Image

ImageView

class datavis.views.ImageView(model=None, **kwargs)

This widget provides functionality for displaying images provided by a ImageModel.

This class also allows to perform basic display operations over the data that is being displayed such as: rotations, zoom, drag and flips, among others.

Example of use:

imageView = datavis.views.ImageView(parent=None, border_color=’#FFAA33’) d = pyqtgraph.gaussianFilter(np.random.normal(size=(512, 512)), (5, 5)) imgModel = dv.models.ImageModel(data) imageView.setModel(imgModel)

__init__(model=None, **kwargs)

Create a new ImageView instance.

Parameters

model – ImageModel instance that will be used to fetch the image data.

Keyword Arguments

  • parent – (QWidget) Is the parent widget to which this ImageView will belong. If None, then the ImageView is created with no parent.

  • toolBar – Bool value to specify if showing or hiding the toolbar. By default, the toolbar is visible.

  • roi – (Bool) If specified, this will be used to set visible the ROI button. False by default.

  • menu – (Bool) If specified, this will be used to set visible the Menu button. False by default.

  • histogram – (Bool) If specified, this will be used to set visible the Menu button. True by default.

  • fit – (Bool) If specified, this will be used to automatically auto-range the image whenever the view is resized. True by default.

  • autoFill – (Bool) This property holds whether the widget background is filled automatically. The color used is defined by the qtg.QPalette::Window color role from the widget’s palette. False by default.

  • hideButtons – (Bool) Hide/show the internal pg buttons. For example, the button used to center an image. False by default.

  • axisPos – (Bool) The axis position. Possible values: AXIS_TOP_LEFT, AXIS_TOP_RIGHT, AXIS_BOTTOM_RIGHT, AXIS_BOTTOM_LEFT

  • axisColor (str) – ‘#00FFAF’

  • axis – (Bool) Show/hide de view’s axes

  • labelX –

    (dict) Dictionary with label properties, like CSS style:

    • labelStyle: (dict) CSS style. Example:

      {'color': '#FFF', 'font-size': '14pt'}

    • labelText: (str) The label text

  • labelY – Same as labelX.

  • levels – (min, max) Pass the min and max range that will be used for image display. By default is None, so the data from the pixel values will be used. Passing a different range is useful for normalization of the slices in volumes.

  • preferredSize – (list of tuples). The first element is the image size and the second element is the preferred size.

  • maskParams –

    Dictionary with mask-related params. Following are some possible values in this dict:

    • type:

      • ROI_CIRCLE (display a circular mask from center) or

      • ROI_RECT (display rectangular mask from center) or

      • CONSTANT (generate data mask with given constant value) or

      • DATA (just provide data mask as numpy array)

    • data: If the type is ROI_CIRCLE or ROI_RECT, it is the value of the radius of the mask. If type is CONSTANT it is the value of entire mask. Finally, if the type is DATA, this should be a numpy array with values of the mask.

    • color: (QColor or str) The color for the mask. Example: ‘#66212a55’ in ARGB format.

    • operation: What operation will be performed in the mask * NONE (the mask editor is not shown) or * ADD (add 1 values to the mask with the pen) or * REMOVE (add 0 values to the mask with the pen)

    • penSize: Size of the pen to be used, only relevant when not operation is not NONE (default 50px).

    • showHandles: (boolean) Enable/Disable the ROI handles

clear()

Clear the view, setting a null image

eventFilter(obj, event)

Filters events if this object has been installed as an event filter for the watched object.

Parameters

  • obj – watched object

  • event – event

Returns

True if this object has been installed, False otherwise.

export(path=None, background=None, antialias=True, exportView=True)

Export the scene to the given path. Image - PNG is the default format. The exact set of image formats supported will depend on qtc.Qt libraries. However, common formats such as PNG, JPG, and TIFF are almost always available.

Parameters

  • path – (str) The image path. If no path is specified, then a save dialog will be displayed

  • background – (str or qtg.QColor) The background color

  • antialias – (boolean) Use antialiasing for render the image

  • exportView – (boolean) If true, all the view area will be exported else export the image

fitToSize()

Fit image to the widget size

getImageItem()

Return the ImageItem object used for in pyqtgraph.ImageView. See pyqtgraph.ImageView.getImageItem

Returns

pyqtgraph.ImageItem

getImageView()

Return the internal pyqtgraph.ImageView

getMask()

Return the current image mask data

getMaskColor()

Return the mask color

getMaskData()

Return the mask data. If mask-type is CONSTANT it is the value of entire mask. If the mask-type is DATA, this is a numpy array with values of the mask. If no mask has been configured, return None

getMaskImage()

Return the mask created by the user using the Mask Creator Tools.

