Merge pull request #257 from oesteban/fix/templateflow

[RF] Updates for templateflow

Dockerfile

@@ -118,9 +118,10 @@ WORKDIR /root/
 COPY . niworkflows/
 RUN find /root/niworkflows/ -name "test*.py" -exec chmod a-x '{}' \;
 RUN cd niworkflows && \
-    pip install -e .[all] && \
-    python -c 'from niworkflows.data.getters import get_mni_icbm152_linear; get_mni_icbm152_linear()' && \
-    python -c 'from niworkflows.data.getters import get_mni_template_ras; get_mni_template_ras()' && \
-    python -c 'from niworkflows.data.getters import get_ds003_downsampled; get_ds003_downsampled()' && \
-    python -c 'from niworkflows.data.getters import get_ants_oasis_template_ras; get_ants_oasis_template_ras()' && \
-    python -c 'from niworkflows.data.getters import get_mni_icbm152_nlin_asym_09c; get_mni_icbm152_nlin_asym_09c()'
+    pip install -e .[all]
+
+# Pre-install templates and data
+RUN python -c 'from niworkflows.data.getters import get_template; get_template("MNI152Lin")' && \
+    python -c 'from niworkflows.data.getters import get_template; get_template("MNI152NLin2009cAsym")' && \
+    python -c 'from niworkflows.data.getters import get_template; get_template("OASIS")' && \
+    python -c 'from niworkflows.data.getters import get_ds003_downsampled; get_ds003_downsampled()'

niworkflows/anat/ants.py

@@ -13,9 +13,9 @@
 import os
 from collections import OrderedDict
 from multiprocessing import cpu_count
+from pathlib import Path
 from pkg_resources import resource_filename as pkgr_fn
 from packaging.version import parse as parseversion, Version
-from pathlib import Path
 
 # nipype
 from nipype.pipeline import engine as pe
@@ -24,7 +24,7 @@
 from nipype.interfaces.ants import N4BiasFieldCorrection, Atropos, MultiplyImages
 
 # niworkflows
-from ..data import TEMPLATE_MAP, get_dataset
+from ..data import OSF_RESOURCES, TEMPLATE_ALIASES, get_template
 from ..interfaces.ants import (
     ImageMath,
     ResampleImageBySpacing,
@@ -163,16 +163,16 @@ def init_brain_extraction_wf(name='brain_extraction_wf',
     wf = pe.Workflow(name)
 
     template_path = None
-    if in_template in TEMPLATE_MAP:
-        template_path = get_dataset(in_template)
+    if in_template in TEMPLATE_ALIASES or in_template in OSF_RESOURCES:
+        template_path = get_template(in_template)
     else:
-        template_path = in_template
+        template_path = Path(in_template)
 
     mod = ('%sw' % modality[:2].upper()
            if modality.upper().startswith('T') else modality.upper())
 
     # Append template modality
-    potential_targets = list(Path(template_path).glob('*_%s.nii.gz' % mod))
+    potential_targets = list(template_path.glob('*_%s.nii.gz' % mod))
     if not potential_targets:
         raise ValueError(
             'No %s template was found under "%s".' % (mod, template_path))

niworkflows/data/__init__.py

@@ -8,20 +8,8 @@
 from .getters import (
     get_brainweb_1mm_normal,
     get_ds003_downsampled,
-    get_mni_template,
-    get_mni_template_ras,
-    get_ants_oasis_template,
-    get_ants_oasis_template_ras,
-    get_mni_epi,
-    get_mni152_nlin_sym_las,
-    get_mni152_nlin_sym_ras,
-    get_mni_icbm152_linear,
-    get_mni_icbm152_nlin_asym_09c,
-    get_oasis_dkt31_mni152,
-    get_hcp32k_files,
-    get_conte69_mesh,
     get_dataset,
     get_template,
     get_bids_examples,
-    TEMPLATE_MAP,
+    TEMPLATE_ALIASES,
 )

