Class _ImageWrapper

Creates a new Image wrapper with the image specified by pixels ID

:param conn: The connection :type conn: BlitzGateway :param pid: Pixles ID :type pid: Long :return: New Image wrapper :rtype: ImageWrapper

Initialisation method which is implemented by subclasses to set their class variables etc.

Overrides: BlitzObjectWrapper.__bstrap__

(inherited documentation)

Loads the object that is wrapped by this class. This includes linked objects. This method can be overwritten by subclasses that want to specify how/which linked objects are loaded.

Overrides: BlitzObjectWrapper.__loadedHotSwap__

(inherited documentation)

Returns the Instrument for this image (or None) making sure the instrument is loaded.

:return: Instrument (microscope) :rtype: InstrumentWrapper

Creates a dict representation of the Image, including author and date info.

:param xtra: controls the optional parts of simpleMarshal;

• thumbUrlPrefix - allows customizing the thumb URL by either a static string prefix or a callable function that will take a single ImgId int argument and return the customized URL string
• tiled - if passed and value evaluates to true, add information on whether this image is tiled on this server.

:type: Dict :return: Dict :rtype: Dict

Overrides: BlitzObjectWrapper.simpleMarshal

Returns the stage label or None

:return: Stage label :rtype: ImageStageLabelWrapper

Provides a truncated name of the image. E.g. ...catedNameOfTheImage.tiff

:param length: The ideal length to return. If truncated, will be ...length :type length: Int :param hist: The amount of leeway allowed before trunction (avoid truncating 1 or 2 letters) :type hist: Int :return: Truncated ...name :type: String

Returns 'Firstname Lastname' of image owner

:return: Image owner :rtype: String

XXX: Deprecated since 4.3.2, use listParents(). (See #6660) Gets the Dataset that image is in, or None. Returns None if Image is in more than one Dataset.

:return: Dataset :rtype: DatasetWrapper

Gets the Project that image is in, or None. TODO: Assumes image is in only 1 Project. Why not use getAncestory()[-1] Returns None if Image is in more than one Dataset & Project.

:return: Project :rtype: ProjectWrapper

If the image is in a Plate/Well hierarchy, returns the parent Plate, otherwise None

:return: Plate :rtype: PlateWrapper

Gets the Ojbective Settings of the Image, or None

:return: Objective Settings :rtype: ObjectiveSettingsWrapper

Gets the Imaging Environment of the Image, or None

:return: Imaging Environment :rtype: ImagingEnvironmentWrapper

Returns the Primary Pixels ID for the image.

:return: Pixels ID :rtype: Long

Decorators:

• @assert_pixels

Gets original metadata from the file annotation. Returns the File Annotation, list of Global Metadata, list of Series Metadata in a tuple. Metadata lists are lists of (key, value) tuples.

:param sort: If True, we sort Metadata by key :return: Tuple of (file-annotation, global-metadata, series-metadata) :rtype: Tuple (FileAnnotationWrapper, [], [])

Returns a string holding a rendered JPEG of the thumbnail.

:type size: tuple or number
:param size: A tuple with one or two ints, or an integer. If a tuple holding a single int,
             or a single int is passed as param, then that will be used as the longest size
             on the rendered thumb, and image aspect ratio is kept.
             If two ints are passed in a tuple, they set the width and height of the
             rendered thumb.
:type z: number
:param z: the Z position to use for rendering the thumbnail. If not provided default is used.
:type t: number
:param t: the T position to use for rendering the thumbnail. If not provided default is used.
:param direct:      If true, force creation of new thumbnail (don't use cached)
:rtype: string or None
:return: the rendered JPEG, or None if there was an error.

Returns (min, max) values for the pixels type of this image. TODO: Does not handle floats correctly, though.

:return: Tuple (min, max)

Decorators:

• @assert_pixels

Decorators:

• @assert_pixels

Loads pixels and returns object in a PixelsWrapper

Decorators:

• @assert_pixels

Returns a list of Channels, each initialised with rendering engine

:return: Channels :rtype: List of ChannelWrapper

Decorators:

• @assert_re(ignoreExceptions= (omero.ConcurrencyException))

Returns a dict of zoomLevels:scale (fraction) for tiled 'Big' images. E.g. {0: 1.0, 1: 0.25, 2: 0.062489446727078291, 3: 0.031237687848258006} Returns None if this image doesn't support tiles.

