vendored code from scikit-image for rescale_intensity

Author: emmanuelle

packages/python/plotly/plotly/express/_imshow.py

@@ -5,7 +5,7 @@
 from PIL import Image
 from io import BytesIO
 import base64
-from skimage.exposure import rescale_intensity
+from .imshow_utils import rescale_intensity, _integer_ranges, _integer_types
 import pandas as pd
 
 try:
@@ -17,21 +17,6 @@
 
 _float_types = []
 
-# Adapted from skimage.util.dtype
-_integer_types = (
-    np.byte,
-    np.ubyte,  # 8 bits
-    np.short,
-    np.ushort,  # 16 bits
-    np.intc,
-    np.uintc,  # 16 or 32 or 64 bits
-    np.int_,
-    np.uint,  # 32 or 64 bits
-    np.longlong,
-    np.ulonglong,
-)  # 64 bits
-_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max) for t in _integer_types}
-
 
 def _array_to_b64str(img, ext="png"):
     pil_img = Image.fromarray(img)

packages/python/plotly/plotly/express/imshow_utils.py

@@ -0,0 +1,248 @@
+"""Vendored code from scikit-image in order to limit the number of dependencies
+Extracted from scikit-image/skimage/exposure/exposure.py
+"""
+
+import numpy as np
+
+from warnings import warn
+
+_integer_types = (
+    np.byte,
+    np.ubyte,  # 8 bits
+    np.short,
+    np.ushort,  # 16 bits
+    np.intc,
+    np.uintc,  # 16 or 32 or 64 bits
+    np.int_,
+    np.uint,  # 32 or 64 bits
+    np.longlong,
+    np.ulonglong,
+)  # 64 bits
+_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max) for t in _integer_types}
+dtype_range = {
+    np.bool_: (False, True),
+    np.bool8: (False, True),
+    np.float16: (-1, 1),
+    np.float32: (-1, 1),
+    np.float64: (-1, 1),
+}
+dtype_range.update(_integer_ranges)
+
+
+DTYPE_RANGE = dtype_range.copy()
+DTYPE_RANGE.update((d.__name__, limits) for d, limits in dtype_range.items())
+DTYPE_RANGE.update(
+    {
+        "uint10": (0, 2 ** 10 - 1),
+        "uint12": (0, 2 ** 12 - 1),
+        "uint14": (0, 2 ** 14 - 1),
+        "bool": dtype_range[np.bool_],
+        "float": dtype_range[np.float64],
+    }
+)
+
+
+def intensity_range(image, range_values="image", clip_negative=False):
+    """Return image intensity range (min, max) based on desired value type.
+
+    Parameters
+    ----------
+    image : array
+        Input image.
+    range_values : str or 2-tuple, optional
+        The image intensity range is configured by this parameter.
+        The possible values for this parameter are enumerated below.
+
+        'image'
+            Return image min/max as the range.
+        'dtype'
+            Return min/max of the image's dtype as the range.
+        dtype-name
+            Return intensity range based on desired `dtype`. Must be valid key
+            in `DTYPE_RANGE`. Note: `image` is ignored for this range type.
+        2-tuple
+            Return `range_values` as min/max intensities. Note that there's no
+            reason to use this function if you just want to specify the
+            intensity range explicitly. This option is included for functions
+            that use `intensity_range` to support all desired range types.
+
+    clip_negative : bool, optional
+        If True, clip the negative range (i.e. return 0 for min intensity)
+        even if the image dtype allows negative values.
+    """
+    if range_values == "dtype":
+        range_values = image.dtype.type
+
+    if range_values == "image":
+        i_min = np.min(image)
+        i_max = np.max(image)
+    elif range_values in DTYPE_RANGE:
+        i_min, i_max = DTYPE_RANGE[range_values]
+        if clip_negative:
+            i_min = 0
+    else:
+        i_min, i_max = range_values
+    return i_min, i_max
+
+
+def _output_dtype(dtype_or_range):
+    """Determine the output dtype for rescale_intensity.
+
+    The dtype is determined according to the following rules:
+    - if ``dtype_or_range`` is a dtype, that is the output dtype.
+    - if ``dtype_or_range`` is a dtype string, that is the dtype used, unless
+      it is not a NumPy data type (e.g. 'uint12' for 12-bit unsigned integers),
+      in which case the data type that can contain it will be used
+      (e.g. uint16 in this case).
+    - if ``dtype_or_range`` is a pair of values, the output data type will be
+      float.
+
+    Parameters
+    ----------
+    dtype_or_range : type, string, or 2-tuple of int/float
+        The desired range for the output, expressed as either a NumPy dtype or
+        as a (min, max) pair of numbers.
+
+    Returns
+    -------
+    out_dtype : type
+        The data type appropriate for the desired output.
+    """
+    if type(dtype_or_range) in [list, tuple, np.ndarray]:
+        # pair of values: always return float.
+        return np.float_
+    if type(dtype_or_range) == type:
+        # already a type: return it
