Editing niftyfit to remove duplicate code from base.py and edit the test/interfaces

Author: byvernault

nipype/interfaces/niftyfit/__init__.py

@@ -9,6 +9,5 @@
 """
 
 from .asl import FitAsl
-from .base import no_niftyfit, get_custom_path
 from .dwi import FitDwi, DwiTool
 from .qt1 import FitQt1

nipype/interfaces/niftyfit/asl.py

@@ -12,7 +12,8 @@
 """
 
 from ..base import TraitedSpec, traits, CommandLineInputSpec
-from .base import NiftyFitCommand, get_custom_path
+from .base import NiftyFitCommand
+from ..niftyreg.base import get_custom_path
 
 
 class FitAslInputSpec(CommandLineInputSpec):
@@ -31,14 +32,14 @@ class FitAslInputSpec(CommandLineInputSpec):
     cbf_file = traits.File(name_source=['source_file'],
                            name_template='%s_cbf.nii.gz',
                            argstr='-cbf %s', desc=desc)
-    desc = 'Filename of the CBF error map.'
     error_file = traits.File(name_source=['source_file'],
                              name_template='%s_error.nii.gz',
-                             argstr='-error %s', desc=desc)
-    desc = 'Filename of the synthetic ASL data.'
+                             argstr='-error %s',
+                             desc='Filename of the CBF error map.')
     syn_file = traits.File(name_source=['source_file'],
                            name_template='%s_syn.nii.gz',
-                           argstr='-syn %s', desc=desc)
+                           argstr='-syn %s',
+                           desc='Filename of the synthetic ASL data.')
 
     # *** Input options (see also fit_qt1 for generic T1 fitting):
     desc = 'Filename of the estimated input T1 map (in ms).'
@@ -150,7 +151,7 @@ class FitAsl(NiftyFitCommand):
 -syn asl_syn.nii.gz'
 
     """
-    _cmd = get_custom_path('fit_asl')
+    _cmd = get_custom_path('fit_asl', env_dir='NIFTYFITDIR')
     input_spec = FitAslInputSpec
     output_spec = FitAslOutputSpec
     _suffix = '_fit_asl'

nipype/interfaces/niftyfit/base.py

@@ -29,25 +29,6 @@
 warnings.filterwarnings('always', category=UserWarning)
 
 
-def get_custom_path(command):
-    """Get path of niftyfit."""
-    try:
-        specific_dir = os.environ['NIFTYFITDIR']
-        command = os.path.join(specific_dir, command)
-        return command
-    except KeyError:
-        return command
-
-
-def no_niftyfit(cmd='fit_dwi'):
-    """Check if niftyfit is installed."""
-    if True in [os.path.isfile(os.path.join(path, cmd)) and
-                os.access(os.path.join(path, cmd), os.X_OK)
-                for path in os.environ["PATH"].split(os.pathsep)]:
-        return False
-    return True
-
-
 class NiftyFitCommand(CommandLine):
     """
     Base support interface for NiftyFit commands.

nipype/interfaces/niftyfit/dwi.py

@@ -12,7 +12,8 @@
 """
 
 from ..base import TraitedSpec, traits, isdefined, CommandLineInputSpec
-from .base import NiftyFitCommand, get_custom_path
+from .base import NiftyFitCommand
+from ..niftyreg.base import get_custom_path
 
 
 class FitDwiInputSpec(CommandLineInputSpec):
@@ -254,7 +255,7 @@ class FitDwi(NiftyFitCommand):
 -tenmap2 dwi_tenmap2.nii.gz  -v1map dwi_v1map.nii.gz'
 
     """
-    _cmd = get_custom_path('fit_dwi')
+    _cmd = get_custom_path('fit_dwi', env_dir='NIFTYFITDIR')
     input_spec = FitDwiInputSpec
     output_spec = FitDwiOutputSpec
     _suffix = '_fit_dwi'
@@ -430,7 +431,7 @@ class DwiTool(NiftyFitCommand):
 -syn dwi_syn.nii.gz -v1map dwi_v1map.nii.gz'
 
