Merge branch 'master' of github.com:nipreps/sdcflows into ci/deploy

Author: mgxd

.circleci/config.yml

@@ -6,8 +6,8 @@ docs_deploy: &docs
     - run:
         name: Check whether this is the original repo
         command: |
-          if [[ "$CIRCLE_PROJECT_USERNAME" != "poldracklab" ]]; then
-              echo "Not in poldracklab/sdcflows - skipping docs deploy."
+          if [[ "$CIRCLE_PROJECT_USERNAME" != "nipreps" ]]; then
+              echo "Not in nipreps/sdcflows - skipping docs deploy."
               circleci step halt
           fi
     - add_ssh_keys:
@@ -21,7 +21,7 @@ docs_deploy: &docs
     - run:
         name: Set git settings
         command: |
-          git config user.email "crn.poldracklab@gmail.com"
+          git config user.email "nipreps@gmail.com"
           git config user.name "Documentation Push"
     - attach_workspace:
         at: docs/_build
@@ -60,8 +60,8 @@ jobs:
               apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
               apt update && apt-get install -y --no-install-recommends git-annex-standalone
             fi
-            git config --global user.name 'CRN'
-            git config --global user.email 'crn.poldracklab@gmail.com'
+            git config --global user.name 'NiPreps Bot'
+            git config --global user.email 'nipreps@gmail.com'
 
       - run:
           name: Setup DataLad & TemplateFlow
@@ -171,14 +171,14 @@ jobs:
                 echo "Pulling from local registry"
                 docker tag localhost:5000/ubuntu ubuntu:xenial-20191010
                 docker pull localhost:5000/sdcflows
-                docker tag localhost:5000/sdcflows poldracklab/sdcflows:latest
-                docker tag localhost:5000/sdcflows poldracklab/sdcflows
+                docker tag localhost:5000/sdcflows nipreps/sdcflows:latest
+                docker tag localhost:5000/sdcflows nipreps/sdcflows
             else
                 echo "Pulling from Docker Hub"
                 docker pull ubuntu:xenial-20191010
                 docker tag ubuntu:xenial-20191010 localhost:5000/ubuntu
                 docker push localhost:5000/ubuntu
-                docker pull poldracklab/sdcflows:latest
+                docker pull nipreps/sdcflows:latest
             fi
       - checkout:
           path: /tmp/src/sdcflows
@@ -201,8 +201,8 @@ jobs:
             # Build docker image
             e=1 && for i in {1..5}; do
               docker build --rm \
-                --cache-from=poldracklab/sdcflows \
-                -t poldracklab/sdcflows:latest \
+                --cache-from=nipreps/sdcflows \
+                -t nipreps/sdcflows:latest \
                 --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
                 --build-arg VCS_REF=`git rev-parse --short HEAD` \
                 --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . \
@@ -212,7 +212,7 @@ jobs:
           name: Docker push to local registry
           no_output_timeout: 40m
           command: |
-            docker tag poldracklab/sdcflows:latest localhost:5000/sdcflows
+            docker tag nipreps/sdcflows:latest localhost:5000/sdcflows
             docker push localhost:5000/sdcflows
       - run:
           name: Docker registry garbage collection
@@ -274,7 +274,7 @@ jobs:
                    -v /tmp/work:/work -e TEST_WORK_DIR=/work \
                    -v /tmp/templateflow:/home/sdcflows/.cache/templateflow \
                    -v /tmp/data:/data:ro -v /tmp/src:/src -v /tmp/tests:/out \
-                   -w /work poldracklab/sdcflows:latest \
+                   -w /work nipreps/sdcflows:latest \
                    pytest -v --junit-xml=/out/pytest.xml /src/sdcflows/sdcflows
       - save_cache:
          key: workdir-v2-{{ .Branch }}-{{ .BuildNum }}
@@ -361,16 +361,16 @@ jobs:
           name: Pull images from local registry
           command: |
             docker pull localhost:5000/sdcflows
-            docker tag localhost:5000/sdcflows poldracklab/sdcflows:latest
+            docker tag localhost:5000/sdcflows nipreps/sdcflows:latest
       - run:
           name: Deploy to Docker Hub
           no_output_timeout: 40m
           command: |
             if [[ -n "$DOCKER_PASS" ]]; then
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker push poldracklab/sdcflows:latest
-              docker tag poldracklab/sdcflows poldracklab/sdcflows:$CIRCLE_TAG
-              docker push poldracklab/sdcflows:$CIRCLE_TAG
+              docker push nipreps/sdcflows:latest
+              docker tag nipreps/sdcflows nipreps/sdcflows:$CIRCLE_TAG
+              docker push nipreps/sdcflows:$CIRCLE_TAG
             fi
 
