Merge pull request #11 from a3sha2/master

step plot for scoreindex

aslprep/cli/run.py

@@ -163,7 +163,7 @@ def get_parser():
     g_conf.add_argument('--smooth_kernel', action='store', default=5, type=int,
                         help='smoothing kernel for M0')
     g_conf.add_argument(
-        '--dummy-vols', required=False, action='store', default=None, type=int,
+        '--dummy-vols', required=False, action='store', default=0, type=int,
         help='Number of first n vol to ingnore.')
 
     #  ANTs options

aslprep/data/reports-spec.yml

@@ -31,7 +31,7 @@ sections:
   reportlets:
   - bids: {datatype: asl, desc: summary, suffix: asl}
   - bids: {datatype: asl, desc: validation, suffix: asl}
-  - bids: {datatype: asl, desc: fieldmap, suffix: asl}
+  - bids: {datatype: asl, desc: fieldmap, suffix: bold}
     caption: The estimated fieldmap was aligned to the corresponding ASL reference
       with a rigid-registration process of the magintude part of the fieldmap,
       using <code>antsRegistration</code>.
@@ -42,12 +42,12 @@ sections:
       orders of magnitude above or below the minimum of blue colors.)
     static: false
     subtitle: Estimated fieldmap and alignment to the corresponding ASL reference
-  - bids: {datatype: asl, desc: sdc, suffix: asl}
+  - bids: {datatype: asl, desc: sdc, suffix: bold}
     caption: Results of performing susceptibility distortion correction (SDC) on the
       ASL
     static: false
     subtitle: Susceptibility distortion correction
-  - bids: {datatype: asl, desc: forcedsyn, suffix: asl}
+  - bids: {datatype: asl, desc: forcedsyn, suffix: bold}
     caption: The dataset contained some fieldmap information, but the argument <code>--force-syn</code>
       was used. The higher-priority SDC method was used. Here, we show the results
       of performing SyN-based SDC on the EPI for comparison.

aslprep/niworkflows/viz/plots.py

@@ -180,7 +180,7 @@ def plot(self, figure=None):
 
         for i, (name, kwargs) in enumerate(self.fd_file.items()):
             tseries = kwargs.pop('values')
-            confoundplot(
+            confoundplotx(
                 tseries, grid[grid_id], tr=self.tr, color=palette[i],
                 name=name, **kwargs)
             grid_id += 1
@@ -673,6 +673,141 @@ def confoundplot(tseries, gs_ts, gs_dist=None, name=None,
               'lw': 0, 'alpha': 0.8}
     )
 
