Merge pull request #90 from fmi-faim/imagexpress-single-channel

ImageXpress: support single-channel acquisitions

src/faim_hcs/hcs/imagexpress/ImageXpressPlateAcquisition.py

@@ -56,7 +56,7 @@ def _list_and_match_files(
         root_dir: Union[Path, str],
         root_re: re.Pattern,
         filename_re: re.Pattern,
-    ) -> list[[dict[dict, str]]]:
+    ) -> list[list[dict[dict, str]]]:
         files = []
         for root, _, filenames in os.walk(root_dir):
             m_root = root_re.fullmatch(root)
@@ -66,6 +66,8 @@ def _list_and_match_files(
                     if m_filename:
                         row = m_root.groupdict()
                         row |= m_filename.groupdict()
+                        if "channel" not in row or row["channel"] is None:
+                            row["channel"] = "w1"
                         row["path"] = str(Path(root).joinpath(f))
                         files.append(row)
         return files

src/faim_hcs/hcs/imagexpress/MixedAcquisition.py

@@ -80,5 +80,5 @@ def _get_root_re(self) -> re.Pattern:
 
     def _get_filename_re(self) -> re.Pattern:
         return re.compile(
-            r"(?P<name>.*)_(?P<well>[A-Z]+\d{2})_(?P<field>s\d+)_(?P<channel>w[1-9]{1})(?!_thumb)(?P<md_id>.*)(?P<ext>.tif)"
+            r"(?P<name>.*)_(?P<well>[A-Z]+\d{2})_?(?P<field>s\d+)?_?(?P<channel>w[1-9]{1})?(?!_thumb)(?P<md_id>[0-9A-F]{8}-[0-9A-F]{4}-[0-9A-F]{4}-[0-9A-F]{4}-[0-9A-F]{12})(?P<ext>.tif)"
         )

src/faim_hcs/hcs/imagexpress/SinglePlaneAcquisition.py

@@ -54,7 +54,7 @@ def _get_root_re(self) -> re.Pattern:
 
     def _get_filename_re(self) -> re.Pattern:
         return re.compile(
-            r"(?P<name>.*)_(?P<well>[A-Z]+\d{2})_(?P<field>s\d+)_(?P<channel>w[1-9]{1})(?!_thumb)(?P<md_id>.*)(?P<ext>.tif)"
+            r"(?P<name>.*)_(?P<well>[A-Z]+\d{2})_?(?P<field>s\d+)?_?(?P<channel>w[1-9]{1})?(?!_thumb)(?P<md_id>[0-9A-F]{8}-[0-9A-F]{4}-[0-9A-F]{4}-[0-9A-F]{4}-[0-9A-F]{12})(?P<ext>.tif)"
         )
 
     def _get_z_spacing(self) -> Optional[float]:

src/faim_hcs/hcs/imagexpress/StackAcquisition.py

@@ -65,15 +65,15 @@ def _get_root_re(self) -> re.Pattern:
 
     def _get_filename_re(self) -> re.Pattern:
         return re.compile(
-            r"(?P<name>.*)_(?P<well>[A-Z]+\d{2})_(?P<field>s\d+)_(?P<channel>w[1-9]{1})(?!_thumb)(?P<md_id>.*)(?P<ext>.tif)"
+            r"(?P<name>.*)_(?P<well>[A-Z]+\d{2})_?(?P<field>s\d+)?_?(?P<channel>w[1-9]{1})?(?!_thumb)(?P<md_id>[0-9A-F]{8}-[0-9A-F]{4}-[0-9A-F]{4}-[0-9A-F]{4}-[0-9A-F]{12})(?P<ext>.tif)"
         )
 
     def _get_z_spacing(self) -> Optional[float]:
         return self._z_spacing
 
     def _compute_z_spacing(self, files: pd.DataFrame) -> Optional[float]:
         assert "z" in files.columns, "No z column in files DataFrame."
-        channel_with_stack = files[files["z"] == "2"]["channel"].unique()[0]
+        channel_with_stack = np.sort(files[files["z"] == "2"]["channel"].unique())[0]
         subset = files[files["channel"] == channel_with_stack]
         subset = subset[subset["well"] == subset["well"].unique()[0]]
         subset = subset[subset["field"] == subset["field"].unique()[0]]
@@ -87,7 +87,7 @@ def _compute_z_spacing(self, files: pd.DataFrame) -> Optional[float]:
                 z_position = metadata["stage-position-z"]
                 plane_positions.append(z_position)
 
