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WIP: Split ImageSequence into a reader per backend. #186

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29 changes: 28 additions & 1 deletion pims/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from warnings import warn

# has to be here for API stuff
from pims.image_sequence import ImageSequence, ImageSequenceND # noqa
from pims.image_sequence import ImageSequenceND # noqa
from .cine import Cine # noqa
from .norpix_reader import NorpixSeq # noqa
from pims.tiff_stack import TiffStack_tifffile # noqa
Expand Down Expand Up @@ -57,6 +57,33 @@ def raiser(*args, **kwargs):
TiffStack = not_available("tifffile, libtiff, or PIL/Pillow")


# As above
from pims.image_sequence import (ImageSequence_skimage, ImageSequence_mpl,
ImageSequence_scipy, ImageSequence_pil,
ImageSequence_tifffile)
if not pims.image_sequence.skimage_available():
ImageSequence_skimage = not_available('skimage')
if not pims.image_sequence.skimage_available():
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@caspervdw caspervdw Oct 19, 2015

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I would opt for an (optional) classmethod pkg_available() for every reader class.

ImageSequence_mpl = not_availabe('matplotlib')
if not pims.image_sequence.scipy_available():
ImageSequence_scipy = not_available('scipy')
if not pims.image_sequence.PIL_available():
ImageSequence_pil = not_available('PIL/Pillow')
if not pims.image_sequence.tifffile_available():
ImageSequence_tifffile = not_available('tifffile')

if pims.image_sequence.skimage_available():
ImageSequence = ImageSequence_skimage
elif pims.image_sequence.mpl_available():
ImageSequence = ImageSequence_mpl
elif pims.iamge_sequence.scipy_avaiable():
ImageSequence = ImageSequence_scipy
elif pims.image_sequence.PIL_avaialble():
ImageSequence = ImageSequence_pil
# Never point ImageSequence to ImageSequence_tifffile; it only works on TIFF.
else:
ImageSequence = not_available("skimage, matplotlib, scipy, or PIL/Pillow")

try:
import pims.bioformats
if pims.bioformats.available():
Expand Down
112 changes: 76 additions & 36 deletions pims/image_sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,19 +17,52 @@
from pims.frame import Frame
from pims.utils.sort import natural_keys

from PIL import Image
# skimage.io.plugin_order() gives a nice hierarchy of implementations of imread.
# If skimage is not available, go down our own hard-coded hierarchy.
try:
from skimage.io import imread
from skimage.io import imread as skimage_imread
except ImportError:
try:
from matplotlib.pyplot import imread
except ImportError:
from scipy.ndimage import imread
skimage_imread = None
try:
from matplotlib.pyplot import imread as mpl_imread
except ImportError:
mpl_imread = None
try:
from scipy.ndimage import imread as scipy_imread
except ImportError:
scipy_imread = None
try:
from tifffile import imread as tifffile_imread
except ImportError:
tifffile_imread = None
try:
from PIL import Image
except ImportError:
pil_imread = None
else:
def pil_imread(filename):
return np.asarray(Image.open(filename))


def skimage_available():
return skimage_imread is not None
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@caspervdw caspervdw Oct 19, 2015

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If you move this to utils then we can make use of this in display.py too



def mpl_available():
return mpl_imread is not None


def scipy_available():
return scipy_imread is not None


def tifffile_available():
return tifffile_imread is not None


def PIL_available():
return pil_imread is not None

class ImageSequence(FramesSequence):

class BaseImageSequence(FramesSequence):
"""Read a directory of sequentially numbered image files into an
iterable that returns images as numpy arrays.

Expand All @@ -48,10 +81,6 @@ class ImageSequence(FramesSequence):
as_grey : boolean, optional
Convert color images to greyscale. False by default.
May not be used in conjection with process_func.
plugin : string
Passed on to skimage.io.imread if scikit-image is available.
If scikit-image is not available, this will be ignored and a warning
will be issued. Not available in combination with zipfiles.

