numpyimage 1.3.0__tar.gz → 2.0.0__tar.gz

numpyimage-2.0.0/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.1
+Name: numpyimage
+Version: 2.0.0
+Summary: Load, save, and manipulate image files as numpy arrays
+Home-page: https://github.com/jasper-tms/npimage
+Author: Jasper Phelps
+Author-email: jasper.s.phelps@gmail.com
+License: GNU GPL v3
+Description: # npimage
+        Need to load pixel values from image files as numpy arrays, and hate having to remember whether you should use PIL, tifffile, matplotlib, or something else? Hate having to deal with the fact that those libraries all use different function names and syntaxes? Wish you could just provide a filename and get back a numpy array? This library's `core.py` does that, with `array = load(filename)`, `save(array, filename)`, and `show(array)` functions that let you easily handle a number of common image file formats without having to remember library-specific syntax. (Another choice of library to consider for accomplishing similar goals is [imageio](https://pypi.org/project/imageio/), which also supports loading videos through the FFmpeg wrapper library [pyav](https://pypi.org/project/av/).)
+        
+        Want to draw simple shapes like lines, triangles, and circles into 3D numpy arrays? Frustrated that the python libraries you can find online like `opencv` and `skimage.draw` work on 2D arrays but not 3D? I wrote some functions in `graphics.py` that do the trick in 3D. (If you know of another library that can do this, please let me know!)
+        
+        
+        ### Documentation
+        - `core.py`: load, save, or show images.
+        - `graphics.py`: draw points, lines, triangles, circles, or spheres into 2D or 3D numpy arrays representing image volumes.
+        - `nrrd_utils.py`: compress or read metadata from `.nrrd` files.
+        - `operations.py`: perform operations on images.
+        
+        For now, check each function's docstring for more. A jupyter notebook demonstrating this package's functions will come later.
+        
+        
+        ### Installation
+        
+        As is always the case in python, consider making a virtual environment (using your preference of conda, virtualenv, or virtualenvwrapper) before installing.
+        
+        **Option 1:** `pip install` from PyPI:
+        
+            pip install numpyimage
+        
+        (Unfortunately the name `npimage` was already taken on PyPI, so `pip install npimage` will get you a different package.)
+        
+        **Option 2:** `pip install` directly from GitHub:
+            
+            pip install git+https://github.com/jasper-tms/npimage.git
+        
+        **Option 3:** First `git clone` this repo and then `pip install` it from your clone:
+        
+            cd ~/repos  # Or wherever on your computer you want to download this code to
+            git clone https://github.com/jasper-tms/npimage.git
+            cd npimage
+            pip install .
+        
+        **After installing,** you can import this package in python using `import npimage` (not `import numpyimage`!)
+        
+Platform: UNKNOWN
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown

{numpyimage-1.3.0 → numpyimage-2.0.0}/npimage/core.py

@@ -15,7 +15,7 @@ from builtins import open as builtin_open
 
 import numpy as np
 
-from . import utils
+from . import operations, utils
 
 supported_extensions = [
     'tif', 'tiff', 'jpg', 'jpeg', 'png', 'pbm',
@@ -30,9 +30,7 @@ def load(filename, dim_order='zyx', **kwargs):
     As is typical for Python, the returned array will by default have
      dimensions ordered as zyx for 3D image volumes, yx for 1-channel 2D
      images, or yxc for multi-channel (RGB/RGBA) 2D images.
-    Set dim_order='xy' if you instead want dimensions ordered as
-     xyz for 3D image volumes, xy for 1-channel 2D images, or
-     xyc for multi-channel 2D images.
+    Set dim_order='xy' if you want to reverse the order of the axes.
     """
     filename = str(filename)
     while filename.endswith('/'):
@@ -109,13 +107,7 @@ def load(filename, dim_order='zyx', **kwargs):
             data = zarr.open(TODO) #TODO check zyx/xyz order
 
     if 'xy' in dim_order:
-        if is_rgb_or_rgba(data):
-            # Can't just transpose because if data is a multi-channel 2D
-            # image, need the channel axis to stay as the last axis.
-            data = data.swapaxes(0, 1)
-        else:
-            data = data.T
-
+        data = data.T
         if extension == 'nrrd':  # TODO check if other formats need this
             utils.transpose_metadata(metadata, inplace=True)
 
