fix: moved nipype imports into function. moved matplotlib.use agg under

Author: akeshavan

preafq/qc.py

@@ -1,4 +1,6 @@
 import matplotlib
+matplotlib.use('agg')
+
 import nibabel as nib
 
 import matplotlib.pyplot as plt
@@ -9,7 +11,7 @@
 from nipype.utils.filemanip import save_json
 import base64
 
-matplotlib.use('agg')
+
 
 
 def reorient_array(data, aff):

preafq/run_1.py

@@ -1,21 +1,22 @@
 import os.path as op
 from shutil import copyfile
 
-import nipype.interfaces.freesurfer as fs
-import nipype.interfaces.fsl as fsl
-import nipype.interfaces.io as nio
-import nipype.interfaces.utility as niu
-import nipype.pipeline.engine as pe
-from nipype.interfaces.dipy import DTI
-from nipype.workflows.dmri.fsl.artifacts import all_fsl_pipeline
-
 
 def run_preAFQ(dwi_file, dwi_file_AP, dwi_file_PA, bvec_file, bval_file,
                subjects_dir, working_dir, out_dir):
     """This is for HBN diffusion data
 
     Assuming phase-encode direction is AP/PA for topup
     """
+
+    import nipype.interfaces.freesurfer as fs
+    import nipype.interfaces.fsl as fsl
+    import nipype.interfaces.io as nio
+    import nipype.interfaces.utility as niu
+    import nipype.pipeline.engine as pe
+    from nipype.interfaces.dipy import DTI
+    from nipype.workflows.dmri.fsl.artifacts import all_fsl_pipeline
+
     # some bookkeeping (getting the filename, gettings the BIDS subject name)
     dwi_fname = op.split(dwi_file)[1].split(".nii.gz")[0]
     bids_sub_name = dwi_fname.split("_")[0]