fix typos

Author: josephmje

MANIFEST.in

@@ -1,6 +1,5 @@
-include AUTHORS.rst
 include CONTRIBUTING.rst
-include HISTORY.rst
+include CHANGES.rst
 include LICENSE
 include README.rst
 

dmriprep/workflows/fieldmap/base.py

@@ -13,8 +13,7 @@ def init_sdc_prep_wf(
     layout,
     bet_mag,
     #synb0,
-    omp_nthreads
-):
+    ):
 
     sdc_prep_wf = pe.Workflow(name='sdc_prep_wf')
 

dmriprep/workflows/fieldmap/fmap.py

@@ -21,7 +21,7 @@ def init_fmap_wf(bet_mag):
         fsl.BinaryMaths(operation='div', operand_value=6.28), name='radToHz'
     )
 
-    mag_bet = pe.Node(fsl.BET(frac=bet_mag, mask=True, robust=True),name='mag_bet')))
+    mag_bet = pe.Node(fsl.BET(frac=bet_mag, mask=True, robust=True), name='mag_bet')
 
     mag_flirt = pe.Node(fsl.FLIRT(dof=6), name='magFlirt')
 

dmriprep/workflows/fieldmap/pepolar.py

@@ -6,7 +6,7 @@
 
 def init_pepolar_wf(subject_id, dwi_meta, epi_fmaps):
 
-    dwi_file_pe = dwi_meta["PhaseEncodingDirection"]
+    dwi_file_pe = dwi_meta['PhaseEncodingDirection']
 
     file2dir = dict()
 
@@ -23,22 +23,22 @@ def init_pepolar_wf(subject_id, dwi_meta, epi_fmaps):
 
     if not usable_fieldmaps_opposite_pe:
         raise Exception(
-            "None of the discovered fieldmaps for "
-            "participant {} has the right phase "
-            "encoding direction".format(subject_id)
+            'None of the discovered fieldmaps for '
+            'participant {} has the right phase '
+            'encoding direction'.format(subject_id)
         )
 
-    wf = pe.Workflow(name="pepolar_wf")
+    wf = pe.Workflow(name='pepolar_wf')
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=["b0_stripped"]), name="inputnode"
+        niu.IdentityInterface(fields=['b0_stripped']), name='inputnode'
     )
 
     outputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["out_topup", "out_movpar", "out_fmap", "out_enc_file"]
+            fields=['out_topup', 'out_movpar', 'out_fmap', 'out_enc_file']
         ),
-        name="outputnode",
+        name='outputnode',
     )
 
     topup_wf = init_topup_wf()
@@ -47,7 +47,7 @@ def init_pepolar_wf(subject_id, dwi_meta, epi_fmaps):
 
     if not usable_fieldmaps_matching_pe:
         wf.connect(
-            [(inputnode, topup_wf, [("b0_stripped", "inputnode.epi_file")])]
+            [(inputnode, topup_wf, [('b0_stripped', 'inputnode.epi_file')])]
         )
     else:
         topup_wf.inputs.inputnode.epi_file = usable_fieldmaps_matching_pe[0]
@@ -57,12 +57,12 @@ def init_pepolar_wf(subject_id, dwi_meta, epi_fmaps):
         topup_wf.inputs.inputnode.altepi_file,
     ]
     dir_map = {
-        "i": "x",
-        "i-": "x-",
-        "j": "y",
-        "j-": "y-",
-        "k": "z",
-        "k-": "z-",
+        'i': 'x',
+        'i-': 'x-',
+        'j': 'y',
+        'j-': 'y-',
+        'k': 'z',
+        'k-': 'z-',
     }
     topup_wf.inputs.inputnode.encoding_directions = [
         dir_map[file2dir[file]] for file in epi_list
@@ -74,10 +74,10 @@ def init_pepolar_wf(subject_id, dwi_meta, epi_fmaps):
                 topup_wf,
                 outputnode,
                 [
-                    ("outputnode.out_fmap", "out_fmap"),
-                    ("outputnode.out_movpar", "out_movpar"),
-                    ("outputnode.out_base", "out_topup"),
-                    ("outputnode.out_enc_file", "out_enc_file"),
+                    ('outputnode.out_fmap', 'out_fmap'),
+                    ('outputnode.out_movpar', 'out_movpar'),
+                    ('outputnode.out_base', 'out_topup'),
+                    ('outputnode.out_enc_file', 'out_enc_file'),
                 ],
             )
         ]
@@ -87,43 +87,43 @@ def init_pepolar_wf(subject_id, dwi_meta, epi_fmaps):
 
 
 def init_synb0_wf(subject_id, dwi_meta, synb0):
-    dwi_file_pe = dwi_meta["PhaseEncodingDirection"]
+    dwi_file_pe = dwi_meta['PhaseEncodingDirection']
 
     file2dir = dict()
 
     usable_fieldmaps_matching_pe = []
     usable_fieldmaps_opposite_pe = []
 
