numpyimage 2.2.0__tar.gz → 2.3.0__tar.gz

{numpyimage-2.2.0 → numpyimage-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: numpyimage
-Version: 2.2.0
+Version: 2.3.0
 Summary: Load, save, & manipulate image files as numpy arrays
 Author-email: Jasper Phelps <jasper.s.phelps@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{numpyimage-2.2.0 → numpyimage-2.3.0}/npimage/core.py

@@ -33,7 +33,7 @@ def load(filename, dim_order='zyx', **kwargs):
      images, or yxc for multi-channel (RGB/RGBA) 2D images.
     Set dim_order='xy' if you want to reverse the order of the axes.
     """
-    filename = str(filename)
+    filename = os.path.expanduser(str(filename))
     while filename.endswith('/'):
         filename = filename[:-1]
     if 'format' in kwargs:
@@ -45,7 +45,7 @@ def load(filename, dim_order='zyx', **kwargs):
                          f' "{filename}". Please specify the file type via'
                          ' the `format` argument, e.g. format="tif"')
     if extension not in supported_extensions:
-        raise ValueError(f'File format "{extension}" not supported/recognized.')
+        raise ValueError(f'File format of "{filename}" not supported/recognized.')
 
     data = None
     metadata = None
@@ -161,7 +161,7 @@ def save(data,
     Currently `pixel_size`, `units`, and `compress` are only recognized
     when saving to .nrrd and .ng files, and ignored otherwise.
     """
-    filename = str(filename)
+    filename = os.path.expanduser(str(filename))
     filename = filename.rstrip('/')
     if os.path.exists(filename) and not overwrite:
         raise FileExistsError(f'File {filename} already exists. '
@@ -352,10 +352,10 @@ write = save  # Function name alias
 to_file = save  # Function name alias
 
 
-def save_video(data, filename, time_axis=0, overwrite=False, dim_order='yx',
-               framerate=30, crf=23, compression_speed='medium'):
+def save_video(data, filename, time_axis=0, color_axis=None, overwrite=False,
+               dim_order='yx', framerate=30, crf=23, compression_speed='medium'):
     """
-    Save a 3D numpy array as a video, with a specified axis as the time axis.
+    Save a 3D numpy array of greyscale values OR a 4D numpy array of RGB values as a video
 
     Follows the PyAV cookbook section on generating video from numpy arrays:
     https://pyav.basswood-io.com/docs/develop/cookbook/numpy.html#generating-video
@@ -363,7 +363,7 @@ def save_video(data, filename, time_axis=0, overwrite=False, dim_order='yx',
     Parameters
     ----------
     data : numpy.ndarray or list of filenames
-        A 3D numpy array of pixel values.
+        A 3D (grayscale) or 4D (RGB) numpy array of pixel values.
 
     filename : str
         The filename to save the video to.
@@ -371,24 +371,44 @@ def save_video(data, filename, time_axis=0, overwrite=False, dim_order='yx',
     time_axis : int, default 0
         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.
+
     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.
     """
-    if not data.ndim == 3:
-        raise ValueError('Input data must be a 3D numpy array.')
     try:
         import av
     except ImportError:
-        raise ImportError('To save videos, you must have PyAV installed. '
-                          'You can install it with "pip install av".')
-    data = np.moveaxis(data, time_axis, 0)
-    if 'xy' in dim_order:
-        data = data.swapaxes(1, 2)
-    n_frames = data.shape[0]
+        raise ImportError('To save videos, you must have PyAV installed. You can install it with "pip install av".')
+
+    if color_axis is not None:
+        if data.ndim != 4:
+            raise ValueError('Input data must be a 4D numpy array for color video.')
+        # Move time axis to 0, color axis to -1
+        data = np.moveaxis(data, time_axis, 0)
+        if color_axis != -1:
+            data = np.moveaxis(data, color_axis, -1)
+        if 'xy' in dim_order:
+            data = data.swapaxes(1, 2)
+        n_frames = data.shape[0]
+        height, width, channels = data.shape[1:]
+        if channels != 3:
+            raise ValueError('Color video must have 3 channels (RGB).')
+    else:
+        if data.ndim != 3:
+            raise ValueError('Input data must be a 3D numpy array for grayscale video.')
+        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:
@@ -397,9 +417,9 @@ def save_video(data, filename, time_axis=0, overwrite=False, dim_order='yx',
     extension = filename.split('.')[-1].lower()
     if extension == 'mp4':
         pad = [[0, 0], [0, 0], [0, 0]]
-        if data.shape[1] % 2 != 0:
+        if height % 2 != 0:
             pad[1][1] = 1
-        if data.shape[2] % 2 != 0:
+        if width % 2 != 0:
             pad[2][1] = 1
         if pad != [[0, 0], [0, 0], [0, 0]]:
             data = np.pad(data, pad, mode='edge')
@@ -412,7 +432,10 @@ def save_video(data, filename, time_axis=0, overwrite=False, dim_order='yx',
     stream.width = data.shape[2]
 