Examples
--------
Expand All @@ -73,19 +102,8 @@ class ImageSequence(FramesSequence):
>>> frame_shape = video.frame_shape # Pixel dimensions of video
"""
def __init__(self, path_spec, process_func=None, dtype=None,
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@caspervdw caspervdw Oct 19, 2015

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If this works:

@classmethod
def pkg_available(cls):
    return cls._imread is not None

as_grey=False, plugin=None):
try:
import skimage
except ImportError:
if plugin is not None:
warn("A plugin was specified but ignored. Plugins can only "
"be specified if scikit-image is available. Instead, "
"ImageSequence will try using matplotlib and scipy "
"in that order.")
self.kwargs = dict()
else:
self.kwargs = dict(plugin=plugin)

as_grey=False, **kwargs):
self.kwargs = kwargs
self._is_zipfile = False
self._zipfile = None
self._get_files(path_spec)
Expand All @@ -104,17 +122,17 @@ def __init__(self, path_spec, process_func=None, dtype=None,
def close(self):
if self._is_zipfile:
self._zipfile.close()
super(ImageSequence, self).close()
super(BaseImageSequence, self).close()

def __del__(self):
self.close()

def imread(self, filename, **kwargs):
if self._is_zipfile:
img = StringIO(self._zipfile.read(filename))
return np.array(Image.open(img))
file_handle = StringIO(self._zipfile.read(filename))
return self._imread(file_handle, **kwargs)
else:
return imread(filename, **kwargs)
return self._imread(filename, **kwargs)

def _get_files(self, path_spec):
# deal with if input is _not_ a string
Expand All @@ -132,9 +150,6 @@ def _get_files(self, path_spec):
if fnmatch.fnmatch(fn, '*.*')]
self._filepaths = sorted(filepaths, key=natural_keys)
self._count = len(self._filepaths)
if 'plugin' in self.kwargs and self.kwargs['plugin'] is not None:
warn("A plugin cannot be combined with reading from an "
"archive. Extract it if you want to use the plugin.")
return

self.pathname = os.path.abspath(path_spec) # used by __repr__
Expand Down Expand Up @@ -193,6 +208,31 @@ def __repr__(self):
dtype=self.pixel_type)


class ImageSequence_skimage(BaseImageSequence):
__doc__ = BaseImageSequence.__doc__
_imread = skimage_imread


class ImageSequence_mpl(BaseImageSequence):
__doc__ = BaseImageSequence.__doc__
_imread = mpl_imread


class ImageSequence_pil(BaseImageSequence):
__doc__ = BaseImageSequence.__doc__
_imread = pil_imread


class ImageSequence_scipy(BaseImageSequence):
__doc__ = BaseImageSequence.__doc__
_imread = scipy_imread


class ImageSequence_tifffile(BaseImageSequence):
__doc__ = BaseImageSequence.__doc__
_imread = tifffile_imread


def filename_to_indices(filename, identifiers='tzc'):
""" Find ocurrences of dimension indices (e.g. t001, z06, c2)
in a filename and returns a list of indices.
Expand Down Expand Up @@ -225,7 +265,7 @@ def filename_to_indices(filename, identifiers='tzc'):
return result


class ImageSequenceND(FramesSequenceND, ImageSequence):
class ImageSequenceND(FramesSequenceND, BaseImageSequence):
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@caspervdw caspervdw Oct 19, 2015

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I think it makes sense to make this BaseImageSequenceND

"""Read a directory of multi-indexed image files into an iterable that
returns images as numpy arrays. By default, the extra dimensions are
denoted with t, z, c.
Expand Down Expand Up @@ -349,8 +389,8 @@ def customize_image_sequence(imread_func, name=None):
>>> MyImageSequence = customize_image_sequence(my_func)
>>> frames = MyImageSequence('path/to/my_weird_files*')
"""
class CustomImageSequence(ImageSequence):
def imread(self, filename, **kwargs):
class CustomImageSequence(BaseImageSequence):
def _imread(self, filename, **kwargs):
return imread_func(filename, **kwargs)
if name is not None:
CustomImageSequence.__name__ = name
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@caspervdw caspervdw Oct 19, 2015

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__doc__ = BaseImageSequence.__doc__

