8-bit conversion flag

loopy/entrypoint.py

@@ -39,9 +39,6 @@ def cli():
 @click.option(
     "scale", "--scale", "-s", default=1, type=float, help="Scale in meters per pixel.", show_default=True
 )
-@click.option(
-    "quality", "--quality", default=90, type=int, help="JPEG compression quality.", show_default=True
-)
 @click.option(
     "translate",
     "--translate",
@@ -50,11 +47,16 @@ def cli():
     type=click.Tuple([float, float]),
     help="Translation to be applied in y and x.",
 )
+@click.option("--convert8bit", is_flag=True, help="Convert the image to 8-bit. ")
+@click.option(
+    "quality", "--quality", default=90, type=int, help="JPEG compression quality. Only applies if image is 8-bit or converting to 8-bit.", show_default=True
+)
 def image(
     tiff: Path,
     out: Path | None = None,
     name: str | None = None,
     channels: str | None = None,
+    convert8bit: bool = False,
     quality: int = 90,
     scale: float = 1,
     translate: tuple[float, float] = (0, 0),
@@ -79,7 +81,7 @@ def image(
 
     (
         Sample(name=name, path=out / name)
-        .add_image(tiff, channels=c, scale=scale, translate=translate, quality=quality)
+        .add_image(tiff, channels=c, scale=scale, translate=translate, quality=quality, convert_to_8bit=convert8bit)
         .write()
     )
 

loopy/image.py

@@ -55,9 +55,9 @@ class Config:
 
     @classmethod
     def from_tiff(
-        cls, tif: Path, *, scale: float, translate: tuple[float, float] = (0, 0), rgb: bool = False
+        cls, tif: Path, *, scale: float, translate: tuple[float, float] = (0, 0), rgb: bool = False, convert_to_8bit: bool = False
     ) -> Self:
-        return cls.from_img(imread(tif), scale=scale, translate=translate, rgb=rgb)
+        return cls.from_img(imread(tif), scale=scale, translate=translate, rgb=rgb, convert_to_8bit=convert_to_8bit)
 
     @classmethod
     def from_img(
@@ -92,7 +92,9 @@ def from_img(
         elif img.dtype == np.uint16:
             if convert_to_8bit:
                 log("Converting uint16 to uint8.", type_="WARNING")
-                dived = np.divide(img, 256, casting="unsafe")  # So that this remains an uint16.
+                maxval = img.max()
+                divide = 2 ** (int(np.log2(maxval)) + 1) // 256
+                dived = np.divide(img, divide, casting="unsafe")  # So that this remains an uint16.
                 del img
                 img = dived.astype(np.uint8)
                 del dived

loopy/sample.py

@@ -145,6 +145,7 @@ def add_image(
         scale: float = 1,
         quality: int = 90,
         translate: tuple[float, float] = (0, 0),
+        convert_to_8bit: bool = False,
         defaultChannels: dict[Colors, str] | None = None,
         save_uncompressed: bool = False,
     ) -> Self:
@@ -161,7 +162,7 @@ def add_image(
         if not tiff.exists():
             raise ValueError(f"Tiff file {tiff} not found")
 
-        geotiff = GeoTiff.from_tiff(tiff, scale=scale, translate=translate, rgb=channels == "rgb")
+        geotiff = GeoTiff.from_tiff(tiff, scale=scale, translate=translate, rgb=channels == "rgb", convert_to_8bit=convert_to_8bit)
 
         if channels is None:
             channels = [f"C{i}" for i in range(1, geotiff.chans + 1)]