@@ -142,6 +134,7 @@ def save(data,
          pixel_size=None,
          units=None,
          compress=None,
+         compression_level=3,
          metadata=None):
     """
     Save a numpy array to file with a file type specified by the
@@ -170,13 +163,15 @@ def save(data,
               '.nrrd. Whether or not compression occurs now will depend on '
               'the format you are saving to.')
 
+    channel_axis = find_channel_axis(data)
     if 'xy' in dim_order:
-        if is_rgb_or_rgba(data):
-            # Can't just transpose because if data is a multi-channel 2D
-            # image, need the channel axis to stay as the last axis.
-            data = data.swapaxes(0, 1)
-        else:
-            data = data.T
+        data = data.T
+        if hasattr(pixel_size, '__iter__') and not isinstance(pixel_size, str):
+            pixel_size = pixel_size[::-1]
+        if hasattr(units, '__iter__') and not isinstance(units, str):
+            units = units[::-1]
+        utils.transpose_metadata(metadata, inplace=True)
+        # The spatial axes and associated metadata are now in zyx order.
 
     if extension in ['tif', 'tiff']:
         import tifffile
@@ -199,30 +194,60 @@ def save(data,
             metadata = {}
         else:
             metadata = metadata.copy()
+        custom_field_map = {}
+
         if compress is True:
             metadata.update({'encoding': 'gzip'})
         if compress is False or 'encoding' not in metadata:
             metadata.update({'encoding': 'raw'})
+
+        if isinstance(metadata.get('space directions', None), str):
+            custom_field_map['space directions'] = 'string'
         if pixel_size is not None:
+            if 'space directions' in metadata:
+                raise ValueError('Cannot specify both "space directions" in'
+                                 ' metadata and "pixel_size" as an argument.')
+
             try:
                 iter(pixel_size)
+                if len(pixel_size) == data.ndim - 1 and channel_axis is not None:
+                    pixel_size.insert(channel_axis, np.nan)
             except TypeError:
-                pixel_size = [pixel_size] * data.ndim
+                if channel_axis is not None:
+                    pixel_size = [pixel_size] * (data.ndim - 1)
+                    pixel_size.insert(channel_axis, np.nan)
+                else:
+                    pixel_size = [pixel_size] * data.ndim
+            if len(pixel_size) != data.ndim:
+                raise ValueError(f'pixel_size has length {len(pixel_size)},'
+                                 ' but data has {data.ndim} dimensions.')
+
+            pixel_size_not_none = [size for size in pixel_size
+                                   if size is not None and size != np.nan]
+            space_directions = np.diag(pixel_size_not_none).astype(float)
+            # nrrd.format_optional_matrix() expects an entire row of
+            # np.nan for non-spatial dimensions, so insert row(s) for that.
+            none_indices = [i for i, size in enumerate(pixel_size)
+                            if size is None or size == np.nan]
+            space_directions = np.insert(space_directions, none_indices, np.nan, axis=0)
+            metadata.update({'space directions': space_directions})
 
-            if 'xy' in dim_order:
-                pixel_size = np.flip(pixel_size)
-            metadata.update({'space directions': np.flip(np.diag(pixel_size),
-                                                         axis=-1)})
         if 'space dimension' not in metadata and 'space' not in metadata:
             # If the number of spatial dimensions is not specified, assume
-            # it's the number of dimensions in the data array, minus the
-            # channel axis if it's present.
-            if is_rgb_or_rgba(data):
+            # it's the number of dimensions in the data array, minus 1 if
+            # a channel axis is present.
+            if find_channel_axis(data) is not None:
                 metadata.update({'space dimension': data.ndim - 1})
             else:
                 metadata.update({'space dimension': data.ndim})
         if units is not None:
-            metadata.update({'space units': [units] * data.ndim})
+            if hasattr(units, '__iter__') and not isinstance(units, str):
+                units = list(units)
+            elif 'space dimension' in metadata:
+                units = [units] * metadata['space dimension']
+            else:
+                units = [units] * data.ndim
+            metadata.update({'space units': units})
 
