Merge pull request #1911 from mmodat/adding_niftyseg

Adding niftyseg

Author: satra

nipype/interfaces/niftyreg/__init__.py

@@ -9,7 +9,7 @@
 Top-level namespace for niftyreg.
 """
 
-from .base import no_niftyreg, get_custom_path
+from .base import no_nifty_package, get_custom_path
 from .reg import RegAladin, RegF3D
 from .regutils import (RegResample, RegJacobian, RegAverage, RegTools,
                        RegTransform, RegMeasure)

nipype/interfaces/niftyreg/base.py

@@ -30,11 +30,11 @@
 from ...utils.filemanip import split_filename
 
 
-def get_custom_path(command):
-    return os.path.join(os.getenv('NIFTYREGDIR', ''), command)
+def get_custom_path(command, env_dir='NIFTYREGDIR'):
+    return os.path.join(os.getenv(env_dir, ''), command)
 
 
-def no_niftyreg(cmd='reg_f3d'):
+def no_nifty_package(cmd='reg_f3d'):
     try:
         return shutil.which(cmd) is None
     except AttributeError:  # Python < 3.3
@@ -64,7 +64,8 @@ def __init__(self, required_version=None, **inputs):
         _version = self.get_version()
         if _version:
             _version = _version.decode("utf-8")
-            if StrictVersion(_version) < StrictVersion(self._min_version):
+            if self._min_version is not None and \
+               StrictVersion(_version) < StrictVersion(self._min_version):
                 msg = 'A later version of Niftyreg is required (%s < %s)'
                 warn(msg % (_version, self._min_version))
             if required_version is not None:
@@ -89,7 +90,7 @@ def check_version(self):
                 raise ValueError(err % (_version, self.required_version))
 
     def get_version(self):
-        if no_niftyreg(cmd=self.cmd):
+        if no_nifty_package(cmd=self.cmd):
             return None
         exec_cmd = ''.join((self.cmd, ' -v'))
         return subprocess.check_output(exec_cmd, shell=True).strip()

nipype/interfaces/niftyreg/tests/test_reg.py

@@ -4,13 +4,13 @@
 
 import pytest
 
-from nipype.interfaces.niftyreg import (no_niftyreg, get_custom_path,
+from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
                                         RegAladin, RegF3D)
 from nipype.testing import example_data
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_aladin'),
+    no_nifty_package(cmd='reg_aladin'),
     reason="niftyreg is not installed. reg_aladin not found.")
 def test_reg_aladin():
     """ tests for reg_aladin interface"""
@@ -48,7 +48,7 @@ def test_reg_aladin():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_f3d'),
+    no_nifty_package(cmd='reg_f3d'),
     reason="niftyreg is not installed. reg_f3d not found.")
 def test_reg_f3d():
     """ tests for reg_f3d interface"""

nipype/interfaces/niftyreg/tests/test_regutils.py

@@ -2,7 +2,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
-from nipype.interfaces.niftyreg import (no_niftyreg, get_custom_path,
+from nipype.interfaces.niftyreg import (no_nifty_package, get_custom_path,
                                         RegAverage, RegResample, RegJacobian,
                                         RegTools, RegMeasure, RegTransform)
 from nipype.testing import example_data
@@ -11,7 +11,7 @@
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_resample'),
+    no_nifty_package(cmd='reg_resample'),
     reason="niftyreg is not installed. reg_resample not found.")
 def test_reg_resample_res():
     """ tests for reg_resample interface """
@@ -68,7 +68,7 @@ def test_reg_resample_res():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_jacobian'),
+    no_nifty_package(cmd='reg_jacobian'),
     reason="niftyreg is not installed. reg_jacobian not found.")
 def test_reg_jacobian_jac():
     """ Test interface for RegJacobian """
@@ -132,7 +132,7 @@ def test_reg_jacobian_jac():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_tools'),
+    no_nifty_package(cmd='reg_tools'),
     reason="niftyreg is not installed. reg_tools not found.")
 def test_reg_tools_mul():
     """ tests for reg_tools interface """
@@ -175,7 +175,7 @@ def test_reg_tools_mul():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_average'),
+    no_nifty_package(cmd='reg_average'),
     reason="niftyreg is not installed. reg_average not found.")
 def test_reg_average():
     """ tests for reg_average interface """
@@ -318,7 +318,7 @@ def test_reg_average():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_transform'),
+    no_nifty_package(cmd='reg_transform'),
     reason="niftyreg is not installed. reg_transform not found.")
 def test_reg_transform_def():
     """ tests for reg_transform interface """
@@ -427,7 +427,7 @@ def test_reg_transform_def():
 