niworkflows/data/getters.py

@@ -12,24 +12,18 @@
 
 OSF_PROJECT_URL = ('https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/')
 OSF_RESOURCES = {
-    'ants_nki_template_ras': ('59cd90f46c613b02b3d79782', 'e5debaee65b8f2c8971577db1327e314'),
-    'ants_oasis_template': ('57f32ae89ad5a101f977eb79', '34d39070b541c416333cc8b6c2fe993c'),
-    'ants_oasis_template_ras': ('584123a29ad5a1020913609d', 'afa21f99c66ae1672320d8aa0408229a'),
     'brainweb': ('57f32b96b83f6901f194c3ca', '384263fbeadc8e2cca92ced98f224c4b'),
+    # Conte69-atlas meshes in 32k resolution
     'conte69': ('5b198ec5ec24e20011b48548', 'bd944e3f9f343e0e51e562b440960529'),
     'ds003_downsampled': ('57f328f6b83f6901ef94cf70', '5a558961c1eb5e5f162696d8afa956e8'),
     'fMRIPrep': ('5bc12155ac011000176bff82', '1aec4d286bd89f4f90316ce2cde63218'),
+    # conversion between fsaverage5/6 and fs_LR(32k)
     'hcpLR32k': ('5b198ec6b796ba000f3e4858', '0ba9adcaa42fa88616a4cea5a1ce0c5a'),
-    'mni_epi': ('57fa09cdb83f6901d93623a0', '9df727e1f742ec55213480434b4c4811'),
-    'mni_icbm152_linear': ('580705eb594d9001ed622649', '72be639e92532def7caad75cb4058e83'),
-    'mni_icbm152_nlin_asym_09c': ('580705089ad5a101f17944a9', '002f9bf24dc5c32de50c03f01fa539ec'),
-    'mni_template': ('57f32ab29ad5a101fb77fd89', 'debfa882b8c301cd6d75dd769e73f727'),
-    'mni_template_RAS': ('57f32a799ad5a101f977eb77', 'a4669f0e7acceae148bb39450b2b21b4'),
-    'mni152_nlin_sym_las': ('57fa7fc89ad5a101e635eeef', '9c4c0cad2a2e99d6799f01abf4107f5a'),
-    'mni152_nlin_sym_ras': ('57fa7fd09ad5a101df35eed0', '65d64ad5a980da86e7d07d95b3ed2ccb'),
+    'MNI152Lin': ('5bc984f8ccdb6b0018abb993', 'a1eb0a121d2aa68fc8a6e75ab148f1db'),
     'MNI152NLin2009cAsym': ('5b0dbce20f461a000db8fa3d', '5d386d7db9c1dec30230623db25e05e1'),
     'NKI': ('5bc3fad82aa873001bc5a553', '092e56fb3700f9f57b8917a0db887db6'),
     'OASIS30ANTs': ('5b0dbce34c28ef0012c7f788', 'f625a0390eb32a7852c7b0d71ac428cd'),
+    # Mindboggle DKT31 label atlas in MNI152NLin2009cAsym space
     'OASISTRT20': ('5b16f17aeca4a80012bd7542', '1b5389bc3a895b2bd5c0d47401107176'),
 }
 
@@ -43,7 +37,8 @@
 }
 
 # Map names of templates to OSF_RESOURCES keys
-TEMPLATE_MAP = {
+TEMPLATE_ALIASES = {
+    'MNI152Lin': 'MNI152Lin',
     'MNI152NLin2009cAsym': 'MNI152NLin2009cAsym',
     'OASIS': 'OASIS30ANTs',
     'NKI': 'NKI',
@@ -54,7 +49,6 @@ def get_dataset(dataset_name, dataset_prefix=None, data_dir=None,
                 url=None, resume=True, verbose=1):
     """Download and load the BIDS-fied brainweb 1mm normal
 
-
     :param str data_dir: path of the data directory. Used to force data storage
         in a non-standard location.
     :param str url: download URL of the dataset. Overwrite the default URL.
@@ -73,15 +67,14 @@ def get_template(template_name, data_dir=None, url=None, resume=True, verbose=1)
         template_name = template_name[4:]
 
     # An aliasing mechanism. Please avoid
-    template_name = TEMPLATE_MAP.get(template_name, template_name)
+    template_name = TEMPLATE_ALIASES.get(template_name, template_name)
     return get_dataset(template_name, dataset_prefix='tpl-', data_dir=data_dir,
                        url=url, resume=resume, verbose=verbose)
 
 
 def get_brainweb_1mm_normal(data_dir=None, url=None, resume=True, verbose=1):
     """Download and load the BIDS-fied brainweb 1mm normal
 
-
     :param str data_dir: path of the data directory. Used to force data storage
         in a non-standard location.
     :param str url: download URL of the dataset. Overwrite the default URL.
@@ -94,7 +87,6 @@ def get_brainweb_1mm_normal(data_dir=None, url=None, resume=True, verbose=1):
 def get_ds003_downsampled(data_dir=None, url=None, resume=True, verbose=1):
     """Download and load the BIDS-fied ds003_downsampled
 
-
     :param str data_dir: path of the data directory. Used to force data storage
         in a non-standard location.
     :param str url: download URL of the dataset. Overwrite the default URL.
@@ -104,144 +96,12 @@ def get_ds003_downsampled(data_dir=None, url=None, resume=True, verbose=1):
                        resume=resume, verbose=verbose)
 
