convert eddy & adding test data

pydra/tasks/fsl/epi/tests/test_run_eddy.py

@@ -0,0 +1,68 @@
+import re, os, shutil, pytest
+from pathlib import Path
+from ..eddy import Eddy
+
+
+@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
+@pytest.mark.parametrize(
+    "inputs, outputs",
+    [
+        (
+            {
+                "in_file": "test.nii.gz",
+                "in_mask": "mask.nii.gz",
+                "in_index": "test_index.txt",
+                "in_acqp": "test_acqp.txt",
+                "in_bvec": "bvecs.scheme",
+                "in_bval": "bvals.scheme",
+            },
+            [
+                "out_corrected",
+                "out_parameter",
+                "out_movement_rms",
+                "out_restricted_movement_rms",
+                "out_shell_alignment_parameters",
+                "out_shell_pe_translation_parameters",
+                "out_outlier_map",
+                "out_outlier_n_stdev_map",
+                "out_outlier_n_sqr_stdev_map",
+                "out_outlier_report",
+            ],
+        )
+    ],
+)
+def test_Eddy(test_data, inputs, outputs):
+    if inputs is None:
+        in_file = Path(test_data) / "test.nii.gz"
+        task = Eddy(in_file=in_file)
+    else:
+        for key, val in inputs.items():
+            try:
+                pattern = r"\.[a-zA-Z]*"
+                if isinstance(val, str):
+                    if re.findall(pattern, val) != []:
+                        inputs[key] = Path(test_data) / val
+                    elif "_dir" in key:
+                        dirpath = Path(test_data) / val
+                        if dirpath.exists() and dirpath.is_dir():
+                            shutil.rmtree(dirpath)
+                        inputs[key] = Path(test_data) / val
+                    else:
+                        inputs[key] = eval(val)
+                elif isinstance(val, list):
+                    if all(re.findall(pattern, _) != [] for _ in val):
+                        inputs[key] = [Path(test_data) / _ for _ in val]
+                else:
+                    inputs[key] = eval(val)
+            except:
+                pass
+        task = Eddy(**inputs)
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)
+    breakpoint()
+    res = task()
+    print("RESULT: ", res)
+    for out_nm in outputs:
+        if isinstance(getattr(res.output, out_nm), list):
+            assert [os.path.exists(x) for x in getattr(res.output, out_nm)]
+        else:
+            assert os.path.exists(getattr(res.output, out_nm))

pydra/tasks/fsl/epi/tests/test_spec_eddy.py

@@ -0,0 +1,59 @@
+import re, os, shutil, pytest
+from pathlib import Path
+from ..eddy import Eddy
+
+
+@pytest.mark.parametrize(
+    "inputs, outputs",
+    [
+        (
+            {
+                "in_file": "test.nii.gz",
+                "in_mask": "mask.nii.gz",
+                "in_index": "test_index.txt",
+                "in_acqp": "test_acqp.txt",
+                "in_bvec": "bvecs.scheme",
+                "in_bval": "bvals.scheme",
+            },
+            [
+                "out_corrected",
+                "out_parameter",
+                "out_movement_rms",
+                "out_restricted_movement_rms",
+                "out_shell_alignment_parameters",
+                "out_shell_pe_translation_parameters",
+                "out_outlier_map",
+                "out_outlier_n_stdev_map",
+                "out_outlier_n_sqr_stdev_map",
+                "out_outlier_report",
+            ],
+        )
+    ],
+)
+def test_Eddy(test_data, inputs, outputs):
+    if inputs is None:
+        in_file = Path(test_data) / "test.nii.gz"
+        task = Eddy(in_file=in_file)
+    else:
+        for key, val in inputs.items():
+            try:
+                pattern = r"\.[a-zA-Z]*"
+                if isinstance(val, str):
+                    if re.findall(pattern, val) != []:
+                        inputs[key] = Path(test_data) / val
+                    elif "_dir" in key:
+                        dirpath = Path(test_data) / val
+                        if dirpath.exists() and dirpath.is_dir():
+                            shutil.rmtree(dirpath)
+                        inputs[key] = Path(test_data) / val
+                    else:
+                        inputs[key] = eval(val)
+                elif isinstance(val, list):
+                    if all(re.findall(pattern, _) != [] for _ in val):
+                        inputs[key] = [Path(test_data) / _ for _ in val]
+                else:
+                    inputs[key] = eval(val)
+            except:
+                pass
+        task = Eddy(**inputs)
+    assert set(task.generated_output_names) == set(["return_code", "stdout", "stderr"] + outputs)