 
 @pytest.mark.skipif(
-    no_niftyreg(cmd='reg_measure'),
+    no_nifty_package(cmd='reg_measure'),
     reason="niftyreg is not installed. reg_measure not found.")
 def test_reg_measure():
     """ tests for reg_measure interface """

nipype/interfaces/niftyseg/__init__.py

@@ -0,0 +1,17 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+The niftyseg module provides classes for interfacing with the `NIFTYSEG
+<https://sourceforge.net/projects/niftyseg/>`_ command line tools.
+
+Top-level namespace for niftyseg.
+"""
+
+from .em import EM
+from .label_fusion import LabelFusion, CalcTopNCC
+from .lesions import FillLesions
+from .maths import (UnaryMaths, BinaryMaths, BinaryMathsInteger, TupleMaths,
+                    Merge)
+from .patchmatch import PatchMatch
+from .stats import UnaryStats, BinaryStats

nipype/interfaces/niftyseg/base.py

@@ -0,0 +1,44 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+The niftyseg module provides classes for interfacing with `niftyseg
+<https://sourceforge.net/projects/niftyseg/>`_ command line tools.
+These are the base tools for working with niftyseg.
+EM Statistical Segmentation tool is found in niftyseg/em.py
+Fill lesions tool is found in niftyseg/lesions.py
+Mathematical operation tool is found in niftyseg/maths.py
+Patch Match tool is found in niftyseg/patchmatch.py
+Statistical operation tool is found in niftyseg/stats.py
+Label Fusion and CalcTopNcc tools are in niftyseg/steps.py
+Examples
+--------
+See the docstrings of the individual classes for examples.
+"""
+
+from nipype.interfaces.niftyreg.base import NiftyRegCommand, no_nifty_package
+import subprocess
+import warnings
+
+
+warn = warnings.warn
+warnings.filterwarnings('always', category=UserWarning)
+
+
+class NiftySegCommand(NiftyRegCommand):
+    """
+    Base support interface for NiftySeg commands.
+    """
+    _suffix = '_ns'
+    _min_version = None
+
+    def __init__(self, **inputs):
+        super(NiftySegCommand, self).__init__(**inputs)
+
+    def get_version(self):
+        if no_nifty_package(cmd=self.cmd):
+            return None
+        # exec_cmd = ''.join((self.cmd, ' --version'))
+        exec_cmd = 'seg_EM --version'
+        # Using seg_EM for version (E.G: seg_stats --version doesn't work)
+        return subprocess.check_output(exec_cmd, shell=True).strip('\n')

