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diff --git a/doc/source/modules/gui/plot/dev.rst b/doc/source/modules/gui/plot/dev.rst new file mode 100644 index 0000000..707d215 --- /dev/null +++ b/doc/source/modules/gui/plot/dev.rst @@ -0,0 +1,204 @@ +Package structure +================= + +The :mod:`silx.gui.plot` package provides plot widgets. +This package is structured as follows. + +.. currentmodule:: silx.gui.plot + +:mod:`.PlotWidget` and :mod:`.PlotWindow` provides the user API. +:class:`PlotWidget` is a Qt widget (actually a :class:`QMainWindow`) displaying a 1D, 2D plot area. +It provides different interaction modes. +:class:`PlotWindow` is a Qt widget (actually a :class:`QMainWindow`) which adds a set of toolbar buttons and associated functionalities to :class:`PlotWidget`. +The toolbar QActions are implemented in :mod:`.PlotActions`. + +:mod:`.Plot`, :mod:`.PlotEvents` and :mod:`.PlotInteraction` implement the plotting API regardless of the rendering backend and regardless of its integration in Qt. +The plotting API in defined in :mod:`.Plot`. +The different interaction modes (zoom, drawing, pan) are implemented in :mod:`.PlotInteraction`. +Each interaction mode is implemented with a state machine structure (implemented in :mod:`.Interaction`). +The different events emitted by :class:`Plot` and by the interaction modes are created with helper functions defined in :mod:`.PlotEvents`. + +The :class:`PlotWindow` uses additional widgets: + +- :mod:`.ColormapDialog` to change colormap settings. +- :mod:`.CurvesROIWidget` to create regions of interest for curves +- :mod:`.LegendSelector` to display a list of curves legends which provides some control on the curves (e.g., select, delete). +- :mod:`.MaskToolsWidget` to provide tools to draw a mask on an image. +- :mod:`.ScatterMaskToolsWidget` to provide tools to draw a mask on a scatter. +- The :mod:`.PlotTools` module provides a set of additional widgets: + + - :class:`.PlotTools.PositionInfo` + - :class:`.PlotTools.LimitsToolBar` + +- The :mod:`.Profile` module provides toolbar for extracting profiles from image and image stack: + + - :class:`.Profile.ProfileToolBar` + - :class:`.Profile.Profile3DToolBar` + +- :mod:`silx.gui.console` to provide an IPython console which can control the plot area content. + +The widgets also use the following miscellaneous modules: + +- :mod:`.Colors` to convert colors from name to RGB(A) +- :mod:`.MPLColormap` to embed recent matplotlib colormaps: 'magma', 'inferno', 'plasma' and 'viridis'. +- :mod:`._utils`: utility functions + +The :mod:`backends` package provide the implementation of the rendering used by the :class:`Plot`. +It contains: +:mod:`.backends.BackendBase` defines the API any plot backend should provide in :class:`BackendBase`. +:mod:`.backends.BackendMatplotlib` implements a `matplotlib <http://matplotlib.org/>`_ backend. +It uses :mod:`.backends.ModestImage` to provide a faster matplotlib AxesImage class using nearest values. +The :mod:`.backends.BackendMatplotlib` the provides two classes: + +.. currentmodule:: silx.gui.plot.backends.BackendMatplotlib + +- :class:`BackendMatplotlib` that provides a matplotlib backend without a specific canvas. +- :class:`BackendMatplotlibQt` which inherits from :class:`BackendMatplotlib` and adds a Qt canvas, and Qt specific functionalities. + +The OpenGL-based backend is implemented in the :mod:`.backends.BackendOpenGL` module and +the :mod:`.backends.glutils` package which provides the different primitives used for rendering and interaction. +It is based on :mod:`silx.gui._glutils`, `PyOpenGL <http://pyopengl.sourceforge.net/>`_ and OpenGL >= 2.1. + +.. |Plot and backend| image:: img/plot_and_backend.png + :align: middle + +|Plot and backend| + +Modules +======= + +.. currentmodule:: silx.gui.plot + +For :mod:`.PlotWidget` and :mod:`.Plot` modules, see their respective documentations: :mod:`.PlotWidget`, :mod:`.Plot`. + +The following modules are the modules used internally by the plot package. + +:mod:`backends.BackendBase` ++++++++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.backends.BackendBase + +.. automodule:: silx.gui.plot.backends.BackendBase + :members: + +:mod:`backends.BackendMatplotlib` ++++++++++++++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.backends.BackendMatplotlib + +.. automodule:: silx.gui.plot.backends.BackendMatplotlib + :members: + +:mod:`backends.ModestImage` ++++++++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.backends.ModestImage + +.. automodule:: silx.gui.plot.backends.ModestImage + :members: + :undoc-members: + +:mod:`ColormapDialog` ++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.ColormapDialog + +.. automodule:: silx.gui.plot.ColormapDialog + :members: + +:mod:`Colors` ++++++++++++++ + +.. currentmodule:: silx.gui.plot.Colors + +.. automodule:: silx.gui.plot.Colors + :members: rgba + +:mod:`CurvesROIWidget` +++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.CurvesROIWidget + +.. automodule:: silx.gui.plot.CurvesROIWidget + :members: + +:mod:`Interaction` +++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.Interaction + +.. automodule:: silx.gui.plot.Interaction + :members: + +:mod:`LegendSelector` ++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.LegendSelector + +.. automodule:: silx.gui.plot.LegendSelector + :members: + +:mod:`_BaseMaskToolsWidget` ++++++++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot._BaseMaskToolsWidget + +.. automodule:: silx.gui.plot._BaseMaskToolsWidget + :members: + +:mod:`MaskToolsWidget` +++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.MaskToolsWidget + +.. automodule:: silx.gui.plot.MaskToolsWidget + :members: + :show-inheritance: + +:mod:`ScatterMaskToolsWidget` ++++++++++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.ScatterMaskToolsWidget + +.. automodule:: silx.gui.plot.ScatterMaskToolsWidget + :members: + :show-inheritance: + +:mod:`MPLColormap` +++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.MPLColormap + +.. automodule:: silx.gui.plot.MPLColormap + :members: + +:mod:`PlotEvents` ++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.PlotEvents + +.. automodule:: silx.gui.plot.PlotEvents + :members: + :undoc-members: + +:mod:`PlotInteraction` +++++++++++++++++++++++ + +.. currentmodule:: silx.gui.plot.PlotInteraction + +.. automodule:: silx.gui.plot.PlotInteraction + :members: + +:mod:`_utils` ++++++++++++++ + +.. currentmodule:: silx.gui.plot._utils + +.. automodule:: silx.gui.plot._utils + :members: + +:mod:`ticklayout` +----------------- + +.. automodule:: silx.gui.plot._utils.ticklayout + :members:
\ No newline at end of file diff --git a/doc/source/modules/gui/plot/getting_started.rst b/doc/source/modules/gui/plot/getting_started.rst new file mode 100644 index 0000000..9e45b70 --- /dev/null +++ b/doc/source/modules/gui/plot/getting_started.rst @@ -0,0 +1,491 @@ +.. currentmodule:: silx.gui + +Getting started with plot widgets +================================= + +This introduction to :mod:`silx.gui.plot` covers the following topics: + +- `Use silx.gui.plot from the console`_ +- `Use silx.gui.plot from a script`_ +- `Plot curves in a widget`_ +- `Plot images in a widget`_ +- `Control plot axes`_ + +For a complete description of the API, see :mod:`silx.gui.plot`. + +Use :mod:`silx.gui.plot` from the console +----------------------------------------- + +From IPython +++++++++++++ + +To run :mod:`silx.gui.plot` widgets from `IPython <http://ipython.org/>`_, IPython must be set to use Qt (and in case of using PyQt4 and Python 2.7, PyQt must be set ti use API version 2, see Explanation_ below). + +As *silx* is performing some configuration of the Qt binding and `matplotlib <http://matplotlib.org/>`_, the safest way to use *silx* from IPython is to import :mod:`silx.gui.plot` first and then run either `%gui <http://ipython.org/ipython-doc/stable/interactive/magics.html#magic-gui>`_ qt or `%pylab <http://ipython.org/ipython-doc/stable/interactive/magics.html#magic-pylab>`_ qt:: + + In [1]: from silx.gui.plot import * + In [2]: %pylab qt + +Alternatively, when using Python 2.7 and PyQt4, you can start IPython with the ``QT_API`` environment variable set to ``pyqt``. + +On Linux and MacOS X, run:: + + QT_API=pyqt ipython + +On Windows, run from the command line:: + + set QT_API=pyqt&&ipython + + +Explanation +........... + +PyQt4 used from Python 2.x provides 2 incompatible versions of QString and QVariant: + +- version 1, the legacy which is the default, and +- version 2, a more pythonic one, which is the only one supported by *silx*. + +All other configurations (i.e., PyQt4 on Python 3.x, PySide, PyQt5, IPython QtConsole widget) uses version 2 only or as the default. + +For more information, see `IPython, PyQt and PySide <http://ipython.org/ipython-doc/stable/interactive/reference.html#pyqt-and-pyside>`_. + + +From Python ++++++++++++ + +The :mod:`silx.sx` package is a convenient module to use silx from the console. +It sets-up Qt and provides functions for the main features of silx. + +>>> from silx import sx + +Alternatively, you can create a QApplication before using silx widgets: + +>>> from silx.gui import qt # Import Qt binding and do some set-up +>>> qapp = qt.QApplication([]) + +>>> from silx.gui.plot import * # Import plot widgets and set-up matplotlib + +.. currentmodule:: silx.sx + +Plot functions +++++++++++++++ + +The :mod:`silx.sx` package provides 2 functions to plot curves and images from the (I)Python console in a widget with a set of tools: + +- :func:`plot`, and +- :func:`imshow`. + +For more features, use widgets directly (see `Plot curves in a widget`_ and `Plot images in a widget`_). + + +Curve: :func:`plot` +................... + +The following examples must run with a Qt QApplication initialized (see `Use silx.gui.plot from the console`_). + +First import :mod:`sx` function: + +>>> from silx import sx +>>> import numpy + +Plot a single curve given some values: + +>>> values = numpy.random.random(100) +>>> plot_1curve = sx.plot(values, title='Random data') + +Plot a single curve given the x and y values: + +>>> angles = numpy.linspace(0, numpy.pi, 100) +>>> sin_a = numpy.sin(angles) +>>> plot_sinus = sx.plot(angles, sin_a, +... xlabel='angle (radian)', ylabel='sin(a)') + +Plot many curves by giving a 2D array, provided xn, yn arrays: + +>>> plot_curves = sx.plot(x0, y0, x1, y1, x2, y2, ...) + +Plot curve with style giving a style string: + +>>> plot_styled = sx.plot(x0, y0, 'ro-', x1, y1, 'b.') + +See :func:`plot` for details. + + +Image: :func:`imshow` +..................... + +This example plot a single image. + +First, import :mod:`silx.sx`: + +>>> from silx import sx +>>> import numpy + +>>> data = numpy.random.random(1024 * 1024).reshape(1024, 1024) +>>> plt = sx.imshow(data, title='Random data') + +See :func:`imshow` for more details. + + +Use :mod:`silx.gui.plot` from a script +-------------------------------------- + +A Qt GUI script must have a QApplication initialized before creating widgets: + +.. code-block:: python + + from silx.gui import qt + + [...] + + qapp = qt.QApplication([]) + + [...] # Widgets initialisation + + if __name__ == '__main__': + [...] + qapp.exec_() + +Unless a Qt binding has already been loaded, :mod:`silx.gui.qt` uses the first Qt binding it founds by probing in the following order: PyQt5, PyQt4 and finally PySide. +If you prefer to choose the Qt binding yourself, import it before importing +a module from :mod:`silx.gui`: + +.. code-block:: python + + import PySide # Importing PySide will force silx to use it + from silx.gui import qt + + +.. warning:: + :mod:`silx.gui.plot` widgets are not thread-safe. + All calls to :mod:`silx.gui.plot` widgets must be made from the main thread. + +Plot curves in a widget +----------------------- + +The :class:`Plot1D` widget provides a plotting area and a toolbar with tools useful for curves such as setting logarithmic scale or defining region of interest. + +First, create a :class:`Plot1D` widget: + +.. code-block:: python + + from silx.gui.plot import Plot1D + + plot = Plot1D() # Create the plot widget + plot.show() # Make the plot widget visible + + +One curve ++++++++++ + +To display a single curve, use the :meth:`.PlotWidget.addCurve` method: + +.. code-block:: python + + plot.addCurve(x=(1, 2, 3), y=(3, 2, 1)) # Add a curve with default style + +When you need to update this curve, call :meth:`.PlotWidget.addCurve` again with the new values to display: + +.. code-block:: python + + plot.addCurve(x=(1, 2, 3), y=(1, 2, 3)) # Replace the existing curve + +To clear the plotting area, call :meth:`.PlotWidget.clear`: + +.. code-block:: python + + plot.clear() + + +Multiple curves ++++++++++++++++ + +In order to display multiple curves at the same time, you need to provide a different ``legend`` string for each of them: + +.. code-block:: python + + import numpy + + x = numpy.linspace(-numpy.pi, numpy.pi, 1000) + plot.addCurve(x, numpy.sin(x), legend='sinus') + plot.addCurve(x, numpy.cos(x), legend='cosinus') + plot.addCurve(x, numpy.random.random(len(x)), legend='random') + + +To update a curve, call :meth:`.PlotWidget.addCurve` with the ``legend`` of the curve you want to udpdate. +By default, the new curve will keep the same color (and style) as the curve it is updating: + +.. code-block:: python + + plot.addCurve(x, numpy.random.random(len(x)) - 1., legend='random') + +To remove a curve from the plot, call :meth:`.PlotWidget.remove` with the ``legend`` of the curve you want to remove from the plot: + +.. code-block:: python + + plot.remove('random') + +To clear the plotting area, call :meth:`.PlotWidget.clear`: + +.. code-block:: python + + plot.clear() + +Curve style ++++++++++++ + +By default, different curves will automatically use different styles to render, and keep the same style when updated. + +It is possible to specify the ``color`` of the curve, its ``linewidth`` and ``linestyle`` as well as the ``symbol`` to use as markers for data points (See :meth:`.PlotWidget.addCurve` for more details): + +.. code-block:: python + + import numpy + + x = numpy.linspace(-numpy.pi, numpy.pi, 100) + + # Curve with a thick dashed line + plot.addCurve(x, numpy.sin(x), legend='sinus', + linewidth=3, linestyle='--') + + # Curve with pink markers only + plot.addCurve(x, numpy.cos(x), legend='cosinus', + color='pink', linestyle=' ', symbol='o') + + # Curve with green line with square markers + plot.addCurve(x, numpy.random.random(len(x)), legend='random', + color='green', linestyle='-', symbol='s') + + + +Histogram ++++++++++ + +Data can be displayed as an histogram. This must be specified when calling the the addCurve function. (using ``histogram``, See :meth:`.PlotWidget.addCurve` for more details ). + +Histogram steps can be centered on x values or set at the left or the right of the given x values. + +.. code-block:: python + + import numpy + x = numpy.arange(0, 20, 1) + plot.addCurve(x, x+1, histogram='center', fill=True, color='green') + +.. note:: You can also give x as edges. For this you must have len(x) = len(y) + 1 + +Plot images in a widget +----------------------- + +The :class:`Plot2D` widget provides a plotting area and a toolbar with tools useful for images, such as keeping aspect ratio, changing the colormap or defining a mask. + +First, create a :class:`Plot2D` widget: + +.. code-block:: python + + from silx.gui.plot import Plot2D + + plot = Plot2D() # Create the plot widget + plot.show() # Make the plot widget visible + + +One image ++++++++++ + +To display a single image, use the :meth:`.PlotWidget.addImage` method: + +.. code-block:: python + + import numpy + + data = numpy.random.random(512 * 512).reshape(512, -1) # Create 2D image + plot.addImage(data) # Plot the 2D data set with default colormap + + +To update this image, call :meth:`.PlotWidget.addImage` again with the new image to display: + +.. code-block:: python + + # Create a RGB image + rgb_image = (numpy.random.random(512*512*3) * 255).astype(numpy.uint8) + rgb_image.shape = 512, 512, 3 + + plot.addImage(rgb_image) # Plot the RGB image instead of the previous data + + +To clear the plotting area, call :meth:`.PlotWidget.clear`: + +.. code-block:: python + + plot.clear() + + +Origin and scale +++++++++++++++++ + +:meth:`.PlotWidget.addImage` supports both 2D arrays of data displayed with a colormap and RGB(A) images as 3D arrays of shape (height, width, color channels). + +When displaying an image, it is possible to specify the ``origin`` and the ``scale`` of the image array in the plot area coordinates: + +.. code-block:: python + + data = numpy.random.random(512 * 512).reshape(512, -1) + plot.addImage(data, origin=(100, 100), scale=(0.1, 0.1)) + +When updating an image, if ``origin`` and ``scale`` are not provided, the previous values will be used: + +.. code-block:: python + + data = numpy.random.random(512 * 512).reshape(512, -1) + plot.addImage(data) # Keep previous origin and scale + + +Colormap +++++++++ + +A ``colormap`` is described with a :class:`dict` as follows (See :mod:`silx.gui.plot.Plot` for full documentation of the colormap): + +.. code-block:: python + + colormap = { + 'name': 'gray', # Name of the colormap + 'normalization': 'linear', # Either 'linear' or 'log' + 'autoscale': True, # True to autoscale colormap to data range, False to use [vmin, vmax] + 'vmin': 0.0, # If not autoscale, data value to bind to min of colormap + 'vmax': 1.0 # If not autoscale, data value to bind to max of colormap + } + + +At least the following colormap names are guaranteed to be available, but any colormap name from `matplotlib <http://matplotlib.org/>`_ (see `Choosing Colormaps <http://matplotlib.org/users/colormaps.html>`_) should work: + +- gray +- reversed gray +- temperature +- red +- green +- blue +- viridis +- magma +- inferno +- plasma + +It is possible to change the default colormap of :meth:`.PlotWidget.addImage` for the plot widget with :meth:`.PlotWidget.setDefaultColormap` (and to get it with :meth:`.PlotWidget.getDefaultColormap`): + +.. code-block:: python + + colormap = {'name': 'viridis', 'normalization': 'linear', + 'autoscale': True, 'vmin': 0.0, 'vmax': 1.0} + plot.setDefaultColormap(colormap) + + data = numpy.arange(512 * 512.).reshape(512, -1) + plot.addImage(data) # Rendered with the default colormap set before + +It is also possible to provide a ``colormap`` to :meth:`.PlotWidget.addImage` to override this default for an image: + +.. code-block:: python + + colormap = {'name': 'magma', 'normalization': 'log', + 'autoscale': False, 'vmin': 1.2, 'vmax': 1.8} + data = numpy.random.random(512 * 512).reshape(512, -1) + 1. + plot.addImage(data, colormap=colormap) + +As for `Origin and scale`_, when updating an image, if ``colormap`` is not provided, the previous colormap will be used: + +.. code-block:: python + + data = numpy.random.random(512 * 512).reshape(512, -1) + 1. + plot.addImage(data) # Keep previous colormap + +The colormap can be changed by the user from the widget's toolbar. + + +Multiple images ++++++++++++++++ + +In order to display multiple images at the same time, you need to provide a different ``legend`` string for each of them and to set the ``replace`` argument to ``False``: + +.. code-block:: python + + data = numpy.random.random(512 * 512).reshape(512, -1) + plot.addImage(data, legend='random', replace=False) + + data = numpy.arange(512 * 512.).reshape(512, -1) + plot.addImage(data, legend='arange', replace=False, origin=(512, 512)) + + +To update an image, call :meth:`.PlotWidget.addImage` with the ``legend`` of the curve you want to udpdate. +By default, the new image will keep the same colormap, origin and scale as the image it is updating: + +.. code-block:: python + + data = (512 * 512. - numpy.arange(512 * 512.)).reshape(512, -1) + plot.addImage(data, legend='arange', replace=False) # Beware of replace=False + + +To remove an image from the plot, call :meth:`.PlotWidget.remove` with the ``legend`` of the image you want to remove: + +.. code-block:: python + + plot.remove('random') + + +Control plot axes +----------------- + +The following examples illustrate the API to control the plot axes. + +Labels and title +++++++++++++++++ + +Use :meth:`.PlotWidget.setGraphTitle` to set the plot main title. +Use :meth:`.PlotWidget.setGraphXLabel` and :meth:`.PlotWidget.setGraphYLabel` to set the axes text labels: + +.. code-block:: python + + plot.setGraphTitle('My