     """
-    _cmd = get_custom_path('dwi_tool')
+    _cmd = get_custom_path('dwi_tool', env_dir='NIFTYFITDIR')
     input_spec = DwiToolInputSpec
     output_spec = DwiToolOutputSpec
     _suffix = '_dwi_tool'

nipype/interfaces/niftyfit/qt1.py

@@ -13,7 +13,8 @@
 """
 
 from ..base import TraitedSpec, File, traits, CommandLineInputSpec
-from .base import get_custom_path, NiftyFitCommand
+from .base import NiftyFitCommand
+from ..niftyreg.base import get_custom_path
 
 
 class FitQt1InputSpec(CommandLineInputSpec):
@@ -169,7 +170,7 @@ class FitQt1(NiftyFitCommand):
 -res TI4D_res.nii.gz -syn TI4D_syn.nii.gz -t1map TI4D_t1map.nii.gz'
 
     """
-    _cmd = get_custom_path('fit_qt1')
+    _cmd = get_custom_path('fit_qt1', env_dir='NIFTYFITDIR')
     input_spec = FitQt1InputSpec
     output_spec = FitQt1OutputSpec
     _suffix = '_fit_qt1'

nipype/interfaces/niftyfit/tests/test_asl.py

@@ -4,19 +4,21 @@
 
 import pytest
 
-from nipype.interfaces.niftyfit import no_niftyfit, get_custom_path, FitAsl
+from nipype.interfaces.niftyfit import FitAsl
+from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
 from nipype.testing import example_data
 
 
-@pytest.mark.skipif(no_niftyfit(cmd='fit_asl'),
+@pytest.mark.skipif(no_nifty_package(cmd='fit_asl'),
                     reason="niftyfit is not installed")
 def test_fit_asl():
     """ Testing FitAsl interface."""
     # Create the test node
     fit_asl = FitAsl()
 
     # Check if the command is properly defined
-    assert fit_asl.cmd == get_custom_path('fit_asl')
+    cmd = get_custom_path('fit_asl', env_dir='NIFTYFIT_DIR')
+    assert fit_asl.cmd == cmd
 
     # test raising error with mandatory args absent
     with pytest.raises(ValueError):
@@ -29,7 +31,7 @@ def test_fit_asl():
 
     cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} -syn {syn}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('fit_asl'),
+        cmd=cmd,
         in_file=in_file,
         cbf='asl_cbf.nii.gz',
         error='asl_error.nii.gz',
@@ -52,7 +54,7 @@ def test_fit_asl():
     cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} \
 -seg {seg} -sig -syn {syn} -t1map {t1map}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('fit_asl'),
+        cmd=cmd,
         in_file=in_file,
         t1map=t1map,
         seg=seg,

nipype/interfaces/niftyfit/tests/test_dwi.py

@@ -3,20 +3,21 @@
 
 import pytest
 
-from nipype.interfaces.niftyfit import (no_niftyfit, get_custom_path, FitDwi,
-                                        DwiTool)
+from nipype.interfaces.niftyfit import FitDwi, DwiTool
+from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
 from nipype.testing import example_data
 
 
-@pytest.mark.skipif(no_niftyfit(cmd='fit_dwi'),
+@pytest.mark.skipif(no_nifty_package(cmd='fit_dwi'),
                     reason="niftyfit is not installed")
 def test_fit_dwi():
     """ Testing FitDwi interface."""
     # Create a node object
     fit_dwi = FitDwi()
 
     # Check if the command is properly defined
-    assert fit_dwi.cmd == get_custom_path('fit_dwi')
+    cmd = get_custom_path('fit_dwi', env_dir='NIFTYFITDIR')
+    assert fit_dwi.cmd == cmd
 