     for frame_i in range(n_frames):
-        frame = av.VideoFrame.from_ndarray(data[frame_i], format='gray')
+        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)
 

{numpyimage-2.2.0 → numpyimage-2.3.0}/npimage/operations.py

@@ -19,12 +19,14 @@ import numpy as np
 from .utils import iround, eq, isint
 
 
-def squeeze_dtype(image: np.ndarray):
+def squeeze_dtype(image: np.ndarray, minimum_bits=1):
     """
     Cast a numpy array to the smallest possible dtype without losing information.
     """
     if not isinstance(image, np.ndarray):
         raise TypeError('image must be a numpy array')
+    if minimum_bits > 64:
+        raise ValueError('minimum_bits must be <= 64')
 
     im_has_fractions = not np.all(image == np.floor(image))
     if im_has_fractions:
@@ -35,17 +37,17 @@ def squeeze_dtype(image: np.ndarray):
         return image
     elif image.min() < 0:
         candidates = [np.int8, np.int16, np.int32, np.int64]
-    elif image.max() <= 1:
+    elif image.max() <= 1 and minimum_bits <= 1:
         return image.astype(bool, copy=False)
     else:
         candidates = [np.uint8, np.uint16, np.uint32, np.uint64]
 
     image_max = image.max()
-    if image_max <= 1:
+    if image_max <= 1 and minimum_bits <= 1:
         return image.astype(bool, copy=False)
     for dtype in candidates:
         info = np.iinfo(dtype)
-        if image_max <= info.max:
+        if image_max <= info.max and info.bits >= minimum_bits:
             return image.astype(dtype, copy=False)
     raise ValueError('Image has values larger than the maximum representable value')
 
@@ -70,7 +72,8 @@ def to_16bit(image: np.ndarray, **kwargs) -> np.ndarray:
 
 def cast(image: np.ndarray,
          output_dtype: Union[str, np.dtype],
-         maximize_contrast=True,
+         maximize_contrast: bool = False,
+         round_before_cast_to_int: bool = True,
          bottom_percentile=0.05,
          top_percentile=99.95,
          bottom_value=None,
@@ -132,11 +135,15 @@ def cast(image: np.ndarray,
         raise TypeError(f'Unsupported dtype: {output_dtype}')
 
     if not maximize_contrast:
+        if (round_before_cast_to_int
+                and np.issubdtype(output_dtype, np.integer)
+                and not np.issubdtype(image.dtype, np.integer)):
+            image = image.round()
         return np.clip(
             image,
             info.min,
             info.max
-        ).astype(output_dtype)
+        ).astype(output_dtype, copy=False)
 
     if bottom_value is None or top_value is None:
         percentiles = np.percentile(image, [bottom_percentile, top_percentile])

{numpyimage-2.2.0 → numpyimage-2.3.0}/numpyimage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: numpyimage
-Version: 2.2.0
+Version: 2.3.0
 Summary: Load, save, & manipulate image files as numpy arrays
 Author-email: Jasper Phelps <jasper.s.phelps@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE

{numpyimage-2.2.0 → numpyimage-2.3.0}/numpyimage.egg-info/SOURCES.txt

@@ -3,7 +3,6 @@ README.md
 pyproject.toml
 npimage/__init__.py
 npimage/align.py
-npimage/align_scratch.py
 npimage/core.py
 npimage/graphics.py
 npimage/nrrd_utils.py
@@ -16,4 +15,5 @@ numpyimage.egg-info/SOURCES.txt
 numpyimage.egg-info/dependency_links.txt
 numpyimage.egg-info/requires.txt
 numpyimage.egg-info/top_level.txt
-tests/test_pbm.py
+tests/test_pbm.py
+tests/tests.py

{numpyimage-2.2.0 → numpyimage-2.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = 'numpyimage'
-version = '2.2.0'
+version = '2.3.0'
 description = 'Load, save, & manipulate image files as numpy arrays'
 readme.file = 'README.md'
 readme.content-type = 'text/markdown'

numpyimage-2.3.0/tests/tests.py

@@ -0,0 +1,39 @@
+#!/usr/bin/env python3
+
+import numpy as np
+import fire
+
+import npimage
+import npimage.operations
+
+test_im = np.zeros((8, 8), dtype=np.uint8)
+test_im[0:1, 0:2] = 255
+test_im[1:3, 2:4] = 255
+test_im[3:7, 3:7] = 255
+
+
+def mplshow(*args):
+    npimage.show(*args, mode='matplotlib')
+
+
+def test_offset():
+    mplshow(test_im)
+    mplshow(npimage.operations.offset(test_im, (0.5, 0)))
+    mplshow(npimage.operations.offset(test_im, (0, 0.5)))
+    mplshow(npimage.operations.offset(test_im, (0.5, 0.5)))
+    mplshow(npimage.operations.offset(test_im, (1, 1)))
+
+
+def test_paste():
+    offsets = [('++', [100, 50]),
+               ('+-', [100, -50]),
+               ('-+', [-100, 50]),
+               ('--', [-100, -50])]
+    for offset in offsets:
+        im = npimage.load('firefox-logo.png', dim_order='xy')
+        npimage.operations.paste(im, im, offset[1])
+        npimage.save(im, 'firefox-logo_paste' + offset[0] + '.png', dim_order='xy')
+
+
+if __name__ == '__main__':
+    fire.Fire()

numpyimage-2.2.0/npimage/align_scratch.py

@@ -1,50 +0,0 @@
-
-
-
-def align(im1, im2, num_divisions=4):
-    """
-    Return a translated version of im1 that is aligned with im2.
-
-    To align the images, this function divides im1 into a grid of
-    num_divisions x num_divisions regions. For each region, we find the
-    region in im2 that is most similar to it. After removing outliers
-    for which the similarity score is too low, we calculate the average
-    translation between the two images. We then shift im1 by this
-    average translation.
-    """
-    # The code below is entirely GitHub copilot generated and needs to
-    # be looked at, finished, tested, etc
-
-    # Divide the image into a grid of num_divisions x num_divisions regions
-    height, width = im1.shape
-    region_height = height // num_divisions
-    region_width = width // num_divisions
-
-    # Initialize lists to store the translations for each region
-    translations = []
-
-    # For each region in im1, find the most similar region in im2
-    for i in range(num_divisions):
-        for j in range(num_divisions):
-            # Define the region in im1
-            top_left = (i * region_height, j * region_width)
-            bottom_right = ((i + 1) * region_height, (j + 1) * region_width)
-            region1 = im1[top_left[0]:bottom_right[0], top_left[1]:bottom_right[1]]
-
-            # Define the search region in im2
-            search_bbox = (slice(max(0, top_left[0] - region_height),
-                                 min(height, bottom_right[0] + region_height)),
-                           slice(max(0, top_left[1] - region_width),
-                                 min(width, bottom_right[1] + region_width)))
-
-            # Find the most similar region in im2
-            top_left2, score = find_landmark(im2, region1, search_bbox=search_bbox)
-
-            # Add the translation to the list of translations
-            translations.append((top_left[0] - top_left2[0], top_left[1] - top_left2[1]))
-
-    # Remove outliers from the list of translations
-    translations = np.array(translations)
-    mean_translations = np.mean(translations)
-    # Shift im1 by the average translation
-    aligned_im1 = np.roll(im1, mean_translations, axis=(0, 1))