numpyimage 3.3.0__tar.gz → 3.4.1__tar.gz

{numpyimage-3.3.0/numpyimage.egg-info → numpyimage-3.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: numpyimage
-Version: 3.3.0
+Version: 3.4.1
 Summary: Load, save, & manipulate image files as numpy arrays
 Author-email: Jasper Phelps <jasper.s.phelps@gmail.com>
 License: MIT License

{numpyimage-3.3.0 → numpyimage-3.4.1}/npimage/graphics.py

@@ -204,29 +204,42 @@ def drawcircle(image, center, perpendicular, radius, value,
     - out_of_bounds: Literal['ignore', 'wrap', 'raise'] = 'ignore'
     - add_missing_dims: Literal[None, 'start', 'end'] = None
     """
-    ndims = 3  # TODO code up logic for determining this from the input
     return_image = False
     if image is None and center is None:
+        ndims = len(perpendicular) if perpendicular is not None else 2
         image = np.zeros((2*iceil(radius) + 1,)*ndims, dtype=np.uint8)
-        center = (radius, radius, radius)
+        center = (radius,) * ndims
         imset_kwargs['convention'] = 'center'
         return_image = True
-
-    norm = lambda v: np.sqrt(sum(v**2))
-    perpendicular = np.array(perpendicular)
-    if eq(norm(perpendicular), 0):
-        print('WARNING: Perpendicular had 0 length. No circle was drawn.')
-    perpendicular = perpendicular / norm(perpendicular)
-
-    ax = np.array((1,) + (0,) * (ndims-1))
-    v0 = np.cross(ax, perpendicular)
-    if eq(norm(v0), 0):
-        v0 = np.cross(np.flip(ax), perpendicular)
-    v1 = np.cross(v0, perpendicular)
-    v0 = v0 / norm(v0)
-    v1 = v1 / norm(v1)
-
-    num_pts = iceil(math.pi*radius/spacing) + 1
+    if image is None:
+        raise ValueError("Specifying center without image doesn't make sense.")
+    ndims = image.ndim
+
+    if ndims == 1:
+        raise ValueError("Can't draw a circle on 1D array.")
+    elif ndims == 2:
+        if perpendicular is not None:
+            print('[npimage.drawcircle] WARNING: perpendicular ignored since ndims is 2.')
+        v0 = np.array((1, 0))
+        v1 = np.array((0, 1))
+    elif perpendicular is None:
+        raise ValueError("Must specify perpendicular for ndims > 2")
+    else:
+        norm = lambda v: np.sqrt(sum(v**2))
+        perpendicular = np.array(perpendicular)
+        if eq(norm(perpendicular), 0):
+            print('WARNING: Perpendicular had 0 length. No circle was drawn.')
+        perpendicular = perpendicular / norm(perpendicular)
+
+        ax = np.array((1,) + (0,) * (ndims-1))
+        v0 = np.cross(ax, perpendicular)
+        if eq(norm(v0), 0):
+            v0 = np.cross(np.flip(ax), perpendicular)
+        v1 = np.cross(v0, perpendicular)
+        v0 = v0 / norm(v0)
+        v1 = v1 / norm(v1)
+
+    num_pts = iceil(math.pi * radius / spacing) + 1
     angles = np.linspace(0, math.pi, num_pts)
     half1 = (np.outer(np.cos(angles), v0)
              + np.outer(np.sin(angles), v1)) * radius + center

{numpyimage-3.3.0 → numpyimage-3.4.1}/npimage/imageio.py

@@ -367,7 +367,8 @@ def show(data,
          dim_order='yx',
          data_type: Literal['image', 'segmentation'] = 'image',
          mode: Literal['PIL', 'mpl'] = 'PIL',
-         convert_to_8bit=True,
+         convert_to_8bit: bool = True,
+         convert_kwargs: dict = {'maximize_contrast': True},
          channel_axis='guess',
          **kwargs) -> None:
     """
@@ -410,8 +411,14 @@ def show(data,
     if utils.isint(channel_axis) and channel_axis != -1:
         data = np.moveaxis(data, utils.find_channel_axis(data), -1)
 
-    if convert_to_8bit and data.dtype != np.uint8:
-        data = operations.to_8bit(data)
+    if data.dtype == np.bool:
+        data = data.astype(np.uint8) * 255
+    elif convert_to_8bit and data.dtype != np.uint8:
+        if any(key in convert_kwargs for key in
+                ['bottom_value', 'bottom_percentile', 'top_value', 'top_percentile']):
+            if 'maximize_contrast' not in convert_kwargs:
+                convert_kwargs['maximize_contrast'] = True
+        data = operations.to_8bit(data, **convert_kwargs)
 
     colorbar = False
     if 'colorbar' in kwargs:

{numpyimage-3.3.0 → numpyimage-3.4.1}/npimage/operations.py

@@ -16,7 +16,7 @@ from typing import Iterable, Literal, Union, Optional, Tuple, List
 import numpy as np
 from tqdm import tqdm
 
-from .utils import iround, eq, isint, find_channel_axis
+from .utils import iround, eq, find_channel_axis
 
 
 def squeeze_dtype(image: np.ndarray, minimum_bits=1):
@@ -266,7 +266,7 @@ def downsample(image: np.ndarray,
     array([[3.5, 5.5]])
     """
     channel_axis = find_channel_axis(image)
-    if isinstance(factor, int):
+    if np.issubdtype(type(factor), np.integer):
         if channel_axis is not None:
             # If RGB/RGBA image, don't downsample the colors axis
             factor = (factor,) * (len(image.shape) - 1)
@@ -617,7 +617,7 @@ def overlay_two_images(im1: np.ndarray,
     """
     Overlay two images, with the second image offset by the given amount.
     """
-    if isint(im2_offset):
+    if any(np.issubdtype(type(im2_offset), t) for t in [np.integer, np.floating]):
         im2_offset = [im2_offset] * im2.ndim
     if expand_bounds:
         offsets = ([max(0, -o) for o in im2_offset],