         # From https://pynrrd.readthedocs.io/en/stable/background/index-ordering.html
         # "C-order is the index order used in Python and many Python libraries
@@ -241,7 +266,12 @@ def save(data,
         # index_order='C' to the nrrd.write command below, we also need to flip
         # the order of any per-axis metadata fields.
         utils.transpose_metadata(metadata, inplace=True)
-        nrrd.write(filename, data, header=metadata, index_order='C')
+        nrrd.write(filename,
+                   data,
+                   header=metadata,
+                   custom_field_map=custom_field_map,
+                   compression_level=compression_level,
+                   index_order='C')
 
     if extension in ['raw', 'vol']:
         raise NotImplementedError
@@ -251,12 +281,10 @@ def save(data,
 
     if extension == 'ng':
         from cloudvolume import CloudVolume
+        from cloudvolume.exceptions import InfoUnavailableError
 
         # CloudVolume expects data in Fortran order
-        if is_rgb_or_rgba(data):
-            data = data.swapaxes(0, 1)
-        else:
-            data = data.T
+        data = data.T
 
         resolution = 1
         if pixel_size is not None:
@@ -265,35 +293,46 @@ def save(data,
             iter(resolution)
         except TypeError:
             resolution = [resolution] * data.ndim
-        if compress is True or compress == 'lossy':
+        if compress is True or compress in ['lossy', 'jpeg', 'jpg']:
             encoding = 'jpeg'
+            gzip = False
+        elif compress is None or compress in ['lossless', 'gzip']:
+            if compress is None:
+                print('Using gzip compression by default for .ng format.')
+            encoding = 'raw'
             gzip = True
-        elif compress == 'lossless':
-            encoding = 'raw',
-            gzip = True
-        elif compress is False or compress is None:
+        elif compress is False:
             encoding = 'raw'
             gzip = False
         else:
-            raise ValueError('For .ng format, compress must be True, False,'
-                             f' "lossy", or "lossless" but was {compress}')
-
-        info = CloudVolume.create_new_info(
-            num_channels=1,
-            layer_type='image',
-            data_type=data.dtype,
-            encoding=encoding,
-            resolution=resolution,
-            voxel_offset=[0, 0, 0],
-            chunk_size=[64, 64, 64],
-            volume_size=data.shape
-        )
+            raise ValueError('For .ng format, compress must be '
+                             'True/"lossy"/"jpeg"/"jpg", "lossless"/"gzip",'
+                             f' or False, but was "{compress}"')
 
         if not any(filename.startswith(prefix)
                    for prefix in ['file://', 'gs://', 's3://']):
             filename = 'file://' + filename
-        vol = CloudVolume(filename, info=info, compress=gzip)
-        vol.commit_info()
+
+        try:
+            vol = CloudVolume(filename, compress=gzip)
+            if (vol.shape[:data.ndim] != data.shape
+                    or any(s != 1 for s in vol.shape[data.ndim:])):
+                raise ValueError('Dataset already exists at the specified path,'
+                                 ' but its shape does not match the given data.')
+        except InfoUnavailableError:
+            info = CloudVolume.create_new_info(
+                num_channels=1,
+                layer_type='image',
+                data_type=data.dtype,
+                encoding=encoding,
+                resolution=resolution,
+                voxel_offset=[0, 0, 0],
+                chunk_size=[64, 64, 64],
+                volume_size=data.shape
+            )
+
+            vol = CloudVolume(filename, info=info, compress=gzip)
+            vol.commit_info()
 
         vol[:] = data
 
@@ -309,11 +348,6 @@ def save_video(data, filename, overwrite=False, dim_order='yx', time_axis=0,
 