nipype/interfaces/niftyseg/em.py

@@ -0,0 +1,146 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+
+"""
+Nipype interface for seg_EM.
+
+The em module provides higher-level interfaces to some of the operations
+that can be performed with the seg_em command-line program.
+
+Examples
+--------
+See the docstrings of the individual classes for examples.
+
+Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+    >>> os.chdir(datadir)
+"""
+
+from ..base import (TraitedSpec, File, traits, CommandLineInputSpec,
+                    InputMultiPath)
+from .base import NiftySegCommand
+from ..niftyreg.base import get_custom_path
+
+
+class EMInputSpec(CommandLineInputSpec):
+    """Input Spec for EM."""
+    in_file = File(argstr='-in %s',
+                   exists=True,
+                   mandatory=True,
+                   desc='Input image to segment',
+                   position=4)
+
+    mask_file = File(argstr='-mask %s',
+                     exists=True,
+                     desc='Filename of the ROI for label fusion')
+
+    # Priors
+    no_prior = traits.Int(argstr='-nopriors %s',
+                          mandatory=True,
+                          desc='Number of classes to use without prior',
+                          xor=['prior_4D', 'priors'])
+
+    prior_4D = File(argstr='-prior4D %s',
+                    exists=True,
+                    mandatory=True,
+                    desc='4D file containing the priors',
+                    xor=['no_prior', 'priors'])
+
+    priors = InputMultiPath(argstr='%s',
+                            mandatory=True,
+                            desc='List of priors filepaths.',
+                            xor=['no_prior', 'prior_4D'])
+
+    # iterations
+    max_iter = traits.Int(argstr='-max_iter %s', default=100,
+                          desc='Maximum number of iterations')
+
+    min_iter = traits.Int(argstr='-min_iter %s', default=0,
+                          desc='Minimun number of iterations')
+
+    # other options
+    bc_order_val = traits.Int(argstr='-bc_order %s', default=3,
+                              desc='Polynomial order for the bias field')
+
+    mrf_beta_val = traits.Float(argstr='-mrf_beta %s',
+                                desc='Weight of the Markov Random Field')
+
+    desc = 'Bias field correction will run only if the ratio of improvement \
+is below bc_thresh. (default=0 [OFF])'
+    bc_thresh_val = traits.Float(argstr='-bc_thresh %s', default=0, desc=desc)
+
+    desc = 'Amount of regularization over the diagonal of the covariance \
+matrix [above 1]'
+    reg_val = traits.Float(argstr='-reg %s', desc=desc)
+
+    desc = 'Outlier detection as in (Van Leemput TMI 2003). <fl1> is the \
+Mahalanobis threshold [recommended between 3 and 7] <fl2> is a convergence \
+ratio below which the outlier detection is going to be done [recommended 0.01]'
+    outlier_val = traits.Tuple(traits.Float(), traits.Float(),
+                               argstr='-outlier %s %s',
+                               desc=desc)
+
+    desc = 'Relax Priors [relaxation factor: 0<rf<1 (recommended=0.5), \
+gaussian regularization: gstd>0 (recommended=2.0)] /only 3D/'
+    relax_priors = traits.Tuple(traits.Float(), traits.Float(),
+                                argstr='-rf %s %s',
+                                desc=desc)
+
+    # outputs
+    out_file = File(name_source=['in_file'],
+                    name_template='%s_em.nii.gz',
+                    argstr='-out %s',
+                    desc='Output segmentation')
+    out_bc_file = File(name_source=['in_file'],
+                       name_template='%s_bc_em.nii.gz',
+                       argstr='-bc_out %s',
+                       desc='Output bias corrected image')
+    out_outlier_file = File(name_source=['in_file'],
+                            name_template='%s_outlier_em.nii.gz',
+                            argstr='-out_outlier %s',
+                            desc='Output outlierness image')
+
+
+class EMOutputSpec(TraitedSpec):
+    """Output Spec for EM."""
+    out_file = File(desc="Output segmentation")
+    out_bc_file = File(desc="Output bias corrected image")
+    out_outlier_file = File(desc='Output outlierness image')
+
+
+class EM(NiftySegCommand):
+    """Interface for executable seg_EM from NiftySeg platform.
+
+    seg_EM is a general purpose intensity based image segmentation tool. In
+    it's simplest form, it takes in one 2D or 3D image and segments it in n
+    classes.
+
+    For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
+    For Documentation, see:
+        http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
+
+    Examples
+    --------
+    >>> from nipype.interfaces import niftyseg
+    >>> node = niftyseg.EM()
+    >>> node.inputs.in_file = 'im1.nii'
+    >>> node.inputs.no_prior = 4
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz \
+-out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
+
+    """
+    _cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')
+    _suffix = '_em'
+    input_spec = EMInputSpec
+    output_spec = EMOutputSpec
+
+    def _format_arg(self, opt, spec, val):
+        """Convert input to appropriate format for seg_EM."""
+        if opt == 'priors':
+            _nb_priors = len(self.inputs.priors)
+            return '-priors %d %s' % (_nb_priors, ' '.join(self.inputs.priors))
+        else:
+            return super(EM, self)._format_arg(opt, spec, val)