Skip to content

Fix/mipav #958

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Oct 15, 2014
Merged

Fix/mipav #958

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
4e3b2e8
tst: added mipav tests
satra Oct 15, 2014
5519045
sty: mipav commit white space fixes and one test script
satra Oct 15, 2014
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion examples/smri_cbs_skullstripping.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import nipype.interfaces.fsl as fsl
import nipype.interfaces.camino2trackvis as cam2trk
import nipype.algorithms.misc as misc
import os
import os
from nipype.interfaces.mipav.developer import JistIntensityMp2rageMasking, MedicAlgorithmSPECTRE2010

wf = pe.Workflow("skullstripping")
Expand Down
6 changes: 3 additions & 3 deletions nipype/interfaces/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -994,13 +994,13 @@ def run(self, **inputs):
raise Exception('Error: Xvfb did not start')
old_displaynum = os.environ['DISPLAY']
runtime.environ['DISPLAY'] = ':%s' % vdisplay_num

runtime = self._run_interface(runtime)

if self._redirect_x:
xvfb_proc.kill()
xvfb_proc.wait()

outputs = self.aggregate_outputs(runtime)
runtime.endTime = dt.isoformat(dt.utcnow())
timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
Expand Down
10 changes: 5 additions & 5 deletions nipype/interfaces/mipav/generate_classes.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
'de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping',
'de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter',
'de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation']

modules_from_chris = ['edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010',
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient',
'edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator',
Expand All @@ -24,14 +24,14 @@
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask',
#'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
'de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation']

modules_from_julia = ['de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking',
'edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010']

modules_from_leonie = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads']

modules_from_yasinyazici = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3']

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))

generate_all_classes(modules_list=modules_list,launcher=["java edu.jhu.ece.iacl.jist.cli.run" ], redirect_x=True, mipav_hacks=True)
88 changes: 88 additions & 0 deletions nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from nipype.testing import assert_equal
from nipype.interfaces.mipav.developer import JistBrainMgdmSegmentation

def test_JistBrainMgdmSegmentation_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inAdjust=dict(argstr='--inAdjust %s',
),
inAtlas=dict(argstr='--inAtlas %s',
),
inCompute=dict(argstr='--inCompute %s',
),
inCurvature=dict(argstr='--inCurvature %f',
),
inData=dict(argstr='--inData %f',
),
inFLAIR=dict(argstr='--inFLAIR %s',
),
inMP2RAGE=dict(argstr='--inMP2RAGE %s',
),
inMP2RAGE2=dict(argstr='--inMP2RAGE2 %s',
),
inMPRAGE=dict(argstr='--inMPRAGE %s',
),
inMax=dict(argstr='--inMax %d',
),
inMin=dict(argstr='--inMin %f',
),
inOutput=dict(argstr='--inOutput %s',
),
inPV=dict(argstr='--inPV %s',
),
inPosterior=dict(argstr='--inPosterior %f',
),
inSteps=dict(argstr='--inSteps %d',
),
inTopology=dict(argstr='--inTopology %s',
),
null=dict(argstr='--null %s',
),
outLevelset=dict(argstr='--outLevelset %s',
hash_files=False,
),
outPosterior2=dict(argstr='--outPosterior2 %s',
hash_files=False,
),
outPosterior3=dict(argstr='--outPosterior3 %s',
hash_files=False,
),
outSegmented=dict(argstr='--outSegmented %s',
hash_files=False,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d',
),
xMaxProcess=dict(argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s',
),
)
inputs = JistBrainMgdmSegmentation.input_spec()

for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value

def test_JistBrainMgdmSegmentation_outputs():
output_map = dict(outLevelset=dict(),
outPosterior2=dict(),
outPosterior3=dict(),
outSegmented=dict(),
)
outputs = JistBrainMgdmSegmentation.output_spec()

for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value

52 changes: 52 additions & 0 deletions nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from nipype.testing import assert_equal
from nipype.interfaces.mipav.developer import JistBrainMp2rageDuraEstimation

