Commit c4f27e31 authored by Thomas Vincent's avatar Thomas Vincent

update qspace view doc

parent e9c27d30
.. _qspace_view:
Fitting peaks (Q-Space view)
============================
Q Space View
============
.. |qspace_window| image:: img/qspace_window.png
.. _figure_qspace_window:
.. figure:: img/qspace_window.png
:width: 100%
:align: center
+-----------------+
| Intensity view |
+=================+
| |qspace_window| |
+-----------------+
Q space view window
This window allows you to visualize the Q space histogram.
You can display the Q space either in 3D (using OpenGL) with `Isosurfaces`_ and a `Cutting plane`_ or as a stack of images.
You can also select a Q space `ROI selection`_ and start `Fitting`_ the selected Q space ROI.
3D view
-------
This window allows you to visualize the q space. You can display one or more
isosurfaces and a cutting plane, select a 3D ROI, and start fitting peaks.
More info about the
The 3D view is available only if OpenGL 2.1 is available.
Isosurfaces
...........
Isosurfaces can be added/removed and configured from the top left tree widget.
Click on the ``+`` (``-``) to add (remove) an isosurface.
Click on the **+** (**-**) to add (remove) an isosurface.
Move the slider or double click on the value and enter a number to change its level.
Tick (untick) the checkbox next to the isosurface color icon to show (hide) that
isosurface.
Toggle the checkbox next to the isosurface color icon to toggle the isosurface visibility.
Cutting plane
.............
A cutting plane can be shown by expanding the ``Cutting plane`` node in the
plot3d parameter tree (top left of the qspace view) and ticking the ``Visible``
node checkbox.
A cutting plane can be displayed by expanding the **Cutting plane** item in the parameter tree (top left of the Q space view) and checking its **Visible** checkbox.
When visible, the cutting plane can be moved around with the mouse.
You can switch between `plane` and `camera` control by clicking on the desired control in the toolbar above the 3D view.
When visible the cutting plane can be moved around with the mouse. You can switch between
`plane` and `camera` control by clicking on the desired control in the toolbar
right above the 3D view.
A view of the cutting plane is also available in the **Cut Plane** tab in the bottom left corner of the window.
Fitting
-------
A vew of the isosurface is also available in the ``Cut Plane`` tab in the
bottom left corner of the window.
Click on **Run** to process the data with selected Q space ROI, background and fit method.
Once done, a :ref:`fit item <fit_item>` is added to the :ref:`project tree <project_tree>`.
The results are displayed in a :ref:`fit view <fit_view>` window.
ROI selection
.............
The widget on the top right corner of the window allows you to select a 3D Region
Of Interest. To enable the ROI, tick the `Roi` checkbox, then move the sliders
to change the ROI ranges. The ROI ranges are displayed as white wires in the 3D
view.
The widget on the top right corner of the window allows you to select a 3D Region Of Interest.
To enable the ROI, check the **Roi** checkbox, then move the sliders to change the ROI ranges.
The ROI bounding box is displayed in white in the 3D view.
Roi intensity
.............
The summed intensity inside the ROI can be visualized in the **ROI Intensity** tab in the bottom left corner of the window.
You have to click on the **Update** button as it is not refreshed in real time.
The summed intensity inside the ROI can be visualized in the ``ROI Intensity``
tab in the bottom left corner of the window. You will have to click on the
``Update`` button as it is not refreshed in real time.
Background selection
....................
Fitting
-------
TODO
Three options are available :
Fit parameters
..............
* **Gaussian** : fits a simple gaussian function on the projected peak along the qx, qy, and qz axis. Results returned are:
* area
* center (qx, qy or qz)
* width
Three options are available :
* **Centroid** : computes the center of mass. Results are:
* center of mass (qx, qy or qz)
* intensity value closest to the center of mass
* maximum intensity
* **Gaussian** : Fits a single gaussian function on the Q space projected on each axes.
Results returned are:
* **Max** : just returns the maximum value and its position
* maximum
* position (qx, qy or qz)
* Area
* Center position
* Width
After selected the desired *"fit"* type, the process can be started by clicking
on ``Run``.
* **Centroid** : Computes the center of mass and maximum. Results are:
When the fit is done, a new :ref:`fit item <fit_item>` is added to the
:ref:`project tree <project_tree>`. You can view the result in
the :ref:`fit view <fit_view>`.
* Center of mass
* Integrated intensity
* Maximum position
* Maximum intensity
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