Merge pull request #9 from djarecka/oesteban-enh/activations-count-map

Oesteban enh/activations count map

Author: oesteban

.circleci/config.yml

@@ -36,9 +36,8 @@ _get_base_image: &get_base_image
       echo "Pulling base image ..."
       docker pull nipype/nipype:base
     elif [ "$GET_BASE" == "BUILD" ]; then
-      e=1 && for i in {1..5}; do
-        docker build -t nipype/nipype:base - < docker/Dockerfile.base  && e=0 && break || sleep 15
-      done && [ "$e" -eq "0" ]
+      tools/retry_cmd.sh -n 5 -s 15 \
+        docker build -t nipype/nipype:base - < docker/Dockerfile.base
     else
       echo "Error: method to get base image not understood"
       exit 1
@@ -48,22 +47,20 @@ _build_main_image_py36: &build_main_image_py36
   name: Build main image (py36)
   no_output_timeout: 60m
   command: |
-    e=1 && for i in {1..5}; do
+    tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:latest \
         --tag nipype/nipype:py36 \
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}" /home/circleci/nipype \
-      && e=0 && break || sleep 15
-    done && [ "$e" -eq "0" ]
 
 _build_main_image_py27: &build_main_image_py27
   name: Build main image (py27)
   no_output_timeout: 60m
   command: |
-    e=1 && for i in {1..5}; do
+    tools/retry_cmd.sh -n 5 -s 15 \
       docker build \
         --rm=false \
         --tag nipype/nipype:py27 \
@@ -72,8 +69,6 @@ _build_main_image_py27: &build_main_image_py27
         --build-arg BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" \
         --build-arg VCS_REF="$(git rev-parse --short HEAD)" \
         --build-arg VERSION="${CIRCLE_TAG}-py27" /home/circleci/nipype \
-      && e=0 && break || sleep 15
-    done && [ "$e" -eq "0" ]
 
 _download_test_data: &_download_test_data
   name: Download test data

nipype/algorithms/tests/test_stats.py

@@ -5,6 +5,7 @@
 import numpy as np
 import nibabel as nb
 from nipype.algorithms.stats import ActivationCount
+import pytest
 
 
 def test_ActivationCount(tmpdir):
@@ -20,3 +21,23 @@ def test_ActivationCount(tmpdir):
     pos = nb.load(res.outputs.acm_pos)
     neg = nb.load(res.outputs.acm_neg)
     assert np.allclose(diff.get_data(), pos.get_data() - neg.get_data())
+
+
+@pytest.mark.parametrize("threshold, above_thresh", [
+        (1, 15.865), # above one standard deviation (one side)
+        (2, 2.275),  # above two standard deviations (one side)
+        (3, 0.135)   # above three standard deviations (one side)
+        ])
+def test_ActivationCount_normaldistr(tmpdir, threshold, above_thresh):
+    tmpdir.chdir()
+    in_files = ['{:d}.nii'.format(i) for i in range(3)]
+    for fname in in_files:
+        nb.Nifti1Image(np.random.normal(size=(100, 100, 100)),
+                       np.eye(4)).to_filename(fname)
+
+    acm = ActivationCount(in_files=in_files, threshold=threshold)
+    res = acm.run()
+    pos = nb.load(res.outputs.acm_pos)
+    neg = nb.load(res.outputs.acm_neg)
+    assert np.isclose(pos.get_data().mean(), above_thresh*1.e-2, rtol=0.1, atol=1.e-4)
+    assert np.isclose(neg.get_data().mean(), above_thresh*1.e-2, rtol=0.1, atol=1.e-4)

nipype/interfaces/afni/tests/test_auto_CatMatvec.py

@@ -38,7 +38,10 @@ def test_CatMatvec_inputs():
         ),
         out_file=dict(
             argstr=' > %s',
+            keep_extension=False,
             mandatory=True,
+            name_source='in_file',
+            name_template='%s_cat.aff12.1D',
             position=-1,
         ),
         outputtype=dict(),

nipype/interfaces/afni/utils.py

@@ -564,8 +564,11 @@ class CatMatvecInputSpec(AFNICommandInputSpec):
         argstr="%s",
         position=-2)
     out_file = File(
-        desc="File to write concattenated matvecs to",
         argstr=" > %s",
+        name_template='%s_cat.aff12.1D',
+        name_source='in_file',
+        keep_extension=False,
+        desc="File to write concattenated matvecs to",
         position=-1,
         mandatory=True)
     matrix = traits.Bool(

nipype/interfaces/fsl/tests/test_auto_ImageMaths.py

@@ -24,19 +24,20 @@ def test_ImageMaths_inputs():
             argstr='%s',
             position=3,
         ),
+        mask_file=dict(argstr='-mas %s', ),
         op_string=dict(
             argstr='%s',
             position=2,
         ),
         out_data_type=dict(
             argstr='-odt %s',
-            position=5,
+            position=-1,
         ),
         out_file=dict(
             argstr='%s',
             genfile=True,
             hash_files=False,
-            position=4,
+            position=-2,
         ),
         output_type=dict(),
         suffix=dict(),