     Follows the PyAV cookbook section on generating video from numpy arrays:
     https://pyav.basswood-io.com/docs/develop/cookbook/numpy.html#generating-video
-
-    Parameters
-    ----------
-    data : numpy.ndarray or list of filenames
-        A 3D numpy array of pixel values, with the time axis as the first axis.
     """
     if not data.ndim == 3:
         raise ValueError('Input data must be a 3D numpy array.')
@@ -351,7 +385,11 @@ def save_video(data, filename, overwrite=False, dim_order='yx', time_axis=0,
     container.close()
 
 
-def show(data, dim_order='yx', mode='PIL', **kwargs):
+def show(data,
+         dim_order='yx',
+         mode='PIL',
+         convert_to_8bit=True,
+         **kwargs):
     """
     Display a numpy array of pixel values as an image. Supported types:
       1-channel (grayscale) : data.shape must be (y, x)
@@ -359,7 +397,7 @@ def show(data, dim_order='yx', mode='PIL', **kwargs):
       4-channel (RGBA)  : data.shape must be (y, x, 4)
 
     If `dim_order` is set to 'xy' (instead of the default 'yx'), then
-    swap the y and x above. The channel axis must come last regardless.
+    swap the y and x above.
 
     Images will be shown using either `PIL.Image.fromarray(data).show()`
     or `matplotlib.pyplot.imshow(data)` depending on 'mode'. Uses PIL by
@@ -374,18 +412,22 @@ def show(data, dim_order='yx', mode='PIL', **kwargs):
         if os.path.exists(data):
             data = load(data)
 
-    if not is_rgb_or_rgba(data) and data.ndim != 2:
-        m = ('Input array must have shape (y, x) for grayscale, '
-            '(y, x, 3) for RGB, or (y, x, 4) for RGBA but had '
-            f'shape {data.shape}')
+    if (not data.ndim == 2) and not (data.ndim == 3 and find_channel_axis(data) is not None):
+        m = ('Data must have shape (y, x) for grayscale, '
+             '(y, x, 3) for RGB, or (y, x, 4) for RGBA but had '
+             f'shape {data.shape}')
         if 'xy' in dim_order:
             m = m.replace('y, x', 'x, y')
         raise ValueError(m)
 
     if 'xy' in dim_order:
-        # Can't just transpose because if data is a multi-channel 2D
-        # image, need the channel axis to stay as the last axis.
-        data = data.swapaxes(0, 1)
+        data = data.T
+    channel_axis = find_channel_axis(data, expected_channel_axis=-1)
+    if channel_axis is not None and channel_axis != -1:
+        data = np.moveaxis(data, find_channel_axis(data), -1)
+
+    if convert_to_8bit and data.dtype != np.uint8:
+        data = operations.to_8bit(data)
 
     colorbar = False
     if 'colorbar' in kwargs:
@@ -407,16 +449,45 @@ def show(data, dim_order='yx', mode='PIL', **kwargs):
 imshow = show  # Function name alias
 
 
-def is_rgb_or_rgba(data):
+def find_channel_axis(data, expected_channel_axis=[0, -1]):
     """
-    Return True if the given numpy array has a shape indicating
-    that it's either an RGB or RGBA image.
-
-    data.shape == (i, j, 3)  ->  it's RGB, return True
-    data.shape == (i, j, 4)  ->  it's RGBA, return True
-    data.shape == anything else -> return False
+    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),
+    3 (RGB), or 4 (RGBA)), return the index of that axis.
 