-    wf = pe.Workflow(name="synb0_wf")
+    wf = pe.Workflow(name='synb0_wf')
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=["b0_stripped"]), name="inputnode"
+        niu.IdentityInterface(fields=['b0_stripped']), name='inputnode'
     )
 
     outputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["out_topup", "out_movpar", "out_fmap", "out_enc_file"]
+            fields=['out_topup', 'out_movpar', 'out_fmap', 'out_enc_file']
         ),
-        name="outputnode",
+        name='outputnode',
     )
 
     topup_wf = init_topup_wf(use_acqp=True)
     topup_wf.inputs.inputnode.altepi_file = synb0
     wf.add_nodes([inputnode])
     wf.connect(
-        [(inputnode, topup_wf, [("b0_stripped", "inputnode.epi_file")])]
+        [(inputnode, topup_wf, [('b0_stripped', 'inputnode.epi_file')])]
     )
-    topup_wf.inputs.inputnode.acqp = "/scratch/smansour/synb0_acqp.txt"
+    topup_wf.inputs.inputnode.acqp = '/scratch/smansour/synb0_acqp.txt'
 
     wf.connect(
         [
             (
                 topup_wf,
                 outputnode,
                 [
-                    ("outputnode.out_fmap", "out_fmap"),
-                    ("outputnode.out_movpar", "out_movpar"),
-                    ("outputnode.out_base", "out_topup"),
+                    ('outputnode.out_fmap', 'out_fmap'),
+                    ('outputnode.out_movpar', 'out_movpar'),
+                    ('outputnode.out_base', 'out_topup'),
                 ],
             )
         ]
@@ -135,77 +135,77 @@ def init_synb0_wf(subject_id, dwi_meta, synb0):
 def init_topup_wf(use_acqp=False):
     from ...interfaces import mrtrix3
 
-    wf = pe.Workflow(name="topup_wf")
+    wf = pe.Workflow(name='topup_wf')
 
     inputnode = pe.Node(
         niu.IdentityInterface(
             fields=[
-                "epi_file",
-                "altepi_file",
-                "encoding_directions",
-                "topup_name",
-                "acqp",
+                'epi_file',
+                'altepi_file',
+                'encoding_directions',
+                'topup_name',
+                'acqp',
             ]
         ),
-        name="inputnode",
+        name='inputnode',
     )
-    inputnode.inputs.topup_name = "topup_base"
+    inputnode.inputs.topup_name = 'topup_base'
 
-    epi_flirt = pe.Node(fsl.FLIRT(), name="epi_flirt")
+    epi_flirt = pe.Node(fsl.FLIRT(), name='epi_flirt')
 
     outputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["out_fmap", "out_movpar", "out_base", "out_enc_file"]
+            fields=['out_fmap', 'out_movpar', 'out_base', 'out_enc_file']
         ),
-        name="outputnode",
+        name='outputnode',
     )
 
-    list_merge = pe.Node(niu.Merge(numinputs=2), name="list_merge")
+    list_merge = pe.Node(niu.Merge(numinputs=2), name='list_merge')
 
-    merge = pe.Node(fsl.Merge(dimension="t"), name="mergeAPPA")
+    merge = pe.Node(fsl.Merge(dimension='t'), name='mergeAPPA')
 
     # Resize (make optional)
-    resize = pe.Node(mrtrix3.MRResize(voxel_size=[1]), name="epi_resize")
+    resize = pe.Node(mrtrix3.MRResize(voxel_size=[1]), name='epi_resize')
 
-    topup = pe.Node(fsl.TOPUP(), name="topup")
+    topup = pe.Node(fsl.TOPUP(), name='topup')
 
-    get_base_movpar = lambda x: x.split("_movpar.txt")[0]
+    get_base_movpar = lambda x: x.split('_movpar.txt')[0]
 
     if use_acqp:
-        wf.connect([(inputnode, topup, [("acqp", "encoding_file")])])
+        wf.connect([(inputnode, topup, [('acqp', 'encoding_file')])])
     else:
         topup.inputs.readout_times = [0.05, 0.05]
         wf.connect(
             [
                 (
                     inputnode,
                     topup,
-                    [("encoding_directions", "encoding_direction")],
+                    [('encoding_directions', 'encoding_direction')],
                 )
             ]
         )
 
     wf.connect(
         [
-            (inputnode, list_merge, [("epi_file", "in1")]),
+            (inputnode, list_merge, [('epi_file', 'in1')]),
             (
                 inputnode,
                 epi_flirt,
-                [("altepi_file", "in_file"), ("epi_file", "reference")],
+                [('altepi_file', 'in_file'), ('epi_file', 'reference')],
             ),
-            (epi_flirt, list_merge, [("out_file", "in2")]),
-            (list_merge, merge, [("out", "in_files")]),
-            # (merge, resize, [("merged_file", "in_file")]),
-            # (resize, topup, [("out_file", "in_file")]),
-            (merge, topup, [("merged_file", "in_file")]),
+            (epi_flirt, list_merge, [('out_file', 'in2')]),
+            (list_merge, merge, [('out', 'in_files')]),
+            # (merge, resize, [('merged_file', 'in_file')]),
+            # (resize, topup, [('out_file', 'in_file')]),
+            (merge, topup, [('merged_file', 'in_file')]),
             (
                 topup,
                 outputnode,
                 [
-                    ("out_field", "out_fmap"),
-                    ("out_movpar", "out_movpar"),
-                    ("out_enc_file", "out_enc_file"),
-                    (("out_movpar", get_base_movpar), "out_base"),
+                    ('out_field', 'out_fmap'),
+                    ('out_movpar', 'out_movpar'),
+                    ('out_enc_file', 'out_enc_file'),
+                    (('out_movpar', get_base_movpar), 'out_base'),
                 ],
             ),
         ]

dmriprep/workflows/fieldmap/phasediff.py

@@ -76,7 +76,7 @@ def init_phdiff_wf(bet_mag):
         (delta, prep_fmap, [('out_value', 'delta_TE')]),
         (prep_fmap, fslroi, [('out_fieldmap', 'in_file')]),
         (fslroi, outputnode, [('roi_file', 'out_fmap')]),
-        (mag_bet, outputnode, [('magnitude1', 'out_mag')])
+        (mag_bet, outputnode, [('out_file', 'out_mag')])
     ])
 
     return wf