+        return dtype_or_range
+    if dtype_or_range in DTYPE_RANGE:
+        # string key in DTYPE_RANGE dictionary
+        try:
+            # if it's a canonical numpy dtype, convert
+            return np.dtype(dtype_or_range).type
+        except TypeError:  # uint10, uint12, uint14
+            # otherwise, return uint16
+            return np.uint16
+    else:
+        raise ValueError(
+            "Incorrect value for out_range, should be a valid image data "
+            f"type or a pair of values, got {dtype_or_range}."
+        )
+
+
+def rescale_intensity(image, in_range="image", out_range="dtype"):
+    """Return image after stretching or shrinking its intensity levels.
+
+    The desired intensity range of the input and output, `in_range` and
+    `out_range` respectively, are used to stretch or shrink the intensity range
+    of the input image. See examples below.
+
+    Parameters
+    ----------
+    image : array
+        Image array.
+    in_range, out_range : str or 2-tuple, optional
+        Min and max intensity values of input and output image.
+        The possible values for this parameter are enumerated below.
+
+        'image'
+            Use image min/max as the intensity range.
+        'dtype'
+            Use min/max of the image's dtype as the intensity range.
+        dtype-name
+            Use intensity range based on desired `dtype`. Must be valid key
+            in `DTYPE_RANGE`.
+        2-tuple
+            Use `range_values` as explicit min/max intensities.
+
+    Returns
+    -------
+    out : array
+        Image array after rescaling its intensity. This image is the same dtype
+        as the input image.
+
+    Notes
+    -----
+    .. versionchanged:: 0.17
+        The dtype of the output array has changed to match the output dtype, or
+        float if the output range is specified by a pair of floats.
+
+    See Also
+    --------
+    equalize_hist
+
+    Examples
+    --------
+    By default, the min/max intensities of the input image are stretched to
+    the limits allowed by the image's dtype, since `in_range` defaults to
+    'image' and `out_range` defaults to 'dtype':
+
+    >>> image = np.array([51, 102, 153], dtype=np.uint8)
+    >>> rescale_intensity(image)
+    array([  0, 127, 255], dtype=uint8)
+
+    It's easy to accidentally convert an image dtype from uint8 to float:
+
+    >>> 1.0 * image
+    array([ 51., 102., 153.])
+
+    Use `rescale_intensity` to rescale to the proper range for float dtypes:
+
+    >>> image_float = 1.0 * image
+    >>> rescale_intensity(image_float)
+    array([0. , 0.5, 1. ])
+
+    To maintain the low contrast of the original, use the `in_range` parameter:
+
+    >>> rescale_intensity(image_float, in_range=(0, 255))
+    array([0.2, 0.4, 0.6])
+
+    If the min/max value of `in_range` is more/less than the min/max image
+    intensity, then the intensity levels are clipped:
+
+    >>> rescale_intensity(image_float, in_range=(0, 102))
+    array([0.5, 1. , 1. ])
+
+    If you have an image with signed integers but want to rescale the image to
+    just the positive range, use the `out_range` parameter. In that case, the
+    output dtype will be float:
+
+    >>> image = np.array([-10, 0, 10], dtype=np.int8)
+    >>> rescale_intensity(image, out_range=(0, 127))
+    array([  0. ,  63.5, 127. ])
+
+    To get the desired range with a specific dtype, use ``.astype()``:
+
+    >>> rescale_intensity(image, out_range=(0, 127)).astype(np.int8)
+    array([  0,  63, 127], dtype=int8)
+
+    If the input image is constant, the output will be clipped directly to the
+    output range:
+    >>> image = np.array([130, 130, 130], dtype=np.int32)
+    >>> rescale_intensity(image, out_range=(0, 127)).astype(np.int32)
+    array([127, 127, 127], dtype=int32)
+    """
+    if out_range in ["dtype", "image"]:
+        out_dtype = _output_dtype(image.dtype.type)
+    else:
+        out_dtype = _output_dtype(out_range)
+
+    imin, imax = map(float, intensity_range(image, in_range))
+    omin, omax = map(
+        float, intensity_range(image, out_range, clip_negative=(imin >= 0))
+    )
+
+    if np.any(np.isnan([imin, imax, omin, omax])):
+        warn(
+            "One or more intensity levels are NaN. Rescaling will broadcast "
+            "NaN to the full image. Provide intensity levels yourself to "
+            "avoid this. E.g. with np.nanmin(image), np.nanmax(image).",
+            stacklevel=2,
+        )
+
+    image = np.clip(image, imin, imax)
+
+    if imin != imax:
+        image = (image - imin) / (imax - imin)
+        return np.asarray(image * (omax - omin) + omin, dtype=out_dtype)
+    else:
+        return np.clip(image, omin, omax).astype(out_dtype)