ImageXpress: support time dimension

fmi-faim · Apr 30, 2024 · 83184eb · 83184eb
1 parent f419135
commit 83184eb
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Showing 4 changed files with 12 additions and 7 deletions.
diff --git a/src/faim_ipa/hcs/imagexpress/ImageXpressWellAcquisition.py b/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 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
diff --git a/src/faim_ipa/hcs/imagexpress/MixedAcquisition.py b/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:

diff --git a/src/faim_ipa/hcs/imagexpress/SinglePlaneAcquisition.py b/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(

diff --git a/src/faim_ipa/hcs/imagexpress/StackAcquisition.py b/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: