Merge branch 'start-gallery-thing' into 'v3'

Start implementing GalleryThing

See merge request openflexure/openflexure-microscope-server!576

ofm_config_full.json

@@ -8,6 +8,7 @@
         },
         "stage": "openflexure_microscope_server.things.stage.sangaboard:SangaboardThing",
         "autofocus": "openflexure_microscope_server.things.autofocus:AutofocusThing",
+        "gallery": "openflexure_microscope_server.things.gallery.GalleryThing",
         "camera_stage_mapping": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
         "system": "openflexure_microscope_server.things.system:OpenFlexureSystem",
         "illumination": "openflexure_microscope_server.things.illumination:SangaIllumination",

ofm_config_simulation.json

@@ -3,6 +3,7 @@
         "camera": "openflexure_microscope_server.things.camera.simulation:SimulatedCamera",
         "stage": "openflexure_microscope_server.things.stage.dummy:DummyStage",
         "autofocus": "openflexure_microscope_server.things.autofocus:AutofocusThing",
+        "gallery": "openflexure_microscope_server.things.gallery.GalleryThing",
         "camera_stage_mapping": "openflexure_microscope_server.things.camera_stage_mapping:CameraStageMapper",
         "illumination": "openflexure_microscope_server.things.illumination.SimulatorIllumination",
         "system": "openflexure_microscope_server.things.system:OpenFlexureSystem",

src/openflexure_microscope_server/scan_directories.py

@@ -335,14 +335,25 @@ class ScanDirectoryManager:
         return [f.name for f in os.scandir(self._base_scan_dir) if f.is_dir()]
 
     @requires_lock
-    def all_scans_info(self, ongoing: Optional[str] = None) -> list[ScanInfo]:
+    def all_scans_info(
-        """Return a lists of ScanInfo objects for each scan."""
+        self, *, ongoing: Optional[str] = None, include_ongoing: bool = True
+    ) -> list[ScanInfo]:
+        """Return a lists of ScanInfo objects for each scan.
+
+        :param ongoing: The name of the ongoing scan (or None if no scan is ongoing).
+        :param include_ongoing: True (dfault) to include the scan info of the ongoing
+            scan in the return. False to exclude it.
+
+        :return: A list of ScanInfo objects for each scan.
+        """
         all_info: list[ScanInfo] = []
         for scan_name in self.all_scans:
-            # If the scan is ongoing send flag to skip reading the json data
+            scan_is_ongoing = scan_name == ongoing
-            skip_json = scan_name == ongoing
+            if scan_is_ongoing and not include_ongoing:
+                continue
             scan_dir = ScanDirectory(scan_name, self.base_dir)
-            info = scan_dir.scan_info(skip_json=skip_json)
+            # If the scan is ongoing send flag to skip reading the json data
+            info = scan_dir.scan_info(skip_json=scan_is_ongoing)
             all_info.append(info)
         return all_info
 

src/openflexure_microscope_server/things/__init__.py

@@ -15,6 +15,13 @@ class OFMThing(lt.Thing):
 
     _data_dir: Optional[str] = None
 
+    _show_data_in_gallery: bool = False
+
+    @property
+    def show_data_in_gallery(self) -> bool:
+        """Whether to show in the Gallery."""
+        return self._show_data_in_gallery
+
     def __enter__(self) -> Self:
         """Set the data directory when the Thing is entered."""
         # Note that the `application_config` was already validated when the

src/openflexure_microscope_server/things/camera/__init__.py

@@ -25,6 +25,7 @@ from pydantic import BaseModel, Field
 import labthings_fastapi as lt
 from labthings_fastapi.types.numpy import NDArray
 
+from openflexure_microscope_server.things import OFMThing
 from openflexure_microscope_server.things.background_detect import (
     BackgroundDetectAlgorithm,
 )
@@ -164,7 +165,7 @@ class CameraMemoryBuffer:
             del self._storage[key]
 
 
-class BaseCamera(lt.Thing):
+class BaseCamera(OFMThing):
     """The base class for all cameras. All cameras must directly inherit from this class.
 
