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130 lines
3.4 KiB
130 lines
3.4 KiB
import six
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class Metadata(object):
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""" A simple container for ND2 metadata. """
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def __init__(self, height, width, channels, date, fields_of_view, frames, z_levels, total_images_per_channel, pixel_microns):
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self._height = height
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self._width = width
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self._channels = channels
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self._date = date
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self._fields_of_view = fields_of_view
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self._frames = frames
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self._z_levels = z_levels
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self._total_images_per_channel = total_images_per_channel
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self._pixel_microns = pixel_microns
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@property
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def height(self):
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"""
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The image height in pixels.
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:rtype: int
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"""
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return self._height
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@property
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def width(self):
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"""
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The image width in pixels.
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:rtype: int
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"""
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return self._width
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@property
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def date(self):
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"""
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The date and time when acquisition began.
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:rtype: datetime.datetime() or None
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"""
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return self._date
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@property
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def channels(self):
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"""
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These are labels created by the NIS Elements user. Typically they may a short description of the filter cube
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used (e.g. "bright field", "GFP", etc.)
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:rtype: list
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"""
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return self._channels
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@property
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def fields_of_view(self):
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"""
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The metadata contains information about fields of view, but it contains it even if some fields
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of view were cropped. We can't find anything that states which fields of view are actually
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in the image data, so we have to calculate it. There probably is something somewhere, since
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NIS Elements can figure it out, but we haven't found it yet.
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:rtype: list
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"""
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return self._fields_of_view
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@property
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def frames(self):
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"""
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The number of cycles.
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:rtype: list
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"""
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return self._frames
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@property
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def z_levels(self):
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"""
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The different levels in the Z-plane. Just a sequence from 0 to n.
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:rtype: list
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"""
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return self._z_levels
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@property
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def total_images_per_channel(self):
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"""
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The total number of images of a particular channel (wavelength, filter, etc) in the entire ND2.
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:rtype: int
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"""
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return self._total_images_per_channel
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@property
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def pixel_microns(self):
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"""
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The width of a pixel in microns.
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:rtype: float
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"""
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return self._pixel_microns
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class CameraSettings(object):
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""" Contains some basic information about a physical camera and its settings. """
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def __init__(self, name, id, exposure, x_binning, y_binning, channel_name):
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self.name = name.decode("utf8")
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self.id = id.decode("utf8")
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self.exposure = exposure
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self.x_binning = int(x_binning)
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self.y_binning = int(y_binning)
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self.channel_name = channel_name
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if six.PY3:
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self.channel_name = self.channel_name.decode("utf8") if channel_name is not None else None
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def __repr__(self):
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return "\n".join(["<Camera Settings: %s>" % self.channel_name,
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"Camera: %s" % self.name,
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"Camera ID: %s" % self.id,
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"Exposure Time (ms): %s" % self.exposure,
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"Binning: %sx%s" % (self.x_binning, self.y_binning)
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])
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