   test_package:

.github/workflows/label.yml

@@ -0,0 +1,19 @@
+# This workflow will triage pull requests and apply a label based on the
+# paths that are modified in the pull request.
+#
+# To use this workflow, you will need to set up a .github/labeler.yml
+# file with configuration.  For more information, see:
+# https://github.com/actions/labeler/blob/master/README.md
+
+name: Labeler
+on: [pull_request]
+
+jobs:
+  label:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/labeler@v2
+      with:
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"

CHANGES.rst

@@ -24,18 +24,18 @@ Bug-fix release.
 A hotfix release preventing downstream dependency collisions on fMRIPrep.
 
 * PIN: niworkflows-1.0.3 `449c2c2
-  <https://github.com/poldracklab/sdcflows/commit/449c2c2b0ab383544f5024de82ca8a80ee70894d>`__
+  <https://github.com/nipreps/sdcflows/commit/449c2c2b0ab383544f5024de82ca8a80ee70894d>`__
 
 1.0.2 (December 18, 2019)
 =========================
 A hotfix release.
 
 * FIX: NiWorkflows' ``IntraModalMerge`` choked with images of shape (x, y, z, 1) (#79, `2e6faa0
-  <https://github.com/poldracklab/sdcflows/commit/2e6faa05ed0f0ec0b4616f33db778a61a1df89d0>`__,
+  <https://github.com/nipreps/sdcflows/commit/2e6faa05ed0f0ec0b4616f33db778a61a1df89d0>`__,
   `717a69e
-  <https://github.com/poldracklab/sdcflows/commit/717a69ef680d556e4d5cde6876d0e60b023924e0>`__,
+  <https://github.com/nipreps/sdcflows/commit/717a69ef680d556e4d5cde6876d0e60b023924e0>`__,
   and `361cd67
-  <https://github.com/poldracklab/sdcflows/commit/361cd678215fca9434baa713fa43f77a2231e632>`__)
+  <https://github.com/nipreps/sdcflows/commit/361cd678215fca9434baa713fa43f77a2231e632>`__)
 
 1.0.1 (December 04, 2019)
 =========================

Dockerfile

@@ -140,6 +140,6 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.description="SDCflows - Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes" \
       org.label-schema.url="http://sdcflows.readthedocs.io" \
       org.label-schema.vcs-ref=$VCS_REF \
-      org.label-schema.vcs-url="https://github.com/poldracklab/sdcflows" \
+      org.label-schema.vcs-url="https://github.com/nipreps/sdcflows" \
       org.label-schema.version=$VERSION \
       org.label-schema.schema-version="1.0"

README.rst

@@ -1,8 +1,8 @@
 SDCflows
 --------
 
-.. image:: https://circleci.com/gh/poldracklab/sdcflows.svg?style=svg
-    :target: https://circleci.com/gh/poldracklab/sdcflows
+.. image:: https://circleci.com/gh/nipreps/sdcflows.svg?style=svg
+    :target: https://circleci.com/gh/nipreps/sdcflows
 
