Update tests to avoid txrm2tiff

Author: stephen-riggs

src/murfey/client/contexts/sxt.py

@@ -61,7 +61,7 @@ def register_sxt_data_collection(
                 "source": str(self._basepath),
                 "tag": tilt_series,
                 "pixel_size_on_image": str(
-                    data_collection_parameters.get("pixel_size", 100) * 1e-10
+                    round(data_collection_parameters.get("pixel_size", 100), 2) * 1e-10
                 ),
                 "image_size_x": data_collection_parameters.get("image_size_x", 0),
                 "image_size_y": data_collection_parameters.get("image_size_y", 0),
@@ -244,7 +244,7 @@ def post_transfer(
                 data={
                     "tag": transferred_file.stem,
                     "source": destination_search_dir,
-                    "pixel_size": metadata.get("pixel_size", 100),
+                    "pixel_size": round(metadata.get("pixel_size", 100), 2),
                     "tilt_offset": midpoint(angles),
                     "tilt_series_length": metadata.get(
                         "tilt_series_length", len(angles)

tests/client/contexts/test_sxt.py

@@ -1,6 +1,8 @@
 from unittest.mock import patch
 from urllib.parse import urlparse
 
+import numpy as np
+
 from murfey.client.contexts.sxt import SXTContext
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 
@@ -36,91 +38,110 @@ def test_sxt_context_xrm(mock_post, tmp_path):
 
 
 @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
-):
+@patch("murfey.client.contexts.sxt.OleFileIO")
+def test_sxt_context_txrm(mock_ole_file, 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
+    mock_ole_file().__enter__().exists.return_value = True
+    # Motor position names
+    mock_ole_file().__enter__().openstream().read.return_value = (
+        "\x00Val1\x00\x00Energy\x00".encode()
+    )
+    # Metadata encoded arrays
+    mock_ole_file().__enter__().openstream().getvalue.side_effect = [
+        np.array([-55, -25, 5, 35, 65], dtype=np.float32).tobytes(),  # Angles
+        np.array([0.01001], dtype=np.float32).tobytes(),  # Pixel size
+        np.array([1024], dtype=np.int32).tobytes(),  # Image Width
+        np.array([2048], dtype=np.int32).tobytes(),  # Image Height
+        np.array([1.5], dtype=np.float32).tobytes(),  # Exposure time
+        np.array([1000], dtype=np.float32).tobytes(),  # Mag
+        np.array([5], dtype=np.int32).tobytes(),  # Image count
+        np.array([0, 519, 2, 3], dtype=np.float32).tobytes(),  # Motor Pos (energy)
     ]
 
     env = MurfeyInstanceEnvironment(
         url=urlparse("http://localhost:8000"),
         client_id=0,
-        sources=[tmp_path],
-        default_destinations={tmp_path: str(tmp_path / "destination")},
+        sources=[tmp_path / "cm12345-6/grid1"],
+        default_destinations={
+            f"{tmp_path}/cm12345-6/grid1": f"{tmp_path}/destination/cm12345-6/grid1"
+        },
         instrument_name="",
-        visit="test",
+        visit="cm12345-6",
         murfey_session=1,
     )
-    context = SXTContext("zeiss", tmp_path, {}, "")
+    context = SXTContext("zeiss", tmp_path / "cm12345-6/grid1", {}, "")
     context.post_transfer(
-        tmp_path / "example.txrm",
+        tmp_path / "cm12345-6/grid1/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()
+    mock_ole_file.assert_any_call(str(tmp_path / "cm12345-6/grid1/example.txrm"))
+    assert mock_ole_file().__enter__().exists.call_count == 10
+    assert mock_ole_file().__enter__().openstream.call_count == 11  # 9 + 2 above
+    mock_ole_file().__enter__().exists.assert_any_call("ReferenceData/Image")
+    for field_name in [
+        "ImageInfo/Angles",
+        "ImageInfo/PixelSize",
+        "ImageInfo/ImageWidth",
+        "ImageInfo/ImageHeight",
+        "ImageInfo/ExpTimes",
+        "ImageInfo/XrayMagnification",
+        "ImageInfo/ImagesTaken",
+        "PositionInfo/AxisNames",
+        "PositionInfo/MotorPositions",
+    ]:
+        mock_ole_file().__enter__().exists.assert_any_call(field_name)
+        mock_ole_file().__enter__().openstream.assert_any_call(field_name)
 
     assert mock_post.call_count == 5
     mock_post.assert_any_call(
-        "http://localhost:8000/workflow/visits/test/sessions/1/register_data_collection_group",
+        "http://localhost:8000/workflow/visits/cm12345-6/sessions/1/register_data_collection_group",
         json={
             "experiment_type_id": 47,
-            "tag": str(tmp_path),
+            "tag": f"{tmp_path}/cm12345-6/grid1",
         },
         headers={"Authorization": "Bearer "},
     )
     mock_post.assert_any_call(
-        "http://localhost:8000/workflow/visits/test/sessions/1/start_data_collection",
+        "http://localhost:8000/workflow/visits/cm12345-6/sessions/1/start_data_collection",
         json={
             "experiment_type": "sxt",
             "file_extension": ".txrm",
             "acquisition_software": "zeiss",
-            "image_directory": f"{tmp_path}/destination",
+            "image_directory": f"{tmp_path}/destination/cm12345-6/grid1",
             "data_collection_tag": "example",
-            "source": str(tmp_path),
+            "source": f"{tmp_path}/cm12345-6/grid1",
             "tag": "example",
-            "pixel_size_on_image": "100.1",
+            "pixel_size_on_image": str(100.1 * 1e-10),
             "image_size_x": 1024,
             "image_size_y": 2048,
             "magnification": 1000,
+            "energy": 519,
             "voltage": 0,
         },
         headers={"Authorization": "Bearer "},
     )
     mock_post.assert_any_call(
-        "http://localhost:8000/workflow/visits/test/sessions/1/register_processing_job",
+        "http://localhost:8000/workflow/visits/cm12345-6/sessions/1/register_processing_job",
         json={
             "tag": "example",
-            "source": str(tmp_path),
+            "source": f"{tmp_path}/cm12345-6/grid1",
             "recipe": "sxt-aretomo",
             "experiment_type": "sxt",
         },
         headers={"Authorization": "Bearer "},
     )
     mock_post.assert_any_call(
-        "http://localhost:8000/workflow/sxt/visits/test/sessions/1/sxt_tilt_series",
+        "http://localhost:8000/workflow/sxt/visits/cm12345-6/sessions/1/sxt_tilt_series",
         json={
-            "session_id": 1,
             "tag": "example",
-            "source": str(tmp_path),
+            "source": f"{tmp_path}/cm12345-6/grid1",
             "pixel_size": 100.1,
             "tilt_offset": 5,
-            "txrm": str(tmp_path / "destination/example.txrm"),
+            "tilt_series_length": 5,
+            "txrm": str(tmp_path / "destination/cm12345-6/grid1/example.txrm"),
         },
         headers={"Authorization": "Bearer "},
     )

tests/workflows/test_register_data_collection.py

@@ -76,6 +76,7 @@ def test_run(
         "experiment_type": "SPA",
         "image_suffix": ".jpg",
         "voltage": 200,
+        "energy": 520,
         "pixel_size": 1e-9,
         "image_size_x": 2048,
         "image_size_y": 2048,