     The connection to the camera hardware should be added to the ``__enter__`` method not

src/openflexure_microscope_server/things/gallery.py

@@ -0,0 +1,99 @@
+"""Server-side gallery functionality.
+
+The types of data that are captured and how they display in the gallery are defined by
+the Things that capture the Data. This thing just provides a unified way for the gallery
+front end to access the data.
+"""
+
+from typing import Any, Mapping, Optional, Protocol, Self, cast, runtime_checkable
+
+from pydantic import BaseModel
+
+import labthings_fastapi as lt
+
+from openflexure_microscope_server.things import OFMThing
+
+
+@runtime_checkable
+class GalleryCompatibleThing(Protocol):
+    """Protocol for checking Things using the gallery are complete.
+
+    Note that runtime checkable protocols only check that the methods exist, not the
+    full signatures. This means that anything attempting to define the methods will
+    be picked up, but may throw an error when used.
+    """
+
+    # Ensure it is a Thing:
+    _thing_server_interface: lt.ThingServerInterface
+
+    # Ensure it is an OFMThing:
+    show_data_in_gallery: bool
+
+    gallery_data_name: str
+
+    gallery_data_schema: type[BaseModel]
+
+    # Ignore D102: No docstrings for the protocol.
+    def get_data_for_gallery(self) -> list[BaseModel]: ...  # noqa: D102
+
+
+class GalleryThing(lt.Thing):
+    """A Thing for communicating with the front end gallery."""
+
+    all_ofm_things: Mapping[str, OFMThing] = lt.thing_slot()
+
+    _gallery_providing_things: Optional[Mapping[str, GalleryCompatibleThing]] = None
+
+    @property
+    def gallery_providing_things(self) -> Mapping[str, GalleryCompatibleThing]:
+        """All Things that provide data to the gallery."""
+        if self._gallery_providing_things is None:
+            raise RuntimeError(
+                "Cannot access gallery_providing_things before server has started."
+            )
+        return self._gallery_providing_things
+
+    def __enter__(self) -> Self:
+        """Check for all gallery providing things on server startup."""
+        self._set_gallery_providers()
+        return self
+
+    def _set_gallery_providers(self) -> None:
+        """Set the mapping of gallery providing things.
+
+        This is called on ``__enter__`` when the server starts.
+        """
+        gallery_providers = {
+            name: thing
+            for name, thing in self.all_ofm_things.items()
+            if thing.show_data_in_gallery
+        }
+        # cache initial list of keys as it may change in the loop
+        keys = list(gallery_providers.keys())
+        for key in keys:
+            if not isinstance(gallery_providers[key], GalleryCompatibleThing):
+                self.logger.error(
+                    f"Data from {key} cannot be shown in gallery as it does not "
+                    "provide all necessary properties/methods for the gallery."
+                )
+                gallery_providers.pop(key)
+
+        # Cast the type of each thing to "GalleryCompatibleThing" as other Things have
+        # been popped.
+        self._gallery_providing_things = cast(
+            Mapping[str, GalleryCompatibleThing], gallery_providers
+        )
+
+    @lt.property
+    def list_data(self) -> list[dict[str, Any]]:
+        """List the data from all registered things.
+
+        Currently only works with `smart_scan` as the UI cards are not customisable.
+
+        This will change to an action (or another type of endpoint) at a
+        later date to enable filtering, and returning only a specific page.
+        """
+        data_list = []
+        for thing in self.gallery_providing_things.values():
+            data_list += [model.model_dump() for model in thing.get_data_for_gallery()]
+        return data_list

src/openflexure_microscope_server/things/smart_scan.py

@@ -71,16 +71,6 @@ class ActiveScanData(scan_directories.BaseScanData):
         self.scan_result = result
 
 
-class ScanListInfo(BaseModel):
-    """The information to be sent to the Scan List tab."""
-
-    scans: list[scan_directories.ScanInfo]
-    """The list of scans as ScanInfo objects"""
-
-    ongoing: Optional[str]
-    """The name of the ongoing scan or None"""
-
-
 class JPEGBlob(lt.blob.Blob):
     """A class representing a JPEG image as a LabThings FastAPI Blob."""
 