plot') + plot.setGraphXLabel('X') + plot.setGraphYLabel('Y') + + +Axes limits ++++++++++++ + +Different methods allows to get and set the data limits displayed on each axis. + +The following code moves the visible plot area to the right: + +.. code-block:: python + + xmin, xmax = plot.getGraphXLimits() + offset = 0.1 * (xmax - xmin) + plot.setGraphXLimits(xmin + offset, xmax + offset) + +:meth:`.PlotWidget.resetZoom` set the plot limits to the bounds of the data: + +.. code-block:: python + + plot.resetZoom() + +See :meth:`.PlotWidget.resetZoom`, :meth:`.PlotWidget.setLimits`, :meth:`.PlotWidget.getGraphXLimits`, :meth:`.PlotWidget.setGraphXLimits`, :meth:`.PlotWidget.getGraphYLimits`, :meth:`.PlotWidget.setGraphYLimits` for details. + + +Axes +++++ + +Different methods allow plot axes modifications: + +.. code-block:: python + + plot.setYAxisInverted(True) # Makes the Y axis pointing downward + plot.setKeepDataAspectRatio(True) # To keep aspect ratio between X and Y axes + +See :meth:`.PlotWidget.setYAxisInverted`, :meth:`.PlotWidget.setKeepDataAspectRatio` for details. + +.. code-block:: python + + plot.setGraphGrid(which='both') # To show a grid for both minor and major axes ticks + + # Use logarithmic axes + plot.setXAxisLogarithmic(True) + plot.setYAxisLogarithmic(True) + +See :meth:`.PlotWidget.setGraphGrid`, :meth:`.PlotWidget.setXAxisLogarithmic`, :meth:`.PlotWidget.setYAxisLogarithmic` for details. diff --git a/doc/source/modules/gui/plot/imageview.rst b/doc/source/modules/gui/plot/imageview.rst new file mode 100644 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b/doc/source/modules/gui/plot/index.rst new file mode 100644 index 0000000..143b85b --- /dev/null +++ b/doc/source/modules/gui/plot/index.rst @@ -0,0 +1,130 @@ + +.. currentmodule:: silx.gui + +:mod:`plot`: 1D and 2D Plot widgets +=================================== + +.. toctree:: + :hidden: + + getting_started.rst + +.. currentmodule:: silx.gui.plot + +.. automodule:: silx.gui.plot + +For an introduction to the widgets of this package, see :doc:`getting_started`. + +For examples of custom plot actions, see :doc:`plotactions_examples`. + +Widgets gallery +--------------- + +The :mod:`silx.gui.plot` package provides the following plotting widgets: + +.. |imgPlotWidget| image:: img/PlotWidget.png + :height: 150px + :align: middle + +.. |imgPlotWindow| image:: img/PlotWindow.png + :height: 150px + :align: middle + +.. |imgPlot1D| image:: img/Plot1D.png + :height: 150px + :align: middle + +.. |imgPlot2D| image:: img/Plot2D.png + :height: 150px + :align: middle + +.. |imgImageView| image:: img/ImageView.png + :height: 150px + :align: middle + +.. |imgStackView| image:: img/StackView.png + :height: 150px + :align: middle + +.. list-table:: + :widths: 1 4 + :header-rows: 1 + + * - Widget + - Description + * - |imgPlotWidget| + - :class:`PlotWidget` is the base Qt widget providing a plot area. + Other plot widgets are based on this one and provides the same API. + * - |imgPlotWindow| + - :class:`PlotWindow` adds a toolbar to :class:`PlotWidget`. + The content of this toolbar can be configured from the + :class:`PlotWindow` constructor or by hiding its content afterward. + * - |imgPlot1D| + - :class:`.Plot1D` is a :class:`PlotWindow` configured with tools useful + for curves. + * - |imgPlot2D| + - :class:`.Plot2D` is a :class:`PlotWindow` configured with tools useful + for images. + * - |imgImageView| + - :class:`ImageView` adds side histograms to a :class:`.Plot2D` widget. + * - |imgStackView| + - :class:`StackView` is a widget designed to display an image from a + stack of images in a :class:`PlotWindow` widget, with a frame browser + to navigate in the stack. The profile tool can do a 2D profile on the + stack of images. + +It also provides (and uses) widgets that can be attached to a :class:`PlotWidget`: + +.. |imgPositionInfo| image:: img/PositionInfo.png + :width: 300px + :align: middle + +.. |imgLimitsToolBar| image:: img/LimitsToolBar.png + :width: 300px + :align: middle + +.. |imgColorbar| image:: img/logColorbar.png + :height: 150px + :align: middle + + +.. list-table:: + :widths: 1 4 + :header-rows: 1 + + * - Widget + - Description + * - |imgPositionInfo| + - :class:`.PlotTools.PositionInfo` is a widget displaying mouse position and + information of a :class:`PlotWidget` associated to the mouse position. + * - |imgLimitsToolBar| + - :class:`.PlotTools.LimitsToolBar` is a QToolBar displaying and + controlling the limits of a :class:`PlotWidget`. + * - |imgColorbar| + - :class:`.ColorBar.ColorBarWidget` display colormap gradient and can be linked with a plot + to display the colormap + +Public modules +-------------- + +.. toctree:: + :maxdepth: 2 + + plotwidget.rst + plotwindow.rst + imageview.rst + stackview.rst + plot.rst + items.rst + plotactions.rst + plottools.rst + profile.rst + roi.rst + +Internals +--------- + +.. toctree:: + :maxdepth: 2 + + dev.rst diff --git a/doc/source/modules/gui/plot/items.rst b/doc/source/modules/gui/plot/items.rst new file mode 100644 index 0000000..beba3a1 --- /dev/null +++ b/doc/source/modules/gui/plot/items.rst @@ -0,0 +1,63 @@ + +.. currentmodule:: silx.gui.plot + +:mod:`items`: Plot primitives +============================= + +.. automodule:: silx.gui.plot.items + +.. currentmodule:: silx.gui.plot.items + +Curve +----- + +.. autoclass:: Curve + :members: + :inherited-members: + +Images +------ + +.. autoclass:: ImageData + :members: + :inherited-members: + +.. autoclass:: ImageRgba + :members: + :inherited-members: + +Scatter +------- + +.. autoclass:: Scatter + :members: + :inherited-members: + +Histogram +--------- + +.. autoclass:: Histogram + :members: + :inherited-members: + +Markers +------- + +.. autoclass:: Marker + :members: + :inherited-members: + +.. autoclass:: XMarker + :members: + :inherited-members: + +.. autoclass:: YMarker + :members: + :inherited-members: + +Item +---- + +.. autoclass:: Shape + :members: + :inherited-members: diff --git a/doc/source/modules/gui/plot/plot.rst b/doc/source/modules/gui/plot/plot.rst new file mode 100644 index 0000000..2b8e096 --- /dev/null +++ b/doc/source/modules/gui/plot/plot.rst @@ -0,0 +1,16 @@ + +.. currentmodule:: silx.gui.plot + +:mod:`Plot`: Full plot API +========================== + +.. automodule:: silx.gui.plot.Plot + +.. currentmodule:: silx.gui.plot.Plot + +:class:`Plot` class +------------------- + +.. autoclass:: Plot + :show-inheritance: + :members: diff --git a/doc/source/modules/gui/plot/plotactions.rst b/doc/source/modules/gui/plot/plotactions.rst new file mode 100644 index 0000000..29a3656 --- /dev/null +++ b/doc/source/modules/gui/plot/plotactions.rst @@ -0,0 +1,20 @@ + +.. currentmodule:: silx.gui.plot + +:mod:`PlotActions`: Actions for PlotWidget +=========================================== + +.. currentmodule:: silx.gui.plot.PlotActions + +The :class:`PlotAction` is a base class used to define plot actions. + +Plot actions serve to add menu items or toolbar items that are associated with a method +that can interact with the associated :class:`PlotWidget`. + +For an introduction to creating custom plot actions, see :doc:`plotactions_examples`. + +PlotActions API +--------------- + +.. automodule:: silx.gui.plot.PlotActions + :members: diff --git a/doc/source/modules/gui/plot/plotactions_examples.rst b/doc/source/modules/gui/plot/plotactions_examples.rst new file mode 100644 index 0000000..f14a42a --- /dev/null +++ b/doc/source/modules/gui/plot/plotactions_examples.rst @@ -0,0 +1,93 @@ +.. currentmodule:: silx.gui + +Adding custom plot actions +========================== + +A :class:`PlotWindow` defines a number of standard plot actions that can be executed +by clicking on toolbar icons. + +Developers can design additional plot actions to be added as toolbar icons or as menu entries, +to be added to a :class:`PlotWindow` or to design their own plot window based on +:class:`PlotWidget`. + +This documentation pages provides examples on how to do this. + +Simple example: Shift a curve +----------------------------- + +The following script is a simplistic example to show the basic required steps: + + - create a new class inheriting from :class:`silx.gui.plot.PlotActions.PlotAction` + - define basic parameters such as the icon, the tooltip... + - write a method that will be triggered by the action + - initialize the new plot action by passing a reference to a plot window + - add the action to a toolbar or a menu + +The method implemented in this action interacts with the plot in a basic way. It gets the active curve, +then it creates a new data array based on the curve data, and finally it replaces the original curve +with a new one using the modified data array. + +.. literalinclude:: ../../../../../examples/shiftPlotAction.py + :lines: 36- + +.. |imgShiftAction0| image:: img/shiftAction0.png + :height: 300px + :align: middle + +.. |imgShiftAction3| image:: img/shiftAction3.png + :height: 300px + :align: middle + +.. list-table:: + :widths: 1 2 + + * - |imgShiftAction0| + - Initial state + * - |imgShiftAction3| + - After triggering the action 3 times, the selected triangle shaped curve + is shifted up by 3 units + +Advanced example: Display amplitude spectrum +-------------------------------------------- + +This more advanced example shows additional ways of interacting with the plot, by changing +labels, storing additional data array along with the curve data. + +This action is *checkable*, meaning that is has two states. When clicking the toolbar icon +or the menu item, it remains in a *pushed* state until it is clicked again. + +In one state (*un-checked*), the original data is displayed. In the other state, the amplitude +spectrum of the original signal is displayed. When the state is changed, the triggered action +computes either the Fast Fourier Transform (FFT), or the reverse FFT. + +This example also illustrates how to store additional data, along with a curve. +The FFT computation returns complex values, but we want to display real data, so we compute +the amplitude spectrum. However, the inverse FFT requires the complete FFT data as input. +We are therefore required to store the complex array of FFT data as curve metadata, +in order to be able to reverse