- add colormap from string to rust code

py/tiffwrite/__init__.py

@@ -6,8 +6,6 @@ from pathlib import Path
 from typing import Any, Callable, Sequence
 from warnings import warn
 
-import colorcet
-import matplotlib
 import numpy as np
 from numpy.typing import ArrayLike, DTypeLike
 from tqdm.auto import tqdm
@@ -77,6 +75,9 @@ class IJTiffFile(rs.IJTiffFile):
             else:
                 return codecs.get(int(idx), 50000)
 
+        if colors is not None and colormap is not None:
+            warn("Cannot have colors and colormap simultaneously.", TiffWriteWarning, stacklevel=2)
+
         self.path = Path(path)
         self.dtype = np.dtype(dtype)
         if compression is not None:
@@ -88,7 +89,7 @@ class IJTiffFile(rs.IJTiffFile):
         if colors is not None:
             self.colors = [str(color) for color in colors]
         if colormap is not None:
-            self.colormap = get_colormap(colormap)
+            self.colormap = str(colormap)
         if pxsize is not None:
             self.px_size = float(pxsize)
         if deltaz is not None:
@@ -96,7 +97,7 @@ class IJTiffFile(rs.IJTiffFile):
         if timeinterval is not None:
             self.time_interval = float(timeinterval)
         if comment is not None:
-            self.comment = comment
+            self.comment = str(comment)
         if extratags is not None:
             for extra_tag in extratags:
                 self.append_extra_tag(extra_tag, None)
@@ -106,8 +107,6 @@ class IJTiffFile(rs.IJTiffFile):
                 TiffWriteWarning,
                 stacklevel=2,
             )
-        if colors is not None and colormap is not None:
-            warn("Cannot have colors and colormap simultaneously.", TiffWriteWarning, stacklevel=2)
 
     def __enter__(self) -> IJTiffFile:
         return self
@@ -146,41 +145,6 @@ class IJTiffFile(rs.IJTiffFile):
                 self.append_extra_tag(extra_tag, (c, z, t))
 
 
-def get_colormap(colormap: str) -> np.ndarray:
-    if hasattr(colorcet, colormap.rstrip("_r")):
-        cm = np.array(
-            [[int("".join(i), 16) for i in zip(*[iter(s[1:])] * 2)] for s in getattr(colorcet, colormap.rstrip("_r"))]
-        ).astype("uint8")
-        if colormap.endswith("_r"):
-            cm = cm[::-1]
-        if colormap.startswith("glasbey") or colormap.endswith("glasbey"):
-            cm[0] = 255, 255, 255
-            cm[-1] = 0, 0, 0
-    else:
-        cmap = matplotlib.colormaps.get_cmap(colormap)
-        if cmap.N < 256:
-            cm = (
-                255
-                * np.vstack(
-                    (
-                        (1, 1, 1),
-                        matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(1, 254), cmap).to_rgba(
-                            np.arange(1, 254)
-                        )[:, :3],
-                        (0, 0, 0),
-                    )
-                )
-            ).astype("uint8")
-        else:
-            cm = (
-                255
-                * matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(0, 255), cmap).to_rgba(np.arange(256))[
-                    :, :3
-                ]
-            ).astype("uint8")
-    return cm
-
-
 def tiffwrite(
     file: str | Path,
     data: np.ndarray,