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@ -10,7 +10,7 @@ import struct |
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log = logging.getLogger(__name__) |
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log = logging.getLogger(__name__) |
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log.addHandler(logging.StreamHandler()) |
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log.addHandler(logging.StreamHandler()) |
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log.setLevel(logging.WARN) |
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log.setLevel(logging.DEBUG) |
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class Nd2(Nd2Parser): |
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class Nd2(Nd2Parser): |
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@ -19,12 +19,6 @@ class Nd2(Nd2Parser): |
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self._use_image_sets = image_sets |
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self._use_image_sets = image_sets |
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def __iter__(self): |
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def __iter__(self): |
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if self._use_image_sets: |
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return self.image_sets() |
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else: |
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return self.images() |
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def images(self): |
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for i in range(self._image_count): |
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for i in range(self._image_count): |
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for fov in range(self.field_of_view_count): |
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for fov in range(self.field_of_view_count): |
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for z_level in range(self.z_level_count): |
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for z_level in range(self.z_level_count): |
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@ -33,6 +27,7 @@ class Nd2(Nd2Parser): |
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if image.is_valid: |
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if image.is_valid: |
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yield image |
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yield image |
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@property |
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def image_sets(self): |
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def image_sets(self): |
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for time_index in xrange(self.time_index_count): |
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for time_index in xrange(self.time_index_count): |
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image_set = ImageSet() |
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image_set = ImageSet() |
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@ -42,7 +37,7 @@ class Nd2(Nd2Parser): |
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image = self.get_image(time_index, fov, channel_name, z_level) |
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image = self.get_image(time_index, fov, channel_name, z_level) |
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if image.is_valid: |
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if image.is_valid: |
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image_set.add(image) |
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image_set.add(image) |
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yield image_set |
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yield image_set |
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def get_image(self, time_index, fov, channel_name, z_level): |
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def get_image(self, time_index, fov, channel_name, z_level): |
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image_set_number = self._calculate_image_set_number(time_index, fov, z_level) |
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image_set_number = self._calculate_image_set_number(time_index, fov, z_level) |
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@ -83,23 +78,22 @@ class Nd2(Nd2Parser): |
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@property |
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@property |
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def absolute_start(self): |
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def absolute_start(self): |
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if self._absolute_start is None: |
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for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values(): |
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absolute_start_12 = None |
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absolute_start_24 = None |
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# ND2s seem to randomly switch between 12- and 24-hour representations. |
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try: |
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absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S") |
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except ValueError: |
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pass |
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try: |
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absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p") |
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except ValueError: |
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pass |
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if not absolute_start_12 and not absolute_start_24: |
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continue |
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self._absolute_start = absolute_start_12 if absolute_start_12 else absolute_start_24 |
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return self._absolute_start |
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for line in self.metadata['ImageTextInfo']['SLxImageTextInfo'].values(): |
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absolute_start_12 = None |
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absolute_start_24 = None |
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# ND2s seem to randomly switch between 12- and 24-hour representations. |
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try: |
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absolute_start_24 = datetime.strptime(line, "%m/%d/%Y %H:%M:%S") |
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except ValueError: |
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pass |
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try: |
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absolute_start_12 = datetime.strptime(line, "%m/%d/%Y %I:%M:%S %p") |
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except ValueError: |
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pass |
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if not absolute_start_12 and not absolute_start_24: |
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continue |
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return absolute_start_12 if absolute_start_12 else absolute_start_24 |
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raise ValueError("This ND2 has no recorded start time. This is probably a bug.") |
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@property |
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@property |
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def channel_count(self): |
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def channel_count(self): |
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@ -182,3 +176,8 @@ class Nd2(Nd2Parser): |
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def _calculate_image_set_number(self, time_index, fov, z_level): |
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def _calculate_image_set_number(self, time_index, fov, z_level): |
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return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level) |
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return time_index * self.field_of_view_count * self.z_level_count + (fov * self.z_level_count + z_level) |
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for image_set in Nd2("FYLM-141111-001.nd2").image_sets: |
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print(image_set.get("", 1).data) |