Merge pull request #2905 from skoudoro/add-all-dipy-wkflw

[ENH] Add all DIPY workflows dynamically

Author: satra

.zenodo.json

@@ -375,6 +375,10 @@
     {
       "name": "Haselgrove, Christian"
     },
+    {
+      "name": "Koudoro, Serge",
+      "affiliation": "Indiana University, IN, USA"
+    },
     {
       "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
       "name": "Glatard, Tristan",

nipype/interfaces/dipy/base.py

@@ -10,7 +10,11 @@
 from ..base import (traits, File, isdefined, LibraryBaseInterface,
                     BaseInterfaceInputSpec, TraitedSpec)
 
+# List of workflows to ignore
+SKIP_WORKFLOWS_LIST = ['Workflow', 'CombinedWorkflow']
+
 HAVE_DIPY = True
+
 try:
     import dipy
     from dipy.workflows.base import IntrospectiveArgumentParser
@@ -211,3 +215,29 @@ def _list_outputs(self):
                      "_run_interface": _run_interface,
                      "_list_outputs:": _list_outputs})
     return newclass
+
+
+def get_dipy_workflows(module):
+    """Search for DIPY workflow class.
+
+    Parameters
+    ----------
+    module : object
+        module object
+
+    Returns
+    -------
+    l_wkflw : list of tuple
+        This a list of tuple containing 2 elements:
+        Worflow name, Workflow class obj
+
+    Examples
+    --------
+    >>> from dipy.workflows import align  # doctest: +SKIP
+    >>> get_dipy_workflows(align)  # doctest: +SKIP
+
+    """
+    return [(m, obj) for m, obj in inspect.getmembers(module)
+            if inspect.isclass(obj) and
+            issubclass(obj, module.Workflow) and
+            m not in SKIP_WORKFLOWS_LIST]

nipype/interfaces/dipy/preprocess.py

@@ -5,15 +5,30 @@
 import os.path as op
 import nibabel as nb
 import numpy as np
+from distutils.version import LooseVersion
 
 from ...utils import NUMPY_MMAP
 
 from ... import logging
 from ..base import (traits, TraitedSpec, File, isdefined)
-from .base import DipyBaseInterface
+from .base import (HAVE_DIPY, dipy_version, dipy_to_nipype_interface,
+                   get_dipy_workflows, DipyBaseInterface)
 
 IFLOGGER = logging.getLogger('nipype.interface')
 
+if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.15'):
+    from dipy.workflows import denoise, mask
+
+    l_wkflw = get_dipy_workflows(denoise) + get_dipy_workflows(mask)
+    for name, obj in l_wkflw:
+        new_name = name.replace('Flow', '')
+        globals()[new_name] = dipy_to_nipype_interface(new_name, obj)
+    del l_wkflw
+
+else:
+    IFLOGGER.info("We advise you to upgrade DIPY version. This upgrade will"
+                  " open access to more function")
+
 
 class ResampleInputSpec(TraitedSpec):
     in_file = File(

nipype/interfaces/dipy/reconstruction.py

@@ -18,24 +18,24 @@
 from ... import logging
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import (DipyDiffusionInterface, DipyBaseInterfaceInputSpec,
-                   HAVE_DIPY, dipy_version, dipy_to_nipype_interface)
+                   HAVE_DIPY, dipy_version, dipy_to_nipype_interface,
+                   get_dipy_workflows)
 
 
 IFLOGGER = logging.getLogger('nipype.interface')
 
 if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.15'):
-    from dipy.workflows.reconst import (ReconstDkiFlow, ReconstCSAFlow,
-                                        ReconstCSDFlow, ReconstMAPMRIFlow,
-                                        ReconstDtiFlow)
-
-    DKIModel = dipy_to_nipype_interface("DKIModel", ReconstDkiFlow)
-    MapmriModel = dipy_to_nipype_interface("MapmriModel", ReconstMAPMRIFlow)
-    DTIModel = dipy_to_nipype_interface("DTIModel", ReconstDtiFlow)
-    CSAModel = dipy_to_nipype_interface("CSAModel", ReconstCSAFlow)
-    CSDModel = dipy_to_nipype_interface("CSDModel", ReconstCSDFlow)
+    from dipy.workflows import reconst
+
+    l_wkflw = get_dipy_workflows(reconst)
+    for name, obj in l_wkflw:
+        new_name = name.replace('Flow', '')
+        globals()[new_name] = dipy_to_nipype_interface(new_name, obj)
+    del l_wkflw
+
 else:
     IFLOGGER.info("We advise you to upgrade DIPY version. This upgrade will"
-                  " activate DKIModel, MapmriModel, DTIModel, CSAModel, CSDModel.")
+                  " open access to more models")
 
 
 class RESTOREInputSpec(DipyBaseInterfaceInputSpec):

nipype/interfaces/dipy/registration.py

@@ -1,18 +1,21 @@
 
 from distutils.version import LooseVersion
 from ... import logging
-from .base import HAVE_DIPY, dipy_version, dipy_to_nipype_interface
+from .base import (HAVE_DIPY, dipy_version, dipy_to_nipype_interface,
+                   get_dipy_workflows)
 