Decorators:

• @assert_re()

Sets the active channels on the rendering engine. Also sets rendering windows and channel colors (for channels that are active)

Examples: # Turn first channel ON, others OFF image.setActiveChannels([1]) # First OFF, second ON, windows and colors for both image.setActiveChannels([-1, 2], [[20, 300], [50, 500]], ['00FF00', 'FF0000']) # Second Channel ON with windows. All others OFF image.setActiveChannels([2], [[20, 300]])

:param channels: List of active channel indexes ** 1-based index ** :type channels: List of int :param windows: Start and stop values for active channel rendering settings :type windows: List of [start, stop]. [[20, 300], [None, None], [50, 500]]. Must be list for each channel :param colors: List of colors. ['F00', None, '00FF00']. Must be item for each channel

Returns list of available keys for projection. E.g. ['intmax', 'intmean']

:return: Projection options :rtype: List of strings

Returns the current projection option (checking it is valid).

:return: Projection key. E.g. 'intmax' :rtype: String

Sets the current projection option.

:param proj: Projection Option. E.g. 'intmax' or 'normal' :type proj: String

Sets the range used for Z-projection. Will only be used if E.g. setProjection('intmax') is not 'normal'

Returns the inverted axis flag

:return: Inverted Axis :rtype: Boolean

Sets the inverted axis flag

:param inverted: Inverted Axis :type inverted: Boolean

Grab a horizontal or vertical line from the image pixel data, for the specified channels (or 'active' if not specified) and using the specified range (or 1:1 relative to the image size). Axis may be 'h' or 'v', for horizontal or vertical respectively.

:param z: Z index :param t: T index :param pos: X or Y position :param axis: Axis 'h' or 'v' :param channels: map of {index: ChannelWrapper } :param range: height of scale (use image height (or width) by default) :return: rv List of lists (one per channel)

Grab a horizontal line from the image pixel data, for the specified channels (or active ones)

:param z: Z index :param t: T index :param y: Y position of row :param channels: map of {index: ChannelWrapper } :param range: height of scale (use image height by default) :return: rv List of lists (one per channel)

Grab a horizontal line from the image pixel data, for the specified channels (or active ones)

:param z: Z index :param t: T index :param x: X position of column :param channels: map of {index: ChannelWrapper } :param range: height of scale (use image width by default) :return: rv List of lists (one per channel)

Gets a list of available rendering models.

:return: Rendering models :rtype: List of BlitzObjectWrapper

Decorators:

• @assert_re()

Get the current rendering model.

:return: Rendering model :rtype: BlitzObjectWrapper

Decorators:

• @assert_re()

Returns True if the current rendering model is 'greyscale'

:return: isGreyscale :rtype: Boolean

Returns the data from rendering the bird's eye view of the image.

:param size: Maximum size of the longest side of the resulting bird's eye view. :return: Data containing a bird's eye view jpeg

Decorators:

• @assert_re()

Return the data from rendering a region of an image plane. NB. Projection not supported by the API currently.

:param z: The Z index. Ignored if projecting image. :param t: The T index. :param x: The x coordinate of region (int) :param y: The y coordinate of region (int) :param width: The width of region (int) :param height: The height of region (int) :param compression: Compression level for jpeg :type compression: Float

Decorators:

• @assert_re()

Return the data from rendering image, compressed (and projected). Projection (or not) is specified by calling setProjection before renderJpeg.

:param z: The Z index. Ignored if projecting image. If None, use defaultZ :param t: The T index. If None, use defaultT :param compression: Compression level for jpeg :type compression: Float

Decorators:

• @assert_re()

Exports the OME-TIFF representation of this image.

:type bufsize: int or tuple
:param bufsize: if 0 return a single string buffer with the whole OME-TIFF
                if >0 return a tuple holding total size and generator of chunks
                (string buffers) of bufsize bytes each
:return:        OME-TIFF file data
:rtype:         String or (size, data generator)

Creates a movie file from this image. TODO: makemovie import is commented out in 4.2+

:type outpath: string :type zstart: int :type zend: int :type tstart: int :type tend: int :type opts: dict :param opts: dictionary of extra options. Currently processed options are:

• watermark:string: path to image to use as watermark
• slides:tuple: tuple of tuples with slides to prefix and postfix video with in format (secs:int, topline:text[, middleline:text[, bottomline:text]]) If more than 2 slides are provided they will be ignored
• fps:int: frames per second
• minsize: tuple of (minwidth, minheight, bgcolor)

• format:string: one of video/mpeg or video/quicktime

:return: Tuple of (file-ext, format) :rtype: (String, String)

Decorators:

• @assert_re()

Render the Image, (projected) and compressed. For projection, call setProjection before renderImage.

