numpyimage 2.4.3__tar.gz → 2.6.0__tar.gz

{numpyimage-2.4.3 → numpyimage-2.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: numpyimage
-Version: 2.4.3
+Version: 2.6.0
 Summary: Load, save, & manipulate image files as numpy arrays
 Author-email: Jasper Phelps <jasper.s.phelps@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -695,6 +695,9 @@ Requires-Dist: tifffile
 Requires-Dist: pynrrd
 Requires-Dist: matplotlib
 Requires-Dist: opencv-python-headless
+Provides-Extra: all
+Requires-Dist: tqdm; extra == "all"
+Requires-Dist: av; extra == "all"
 Dynamic: license-file
 
 # npimage

{numpyimage-2.4.3 → numpyimage-2.6.0}/npimage/core.py

@@ -9,7 +9,7 @@ Function list:
 - show(np_array) -> Displays a numpy array of pixel values as an image
 """
 
-from typing import Literal
+from typing import Literal, Union, Tuple, Iterator
 import os
 import glob
 from builtins import open as builtin_open
@@ -24,7 +24,7 @@ supported_extensions = [
 ]
 
 
-def load(filename, dim_order='zyx', **kwargs):
+def load(filename, dim_order='zyx', **kwargs) -> Union[np.ndarray, Tuple[np.ndarray, dict]]:
     """
     Open a 2D or 3D image file and return its pixel values as a numpy array.
 
@@ -52,16 +52,16 @@ def load(filename, dim_order='zyx', **kwargs):
 
     if extension in ['jpg', 'jpeg', 'png']:
         from PIL import Image
-        data = np.array(Image.open(filename)) #PIL.Image.open returns zyx order
+        data = np.array(Image.open(filename))  # PIL.Image.open returns zyx order
 
     if extension == 'heic':
         _ensure_heif_opener_registered()
         from PIL import Image
-        data = np.array(Image.open(filename)) #PIL.Image.open returns zyx order
+        data = np.array(Image.open(filename))  # PIL.Image.open returns zyx order
 
     if extension in ['tif', 'tiff']:
         import tifffile
-        data = tifffile.imread(filename) #tifffile.imread returns zyx order
+        data = tifffile.imread(filename)  # tifffile.imread returns zyx order
 
     if extension == 'pbm':
         from .filetypes import pbm
@@ -151,7 +151,7 @@ def save(data,
          units=None,
          compress=None,
          compression_level=3,
-         metadata=None):
+         metadata=None) -> None:
     """
     Save a numpy array to file with a file type specified by the
     filename extension.
@@ -357,12 +357,13 @@ def save(data,
 
         vol[:] = data
 
-
 write = save  # Function name alias
 to_file = save  # Function name alias
 
 
-def load_video(filename, force_rgb=False, progress_bar=True):
+def load_video(filename,
+               return_framerate=False,
+               progress_bar=True) -> Union[np.ndarray, Tuple[np.ndarray, float]]:
     """
     Load all images in a video file as a numpy array.
 
@@ -370,53 +371,57 @@ def load_video(filename, force_rgb=False, progress_bar=True):
     ----------
     filename : str
         Path to the video file
-    force_rgb : bool, default False
-        If True, always return frames as RGB arrays (shape=(H, W, 3))
-        If False, return frames in their native format (e.g., grayscale if possible)
+    return_framerate : bool, default False
+        If True, return the frame rate of the video
     progress_bar : bool, default True
         If True, display a progress bar
 
