Merge pull request #834 from 36000/nightly_fixes_1

[FIX] update nightly tests and fix kwargs

AFQ/definitions/image.py

@@ -170,7 +170,9 @@ def image_getter(dwi, bids_info):
                 dwi_img.get_fdata(),
                 image_affine,
                 dwi_img.affine)
-            return nib.Nifti1Image(image_data, dwi_img.affine), meta
+            return nib.Nifti1Image(
+                image_data.astype(np.float32),
+                dwi_img.affine), meta
         return image_getter
 
     def get_image_direct(self, dwi, bids_info, b0_file, data_imap=None):
@@ -200,7 +202,7 @@ def get_image_getter(self, task_name):
         def image_getter(dwi):
             dwi_img = nib.load(dwi)
             return nib.Nifti1Image(
-                np.ones(dwi_img.get_fdata()[..., 0].shape),
+                np.ones(dwi_img.get_fdata()[..., 0].shape, dtype=np.float32),
                 dwi_img.affine), dict(source="Entire Volume")
         return image_getter
 
@@ -328,7 +330,8 @@ def image_getter_helper(b0):
             mean_b0 = mean_b0_img.get_fdata()
             _, image_data = median_otsu(mean_b0, **self.median_otsu_kwargs)
             return nib.Nifti1Image(
-                image_data.astype(int), mean_b0_img.affine), dict(
+                image_data.astype(np.float32),
+                mean_b0_img.affine), dict(
                     source=b0,
                     technique="median_otsu applied to b0",
                     median_otsu_kwargs=self.median_otsu_kwargs)
@@ -645,7 +648,8 @@ def _image_getter_helper(mapping, reg_template):
             scalar_data = mapping.transform_inverse(
                 img_data, interpolation='nearest')
             return nib.Nifti1Image(
-                scalar_data, reg_template.affine), dict(source=self.path)
+                scalar_data.astype(np.float32),
+                reg_template.affine), dict(source=self.path)
 
         if task_name == "mapping":
             def image_getter(mapping, data_imap):

AFQ/tasks/data.py

@@ -495,7 +495,7 @@ def brain_mask(base_fname, dwi, b0,
             bids_info["subject"],
             bids_info["session"])
     return brain_mask_definition.get_image_direct(
-        base_fname, bids_info, b0, data_imap=None)
+        dwi, bids_info, b0, data_imap=None)
 
 
 @pimms.calc("bundle_dict", "reg_template")
@@ -586,7 +586,7 @@ def roi_scalar_to_info(roi):
             bids_info["subject"],
             bids_info["session"])
         roi_img, _ = roi.get_image_direct(
-            base_fname, bids_info, b0, data_imap=None)
+            dwi, bids_info, b0, data_imap=None)
         return roi_img
     for b_name, b_info in bundle_dict._dict.items():
         if "space" in b_info and b_info["space"] == "subject":

AFQ/tasks/decorators.py

@@ -65,7 +65,7 @@ def _has_args(func):
                     header += f"{name}='{default}', "
                 else:
                     header += f"{name}={default}, "
-                content += f"{name}, "
+                content += f"{name}={name}, "
 
         header = header[:-2]
         content = content[:-2]

AFQ/tasks/mapping.py

@@ -218,7 +218,7 @@ def get_reg_subject(data_imap, bids_info, base_fname, dwi,
             bids_info["subject"],
             bids_info["session"])
         img, _ = reg_subject_spec.get_image_direct(
-            base_fname, bids_info, data_imap["b0"],
+            dwi, bids_info, data_imap["b0"],
             data_imap=data_imap)
     else:
         if reg_subject_spec in filename_dict:

AFQ/tests/test_api.py

@@ -250,15 +250,15 @@ def test_AFQ_custom_tract():
             'subsampled_tractography.trk'
             )
     )
-    my_afq = GroupAFQ(
+    myafq = GroupAFQ(
         bids_path,
         preproc_pipeline='vistasoft',
         bundle_info=bundle_names,
         import_tract={
             "suffix": "tractography",
             "scope": "vistasoft"
         })
-    my_afq.export_streamlines()
+    myafq.export("streamlines")
 
 
 @pytest.mark.nightly_basic
@@ -315,12 +315,12 @@ def test_AFQ_init():
                     match="No subjects specified in `participant_labels` "
                     + " found in BIDS derivatives folders."
                         + " See above warnings."):
-                    my_afq = GroupAFQ(
+                    myafq = GroupAFQ(
                         bids_path,
                         preproc_pipeline="synthetic",
                         participant_labels=participant_labels)
             else:
-                my_afq = GroupAFQ(
+                myafq = GroupAFQ(
                     bids_path,
                     preproc_pipeline="synthetic",
                     participant_labels=participant_labels)
@@ -329,7 +329,7 @@ def test_AFQ_init():
                     sub = f"0{subject+1}"
                     if n_subjects == n_sessions:
                         npt.assert_equal(
-                            len(my_afq.wf_dict[sub][sub]),
+                            len(myafq.wf_dict[sub][sub]),
                             27)
                     else:
                         for session in range(n_sessions):
@@ -338,7 +338,7 @@ def test_AFQ_init():
                             else:
                                 sess = f"0{session+1}"
                             npt.assert_equal(
-                                len(my_afq.wf_dict[sub][sess]),
+                                len(myafq.wf_dict[sub][sess]),
                                 27)
 
 
@@ -531,7 +531,7 @@ def test_AFQ_pft():
         ImageFile(suffix="CSFprobseg"))
 
     with nbtmp.InTemporaryDirectory() as t_output_dir:
-        my_afq = GroupAFQ(
+        myafq = GroupAFQ(
             bids_path,
             preproc_pipeline='vistasoft',
             bundle_info=bundle_names,
@@ -541,7 +541,7 @@ def test_AFQ_pft():
                 "stop_threshold": "CMC",
                 "tracker": "pft"
             })
-        my_afq.export_streamlines()
+        myafq.export("streamlines")
 
 
 @pytest.mark.nightly_custom
@@ -558,22 +558,22 @@ def test_AFQ_custom_subject_reg():
     b0_file = GroupAFQ(
         bids_path,
         preproc_pipeline='vistasoft',
-        bundle_info=bundle_info).b0["01"]
+        bundle_info=bundle_info).export("b0")["01"]
 
     # make a different temporary directly to test this custom file in
     _, bids_path, sub_path = get_temp_hardi()
 
     os.rename(b0_file, op.join(sub_path, "sub-01_ses-01_customb0.nii.gz"))
 
-    my_afq = GroupAFQ(
+    myafq = GroupAFQ(
         bids_path,
         preproc_pipeline='vistasoft',
         bundle_info=bundle_info,
         reg_template_spec="mni_T2",
         reg_subject_spec=ImageFile(
             suffix="customb0",
             filters={"scope": "vistasoft"}))
-    my_afq.export_rois()
+    myafq.export("rois")
 
 
 # Requires large download

bin/pyAFQ

@@ -36,9 +36,8 @@ def parse_cli(arg_dict):
     cli_parser.add_argument(
         dest='config',
         action="store",
-        help=(
-            "Path to config file or folder. ",
-            "For example, /path/to/afq_config.toml"))
+        help="Path to config file or folder. "
+        + "For example, /path/to/afq_config.toml")
 
     cli_parser.add_argument(
         '-g',