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chrisgorgochrisgorgo
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Merge pull request #958 from satra/fix/mipav
Fix/mipav
2 parents 5dbb5eb + 5519045 commit 7de9363

23 files changed

+1240
-24
lines changed

‎examples/smri_cbs_skullstripping.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
import nipype.interfaces.fsl as fsl
66
import nipype.interfaces.camino2trackvis as cam2trk
77
import nipype.algorithms.misc as misc
8-
import os
8+
import os
99
from nipype.interfaces.mipav.developer import JistIntensityMp2rageMasking, MedicAlgorithmSPECTRE2010
1010

1111
wf = pe.Workflow("skullstripping")

‎nipype/interfaces/base.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -994,13 +994,13 @@ def run(self, **inputs):
994994
raise Exception('Error: Xvfb did not start')
995995
old_displaynum = os.environ['DISPLAY']
996996
runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
997-
997+
998998
runtime = self._run_interface(runtime)
999-
999+
10001000
if self._redirect_x:
10011001
xvfb_proc.kill()
10021002
xvfb_proc.wait()
1003-
1003+
10041004
outputs = self.aggregate_outputs(runtime)
10051005
runtime.endTime = dt.isoformat(dt.utcnow())
10061006
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)

‎nipype/interfaces/mipav/generate_classes.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@
1515
'de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping',
1616
'de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter',
1717
'de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation']
18-
18+
1919
modules_from_chris = ['edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010',
2020
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient',
2121
'edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator',
@@ -24,14 +24,14 @@
2424
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask',
2525
#'de.mpg.cbs.jist.cortex.JistCortexFullCRUISE', # waiting for http://www.nitrc.org/tracker/index.php?func=detail&aid=7236&group_id=228&atid=942 to be fixed
2626
'de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation']
27-
27+
2828
modules_from_julia = ['de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking',
2929
'edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010']
30-
30+
3131
modules_from_leonie = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads']
32-
32+
3333
modules_from_yasinyazici = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3']
34-
34+
3535
modules_list = list(set(modules_list).union(modules_from_chris).union(modules_from_leonie).union(modules_from_julia).union(modules_from_yasinyazici).union(modules_list))
3636

3737
generate_all_classes(modules_list=modules_list,launcher=["java edu.jhu.ece.iacl.jist.cli.run" ], redirect_x=True, mipav_hacks=True)

‎nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py

Lines changed: 88 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,88 @@
1+
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2+
from nipype.testing import assert_equal
3+
from nipype.interfaces.mipav.developer import JistBrainMgdmSegmentation
4+
5+
def test_JistBrainMgdmSegmentation_inputs():
6+
input_map = dict(args=dict(argstr='%s',
7+
),
8+
environ=dict(nohash=True,
9+
usedefault=True,
10+
),
11+
ignore_exception=dict(nohash=True,
12+
usedefault=True,
13+
),
14+
inAdjust=dict(argstr='--inAdjust %s',
15+
),
16+
inAtlas=dict(argstr='--inAtlas %s',
17+
),
18+
inCompute=dict(argstr='--inCompute %s',
19+
),
20+
inCurvature=dict(argstr='--inCurvature %f',
21+
),
22+
inData=dict(argstr='--inData %f',
23+
),
24+
inFLAIR=dict(argstr='--inFLAIR %s',
25+
),
26+
inMP2RAGE=dict(argstr='--inMP2RAGE %s',
27+
),
28+
inMP2RAGE2=dict(argstr='--inMP2RAGE2 %s',
29+
),
30+
inMPRAGE=dict(argstr='--inMPRAGE %s',
31+
),
32+
inMax=dict(argstr='--inMax %d',
33+
),
34+
inMin=dict(argstr='--inMin %f',
35+
),
36+
inOutput=dict(argstr='--inOutput %s',
37+
),
38+
inPV=dict(argstr='--inPV %s',
39+
),
40+
inPosterior=dict(argstr='--inPosterior %f',
41+
),
42+
inSteps=dict(argstr='--inSteps %d',
43+
),
44+
inTopology=dict(argstr='--inTopology %s',
45+
),
46+
null=dict(argstr='--null %s',
47+
),
48+
outLevelset=dict(argstr='--outLevelset %s',
49+
hash_files=False,
50+
),
51+
outPosterior2=dict(argstr='--outPosterior2 %s',
52+
hash_files=False,
53+
),
54+
outPosterior3=dict(argstr='--outPosterior3 %s',
55+
hash_files=False,
56+
),
57+
outSegmented=dict(argstr='--outSegmented %s',
58+
hash_files=False,
59+
),
60+
terminal_output=dict(mandatory=True,
61+
nohash=True,
62+
),
63+
xDefaultMem=dict(argstr='-xDefaultMem %d',
64+
),
65+
xMaxProcess=dict(argstr='-xMaxProcess %d',
66+
usedefault=True,
67+
),
68+
xPrefExt=dict(argstr='--xPrefExt %s',
69+
),
70+
)
71+
inputs = JistBrainMgdmSegmentation.input_spec()
72+
73+
for key, metadata in input_map.items():
74+
for metakey, value in metadata.items():
75+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
76+
77+
def test_JistBrainMgdmSegmentation_outputs():
78+
output_map = dict(outLevelset=dict(),
79+
outPosterior2=dict(),
80+
outPosterior3=dict(),
81+
outSegmented=dict(),
82+
)
83+
outputs = JistBrainMgdmSegmentation.output_spec()
84+
85+
for key, metadata in output_map.items():
86+
for metakey, value in metadata.items():
87+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
88+