 
-def get_mni_template(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the mni template
-
-
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-
-    """
-    return get_dataset('mni_template', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_mni_template_ras(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the mni template
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('mni_template_RAS', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_mni_epi(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the mni template
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('mni_epi', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_ants_oasis_template(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the ANTs template of the OASIS dataset.
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('ants_oasis_template', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_ants_oasis_template_ras(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the ANTs template of the OASIS dataset.
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('ants_oasis_template_ras', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_ants_nki_template_ras(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the ANTs template of the NKI dataset.
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('ants_nki_template_ras', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_mni152_nlin_sym_las(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the mni template
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('mni152_nlin_sym_las', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_mni152_nlin_sym_ras(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the mni template
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('mni152_nlin_sym_ras', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_mni_icbm152_nlin_asym_09c(data_dir=None, url=None, resume=True, verbose=1):
-    return get_dataset('mni_icbm152_nlin_asym_09c', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
-def get_mni_icbm152_linear(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the mni template
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_dataset('mni_icbm152_linear', data_dir=data_dir, url=url,
-                       resume=resume, verbose=verbose)
-
-
 def get_bids_examples(data_dir=None, url=None, resume=True, verbose=1,
                       variant='BIDS-examples-1-1.0.0-rc3u5'):
-    """
-    Download BIDS-examples-1
-    """
+    """Download BIDS-examples-1"""
     variant = 'BIDS-examples-1-1.0.0-rc3u5' if variant not in BIDS_EXAMPLES else variant
     if url is None:
         url = BIDS_EXAMPLES[variant][0]
     md5 = BIDS_EXAMPLES[variant][1]
     return fetch_file(variant, url, data_dir, resume=resume, verbose=verbose,
                       md5sum=md5)
-
-
-def get_oasis_dkt31_mni152(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files from the Mindboggle DKT31 label
-    atlas in MNI152NLin2009cAsym space
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_template('OASISTRT20', data_dir=data_dir, url=url,
-                        resume=resume, verbose=verbose)
-
-
-def get_hcp32k_files(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load the necessary files for conversion between fsaverage5/6
-    and fs_LR(32k)
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_template('hcpLR32k', data_dir=data_dir, url=url,
-                        resume=resume, verbose=verbose)
-
-
-def get_conte69_mesh(data_dir=None, url=None, resume=True, verbose=1):
-    """Download and load Conte69-atlas meshes in 32k resolution
-    :param str data_dir: path of the data directory. Used to force data storage
-        in a non-standard location.
-    :param str url: download URL of the dataset. Overwrite the default URL.
-    """
-    return get_template('conte69', data_dir=data_dir, url=url,
-                        resume=resume, verbose=verbose)

niworkflows/interfaces/masks.py

@@ -20,6 +20,7 @@
 from nipype.interfaces.mixins import reporting
 from nipype.algorithms import confounds
 from . import report_base as nrc
+from seaborn import color_palette
 
 
 class BETInputSpecRPT(nrc.SVGReportCapableInputSpec,
@@ -250,6 +251,9 @@ class ROIsPlotInputSpecRPT(nrc.SVGReportCapableInputSpec):
     masked = traits.Bool(False, usedefault=True, desc='mask in_file prior plotting')
     colors = traits.Either(None, traits.List(Str), usedefault=True,
                            desc='use specific colors for contours')
+    levels = traits.Either(None, traits.List(traits.Float),
+                           usedefault=True, desc='pass levels to nilearn.plotting')
+    mask_color = Str('r', usedefault=True, desc='color for mask')
 
 
 class ROIsPlot(nrc.ReportingInterface):
@@ -258,21 +262,51 @@ class ROIsPlot(nrc.ReportingInterface):
     def _generate_report(self):
         from niworkflows.viz.utils import plot_segs, compose_view
         seg_files = self.inputs.in_rois
-        mask_file = None
-        if isdefined(self.inputs.in_mask):
-            mask_file = self.inputs.in_mask
-            seg_files.insert(0, self.inputs.in_mask)
+        mask_file = None if not isdefined(self.inputs.in_mask) \
+            else self.inputs.in_mask
+
+        # Remove trait decoration and replace None with []
+        levels = [l for l in self.inputs.levels or []]
+        colors = [c for c in self.inputs.colors or []]
+
+        if len(seg_files) == 1:  # in_rois is a segmentation
+            nsegs = len(levels)
+            if nsegs == 0:
+                levels = np.unique(np.round(
+                    nb.load(seg_files[0]).get_data()).astype(int))
+                levels = (levels[levels > 0] - 0.5).tolist()
+                nsegs = len(levels)
+
+            levels = [levels]
+            missing = nsegs - len(colors)
+            if missing > 0:
+                colors = colors + color_palette("husl", missing)
+            colors = [colors]
+        else:  # in_rois is a list of masks
+            nsegs = len(seg_files)
+            levels = [[0.5]] * nsegs
+            missing = nsegs - len(colors)
+            if missing > 0:
+                colors = [[c] for c in colors + color_palette("husl", missing)]
+
+        if mask_file:
+            seg_files.insert(0, mask_file)
+            if levels:
+                levels.insert(0, [0.5])
+            colors.insert(0, [self.inputs.mask_color])
+            nsegs += 1
 
         self._out_report = os.path.abspath(self.inputs.out_report)
         compose_view(
             plot_segs(
                 image_nii=self.inputs.in_file,
                 seg_niis=seg_files,
                 bbox_nii=mask_file,
+                levels=levels,
+                colors=colors,
                 out_file=self.inputs.out_report,
                 masked=self.inputs.masked,
-                colors=self.inputs.colors,
-                compress=self.inputs.compress_report
+                compress=self.inputs.compress_report,
             ),
             fg_svgs=None,
             out_file=self._out_report