-        plane_positions = sorted(plane_positions)
+        plane_positions = np.array(sorted(plane_positions), dtype=np.float32)
 
         precision = -Decimal(str(plane_positions[0])).as_tuple().exponent
         z_step = np.round(np.mean(np.diff(plane_positions)), decimals=precision)

tests/hcs/imagexpress/test_ImageXpress.py

@@ -119,7 +119,7 @@ def test_stack_acquistion(stack_acquisition: PlateAcquisition):
     assert ch.spatial_calibration_x == 1.3668
     assert ch.spatial_calibration_y == 1.3668
     assert ch.wavelength == 536
-    assert_almost_equal(ch.z_spacing, 5.0, decimal=4)
+    assert_almost_equal(ch.z_spacing, 5.0, decimal=2)
 
     ch = channels[1]
     assert ch.channel_index == 1
@@ -132,7 +132,7 @@ def test_stack_acquistion(stack_acquisition: PlateAcquisition):
     assert ch.spatial_calibration_x == 1.3668
     assert ch.spatial_calibration_y == 1.3668
     assert ch.wavelength == 536
-    assert_almost_equal(ch.z_spacing, 5.0, decimal=4)
+    assert_almost_equal(ch.z_spacing, 5.0, decimal=2)
 
     ch = channels[3]
     assert ch.channel_index == 3
@@ -145,7 +145,7 @@ def test_stack_acquistion(stack_acquisition: PlateAcquisition):
     assert ch.spatial_calibration_x == 1.3668
     assert ch.spatial_calibration_y == 1.3668
     assert ch.wavelength == 536
-    assert_almost_equal(ch.z_spacing, 5.0, decimal=4)
+    assert_almost_equal(ch.z_spacing, 5.0, decimal=2)
 
     for well in stack_acquisition.get_well_acquisitions():
         assert isinstance(well, WellAcquisition)
@@ -266,3 +266,51 @@ def test_raise_not_implemented_error(dummy_plate):
 
     with pytest.raises(NotImplementedError):
         dummy_plate._get_z_spacing()
+
+
+@pytest.fixture
+def acquisition_dir_single_channel():
+    return Path(__file__).parent.parent.parent.parent / "resources" / "SingleChannel"
+
+
+@pytest.fixture
+def single_channel_acquisition(acquisition_dir_single_channel):
+    return SinglePlaneAcquisition(
+        acquisition_dir_single_channel, alignment=TileAlignmentOptions.GRID
+    )
+
+
+def test_single_channel_acquistion(single_channel_acquisition: PlateAcquisition):
+    wells = single_channel_acquisition.get_well_acquisitions()
+
+    assert wells is not None
+    assert len(wells) == 2
+    # MIPs: 1 well has 2 fields * 1 channels = 2 files
+    assert len(wells[0]._files) == 2
+    assert len(wells[0]._files) == 2
+
+    channels = single_channel_acquisition.get_channel_metadata()
+    assert len(channels) == 1
+    ch = channels[0]
+    assert ch.channel_index == 0
+    assert ch.channel_name == "Maximum-Projection_FITC_05"
+    assert ch.display_color == "73ff00"
+    assert ch.exposure_time == 15.0
+    assert ch.exposure_time_unit == "ms"
+    assert ch.objective == "20X Plan Apo Lambda"
+    assert ch.spatial_calibration_units == "um"
+    assert ch.spatial_calibration_x == 1.3668
+    assert ch.spatial_calibration_y == 1.3668
+    assert ch.wavelength == 536
+    assert ch.z_spacing is None
+
+    for well in single_channel_acquisition.get_well_acquisitions():
+        assert isinstance(well, WellAcquisition)
+        assert len(well.get_tiles()) == 2
+        for tile in well.get_tiles():
+            assert tile.position.time == 0
+            assert tile.position.channel in [0]
+            assert tile.position.z == 0
+            assert tile.position.y in [0]
+            assert tile.position.x in [0, 512]
+            assert tile.shape == (512, 512)