Expand Down
97 changes: 58 additions & 39 deletions pims/tests/test_common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -510,54 +510,70 @@ def setUp(self):
self.expected_len = 5


class TestImageSequenceWithSkimage(_image_series):
def setUp(self):
self.klass = ImageSequence_skimage
try:
import skimage
except ImportError:
self.skip = True
else:
self.skip = False
super(TestImageSequenceWithPIL, self).setUp()


class TestImageSequenceWithPIL(_image_series):
def setUp(self):
self.filepath = os.path.join(path, 'image_sequence')
self.filenames = ['T76S3F00001.png', 'T76S3F00002.png',
'T76S3F00003.png', 'T76S3F00004.png',
'T76S3F00005.png']
shape = (10, 11)
frames = save_dummy_png(self.filepath, self.filenames, shape)
self.klass = ImageSequence_pil
try:
from PIL import Image
except ImportError:
self.skip = 'PIL'
else:
self.skip = False
super(TestImageSequenceWithPIL, self).setUp()

self.filename = os.path.join(self.filepath, '*.png')
self.frame0 = frames[0]
self.frame1 = frames[1]
self.kwargs = dict(plugin='pil')
self.klass = pims.ImageSequence
self.v = self.klass(self.filename, **self.kwargs)
self.expected_shape = shape
self.expected_len = 5

def test_bad_path_raises(self):
raises = lambda: pims.ImageSequence('this/path/does/not/exist/*.jpg')
self.assertRaises(IOError, raises)
class TestImageSequenceWithMPL(_image_series):
def setUp(self):
try:
import matplotlib
except ImportError:
self.skip = 'matplotlib'
else:
self.skip = False
self.klass = ImageSequence_mpl
super(TestImageSequenceWithMPL, self).setUp()

def tearDown(self):
clean_dummy_png(self.filepath, self.filenames)

class TestImageSequenceWithTifffile(_image_series):
def setUp(self):
try:
import tifffile
except ImportError:
self.skip = 'tifffile'
else:
self.skip = False
self.klass = ImageSequence_tifffile
super(TestImageSequenceWithTifffile, self).setUp()

class TestImageSequenceWithMPL(_image_series):

class TestImageSequenceWithScipy(_image_series):
def setUp(self):
self.filepath = os.path.join(path, 'image_sequence')
self.filenames = ['T76S3F00001.png', 'T76S3F00002.png',
'T76S3F00003.png', 'T76S3F00004.png',
'T76S3F00005.png']
shape = (10, 11)
frames = save_dummy_png(self.filepath, self.filenames, shape)
self.filename = os.path.join(self.filepath, '*.png')
self.frame0 = frames[0]
self.frame1 = frames[1]
self.kwargs = dict(plugin='matplotlib')
self.klass = pims.ImageSequence
self.v = self.klass(self.filename, **self.kwargs)
self.expected_shape = shape
self.expected_len = 5
try:
import scipy
except ImportError:
self.skip = 'scipy'
else:
self.skip = False
self.klass = ImageSequence_scipy
super(TestImageSequenceWithScipy, self).setUp()

def tearDown(self):
clean_dummy_png(self.filepath, self.filenames)

class TestImageSequenceAcceptsList(_image_series):
class ImageSequenceBase(_image_series):
def setUp(self):
if self.skip:
raise nose.SkipTest('{0} is not installed'.format(self.skip))
self.filepath = os.path.join(path, 'image_sequence')
self.filenames = ['T76S3F00001.png', 'T76S3F00002.png',
'T76S3F00003.png', 'T76S3F00004.png',
Expand All @@ -569,12 +585,15 @@ def setUp(self):
for fn in self.filenames]
self.frame0 = frames[0]
self.frame1 = frames[1]
self.kwargs = dict(plugin='matplotlib')
self.klass = pims.ImageSequence
self.v = self.klass(self.filename, **self.kwargs)
self.expected_shape = shape
self.expected_len = len(self.filenames)

def test_bad_path_raises(self):
raises = lambda: pims.ImageSequence('this/path/does/not/exist/*.jpg')
self.assertRaises(IOError, raises)


def tearDown(self):
clean_dummy_png(self.filepath, self.filenames)

Expand Down