[ENH] create useful error message when images are not found (#246)

* pin dependencies relative to niworkflows

* add more informative error message when preprocessed images are not found

* add tests to make sure error is raised

- also refactor other test in test_base

* increase number of testing scenerios

Author: jdkent

setup.cfg

@@ -28,14 +28,14 @@ keywords =
 [options]
 python_requires = >=3.5
 install_requires =
-    nipype ~= 1.1.5
+    nipype ~= 1.3.0
     pybids ~= 0.9.3
-    nibabel ~= 2.3.0
+    nibabel ~= 2.4.0
     nistats == 0.0.1b1
     nilearn ~= 0.4.2
     pandas ~= 0.24.0
     numpy
-    niworkflows
+    niworkflows ~= 1.0.2
     duecredit ~= 0.6.4
     scikit-learn ~= 0.19.2
     matplotlib ~= 2.2.4

src/nibetaseries/workflows/tests/test_base.py

@@ -1,13 +1,18 @@
 import os.path as op
 from nipype import config as ncfg
+import pytest
 
 from ..base import init_nibetaseries_participant_wf
 
 
-def test_init_nibetaseries_participant_wf(
+@pytest.mark.parametrize("estimator,fir_delays,hrf_model",
+                         [('lsa', None, 'spm'),
+                          ('lss', None, 'spm'),
+                          ('lss', [0, 1, 2, 3, 4], 'fir')])
+def test_valid_init_nibetaseries_participant_wf(
         bids_dir, deriv_dir, sub_fmriprep, sub_metadata, bold_file, preproc_file,
         sub_events, confounds_file, brainmask_file, atlas_file, atlas_lut,
-        ):
+        estimator, fir_delays, hrf_model):
 
     output_dir = op.join(str(bids_dir), 'derivatives', 'atlasCorr')
     work_dir = op.join(str(bids_dir), 'derivatives', 'work')
@@ -19,16 +24,16 @@ def test_init_nibetaseries_participant_wf(
                       'crashfile_format': 'txt',
                       'parameterize_dirs': False},
     })
-    # LSS test
+
     test_np_wf = init_nibetaseries_participant_wf(
-        estimator='lss',
-        fir_delays=None,
+        estimator=estimator,
+        fir_delays=fir_delays,
         atlas_img=str(atlas_file),
         atlas_lut=str(atlas_lut),
         bids_dir=str(bids_dir),
         derivatives_pipeline_dir=deriv_dir,
         exclude_description_label=None,
-        hrf_model='spm',
+        hrf_model=hrf_model,
         high_pass=0.008,
         output_dir=output_dir,
         run_label=None,
@@ -43,50 +48,45 @@ def test_init_nibetaseries_participant_wf(
 
     assert test_np_wf.run()
 
-    # FS test
-    test_np_wf = init_nibetaseries_participant_wf(
-        estimator='lss',
-        fir_delays=[0, 1, 2, 3, 4],
-        atlas_img=str(atlas_file),
-        atlas_lut=str(atlas_lut),
-        bids_dir=str(bids_dir),
-        derivatives_pipeline_dir=deriv_dir,
-        exclude_description_label=None,
-        hrf_model='fir',
-        high_pass=0.008,
-        output_dir=output_dir,
-        run_label=None,
-        selected_confounds=['WhiteMatter', 'CSF'],
-        session_label=None,
-        smoothing_kernel=None,
-        space_label=None,
-        subject_list=["01"],
-        task_label=None,
-        description_label=None,
-        work_dir=work_dir)
 
-    assert test_np_wf.run()
+@pytest.mark.parametrize("session_label,task_label,run_label,space_label,description_label",
+                         [('these', 'are', 'not', 'valid', 'filters'),
+                          (123, 123, 123, 123, 123)])
+def test_filters_init_nibetaseries_participant_wf(
+        bids_dir, deriv_dir, sub_fmriprep, sub_metadata, bold_file, preproc_file,
+        sub_events, confounds_file, brainmask_file,
+        session_label, task_label, run_label, space_label, description_label):
 
-    # LSA test
-    test_np_wf = init_nibetaseries_participant_wf(
-        estimator='lsa',
-        fir_delays=None,
-        atlas_img=None,
-        atlas_lut=None,
-        bids_dir=str(bids_dir),
-        derivatives_pipeline_dir=deriv_dir,
-        exclude_description_label=None,
-        hrf_model='spm',
-        high_pass=0.008,
-        output_dir=output_dir,
-        run_label=None,
-        selected_confounds=['WhiteMatter', 'CSF'],
-        session_label=None,
-        smoothing_kernel=None,
-        space_label=None,
-        subject_list=["01"],
-        task_label=None,
-        description_label=None,
-        work_dir=work_dir)
+    output_dir = op.join(str(bids_dir), 'derivatives', 'atlasCorr')
+    work_dir = op.join(str(bids_dir), 'derivatives', 'work')
+    deriv_dir = op.join(str(bids_dir), 'derivatives', 'fmriprep')
+    ncfg.update_config({
+        'logging': {'log_directory': work_dir,
+                    'log_to_file': True},
+        'execution': {'crashdump_dir': work_dir,
+                      'crashfile_format': 'txt',
+                      'parameterize_dirs': False},
+    })
+    with pytest.raises(ValueError) as val_err:
+        init_nibetaseries_participant_wf(
+            estimator='lsa',
+            fir_delays=None,
+            atlas_img=None,
+            atlas_lut=None,
+            bids_dir=str(bids_dir),
+            derivatives_pipeline_dir=deriv_dir,
+            exclude_description_label=None,
+            hrf_model='spm',
+            high_pass=0.008,
+            output_dir=output_dir,
+            run_label=run_label,
+            selected_confounds=['WhiteMatter', 'CSF'],
+            session_label=session_label,
+            smoothing_kernel=None,
+            space_label=space_label,
+            subject_list=["01"],
+            task_label=task_label,
+            description_label=description_label,
+            work_dir=work_dir)
 
-    assert test_np_wf.run()
+    assert "could not find preprocessed outputs:" in str(val_err.value)

src/nibetaseries/workflows/utils.py

@@ -37,6 +37,10 @@ def collect_data(layout, participant_label, ses=None,
 
     preprocs = layout.get(**preproc_query)
 
+    if not preprocs:
+        msg = "could not find preprocessed outputs: " + str(preproc_query)
+        raise ValueError(msg)
+
     # get the relevant files for each preproc
     preproc_collector = []
     # common across all queries