+    Parameters
+    ----------
+    data : numpy.ndarray
+        The numpy array to check for a channel axis.
+
+    expected_channel_axis : 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
+        almost always where a channel axis will be found.
+
+    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 expected_channel_axis 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
+        axis, so be careful not to do a test like `if find_channel_axis(data):`
+        because 0 will evaluate to False even though the data has a channel axis.
     """
-    if data.ndim == 3 and data.shape[2] in [3, 4]:
-        return True
-    return False
+    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]:
+            return axis
+    return None

{numpyimage-1.3.0 → numpyimage-2.0.0}/npimage/operations.py

@@ -11,7 +11,7 @@ Function list:
 - overlay_two_images: Overlay two images with the second one offset.
 """
 
-from typing import Iterable, Literal, Union, Optional
+from typing import Iterable, Literal, Union, Optional, Tuple, List
 import gc
 
 import numpy as np
@@ -136,8 +136,8 @@ def cast(image: np.ndarray,
 
 
 def adjust_brightness(image: np.ndarray,
-                      starting_range: tuple[float, float],
-                      target_range: tuple[float, float],
+                      starting_range: Tuple[float, float],
+                      target_range: Tuple[float, float],
                       output_dtype: Optional[Union[str, np.dtype]] = None,
                       clip: bool = False) -> np.ndarray:
     """
@@ -436,8 +436,8 @@ def paste(image: np.ndarray,
     target[tuple(target_range)] = image[tuple(source_range)]
 
 
-def overlay(ims: list[np.ndarray],
-            offsets: list[tuple[float]],
+def overlay(ims: List[np.ndarray],
+            offsets: List[Tuple[float]],
             later_images_on_top=True,
             expand_bounds=False,
             fill_value=0):

{numpyimage-1.3.0 → numpyimage-2.0.0}/npimage/utils.py

@@ -68,10 +68,17 @@ def transpose_metadata(metadata: dict or OrderedDict,
     Designed to work with OrderedDicts that contain nrrd files'
     metadata, but may be useful for metadata from other formats.
     """
+    if metadata is None:
+        return None
     if not inplace:
         metadata = metadata.copy()
-    for key in metadata:
-        if hasattr(metadata[key], '__iter__') and not isinstance(metadata[key], str):
-            metadata[key] = metadata[key][::-1]
+    for key, value in metadata.items():
+        if isinstance(value, str) or not hasattr(value, '__iter__'):
+            continue
+        if isinstance(value, np.ndarray):
+            value = np.flip(value)
+        else:
+            value = value[::-1]
+        metadata[key] = value
     if not inplace:
         return metadata

numpyimage-2.0.0/numpyimage.egg-info/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.1
+Name: numpyimage
+Version: 2.0.0
+Summary: Load, save, and manipulate image files as numpy arrays
+Home-page: https://github.com/jasper-tms/npimage
+Author: Jasper Phelps
+Author-email: jasper.s.phelps@gmail.com
+License: GNU GPL v3
+Description: # npimage
+        Need to load pixel values from image files as numpy arrays, and hate having to remember whether you should use PIL, tifffile, matplotlib, or something else? Hate having to deal with the fact that those libraries all use different function names and syntaxes? Wish you could just provide a filename and get back a numpy array? This library's `core.py` does that, with `array = load(filename)`, `save(array, filename)`, and `show(array)` functions that let you easily handle a number of common image file formats without having to remember library-specific syntax. (Another choice of library to consider for accomplishing similar goals is [imageio](https://pypi.org/project/imageio/), which also supports loading videos through the FFmpeg wrapper library [pyav](https://pypi.org/project/av/).)
+        
+        Want to draw simple shapes like lines, triangles, and circles into 3D numpy arrays? Frustrated that the python libraries you can find online like `opencv` and `skimage.draw` work on 2D arrays but not 3D? I wrote some functions in `graphics.py` that do the trick in 3D. (If you know of another library that can do this, please let me know!)
+        
+        
+        ### Documentation
+        - `core.py`: load, save, or show images.
+        - `graphics.py`: draw points, lines, triangles, circles, or spheres into 2D or 3D numpy arrays representing image volumes.
+        - `nrrd_utils.py`: compress or read metadata from `.nrrd` files.
+        - `operations.py`: perform operations on images.
+        
+        For now, check each function's docstring for more. A jupyter notebook demonstrating this package's functions will come later.
+        
+        
+        ### Installation
+        
+        As is always the case in python, consider making a virtual environment (using your preference of conda, virtualenv, or virtualenvwrapper) before installing.
+        
+        **Option 1:** `pip install` from PyPI:
+        
+            pip install numpyimage
+        
+        (Unfortunately the name `npimage` was already taken on PyPI, so `pip install npimage` will get you a different package.)
+        
+        **Option 2:** `pip install` directly from GitHub:
+            
+            pip install git+https://github.com/jasper-tms/npimage.git
+        
+        **Option 3:** First `git clone` this repo and then `pip install` it from your clone:
+        
+            cd ~/repos  # Or wherever on your computer you want to download this code to
+            git clone https://github.com/jasper-tms/npimage.git
+            cd npimage
+            pip install .
+        
+        **After installing,** you can import this package in python using `import npimage` (not `import numpyimage`!)
+        
+Platform: UNKNOWN
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown

{numpyimage-1.3.0 → numpyimage-2.0.0}/numpyimage.egg-info/SOURCES.txt

@@ -16,5 +16,4 @@ numpyimage.egg-info/PKG-INFO
 numpyimage.egg-info/SOURCES.txt
 numpyimage.egg-info/dependency_links.txt
 numpyimage.egg-info/requires.txt
-numpyimage.egg-info/top_level.txt
-tests/tests.py
+numpyimage.egg-info/top_level.txt

{numpyimage-1.3.0 → numpyimage-2.0.0}/setup.py

@@ -9,7 +9,7 @@ with open("requirements.txt", "r") as f:
 
 setuptools.setup(
     name="numpyimage",
-    version="1.3.0",
+    version="2.0.0",
     author="Jasper Phelps",
     author_email="jasper.s.phelps@gmail.com",
     description="Load, save, and manipulate image files as numpy arrays",

numpyimage-1.3.0/PKG-INFO

@@ -1,58 +0,0 @@
-Metadata-Version: 2.1
-Name: numpyimage
-Version: 1.3.0
-Summary: Load, save, and manipulate image files as numpy arrays
-Home-page: https://github.com/jasper-tms/npimage
-Author: Jasper Phelps
-Author-email: jasper.s.phelps@gmail.com
-License: GNU GPL v3
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: pillow
-Requires-Dist: tifffile
-Requires-Dist: pynrrd
-Requires-Dist: matplotlib
-Requires-Dist: opencv-python-headless
-
-# npimage
-Need to load pixel values from image files as numpy arrays, and hate having to remember whether you should use PIL, tifffile, matplotlib, or something else? Hate having to deal with the fact that those libraries all use different function names and syntaxes? Wish you could just provide a filename and get back a numpy array? This library's `core.py` does that, with `array = load(filename)`, `save(array, filename)`, and `show(array)` functions that let you easily handle a number of common image file formats without having to remember library-specific syntax. (Another choice of library to consider for accomplishing similar goals is [imageio](https://pypi.org/project/imageio/), which also supports loading videos through the FFmpeg wrapper library [pyav](https://pypi.org/project/av/).)
-
-Want to draw simple shapes like lines, triangles, and circles into 3D numpy arrays? Frustrated that the python libraries you can find online like `opencv` and `skimage.draw` work on 2D arrays but not 3D? I wrote some functions in `graphics.py` that do the trick in 3D. (If you know of another library that can do this, please let me know!)
-
-
-### Documentation
-- `core.py`: load, save, or show images.
-- `graphics.py`: draw points, lines, triangles, circles, or spheres into 2D or 3D numpy arrays representing image volumes.
-- `nrrd_utils.py`: compress or read metadata from `.nrrd` files.
-- `operations.py`: perform operations on images.
-
-For now, check each function's docstring for more. A jupyter notebook demonstrating this package's functions will come later.
-
-
-### Installation
-
-As is always the case in python, consider making a virtual environment (using your preference of conda, virtualenv, or virtualenvwrapper) before installing.
-
-**Option 1:** `pip install` from PyPI:
-
-    pip install numpyimage
-
-(Unfortunately the name `npimage` was already taken on PyPI, so `pip install npimage` will get you a different package.)
-
-**Option 2:** `pip install` directly from GitHub:
-    
-    pip install git+https://github.com/jasper-tms/npimage.git
-
-**Option 3:** First `git clone` this repo and then `pip install` it from your clone:
-
-    cd ~/repos  # Or wherever on your computer you want to download this code to
-    git clone https://github.com/jasper-tms/npimage.git
-    cd npimage
-    pip install .
-
-**After installing,** you can import this package in python using `import npimage` (not `import numpyimage`!)

