Merge pull request #270 from oesteban/fix/upstreamed-read-crashfiles

[FIX] ``read_crashfile`` stopped working after migration

Author: oesteban

niworkflows/data/tests/crashfile.txt

@@ -0,0 +1,33 @@
+Node: fmriprep_wf.single_subject_100185_wf.func_preproc_task_machinegame_run_02_wf.carpetplot_wf.conf_plot
+Working directory: /home/oesteban/tmp/fmriprep-ds005/work/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/carpetplot_wf/conf_plot
+
+Node inputs:
+
+confounds_file = /home/oesteban/tmp/fmriprep-ds005/work/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/bold_confounds_wf/concat/confounds.tsv
+confounds_list = [('global_signal', None, 'GS'), ('csf', None, 'GSCSF'), ('white_matter', None, 'GSWM'), ('std_dvars', None, 'DVARS'), ('framewise_displacement', 'mm', 'FD')]
+in_func = /home/oesteban/tmp/fmriprep-ds005/work/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz
+in_mask = /home/oesteban/tmp/fmriprep-ds005/work/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz
+in_segm = /home/oesteban/tmp/fmriprep-ds005/work/fmriprep_wf/single_subject_100185_wf/func_preproc_task_machinegame_run_02_wf/carpetplot_wf/resample_parc/tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-carpet_atlas_trans.nii.gz
+str_or_tuple = <undefined>
+tr = 1.0
+
+Traceback (most recent call last):
+  File "/home/oesteban/workspace/nipype/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
+    result['result'] = node.run(updatehash=updatehash)
+  File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 473, in run
+    result = self._run_interface(execute=True)
+  File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
+    return self._run_command(execute)
+  File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 637, in _run_command
+    result = self._interface.run(cwd=outdir)
+  File "/home/oesteban/workspace/nipype/nipype/interfaces/base/core.py", line 511, in run
+    runtime = self._run_interface(runtime)
+  File "/home/oesteban/workspace/fmriprep/fmriprep/interfaces/confounds.py", line 342, in _run_interface
+    units=units,
+  File "/home/oesteban/workspace/niworkflows/niworkflows/viz/plots.py", line 101, in plot
+    name=name, **kwargs)
+  File "/home/oesteban/workspace/niworkflows/niworkflows/viz/plots.py", line 483, in confoundplot
+    def_ylims = [nonnan.min() - 0.1 * abs(nonnan.min()), 1.1 * nonnan.max()]
+  File "/home/oesteban/.anaconda3/lib/python3.7/site-packages/numpy/core/_methods.py", line 32, in _amin
+    return umr_minimum(a, axis, None, out, keepdims, initial)
+ValueError: zero-size array to reduction operation minimum which has no identity

niworkflows/utils/misc.py

@@ -68,9 +68,20 @@ def _read_pkl(path):
 
 
 def _read_txt(path):
+    """Read a txt crashfile
+
+    >>> new_path = Path(__file__).resolve().parent.parent
+    >>> test_data_path = new_path / 'data' / 'tests'
+    >>> info = _read_txt(test_data_path / 'crashfile.txt')
+    >>> info['node']  # doctest: +ELLIPSIS
+    '...func_preproc_task_machinegame_run_02_wf.carpetplot_wf.conf_plot'
+    >>> info['traceback']  # doctest: +ELLIPSIS
+    '...ValueError: zero-size array to reduction operation minimum which has no identity'
+
+    """
     from pathlib import Path
     lines = Path(path).read_text().splitlines()
-    data = {'file': path}
+    data = {'file': str(path)}
     traceback_start = 0
     if lines[0].startswith('Node'):
         data['node'] = lines[0].split(': ', 1)[1].strip()
@@ -79,6 +90,9 @@ def _read_txt(path):
         cur_key = ''
         cur_val = ''
         for i, line in enumerate(lines[5:]):
+            if not line.strip():
+                continue
+
             if line[0].isspace():
                 cur_val += line
                 continue
@@ -95,7 +109,7 @@ def _read_txt(path):
         data['inputs'] = sorted(inputs)
     else:
         data['node_dir'] = "Node crashed before execution"
-    data['traceback'] = ''.join(lines[traceback_start:]).strip()
+    data['traceback'] = '\n'.join(lines[traceback_start:]).strip()
     return data
 
 

niworkflows/viz/plots.py

@@ -473,7 +473,6 @@ def confoundplot(tseries, gs_ts, gs_dist=None, name=None,
     ax_ts.spines["left"].set_visible(False)
     # ax_ts.yaxis.set_ticks_position('left')
 
-
     ax_ts.set_yticks([])
     ax_ts.set_yticklabels([])