Returns: (u8bit numpy array) or None

getMaskSize()

Return the image mask size. This function si valid only if a roi mask has been configured and return None in other case

getMaskType()

Return the mask-type. Possible values are: ROI_CIRCLE, ROI_RECT, CONSTANT, DATA or None if no mask has been configured.

getPreferredSize()

Returns a tuple (width, height), which represents the preferred dimensions to contain all the image

getScale()

Return the image scale.

getToolBar()

Get the left side toolbar.

getView()

Returns the widget used for the internal pyqtgraph.ImageView to display image data.

Returns: pyqtgraph.ViewBox (or other compatible object)

used by pyqtgraph.ImageView to display the image data

getViewBox()

Return the pyqtgraph.ViewBox used for the internal pyqtgraph.ImageView. See pyqtgraph.ImageView

getViewRect()

Returns the view rect area. See pyqtgraph.ViewBox.viewRect()

getViewSize()

Returns the image view size.

Returns: A tupple (width, height) representing the view size

horizontalFlip()

Flip the image horizontally (Image data is not modified).

imageModelChanged()

Call this function when the image model has been modified externally

In this case, the ImageView will need to be notified so that the view can be updated.

isEmpty()

Return True if the ImageView is empty

rotate(angle)

Make a rotation according to the given angle. Does not modify the image. :param angle: (int) The angle(in degrees)

setAxisOrientation(orientation)

Sets the axis orientation for this ImageView.

Parameters

orientation –

Orientation of the axis. Possible values are:

  • AXIS_TOP_LEFT: axis in top-left

  • AXIS_TOP_RIGHT: axis in top-right

  • AXIS_BOTTOM_RIGHT: axis in bottom-right

  • AXIS_BOTTOM_LEFT: axis in bottom-left

setImageInfo(**kwargs)

Set the image info that will be displayed.

Keyword Arguments

  • text – (str) if passed, it will be used as the info to be displayed, if not, other arguments are considered

  • path – (str) the image path

  • format – (str) the image format

  • dataType – (str) the image data type

setImageMask(**kwargs)

Set the mask to use in this ImageView.

If mask=None, the current mask will be removed.

Keyword Arguments

  • type – ROI_CIRCLE (display a circular mask from center) or ROI_RECT (display rectangular mask from center) or CONSTANT (generate a data mask with given constant value) or DATA (just provide a data mask as numpy array)

  • color – (str or QColor) The color in #ARGB format. Example: #22AAFF00. Default value: ‘#2200FF55’

  • data – If the type is ROI_CIRCLE or ROI_RECT, it is the value of the radius of the mask. If type is CONSTANT it is the value of entire mask. Finally, if the type is DATA, this should be a numpy array with values of the mask.

  • showHandles – (boolean) Enable/Disable the ROI handles

setLevels(levels)

Set levels for the display.

setMaskColor(color)

Set the mask color.

Parameters

color – (str) The color in #ARGB format. Example: #22AAFF00 or (qtg.QColor)

setModel(imageModel, fitToSize=True)

Set the image model to be used for this ImageView.

Parameters

imageModel – Input ImageModel

setRoiMaskSize(size)

Sets the size to the roi mask. If the ROI mask has been configured, then sets a new size to the roi mask. :param size: (int) The roi size

setRoiMaskSizeVisible(visible)

Show or hide the TextItem used to display the roi mask size

setScale(scale)

Set de image scale.

Parameters

scale – (float) The new image scale.

setViewRect(rect)

Set the current view rect. The view rect is the rect region that will be visible in the view.

Parameters

rect – (QRect) The view rect

Link the X axis to another ImageView.

Parameters

imageView – (ImageView) The ImageView widget to be linked

Link the Y axis to another ImageView. :param imageView: (ImageView) The ImageView widget to be linked

showHistogram(visible=True)

Show or hide the histogram widget used by the internal pyqtgraph.ImageView.

showMenuButton(visible=True)

Show or hide the menu button used by the internal pyqtgraph.ImageView

showRoiButton(visible=True)

Show or hide the ROI button. used by the internal pyqtgraph.ImageView

showToolBar(visible=True)

Show or hide the tool bar.

sigScaleChanged

Signal emitted when the mask ROI size changed

updateImageScale()

Update the image scale, calculating the current scale.

verticalFlip()

Flips the image vertically. (Image data is not modified).

SlicesView

class datavis.views.SlicesView(model, **kwargs)

This view can be used when displaying 3D data: (a) a single volume (x, y, z, 1) (b) stacks of particles (x, y, 1, n). In the case (b) for particles, usually the gallery view will be preferred, but for movies (stacks of frames), this view is very useful since these are big images and will take much memory loading all of them at once.