pydra/tasks/fsl/tests/data/bvals.scheme

@@ -0,0 +1 @@
+0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000

pydra/tasks/fsl/tests/data/bvecs.scheme

@@ -0,0 +1,3 @@
+0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0 1 0 -1 0
+0 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

pydra/tasks/fsl/tests/data/test_acqp.txt

@@ -0,0 +1,12 @@
+0 1 0 0.1
+0 1 0 0.1
+0 1 0 0.1
+1 0 0 0.1
+1 0 0 0.1
+1 0 0 0.1
+0 -1 0 0.1
+0 -1 0 0.1
+0 -1 0 0.1
+-1 0 0 0.1
+-1 0 0 0.1
+-1 0 0 0.1

pydra/tasks/fsl/tests/data/test_index.txt

@@ -0,0 +1 @@
+1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 11 11 11

specs/callables.py

@@ -148,6 +148,9 @@ def FAST_output_infile(field, in_files, out_basename):
 
 
 def FEAT_output(fsf_file):
+    import os
+    from glob import glob
+
     is_ica = False
     with open(fsf_file, "rt") as fp:
         text = fp.read()
@@ -173,6 +176,7 @@ def FEAT_output(fsf_file):
 
 def FEATModel_output(field, fsf_file):
     import os
+    from glob import glob
 
     # TODO: figure out file names and get rid off the globs
     outputs = {}

specs/fsl_epi_param.yml

@@ -16,14 +16,58 @@
 #   tests_inputs:
 #   tests_outputs:
 
-# Eddy:
-#   output_requirements:
-#   output_callables:
-#   output_templates:
-#   inputs_drop:
-#   doctest:
-#   tests_inputs:
-#   tests_outputs:
+Eddy:
+  output_requirements:
+    out_corrected:
+    out_parameter:
+    out_rotated_bvec:
+    out_movement_rms:
+    out_restricted_movement_rms:
+    out_shell_alignment_parameters:
+    out_shell_pe_translation_parameters:
+    out_outlier_map:
+    out_outlier_n_stdev_map:
+    out_outlier_n_sqr_stdev_map:
+    out_outlier_report:
+    out_outlier_free: [repol]
+    out_movement_over_time: [mporder]
+    out_cnr_maps: [cnr_maps]
+    out_residuals: [residuals]
+  output_callables:
+  output_templates:
+    out_corrected: "{out_base}.nii.gz"
+    out_parameter: "{out_base}.eddy_parameters"
+    out_rotated_bvec: "{out_base}.eddy_rotated_bvecs"
+    out_movement_rms: "{out_base}.eddy_movement_rms"
+    out_restricted_movement_rms: "{out_base}.eddy_restricted_movement_rms"
+    out_shell_alignment_parameters: "{out_base}.eddy_post_eddy_shell_alignment_parameters"
+    out_shell_pe_translation_parameters: "{out_base}.eddy_post_eddy_shell_PE_translation_parameters"
+    out_outlier_map: "{out_base}.eddy_outlier_map"
+    out_outlier_n_stdev_map: "{out_base}.eddy_outlier_n_stdev_map"
+    out_outlier_n_sqr_stdev_map: "{out_base}.eddy_outlier_n_sqr_stdev_map"
+    out_outlier_report: "{out_base}.eddy_outlier_report"
+    out_outlier_free: "{out_base}.eddy_outlier_free_data"
+    out_movement_over_time: "{out_base}.eddy_movement_over_time"
+    out_cnr_maps: "{out_base}.eddy_cnr_maps"
+    out_residuals: "{out_base}.eddy_residuals"
+  inputs_drop:
+  doctest:
+    in_file: test.nii.gz
+    in_mask: mask.nii.gz
+    in_index: test_index.txt
+    in_acqp: test_acqp.txt
+    in_bvec: bvecs.scheme
+    in_bval: bvals.scheme
+    cmdline: eddy_openmp --imain=test.nii.gz --mask=test_mask.nii.gz --index=test_index.txt --acqp=test_acqp.txt --bvecs=bvecs.scheme --bvals=bvals.scheme --verbose
+  tests_inputs:
+    - in_file: test.nii.gz
+      in_mask: mask.nii.gz
+      in_index: test_index.txt
+      in_acqp: test_acqp.txt
+      in_bvec: bvecs.scheme
+      in_bval: bvals.scheme
+  tests_outputs:
+    - [out_corrected, out_parameter, out_movement_rms, out_restricted_movement_rms, out_shell_alignment_parameters, out_shell_pe_translation_parameters, out_outlier_map, out_outlier_n_stdev_map, out_outlier_n_sqr_stdev_map, out_outlier_report]
 
 # EddyCorrect:
 #   output_requirements: