mergechannels 0.3.0__tar.gz → 0.4.0__tar.gz

{mergechannels-0.3.0 → mergechannels-0.4.0}/Cargo.lock

@@ -1,6 +1,6 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 4
+version = 3
 
 [[package]]
 name = "autocfg"
@@ -59,7 +59,7 @@ dependencies = [
 
 [[package]]
 name = "mergechannels"
-version = "0.3.0"
+version = "0.4.0"
 dependencies = [
  "lazy_static",
  "ndarray",

{mergechannels-0.3.0 → mergechannels-0.4.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mergechannels"
-version = "0.3.0"
+version = "0.4.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

{mergechannels-0.3.0 → mergechannels-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mergechannels
-Version: 0.3.0
+Version: 0.4.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -50,6 +50,7 @@ pip install git+https://github.com/zacswider/mergechannels.git
 
 ```python
 from skimage import data
+import matplotlib.pyplot as plt
 import mergechannels as mc
 
 img = data.camera()
@@ -116,10 +117,10 @@ b.imshow(
         channels,
         colormaps,
         blending='min',
-        saturation_limits=(
-            0.01,  # bottom 1% of pixels set to black point
-            0.97,  # top 3% of pixels set to white point
-        ),
+        percentiles=[(
+            1,  # bottom 1% of pixels set to black point
+            97,  # top 3% of pixels set to white point
+        )]*len(channels),
     ),
 )
 fig.tight_layout()

{mergechannels-0.3.0 → mergechannels-0.4.0}/README.md

@@ -28,6 +28,7 @@ pip install git+https://github.com/zacswider/mergechannels.git
 
 ```python
 from skimage import data
+import matplotlib.pyplot as plt
 import mergechannels as mc
 
 img = data.camera()
@@ -94,10 +95,10 @@ b.imshow(
         channels,
         colormaps,
         blending='min',
-        saturation_limits=(
-            0.01,  # bottom 1% of pixels set to black point
-            0.97,  # top 3% of pixels set to white point
-        ),
+        percentiles=[(
+            1,  # bottom 1% of pixels set to black point
+            97,  # top 3% of pixels set to white point
+        )]*len(channels),
     ),
 )
 fig.tight_layout()

{mergechannels-0.3.0 → mergechannels-0.4.0}/python/mergechannels/__init__.py

@@ -3,11 +3,12 @@ from .mergechannels import (  # type: ignore
 	dispatch_single_channel,
 	dispatch_multi_channel,
 )
-from ._internal import merge
+from ._internal import merge, apply_color_map
 
 
 __all__ = [
 	'dispatch_single_channel',
 	'dispatch_multi_channel',
 	'merge',
+	'apply_color_map',
 ]

{mergechannels-0.3.0 → mergechannels-0.4.0}/python/mergechannels/__init__.pyi

@@ -6,11 +6,20 @@ from python.mergechannels._blending import BLENDING_OPTIONS
 from python.mergechannels._luts import COLORMAPS
 
 
+def apply_color_map(
+	arr: np.ndarray,
+	color: COLORMAPS,
+	percentiles: tuple[float, float] | None = None,
+	saturation_limits: tuple[float, float] | None = None,
+) -> np.ndarray:
+    ...
+
 def merge(
-    arrs: np.ndarray | Sequence[np.ndarray],
-    colors: Sequence[COLORMAPS] = (),
-    blending: Literal[BLENDING_OPTIONS] = 'max',
-    saturation_limits: tuple[float, float] = (0.2, 99.8),
+	arrs: Sequence[np.ndarray],
+	colors: Sequence[COLORMAPS],
+	blending: BLENDING_OPTIONS = 'max',
+	percentiles: tuple[float, float] | Sequence[tuple[float, float]] | None = None,
+	saturation_limits: tuple[float, float] | Sequence[tuple[float, float]] | None = None,
 ) -> np.ndarray:
     ...
 

mergechannels-0.4.0/python/mergechannels/_internal.py

@@ -0,0 +1,59 @@
+from typing import (
+	Sequence,
+	Union,
+)
+
+import numpy as np
+
+from mergechannels import (
+	dispatch_single_channel,
+	dispatch_multi_channel,
+)
+from ._luts import COLORMAPS
+from ._blending import BLENDING_OPTIONS
+
+def apply_color_map(
+	arr: np.ndarray,
+	color: COLORMAPS,
+	percentiles: Union[tuple[float, float], None] = None,
+	saturation_limits: Union[tuple[float, float], None] = None,
+) -> np.ndarray:
+	'''
+	apply a color map to an array
+	'''
+	if saturation_limits is None:
+		if percentiles is None:
+			percentiles = (1.1, 99.9)
+		low, high = np.percentile(arr, percentiles)
+		saturation_limits = (low, high)
+
+	return dispatch_single_channel(
+		array_reference=arr,
+		cmap_name=color,
+		limits=saturation_limits,
+	)
+
+
+def merge(
+	arrs: Sequence[np.ndarray],
+	colors: Sequence[COLORMAPS],
+	blending: BLENDING_OPTIONS = 'max',
+	percentiles: Union[Sequence[tuple[float, float]], None] = None,
+	saturation_limits: Union[Sequence[tuple[float, float]], None] = None,
+) -> np.ndarray:
+	'''
+	apply cmaps to arrays and blend the colors
+	'''
+	if saturation_limits is None:
+		if percentiles is None:
+			percentiles = [(1.1, 99.9)] * len(arrs)
+		saturation_limits = tuple(
+			np.percentile(arr, ch_percentiles)
+			for arr, ch_percentiles in zip(arrs, percentiles)  # type: ignore
+		)
+	return dispatch_multi_channel(
+		array_references=arrs,
+		cmap_names=colors,
+		blending=blending,
+		limits=saturation_limits,  # type: ignore
+	)

{mergechannels-0.3.0 → mergechannels-0.4.0}/src/blend.rs

@@ -1,32 +1,9 @@
 use smallvec::SmallVec;
-use std::error::Error;
-use std::fmt;
 
 pub const MAX_N_CH: usize = 5;
 
 pub type BlendFn = fn(&SmallVec<[[u8; 3]; 5]>) -> [u8; 3];
 
-#[derive(Debug)]
-pub enum MergeError {
-    InvalidBlendingMode(String),
-}
-
-impl fmt::Display for MergeError {
-    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        match self {
-            MergeError::InvalidBlendingMode(mode) => {
-                write!(
-                    f,
-                    "Invalid blending mode: `{}`. Valid modes are 'max', 'sum', 'min', and 'mean'.",
-                    mode
-                )
-            }
-        }
-    }
-}
-
-impl Error for MergeError {}
-
 pub fn max_blending(px_vals: &SmallVec<[[u8; 3]; 5]>) -> [u8; 3] {
     let mut r: u8 = 0;
     let mut g: u8 = 0;

{mergechannels-0.3.0 → mergechannels-0.4.0}/src/colorize.rs

@@ -1,4 +1,5 @@
-use crate::blend::{self, MergeError};
+use crate::blend::{self};
+use crate::errors::MergeError;
 use numpy::ndarray::{Array, Array3, Array4, ArrayView2, ArrayView3};
 use smallvec::SmallVec;
 

mergechannels-0.4.0/src/errors.rs

@@ -0,0 +1,51 @@
+use pyo3::exceptions::PyValueError;
+use pyo3::prelude::*;
+use std::error::Error;
+
+#[derive(Debug)]
+pub enum DispatchError {
+    UnsupportedDataType(String),
+    UnsupportedNumberOfDimensions(usize),
+}
+
+impl std::fmt::Display for DispatchError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            DispatchError::UnsupportedDataType(dtype) => {
+                write!(f, "Received unsupported dtype: {}", dtype)
+            }
+            DispatchError::UnsupportedNumberOfDimensions(ndim) => {
+                write!(f, "Received unsupported number of dimensions: {}", ndim)
+            }
+        }
+    }
+}
+
+impl std::error::Error for DispatchError {}
+
+impl From<DispatchError> for PyErr {
+    fn from(err: DispatchError) -> Self {
+        PyValueError::new_err(err.to_string())
+    }
+}
+
+#[derive(Debug)]
+pub enum MergeError {
+    InvalidBlendingMode(String),
+}
+
+impl std::fmt::Display for MergeError {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            MergeError::InvalidBlendingMode(mode) => {
+                write!(
+                    f,
+                    "Invalid blending mode: `{}`. Valid modes are 'max', 'sum', 'min', and 'mean'.",
+                    mode
+                )
+            }
+        }
+    }
+}
+
+impl Error for MergeError {}

{mergechannels-0.3.0 → mergechannels-0.4.0}/src/interface.rs

@@ -1,43 +1,16 @@
 use crate::cmaps;
 use crate::colorize;
+use crate::errors;
 use ndarray::ArrayView2;
 use ndarray::ArrayView3;
 use numpy::{
     IntoPyArray, PyArrayDyn, PyReadonlyArray2, PyReadonlyArray3, PyUntypedArray,
     PyUntypedArrayMethods,
 };
-use pyo3::exceptions::PyValueError;
 use pyo3::prelude::*;
 use pyo3::types::PyAny;
 use pyo3::{Bound, Python};
 
-#[derive(Debug)]
-pub enum DispatchError {
-    UnsupportedDataType(String),
-    UnsupportedNumberOfDimensions(usize),
-}
-
-impl std::fmt::Display for DispatchError {
-    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
-        match self {
-            DispatchError::UnsupportedDataType(dtype) => {
-                write!(f, "Received unsupported dtype: {}", dtype)
-            }
-            DispatchError::UnsupportedNumberOfDimensions(ndim) => {
-                write!(f, "Received unsupported number of dimensions: {}", ndim)
-            }
-        }
-    }
-}
-
-impl std::error::Error for DispatchError {}
-
-impl From<DispatchError> for PyErr {
-    fn from(err: DispatchError) -> Self {
-        PyValueError::new_err(err.to_string())
-    }
-}
-
 #[pyfunction]
 #[pyo3(name = "dispatch_single_channel")]
 pub fn dispatch_single_channel_py<'py>(
@@ -65,7 +38,7 @@ pub fn dispatch_single_channel_py<'py>(
                 let rgb = colorize::colorize_stack_8bit(arr, cmap, limits);
                 Ok(rgb.into_dyn().into_pyarray(py))
             }
-            _ => Err(DispatchError::UnsupportedNumberOfDimensions(ndim).into()),
+            _ => Err(errors::DispatchError::UnsupportedNumberOfDimensions(ndim).into()),
         },
         "uint16" => match ndim {
             2 => {
@@ -82,9 +55,9 @@ pub fn dispatch_single_channel_py<'py>(
                 let rgb = colorize::colorize_stack_16bit(arr, cmap, limits);
                 Ok(rgb.into_dyn().into_pyarray(py))
             }
-            _ => Err(DispatchError::UnsupportedNumberOfDimensions(ndim).into()),
+            _ => Err(errors::DispatchError::UnsupportedNumberOfDimensions(ndim).into()),
         },
-        _ => Err(DispatchError::UnsupportedDataType(dtype).into()),
+        _ => Err(errors::DispatchError::UnsupportedDataType(dtype).into()),
     }
 }
 
@@ -215,7 +188,7 @@ pub fn dispatch_multi_channel_py<'py>(
                 let rgb = colorize::merge_3d_u8(arrs, cmaps, blending, limits).unwrap();
                 Ok(rgb.into_dyn().into_pyarray(py))
             }
-            _ => Err(DispatchError::UnsupportedNumberOfDimensions(*ndim).into()),
+            _ => Err(errors::DispatchError::UnsupportedNumberOfDimensions(*ndim).into()),
         },
         "uint16" => match ndim {
             2 => {
@@ -232,8 +205,8 @@ pub fn dispatch_multi_channel_py<'py>(
                 let rgb = colorize::merge_3d_u16(arrs, cmaps, blending, limits).unwrap();
                 Ok(rgb.into_dyn().into_pyarray(py))
             }
-            _ => Err(DispatchError::UnsupportedNumberOfDimensions(*ndim).into()),
+            _ => Err(errors::DispatchError::UnsupportedNumberOfDimensions(*ndim).into()),
         },
-        _ => Err(DispatchError::UnsupportedDataType(dtype.clone()).into()),
+        _ => Err(errors::DispatchError::UnsupportedDataType(dtype.clone()).into()),
     }
 }

{mergechannels-0.3.0 → mergechannels-0.4.0}/src/lib.rs

@@ -1,6 +1,7 @@
 mod blend;
 mod cmaps;
 mod colorize;
+mod errors;
 mod interface;
 
 use interface::{dispatch_multi_channel_py, dispatch_single_channel_py};

mergechannels-0.3.0/python/mergechannels/_internal.py

@@ -1,65 +0,0 @@
-from typing import Sequence
-
-import numpy as np
-
-from mergechannels import (
-	dispatch_single_channel,
-	dispatch_multi_channel,
-)
-from ._luts import COLORMAPS
-from ._blending import BLENDING_OPTIONS
-
-def merge(
-	arrs: Sequence[np.ndarray],
-	colors: Sequence[COLORMAPS],
-	blending: BLENDING_OPTIONS = 'max',
-    saturation_limits: tuple[float, float] = (0.011, 0.999),
-) -> np.ndarray:
-	'''
-	apply cmaps to arrays and blend the colors
-	'''
-	# region validation
-	n_arrs = len(arrs)
-	n_colors = len(colors)
-	if not n_arrs == n_colors and n_arrs > 0:
-		raise ValueError(
-			'Expected an equal number of arrays to colorize and colormap names to apply. '
-			f'Got {n_arrs} arrays and {n_colors} colors'
-		)
-	arr_shapes = [arr.shape for arr in arrs]
-	if not len(set(arr_shapes)) == 1:
-		raise ValueError(
-			f'Expected every array to have the same shape, got {arr_shapes}'
-		)
-	if len(arr_shapes[0]) not in (2, 3):
-		raise ValueError(
-			f'Expected every array to be 2D or 3D, got {arr_shapes[0]}'
-		)
-	arr_dtypes = [arr.dtype for arr in arrs]
-	if not len(set(arr_dtypes)) == 1:
-		raise ValueError(
-			f'Expected every array to have the same dtype, got {arr_dtypes}'
-		)
-	# endregion
-	if n_arrs == 1:
-		if arrs[0].dtype == 'uint8':
-			limits = (0, 255)
-		else:
-			low, high = np.percentile(arrs[0], np.array(saturation_limits) * 100)
-			limits = (low, high)
-		return dispatch_single_channel(
-			array_reference=arrs[0],
-			cmap_name=colors[0],
-			limits=limits,
-		)
-	else:
-		if all(arr.dtype == 'uint8' for arr in arrs):
-			limits = (0, 255)
-		else:
-			limits = tuple(np.percentile(arr, np.array(saturation_limits) * 100) for arr in arrs)
-		return dispatch_multi_channel(
-			array_references=arrs,
-			cmap_names=colors,
-			blending=blending,
-			limits=limits,  # type: ignore
-		)