     Returns
     -------
     data : numpy.ndarray
-        The video frames as a numpy array, shape (num_frames, height, width[, channels])
+        The video frames as a numpy array, shape (num_frames, height, width, colors)
     """
     try:
         import av
+        from tqdm import tqdm
     except ImportError:
-        raise ImportError('To use load_video, install PyAV: pip install av')
-    from tqdm import tqdm
+        raise ImportError('Missing optional dependency for video processing,'
+                          ' run `pip install av tqdm`')
+
     container = av.open(filename)
     stream = container.streams.video[0]
     num_frames = stream.frames
     if not num_frames or num_frames == 0:
         # If we don't know the number of frames, we can't preallocate, so
-        # it's hard to do better than the following approach (which temporarily
-        # uses double the amount of RAM than the preallocated approach uses).
-        return np.array(list(lazy_load_video(filename, force_rgb=force_rgb)))
+        # it's hard to do better than the following approach which temporarily
+        # uses double the amount of RAM compared to the preallocated approach.
+        data = np.array(list(lazy_load_video(filename)))
+        if return_framerate:
+            return data, float(stream.average_rate)
+        else:
+            return data
     else:
         # Load first image to get shape and dtype
         frame_iter = container.decode(stream)
         first_frame = next(frame_iter)
-        if force_rgb:
-            first_img = first_frame.to_ndarray(format='rgb24')
-        else:
-            first_img = first_frame.to_ndarray()
+        first_img = first_frame.to_ndarray(format='rgb24')
         # Preallocate memory for the entire array
         data = np.empty((num_frames, *first_img.shape), dtype=first_img.dtype)
         # Then fill it up frame by frame
         data[0] = first_img
-        for i, frame in tqdm(enumerate(frame_iter, start=1), total=num_frames,
+        for i, frame in tqdm(enumerate(frame_iter), total=num_frames,
                              desc='Loading video', disable=not progress_bar):
-            if force_rgb:
-                img = frame.to_ndarray(format='rgb24')
-            else:
-                img = frame.to_ndarray()
+            if i == 0:
+                continue
+            img = frame.to_ndarray(format='rgb24')
             data[i] = img
-        return data
+        if return_framerate:
+            return data, float(stream.average_rate)
+        else:
+            return data
 
 
-def lazy_load_video(filename, force_rgb=False):
+def lazy_load_video(filename) -> Iterator[np.ndarray]:
     """
     Lazily load video frames as numpy arrays using PyAV.
 
@@ -424,31 +429,112 @@ def lazy_load_video(filename, force_rgb=False):
     ----------
     filename : str
         Path to the video file.
-    force_rgb : bool, default False
-        If True, always return frames as RGB arrays (shape=(H, W, 3)).
-        If False, return frames in their native format (e.g., grayscale if possible).
 
     Yields
     ------
     frame : np.ndarray
-        Video frame as a numpy array, shape (height, width[, colors]).
+        Video frame as a numpy array, shape (height, width, colors).
     """
     try:
         import av
     except ImportError:
-        raise ImportError('To use lazy_load_video, install PyAV: pip install av')
+        raise ImportError('Missing optional dependency for video processing,'
+                          ' run `pip install av tqdm`')
     container = av.open(filename)
     stream = container.streams.video[0]
     for frame in container.decode(stream):
-        if force_rgb:
-            img = frame.to_ndarray(format='rgb24')
-        else:
-            img = frame.to_ndarray()
+        img = frame.to_ndarray(format='rgb24')
         yield img
 
 
+codec_aliases = {
+    "libx264": "libx264",
+    "avc1": "libx264",
+    "h264": "libx264",
+    "H.264": "libx264",
+    "libx265": "libx265",
+    "hevc": "libx265",
+    "hvc1": "libx265",
+    "hev1": "libx265",
+    "h265": "libx265",
+    "H.265": "libx265",
+}
+
+
+class VideoWriter:
+    """
+    Create a video writer object for saving frames to a video file.
+
+    Parameters
+    ----------
+    filename : str
+        The filename to save the video to.
+    framerate : int, default 30
+        The frame rate of the video.
+    crf : int, default 23
+        Constant Rate Factor for encoding quality (lower is better quality).
+    compression_speed : str, default 'medium'
+        Compression speed preset: 'ultrafast', 'superfast', 'veryfast',
+        'faster', 'fast', 'medium', 'slow', 'slower', 'veryslow'.
+    codec : Literal['libx264', 'libx265'], default 'libx264'
+        The video codec to use for encoding. Can be any of a number of aliases for
+        these two codecs, including avc1/h264 vs hevc/hvc1/hev1/h265.
+    """
+    def __init__(self, filename, framerate=30, crf=23, compression_speed='medium',
+                 codec: Literal['libx264', 'libx265'] = 'libx264',
+                 overwrite=False):
+        try:
+            import av
+        except ImportError:
+            raise ImportError('Missing optional dependency for video processing,'
+                              ' run `pip install av tqdm`')
+        self.av = av
+        filename = os.path.expanduser(str(filename))
+        if os.path.exists(filename) and not overwrite:
+            raise FileExistsError(f'File {filename} already exists. '
+                                  'Set overwrite=True to overwrite.')
+        self.filename = filename
+        self.framerate = framerate
+        self.crf = crf
+        self.compression_speed = compression_speed
+        self.codec = codec_aliases[codec.lower()]
+        self.container = av.open(filename, mode='w')
+        self.stream = self.container.add_stream(self.codec, rate=framerate)
+        self.stream.pix_fmt = 'yuv420p'
+        self.stream.options = {'crf': str(crf), 'preset': compression_speed}
+        self._closed = False
+        self.stream.width = 0
+        self.stream.height = 0
+
+    def write(self, frame):
+        if not isinstance(frame, self.av.VideoFrame):
+            if frame.ndim == 3 and frame.shape[-1] == 3:
+                frame = self.av.VideoFrame.from_ndarray(frame, format='rgb24')
+            elif frame.ndim == 2:
+                frame = self.av.VideoFrame.from_ndarray(frame, format='gray')
+            else:
+                raise ValueError(f'Frame must be (H, W) or (H, W, 3) but was {frame.shape}')
+        if self.stream.width == 0:
+            self.stream.width = frame.width
+        if self.stream.height == 0:
+            self.stream.height = frame.height
+        for packet in self.stream.encode(frame):
+            self.container.mux(packet)
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        # Flush stream
+        for packet in self.stream.encode():
+            self.container.mux(packet)
+        self.container.close()
+        self._closed = True
+
+
 def save_video(data, filename, time_axis=0, color_axis=None, overwrite=False,
-               dim_order='yx', framerate=30, crf=23, compression_speed='medium'):
+               dim_order='yx', framerate=30, crf=23, compression_speed='medium',
+               progress_bar=True, codec: Literal['libx264', 'libx265'] = 'libx264') -> None:
     """
     Save a 3D numpy array of greyscale values OR a 4D numpy array of RGB values as a video
 
