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ENH: interface for whitestripe normalization #3351

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11 changes: 10 additions & 1 deletion docker/generate_dockerfiles.sh
View file Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,7 @@ function generate_base_dockerfile() {
--install afni ants apt-utils bzip2 convert3d file fsl-core \
fsl-mni152-templates fusefat g++ git graphviz make python ruby \
unzip xvfb git-annex-standalone liblzma-dev \
gfortran libreadline-dev libx11-dev libxt-dev libpng-dev libjpeg-dev libcairo2-dev libssl-dev libxml2-dev libudunits2-dev libgdal-dev libbz2-dev libzstd-dev liblzma-dev libpcre2-dev \
--add-to-entrypoint "source /etc/fsl/fsl.sh && source /etc/afni/afni.sh" \
--env ANTSPATH='/usr/lib/ants' \
PATH='/usr/lib/ants:$PATH' \
Expand All @@ -87,7 +88,15 @@ function generate_main_dockerfile() {
--label maintainer="The nipype developers https://github.com/nipy/nipype" \
--env MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1 \
--arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=8 BUILD_DATE VCS_REF VERSION \
--arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=8 R_VERSION_MAJOR=4 R_VERSION_MINOR=1 R_VERSION_PATCH=0 R_CONFIGURE_OPTS=CONFIGURE_OPTIONS="--with-cairo --with-jpeglib --enable-R-shlib --with-blas --with-lapack" BUILD_DATE VCS_REF VERSION \
--run 'curl -LO https://cran.rstudio.com/src/base/R-${R_VERSION_MAJOR}/R-${R_VERSION_MAJOR}.${R_VERSION_MINOR}.${R_VERSION_PATCH}.tar.gz
&& tar zxvf R-${R_VERSION_MAJOR}.${R_VERSION_MINOR}.${R_VERSION_PATCH}.tar.gz
&& rm R-${R_VERSION_MAJOR}.${R_VERSION_MINOR}.${R_VERSION_PATCH}.tar.gz
&& cd R-${R_VERSION_MAJOR}.${R_VERSION_MINOR}.${R_VERSION_PATCH}
&& ./configure ${CONFIGURE_OPTIONS}
&& make && make install && cd .. && rm -rf R-${R_VERSION_MAJOR}.${R_VERSION_MINOR}.${R_VERSION_PATCH}
&& echo '"'"'options(repos = c(CRAN = "https://cran.rstudio.com/"), download.file.method = "libcurl")'"'"' >> /usr/local/lib/R/etc/Rprofile.site
&& Rscript -e "source('"'"'https://neuroconductor.org/neurocLite.R'"'"'); neuro_install(c('"'"'WhiteStripe'"'"'));"' \
--user neuro \
--workdir /home/neuro \
--miniconda create_env=neuro \
Expand Down
17 changes: 11 additions & 6 deletions nipype/interfaces/r.py
View file Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,13 +97,18 @@ def _format_arg(self, name, trait_spec, value):
def _gen_r_command(self, argstr, script_lines):
"""Generates commands and, if rfile specified, writes it to disk."""
if not self.inputs.rfile:
# replace newlines with ;, strip comments
# replace newlines with ;
script = "; ".join(
[
line
for line in script_lines.split("\n")
if not line.strip().startswith("#")
]
list(
filter(
None, # drop empty lines
[
line
for line in script_lines.split("\n")
if not line.strip().startswith("#") # strip comments
],
)
)
)
# escape " and $
script = script.replace('"', '\\"')
Expand Down
39 changes: 39 additions & 0 deletions nipype/interfaces/tests/test_auto_WhiteStripe.py
View file Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,39 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from ..whitestripe import WhiteStripe


def test_WhiteStripe_inputs():
input_map = dict(
img_type=dict(
mandatory=False,
),
in_file=dict(
extensions=None,
mandatory=True,
),
indices=dict(
mandatory=False,
),
out_file=dict(
extensions=None,
usedefault=True,
),
)
inputs = WhiteStripe.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value


def test_WhiteStripe_outputs():
output_map = dict(
out_file=dict(
extensions=None,
),
)
outputs = WhiteStripe.output_spec()

for key, metadata in list(output_map.items()):
for metakey, value in list(metadata.items()):
assert getattr(outputs.traits()[key], metakey) == value
47 changes: 47 additions & 0 deletions nipype/interfaces/tests/test_whitestripe.py
View file Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os

import pytest
import requests
from pathlib import Path
from string import Template
from nipype.interfaces import whitestripe
from nipype.interfaces.r import get_r_command


def test_whitestripe(tmpdir):
cwd = tmpdir.chdir()

