adding seam blender wrapper for 2pco virtual datasets

httomo/method_wrappers/__init__.py

@@ -9,6 +9,7 @@
 import httomo.method_wrappers.datareducer
 import httomo.method_wrappers.dezinging
 import httomo.method_wrappers.distortion_correction
+import httomo.method_wrappers.seam_blender
 import httomo.method_wrappers.images
 import httomo.method_wrappers.reconstruction
 import httomo.method_wrappers.rotation

httomo/method_wrappers/seam_blender.py

@@ -0,0 +1,56 @@
+from typing import Dict, Optional
+
+from mpi4py.MPI import Comm
+
+from httomo.method_wrappers.generic import GenericMethodWrapper
+from httomo.preview import PreviewConfig
+from httomo.runner.methods_repository_interface import MethodRepository
+
+
+class SeamBlenderWrapper(GenericMethodWrapper):
+    """
+    Wrapper for seam blender.
+    """
+
+    @classmethod
+    def should_select_this_class(cls, module_path: str, method_name: str) -> bool:
+        return "seam_blend" in method_name
+
+    @classmethod
+    def requires_preview(cls) -> bool:
+        return True
+
+    def __init__(
+        self,
+        method_repository: MethodRepository,
+        module_path: str,
+        method_name: str,
+        comm: Comm,
+        preview_config: PreviewConfig,
+        save_result: Optional[bool] = None,
+        output_mapping: Dict[str, str] = {},
+        **kwargs,
+    ):
+        super().__init__(
+            method_repository,
+            module_path,
+            method_name,
+            comm,
+            save_result,
+            output_mapping,
+            **kwargs,
+        )
+        self._update_params_from_preview(preview_config)
+
+    def _update_params_from_preview(self, preview_config: PreviewConfig) -> None:
+        """
+        Extract information from preview config to modify seam index parameter required for `seam_blend_stitched_data` method.
+        """
+        SHIFT_PARAM_NAME = "shift_seam_index"
+        det_x_start = preview_config.detector_x.start
+
+        self.append_config_params(
+            {
+                SHIFT_PARAM_NAME: det_x_start,
+            }
+        )

httomo/runner/task_runner.py

@@ -81,11 +81,18 @@ def execute(self) -> None:
     def _pipeline_inspector(self) -> None:
         phase_in_pipeline = False
         minus_log_in_pipeline = False
+        seam_blend_in_pipeline = False
         for i, method in enumerate(self.pipeline._methods):
             if "phase" in method.module_path:
                 phase_in_pipeline = True
             if "minus_log" == method.method_name:
                 minus_log_in_pipeline = True
+            if "seam_blend" in method.method_name:
+                seam_blend_in_pipeline = True
+            if "dark_flat" in method.method_name and seam_blend_in_pipeline:
+                raise RuntimeError(
+                    "Seam blending method should be used only after the dark/flat field correction"
+                )
             if "rotation" in method.module_path:
                 if self.pipeline[i - 1].method_name == "data_reducer":
                     log_once(

tests/method_wrappers/test_seam_blender.py

@@ -0,0 +1,73 @@
+import pytest
+from mpi4py import MPI
+from pytest_mock import MockerFixture
+
+from httomo.method_wrappers.seam_blender import SeamBlenderWrapper
+from httomo.preview import PreviewConfig, PreviewDimConfig
+from tests.testing_utils import make_mock_repo
+
+
+@pytest.mark.parametrize(
+    "method_name, expected_result",
+    [("seam_blend", True), ("other_method", False)],
+    ids=["should-select", "shouldn't-select"],
+)
+def test_class_only_selected_for_methods_with_seam_blend_in_name(
+    method_name: str, expected_result: bool
+):
+    assert (
+        SeamBlenderWrapper.should_select_this_class("dummy.module.path", method_name)
+        is expected_result
+    )
+
+
+def test_requires_preview_is_true():
+    assert SeamBlenderWrapper.requires_preview() is True
+
+
+@pytest.mark.parametrize(
+    "preview_config",
+    [
+        PreviewConfig(
+            angles=PreviewDimConfig(start=0, stop=180),
+            detector_y=PreviewDimConfig(start=0, stop=128),
+            detector_x=PreviewDimConfig(start=0, stop=160),
+        ),
+        PreviewConfig(
+            angles=PreviewDimConfig(start=0, stop=180),
+            detector_y=PreviewDimConfig(start=0, stop=128),
+            detector_x=PreviewDimConfig(start=5, stop=155),
+        ),
+    ],
+    ids=["no_cropping", "crop_det_x_both_ends"],
+)
+def test_sets_shiftx_params_correctly(
+    preview_config: PreviewConfig, mocker: MockerFixture
+):
+    MODULE_PATH = "dummy.module.path"
+    METHOD_NAME = "seam_blend_dummy"
+    COMM = MPI.COMM_WORLD
+
+    # Patch method function import that occurs when the wrapper object is created, to instead
+    # import the below dummy method function
+    class FakeModule:
+        def seam_blend_dummy(shift_seam_index):  # type: ignore
+            return shift_seam_index
+
+    mocker.patch(
+        "httomo.method_wrappers.generic.import_module", return_value=FakeModule
+    )
+
+    wrapper = SeamBlenderWrapper(
+        method_repository=make_mock_repo(mocker),
+        module_path=MODULE_PATH,
+        method_name=METHOD_NAME,
+        comm=COMM,
+        preview_config=preview_config,
+    )
+
+    expected_shift_values = preview_config.detector_x.start
+
+    SHIFT_PARAM_NAME = "shift_seam_index"
+    assert SHIFT_PARAM_NAME in wrapper.config_params
+    assert wrapper.config_params[SHIFT_PARAM_NAME] == expected_shift_values