Add plugin to make thumbnails of xrm files

pyproject.toml

@@ -134,6 +134,7 @@ torch = [
     "picked_particles_3d_central_slice" = "cryoemservices.services.images_plugins:picked_particles_3d_central_slice"
     "tiff_to_apng" = "cryoemservices.services.images_plugins:tiff_to_apng"
     "tilt_series_alignment" = "cryoemservices.services.images_plugins:tilt_series_alignment"
+    "xrm_to_jpeg" = "cryoemservices.services.images_plugins:xrm_to_jpeg"
 [project.entry-points."cryoemservices.services.process_recipe.filters"]
     ispyb = "cryoemservices.util.process_recipe_tools:ispyb_filter"
 [project.entry-points."cryoemservices.wrappers"]

src/cryoemservices/services/images_plugins.py

@@ -10,8 +10,9 @@
 import pandas as pd
 import PIL.Image
 import starfile
-import tifffile as tf
+import tifffile
 from PIL import ImageDraw, ImageEnhance, ImageFilter, ImageFont
+from txrm2tiff.main import convert_and_save
 
 from cryoemservices.services.cryolo import grid_bar_histogram
 from cryoemservices.util.image_processing.shared import convert_to_rgb
@@ -686,7 +687,7 @@ def tiff_to_apng(plugin_params: Callable):
     img = PIL.Image.open(input_file)
 
     # Determine number of frames in image
-    with tf.TiffFile(input_file) as tiff_file:
+    with tifffile.TiffFile(input_file) as tiff_file:
         num_frames = len(tiff_file.pages)
 
     # Collect image frames
@@ -924,3 +925,27 @@ def tilt_series_alignment(plugin_params: Callable):
         extra={"image-processing-time": timing},
     )
     return outfile
+
+
+def xrm_to_jpeg(plugin_params: Callable):
+    if not required_parameters(plugin_params, ["xrm_file", "tiff_destination"]):
+        return False
+    xrm_path = Path(plugin_params("xrm_file"))
+    tiff_path = Path(plugin_params("tiff_destination"))
+    annotate = plugin_params("annotate")
+    if not xrm_path.is_file():
+        logger.error(f"File {xrm_path} not found")
+        return False
+
+    convert_and_save(
+        xrm_path, str(tiff_path).replace("_Annotated", ""), annotate=annotate or False
+    )
+    data = tifffile.imread(tiff_path)
+    if len(data.shape) == 4:
+        # Take first frame if 3D RGB
+        data = data[0]
+    with PIL.Image.fromarray(data) as thumb_im:
+        thumb_im.thumbnail((1024, 1024))
+        thumbnail_jpg = tiff_path.parent / (tiff_path.stem + "_thumbnail.jpg")
+        thumb_im.save(thumbnail_jpg)
+    return tiff_path

tests/services/test_images_plugins.py

@@ -21,6 +21,7 @@
     picked_particles_3d_central_slice,
     tiff_to_apng,
     tilt_series_alignment,
+    xrm_to_jpeg,
 )
 from cryoemservices.util.image_processing.shared import convert_to_rgb
 
@@ -103,6 +104,19 @@ def params(key):
     return params
 
 
+def plugin_params_xrm(input_file, output_file, command):
+    def params(key):
+        p = {
+            "parameters": {"images_command", command},
+            "xrm_file": input_file,
+            "tiff_destination": output_file,
+            "annotate": True,
+        }
+        return p.get(key)
+
+    return params
+
+
 def test_mrc_to_jpeg_nack_when_file_not_found(tmp_path):
     jpeg_path = tmp_path / "new_folder/new_job/new_file.jpeg"
     assert not mrc_to_jpeg(plugin_params(jpeg_path, False))
@@ -808,6 +822,23 @@ def test_tilt_image_alignment_works_2d(mock_imagedraw, tmp_path):
     assert ellipse_calls[1][1] == {"width": 20, "outline": "#f5a927"}
 
 
+@mock.patch("cryoemservices.services.images_plugins.convert_and_save")
+def test_xrm_to_jpeg(mock_convert, tmp_path):
+    input_xrm = tmp_path / "example.xrm"
+    input_xrm.touch()
+    output_tiff = tmp_path / "example_Annotated.tiff"
+    data_2d = np.linspace(0, 255, 100).reshape((10, 10))
+    im = PIL.Image.fromarray(data_2d)
+    im.convert("RGB").save(output_tiff)
+
+    assert xrm_to_jpeg(plugin_params_xrm(input_xrm, output_tiff, "xrm_to_tiff"))
+
+    mock_convert.assert_called_once_with(
+        input_xrm, f"{tmp_path}/example.tiff", annotate=True
+    )
+    assert (tmp_path / "example_Annotated_thumbnail.jpg").is_file()
+
+
 def test_interfaces_without_keys():
     """Test that file path keys are required"""
     assert not mrc_to_jpeg(lambda x: None)
@@ -818,6 +849,7 @@ def test_interfaces_without_keys():
     assert not picked_particles_3d_central_slice(lambda x: None)
     assert not picked_particles_3d_apng(lambda x: None)
     assert not tilt_series_alignment(lambda x: None)
+    assert not xrm_to_jpeg(lambda x: None)
 
 
 def test_interfaces_without_files(tmp_path):
@@ -853,3 +885,6 @@ def test_interfaces_without_files(tmp_path):
         )
     )
     assert not tilt_series_alignment(plugin_params(tmp_path / "not.mrc", True, 1))
+    assert not xrm_to_jpeg(
+        plugin_params_xrm(tmp_path / "not.xrm", tmp_path / "out.tiff", "xrm_to_tiff")
+    )

tests/services/test_images_service.py

@@ -24,7 +24,7 @@ def test_plugins_exist():
     service.initializing()
 
     # Check the expected images plugins are present
-    assert len(service.image_functions.keys()) == 10
+    assert len(service.image_functions.keys()) == 11
     assert service.image_functions.get("mrc_central_slice", "")
     assert service.image_functions.get("mrc_projection", "")
     assert service.image_functions.get("mrc_to_apng", "")
@@ -35,6 +35,7 @@ def test_plugins_exist():
     assert service.image_functions.get("picked_particles_3d_central_slice", "")
     assert service.image_functions.get("tiff_to_apng", "")
     assert service.image_functions.get("tilt_series_alignment", "")
+    assert service.image_functions.get("xrm_to_jpeg", "")
 
 
 @pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")