Merge branch 'roi'

bin/qipipe

@@ -63,6 +63,8 @@ def _parse_arguments():
     # The actions.
     parser.add_argument('--stage', dest='actions', action='append_const',
                         const='stage', help='stage the input DICOM files')
+    parser.add_argument('--roi', dest='actions', action='append_const',
+                        const='roi', help='generate the ROI mask files')
     parser.add_argument('--register', dest='actions', action='append_const',
                         const='register', help='register the scans')
     parser.add_argument('--model', dest='actions', action='append_const',
@@ -115,10 +117,9 @@ def _parse_arguments():
                         help='the XNAT modeling resource name',
                         metavar='RESOURCE')
 
-    # The input subject directories or XNAT labels to process.
+    # The input directories or XNAT labels to process.
     parser.add_argument('input', nargs='+',
-                        help='the AIRC DICOM subject directory to stage'
-                             ' or XNAT session label to process')
+                        help='the directory or XNAT session label to process')
 
     args = vars(parser.parse_args())
     nonempty_args = dict((k, v) for k, v in args.iteritems() if v != None)

conf/roi.cfg

@@ -0,0 +1,3 @@
+[SGE]
+# The Sun Grid Engine parameters.
+plugin_args = {'qsub_args': '-l h_rt=0:30:00,mf=4G'}

qipipe/interfaces/__init__.py

@@ -13,6 +13,7 @@
 
 from .compress import Compress
 from .copy import Copy
+from .convert_bolero_mask import ConvertBoleroMask
 from .fix_dicom import FixDicom
 from .gate import Gate
 from .group_dicom import GroupDicom
@@ -26,4 +27,5 @@
 from .xnat_download import XNATDownload
 from .xnat_upload import XNATUpload
 from .xnat_find import XNATFind
+# TODO - enable QuIP update
 #from .update_qiprofile import UpdateQIProfile

qipipe/interfaces/convert_bolero_mask.py

@@ -0,0 +1,53 @@
+"""
+This module wraps the proprietary OHSU AIRC ``bolero_mask_conv``
+utility. ``bolero_mask_conv`` converts a proprietary OHSU format
+mask file into a NiFTI mask file.
+"""
+import os
+from os import path
+from glob import glob
+import traits.api as traits
+from nipype.interfaces.base import (TraitedSpec, CommandLine,
+                                    CommandLineInputSpec)
+from nipype.interfaces.traits_extension import Undefined
+
+
+class ConvertBoleroMaskInputSpec(CommandLineInputSpec):
+    time_series = traits.File(desc='Input 4D DCE series NiFTI file',
+                              mandatory=True, exists=True, position=1,
+                              argstr='%s')
+    slice_index = traits.Int(desc='One-based slice index', mandatory=True,
+                             position=2, argstr='%d')
+    in_file = traits.Int(desc='BOLERO .bqf mask file', mandatory=True,
+                         position=3, argstr='%d')
+    out_base = traits.Str(desc='Output file base name without extension',
+                          argstr='-o %s')
+
+
+class ConvertBoleroMaskOutputSpec(TraitedSpec):
+    out_file = traits.File(desc='NiFTI mask file', exists=True)
+
+
+class ConvertBoleroMask(CommandLine):
+    """
+    Interface to the proprietary OHSU AIRC ``bolero_mask_conv`` utility.
+    """
+
+    _cmd = 'bolero_mask_conv'
+    input_spec = ConvertBoleroMaskInputSpec
+    output_spec = ConvertBoleroMaskOutputSpec
+
+    def __init__(self, **inputs):
+        super(ConvertBoleroMask, self).__init__(**inputs)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+
+        # The default output base name is slice_<slice>_lesion.
+        out_base = self.inputs.out_base or "slice_%d_lesion" % self.inputs.slice_index
+        # The output is compressed.
+        out_file = out_base + '.nii.gz'
+        # Expand the output path.
+        outputs['out_file'] = os.path.abspath(out_file)
+
+        return outputs