:param z: Z index :param t: T index

Prepares a jpeg representation of a 2d grid holding a render of each channel, along with one for all channels at the set Z and T points.

:param z: Z index :param t: T index :param compression: Image compression level :param border: :return: value

Returns a dict of layout parameters for generating split channel image. E.g. row count, column count etc. for greyscale and color layouts.

:param border: spacing between panels :type border: int :return: Dict of parameters :rtype: Dict

Prepares a PIL Image with a 2d grid holding a render of each channel, along with one for all channels at the set Z and T points.

:param z: Z index :param t: T index :param compression: Compression level :param border: space around each panel (int) :return: canvas :rtype: PIL Image

Common part of horizontal and vertical line plot rendering.

:returns: (Image, width, height).

Draws the Row plot as a gif file. Returns gif data.

:param z: Z index :param t: T index :param y: Y position :param linewidth: Width of plot line :return: gif data as String :rtype: String

Decorators:

• @assert_re()

Draws the Column plot as a gif file. Returns gif data.

:param z: Z index :param t: T index :param x: X position :param linewidth: Width of plot line :return: gif data as String :rtype: String

Decorators:

• @assert_re()

Returns the last used value of Z (E.g. for renderingJpeg or line plot) Returns 0 if these methods not been used yet. TODO: How to get default-Z?

:return: current Z index :rtype: int

Decorators:

• @assert_re()

Returns the last used value of T (E.g. for renderingJpeg or line plot) Returns 0 if these methods not been used yet. TODO: How to get default-T?

:return: current T index :rtype: int

Decorators:

• @assert_re()

Gets the default Z index from the rendering engine

Decorators:

• @assert_re()

Gets the default T index from the rendering engine

Decorators:

• @assert_re()

Gets name of pixel data type.

:return: name of the image precision, e.g., float, uint8, etc. :rtype: String

Decorators:

• @assert_pixels

Gets the physical size X of pixels in microns

:return: Size of pixel in x or O :rtype: float

Decorators:

• @assert_pixels

Gets the physical size Y of pixels in microns

:return: Size of pixel in y or O :rtype: float

Decorators:

• @assert_pixels

Gets the physical size Z of pixels in microns

:return: Size of pixel in z or O :rtype: float

Decorators:

• @assert_pixels

Gets width (size X) of the image (in pixels)

:return: width :rtype: int

Decorators:

• @assert_pixels

Gets height (size Y) of the image (in pixels)

:return: height :rtype: int

Decorators:

• @assert_pixels

Gets Z count of the image

:return: size Z :rtype: int

Decorators:

• @assert_pixels

Gets T count of the image

:return: size T :rtype: int

Decorators:

• @assert_pixels

Gets C count of the image (number of channels)

:return: size C :rtype: int

Decorators:

• @assert_pixels

Removes specific color settings from channels

:return: True if allowed to do this :rtype: Boolean

Loads rendering options from an Annotation on the Image and applies them to the Image.

:return: True! TODO: Always True??

Limited support for saving the current prepared image rendering defs. Right now only channel colors are saved back.

:return: Boolean

Decorators:

• @assert_re()

Decorators:

• @assert_re()

Returns the number of Original 'archived' Files linked to primary pixels. Used by self.countImportedImageFiles which also handles FS files.

Returns a dict of 'count' and 'size' of the Fileset files (OMERO 5) or the Original Archived files (OMERO 4)

:return: A dict of 'count' and sum 'size' of the files.

Returns the Fileset linked to this Image. Fileset images, usedFiles and originalFiles are loaded.

Count number of ROIs associated to an image

:param shapeType: Filter by shape type ("Rect",...). :param filterByCurrentUser: Whether or not to filter the count by the currently logged in user. :return: Number of ROIs found for the currently logged in user if filterByCurrentUser is True, otherwise the total number found.

PROJECTIONS

Value:

{'normal':-1, 'intmax': omero.constants.projection.ProjectionType.MAXI MUMINTENSITY, 'intmean': omero.constants.projection.ProjectionType.MEA NINTENSITY, 'intsum': omero.constants.projection.ProjectionType.SUMINT ENSITY,}

LINE_PLOT_DTYPES

Value:

{(4, True, True): 'f', (2, False, False): 'H', (2, False, True): 'h', (1, False, False): 'B', (1, False, True): 'b',}