Merge branch 'atlas-dcg' into match-atlas-dcgs

Author: stephen-riggs

src/murfey/client/contexts/atlas.py

@@ -2,6 +2,8 @@
 from pathlib import Path
 from typing import Optional
 
+import xmltodict
+
 from murfey.client.context import Context, _atlas_destination
 from murfey.client.contexts.spa import _get_source
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
@@ -43,8 +45,60 @@ def post_transfer(
                     function_name="make_atlas_jpg",
                     token=self._token,
                     session_id=environment.murfey_session,
-                    data={"path": str(transferred_atlas_name)},
+                    data={"path": str(transferred_atlas_name).replace("//", "/")},
                 )
                 logger.info(
                     f"Submitted request to create JPG image of atlas {str(transferred_atlas_name)!r}"
                 )
+        elif (
+            environment
+            and "Atlas_" in transferred_file.stem
+            and transferred_file.suffix == ".xml"
+        ):
+            source = _get_source(transferred_file, environment)
+            if source:
+                atlas_mrc = transferred_file.with_suffix(".mrc")
+                transferred_atlas_jpg = _atlas_destination(
+                    environment, source, self._token
+                ) / atlas_mrc.relative_to(source.parent).with_suffix(".jpg")
+
+                with open(transferred_file, "rb") as atlas_xml:
+                    atlas_xml_data = xmltodict.parse(atlas_xml)
+                    atlas_original_pixel_size = float(
+                        atlas_xml_data["MicroscopeImage"]["SpatialScale"]["pixelSize"][
+                            "x"
+                        ]["numericValue"]
+                    )
+
+                # need to calculate the pixel size of the downscaled image
+                atlas_pixel_size = atlas_original_pixel_size * 7.8
+
+                for p in transferred_file.parts:
+                    if p.startswith("Sample"):
+                        sample = int(p.replace("Sample", ""))
+                        break
+                else:
+                    logger.warning(
+                        f"Sample could not be identified for {transferred_file}"
+                    )
+                    return
+
+                dcg_data = {
+                    "experiment_type_id": 44,  # Atlas
+                    "tag": str(transferred_file.parent),
+                    "atlas": str(transferred_atlas_jpg).replace("//", "/"),
+                    "sample": sample,
+                    "atlas_pixel_size": atlas_pixel_size,
+                }
+                capture_post(
+                    base_url=str(environment.url.geturl()),
+                    router_name="workflow.router",
+                    function_name="register_dc_group",
+                    token=self._token,
+                    visit_name=environment.visit,
+                    session_id=environment.murfey_session,
+                    data=dcg_data,
+                )
+                logger.info(
+                    f"Registered data collection group for atlas {str(transferred_atlas_jpg)!r}"
+                )

tests/client/contexts/test_atlas.py

@@ -0,0 +1,92 @@
+from unittest.mock import patch
+from urllib.parse import urlparse
+
+from murfey.client.contexts.atlas import AtlasContext
+from murfey.client.instance_environment import MurfeyInstanceEnvironment
+
+
+def test_atlas_context_initialisation(tmp_path):
+    context = AtlasContext("tomo", tmp_path, "token")
+    assert context.name == "Atlas"
+    assert context._acquisition_software == "tomo"
+    assert context._basepath == tmp_path
+    assert context._token == "token"
+
+
+@patch("murfey.client.contexts.atlas.capture_post")
+def test_atlas_context_mrc(mock_capture_post, tmp_path):
+    env = MurfeyInstanceEnvironment(
+        url=urlparse("http://localhost:8000"),
+        client_id=0,
+        sources=[tmp_path / "cm12345-6"],
+        default_destinations={
+            tmp_path / "cm12345-6": f"{tmp_path}/destination/cm12345-6"
+        },
+        instrument_name="",
+        visit="cm12345-6",
+        murfey_session=1,
+    )
+    context = AtlasContext("tomo", tmp_path, "token")
+
+    atlas_mrc = tmp_path / "cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas_1.mrc"
+    atlas_mrc.parent.mkdir(parents=True)
+    atlas_mrc.touch()
+
+    context.post_transfer(
+        atlas_mrc,
+        environment=env,
+    )
+    mock_capture_post.assert_called_once_with(
+        base_url="http://localhost:8000",
+        router_name="session_control.spa_router",
+        function_name="make_atlas_jpg",
+        token="token",
+        session_id=1,
+        data={"path": f"{tmp_path}/destination/{atlas_mrc.relative_to(tmp_path)}"},
+    )
+
+
+@patch("murfey.client.contexts.atlas.capture_post")
+def test_atlas_context_xml(mock_capture_post, tmp_path):
+    env = MurfeyInstanceEnvironment(
+        url=urlparse("http://localhost:8000"),
+        client_id=0,
+        sources=[tmp_path / "cm12345-6"],
+        default_destinations={
+            tmp_path / "cm12345-6": f"{tmp_path}/destination/cm12345-6"
+        },
+        instrument_name="",
+        visit="cm12345-6",
+        murfey_session=1,
+    )
+    context = AtlasContext("tomo", tmp_path, "token")
+
+    atlas_pixel_size = 4.6
+    atlas_xml = tmp_path / "cm12345-6/Supervisor_atlas/Sample2/Atlas/Atlas_1.xml"
+    atlas_xml.parent.mkdir(parents=True)
+    with open(atlas_xml, "w") as new_xml:
+        new_xml.write(
+            f"<MicroscopeImage><SpatialScale><pixelSize><x><numericValue>{atlas_pixel_size}"
+            "</numericValue></x></pixelSize></SpatialScale></MicroscopeImage>"
+        )
+
+    context.post_transfer(
+        atlas_xml,
+        environment=env,
+    )
+    dcg_data = {
+        "experiment_type_id": 44,  # Atlas
+        "tag": str(atlas_xml.parent),
+        "atlas": f"{tmp_path}/destination/{atlas_xml.relative_to(tmp_path).with_suffix('.jpg')}",
+        "sample": 2,
+        "atlas_pixel_size": atlas_pixel_size * 7.8,
+    }
+    mock_capture_post.assert_called_once_with(
+        base_url="http://localhost:8000",
+        router_name="workflow.router",
+        function_name="register_dc_group",
+        token="token",
+        visit_name="cm12345-6",
+        session_id=1,
+        data=dcg_data,
+    )