@@ -467,23 +553,57 @@ def save_video(data, filename, time_axis=0, color_axis=None, overwrite=False,
         The axis of the data array that will be played as time in the video.
 
     color_axis : int or None, default None
-        If not None, specifies the axis of the color channels (e.g., -1 for last axis, 1 for second axis).
-        If None, data is assumed to be grayscale.
+        If not None, specifies the axis of the color channels (e.g., -1 for last axis,
+        1 for second axis).
+        If None, data must be 3D (greyscale) or 4D with one length 3 axis (RGB).
 
     overwrite : bool, default False
         Whether to overwrite the file if it already exists.
 
     dim_order : 'yx' (default) or 'xy'
         The order of the spatial dimensions in the input data.
+
+    framerate : int, default 30
+        The frame rate of the video.
+
+    crf : int, default 23
+        Constant Rate Factor that specifies amount of lossiness allowed in compression.
+        Lower values produce better quality, larger videos. crf=17 has no human-visible
+        compression artifacts. File size approximately doubles/halves each time you
+        add/subtract 6 from crf, so crf=17 produces files about twice as large as
+        the default crf=23.
+
+    compression_speed : str, default 'medium'
+        Compression speed preset: 'ultrafast', 'superfast', 'veryfast',
+        'faster', 'fast', 'medium', 'slow', 'slower', 'veryslow'.
+
+    progress_bar : bool, default True
+        If True, display a progress bar.
+
+    codec : Literal['libx264', 'libx265'], default 'libx264'
+        The video codec to use for encoding. Can be any of a number of aliases for
+        these two codecs, including avc1/h264 vs hevc/hvc1/hev1/h265.
     """
     try:
-        import av
+        from tqdm import tqdm
     except ImportError:
-        raise ImportError('To save videos, you must have PyAV installed. You can install it with "pip install av".')
+        raise ImportError('Missing optional dependency for video processing,'
+                          ' run `pip install av tqdm`')
+
+    filename = os.path.expanduser(str(filename))
+    if filename.split('.')[-1].lower() not in ['mp4', 'mkv', 'avi', 'mov']:
+        filename += '.mp4'
+    if os.path.exists(filename) and not overwrite:
+        raise FileExistsError(f'File {filename} already exists. '
+                              'Set overwrite=True to overwrite.')
 
+    if color_axis is None and data.ndim == 4:
+        color_axis = find_channel_axis(data, possible_channel_lengths=3)
+        if color_axis is None:
+            raise ValueError('4D input data must have an RGB (length 3) axis.')
     if color_axis is not None:
         if data.ndim != 4:
-            raise ValueError('Input data must be a 4D numpy array for color video.')
+            raise ValueError('Input data must be 4D when color_axis is specified.')
         # Move time axis to 0, color axis to -1
         data = np.moveaxis(data, time_axis, 0)
         if color_axis != -1:
@@ -493,22 +613,16 @@ def save_video(data, filename, time_axis=0, color_axis=None, overwrite=False,
         n_frames = data.shape[0]
         height, width, channels = data.shape[1:]
         if channels != 3:
-            raise ValueError('Color video must have 3 channels (RGB).')
+            raise ValueError(f'Color video must have 3 channels (RGB) but had {channels}.')
     else:
         if data.ndim != 3:
-            raise ValueError('Input data must be a 3D numpy array for grayscale video.')
+            raise ValueError('Input data must be 3D when color_axis is not specified.')
         data = np.moveaxis(data, time_axis, 0)
         if 'xy' in dim_order:
             data = data.swapaxes(1, 2)
         n_frames = data.shape[0]
         height, width = data.shape[1:]
 
-    filename = os.path.expanduser(str(filename))
-    if filename.split('.')[-1].lower() not in ['mp4', 'mkv', 'avi', 'mov']:
-        filename += '.mp4'
-    if os.path.exists(filename) and not overwrite:
-        raise FileExistsError(f'File {filename} already exists. '
-                              'Set overwrite=True to overwrite.')
     extension = filename.split('.')[-1].lower()
     if extension == 'mp4':
         pad = [[0, 0], [0, 0], [0, 0]]
@@ -519,25 +633,12 @@ def save_video(data, filename, time_axis=0, color_axis=None, overwrite=False,
         if pad != [[0, 0], [0, 0], [0, 0]]:
             data = np.pad(data, pad, mode='edge')
 
-    container = av.open(filename, mode='w')
-    stream = container.add_stream('libx264', rate=framerate)
-    stream.pix_fmt = 'yuv420p'
-    stream.options = {'crf': str(crf), 'preset': compression_speed}
-    stream.height = data.shape[1]
-    stream.width = data.shape[2]
-
-    for frame_i in range(n_frames):
-        if color_axis is not None:
-            frame = av.VideoFrame.from_ndarray(data[frame_i], format='rgb24')
-        else:
-            frame = av.VideoFrame.from_ndarray(data[frame_i], format='gray')
-        for packet in stream.encode(frame):
-            container.mux(packet)
-
-    for packet in stream.encode():
-        container.mux(packet)
-
-    container.close()
+    with VideoWriter(filename, framerate=framerate, crf=crf,
+                     compression_speed=compression_speed, codec=codec,
+                     overwrite=overwrite) as writer:
+        for frame_i in tqdm(range(n_frames), total=n_frames,
+                            desc='Saving video', disable=not progress_bar):
+            writer.write(data[frame_i])
 
 
 def show(data,
@@ -546,7 +647,7 @@ def show(data,
          mode: Literal['PIL', 'mpl'] = 'PIL',
          convert_to_8bit=True,
          channel_axis='guess',
-         **kwargs):
+         **kwargs) -> None:
     """
     Display a numpy array of pixel values as an image. Supported types:
       1-channel (grayscale) : data.shape must be (y, x)
@@ -610,7 +711,9 @@ def show(data,
 imshow = show  # Function name alias
 
 
-def find_channel_axis(data, expected_channel_axis=[0, -1]):
+def find_channel_axis(data,
+                      possible_channel_axes=[-1, 0],
+                      possible_channel_lengths=[2, 3, 4]) -> Union[int, None]:
     """
     If the given numpy array has a shape suggesting that it has a
     channel (color) axis (that is, any axis with length 2 (2-color),
@@ -621,23 +724,28 @@ def find_channel_axis(data, expected_channel_axis=[0, -1]):
     data : numpy.ndarray
         The numpy array to check for a channel axis.
 
-    expected_channel_axis : int or list of int, default [0, -1]
+    possible_channel_axes : int or list of int, default [0, -1]
         If None, any axis having length 2, 3, or 4 will be considered
         a channel axis.
         If an int, only that axis index will be checked.
         If a list of ints, all axes with those indices will be checked.
-        The default value of [0, -1] checks the first and last axes, which is
+        The default value of [-1, 0] checks the last and first axes, which is
         almost always where a channel axis will be found.
 
+    possible_channel_lengths : int or list of int, default [2, 3, 4]
+        If an int, only that length will be considered a channel axis.
+        If a list of ints, an axis with any of those lengths will be considered
+        a channel axis.
+
     Returns
     -------
     int or None
         The index of the channel axis, or None if no channel axis was found.
 
-        If expected_channel_axis is given, the returned value will be one of
-        the expected_channel_axis values, or None if no channel axis was found.
+        If possible_channel_axes is given, the returned value will be one of
+        the possible_channel_axes values, or None if no channel axis was found.
 
-        If expected_channel_axis is None, the returned value will be between
+        If possible_channel_axes is None, the returned value will be between
         0 and data.ndim - 1, inclusive, or None if no channel axis was found.
 
