Commit 2f9aa4b

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fix eddy command and multithreading

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+17

-7

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nipype/interfaces/fsl
- epi.py

1 file changed

+17

-7

lines changed

`‎nipype/interfaces/fsl/epi.py`

Lines changed: 17 additions & 7 deletions

Original file line number	Diff line number	Diff line change
`@@ -5,11 +5,13 @@`
`5`	`5`	`was written to work with FSL version 5.0.4.`
`6`	`6`	`"""`
`7`	`7`	`import os`
	`8`	`+from shutil import which`
`8`	`9`	`import numpy as np`
`9`	`10`	`import nibabel as nb`
`10`	`11`	`import warnings`
`11`	`12`
`12`	`13`	`from ...utils.filemanip import split_filename, fname_presuffix`
	`14`	`+from ...utils.gpu_count import gpu_count`
`13`	`15`
`14`	`16`	`from ..base import traits, TraitedSpec, InputMultiPath, File, isdefined`
`15`	`17`	`from .base import FSLCommand, FSLCommandInputSpec, Info`
`@@ -793,9 +795,12 @@ class EddyInputSpec(FSLCommandInputSpec):`
`793`	`795`	`requires=["estimate_move_by_susceptibility"],`
`794`	`796`	`min_ver="6.0.1",`
`795`	`797`	`)`
`796`		`-`
`797`	`798`	`num_threads = traits.Int(`
`798`		`- 1, usedefault=True, nohash=True, desc="Number of openmp threads to use"`
	`799`	`+ argstr="--nthr=%d",`
	`800`	`+ default_value=1,`
	`801`	`+ usedefault=True,`
	`802`	`+ nohash=True,`
	`803`	`+ desc="Number of openmp threads to use"`
`799`	`804`	`)`
`800`	`805`	`is_shelled = traits.Bool(`
`801`	`806`	`False,`
`@@ -937,7 +942,7 @@ class Eddy(FSLCommand):`
`937`	`942`
`938`	`943`	`"""`
`939`	`944`
`940`		`- _cmd = "eddy_openmp"`
	`945`	`+ _cmd = "eddy_openmp"ifwhich("eddy_openmp") else"eddy_cpu"`
`941`	`946`	`input_spec = EddyInputSpec`
`942`	`947`	`output_spec = EddyOutputSpec`
`943`	`948`
`@@ -963,17 +968,22 @@ def _num_threads_update(self):`
`963`	`968`	`self.inputs.environ["OMP_NUM_THREADS"] = str(self.inputs.num_threads)`
`964`	`969`
`965`	`970`	`def _use_cuda(self):`
`966`		`- self._cmd = "eddy_cuda" if self.inputs.use_cuda else "eddy_openmp"`
	`971`	`+ if self.inputs.use_cuda and gpu_count()>0:`
	`972`	`+ # eddy_cuda usually link to eddy_cudaX.X but some versions miss the symlink`
	`973`	`+ # anyway in newer fsl versions eddy automatically use cuda on cuda-capable systems`
	`974`	`+ self._cmd = "eddy_cuda" if which("eddy_cuda") else "eddy"`
	`975`	`+ else:`
	`976`	`+ # older fsl versions has cuda_openmp, newer versions has eddy_cpu`
	`977`	`+ _cmd = "eddy_openmp" if which("eddy_openmp") else "eddy_cpu"`
`967`	`978`
`968`	`979`	`def _run_interface(self, runtime):`
`969`		`- # If 'eddy_openmp' is missing, use 'eddy'`
	`980`	`+ # If selected command is missing, use generic 'eddy'`
`970`	`981`	`FSLDIR = os.getenv("FSLDIR", "")`
`971`	`982`	`cmd = self._cmd`
`972`	`983`	`if all(`
`973`	`984`	`(`
`974`	`985`	`FSLDIR != "",`
`975`		`- cmd == "eddy_openmp",`
`976`		`- not os.path.exists(os.path.join(FSLDIR, "bin", cmd)),`
	`986`	`+ not os.path.exists(os.path.join(FSLDIR, "bin", self._cmd)),`
`977`	`987`	`)`
`978`	`988`	`):`
`979`	`989`	`self._cmd = "eddy"`

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`‎nipype/interfaces/fsl/epi.py`

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