     # test raising error with mandatory args absent
     with pytest.raises(ValueError):
@@ -36,7 +37,7 @@ def test_fit_dwi():
 {nodiff} -res {res} -rgbmap {rgb} -syn {syn} -tenmap2 {ten2}  -v1map {v1}'
 
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('fit_dwi'),
+        cmd=cmd,
         in_file=in_file,
         bval=bval_file,
         bvec=bvec_file,
@@ -55,15 +56,16 @@ def test_fit_dwi():
     assert fit_dwi.cmdline == expected_cmd
 
 
-@pytest.mark.skipif(no_niftyfit(cmd='dwi_tool'),
+@pytest.mark.skipif(no_nifty_package(cmd='dwi_tool'),
                     reason="niftyfit is not installed")
 def test_dwi_tool():
     """ Testing DwiTool interface."""
     # Create a node object
     dwi_tool = DwiTool()
 
     # Check if the command is properly defined
-    assert dwi_tool.cmd == get_custom_path('dwi_tool')
+    cmd = get_custom_path('dwi_tool', env_dir='NIFTYFITDIR')
+    assert dwi_tool.cmd == cmd
 
     # test raising error with mandatory args absent
     with pytest.raises(ValueError):
@@ -86,7 +88,7 @@ def test_dwi_tool():
 -mask {mask} -dti -famap {fa} -logdti2 {log} -mcmap {mc} -mdmap {md} \
 -rgbmap {rgb} -syn {syn} -v1map {v1}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('dwi_tool'),
+        cmd=cmd,
         in_file=in_file,
         bval=bval_file,
         bvec=bvec_file,

nipype/interfaces/niftyfit/tests/test_qt1.py

@@ -4,19 +4,21 @@
 
 import pytest
 
-from nipype.interfaces.niftyfit import no_niftyfit, get_custom_path, FitQt1
+from nipype.interfaces.niftyfit import FitQt1
+from nipype.interfaces.niftyreg import no_nifty_package, get_custom_path
 from nipype.testing import example_data
 
 
-@pytest.mark.skipif(no_niftyfit(cmd='fit_qt1'),
+@pytest.mark.skipif(no_nifty_package(cmd='fit_qt1'),
                     reason="niftyfit is not installed")
 def test_fit_qt1():
     """ Testing FitQt1 interface."""
     # Create a node object
     fit_qt1 = FitQt1()
 
     # Check if the command is properly defined
-    assert fit_qt1.cmd == get_custom_path('fit_qt1')
+    cmd = get_custom_path('fit_qt1', env_dir='NIFTYFITDIR')
+    assert fit_qt1.cmd == cmd
 
     # test raising error with mandatory args absent
     with pytest.raises(ValueError):
@@ -29,7 +31,7 @@ def test_fit_qt1():
     cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} -m0map \
 {map0} -mcmap {cmap} -res {res} -syn {syn} -t1map {t1map}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('fit_qt1'),
+        cmd=cmd,
         in_file=in_file,
         comp='TI4D_comp.nii.gz',
         map0='TI4D_m0map.nii.gz',
@@ -51,7 +53,7 @@ def test_fit_qt1():
 -comp {comp} -error {error} -m0map {map0} -mcmap {cmap} -res {res} \
 -syn {syn} -t1map {t1map}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('fit_qt1'),
+        cmd=cmd,
         in_file=in_file,
         comp='TI4D_comp.nii.gz',
         map0='TI4D_m0map.nii.gz',
@@ -73,7 +75,7 @@ def test_fit_qt1():
 -flips 2.0 4.0 8.0 -m0map {map0} -mcmap {cmap} -res {res} -SPGR -syn {syn} \
 -t1map {t1map}'
     expected_cmd = cmd_tmp.format(
-        cmd=get_custom_path('fit_qt1'),
+        cmd=cmd,
         in_file=in_file,
         comp='TI4D_comp.nii.gz',
         map0='TI4D_m0map.nii.gz',