- add colormap from string to rust code

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "tiffwrite"
-version = "2025.8.0"
+version = "2025.8.1"
 edition = "2024"
 rust-version = "1.85.1"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
@@ -18,6 +18,8 @@ crate-type = ["cdylib", "rlib"]
 
 [dependencies]
 anyhow = "1.0.98"
+colorcet = "0.2.1"
+colorgrad = "0.7.2"
 chrono = "0.4.41"
 css-color = "0.2.8"
 flate2 = "1.1.1"

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,

pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
     "Programming Language :: Python :: 3.14",
 ]
 
-dependencies = ["colorcet", "matplotlib", "numpy", "tqdm"]
+dependencies = ["numpy", "tqdm"]
 
 [project.optional-dependencies]
 test = ["pytest", "tifffile", "imagecodecs"]

src/lib.rs

@@ -3,6 +3,8 @@ mod py;
 
 use anyhow::{Result, anyhow};
 use chrono::Utc;
+use colorcet::ColorMap;
+use colorgrad::{Gradient, LinearGradient};
 use css_color::Srgb;
 use flate2::write::ZlibEncoder;
 use ndarray::{ArcArray2, AsArray, Ix2, s};
@@ -709,11 +711,12 @@ impl IJTiffFile {
     }
 
     /// set colors from css color names and #C01085
-    pub fn set_colors(&mut self, colors: &[String]) -> Result<()> {
+    pub fn set_colors<S: AsRef<str>>(&mut self, colors: &[S]) -> Result<()> {
         self.colors = Colors::Colors(
             colors
                 .iter()
                 .map(|c| {
+                    let c = c.as_ref();
                     let lc = c.to_lowercase();
                     let c = match lc.as_str() {
                         "r" => "#ff0000",
@@ -740,6 +743,28 @@ impl IJTiffFile {
         Ok(())
     }
 
+    pub fn set_colormap<S: AsRef<str>>(&mut self, name: S) -> Result<()> {
+        let name = name.as_ref();
+        let colormap: LinearGradient = name.parse::<ColorMap>()?.try_into()?;
+        let mut colormap = colormap
+            .colors(256)
+            .into_iter()
+            .map(|c| {
+                vec![
+                    (c.r * 255.0).round() as u8,
+                    (c.g * 255.0).round() as u8,
+                    (c.b * 255.0).round() as u8,
+                ]
+            })
+            .collect::<Vec<_>>();
+        if name.starts_with("glasbey") || name.ends_with("glasbey") {
+            colormap[0] = vec![255, 255, 255];
+            colormap[255] = vec![0, 0, 0];
+        }
+        self.colors = Colors::Colormap(colormap);
+        Ok(())
+    }
+
     /// to be saved in description tag (270)
     pub fn description(&self, c_size: usize, z_size: usize, t_size: usize) -> String {
         let mut desc: String = String::from("ImageJ=1.11a");

src/py.rs

@@ -1,7 +1,6 @@
 use crate::{Colors, Compression, IJTiffFile, Tag};
-use ndarray::s;
 use num::{Complex, FromPrimitive, Rational32};
-use numpy::{PyArrayMethods, PyReadonlyArray2};
+use numpy::PyReadonlyArray2;
 use pyo3::exceptions::PyValueError;
 use pyo3::prelude::*;
 
@@ -221,14 +220,9 @@ impl PyIJTiffFile {
     }
 
     #[setter]
-    fn set_colormap(&mut self, colormap: PyReadonlyArray2<u8>) -> PyResult<()> {
+    fn set_colormap(&mut self, colormap: &str) -> PyResult<()> {
         if let Some(ijtifffile) = &mut self.ijtifffile {
-            let a = colormap.to_owned_array();
+            ijtifffile.set_colormap(colormap)?;
-            ijtifffile.colors = Colors::Colormap(
-                (0..a.shape()[0])
-                    .map(|i| Vec::from(a.slice(s![i, ..]).as_slice().unwrap()))
-                    .collect(),
-            );
         }
         Ok(())
     }