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Fix ImageIOReader for images with channels and reordered axes #430

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Fix ImageIOReader for images with channels and reordered axes #430

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3bdfe6d
Fix ImageIOReader for images with channels and reordered axes
jstriebel Nov 16, 2022
b497107
Update imageio_reader.py
jstriebel Nov 16, 2022
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24 changes: 12 additions & 12 deletions pims/imageio_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,20 +72,24 @@ def __init__(self, filename, **kwargs):
)

first_frame = self.get_frame_2D(t=0)
self._shape = first_frame.shape
self._dtype = first_frame.dtype

self._setup_axes()
self._register_get_frame(self.get_frame_2D, 'yx')
self._setup_axes(first_frame.shape)
if len(first_frame.shape) == 2:
self._register_get_frame(self.get_frame_2D, 'yx')
else:
self._register_get_frame(self.get_frame_2D, 'yxc')

def _setup_axes(self):
def _setup_axes(self, frame_shape):
"""Setup the xyctz axes, iterate over t axis by default

"""
if self._shape[1] > 0:
self._init_axis('x', self._shape[1])
if self._shape[0] > 0:
self._init_axis('y', self._shape[0])
if frame_shape[1] > 0:
self._init_axis('x', frame_shape[1])
if frame_shape[0] > 0:
self._init_axis('y', frame_shape[0])
if len(frame_shape) > 2:
self._init_axis('c', frame_shape[3])
if self._len > 0:
self._init_axis('t', self._len)

Expand Down Expand Up @@ -138,10 +142,6 @@ def __iter__(self):
def frame_rate(self):
return self.get_metadata()['fps']

@property
def frame_shape(self):
return self._shape

@property
def pixel_type(self):
return self._dtype
Expand Down