 IFLOGGER = logging.getLogger('nipype.interface')
 
-if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.15'):
 
-    from dipy.workflows.align import ResliceFlow, SlrWithQbxFlow
+if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.15'):
+    from dipy.workflows import align
 
-    Reslice = dipy_to_nipype_interface("Reslice", ResliceFlow)
-    StreamlineRegistration = dipy_to_nipype_interface("StreamlineRegistration",
-                                                      SlrWithQbxFlow)
+    l_wkflw = get_dipy_workflows(align)
+    for name, obj in l_wkflw:
+        new_name = name.replace('Flow', '')
+        globals()[new_name] = dipy_to_nipype_interface(new_name, obj)
+    del l_wkflw
 
 else:
     IFLOGGER.info("We advise you to upgrade DIPY version. This upgrade will"
-                  " activate Reslice, StreamlineRegistration.")
+                  " open access to more function")

nipype/interfaces/dipy/stats.py

@@ -0,0 +1,20 @@
+
+from distutils.version import LooseVersion
+from ... import logging
+from .base import (HAVE_DIPY, dipy_version, dipy_to_nipype_interface,
+                   get_dipy_workflows)
+
+IFLOGGER = logging.getLogger('nipype.interface')
+
+if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.16'):
+    from dipy.workflows import stats
+
+    l_wkflw = get_dipy_workflows(stats)
+    for name, obj in l_wkflw:
+        new_name = name.replace('Flow', '')
+        globals()[new_name] = dipy_to_nipype_interface(new_name, obj)
+    del l_wkflw
+
+else:
+    IFLOGGER.info("We advise you to upgrade DIPY version. This upgrade will"
+                  " open access to more function")

nipype/interfaces/dipy/tests/test_base.py

@@ -2,7 +2,8 @@
 from collections import namedtuple
 from ...base import traits, TraitedSpec, BaseInterfaceInputSpec
 from ..base import (convert_to_traits_type, create_interface_specs,
-                    dipy_to_nipype_interface, DipyBaseInterface, no_dipy)
+                    dipy_to_nipype_interface, DipyBaseInterface, no_dipy,
+                    get_dipy_workflows)
 
 
 def test_convert_to_traits_type():
@@ -136,6 +137,16 @@ def run(self, in_files, param1=1, out_dir='', out_ref='out1.txt'):
         new_specs().run()
 
 
+@pytest.mark.skipif(no_dipy(), reason="DIPY is not installed")
+def test_get_dipy_workflows():
+    from dipy.workflows import align
+
+    l_wkflw = get_dipy_workflows(align)
+    for name, obj in l_wkflw:
+        assert name.endswith('Flow')
+        assert issubclass(obj, align.Workflow)
+
+
 if __name__ == "__main__":
     test_convert_to_traits_type()
     test_create_interface_specs()

nipype/interfaces/dipy/tracks.py

@@ -12,28 +12,32 @@
 from ..base import (TraitedSpec, BaseInterfaceInputSpec, File, isdefined,
                     traits)
 from .base import (DipyBaseInterface, HAVE_DIPY, dipy_version,
-                   dipy_to_nipype_interface)
+                   dipy_to_nipype_interface, get_dipy_workflows)
 
 IFLOGGER = logging.getLogger('nipype.interface')
 
 
-if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.15'):
-
-    from dipy.workflows.segment import RecoBundlesFlow, LabelsBundlesFlow
+if HAVE_DIPY and (LooseVersion('0.15') >= LooseVersion(dipy_version()) >= LooseVersion('0.16')):
     try:
         from dipy.workflows.tracking import LocalFiberTrackingPAMFlow as DetTrackFlow
     except ImportError:  # different name in 0.15
         from dipy.workflows.tracking import DetTrackPAMFlow as DetTrackFlow
 
-    RecoBundles = dipy_to_nipype_interface("RecoBundles", RecoBundlesFlow)
-    LabelsBundles = dipy_to_nipype_interface("LabelsBundles",
-                                             LabelsBundlesFlow)
     DeterministicTracking = dipy_to_nipype_interface("DeterministicTracking",
                                                      DetTrackFlow)
 
+if HAVE_DIPY and LooseVersion(dipy_version()) >= LooseVersion('0.15'):
+    from dipy.workflows import segment, tracking
+
+    l_wkflw = get_dipy_workflows(segment) + get_dipy_workflows(tracking)
+    for name, obj in l_wkflw:
+        new_name = name.replace('Flow', '')
+        globals()[new_name] = dipy_to_nipype_interface(new_name, obj)
+    del l_wkflw
+
 else:
     IFLOGGER.info("We advise you to upgrade DIPY version. This upgrade will"
-                  " activate RecoBundles, LabelsBundles, DeterministicTracking.")
+                  " open access to more function")
 
 
 class TrackDensityMapInputSpec(BaseInterfaceInputSpec):