[WIP] Task generation

.github/workflows/pythonpackage.yml

@@ -29,4 +29,4 @@ jobs:
         pip install ".[dev]"
     - name: Test with pytest
       run: |
-        pytest -sv --doctest-modules pydra/tasks/TODO
+        pytest -sv --doctest-modules pydra/tasks/sem

MANIFEST.in

@@ -1,2 +1,2 @@
 include versioneer.py
-include pydra/tasks/TODO/_version.py
+include pydra/tasks/sem/_version.py

pydra/tasks/sem/__init__.py

@@ -0,0 +1,30 @@
+from registration import *
+from filtering import *
+from segmentation import *
+from utilities import *
+from diffusion import *
+from quantification import BRAINSLabelStats, PETStandardUptakeValueComputation
+from brains import *
+from testing import (
+    CLIROITest,
+    ComputeReflectiveCorrelationMetric,
+    GenerateAverageLmkFile,
+    LandmarksCompare,
+)
+from converters import (
+    CreateDICOMSeries,
+    DWICompare,
+    DWISimpleCompare,
+    OrientScalarVolume,
+)
+from legacy import *
+from superresolution import GenerateEdgeMapImage
+from classification import GeneratePurePlugMask
+from surface import (
+    GrayscaleModelMaker,
+    LabelMapSmoothing,
+    MergeModels,
+    ModelMaker,
+    ModelToLabelMap,
+    ProbeVolumeWithModel,
+)

pydra/tasks/TODO/_version.py → pydra/tasks/sem/_version.py

@@ -42,7 +42,7 @@ def get_config():
     cfg.style = "pep440"
     cfg.tag_prefix = ""
     cfg.parentdir_prefix = ""
-    cfg.versionfile_source = "pydra/tasks/TODO/_version.py"
+    cfg.versionfile_source = "pydra/tasks/sem/_version.py"
     cfg.verbose = False
     return cfg
 

pydra/tasks/sem/brains/__init__.py

@@ -0,0 +1,2 @@
+from classify import BRAINSPosteriorToContinuousClass
+from segmentation import BRAINSTalairach, BRAINSTalairachMask

pydra/tasks/sem/brains/classify.py

@@ -0,0 +1,141 @@
+"""
+Autogenerated file - DO NOT EDIT
+If you spot a bug, please report it on the mailing list and/or change the generator.
+"""
+
+import attr
+from nipype.interfaces.base import (
+    Directory,
+    File,
+    InputMultiPath,
+    OutputMultiPath,
+    traits,
+)
+from pydra import ShellCommandTask
+from pydra.engine.specs import SpecInfo, ShellSpec
+
+
+class BRAINSPosteriorToContinuousClass:
+    """
+    title: Tissue Classification
+    category: BRAINS.Classify
+    description: This program will generate an 8-bit continuous tissue classified image based on BRAINSABC posterior images.
+    version: 5.2.0
+    documentation-url: http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSClassify
+    license: https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt
+    contributor: Vincent A. Magnotta
+    acknowledgements: Funding for this work was provided by NIH/NINDS award NS050568
+    """
+
+    input_fields = [
+        (
+            "inputWhiteVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputWhiteVolume %s",
+                    "help_string": "White Matter Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "inputBasalGmVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputBasalGmVolume %s",
+                    "help_string": "Basal Grey Matter Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "inputSurfaceGmVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputSurfaceGmVolume %s",
+                    "help_string": "Surface Grey Matter Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "inputCsfVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputCsfVolume %s",
+                    "help_string": "CSF Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "inputVbVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputVbVolume %s",
+                    "help_string": "Venous Blood Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "inputCrblGmVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputCrblGmVolume %s",
+                    "help_string": "Cerebellum Grey Matter Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "inputCrblWmVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--inputCrblWmVolume %s",
+                    "help_string": "Cerebellum White Matter Posterior Volume",
+                    "exists": "True",
+                },
+            ),
+        ),
+        (
+            "outputVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "argstr": "--outputVolume %s",
+                    "help_string": "Output Continuous Tissue Classified Image",
+                    "hash_files": "False",
+                },
+            ),
+        ),
+    ]
+    output_fields = [
+        (
+            "outputVolume",
+            attr.ib(
+                type=File,
+                metadata={
+                    "help_string": "Output Continuous Tissue Classified Image",
+                    "exists": "True",
+                },
+            ),
+        )
+    ]
+
+    input_spec = SpecInfo(name="Input", fields=input_fields, bases=(ShellSpec,))
+    output_spec = SpecInfo(name="Output", fields=output_fields, bases=(ShellSpec,))
+
+    task = ShellCommandTask(
+        name="BRAINSPosteriorToContinuousClass",
+        executable=" BRAINSPosteriorToContinuousClass ",
+        input_spec=input_spec,
+        output_spec=output_spec,
+    )