__init__(model, **kwargs)

Construct an SlicesView instance. SlicesView use an ImageView to display the slices, see ImageView class for initialization params.

Parameters

model – The SlicesModel

Keyword Arguments

  • parent – (QWidget) Specifies the parent widget to which this ImageView will belong. If None, then the SlicesView is created with no parent.

  • text – (str) Text to be display in the slider.

  • currentValue – (int) The index (starting at 1) of the initial slice.

  • imageViewKwargs – The ImageView arguments

clear()

Clear the view

getImageView()

Return the ImageView widget, used to visualize the slices.

getPreferredSize()

Returns a tuple (width, height), which represents the preferred dimensions to contain all the data.

getRange()

Returns a tuple (min, max) with the slices range.

getScale()

Return the current scale

getText()

Returns the label text for the internal slider

getValue()

Returns the value of the current slice.

setModel(model, **kwargs)

Set the SlicesModel

Parameters

model – The model or None for clear the view

Keyword Arguments

  • normalize – (bool) If true, set the ImageView levels

  • slice – (int) If not None, set this as the initial slice

setScale(scale)

Set the image scale

Parameters

scale – (float) The scale

setText(text)

Set the label text for the internal slider

setValue(value)

Set the current value to a different one.

MultiSliceView

class datavis.views.MultiSliceView(parent, slicesKwargs, mode=3)

This view is currently used for displaying 3D volumes and it is composed by 3 SlicesView and a custom 2D plot showing the axis and the slider position. This view is the default for Volumes.

__init__(parent, slicesKwargs, mode=3)

Create a new MultiSliceView instance

Parameters

  • parent – (QWidget) Parent widget

  • slicesKwargs – (dict) A dict with keys of axis(AXIS_X, AXIS_Y, AXIS_Z) and values for the model for each axis. See SlicesView

  • mode – (int) Specifies which axis will be visible. Possible values: AXIS_X, AXIS_Y, AXIS_Z, AXIS_XYZ

clear()

Clear the view

fitToSize()

Fit images to the widget size

getAxis()

Returns the current axis

getMode()

Return the current mode. Possible values: AXIS_X, AXIS_Y, AXIS_Z, AXIS_XYZ

getPreferredSize()

Returns a tuple (width, height), which represents the preferred dimensions to contain all the data

getSliceView(axis=None)

Return the SlicesView widget for the given axis

getText(axis)

Returns the label text for the given axis

Parameters

axis – (int) The axis. (AXIS_X or AXIS_Y or AXIS_Z)

Returns: (str) The label text

Raises

Exception If the axis is not anyone of the following – datavis.models.AXIS_X, datavis.models.AXIS_Y, datavis.models.AXIS_Z

getValue(axis=None)
Return the current slice index for the given axis.

(If axis=None, the last changed axis is used)

Parameters

axis – AXIS_X or AXIS_Y or AXIS_Z

setAxis(axis)

Sets the current axis. Updates the axis graphic.

Parameters

axis – (int) The axis (AXIS_X or AXIS_Y or AXIS_Z)

setModel(models, **kwargs)

Set the data models for display.

Parameters

models – (tuple) The models (AXIS_X, AXIS_Y, AXIS_Z) for views or None for clear the view.

Keyword Arguments

  • normalize – (bool) If True, each of the SlicesView will be normalized, levels of the image will be set all range

  • slice – (int) Default slice

setScale(scale)

Set the image scale for all axis :param scale: (float) The new image scale.

setValue(value, axis=None)

Sets the slice value for the given axis. (If axis is None the last modified axis is used)

VolumeView

class datavis.views.VolumeView(model, **kwargs)

View to display a volume and allows to switch between MultiSliceView and GalleryView.

In case of multiple volumes, this view could be extended with a way to select which volume to display.

__init__(model, **kwargs)

Create a new VolumeView instance.

Parameters

model – Input VolumeModel instance.

Keyword Arguments

  • parent – (QWidget) Parent widget.

  • cellSize – (int) The default cell size

  • maxCellSize – (int) The maximum value for cell size

  • minCellSize – (int) The minimum value for cell size

  • zoomUnits – (int) The zoom type for GalleryView cells: PIXEL_UNITS or PERCENT_UNITS

  • galleryKwargs – Configuration params for the internal GalleryView.

  • slicesKwargs – Configuration params for the internal MultiSliceView.

  • slicesMode – (int) Specifies which axis will be visible. Possible values: AXIS_X, AXIS_Y, AXIS_Z, AXIS_XYZ

clear()

Clear the volume view

fitToSize()

Fit the images to the widget size in MultiSliceView

getModel()

Return the current model

setModel(model)

Sets the VolumeModel

Raises

Exception if model is None. –

setView(view)

Sets the current view: GALLERY or SLICES