SXT context test

Author: stephen-riggs

src/murfey/client/context.py

@@ -99,6 +99,10 @@ def ensure_dcg_exists(
                     )
             except Exception as e:
                 logger.warning(f"Get EPU session hook failed: {e}")
+    elif collection_type == "sxt":
+        experiment_type_id = 47
+        session_file = metadata_source / "Session.dm"
+        source_visit_dir = metadata_source.parent
     else:
         logger.error(f"Unknown collection type {collection_type}")
         return None

src/murfey/client/contexts/sxt.py

@@ -58,7 +58,7 @@ def register_sxt_data_collection(
                 "source": str(self._basepath),
                 "tag": tilt_series,
                 "pixel_size_on_image": str(
-                    data_collection_parameters.get("pixel_size_on_image", 100)
+                    data_collection_parameters.get("pixel_size", 100)
                 ),
                 "image_size_x": data_collection_parameters.get("image_size_x", 0),
                 "image_size_y": data_collection_parameters.get("image_size_y", 0),
@@ -142,7 +142,7 @@ def post_transfer(
                     strict=True,
                 )
                 if pixel_size_txrm:
-                    metadata["pixel_size_microns"] = pixel_size_txrm[0]
+                    metadata["pixel_size"] = pixel_size_txrm[0] * 1e4
 
                 image_width_txrm = read_stream(
                     inspector.txrm.ole,

tests/client/contexts/test_sxt.py

@@ -0,0 +1,125 @@
+from unittest.mock import patch
+from urllib.parse import urlparse
+
+from murfey.client.contexts.sxt import SXTContext
+from murfey.client.instance_environment import MurfeyInstanceEnvironment
+
+
+def test_sxt_context_initialisation(tmp_path):
+    context = SXTContext("zeiss", tmp_path, "")
+    assert context._acquisition_software == "zeiss"
+    assert context._basepath == tmp_path
+
+
+@patch("requests.post")
+def test_sxt_context_xrm(mock_post, tmp_path):
+    """Currently nothing happens with an xrm file"""
+    env = MurfeyInstanceEnvironment(
+        url=urlparse("http://localhost:8000"),
+        client_id=0,
+        sources=[tmp_path],
+        default_destinations={tmp_path: str(tmp_path)},
+        instrument_name="",
+        visit="test",
+        murfey_session=1,
+    )
+    context = SXTContext("zeiss", tmp_path, "")
+    return_value = context.post_transfer(
+        tmp_path / "example.xrm",
+        required_position_files=[],
+        required_strings=["fractions"],
+        environment=env,
+    )
+    assert return_value
+    mock_post.assert_not_called()
+
+
+@patch("requests.post")
+@patch("murfey.client.contexts.sxt.Inspector")
+@patch("murfey.client.contexts.sxt.open_txrm")
+@patch("murfey.client.contexts.sxt.read_stream")
+def test_sxt_context_txrm(
+    mock_read_stream, mock_open_txrm, mock_inspector, mock_post, tmp_path
+):
+    mock_post().status_code = 200
+    mock_read_stream.side_effect = [
+        [-55, -25, 5, 35, 65],  # Angles
+        [0.01001],  # Pixel size
+        [1024],  # Image Width
+        [2048],  # Image Height
+        [1.5],  # Exposure time
+        [1000],  # Mag
+        [5],  # Image count
+    ]
+
+    env = MurfeyInstanceEnvironment(
+        url=urlparse("http://localhost:8000"),
+        client_id=0,
+        sources=[tmp_path],
+        default_destinations={tmp_path: str(tmp_path / "destination")},
+        instrument_name="",
+        visit="test",
+        murfey_session=1,
+    )
+    context = SXTContext("zeiss", tmp_path, "")
+    context.post_transfer(
+        tmp_path / "example.txrm",
+        required_position_files=[],
+        required_strings=["fractions"],
+        environment=env,
+    )
+
+    mock_open_txrm.assert_called_once_with(
+        tmp_path / "example.txrm", load_images=False, load_reference=False, strict=False
+    )
+    mock_inspector.assert_called_once()
+
+    assert mock_post.call_count == 5
+    mock_post.assert_any_call(
+        "http://localhost:8000/workflow/visits/test/sessions/1/register_data_collection_group",
+        json={
+            "experiment_type_id": 47,
+            "tag": str(tmp_path),
+        },
+        headers={"Authorization": "Bearer "},
+    )
+    mock_post.assert_any_call(
+        "http://localhost:8000/workflow/visits/test/sessions/1/start_data_collection",
+        json={
+            "experiment_type": "sxt",
+            "file_extension": ".txrm",
+            "acquisition_software": "zeiss",
+            "image_directory": f"{tmp_path}/destination",
+            "data_collection_tag": "example",
+            "source": str(tmp_path),
+            "tag": "example",
+            "pixel_size_on_image": "100.1",
+            "image_size_x": 1024,
+            "image_size_y": 2048,
+            "magnification": 1000,
+            "voltage": 0,
+        },
+        headers={"Authorization": "Bearer "},
+    )
+    mock_post.assert_any_call(
+        "http://localhost:8000/workflow/visits/test/sessions/1/register_processing_job",
+        json={
+            "tag": "example",
+            "source": str(tmp_path),
+            "recipe": "sxt-tomo-align",
+            "experiment_type": "sxt",
+        },
+        headers={"Authorization": "Bearer "},
+    )
+    mock_post.assert_any_call(
+        "http://localhost:8000/workflow/sxt/visits/test/sessions/1/sxt_tilt_series",
+        json={
+            "session_id": 1,
+            "tag": "example",
+            "source": str(tmp_path),
+            "pixel_size": 100.1,
+            "tilt_offset": 5,
+            "txrm": str(tmp_path / "destination/example.txrm"),
+        },
+        headers={"Authorization": "Bearer "},
+    )