 .. image:: https://img.shields.io/pypi/v/sdcflows.svg
   :target: https://pypi.python.org/pypi/sdcflows/

docs/installation.rst

@@ -8,7 +8,7 @@ Make sure all of *SDCflows*' `External Dependencies`_ are installed.
 These tools must be installed and their binaries available in the
 system's ``$PATH``.
 A relatively interpretable description of how your environment can be set-up
-is found in the `Dockerfile <https://github.com/poldracklab/sdcflows/blob/master/Dockerfile>`_.
+is found in the `Dockerfile <https://github.com/nipreps/sdcflows/blob/master/Dockerfile>`_.
 As an additional installation setting, FreeSurfer_ requires a license file.
 
 On a functional Python 3.5 (or above) environment with ``pip`` installed,

sdcflows/__about__.py

@@ -11,8 +11,8 @@
 __copyright__ = 'Copyright 2019, Center for Reproducible Neuroscience, Stanford University'
 __credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder'
                'of the repository')
-__url__ = 'https://github.com/poldracklab/sdcflows'
+__url__ = 'https://github.com/nipreps/sdcflows'
 
 DOWNLOAD_URL = (
-    'https://github.com/poldracklab/{name}/archive/{ver}.tar.gz'.format(
+    'https://github.com/nipreps/{name}/archive/{ver}.tar.gz'.format(
         name=__packagename__, ver=__version__))

sdcflows/interfaces/fmap.py

@@ -661,42 +661,20 @@ def _delta_te(in_values, te1=None, te2=None):
 
 def au2rads(in_file, newpath=None):
     """Convert the input phase difference map in arbitrary units (a.u.) to rads."""
-    from scipy import stats
     im = nb.load(in_file)
-    data = im.get_fdata(dtype='float32')
+    data = im.get_fdata(caching='unchanged')  # Read as float64 for safety
     hdr = im.header.copy()
 
-    dmin, dmax = data.min(), data.max()
+    # Rescale to [0, 2*pi]
+    data = (data - data.min()) * (2 * np.pi / (data.max() - data.min()))
 
-    # Find the mode ignoring outliers on the far max/min, to allow for junk outside the FoV
-    fudge = 0.05 * (dmax - dmin)
-    mode = stats.mode(data[(data > dmin + fudge) & (data < dmax - fudge)])[0][0]
-
-    # Center data around 0.0
-    data -= mode
-
-    # Provide a less opaque error if we still can't figure it out
-    neg = data < 0
-    pos = data > 0
-    if not (neg.any() and pos.any()):
-        raise ValueError("Could not find an appropriate mode to center phase values around")
-
-    # Scale lower tail
-    data[neg] = - np.pi * data[neg] / data[neg].min()
-
-    # Scale upper tail
-    data[pos] = np.pi * data[pos] / data[pos].max()
-
-    # Offset to 0 - 2pi
-    data += np.pi
-
-    # Clip
-    data = np.clip(data, 0.0, 2 * np.pi)
+    # Round to float32 and clip
+    data = np.clip(np.float32(data), 0.0, 2 * np.pi)
 
     hdr.set_data_dtype(np.float32)
     hdr.set_xyzt_units('mm')
     out_file = fname_presuffix(in_file, suffix='_rads', newpath=newpath)
-    nb.Nifti1Image(data, im.affine, hdr).to_filename(out_file)
+    nb.Nifti1Image(data, None, hdr).to_filename(out_file)
     return out_file
 
 

setup.cfg

@@ -1,9 +1,9 @@
 [metadata]
-url = https://github.com/poldracklab/sdcflows
+url = https://github.com/nipreps/sdcflows
 author = The SDCflows developers
-author_email = [email protected]
+author_email = [email protected]
 maintainer = Oscar Esteban
-maintainer_email = [email protected]
+maintainer_email = [email protected]
 description = Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes.
 long_description = file:README.rst
 long_description_content_type = text/x-rst; charset=UTF-8