+    # Annotate percentile 95
+    ax_ts.plot((0, ntsteps - 1), [p95] * 2, linewidth=.1, color='lightgray')
+    ax_ts.annotate(
+        '%.2f' % p95, xy=(0, p95), xytext=(-1, 0),
+        textcoords='offset points', va='center', ha='right',
+        color='lightgray', size=3)
+
+    if cutoff is None:
+        cutoff = []
+
+    for i, thr in enumerate(cutoff):
+        ax_ts.plot((0, ntsteps - 1), [thr] * 2,
+                   linewidth=.2, color='dimgray')
+
+        ax_ts.annotate(
+            '%.2f' % thr, xy=(0, thr), xytext=(-1, 0),
+            textcoords='offset points', va='center', ha='right',
+            color='dimgray', size=3)
+
+    ax_ts.plot(tseries, color=color, linewidth=.8)
+    ax_ts.set_xlim((0, ntsteps - 1))
+    #ax_ts.step(range(0,ntsteps),tseries,color=color)
+    #ax_ts.set_xlim((0, ntsteps - 1))
+    if gs_dist is not None:
+        ax_dist = plt.subplot(gs_dist)
+        sns.displot(tseries, vertical=True, ax=ax_dist)
+        ax_dist.set_xlabel('Timesteps')
+        ax_dist.set_ylim(ax_ts.get_ylim())
+        ax_dist.set_yticklabels([])
+
+        return [ax_ts, ax_dist], gs
+    return ax_ts, gs
+
+def confoundplotx(tseries, gs_ts, gs_dist=None, name=None,
+                 units=None, tr=None, hide_x=True, color='b', nskip=0,
+                 cutoff=None, ylims=None):
+
+    # Define TR and number of frames
+    notr = False
+    if tr is None:
+        notr = True
+        tr = 1.
+    ntsteps = len(tseries)
+    tseries = np.array(tseries)
+
+    # Define nested GridSpec
+    gs = mgs.GridSpecFromSubplotSpec(1, 2, subplot_spec=gs_ts,
+                                     width_ratios=[1, 100], wspace=0.0)
+
+    ax_ts = plt.subplot(gs[1])
+    ax_ts.grid(False)
+
+    # Set 10 frame markers in X axis
+    interval = max((ntsteps // 10, ntsteps // 5, 1))
+    xticks = list(range(0, ntsteps)[::interval])
+    ax_ts.set_xticks(xticks)
+
+    if not hide_x:
+        if notr:
+            ax_ts.set_xlabel('time (frame #)')
+        else:
+            ax_ts.set_xlabel('time (s)')
+            labels = tr * np.array(xticks)
+            ax_ts.set_xticklabels(['%.02f' % t for t in labels.tolist()])
+    else:
+        ax_ts.set_xticklabels([])
+
+    if name is not None:
+        if units is not None:
+            name += ' [%s]' % units
+
+        ax_ts.annotate(
+            name, xy=(0.0, 0.7), xytext=(0, 0), xycoords='axes fraction',
+            textcoords='offset points', va='center', ha='left',
+            color=color, size=8,
+            bbox={'boxstyle': 'round', 'fc': 'w', 'ec': 'none',
+                  'color': 'none', 'lw': 0, 'alpha': 0.8})
+
+    for side in ["top", "right"]:
+        ax_ts.spines[side].set_color('none')
+        ax_ts.spines[side].set_visible(False)
+
+    if not hide_x:
+        ax_ts.spines["bottom"].set_position(('outward', 20))
+        ax_ts.xaxis.set_ticks_position('bottom')
+    else:
+        ax_ts.spines["bottom"].set_color('none')
+        ax_ts.spines["bottom"].set_visible(False)
+
+    # ax_ts.spines["left"].set_position(('outward', 30))
+    ax_ts.spines["left"].set_color('none')
+    ax_ts.spines["left"].set_visible(False)
+    # ax_ts.yaxis.set_ticks_position('left')
+
+    ax_ts.set_yticks([])
+    ax_ts.set_yticklabels([])
+
+    nonnan = tseries[~np.isnan(tseries)]
+    if nonnan.size > 0:
+        # Calculate Y limits
+        valrange = (nonnan.max() - nonnan.min())
+        def_ylims = [nonnan.min() - 0.1 * valrange, nonnan.max() + 0.1 * valrange]
+        if ylims is not None:
+            if ylims[0] is not None:
+                def_ylims[0] = min([def_ylims[0], ylims[0]])
+            if ylims[1] is not None:
+                def_ylims[1] = max([def_ylims[1], ylims[1]])
+
+        # Add space for plot title and mean/SD annotation
+        def_ylims[0] -= 0.1 * (def_ylims[1] - def_ylims[0])
+
+        ax_ts.set_ylim(def_ylims)
+
+        # Annotate stats
+        maxv = nonnan.max()
+        mean = nonnan.mean()
+        stdv = nonnan.std()
+        p95 = np.percentile(nonnan, 95.0)
+    else:
+        maxv = 0
+        mean = 0
+        stdv = 0
+        p95 = 0
+
+    stats_label = (r'max: {max:.3f}{units} $\bullet$ mean: {mean:.3f}{units} '
+                   r'$\bullet$ $\sigma$: {sigma:.3f}').format(
+        max=maxv, mean=mean, units=units or '', sigma=stdv)
+    ax_ts.annotate(
+        stats_label, xy=(0.98, 0.7), xycoords='axes fraction',
+        xytext=(0, 0), textcoords='offset points',
+        va='center', ha='right', color=color, size=4,
+        bbox={'boxstyle': 'round', 'fc': 'w', 'ec': 'none', 'color': 'none',
+              'lw': 0, 'alpha': 0.8}
+    )
+
     # Annotate percentile 95
     ax_ts.plot((0, ntsteps - 1), [p95] * 2, linewidth=.1, color='lightgray')
     ax_ts.annotate(
@@ -707,6 +842,7 @@ def confoundplot(tseries, gs_ts, gs_dist=None, name=None,
     return ax_ts, gs
 
 
+
 def compcor_variance_plot(metadata_files, metadata_sources=None,
                           output_file=None, varexp_thresh=(0.5, 0.7, 0.9),
                           fig=None):

docs/conf.py

@@ -19,12 +19,12 @@
 from packaging import version as pver  # Avoid distutils.LooseVersion which is deprecated
 import sphinx
 
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.append(os.path.abspath("sphinxext")) 
 sys.path.insert(0, os.path.abspath("../wrapper"))
-sys.path.append(os.path.abspath('../..'))
 
 from github_link import make_linkcode_resolve
 
@@ -54,13 +54,15 @@
     "numpy",
     "nitime",
     "matplotlib",
+    "aslprep"
 ]
 
 if pver.parse(sphinxversion) >= pver.parse("1.7.0"):
     autodoc_mock_imports += [
         "pandas",
         "nilearn",
         "seaborn",
+        "aslprep"
     ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/index.rst

@@ -1,4 +1,4 @@
-.. fmriprep documentation master file, created by
+.. aslprep documentation master file, created by
    sphinx-quickstart on Mon May  9 09:04:25 2016.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
@@ -11,6 +11,9 @@
 Contents
 --------
 
+.. automodule:: aslprep
+   :members:
+
 .. toctree::
    :maxdepth: 3