Merge pull request #121 from fmi-faim/imagexpress-patterns

ImageXpress: support time dimension

examples/ImageXpressSinglePlaneAcquisitionExample.py

@@ -14,7 +14,10 @@ def main():
 
     # Parse MD plate acquisition.
     plate_acquisition = SinglePlaneAcquisition(
-        acquisition_dir=Path(__file__).parent.parent / "resources" / "Projection-Mix",
+        acquisition_dir=Path(__file__).parent.parent
+        / "resources"
+        / "ImageXpress"
+        / "Projection-Mix",
         alignment=TileAlignmentOptions.GRID,
     )
 

examples/ImageXpressStackAcquisitionExample.py

@@ -22,7 +22,10 @@ def main():
 
     # Parse MD plate acquisition.
     plate_acquisition = StackAcquisition(
-        acquisition_dir=Path(__file__).parent.parent / "resources" / "Projection-Mix",
+        acquisition_dir=Path(__file__).parent.parent
+        / "resources"
+        / "ImageXpress"
+        / "Projection-Mix",
         alignment=TileAlignmentOptions.GRID,
     )
 

src/faim_ipa/hcs/imagexpress/ImageXpressWellAcquisition.py

@@ -30,7 +30,7 @@ def _assemble_tiles(self) -> list[Tile]:
         tiles = []
         for i, row in self._files.iterrows():
             file = row["path"]
-            time_point = 0
+            time_point = row["t"] if "t" in row.index and row["t"] is not None else 0
             channel = row["channel"]
             metadata = load_metaseries_tiff_metadata(file)
             if self._z_spacing is None:
@@ -77,12 +77,15 @@ def get_z_spacing(self) -> Optional[float]:
         return self._z_spacing
 
     def get_axes(self) -> list[str]:
+        axes = ["y", "x"]
+
         if "z" in self._files.columns:
-            axes = ["z", "y", "x"]
-        else:
-            axes = ["y", "x"]
+            axes = ["z"] + axes
 
         if self._files["channel"].nunique() > 1:
             axes = ["c"] + axes
 
+        if "t" in self._files.columns and self._files["t"].nunique() > 1:
+            axes = ["t"] + axes
+
         return axes

src/faim_ipa/hcs/imagexpress/MixedAcquisition.py

@@ -76,7 +76,7 @@ def _filter_mips(self, files: pd.DataFrame) -> pd.DataFrame:
 
     def _get_root_re(self) -> re.Pattern:
         return re.compile(
-            r".*[\/\\](?P<date>\d{4}-\d{2}-\d{2})[\/\\](?P<acq_id>\d+)(?:[\/\\]ZStep_(?P<z>\d+))?.*"
+            r".*[\/\\](?P<date>\d{4}-\d{2}-\d{2})[\/\\](?P<acq_id>\d+)(?:[\/\\]TimePoint_(?P<t>\d+))?(?:[\/\\]ZStep_(?P<z>\d+))?.*"
         )
 
     def _get_filename_re(self) -> re.Pattern:

src/faim_ipa/hcs/imagexpress/SinglePlaneAcquisition.py

@@ -50,7 +50,9 @@ def __init__(
         )
 
     def _get_root_re(self) -> re.Pattern:
-        return re.compile(r".*[\/\\](?P<date>\d{4}-\d{2}-\d{2})[\/\\](?P<acq_id>\d+)")
+        return re.compile(
+            r".*[\/\\](?P<date>\d{4}-\d{2}-\d{2})[\/\\](?P<acq_id>\d+)(?:[\/\\]TimePoint_(?P<t>\d+))?"
+        )
 
     def _get_filename_re(self) -> re.Pattern:
         return re.compile(

src/faim_ipa/hcs/imagexpress/StackAcquisition.py

@@ -60,7 +60,7 @@ def _parse_files(self) -> pd.DataFrame:
 
     def _get_root_re(self) -> re.Pattern:
         return re.compile(
-            r".*[\/\\](?P<date>\d{4}-\d{2}-\d{2})[\/\\](?P<acq_id>\d+)(?:[\/\\]ZStep_(?P<z>\d+))"
+            r".*[\/\\](?P<date>\d{4}-\d{2}-\d{2})[\/\\](?P<acq_id>\d+)(?:[\/\\]TimePoint_(?P<t>\d+))?(?:[\/\\]ZStep_(?P<z>\d+))"
         )
 
     def _get_filename_re(self) -> re.Pattern:

tests/hcs/imagexpress/test_ImageXpress.py

@@ -19,7 +19,12 @@
 
 @pytest.fixture
 def acquisition_dir():
-    return Path(__file__).parent.parent.parent.parent / "resources" / "Projection-Mix"
+    return (
+        Path(__file__).parent.parent.parent.parent
+        / "resources"
+        / "ImageXpress"
+        / "Projection-Mix"
+    )
 
 
 @pytest.fixture
@@ -270,7 +275,12 @@ def test_raise_not_implemented_error(dummy_plate):
 
 @pytest.fixture
 def acquisition_dir_single_channel():
-    return Path(__file__).parent.parent.parent.parent / "resources" / "SingleChannel"
+    return (
+        Path(__file__).parent.parent.parent.parent
+        / "resources"
+        / "ImageXpress"
+        / "SingleChannel"
+    )
 
 
 @pytest.fixture
@@ -314,3 +324,34 @@ def test_single_channel_acquistion(single_channel_acquisition: PlateAcquisition)
             assert tile.position.y in [0]
             assert tile.position.x in [0, 512]
             assert tile.shape == (512, 512)
+
+
+@pytest.fixture
+def acquisition_dir_time_lapse():
+    return (
+        Path(__file__).parent.parent.parent.parent
+        / "resources"
+        / "ImageXpress"
+        / "1well-3C-2S-Zmix-T"
+    )
+
+
+@pytest.fixture
+def time_lapse_acquisition(acquisition_dir_time_lapse):
+    return SinglePlaneAcquisition(
+        acquisition_dir_time_lapse, alignment=TileAlignmentOptions.STAGE_POSITION
+    )
+
+
+def test_time_lapse_acquistion(time_lapse_acquisition: PlateAcquisition):
+    wells = time_lapse_acquisition.get_well_acquisitions()
+    for well in wells:
+        assert isinstance(well, WellAcquisition)
+        assert len(well.get_tiles()) == 12
+        for tile in well.get_tiles():
+            assert tile.position.time in [0, 1]
+            assert tile.position.channel in [0, 1, 2]
+            assert tile.position.z == 0
+            assert tile.position.y in [0, 256]
+            assert tile.position.x in [0]
+            assert tile.shape == (256, 256)

tests/io/test_MetaSeriesTiff.py

@@ -18,6 +18,7 @@ def test_load_metaseries_tiff(self):
         path = join(
             ROOT_DIR.parent,
             "resources",
+            "ImageXpress",
             "Projection-Mix",
             "2023-02-21",
             "1334",