fix: fix to avoid IO error

lib/buildTemplate.py

@@ -115,7 +115,7 @@ def antsMult(caselist, outPrefix):
                            '-o', outPrefix,
                            caselist]), shell= True, stdout= f, stderr= sys.stdout)
 
-    if f.name!='<sys.stdout>':
+    if f is not sys.stdout:
         f.close()
 
 def dti_stat(siteName, imgs, masks, templatePath, templateHdr):

lib/consistencyCheck.py

@@ -66,7 +66,7 @@ def check_resolution(ref_imgs, ref_res):
 
         res= load(imgPath._path).header['pixdim'][1:4]
 
-        if (res-ref_res).sum()<=10e-6:
+        if (res-ref_res).sum()<=0.001:
             print('spatial resolution matched for', imgPath.name)
 
         else:

lib/joinBshells.py

@@ -16,7 +16,7 @@
 from plumbum import cli, local
 from conversion import read_bvals, read_imgs, read_imgs_masks
 from nibabel import load
-from util import abspath, pjoin, save_nifti, copyfile, RAISE, basename, dirname, isfile
+from util import abspath, pjoin, save_nifti, copyfile, basename, dirname, isfile
 import numpy as np
 from multiprocessing import Pool
 from findBshells import BSHELL_MIN_DIST
@@ -86,13 +86,16 @@ def joinAllBshells(tar_csv, ref_bvals_file, separatedPrefix=None, ncpu=4):
             imgs = read_imgs(tar_csv)
 
         pool = Pool(int(ncpu))
+        results = []
         for imgPath in imgs:
-            pool.apply_async(joinBshells, kwds=({'imgPath': imgPath, 'ref_bvals': ref_bvals, 'sep_prefix': separatedPrefix}),
-                             error_callback=RAISE)
+            results.append(pool.apply_async(joinBshells, kwds=({'imgPath': imgPath, 'ref_bvals': ref_bvals, 'sep_prefix': separatedPrefix})))
 
         pool.close()
         pool.join()
 
+        for r in results:
+            r.get()
+
 
 
 class joinDividedShells(cli.Application):

lib/reconstSignal.py

@@ -61,7 +61,7 @@ def antsReg(img, mask, mov, outPrefix):
                                '-e', '123456']), shell= True, stdout= f, stderr= sys.stdout)
         p.wait()
 
-    if f.name!='<sys.stdout>':
+    if f is not sys.stdout:
         f.close()
 
 

lib/separateBshells.py

@@ -17,7 +17,7 @@
 from plumbum import cli, local
 from conversion import read_bvals, read_bvecs, write_bvals, write_bvecs, read_imgs, read_imgs_masks
 from nibabel import load
-from util import abspath, pjoin, save_nifti, RAISE, isfile
+from util import abspath, pjoin, save_nifti, isfile
 import numpy as np
 from multiprocessing import Pool
 from findBshells import BSHELL_MIN_DIST
@@ -51,13 +51,19 @@ def separateBshells(imgPath, ref_bvals_file=None, ref_bvals=None):
         if bval==0.:
             b0 = find_b0(dwi, ind)
 
-        if isfile(bPrefix + '.nii.gz'):
-            continue
-
+        nii_file = bPrefix + '.nii.gz'
+        bval_file = bPrefix + '.bval'
+        bvec_file = bPrefix + '.bvec'
+
         if bval==0.:
-            save_nifti(bPrefix + '.nii.gz', b0, img.affine, img.header)
+            if isfile(nii_file):
+                continue
+            save_nifti(nii_file, b0, img.affine, img.header)
 
         else:
+            if isfile(nii_file) and isfile(bval_file) and isfile(bvec_file):
+                continue
+
             b0_bshell = np.zeros((dwi.shape[0],dwi.shape[1],dwi.shape[2],N_b+1), dtype='float32')
             b0_bshell[:,:,:,0]= b0
             b0_bshell[:,:,:,1:]= dwi[:,:,:,ind]
@@ -67,9 +73,12 @@ def separateBshells(imgPath, ref_bvals_file=None, ref_bvals=None):
             b0_bvecs= np.zeros((N_b+1,3), dtype='float32')
             b0_bvecs[1:,]= bvecs[ind,: ]
 
-            save_nifti(bPrefix+'.nii.gz', b0_bshell, img.affine, img.header)
-            write_bvals(bPrefix+'.bval', b0_bvals)
-            write_bvecs(bPrefix+'.bvec', b0_bvecs)
+            if not isfile(nii_file):
+                save_nifti(nii_file, b0_bshell, img.affine, img.header)
+            if not isfile(bval_file):
+                write_bvals(bval_file, b0_bvals)
+            if not isfile(bvec_file):
+                write_bvecs(bvec_file, b0_bvecs)
 
 
 
@@ -84,13 +93,17 @@ def separateAllBshells(ref_csv, ref_bvals_file, ncpu=4, outPrefix= None):
         masks = None
 
     pool = Pool(int(ncpu))
+    results = []
     for imgPath in imgs:
-        pool.apply_async(separateBshells,
-                         kwds={'imgPath': imgPath, 'ref_bvals': ref_bvals}, error_callback=RAISE)
+        results.append(pool.apply_async(separateBshells,
+                         kwds={'imgPath': imgPath, 'ref_bvals': ref_bvals}))
 
     pool.close()
     pool.join()
 
+    for r in results:
+        r.get()
+
 
     if outPrefix:
         outPrefix = abspath(outPrefix)

lib/tests/shellEquate.py

@@ -17,7 +17,7 @@
 from plumbum import cli, local
 from conversion import read_bvals, read_bvecs, write_bvals, write_bvecs, read_imgs, read_imgs_masks
 from nibabel import load
-from util import abspath, pjoin, save_nifti, RAISE, isfile
+from util import abspath, pjoin, save_nifti, isfile
 import numpy as np
 from multiprocessing import Pool
 from findBshells import BSHELL_MIN_DIST
@@ -83,12 +83,16 @@ def separateAllBshells(ref_csv, ref_bvals_file, ncpu=4, outPrefix= None):
         masks = None
 
     pool = Pool(int(ncpu))
+    results = []
     for imgPath in imgs:
-        pool.apply_async(separateBshells,
-                         kwds={'imgPath': imgPath, 'ref_bvals': ref_bvals}, error_callback=RAISE)
+        results.append(pool.apply_async(separateBshells,
+                         kwds={'imgPath': imgPath, 'ref_bvals': ref_bvals}))
 
     pool.close()
     pool.join()
+
+    for r in results:
+        r.get()
 
 
     if outPrefix: