin(templatePath, 'templateMask.nii.gz'), templateMask.astype('uint8'), ref.affine, ref.header)
 
     for dm in diffusionMeasures:
         fileName= pjoin(templatePath, f'Mean_{siteName}_{dm}_b{bshell_b}.nii.gz')
         img= load(fileName)
-        save_nifti(fileName, applymask(img.get_data(), templateMask), img.affine, img.header)
+        save_nifti(fileName, applymask(img.get_fdata(), templateMask), img.affine, img.header)
 
         fileName= pjoin(templatePath, f'Std_{siteName}_{dm}_b{bshell_b}.nii.gz')
         img= load(fileName)
-        save_nifti(fileName, applymask(img.get_data(), templateMask), img.affine, img.header)
+        save_nifti(fileName, applymask(img.get_fdata(), templateMask), img.affine, img.header)
 
 
     return templateMask

lib/buildTemplate.py

@@ -170,7 +170,7 @@ def sub2tmp2mni(templatePath, siteName, caselist, ref= False, tar_unproc= False,
 def analyzeStat(file, templatePath):
 
     skel= load(pjoin(ROOTDIR, 'IITAtlas', 'IITmean_FA_skeleton.nii.gz'))
-    skel_mask= (skel.get_data()>0)*1.
+    skel_mask= (skel.get_fdata()>0)*1.
 
     imgs, _ = read_caselist(file)
 
@@ -180,7 +180,7 @@ def analyzeStat(file, templatePath):
         prefix = basename(inPrefix)
 
         faImg= pjoin(templatePath, prefix + f'_InMNI_FA.nii.gz')
-        data= load(faImg).get_data()
+        data= load(faImg).get_fdata()
         temp= data*skel_mask
         meanAttr.append(temp[temp>0].mean())
 

lib/debug_fa.py

@@ -17,7 +17,7 @@ def dti(imgPath, maskPath, inPrefix, outPrefix, tool='FSL'):
 
     vol = load(imgPath)
     mask = load(maskPath)
-    masked_vol = applymask(vol.get_data(), mask.get_data())
+    masked_vol = applymask(vol.get_fdata(), mask.get_fdata())
 
     if tool=='DIPY':
         print('dipy dtifit ', imgPath)

lib/dti.py

@@ -14,15 +14,15 @@
 # ===============================================================================
 
 from plumbum import cli
-from distutils.spawn import find_executable
-import multiprocessing, psutil
+from shutil import which
+import multiprocessing
 import io
 
 from determineNshm import verifyNshmForAll, determineNshm
 from util import *
 from fileUtil import read_caselist, check_dir, check_csv
 
-N_CPU= psutil.cpu_count()
+N_CPU= multiprocessing.cpu_count()
 SCRIPTDIR= dirname(__file__)
 
 
@@ -365,22 +365,22 @@ def showStat(self):
         from harm_plot import generate_csv, harm_plot
         import pandas as pd
 
-        print('\n\nComputing statistics\n\n')
+        print('\n\nComputing statistics:')
 
-        print(f'{self.reference} site: ')
+        print(f'{self.reference} site')
         ref_mean = analyzeStat(self.ref_csv, self.templatePath)
         generate_csv(self.ref_csv, ref_mean, pjoin(self.templatePath, self.reference), self.bshell_b)
 
-        print(f'{self.target} site before harmonization: ')
+        print(f'{self.target} site before harmonization')
         target_mean_before = analyzeStat(self.tar_unproc_csv, self.templatePath)
         generate_csv(self.tar_unproc_csv, target_mean_before, pjoin(self.templatePath, self.target)+'_before', self.bshell_b)
 
-        print(f'{self.target} site after harmonization: ')
+        print(f'{self.target} site after harmonization')
         target_mean_after = analyzeStat(self.harm_csv, self.templatePath)
         generate_csv(self.harm_csv, target_mean_after, pjoin(self.templatePath, self.target)+'_after', self.bshell_b)
 
 
-        print('\n\nPrinting statistics\n\n')
+        print('\n\nPrinting statistics:')
         # save statistics for future
         statFile= pjoin(self.templatePath, 'meanFAstat.csv')
         if isfile(statFile):
@@ -428,7 +428,7 @@ def sanityCheck(self):
             'unring.a64']
 
         for cmd in external_commands:
-            exe= find_executable(cmd)
+            exe= which(cmd)
             if not exe:
                 raise EnvironmentError(f'{cmd} not found')
 

lib/harmonization.py

@@ -63,12 +63,12 @@ def joinBshells(imgPath, ref_bvals_file=None, ref_bvals=None, sep_prefix=None):
 
         if bval==0.:
             b0Img = load(inPrefix+'_b0.nii.gz')
-            b0 = b0Img.get_data()
+            b0 = b0Img.get_fdata()
             for i in ind:
                 joinedDwi[:,:,:,i]= b0
 
         else:
-            b0_bshell= load(harmPrefix+f'_b{int(bval)}.nii.gz').get_data()
+            b0_bshell= load(harmPrefix+f'_b{int(bval)}.nii.gz').get_fdata()
 
             joinedDwi[:,:,:,ind] = b0_bshell[:,:,:,1:]
 

lib/joinBshells.py

@@ -14,8 +14,8 @@
 # ===============================================================================
 
 from plumbum import cli
-import psutil
-N_CPU= str(psutil.cpu_count())
+import multiprocessing
+N_CPU= str(multiprocessing.cpu_count())
 from conversion import read_bvals
 from util import dirname, basename, pjoin, SCRIPTDIR, remove, isfile
 from subprocess import check_call

lib/multi-shell-harmonization.py

@@ -59,12 +59,12 @@ def preprocessing(imgPath, maskPath):
     # load signal attributes for pre-processing
     # imgPath= nrrd2nifti(imgPath)
     lowRes = load(imgPath)
-    lowResImg = lowRes.get_data().astype('float')
+    lowResImg = lowRes.get_fdata().astype('float')
     lowResImgHdr = lowRes.header
 
     # maskPath= nrrd2nifti(maskPath)
     lowRes = load(maskPath)
-    lowResMask = lowRes.get_data()
+    lowResMask = lowRes.get_fdata()
     lowResMaskHdr = lowRes.header
 
     lowResImg = applymask(lowResImg, lowResMask)

lib/preprocess.py

@@ -154,12 +154,12 @@ def ring_masking(directory, prefix, maskPath, shm_coeff, b0, qb_model, hdr):
     mapped_cs= []
     shs_same_level= [[0, 1], [1, 6], [6, 15], [15, 28], [28, 45]]
 
-    mask= load(maskPath).get_data()
+    mask= load(maskPath).get_fdata()
     for i in range(0, N_shm+1, 2):
 
         # load data and mask
         fileName= pjoin(directory, 'harm', f'Scale_L{i}_{prefix}.nii.gz')
-        img= load(fileName).get_data()
+        img= load(fileName).get_fdata()
 
         if i==0: # compute the skullRingMask from 0th shm
 

lib/reconstSignal.py

@@ -18,6 +18,7 @@
 from scipy.io import loadmat, savemat
 from normalize import normalize_data, find_b0
 from util import *
+from os import getenv
 
 
 def resize_spm(lowResImg, inPrefix):
@@ -27,7 +28,7 @@ def resize_spm(lowResImg, inPrefix):
     savemat(dataFile, {'lowResImg': lowResImg})
 
     # call MATLAB_Runtime based spm bspline interpolation
-    p= Popen((' ').join([pjoin(SCRIPTDIR,'spm_bspline_exec', 'bspline'), inPrefix]), shell= True)
+    p= Popen((' ').join([pjoin(SCRIPTDIR,'spm_bspline_exec', 'run_bspline.sh'), getenv('MCRROOT'), inPrefix]), shell= True)
     p.wait()
     highResImg= np.nan_to_num(loadmat(inPrefix+'_resampled.mat')['highResImg'])
 
@@ -139,7 +140,7 @@ def resampling(lowResImgPath, lowResMaskPath, lowResImg, lowResImgHdr, lowResMas
     p= Popen((' ').join(['unring.a64', highResB0PathTmp, highResB0Path]), shell=True)
     p.wait()
     check_call(['rm', highResB0PathTmp])
-    b0_gibs = load(highResB0Path).get_data()
+    b0_gibs = load(highResB0Path).get_fdata()
     np.nan_to_num(b0_gibs).clip(min= 0., out= b0_gibs) # using min= 1. is unnecessary
 
     # defining lh_max and lh_min separately to deal with memory error