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Merge pull request #287 from European-XFEL/documentation
[DOC] Update documentation
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Diff for: ‎docs/image_tool.rst

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@@ -11,7 +11,7 @@ IMAGE TOOL
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The *ImageTool* window is the second control window which provides various image-related
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information and controls.
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.. image:: images/ImageTool.png
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.. image:: images/image_tool.jpg
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:width: 800
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Image control
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| ``Update automatically`` | Automatically update the current displayed image in the |
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| | *ImageTool* window. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Moving average`` | Apply moving average to the image data. It affects both the |
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| | individual images in a train and the averaged image, as well as |
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| | the subsequent analysis. If a new window size is smaller than |
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| | the old one, the moving average calculation will start from the |
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| | scratch. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Auto level`` | Update the detector images (not only in the *ImageTool* window, |
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| | but also in other plot windows) by automatically selecting levels |
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| | based on the maximum and minimum values in the data. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Save image`` | Save the current image to file. Please also see ImageFileFormat_ |
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+----------------------------+--------------------------------------------------------------------+
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.. Warning::
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The moving average here is not calculated by nanmean_, which means that if a pixel of the image
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in a certain pulse is *NaN*, the moving average of that pixel will be *NaN* for that pulse.
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.. Warning::
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Please be aware that there is another moving average setup in the :ref:`Global setup` in the
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main GUI.
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Mask panel
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""""""""""
@@ -173,6 +188,8 @@ Gain / offset
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.. _nanmean: https://docs.scipy.org/doc/numpy/reference/generated/numpy.nanmean.html
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.. image:: images/gain_offset_correction.jpg
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Apply pixel-wised gain and offset correction, where
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.. math::
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of trains. The moving average of the each "dark pulse" in the train will be calculated,
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which will then be used to apply dark subtraction to image data pulse-by-pulse.
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+----------------------------+--------------------------------------------------------------------+
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| Input | Description |
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+============================+====================================================================+
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| ``Gain correction`` | Check to activate gain correction. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Offset correction`` | Check to activate offset correction. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Use dark as offset`` | Check to use recorded dark images as offset. The already loaded |
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| | offset constants will be ignored. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Record dark`` | Start and stop dark run recording. |
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+----------------------------+--------------------------------------------------------------------+
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| ``Remove dark`` | Remove the recorded dark run. |
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+----------------------------+--------------------------------------------------------------------+
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.. Note::
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+-----------------------------+--------------------------------------------------------------------+
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| Input | Description |
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+=============================+====================================================================+
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| ``Apply gain correction`` | Check to activate gain correction. |
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+-----------------------------+--------------------------------------------------------------------+
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| ``Apply offset correction`` | Check to activate offset correction. Since version 1.10, a |
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| | variation of offset correction has been introduced: |
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| | |
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| | - ``+intra-dark``: |
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| | |
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| | After the pulse-by-pulse offset correction, every other pulse |
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| | will be subtracted by the following one starting from the |
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| | first pulse. For instance, imaging a pulse train consisting of |
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| | four pulses *ABAB*, the extra intra-dark correction will |
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| | result in a train *A'BA'B*, where *A'* = *A* - *B*. |
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| | Then one can make use of the pulse slicer in the |
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| | :ref:`Data source tree` to remove the intra-dark pulses. |
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+-----------------------------+--------------------------------------------------------------------+
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| ``Use dark as offset`` | Check to use recorded dark images as offset. The already loaded |
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| | offset constants will be ignored. |
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+-----------------------------+--------------------------------------------------------------------+
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| ``Record dark`` | Start and stop dark run recording. |
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+-----------------------------+--------------------------------------------------------------------+
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| ``Remove dark`` | Remove the recorded dark run. |
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+-----------------------------+--------------------------------------------------------------------+
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.. Warning::
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The moving average here is not calculated by nanmean_, which means that if a pixel of the image
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in a certain pulse is *NaN*, the moving average of that pixel will be *NaN* for that pulse.
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.. Note::
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Some detectors have its own special treatment for gain/offset correction:
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- DSSC:
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Due to the readout issue, pixels with value 0 will be converted to 256.
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Reference image
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---------------

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Diff for: ‎docs/installation.rst

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@@ -66,11 +66,9 @@ accelerate your analysis, please feel free to dig into the code and ask question
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# Now you should be able to load the newly created kernel on max-jhub.
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Install C++ API of **EXtra-foam** only
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--------------------------------------
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Install C++ API only
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--------------------
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.. code-block:: bash
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.. _foamalgo: https://github.com/zhujun98/foamalgo
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$ mkdir build && cd build
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$ cmake -DFOAM_USE_XSIMD=ON -DCMAKE_INSTALL_PREFIX=/YOUR/INSTALL/PREFIX
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$ make && make install
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Please check foamalgo_.

Diff for: ‎docs/main_gui.rst

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MAIN GUI
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========
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| ``Port`` | Port number of the TCP connection. |
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+----------------------------+--------------------------------------------------------------------+
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.. _Data source tree:
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Data source tree
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""""""""""""""""
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General analysis
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----------------
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.. _Global setup:
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Global setup
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""""""""""""
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+----------------------------+--------------------------------------------------------------------+
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| ``Moving average window`` | Moving average window size. If the moving average window size is |
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| | larger than 1, moving average will be applied to all the |
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| | registered analysis types. If the new window size is smaller than |
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| | registered analysis types. If a new window size is smaller than |
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| | the old one, the moving average calculation will start from the |
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| | scratch. |
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| | scratch. Currently, this setup will affect the calculations of: |
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| | |
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| | - Pulse intensity of XGM |
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| | - Pulse integral of Digitizer |
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| | - Train-resolved (pump/probe) azimuthal integration |
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| | - Train-resolved (pump/probe) ROI FOM |
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| | - Train-resolved (pump/probe) ROI 1D projection |
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| | |
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+----------------------------+--------------------------------------------------------------------+
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| ``Reset`` | Reset the moving average counts of all registered analysis types. |
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+----------------------------+--------------------------------------------------------------------+
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.. Warning::
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Since version 1.10, another moving average was re-activated in :ref:`Image tool`. If both the
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moving averages are set, the result of azimuthal integration, ROI FOM and ROI 1D projection
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will be a moving average on top of the moving averaged image! This is due to some historical
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reason and it will be fixed in the future.
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Pump-probe setup
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""""""""""""""""
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