clean(imageviewer): remove unused class

src/aliby/utils/imageViewer.py

@@ -30,7 +30,7 @@ from agora.io.cells import Cells
 from agora.io.writer import load_attributes
 from aliby.io.image import dispatch_image
 from aliby.tile.tiler import Tiler, TilerParameters
-from aliby.utils.plot import stretch_image
+from aliby.utils.plot import stretch_clip
 
 default_colours = {
     "Brightfield": "Greys_r",
@@ -56,28 +56,6 @@ def custom_imshow(a, norm=None, cmap=None, *args, **kwargs):
     )
 
 
-class localImageViewer:
-    """
-    Fast access to Images segmented locally without tiling
-    from image.h5 objects.
-    """
-
-    def __init__(self, h5file, data_source=None):
-        self._hdf = h5py.File(h5file)
-        self.positions = list(self._hdf.keys())
-        self.current_position = self.positions[0]
-
-    def plot_position(self, channel=0, tp=0, z=0, stretch=True):
-        pixvals = self._hdf[self.current_position][channel, tp, ..., z]
-        if stretch:
-            minval = np.percentile(pixvals, 0.5)
-            maxval = np.percentile(pixvals, 99.5)
-            pixvals = np.clip(pixvals, minval, maxval)
-            pixvals = ((pixvals - minval) / (maxval - minval)) * 255
-
-        Image.fromarray(pixvals.astype(np.uint8))
-
-
 class BaseImageViewer(ABC):
     def __init__(self, fpath):
 
@@ -112,6 +90,7 @@ class LocalImageViewer(BaseImageViewer):
     """
     Tool to generate figures from local files, either zarr or files organised
     in directories.
+    TODO move common functionality from RemoteImageViewer to BaseImageViewer
     """
 
     def __init__(self, results_path: str, data_path: str):
@@ -133,7 +112,7 @@ class LocalImageViewer(BaseImageViewer):
         self.cells = Cells.from_source(results_path)
 
 
-class remoteImageViewer(BaseImageViewer):
+class RemoteImageViewer(BaseImageViewer):
     """
     This ImageViewer combines fetching remote images with tiling and outline display.
     """
@@ -364,7 +343,7 @@ class remoteImageViewer(BaseImageViewer):
         ), "Invalid norm argument."
 
         if norm and norm in ("l1", "l2", "max"):
-            images = {k: stretch_image(v) for k, v in images.items()}
+            images = {k: stretch_clip(v) for k, v in images.items()}
 
         images = [concat_pad(img, width, nrows) for img in images.values()]
         # TODO convert to RGB to draw fluorescence with colour

src/extraction/core/extractor.py

@@ -61,23 +61,6 @@ class ExtractorParameters(ParametersABC):
         self.sub_bg = sub_bg
         self.multichannel_ops = multichannel_ops
 
-    @staticmethod
-    def guess_from_meta(store_name: str, suffix="fast"):
-        """
-        Find the microscope name from the h5 metadata.
-
-        Parameters
-        ----------
-        store_name : str or Path
-            For a h5 file
-        suffix : str
-            Added at the end of the predicted parameter set
-        """
-        with h5py.File(store_name, "r") as f:
-            microscope = f["/"].attrs.get("microscope")
-        assert microscope, "No metadata found"
-        return "_".join((microscope, suffix))
-
     @classmethod
     def default(cls):
         return cls({})