@@ -176,6 +166,31 @@ class SmartScanThing(OFMThing):
         In this case it doesn't need to do anything.
         """
 
+    # Register with gallery.
+    _show_data_in_gallery = True
+
+    @property
+    def gallery_data_name(self) -> str:
+        """Name under which data shows up in gallery."""
+        return "Scans"
+
+    @property
+    def gallery_data_schema(self) -> type[scan_directories.ScanInfo]:
+        """The schema (BaseModel) for passing data to the gallery."""
+        return scan_directories.ScanInfo
+
+    def get_data_for_gallery(self) -> list[scan_directories.ScanInfo]:
+        """Return all the information from the scan directories.
+
+        It is preferable to use the method rather than calling
+        _scan_dir_manager.all_scans_info() directly as it will handle stopping the json
+        in any ongoing scans being read.
+        """
+        ongoing_name = None if self._ongoing_scan is None else self.ongoing_scan.name
+        return self._scan_dir_manager.all_scans_info(
+            ongoing=ongoing_name, include_ongoing=False
+        )
+
     # Note that the default detector name is set at init. This is over written if
     # setting is loaded from disk.
     @lt.setting
@@ -544,31 +559,6 @@ class SmartScanThing(OFMThing):
     stitch_automatically: bool = lt.setting(default=True)
     """Whether to run a final stitch at the end of a successful scan."""
 
-    def _get_all_scan_info(self) -> list[scan_directories.ScanInfo]:
-        """Return all the information from the scan directories.
-
-        It is preferable to use the method rather than calling
-        _scan_dir_manager.all_scans_info() directly as it will handle stopping the json
-        in any ongoing scans being read.
-        """
-        ongoing_name = None if self._ongoing_scan is None else self.ongoing_scan.name
-        return self._scan_dir_manager.all_scans_info(ongoing=ongoing_name)
-
-    @lt.property
-    def scans(self) -> ScanListInfo:
-        """All the available scans.
-
-        Each scan has a name (which can be used to access it), along with
-        its modified and created times (according to the filesystem) and
-        the number of items in the ``images`` folder. Note that image count
-        uses a regular expression, and changes to the naming scheme will
-        break it.
-        """
-        return ScanListInfo(
-            scans=self._get_all_scan_info(),
-            ongoing=None if self._ongoing_scan is None else self.ongoing_scan.name,
-        )
-
     @lt.endpoint(
         "get",
         "get_stitch/{scan_name}",
@@ -632,8 +622,8 @@ class SmartScanThing(OFMThing):
     @lt.action
     def purge_empty_scans(self) -> None:
         """Delete all scan folders containing no images at the top level."""
-        # JSON is ignored as it's created before any images are captured
+        # Use the scan list (the data read by the gallery) to check for empty scans.
-        for scan_info in self._get_all_scan_info():
+        for scan_info in self.get_data_for_gallery():
             if scan_info.number_of_images == 0:
                 self._delete_scan(scan_info.name)
 
@@ -748,6 +738,8 @@ class SmartScanThing(OFMThing):
         """
         if self._scan_lock.locked():
             raise RuntimeError("Can't stitch previous scans while a scan is ongoing")
-        for scan in self._get_all_scan_info():
+        # Use the scan list (the data read by the gallery) to find any scans that
+        # need stitching.
+        for scan in self.get_data_for_gallery():
             if scan.dzi is None:
                 self.stitch_scan(scan_name=scan.name)

tests/conftest.py

@@ -1,6 +1,8 @@
 """Fixtures for all test suites."""
 
+import json
 import logging
+import os
 import re
 from collections.abc import Iterable
 from contextlib import contextmanager
@@ -10,6 +12,24 @@ import pytest
 
 from labthings_fastapi.testing import create_thing_without_server
 
+from .shared_utils.lt_test_utils import LabThingsTestEnv
+
+THIS_DIR = os.path.dirname(os.path.abspath(__file__))
+REPO_ROOT = os.path.dirname(THIS_DIR)
+SIM_CONFIG = os.path.join(REPO_ROOT, "ofm_config_simulation.json")
+
+
+@pytest.fixture
+def simulation_test_env():
+    """Yield a server with the configuration from the simulation json."""
+    with open(SIM_CONFIG, "r", encoding="utf-8") as f_obj:
+        config_dict = json.load(f_obj)
+    with LabThingsTestEnv(
+        things=config_dict["things"],
+        application_config=config_dict["application_config"],
+    ) as env:
+        yield env
+
 