         Note that returning 0 means the channel axis was found and is the first
@@ -645,25 +753,24 @@ def find_channel_axis(data, expected_channel_axis=[0, -1]):
         because 0 will evaluate to False even though the data has a channel axis.
         Instead write `if find_channel_axis(data) is not None:`
     """
-    if isinstance(expected_channel_axis, int):
-        expected_channel_axis = [expected_channel_axis]
-    if expected_channel_axis is None:
-        expected_channel_axis = range(data.ndim)
-    for axis in expected_channel_axis:
-        if data.shape[axis] in [2, 3, 4]:
+    if isinstance(possible_channel_axes, int):
+        possible_channel_axes = [possible_channel_axes]
+    if possible_channel_axes is None:
+        possible_channel_axes = range(data.ndim)
+    if isinstance(possible_channel_lengths, int):
+        possible_channel_lengths = [possible_channel_lengths]
+    for axis in possible_channel_axes:
+        if data.shape[axis] in possible_channel_lengths:
             return axis
     return None
 
 
 # Flag to track if HEIF opener has been registered
 _heif_opener_registered = False
-
-
-def _ensure_heif_opener_registered():
+def _ensure_heif_opener_registered() -> None:
     """Register the HEIF opener if not already registered."""
     global _heif_opener_registered
     if not _heif_opener_registered:
         from pillow_heif import register_heif_opener
         register_heif_opener()
         _heif_opener_registered = True
-

{numpyimage-2.4.3 → numpyimage-2.6.0}/numpyimage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: numpyimage
-Version: 2.4.3
+Version: 2.6.0
 Summary: Load, save, & manipulate image files as numpy arrays
 Author-email: Jasper Phelps <jasper.s.phelps@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -695,6 +695,9 @@ Requires-Dist: tifffile
 Requires-Dist: pynrrd
 Requires-Dist: matplotlib
 Requires-Dist: opencv-python-headless
+Provides-Extra: all
+Requires-Dist: tqdm; extra == "all"
+Requires-Dist: av; extra == "all"
 Dynamic: license-file
 
 # npimage

{numpyimage-2.4.3 → numpyimage-2.6.0}/numpyimage.egg-info/SOURCES.txt

@@ -14,4 +14,5 @@ numpyimage.egg-info/dependency_links.txt
 numpyimage.egg-info/requires.txt
 numpyimage.egg-info/top_level.txt
 tests/test_heic.py
-tests/test_pbm.py
+tests/test_pbm.py
+tests/test_video.py

{numpyimage-2.4.3 → numpyimage-2.6.0}/numpyimage.egg-info/requires.txt

@@ -5,3 +5,7 @@ tifffile
 pynrrd
 matplotlib
 opencv-python-headless
+
+[all]
+tqdm
+av

{numpyimage-2.4.3 → numpyimage-2.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'numpyimage'
-version = '2.4.3'
+version = '2.6.0'
 description = 'Load, save, & manipulate image files as numpy arrays'
 readme.file = 'README.md'
 readme.content-type = 'text/markdown'
@@ -30,5 +30,11 @@ dependencies = [
     'opencv-python-headless',
 ]
 
+[project.optional-dependencies]
+all = [
+    "tqdm",
+    "av"
+]
+
 [tool.setuptools.packages.find]
 include = ['npimage']

numpyimage-2.6.0/tests/test_video.py

@@ -0,0 +1,31 @@
+#! /usr/bin/env python3
+
+import numpy as np
+import npimage
+from pathlib import Path
+
+
+def test_save_and_load_video(tmp_path=Path.cwd()):
+    # Create synthetic video data
+    data = np.full((120, 128, 256, 3), 255, dtype=np.uint8)
+    for i in range(120):
+        # Zero out the green (channel 1) channel along a moving line
+        npimage.drawline(
+            data[i],
+            pt1=(10 + i / 4, 10 + i, 1),
+            pt2=(90 + i / 4, 128 + i, 1),
+            value=0,
+            thickness=(3, 3, 1)  # Thickness 1 along the color axis
+        )
+    video_path = tmp_path / 'test_video.mp4'
+    npimage.save_video(data, str(video_path), crf=15, overwrite=True)
+    loaded = npimage.load_video(str(video_path), progress_bar=False)
+    # Check shape
+    assert loaded.shape == data.shape
+    # Allow for some difference due to lossy encoding/decoding
+    assert np.allclose(loaded.mean(axis=-1), data.mean(axis=-1), atol=64)
+    print('test_save_and_load_video PASSED')
+
+
+if __name__ == '__main__':
+    test_save_and_load_video()