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Merge pull request #51 from jimrybarski/40-feature-slices

resolves #40: adds slicing semantics
zolfa-add_slices_loading
Jim Rybarski 10 years ago
parent
commit
c78d367c54
1 changed files with 43 additions and 7 deletions
  1. +43
    -7
      nd2reader/__init__.py

+ 43
- 7
nd2reader/__init__.py View File

@ -34,19 +34,55 @@ class Nd2(Nd2Parser):
""" """
return self._image_count * self._channel_count return self._image_count * self._channel_count
def __getitem__(self, frame_number):
if isinstance(frame_number, int):
def __getitem__(self, item):
"""
Allows slicing ND2s.
>>> nd2 = Nd2("my_images.nd2")
>>> image = nd2[16] # gets 17th frame
>>> for image in nd2[100:200]: # iterate over the 100th to 200th images
>>> do_something(image.data)
>>> for image in nd2[::-1]: # iterate backwards
>>> do_something(image.data)
>>> for image in nd2[37:422:17]: # do something super weird if you really want to
>>> do_something(image.data)
:type item: int or slice
:rtype: nd2reader.model.Image() or generator
"""
if isinstance(item, int):
try: try:
channel_offset = frame_number % len(self.channels)
fov = self._calculate_field_of_view(frame_number)
channel = self._calculate_channel(frame_number)
z_level = self._calculate_z_level(frame_number)
timestamp, raw_image_data = self._get_raw_image_data(frame_number, channel_offset)
channel_offset = item % len(self.channels)
fov = self._calculate_field_of_view(item)
channel = self._calculate_channel(item)
z_level = self._calculate_z_level(item)
timestamp, raw_image_data = self._get_raw_image_data(item, channel_offset)
image = Image(timestamp, raw_image_data, fov, channel, z_level, self.height, self.width) image = Image(timestamp, raw_image_data, fov, channel, z_level, self.height, self.width)
except (TypeError, ValueError): except (TypeError, ValueError):
return None return None
else: else:
return image return image
elif isinstance(item, slice):
return self._slice(item.start, item.stop, item.step)
raise IndexError
def _slice(self, start, stop, step):
"""
Allows for iteration over a selection of the entire dataset.
:type start: int
:type stop: int
:type step: int
:rtype: nd2reader.model.Image() or None
"""
start = start if start is not None else 0
step = step if step is not None else 1
stop = stop if stop is not None else len(self)
# This weird thing with the step allows you to iterate backwards over the images
for i in range(start, stop)[::step]:
yield self[i]
@property @property
def image_sets(self): def image_sets(self):


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