Added tests and placeholder tests for the FIBContext class

Author: tieneupin

tests/client/contexts/test_fib.py

@@ -0,0 +1,249 @@
+import xml.etree.ElementTree as ET
+from pathlib import Path
+from typing import Any
+
+import pytest
+
+from murfey.client.contexts.fib import FIBContext
+
+# -------------------------------------------------------------------------------------
+# FIBContext test utilty functions and fixtures
+# -------------------------------------------------------------------------------------
+
+
+def create_fib_maps_dataset_element(
+    id: int,
+    name: str,
+    relative_path: str,
+    center_x: float,
+    center_y: float,
+    center_z: float,
+    size_x: float,
+    size_y: float,
+    size_z: float,
+    rotation_angle: float,
+):
+    # Create dataset node
+    dataset = ET.Element("Dataset")
+    # ID node
+    id_node = ET.Element("Id")
+    id_node.text = str(id)
+    dataset.append(id_node)
+
+    # Name node
+    name_node = ET.Element("Name")
+    name_node.text = name
+    dataset.append(name_node)
+
+    # Stage position node
+    box_center = ET.Element("BoxCenter")
+    for tag, value in (
+        ("CenterX", center_x),
+        ("CenterY", center_y),
+        ("CenterZ", center_z),
+    ):
+        node = ET.Element(tag)
+        node.text = str(value)
+        box_center.append(node)
+    dataset.append(box_center)
+
+    # Image size node
+    box_size = ET.Element("BoxSize")
+    for tag, value in (
+        ("SizeX", size_x),
+        ("SizeY", size_y),
+        ("SizeZ", size_z),
+    ):
+        node = ET.Element(tag)
+        node.text = str(value)
+        box_size.append(node)
+    dataset.append(box_size)
+
+    # Rotation angle
+    angle_node = ET.Element("RotationAngle")
+    angle_node.text = str(rotation_angle)
+    dataset.append(angle_node)
+
+    # Relative path
+    image_path_node = ET.Element("FinalImages")
+    image_path_node.text = relative_path.replace("/", "\\")
+    dataset.append(image_path_node)
+
+    return dataset
+
+
+def create_fib_maps_xml_metadata(
+    project_name: str,
+    datasets: list[dict[str, Any]],
+):
+    # Create root node
+    root = ET.Element("EMProject")
+
+    # Project name node
+    project_name_node = ET.Element("ProjectName")
+    project_name_node.text = project_name
+    root.append(project_name_node)
+
+    # Datasets node
+    datasets_node = ET.Element("Datasets")
+    for id, dataset in enumerate(datasets):
+        datasets_node.append(create_fib_maps_dataset_element(id, **dataset))
+    root.append(datasets_node)
+
+    return root
+
+
+fib_maps_test_datasets = [
+    {
+        "name": name,
+        "relative_path": relative_path,
+        "center_x": cx,
+        "center_y": cy,
+        "center_z": cz,
+        "size_x": sx,
+        "size_y": sy,
+        "size_z": sz,
+        "rotation_angle": ra,
+    }
+    for (name, relative_path, cx, cy, cz, sx, sy, sz, ra) in (
+        (
+            "Electron Snapshot",
+            "LayersData/Layer/Electron Snapshot",
+            -0.002,
+            -0.004,
+            0.00000008,
+            0.0036,
+            0.0024,
+            0.0,
+            3.1415926535897931,
+        ),
+        (
+            "Electron Snapshot (2)",
+            "LayersData/Layer/Electron Snapshot (2)",
+            -0.002,
+            -0.004,
+            0.00000008,
+            0.0036,
+            0.0024,
+            0.0,
+            3.1415926535897931,
+        ),
+        (
+            "Electron Snapshot (3)",
+            "LayersData/Layer/Electron Snapshot (3)",
+            0.002,
+            0.004,
+            0.00000008,
+            0.0036,
+            0.0024,
+            0.0,
+            3.1415926535897931,
+        ),
+        (
+            "Electron Snapshot (4)",
+            "LayersData/Layer/Electron Snapshot (4)",
+            0.002,
+            0.004,
+            0.00000008,
+            0.0036,
+            0.0024,
+            0.0,
+            3.1415926535897931,
+        ),
+    )
+]
+
+
+@pytest.fixture
+def fib_maps_metadata_file(tmp_path: Path):
+    metadata = create_fib_maps_xml_metadata(
+        "test-project",
+        fib_maps_test_datasets,
+    )
+    tree = ET.ElementTree(metadata)
+    ET.indent(tree, space="  ")
+    save_path = tmp_path / "EMproject.emxml"
+    tree.write(save_path, encoding="utf-8")
+    return save_path
+
+
+@pytest.fixture
+def fib_maps_images(tmp_path: Path):
+    image_list = []
+    for dataset in fib_maps_test_datasets:
+        name = str(dataset["name"])
+        relative_path = str(dataset["relative_path"])
+        file = tmp_path / relative_path / f"{name}.tiff"
+        if not file.exists():
+            file.parent.mkdir(parents=True, exist_ok=True)
+            file.touch()
+        image_list.append(file)
+    return image_list
+
+
+# -------------------------------------------------------------------------------------
+# Tests
+# -------------------------------------------------------------------------------------
+def test_fib_autotem_context():
+    pass
+
+
+@pytest.mark.parametrize("metadata_first", ((False, True)))
+def test_fib_maps_context(
+    tmp_path: Path,
+    fib_maps_metadata_file: Path,
+    fib_maps_images: list[Path],
+    metadata_first: bool,
+):
+    # Initialise the FIBContext
+    basepath = tmp_path
+    context = FIBContext(
+        acquisition_software="maps",
+        basepath=basepath,
+        token="",
+    )
+    # Assert that its initial state is correct
+    assert not context._electron_snapshots
+    assert not context._electron_snapshot_metadata
+    assert not context._electron_snapshots_submitted
+
+    if metadata_first:
+        # Read the metadata first
+        context.post_transfer(fib_maps_metadata_file)
+        # Metadata field should now be populated
+        assert all(
+            name in context._electron_snapshot_metadata.keys()
+            for name in [image.stem for image in fib_maps_images]
+        )
+        # Parse the images one-by-one
+        for image in fib_maps_images:
+            name = image.stem
+            context.post_transfer(image)
+            # Entries should now start being removed from 'metadata' and 'images' fields
+            assert (
+                name not in context._electron_snapshots.keys()
+                and name not in context._electron_snapshot_metadata.keys()
+                and name in context._electron_snapshots_submitted
+            )
+    else:
+        # Read in images first
+        for image in fib_maps_images:
+            name = image.stem
+            context.post_transfer(image)
+            assert (
+                name in context._electron_snapshots.keys()
+                and name not in context._electron_snapshot_metadata.keys()
+                and name not in context._electron_snapshots_submitted
+            )
+        # Read in the metadata
+        context.post_transfer(fib_maps_metadata_file)
+        assert all(
+            name in context._electron_snapshots_submitted
+            and name not in context._electron_snapshots.keys()
+            and name not in context._electron_snapshot_metadata.keys()
+            for name in [file.stem for file in fib_maps_images]
+        )
+
+
+def test_fib_meteor_context():
+    pass