 @pytest.fixture
 def check_side_effect(caplog):

tests/integration_tests/test_actions.py

@@ -12,7 +12,6 @@ it has been moved as it artificaially inflated coverage.
 """
 
 import json
-import os
 
 import numpy as np
 import piexif
@@ -21,29 +20,11 @@ from PIL import Image
 
 import labthings_fastapi as lt
 
-from ..shared_utils.lt_test_utils import LabThingsTestEnv
 
-THIS_DIR = os.path.dirname(os.path.abspath(__file__))
+def test_autofocus(simulation_test_env):
-REPO_ROOT = os.path.dirname(os.path.dirname(THIS_DIR))
-SIM_CONFIG = os.path.join(REPO_ROOT, "ofm_config_simulation.json")
-
-
-@pytest.fixture
-def test_env():
-    """Yield a server with a very basic configuration."""
-    with open(SIM_CONFIG, "r", encoding="utf-8") as f_obj:
-        config_dict = json.load(f_obj)
-    with LabThingsTestEnv(
-        things=config_dict["things"],
-        application_config=config_dict["application_config"],
-    ) as env:
-        yield env
-
-
-def test_autofocus(test_env):
     """Test Fast Autofocus can run doesn't raise an exception."""
-    stage = test_env.get_thing_client("stage")
+    stage = simulation_test_env.get_thing_client("stage")
-    autofocus = test_env.get_thing_client("autofocus")
+    autofocus = simulation_test_env.get_thing_client("autofocus")
     assert stage.position["z"] == 0
     # Autofocus 5 times and check each ends within 500 steps
     for i in range(5):
@@ -51,17 +32,17 @@ def test_autofocus(test_env):
         assert abs(stage.position["z"]) < 500, f"Autofocus failed on iteration {i}"
 
 
-def test_grab_jpeg(test_env):
+def test_grab_jpeg(simulation_test_env):
     """Check that grab_jpeg returns a blob that can be opened."""
-    camera = test_env.get_thing_client("camera")
+    camera = simulation_test_env.get_thing_client("camera")
     blob = camera.grab_jpeg()
     image = Image.open(blob.open())
     assert image.size == (820, 616)
 
 
-def test_capture_jpeg_metadata(test_env):
+def test_capture_jpeg_metadata(simulation_test_env):
     """Check that the position is encoded into the image metadata."""
-    camera = test_env.get_thing_client("camera")
+    camera = simulation_test_env.get_thing_client("camera")
     blob = camera.capture_jpeg()
     image = Image.open(blob.open())
     exif_dict = piexif.load(image.info["exif"])
@@ -72,9 +53,9 @@ def test_capture_jpeg_metadata(test_env):
     assert image.size == (820, 616)
 
 
-def test_stage(test_env):
+def test_stage(simulation_test_env):
     """Test moving the stage forwards and backwards."""
-    stage = test_env.get_thing_client("stage")
+    stage = simulation_test_env.get_thing_client("stage")
     start = stage.position
     move = {"x": 1, "y": 2, "z": 3}
     move_back = {"x": -1, "y": -2, "z": -3}
@@ -95,20 +76,20 @@ def test_stage(test_env):
     assert start["z"] == pos["z"]
 
 
-def test_capture_array(test_env):
+def test_capture_array(simulation_test_env):
     """Capture array from simulation and check the size is as expected."""
-    camera = test_env.get_thing_client("camera")
+    camera = simulation_test_env.get_thing_client("camera")
     array = np.asarray(camera.capture_array())
     assert array.shape == (616, 820, 3)
 
 
-def test_camera_stage_mapping_calibration(test_env):
+def test_camera_stage_mapping_calibration(simulation_test_env):
     """Check that camera stage mapping runs and returns the expected result."""
-    camera = test_env.get_thing_client("camera")
+    camera = simulation_test_env.get_thing_client("camera")
     # Remove camera settling time for speed.
     camera.settling_time = 0
-    csm = test_env.get_thing_client("camera_stage_mapping")
+    csm = simulation_test_env.get_thing_client("camera_stage_mapping")
-    stage = test_env.get_thing_client("stage")
+    stage = simulation_test_env.get_thing_client("stage")
 