nipype/interfaces/fsl/utils.py

@@ -500,7 +500,9 @@ def _list_outputs(self):
 class ImageMathsInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr="%s", mandatory=True, position=1)
     in_file2 = File(exists=True, argstr="%s", position=3)
-    out_file = File(argstr="%s", position=4, genfile=True, hash_files=False)
+    mask_file = File(exists=True, argstr='-mas %s',
+                     desc='use (following image>0) to mask current image')
+    out_file = File(argstr="%s", position=-2, genfile=True, hash_files=False)
     op_string = traits.Str(
         argstr="%s",
         position=2,
@@ -514,7 +516,7 @@ class ImageMathsInputSpec(FSLCommandInputSpec):
         'double',
         'input',
         argstr="-odt %s",
-        position=5,
+        position=-1,
         desc=("output datatype, one of (char, short, "
               "int, float, double, input)"))
 

nipype/pipeline/engine/nodes.py

@@ -27,7 +27,7 @@
 from ...utils.filemanip import (md5, FileNotFoundError, filename_to_list,
                                 list_to_filename, copyfiles, fnames_presuffix,
                                 loadpkl, split_filename, load_json, makedirs,
-                                emptydirs, savepkl, to_str)
+                                emptydirs, savepkl, to_str, indirectory)
 
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
                                 DynamicTraitedSpec, Bunch, InterfaceResult,
@@ -627,7 +627,8 @@ def _run_command(self, execute, copyfiles=True):
             self._interface.__class__.__name__)
         if issubclass(self._interface.__class__, CommandLine):
             try:
-                cmd = self._interface.cmdline
+                with indirectory(outdir):
+                    cmd = self._interface.cmdline
             except Exception as msg:
                 result.runtime.stderr = '{}\n\n{}'.format(
                     getattr(result.runtime, 'stderr', ''), msg)

nipype/utils/filemanip.py

@@ -18,6 +18,7 @@
 import os.path as op
 import re
 import shutil
+import contextlib
 import posixpath
 import simplejson as json
 import numpy as np
@@ -916,3 +917,13 @@ def relpath(path, start=None):
     if not rel_list:
         return os.curdir
     return op.join(*rel_list)
+
+
+@contextlib.contextmanager
+def indirectory(path):
+    cwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(cwd)

nipype/utils/tests/test_filemanip.py

@@ -14,7 +14,7 @@
     save_json, load_json, fname_presuffix, fnames_presuffix, hash_rename,
     check_forhash, _parse_mount_table, _cifs_table, on_cifs, copyfile,
     copyfiles, filename_to_list, list_to_filename, check_depends,
-    split_filename, get_related_files)
+    split_filename, get_related_files, indirectory)
 
 
 def _ignore_atime(stat):
@@ -490,3 +490,34 @@ def test_cifs_check():
 
     _cifs_table[:] = []
     _cifs_table.extend(orig_table)
+
+
+def test_indirectory(tmpdir):
+    tmpdir.chdir()
+
+    os.makedirs('subdir1/subdir2')
+    sd1 = os.path.abspath('subdir1')
+    sd2 = os.path.abspath('subdir1/subdir2')
+
+    assert os.getcwd() == tmpdir.strpath
+    with indirectory('/'):
+        assert os.getcwd() == '/'
+    assert os.getcwd() == tmpdir.strpath
+    with indirectory('subdir1'):
+        assert os.getcwd() == sd1
+        with indirectory('subdir2'):
+            assert os.getcwd() == sd2
+            with indirectory('..'):
+                assert os.getcwd() == sd1
+                with indirectory('/'):
+                    assert os.getcwd() == '/'
+                assert os.getcwd() == sd1
+            assert os.getcwd() == sd2
+        assert os.getcwd() == sd1
+    assert os.getcwd() == tmpdir.strpath
+    try:
+        with indirectory('subdir1'):
+            raise ValueError("Erroring out of context")
+    except ValueError:
+        pass
+    assert os.getcwd() == tmpdir.strpath

tools/retry_cmd.sh

@@ -0,0 +1,36 @@
+#!/bin/sh
+#
+# retry_cmd.sh [-n NLOOPS] [-s SLEEP] CMD
+#
+# Retry command until success or pre-specified number of failures
+#
+# 2018 Chris Markiewicz
+# Released into public domain
+
+NLOOPS=3
+TOSLEEP=5
+
+while true; do
+    case "$1" in
+        -n ) NLOOPS="$2"; shift 2 ;;
+        -s ) TOSLEEP="$2"; shift 2 ;;
+        -- ) shift; break ;;
+        * ) break ;;
+    esac
+done
+
+# Normalize whitespace in command, preserving quotes
+CMD=""
+for ARG; do
+    CMD="$CMD \"$ARG\"";
+done
+
+RET=0
+for i in `seq $NLOOPS`; do
+    sh -c "$CMD"
+    RET="$?"
+    if [ "$RET" -eq 0 ]; then break; fi
+    if [ "$i" -ne "$NLOOPS" ]; then sleep $TOSLEEP; fi
+done
+
+exit $RET