numpyimage-1.3.0/numpyimage.egg-info/PKG-INFO

@@ -1,58 +0,0 @@
-Metadata-Version: 2.1
-Name: numpyimage
-Version: 1.3.0
-Summary: Load, save, and manipulate image files as numpy arrays
-Home-page: https://github.com/jasper-tms/npimage
-Author: Jasper Phelps
-Author-email: jasper.s.phelps@gmail.com
-License: GNU GPL v3
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: pillow
-Requires-Dist: tifffile
-Requires-Dist: pynrrd
-Requires-Dist: matplotlib
-Requires-Dist: opencv-python-headless
-
-# npimage
-Need to load pixel values from image files as numpy arrays, and hate having to remember whether you should use PIL, tifffile, matplotlib, or something else? Hate having to deal with the fact that those libraries all use different function names and syntaxes? Wish you could just provide a filename and get back a numpy array? This library's `core.py` does that, with `array = load(filename)`, `save(array, filename)`, and `show(array)` functions that let you easily handle a number of common image file formats without having to remember library-specific syntax. (Another choice of library to consider for accomplishing similar goals is [imageio](https://pypi.org/project/imageio/), which also supports loading videos through the FFmpeg wrapper library [pyav](https://pypi.org/project/av/).)
-
-Want to draw simple shapes like lines, triangles, and circles into 3D numpy arrays? Frustrated that the python libraries you can find online like `opencv` and `skimage.draw` work on 2D arrays but not 3D? I wrote some functions in `graphics.py` that do the trick in 3D. (If you know of another library that can do this, please let me know!)
-
-
-### Documentation
-- `core.py`: load, save, or show images.
-- `graphics.py`: draw points, lines, triangles, circles, or spheres into 2D or 3D numpy arrays representing image volumes.
-- `nrrd_utils.py`: compress or read metadata from `.nrrd` files.
-- `operations.py`: perform operations on images.
-
-For now, check each function's docstring for more. A jupyter notebook demonstrating this package's functions will come later.
-
-
-### Installation
-
-As is always the case in python, consider making a virtual environment (using your preference of conda, virtualenv, or virtualenvwrapper) before installing.
-
-**Option 1:** `pip install` from PyPI:
-
-    pip install numpyimage
-
-(Unfortunately the name `npimage` was already taken on PyPI, so `pip install npimage` will get you a different package.)
-
-**Option 2:** `pip install` directly from GitHub:
-    
-    pip install git+https://github.com/jasper-tms/npimage.git
-
-**Option 3:** First `git clone` this repo and then `pip install` it from your clone:
-
-    cd ~/repos  # Or wherever on your computer you want to download this code to
-    git clone https://github.com/jasper-tms/npimage.git
-    cd npimage
-    pip install .
-
-**After installing,** you can import this package in python using `import npimage` (not `import numpyimage`!)

numpyimage-1.3.0/tests/tests.py

@@ -1,39 +0,0 @@
-#!/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()