🎨 DRY: raise scope of repeated inner function convert_pedir (#1648)

Author: shnizzedy

CPAC/info.py

@@ -161,6 +161,5 @@ def get_cpac_gitversion():
     "simplejson==3.15.0",
     "traits==4.6.0",
     "PyBASC==0.4.5",
-    "pathlib==1.0.1",
     "voluptuous>=0.12.0",
 ]

CPAC/registration/registration.py

@@ -278,6 +278,25 @@ def transform_derivative(wf_name, label, reg_tool, num_cpus, num_ants_cores,
     return wf
 
 
+def convert_pedir(pedir):
+    '''FSL Flirt requires pedir input encoded as an int'''
+    conv_dct = {'x': 1, 'y': 2, 'z': 3, 'x-': -1, 'y-': -2, 'z-': -3,
+                'i': 1, 'j': 2, 'k': 3, 'i-': -1, 'j-': -2, 'k-': -3,
+                '-x': -1, '-i': -1, '-y': -2,
+                '-j': -2, '-z': -3, '-k': -3}
+
+    if isinstance(pedir, bytes):
+        pedir = pedir.decode()
+    if not isinstance(pedir, str):
+        raise Exception("\n\nPhase-encoding direction must be a "
+                        "string value.\n\nValue: {0}"
+                        "\n\n".format(pedir))
+    if pedir not in conv_dct.keys():
+        raise Exception("\n\nInvalid phase-encoding direction "
+                        "entered: {0}\n\n".format(pedir))
+    return conv_dct[pedir]
+
+
 def create_fsl_flirt_linear_reg(name='fsl_flirt_linear_reg'):
 
     linear_register = pe.Workflow(name=name)
@@ -683,26 +702,6 @@ def create_register_func_to_anat(config, phase_diff_distcor=False,
     if config.registration_workflows['functional_registration']['coregistration']['arguments'] is not None:
         linear_reg.inputs.args = config.registration_workflows['functional_registration']['coregistration']['arguments']
 
-    # if fieldmap_distortion:
-
-    def convert_pedir(pedir):
-        # FSL Flirt requires pedir input encoded as an int
-        conv_dct = {'x': 1, 'y': 2, 'z': 3, 'x-': -1, 'y-': -2, 'z-': -3,
-                    'i': 1, 'j': 2, 'k': 3, 'i-': -1, 'j-': -2, 'k-': -3,
-                    '-x': -1, '-i': -1, '-y': -2,
-                    '-j': -2, '-z': -3, '-k': -3}
-
-        if isinstance(pedir, bytes):
-            pedir = pedir.decode()
-        if not isinstance(pedir, str):
-            raise Exception("\n\nPhase-encoding direction must be a "
-                            "string value.\n\nValue: {0}"
-                            "\n\n".format(pedir))
-        if pedir not in conv_dct.keys():
-            raise Exception("\n\nInvalid phase-encoding direction "
-                            "entered: {0}\n\n".format(pedir))
-        return conv_dct[pedir]
-
     if phase_diff_distcor:
         register_func_to_anat.connect(
             inputNode_pedir, ('pedir', convert_pedir),
@@ -973,24 +972,6 @@ def bbreg_args(bbreg_target):
         inputspec, 'linear_reg_matrix',
         bbreg_func_to_anat, 'in_matrix_file')
 
-    def convert_pedir(pedir):
-        # FSL Flirt requires pedir input encoded as an int
-        conv_dct = {'x': 1, 'y': 2, 'z': 3, 'x-': -1, 'y-': -2, 'z-': -3,
-                    'i': 1, 'j': 2, 'k': 3, 'i-': -1, 'j-': -2, 'k-': -3,
-                    '-x': -1, '-i': -1, '-y': -2,
-                    '-j': -2, '-z': -3, '-k': -3}
-
-        if isinstance(pedir, bytes):
-            pedir = pedir.decode()
-        if not isinstance(pedir, str):
-            raise Exception("\n\nPhase-encoding direction must be a "
-                            "string value.\n\nValue: {0}"
-                            "\n\n".format(pedir))
-        if pedir not in conv_dct.keys():
-            raise Exception("\n\nInvalid phase-encoding direction "
-                            "entered: {0}\n\n".format(pedir))
-        return conv_dct[pedir]
-
     if phase_diff_distcor:
         register_bbregister_func_to_anat.connect(
             inputNode_pedir, ('pedir', convert_pedir),

cpac_install.sh

@@ -108,7 +108,6 @@ pip_packages=(
     "simplejson==3.15.0"
     "python-dateutil==2.7.3"
     "PyBASC==0.4.5"
-    "pathlib==1.0.1"
 )
 
 ##### Helper functions for installing system dependencies.