def test_JistBrainMp2rageDuraEstimation_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inDistance=dict(argstr='--inDistance %f',
),
inSecond=dict(argstr='--inSecond %s',
),
inSkull=dict(argstr='--inSkull %s',
),
inoutput=dict(argstr='--inoutput %s',
),
null=dict(argstr='--null %s',
),
outDura=dict(argstr='--outDura %s',
hash_files=False,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d',
),
xMaxProcess=dict(argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s',
),
)
inputs = JistBrainMp2rageDuraEstimation.input_spec()

for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value

def test_JistBrainMp2rageDuraEstimation_outputs():
output_map = dict(outDura=dict(),
)
outputs = JistBrainMp2rageDuraEstimation.output_spec()

for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value

66 changes: 66 additions & 0 deletions nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from nipype.testing import assert_equal
from nipype.interfaces.mipav.developer import JistBrainMp2rageSkullStripping

def test_JistBrainMp2rageSkullStripping_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inFilter=dict(argstr='--inFilter %s',
),
inSecond=dict(argstr='--inSecond %s',
),
inSkip=dict(argstr='--inSkip %s',
),
inT1=dict(argstr='--inT1 %s',
),
inT1weighted=dict(argstr='--inT1weighted %s',
),
null=dict(argstr='--null %s',
),
outBrain=dict(argstr='--outBrain %s',
hash_files=False,
),
outMasked=dict(argstr='--outMasked %s',
hash_files=False,
),
outMasked2=dict(argstr='--outMasked2 %s',
hash_files=False,
),
outMasked3=dict(argstr='--outMasked3 %s',
hash_files=False,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d',
),
xMaxProcess=dict(argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s',
),
)
inputs = JistBrainMp2rageSkullStripping.input_spec()

for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value

def test_JistBrainMp2rageSkullStripping_outputs():
output_map = dict(outBrain=dict(),
outMasked=dict(),
outMasked2=dict(),
outMasked3=dict(),
)
outputs = JistBrainMp2rageSkullStripping.output_spec()

for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value

50 changes: 50 additions & 0 deletions nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from nipype.testing import assert_equal
from nipype.interfaces.mipav.developer import JistBrainPartialVolumeFilter

def test_JistBrainPartialVolumeFilter_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inInput=dict(argstr='--inInput %s',
),
inPV=dict(argstr='--inPV %s',
),
inoutput=dict(argstr='--inoutput %s',
),
null=dict(argstr='--null %s',
),
outPartial=dict(argstr='--outPartial %s',
hash_files=False,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d',
),
xMaxProcess=dict(argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s',
),
)
inputs = JistBrainPartialVolumeFilter.input_spec()

for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value

def test_JistBrainPartialVolumeFilter_outputs():
output_map = dict(outPartial=dict(),
)
outputs = JistBrainPartialVolumeFilter.output_spec()

for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value

62 changes: 62 additions & 0 deletions nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from nipype.testing import assert_equal
from nipype.interfaces.mipav.developer import JistCortexSurfaceMeshInflation

def test_JistCortexSurfaceMeshInflation_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inLevelset=dict(argstr='--inLevelset %s',
),
inLorentzian=dict(argstr='--inLorentzian %s',
),
inMax=dict(argstr='--inMax %d',
),
inMean=dict(argstr='--inMean %f',
),
inSOR=dict(argstr='--inSOR %f',
),
inStep=dict(argstr='--inStep %d',
),
inTopology=dict(argstr='--inTopology %s',
),
null=dict(argstr='--null %s',
),
outInflated=dict(argstr='--outInflated %s',
hash_files=False,
),
outOriginal=dict(argstr='--outOriginal %s',
hash_files=False,
),
terminal_output=dict(mandatory=True,
nohash=True,
),
xDefaultMem=dict(argstr='-xDefaultMem %d',
),
xMaxProcess=dict(argstr='-xMaxProcess %d',
usedefault=True,
),
xPrefExt=dict(argstr='--xPrefExt %s',
),
)
inputs = JistCortexSurfaceMeshInflation.input_spec()

for key, metadata in input_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(inputs.traits()[key], metakey), value

def test_JistCortexSurfaceMeshInflation_outputs():
output_map = dict(outInflated=dict(),
outOriginal=dict(),
)
outputs = JistCortexSurfaceMeshInflation.output_spec()

for key, metadata in output_map.items():
for metakey, value in metadata.items():
yield assert_equal, getattr(outputs.traits()[key], metakey), value

Loading