Path("T1W.nii.gz").touch()

normalizer = whitestripe.WhiteStripe()
normalizer.inputs.img_type = "T1"
normalizer.inputs.in_file = "T1W.nii.gz"
normalizer.inputs.out_file = "T1W_ws.nii.gz"
tmpfile, script = normalizer._cmdline(normalizer)

expected_script = Template(
# the level of indentation needs to match what's in the whitestripe interface
"""
library(neurobase)
library(WhiteStripe)
in_file = readnii('$in_file')
ind = whitestripe(in_file, "$img_type")$$whitestripe.ind
norm = whitestripe_norm(in_file, ind)
out_file = '$out_file'
writenii(norm, out_file)
"""
).substitute(
{
"in_file": normalizer.inputs.in_file,
"out_file": normalizer.inputs.out_file,
"img_type": normalizer.inputs.img_type,
}
)
assert tmpfile is False
assert script == expected_script
os.remove(normalizer.inputs.in_file)

cwd.chdir()
130 changes: 130 additions & 0 deletions nipype/interfaces/whitestripe.py
View file Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,130 @@
from nipype.interfaces.r import RCommand
from nipype.interfaces.base import (
TraitedSpec,
BaseInterface,
BaseInterfaceInputSpec,
File,
traits,
)
import os
import tempfile
from string import Template


class WhiteStripeInputSpec(BaseInterfaceInputSpec):
in_file = File(exists=True, mandatory=True)
out_file = File("out.nii.gz", usedefault=True)
indices = traits.Array(desc="WhiteStripe indices", mandatory=False)
img_type = traits.String(
desc="WhiteStripe image type", mandatory=False, default="T1"
)


class WhiteStripeOutputSpec(TraitedSpec):
out_file = File(exists=True)


class WhiteStripe(BaseInterface):
input_spec = WhiteStripeInputSpec
output_spec = WhiteStripeOutputSpec

def _run_interface(self, runtime):
tmpfile, script = self._cmdline(runtime)

# rfile = True will create a .R file with your script and executed.
# Alternatively
# rfile can be set to False which will cause the R code to be
# passed
# as a commandline argument to the R executable
# (without creating any files).
# This, however, is less reliable and harder to debug
# (code will be reduced to
# a single line and stripped of any comments).
rcmd = RCommand(script=script, rfile=False)
result = rcmd.run()
if tmpfile:
os.remove(tmpfile)
return result.runtime

def _list_outputs(self):
outputs = self._outputs().get()
outputs["out_file"] = os.path.abspath(self.inputs.out_file)
return outputs

def _cmdline(self, runtime):
d = dict(
in_file=self.inputs.in_file,
out_file=self.inputs.out_file,
img_type=self.inputs.img_type,
)
if len(self.inputs.indices) == 0:
tmpfile = False
script = Template(
"""
library(neurobase)
library(WhiteStripe)
in_file = readnii('$in_file')
ind = whitestripe(in_file, "$img_type")$$whitestripe.ind
norm = whitestripe_norm(in_file, ind)
out_file = '$out_file'
writenii(norm, out_file)
"""
).substitute(d)
else:
# d['indices'] = ",".join(map(str, self.inputs.indices))
tmpfile = tempfile.mkstemp()[1]
self._write_indices(tmpfile, self.inputs.indices)
d["indices"] = tmpfile
script = Template(
"""
library(neurobase)
library(WhiteStripe)
in_file = readnii('$in_file')
# ind = c($indices)
ind = as.vector(read.table("$indices")[[1]], mode='numeric')
norm = whitestripe_norm(in_file, ind)
out_file = '$out_file'
writenii(norm, out_file)
"""
).substitute(d)

return tmpfile, script

def gen_indices(self):
path = tempfile.mkstemp()[1]
d = dict(
in_file=self.inputs.in_file, out_file=path, img_type=self.inputs.img_type
)
script = Template(
"""
library(neurobase)
library(WhiteStripe)
in_file = readnii('$in_file')
t1_ind = whitestripe(in_file, "$img_type")$$whitestripe.ind
write.table(t1_ind, file = "$out_file", row.names = F, col.names = F)
"""
).substitute(d)
RCommand(script=script, rfile=False).run()
ret = self._read_indices(path)
os.remove(path)
return ret

def _read_indices(self, fn):
with open(fn) as f:
# read lines as ints
return list(map(int, f))

def _write_indices(self, fn, indices):
with open(fn, "w") as f:
for idx in indices:
f.write("{}\n".format(idx))


if __name__ == "__main__":
w = WhiteStripe()
w.inputs.img_type = "T1"
w.inputs.in_file = "T1W.nii.gz"
# w.inputs.indices = [1,2,3]
w.inputs.indices = w.gen_indices()
w.inputs.out_file = "T1W_ws.nii.gz"
w.run()

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