fix: resolved conflict

Author: satra

nipype/algorithms/misc.py

@@ -1165,7 +1165,172 @@ def normalize_tpms(in_files, in_mask=None, out_files=[]):
     return out_files
 
 
-# Deprecated interfaces ---------------------------------------------------------
+def split_rois(in_file, mask=None, roishape=None):
+    """
+    Splits an image in ROIs for parallel processing
+    """
+    import nibabel as nb
+    import numpy as np
+    from math import sqrt, ceil
+    import os.path as op
+
+    if roishape is None:
+        roishape = (10, 10, 1)
+
+    im = nb.load(in_file)
+    imshape = im.get_shape()
+    dshape = imshape[:3]
+    nvols = imshape[-1]
+    roisize = roishape[0] * roishape[1] * roishape[2]
+    droishape = (roishape[0], roishape[1], roishape[2], nvols)
+
+    if mask is not None:
+        mask = nb.load(mask).get_data()
+        mask[mask > 0] = 1
+        mask[mask < 1] = 0
+    else:
+        mask = np.ones(dshape)
+
+    mask = mask.reshape(-1).astype(np.uint8)
+    nzels = np.nonzero(mask)
+    els = np.sum(mask)
+    nrois = int(ceil(els/roisize))
+
+    data = im.get_data().reshape((mask.size, -1))
+    data = np.squeeze(data.take(nzels, axis=0))
+    nvols = data.shape[-1]
+
+    roidefname = op.abspath('onesmask.nii.gz')
+    nb.Nifti1Image(np.ones(roishape, dtype=np.uint8), None,
+                   None).to_filename(roidefname)
+
+    out_files = []
+    out_mask = []
+    out_idxs = []
+
+    for i in xrange(nrois):
+        first = i * roisize
+        last = (i+1) * roisize
+        fill = 0
+
+        if last > els:
+            fill = last - els
+            last = els
+
+        droi = data[first:last, ...]
+        iname = op.abspath('roi%010d_idx' % i)
+        out_idxs.append(iname+'.npz')
+        np.savez(iname, (nzels[0][first:last],))
+
+        if fill > 0:
+            droi = np.vstack((droi, np.zeros((fill, nvols), dtype=np.float32)))
+            partialmsk = np.ones((roisize,), dtype=np.uint8)
+            partialmsk[-fill:] = 0
+            partname = op.abspath('partialmask.nii.gz')
+            nb.Nifti1Image(partialmsk.reshape(roishape), None,
+                           None).to_filename(partname)
+            out_mask.append(partname)
+        else:
+            out_mask.append(roidefname)
+
+        fname = op.abspath('roi%010d.nii.gz' % i)
+        nb.Nifti1Image(droi.reshape(droishape),
+                       None, None).to_filename(fname)
+        out_files.append(fname)
+    return out_files, out_mask, out_idxs
+
+
+def merge_rois(in_files, in_idxs, in_ref,
+               dtype=None, out_file=None):
+    """
+    Re-builds an image resulting from a parallelized processing
+    """
+    import nibabel as nb
+    import numpy as np
+    import os.path as op
+    import subprocess as sp
+
+    if out_file is None:
+        out_file = op.abspath('merged.nii.gz')
+
+    if dtype is None:
+        dtype = np.float32
+
+    # if file is compressed, uncompress using os
+    # to avoid memory errors
+    if op.splitext(in_ref)[1] == '.gz':
+        try:
+            iflogger.info('uncompress %i' % in_ref)
+            sp.check_call(['gunzip', in_ref], stdout=sp.PIPE, shell=True)
+            in_ref = op.splitext(in_ref)[0]
+        except:
+            pass
+
+    ref = nb.load(in_ref)
+    aff = ref.get_affine()
+    hdr = ref.get_header().copy()
+    rsh = ref.get_shape()
+    del ref
+    npix = rsh[0] * rsh[1] * rsh[2]
+    fcdata = nb.load(in_files[0]).get_data()
+
+    if fcdata.ndim == 4:
+        ndirs = fcdata.shape[-1]
+    else:
+        ndirs = 1
+    newshape = (rsh[0], rsh[1], rsh[2], ndirs)
+    hdr.set_data_dtype(dtype)
+    hdr.set_xyzt_units('mm', 'sec')
+
+    if ndirs < 300:
+        data = np.zeros((npix, ndirs))
+        for cname, iname in zip(in_files, in_idxs):
+            with np.load(iname) as f:
+                idxs = np.squeeze(f['arr_0'])
+            cdata = nb.load(cname).get_data().reshape(-1, ndirs)
+            nels = len(idxs)
+            idata = (idxs, )
+            try:
+                data[idata, ...] = cdata[0:nels, ...]
+            except:
+                print(data.shape, cdata.shape)
+                raise
+
+        hdr.set_data_shape(newshape)
+
+        nb.Nifti1Image(data.reshape(newshape).astype(dtype),
+                       aff, hdr).to_filename(out_file)
+
+
+    else:
+        hdr.set_data_shape(rsh[:3])
+        nii = []
+        for d in xrange(ndirs):
+            fname = op.abspath('vol%06d.nii' % d)
+            nb.Nifti1Image(np.zeros(rsh[:3]), aff, hdr).to_filename(fname)
+            nii.append(fname)
+
+        for cname, iname in zip(in_files, in_idxs):
+            with np.load(iname) as f:
+                idxs = np.squeeze(f['arr_0'])
+
+            for d, fname in enumerate(nii):
+                data = nb.load(fname).get_data().reshape(-1)
+                cdata = nb.load(cname).get_data().reshape(-1, ndirs)[:, d]
+                nels = len(idxs)
+                idata = (idxs, )
+                data[idata] = cdata[0:nels]
+                nb.Nifti1Image(data.reshape(rsh[:3]), aff, hdr).to_filename(fname)
+
+        imgs = [nb.load(im) for im in nii]
+        allim = nb.concat_images(imgs)
+        allim.to_filename(out_file)
+
+    return out_file
+
+
+# Deprecated interfaces ------------------------------------------------------
+
 class Distance(nam.Distance):
     """Calculates distance between two volumes.
 

nipype/algorithms/tests/test_auto_Overlap.py

@@ -109,7 +109,6 @@ class SVMTestInputSpec(AFNICommandInputSpec):
     #testing options
     model = traits.Str(desc='modname is the basename for the brik containing the SVM model',
                 argstr='-model %s',
-                exists=True,
                 mandatory=True)
     in_file = File(desc='A 3D or 3D+t AFNI brik dataset to be used for testing.',
                 argstr='-testvol %s',

nipype/interfaces/afni/svm.py

@@ -17,7 +17,6 @@ def test_SVMTest_inputs():
     mandatory=True,
     ),
     model=dict(argstr='-model %s',
-    exists=True,
     mandatory=True,
     ),
     multiclass=dict(argstr='-multiclass %s',

nipype/interfaces/afni/tests/test_auto_SVMTest.py

@@ -127,7 +127,7 @@ class Denoise(BaseInterface):
     """
     input_spec = DenoiseInputSpec
     output_spec = DenoiseOutputSpec
-    
+
     def _run_interface(self, runtime):
         out_file = op.abspath(self._gen_outfilename())