the process when the action is unchecked. + +.. literalinclude:: ../../../../../examples/fftPlotAction.py + :lines: 44- + +.. |imgFftAction0| image:: img/fftAction0.png + :height: 300px + :align: middle + +.. |imgFftAction1| image:: img/fftAction1.png + :height: 300px + :align: middle + +.. list-table:: + :widths: 1 2 + + * - |imgFftAction0| + - Original signals (zoom applied). In red, a cosine wave at 7 Hz. + In black, a sum of sines with frequencies of 3, 20 and 42 Hz. + In green, a square wave with a fundamental frequency of 0.5 Hz + (wavelength of 2 seconds). + * - |imgFftAction1| + - Amplitude spectra (zoom applied), with peaks visible at + the expected frequencies of 3, 7, 20 and 42 Hz for the sine and cosine + signals. In green, we see the complete series of peaks related to the square wave, + with a fundamental frequency at 0.5 Hz and harmonic frequencies at every + odd multiple of the fundamental. diff --git a/doc/source/modules/gui/plot/plottools.rst b/doc/source/modules/gui/plot/plottools.rst new file mode 100644 index 0000000..4cf8f88 --- /dev/null +++ b/doc/source/modules/gui/plot/plottools.rst @@ -0,0 +1,36 @@ +:mod:`PlotTools`: Tool widgets for PlotWidget +============================================= + +.. currentmodule:: silx.gui.plot.PlotTools + +.. automodule:: silx.gui.plot.PlotTools + +:class:`PositionInfo` class +--------------------------- + +.. autoclass:: PositionInfo + :show-inheritance: + :members: + +:class:`LimitsToolBar` class +---------------------------- + +.. autoclass:: LimitsToolBar + :show-inheritance: + :members: + + +.. currentmodule:: silx.gui.plot + +:mod:`ColorBar`: ColorBar Widget +================================ + +.. currentmodule:: silx.gui.plot.ColorBar + +.. automodule:: silx.gui.plot.ColorBar + +:class:`ColorBarWidget` class +----------------------------- + +.. autoclass:: ColorBarWidget + :members: diff --git a/doc/source/modules/gui/plot/plotwidget.rst b/doc/source/modules/gui/plot/plotwidget.rst new file mode 100644 index 0000000..df576fc --- /dev/null +++ b/doc/source/modules/gui/plot/plotwidget.rst @@ -0,0 +1,173 @@ + +.. currentmodule:: silx.gui.plot + +:mod:`PlotWidget`: Base class for plotting widgets +================================================== + +.. module:: silx.gui.plot.PlotWidget + +.. currentmodule:: silx.gui.plot.PlotWidget + +The :class:`PlotWidget` is a Qt widget providing the plot API initially +provided in `PyMca <http://pymca.sourceforge.net/>`_. +It is the basis of other plot widget, thus all plot widgets share the same API. + +For an introduction and examples of the plot API, see :doc:`getting_started`. + +Plot API +-------- + +.. currentmodule:: silx.gui.plot.Plot + +This is a choosen subset of the complete plot API, the full API is +documented in :class:`silx.gui.plot.Plot`. + +.. currentmodule:: silx.gui.plot.PlotWidget + +.. autoclass:: PlotWidget + :show-inheritance: + +Plot data +......... + +Those methods allow to add and update plotted data: + +.. automethod:: PlotWidget.addCurve +.. automethod:: PlotWidget.addImage +.. automethod:: PlotWidget.addScatter +.. automethod:: PlotWidget.addHistogram + +Plot markers +............ + +It is also possible to add point or line markers to the plot: + +.. automethod:: PlotWidget.addMarker +.. automethod:: PlotWidget.addXMarker +.. automethod:: PlotWidget.addYMarker + +Remove data from the plot +......................... + +.. automethod:: PlotWidget.clear +.. automethod:: PlotWidget.remove + +Title and labels +................ + +Those methods handle the text labels of the axes and the plot title: + +.. automethod:: PlotWidget.getGraphTitle +.. automethod:: PlotWidget.setGraphTitle +.. automethod:: PlotWidget.getGraphXLabel +.. automethod:: PlotWidget.setGraphXLabel +.. automethod:: PlotWidget.getGraphYLabel +.. automethod:: PlotWidget.setGraphYLabel + +Axes limits +........... + +Those methods change the range of data values displayed on each axis. + +.. automethod:: PlotWidget.getGraphXLimits +.. automethod:: PlotWidget.setGraphXLimits +.. automethod:: PlotWidget.getGraphYLimits +.. automethod:: PlotWidget.setGraphYLimits +.. automethod:: PlotWidget.setLimits + +Axes +.... + +The following methods handle the display properties of the axes: + +.. automethod:: PlotWidget.isXAxisLogarithmic +.. automethod:: PlotWidget.setXAxisLogarithmic +.. automethod:: PlotWidget.isYAxisLogarithmic +.. automethod:: PlotWidget.setYAxisLogarithmic + +.. automethod:: PlotWidget.isYAxisInverted +.. automethod:: PlotWidget.setYAxisInverted +.. automethod:: PlotWidget.isKeepDataAspectRatio +.. automethod:: PlotWidget.setKeepDataAspectRatio +.. automethod:: PlotWidget.getGraphGrid +.. automethod:: PlotWidget.setGraphGrid + +Reset zoom +.......... + +.. automethod:: PlotWidget.resetZoom + +Those methods change the behavior of :meth:`PlotWidget.resetZoom`. + +.. automethod:: PlotWidget.getDataMargins +.. automethod:: PlotWidget.setDataMargins +.. automethod:: PlotWidget.isXAxisAutoScale +.. automethod:: PlotWidget.setXAxisAutoScale +.. automethod:: PlotWidget.isYAxisAutoScale +.. automethod:: PlotWidget.setYAxisAutoScale + +Defaults +........ + +Those methods set-up default values for :meth:`PlotWidget.addCurve` and +:meth:`PlotWidget.addImage`: + +.. automethod:: PlotWidget.getDefaultColormap +.. automethod:: PlotWidget.setDefaultColormap +.. automethod:: PlotWidget.getSupportedColormaps +.. automethod:: PlotWidget.setDefaultPlotPoints +.. automethod:: PlotWidget.setDefaultPlotLines + +Interaction +........... + +Those methods allow to change the interaction mode (e.g., drawing mode) +of the plot and to toggle the use of a crosshair cursor: + +.. automethod:: PlotWidget.getInteractiveMode +.. automethod:: PlotWidget.setInteractiveMode + +.. automethod:: PlotWidget.getGraphCursor +.. automethod:: PlotWidget.setGraphCursor + +Misc. +..... + +.. automethod:: PlotWidget.saveGraph + +Signals +....... + +The :class:`PlotWidget` provides the following Qt signals: + +.. autoattribute:: PlotWidget.sigPlotSignal +.. autoattribute:: PlotWidget.sigSetYAxisInverted +.. autoattribute:: PlotWidget.sigSetXAxisLogarithmic +.. autoattribute:: PlotWidget.sigSetYAxisLogarithmic +.. autoattribute:: PlotWidget.sigSetXAxisAutoScale +.. autoattribute:: PlotWidget.sigSetYAxisAutoScale +.. autoattribute:: PlotWidget.sigSetKeepDataAspectRatio +.. autoattribute:: PlotWidget.sigSetGraphGrid +.. autoattribute:: PlotWidget.sigSetGraphCursor +.. autoattribute:: PlotWidget.sigSetPanWithArrowKeys +.. autoattribute:: PlotWidget.sigContentChanged +.. autoattribute:: PlotWidget.sigActiveCurveChanged +.. autoattribute:: PlotWidget.sigActiveImageChanged +.. autoattribute:: PlotWidget.sigInteractiveModeChanged + +.. Not documented: + addItem, removeItem, clearItems + isActiveCurveHandling, enableActiveCurveHandling, + getActiveCurveColor, setActiveCurveColor, + getActiveCurve, setActiveCurve, + isCurveHidden, hideCurve, + getActiveImage, setActiveImage, + getAllCurves, getCurve, getImage, getAllImages, + getScatter, getHistogram, + setDefaultPlotPoints, setDefaultPlotLines, + getWidgetHandle, notify, setCallback, graphCallback, + dataToPixel, pixelToData, getPlotBoundsInPixels, + setGraphCursorShape, pickMarker, moveMarker, pickImageOrCurve, moveImage, + onMousePress, onMouseMove, onMouseRelease, onMouseWheel, + isDrawModeEnabled, setDrawModeEnabled, getDrawMode, + isZoomModeEnabled, setZoomModeEnabled, diff --git a/doc/source/modules/gui/plot/plotwindow.rst b/doc/source/modules/gui/plot/plotwindow.rst new file mode 100644 index 0000000..1447403 --- /dev/null +++ b/doc/source/modules/gui/plot/plotwindow.rst @@ -0,0 +1,30 @@ + +.. currentmodule:: silx.gui.plot + +:mod:`PlotWindow`: Plot widget with toolbar +=========================================== + +.. automodule:: silx.gui.plot.PlotWindow + +.. currentmodule:: silx.gui.plot.PlotWindow + +:class:`PlotWindow` class +------------------------- + +.. autoclass:: PlotWindow + :show-inheritance: + :members: + +:class:`Plot1D`: Plot curves +---------------------------- + +.. autoclass:: Plot1D + :show-inheritance: + :members: + +:class:`Plot2D`: Plot images +---------------------------- + +.. autoclass:: Plot2D + :show-inheritance: + :members: diff --git a/doc/source/modules/gui/plot/profile.rst b/doc/source/modules/gui/plot/profile.rst new file mode 100644 index 0000000..56530f3 --- /dev/null +++ b/doc/source/modules/gui/plot/profile.rst @@ -0,0 +1,20 @@ +:mod:`Profile`: Toolbars with profile tools +=========================================== + +.. currentmodule:: silx.gui.plot.Profile + +.. automodule:: silx.gui.plot.Profile + +:class:`ProfileToolBar` class +----------------------------- + +.. autoclass:: ProfileToolBar + :show-inheritance: + :members: + +:class:`Profile3DToolBar` class +------------------------------- + +.. autoclass:: Profile3DToolBar + :show-inheritance: + :members: diff --git a/doc/source/modules/gui/plot/roi.rst b/doc/source/modules/gui/plot/roi.rst new file mode 100644 index 0000000..77b5c2a --- /dev/null +++ b/doc/source/modules/gui/plot/roi.rst @@ -0,0 +1,17 @@ +.. currentmodule:: silx.gui.plot + +:mod:`CurvesROIWidget`: ROI from curves +======================================= + +.. |roiWidgetImage| image:: img/roiwidget.png + :height: 400px + :align: middle + +You can access to the ROIWidget from a Plot window by : + +- using the tool button 'ROI' +- using the options button then by selecting region of interest. + +|roiWidgetImage| + +.. automodule:: silx.gui.plot.CurvesROIWidget diff --git a/doc/source/modules/gui/plot/stackview.rst b/doc/source/modules/gui/plot/stackview.rst new file mode 100644 index 0000000..7f2442a --- /dev/null +++ b/doc/source/modules/gui/plot/stackview.rst @@ -0,0 +1,24 @@ + +.. currentmodule:: silx.gui.plot + +:mod:`StackView`: Plot a stack of images +========================================= + +.. automodule:: silx.gui.plot.StackView + +.. currentmodule:: silx.gui.plot.StackView + +:class:`StackView` class +------------------------ + +.. autoclass:: StackView + :members: + :exclude-members: remove, setInteractiveMode, addItem + +:class:`StackViewMainWindow` class +---------------------------------- + +.. autoclass:: StackViewMainWindow + :show-inheritance: + :members: + |
