diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py index 7feb90e..2bfa070 100644 --- a/nd2reader/__init__.py +++ b/nd2reader/__init__.py @@ -1,6 +1,6 @@ import logging from nd2reader.service import BaseNd2 -from nd2reader.model import Image +from nd2reader.model import Image, ImageSet log = logging.getLogger("nd2reader") log.addHandler(logging.StreamHandler()) @@ -14,11 +14,12 @@ class Nd2(BaseNd2): def get_image(self, timepoint, fov, channel_name, z_level): image_set_number = self._calculate_image_set_number(timepoint, fov, z_level) timestamp, raw_image_data = self._reader.get_raw_image_data(image_set_number, self.channel_offset[channel_name]) - return Image(timestamp, raw_image_data, self.height, self.width) + return Image(timestamp, raw_image_data, fov, channel_name, z_level, self.height, self.width) def __iter__(self): """ - Just return every image. + Just return every image in order (might not be exactly the order that the images were physically taken, but it will + be within a few seconds). A better explanation is probably needed here. """ for i in range(self._image_count): @@ -27,4 +28,21 @@ class Nd2(BaseNd2): for channel in self.channels: image = self.get_image(i, fov, channel.name, z_level) if image.is_valid: - yield image \ No newline at end of file + yield image + + def image_sets(self, field_of_view, timepoints=None, channels=None, z_levels=None): + """ + Gets all the images for a given field of view and + """ + timepoint_set = xrange(self._timepoint_count) if timepoints is None else timepoints + channel_set = [channel.name for channel in self.channels] if channels is None else channels + z_level_set = xrange(self._z_level_count) if z_levels is None else z_levels + + for timepoint in timepoint_set: + image_set = ImageSet() + for channel_name in channel_set: + for z_level in z_level_set: + image = self.get_image(timepoint, field_of_view, channel_name, z_level) + if image.is_valid: + image_set.add(image) + yield image_set \ No newline at end of file diff --git a/nd2reader/model/__init__.py b/nd2reader/model/__init__.py index caf6f6b..56d0d90 100644 --- a/nd2reader/model/__init__.py +++ b/nd2reader/model/__init__.py @@ -1,5 +1,8 @@ import numpy as np import skimage.io +import logging + +log = logging.getLogger("nd2reader") class Channel(object): @@ -43,23 +46,30 @@ class ImageSet(object): class Image(object): - def __init__(self, timestamp, raw_array, height, width): + def __init__(self, timestamp, raw_array, field_of_view, channel, z_level, height, width): self._timestamp = timestamp self._raw_data = raw_array - self._data = np.reshape(self._raw_data, (height, width)) + self._field_of_view = field_of_view + self._channel = channel + self._z_level = z_level + self._height = height + self._width = width + self._data = None @property def timestamp(self): # TODO: Convert to datetime object - return self._timestamp + return self._timestamp / 1000.0 @property def data(self): + if self._data is None: + self._data = np.reshape(self._raw_data, (self._height, self._width)) return self._data @property def is_valid(self): - return np.any(self._data) + return np.any(self.data) def show(self): skimage.io.imshow(self.data) diff --git a/nd2reader/service/__init__.py b/nd2reader/service/__init__.py index ade86f9..bb7bd19 100644 --- a/nd2reader/service/__init__.py +++ b/nd2reader/service/__init__.py @@ -71,6 +71,10 @@ class BaseNd2(object): """ return sum(self._metadata['ImageMetadata']['SLxExperiment']['ppNextLevelEx']['']['pItemValid']) + @property + def _channel_count(self): + return self._reader.channel_count + @property def channel_offset(self): if self._channel_offset is None: diff --git a/run.py b/run.py index bd45aea..0c1f76b 100644 --- a/run.py +++ b/run.py @@ -4,9 +4,11 @@ import numpy as np from skimage import io -for image in Nd2("/home/jim/Desktop/nd2hacking/YFP-dsRed-GFP-BF.nd2"): +for image_set in Nd2("/home/jim/Desktop/nd2hacking/YFP-dsRed-GFP-BF.nd2").image_sets(0): + for image in image_set: + print(image.timestamp, image._channel, image._z_level) + print("") # n = Nd2("/home/jim/Desktop/nd2hacking/test-141111.nd2") - image.show() \ No newline at end of file