‎nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py

Lines changed: 52 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,52 @@
1+
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2+
from nipype.testing import assert_equal
3+
from nipype.interfaces.mipav.developer import JistBrainMp2rageDuraEstimation
4+
5+
def test_JistBrainMp2rageDuraEstimation_inputs():
6+
input_map = dict(args=dict(argstr='%s',
7+
),
8+
environ=dict(nohash=True,
9+
usedefault=True,
10+
),
11+
ignore_exception=dict(nohash=True,
12+
usedefault=True,
13+
),
14+
inDistance=dict(argstr='--inDistance %f',
15+
),
16+
inSecond=dict(argstr='--inSecond %s',
17+
),
18+
inSkull=dict(argstr='--inSkull %s',
19+
),
20+
inoutput=dict(argstr='--inoutput %s',
21+
),
22+
null=dict(argstr='--null %s',
23+
),
24+
outDura=dict(argstr='--outDura %s',
25+
hash_files=False,
26+
),
27+
terminal_output=dict(mandatory=True,
28+
nohash=True,
29+
),
30+
xDefaultMem=dict(argstr='-xDefaultMem %d',
31+
),
32+
xMaxProcess=dict(argstr='-xMaxProcess %d',
33+
usedefault=True,
34+
),
35+
xPrefExt=dict(argstr='--xPrefExt %s',
36+
),
37+
)
38+
inputs = JistBrainMp2rageDuraEstimation.input_spec()
39+
40+
for key, metadata in input_map.items():
41+
for metakey, value in metadata.items():
42+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
43+
44+
def test_JistBrainMp2rageDuraEstimation_outputs():
45+
output_map = dict(outDura=dict(),
46+
)
47+
outputs = JistBrainMp2rageDuraEstimation.output_spec()
48+
49+
for key, metadata in output_map.items():
50+
for metakey, value in metadata.items():
51+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
52+

‎nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py

Lines changed: 66 additions & 0 deletions
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@@ -0,0 +1,66 @@
1+
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2+
from nipype.testing import assert_equal
3+
from nipype.interfaces.mipav.developer import JistBrainMp2rageSkullStripping
4+
5+
def test_JistBrainMp2rageSkullStripping_inputs():
6+
input_map = dict(args=dict(argstr='%s',
7+
),
8+
environ=dict(nohash=True,
9+
usedefault=True,
10+
),
11+
ignore_exception=dict(nohash=True,
12+
usedefault=True,
13+
),
14+
inFilter=dict(argstr='--inFilter %s',
15+
),
16+
inSecond=dict(argstr='--inSecond %s',
17+
),
18+
inSkip=dict(argstr='--inSkip %s',
19+
),
20+
inT1=dict(argstr='--inT1 %s',
21+
),
22+
inT1weighted=dict(argstr='--inT1weighted %s',
23+
),
24+
null=dict(argstr='--null %s',
25+
),
26+
outBrain=dict(argstr='--outBrain %s',
27+
hash_files=False,
28+
),
29+
outMasked=dict(argstr='--outMasked %s',
30+
hash_files=False,
31+
),
32+
outMasked2=dict(argstr='--outMasked2 %s',
33+
hash_files=False,
34+
),
35+
outMasked3=dict(argstr='--outMasked3 %s',
36+
hash_files=False,
37+
),
38+
terminal_output=dict(mandatory=True,
39+
nohash=True,
40+
),
41+
xDefaultMem=dict(argstr='-xDefaultMem %d',
42+
),
43+
xMaxProcess=dict(argstr='-xMaxProcess %d',
44+
usedefault=True,
45+
),
46+
xPrefExt=dict(argstr='--xPrefExt %s',
47+
),
48+
)
49+
inputs = JistBrainMp2rageSkullStripping.input_spec()
50+
51+
for key, metadata in input_map.items():
52+
for metakey, value in metadata.items():
53+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
54+
55+
def test_JistBrainMp2rageSkullStripping_outputs():
56+
output_map = dict(outBrain=dict(),
57+
outMasked=dict(),
58+
outMasked2=dict(),
59+
outMasked3=dict(),
60+
)
61+
outputs = JistBrainMp2rageSkullStripping.output_spec()
62+
63+
for key, metadata in output_map.items():
64+
for metakey, value in metadata.items():
65+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
66+

