Fix

Author: hangyinn

imc/data_models/roi.py

@@ -1219,27 +1219,7 @@ def quantify_cell_intensity(
         layers: tp.Sequence[str] = ["cell"],
         **kwargs,
     ) -> DataFrame:
-        """
-        Quantify intensity of each cell in each channel.
-
-        Parameters
-        ----------
-
-        channel_include: list[str]
-            Channels to include in quantification.
-            Default is all.
-        channel_exclude: list[str]
-            Channels to exclude from quantification.
-            Default is non.
-        layers: list[str]
-            What mask layer to quantify. The masks must exist for the ROI. Options are:
-            - 'cell': Whole cell mask.
-            - 'nuclei': Nuclear mask.
-            - 'membrane': Membrane mask - this is usually not a real mask but cell mask minus a fixed value.
-            - 'cytoplasm':  Mask of the cell cytoplasm.
-            - 'extracellular': Mask of the local neighborhood of the cell excluding other cells.
-            Default is value of ROI.mask_layer which is by default 'cell.
-        """
+        """Quantify intensity of each cell in each channel."""
         from imc.ops.quant import quantify_cell_intensity
 
         if channel_include is not None:

imc/utils.py

@@ -1507,48 +1507,3 @@ def mask_to_labelme(
     }
     with open(output_file.as_posix(), "w") as fp:
         json.dump(payload, fp, indent=2)
-
-
-def get_channel_names_from_ome_tiff(ome_tiff_file: tp.Union[str, Path]) -> tp.List[str]:
-    """
-    Parse channel names from OME metadata in OME-TIFF file.
-    Assumes hierarchy of OME metadata is OME->Image->[Description->]Pixels->Channel.
-    The "Name" attribute of Channel is returned.
-
-    Parameters
-    ----------
-    ome_tiff_file: str | Path
-        Either a pathlib.Path to a file or a string with OME XML information.
-
-    Returns
-    -------
-    list[str]
-        A list of channel names
-    """
-    from xml.etree import ElementTree
-
-    if isinstance(ome_tiff_file, Path):
-        f = tifffile.TiffFile(ome_tiff_file)
-        root = ElementTree.fromstring(f.ome_metadata)
-    else:
-        root = ElementTree.fromstring(ome_tiff_file)
-
-    # "OME" is the tag of the root
-    path_to_channels = ["Image", "Description", "Pixels"]
-
-    i = 0
-    t = 0
-    obj = root
-    while i < len(path_to_channels):
-        for c in obj:
-            tag = c.tag.split("}")[-1]
-            if tag == path_to_channels[i]:
-                obj = c
-                i += 1
-        t += 1
-
-        # If loop not working, most likely XML does not have the "Description" tag, so try skipping it
-        if (t > 200) and (i == 1):
-            path_to_channels = ["Image", "Pixels"]
-    channels = [c.attrib["Name"] for c in obj if c.tag.split("}")[-1] == "Channel"]
-    return channels