     # Check it starts uncalibrated
     assert csm.calibration_required

tests/unit_tests/test_gallery.py

@@ -0,0 +1,122 @@
+"""Tests that captures have the expected metadata."""
+
+import logging
+
+from pydantic import BaseModel
+
+from labthings_fastapi.testing import create_thing_without_server
+
+from openflexure_microscope_server.things import OFMThing
+from openflexure_microscope_server.things.gallery import (
+    GalleryCompatibleThing,
+    GalleryThing,
+)
+
+from ..shared_utils.lt_test_utils import LabThingsTestEnv
+
+
+class MockGalleryData(BaseModel):
+    """Mock gallery data."""
+
+    mock: str
+    foobar: int
+
+
+class MinimalGalleryClass:
+    """A class that provides data to the gallery but is NOT a thing.
+
+    This should fail the protocol check as it is not an OFMThing
+    """
+
+    gallery_data_name: str = "Mock"
+
+    gallery_data_schema: type[BaseModel] = MockGalleryData
+
+    def get_data_for_gallery(self) -> list[BaseModel]:
+        """Return a list of Mock Gallery Data."""
+        return [MockGalleryData(mock="mock", foobar="foobar")]
+
+
+class MinimalGallerySource(OFMThing, MinimalGalleryClass):
+    """Minimal example of a Thing that can show data in the gallery.
+
+    Mixes MinimalGalleryClass into OFMThing to be recognised by the protocol.
+    """
+
+    show_data_in_gallery = True
+
+
+class BadGallerySource(OFMThing):
+    """An OFMThing that almost defines enough to show in the gallery.
+
+    Shouldn't match the protocol as ``gallery_data_name`` is missing.
+    """
+
+    show_data_in_gallery = True
+
+    gallery_data_schema: type[BaseModel] = MockGalleryData
+
+    def get_data_for_gallery(self) -> list[BaseModel]:
+        """Return a list of Mock Gallery Data."""
+        return [MockGalleryData(mock="mock", foobar="foobar")]
+
+
+def test_gallery_compatible_protocol():
+    """Check the gallery compatible protocol detects compatible classes only."""
+    # Minimal class has the gallery specific methods but is not an OFMThing.
+    assert not isinstance(MinimalGalleryClass(), GalleryCompatibleThing)
+
+    # BadGallerySource is an OFM Thing but is missing one of the required properties.
+    assert not isinstance(
+        create_thing_without_server(BadGallerySource), GalleryCompatibleThing
+    )
+
+    # MinimalGallerySource should match!
+    assert isinstance(
+        create_thing_without_server(MinimalGallerySource), GalleryCompatibleThing
+    )
+
+
+def test_gallery_thing_finds_all_providers(simulation_test_env):
+    """Check the gallery identifies the correct Things that will provide data."""
+    gallery = simulation_test_env.get_thing_by_name("gallery")
+    snake_workflow = simulation_test_env.get_thing_by_name("snake_workflow")
+    smart_scan = simulation_test_env.get_thing_by_name("smart_scan")
+    camera = simulation_test_env.get_thing_by_name("camera")
+
+    assert snake_workflow not in gallery.all_ofm_things.values()
+    assert camera in gallery.all_ofm_things.values()
+    assert smart_scan in gallery.all_ofm_things.values()
+
+    assert snake_workflow not in gallery.gallery_providing_things.values()
+    assert camera not in gallery.gallery_providing_things.values()
+    assert smart_scan in gallery.gallery_providing_things.values()
+
+    assert not isinstance(snake_workflow, GalleryCompatibleThing)
+    assert isinstance(smart_scan, GalleryCompatibleThing)
+
+
+def test_gallery_logs_for_bad_providers(caplog):
+    """Test that an error is logged if a gallery source doesn't match the protocol."""
+    # Create a config with the minimal Thing and the bad Thing
+    things = {
+        "minimal_thing": MinimalGallerySource,
+        "bad_thing": BadGallerySource,
+        "gallery": GalleryThing,
+    }
+    with caplog.at_level(logging.INFO):
+        # Start the server
+        with LabThingsTestEnv(
+            things=things, application_config={"data_folder": "./openflexure/data/"}
+        ) as env:
+            gallery = env.get_thing_by_name("gallery")
+            # Minimal thing is listed as a gallery provider
+            assert "minimal_thing" in gallery.gallery_providing_things
+            # Bad thing isn't as the protocol doesn't match
+            assert "bad_thing" not in gallery.gallery_providing_things
+
+        # There is an error logged about bad_thing
+        assert len(caplog.records) == 1
+        record = caplog.records[0]
+        assert "Data from bad_thing cannot be shown in gallery" in record.message
+        assert record.levelname == "ERROR"

webapp/src/components/tabContentComponents/scanListComponents/scanCard.vue

@@ -13,8 +13,7 @@
         </div>
       </div>
       <h3 class="uk-card-title scan-card-title">{{ scanData.name }}</h3>
-      <h4 v-if="ongoing" class="ongoing-msg">Scan in progress</h4>
+      <div class="button-container">
-      <div v-if="!ongoing" class="button-container">
         <div class="uk-button-group scan-card-buttons">
           <action-button
             class="uk-width-1-2"
@@ -59,10 +58,9 @@
         <ul>
           <li>{{ scanData.number_of_images }} images</li>
           <li>Created: {{ formatDate(scanData.created) }}</li>
-          <li v-if="!ongoing">Duration: {{ formatDuration(scanData.duration) }}</li>
+          <li>Duration: {{ formatDuration(scanData.duration) }}</li>
-          <li v-if="ongoing">Duration: <i>Ongoing</i></li>
         </ul>
-        <ul v-if="!ongoing">
+        <ul>
           <li v-if="scanData.number_of_images < 3" class="warning-msg">
             Not enough images to stitch
           </li>
@@ -102,10 +100,6 @@ export default {
       type: String,
       required: true,
     },
-    ongoing: {
-      type: Boolean,
-      required: true,
-    },
   },
 
   emits: ["viewer-requested", "update-requested"],
@@ -148,9 +142,7 @@ export default {
     },
     requestViewer() {
       // Notify parent that thumbnail was clicked
-      if (!this.ongoing) {
+      this.$emit("viewer-requested", this.scanData);
-        this.$emit("viewer-requested", this.scanData);
-      }
     },
     async deleteScan() {
       try {
@@ -204,9 +196,4 @@ ul {
 .scan-card-title {
   text-align: center;
 }
-
-.ongoing-msg {
-  text-align: center;
-  padding: 2rem 0;
-}
 </style>

webapp/src/components/tabContentComponents/scanListContent.vue

@@ -55,7 +55,6 @@
           <scan-card
             :scan-data="scanData"
             :scans-uri="scansUri"
-            :ongoing="isOngoing(scanData.name)"
             @viewer-requested="showScan"
             @update-requested="updateScans"
           />
@@ -97,7 +96,6 @@ export default {
   data: function () {
     return {
       scans: [],
-      ongoing: null,
       selectedScan: null,
       osdViewer: null,
       currentPage: 1,
@@ -108,7 +106,9 @@ export default {
   computed: {
     ...mapState(useSettingsStore, ["baseUri", "ready"]),
     scansUri() {
-      return this.thingPropertyUrl("smart_scan", "scans");
+      // The scans URI is currently used for creating endpoint URIs.
+      // The actual property does not exist. So allowUndefined=true
+      return this.thingPropertyUrl("smart_scan", "scans", true);
     },
     scansEmpty() {
       return this.scans.length == 0;
@@ -179,9 +179,7 @@ export default {
     },
     async updateScans() {
       try {
-        let scans_information = await this.readThingProperty("smart_scan", "scans");
+        let scans = await this.readThingProperty("gallery", "list_data");
-        let scans = scans_information.scans;
-        this.ongoing = scans_information.ongoing;
         if (!scans | (scans.length == 0)) {
           this.scans = scans;
         }
@@ -198,9 +196,6 @@ export default {
         this.scans = [];
       }
     },
-    isOngoing(name) {
-      return name === this.ongoing;
-    },
     async deleteAllScans() {
       try {
         await this.modalConfirm(