{numpyimage-3.3.0 → numpyimage-3.4.1}/npimage/utils.py

@@ -49,13 +49,28 @@ def eq(a, b, tolerance=1e-8):
     return abs(a - b) < tolerance
 
 
-#TODO duck type this to accept a more general class of objects that extend ints
 def isint(n):
+    """
+    Check whether the given variable is an integer (either a built-in
+    int or a numpy integer type). If the argument is iterable, return
+    a list of booleans indicating whether each element is an integer
+    (again either a built-in int or a numpy integer type).
+
+    Notes
+    -----
+    You might think that isinstance(n, int) is what you want, but that
+      has the undesirable behavior of returning True for bools, and
+      returning False for numpy integer types.
+    To check whether n is a built-in int or np.integer _but not an iterable
+      of them_, use `if npimage.isint(n) is True`, or just
+      call `if np.issubdtype(type(n), np.integer)` yourself.
+    This function does NOT recognize integer types from other packages
+      including TensorFlow, PyTorch, or JAX.
+    """
     try:
-        return [isinstance(a, int) or np.issubdtype(type(a), np.integer)
-                for a in n]
+        return [np.issubdtype(type(a), np.integer) for a in n]
     except TypeError:
-        return isinstance(n, int) or np.issubdtype(type(n), np.integer)
+        return np.issubdtype(type(n), np.integer)
 
 
 def find_channel_axis(data,
@@ -133,15 +148,15 @@ def find_channel_axis(data,
     >>> npimage.find_channel_axis(np.empty((30, 4)), minimum_image_size=0)
     1
     """
-    if isinstance(possible_channel_axes, int):
+    if np.issubdtype(type(possible_channel_axes), np.integer):
         possible_channel_axes = [possible_channel_axes]
     if possible_channel_axes is None:
         possible_channel_axes = range(data.ndim)
 
-    if isinstance(possible_channel_lengths, int):
+    if np.issubdtype(type(possible_channel_lengths), np.integer):
         possible_channel_lengths = [possible_channel_lengths]
 
-    if isinstance(minimum_image_size, int):
+    if np.issubdtype(type(minimum_image_size), np.integer):
         minimum_image_size = (minimum_image_size,)
 
     for axis in possible_channel_axes:

{numpyimage-3.3.0 → numpyimage-3.4.1}/npimage/vidio.py

@@ -280,7 +280,7 @@ class VideoStreamer:
             self.frames_pts = index['frames_pts']
         else:
             self.pts0 = index['pts0']
-            if isinstance(index['framerate'], int):
+            if np.issubdtype(type(index['framerate']), np.integer):
                 self._framerate = index['framerate']
             else:
                 self._framerate = Fraction(index['framerate']['numerator'],
@@ -343,15 +343,29 @@ class VideoStreamer:
             return (pts - self.pts0) // self.pts_delta
 
     def __getitem__(self, key) -> np.ndarray:
-        if isinstance(key, tuple):
-            frame_idx = key[0]
-            frame = self._get_frame(frame_idx)
-            if len(key) == 1:
-                return frame
-            else:
-                return frame[key[1:]]
-        else:
+        if np.issubdtype(type(key), np.integer):
             return self._get_frame(key)
+        if isinstance(key, slice):  # Support slicing
+            key = (key,)  # Logic is handled in the tuple case below
+        if not isinstance(key, tuple):
+            raise TypeError('Key must be an int, slice, or a tuple of ints/slices')
+
+        frame_idx = key[0]
+        if np.issubdtype(type(frame_idx), np.integer):
+            frames = self._get_frame(frame_idx)
+            key = key[1:]
+        elif isinstance(frame_idx, slice):  # Support slicing
+            start, stop, step = frame_idx.indices(self.n_frames)
+            frames = np.array([self._get_frame(i) for i in range(start, stop, step)])
+            key = (slice(None),) + key[1:]
+        elif isinstance(frame_idx, (list, tuple, np.ndarray)):  # Support sequences of ints
+            if not all(utils.isint(frame_idx)):
+                raise TypeError('Sequences of frame indices must contain only integers')
+            frames = np.array([self._get_frame(i) for i in frame_idx])
+            key = (slice(None),) + key[1:]
+        else:
+            raise TypeError("Key's first element must be an int, slice, or sequence of ints")
+        return frames[key]
 
     def _get_frame(self, frame_number) -> np.ndarray:
         """
@@ -390,9 +404,6 @@ class VideoStreamer:
                                  f'{target_pts}). Last seen frame was {self._current_frame_number}'
                                  f' (PTS {self.frame_number_to_pts(self._current_frame_number)}')
 
-        if isinstance(frame_number, slice):  # Support slicing
-            start, stop, step = frame_number.indices(self.n_frames)
-            return np.array([self._get_frame(i) for i in range(start, stop, step)])
         with self._lock:
             frame_number = self._normalize_frame_number(frame_number)
             if (self._current_frame_number is None

{numpyimage-3.3.0 → numpyimage-3.4.1/numpyimage.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: numpyimage
-Version: 3.3.0
+Version: 3.4.1
 Summary: Load, save, & manipulate image files as numpy arrays
 Author-email: Jasper Phelps <jasper.s.phelps@gmail.com>
 License: MIT License

{numpyimage-3.3.0 → numpyimage-3.4.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'numpyimage'
-version = '3.3.0'
+version = '3.4.1'
 description = 'Load, save, & manipulate image files as numpy arrays'
 readme.file = 'README.md'
 readme.content-type = 'text/markdown'