‎nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py

Lines changed: 50 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,50 @@
1+
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2+
from nipype.testing import assert_equal
3+
from nipype.interfaces.mipav.developer import JistBrainPartialVolumeFilter
4+
5+
def test_JistBrainPartialVolumeFilter_inputs():
6+
input_map = dict(args=dict(argstr='%s',
7+
),
8+
environ=dict(nohash=True,
9+
usedefault=True,
10+
),
11+
ignore_exception=dict(nohash=True,
12+
usedefault=True,
13+
),
14+
inInput=dict(argstr='--inInput %s',
15+
),
16+
inPV=dict(argstr='--inPV %s',
17+
),
18+
inoutput=dict(argstr='--inoutput %s',
19+
),
20+
null=dict(argstr='--null %s',
21+
),
22+
outPartial=dict(argstr='--outPartial %s',
23+
hash_files=False,
24+
),
25+
terminal_output=dict(mandatory=True,
26+
nohash=True,
27+
),
28+
xDefaultMem=dict(argstr='-xDefaultMem %d',
29+
),
30+
xMaxProcess=dict(argstr='-xMaxProcess %d',
31+
usedefault=True,
32+
),
33+
xPrefExt=dict(argstr='--xPrefExt %s',
34+
),
35+
)
36+
inputs = JistBrainPartialVolumeFilter.input_spec()
37+
38+
for key, metadata in input_map.items():
39+
for metakey, value in metadata.items():
40+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
41+
42+
def test_JistBrainPartialVolumeFilter_outputs():
43+
output_map = dict(outPartial=dict(),
44+
)
45+
outputs = JistBrainPartialVolumeFilter.output_spec()
46+
47+
for key, metadata in output_map.items():
48+
for metakey, value in metadata.items():
49+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
50+

‎nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py

Lines changed: 62 additions & 0 deletions
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@@ -0,0 +1,62 @@
1+
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2+
from nipype.testing import assert_equal
3+
from nipype.interfaces.mipav.developer import JistCortexSurfaceMeshInflation
4+
5+
def test_JistCortexSurfaceMeshInflation_inputs():
6+
input_map = dict(args=dict(argstr='%s',
7+
),
8+
environ=dict(nohash=True,
9+
usedefault=True,
10+
),
11+
ignore_exception=dict(nohash=True,
12+
usedefault=True,
13+
),
14+
inLevelset=dict(argstr='--inLevelset %s',
15+
),
16+
inLorentzian=dict(argstr='--inLorentzian %s',
17+
),
18+
inMax=dict(argstr='--inMax %d',
19+
),
20+
inMean=dict(argstr='--inMean %f',
21+
),
22+
inSOR=dict(argstr='--inSOR %f',
23+
),
24+
inStep=dict(argstr='--inStep %d',
25+
),
26+
inTopology=dict(argstr='--inTopology %s',
27+
),
28+
null=dict(argstr='--null %s',
29+
),
30+
outInflated=dict(argstr='--outInflated %s',
31+
hash_files=False,
32+
),
33+
outOriginal=dict(argstr='--outOriginal %s',
34+
hash_files=False,
35+
),
36+
terminal_output=dict(mandatory=True,
37+
nohash=True,
38+
),
39+
xDefaultMem=dict(argstr='-xDefaultMem %d',
40+
),
41+
xMaxProcess=dict(argstr='-xMaxProcess %d',
42+
usedefault=True,
43+
),
44+
xPrefExt=dict(argstr='--xPrefExt %s',
45+
),
46+
)
47+
inputs = JistCortexSurfaceMeshInflation.input_spec()
48+
49+
for key, metadata in input_map.items():
50+
for metakey, value in metadata.items():
51+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
52+
53+
def test_JistCortexSurfaceMeshInflation_outputs():
54+
output_map = dict(outInflated=dict(),
55+
outOriginal=dict(),
56+
)
57+
outputs = JistCortexSurfaceMeshInflation.output_spec()
58+
59+
for key, metadata in output_map.items():
60+
for metakey, value in metadata.items():
61+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
62+

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