Order doc inputparam

doc/index.rst

@@ -55,7 +55,7 @@ Welcome to BioEM's documentation!
    David Rohr, Fabio Baruffa, Markus Rampp, Volker Linderstruth and
    Gerhard Hummer.
 
-   **BioEM 2.0** Copyright (C) 2017 Pilar Cossio, Luka Stanisic,
+   **BioEM 2.0** Copyright (C) 2018 Pilar Cossio, Luka Stanisic,
    Markus Rampp and Gerhard Hummer.
 
    The BioEM program is a free software, under the terms of the GNU
@@ -832,6 +832,104 @@ With this feature there is an additional output file
 are written. The orientations in this file are sorted in decreasing log-posterior
 order.
 
+Overview of keywords for the input-parameter file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In the following, we provide a list of the possible keywords read from
+the input-parameter.
+
+BioEM posterior probability computation:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+-  :inpar:`PIXEL_SIZE` ``(float)``: Micrograph pixel size in Å.
+
+-  :inpar:`NUMBER_PIXELS` ``(int)``: Assuming a square particle-image,
+   it is the number of pixels along an axis. This should coincide with
+   the number of pixels read from the micrograph.
+
+-  :inpar:`CTF_DEFOCUS` ``(float) (float) (int)``: (CTF integration)
+   Grid sampling of CTF defocus, :math:`\Delta f`. Units of
+   micro-meters.  ``(float) (float)`` are the starting and ending
+   limits, respectively, and ``(int)`` is the number of grid points.
+
+-  :inpar:`CTF_B_ENV` ``(float) (float) (int)``: (CTF integration)
+   Grid sampling of envelope parameter :math:`b`. Units of Å\
+   :math:`^2`.  ``(float) (float)`` are the starting and ending
+   limits, respectively, and ``(int)`` is the number of grid points.
+
+-  :inpar:`CTF_AMPLITUDE` ``(float) (float) (int)``: (CTF integration)
+   Grid sampling of the CTF amplitude, :math:`A` (adimensional
+   :math:`\in [0,1]`). ``(float) (float)`` are the starting and ending
+   limits, respectively, and ``(int)`` is the number of grid points.
+
+-  :inpar:`DISPLACE_CENTER` ``(int) (int)``: (Integration of particle
+   center displacement) Sampling within a square grid. Units of
+   pixels.  ``(int) (int)`` are the maximum displacement from the
+   center in both directions, and the grid spacing, respectively.
+
+Optional keywords:
+^^^^^^^^^^^^^^^^^^
+
+-  :inpar:`GRIDPOINTS_ALPHA` ``(int)``: (Integration of orientations,
+   mandatory if quaterionions or `--ReadOrientation` are not used)
+   Number of grid points used in the integration over Euler angle
+   :math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle
+   space is performed. The integral over Euler angle :math:`\gamma` is
+   identical to that of :math:`\alpha`.
+
+-  :inpar:`GRIDPOINTS_BETA` ``(int)``: (Integration of orientations,
+   mandatory if quaterionions or `--ReadOrientation` are not used)
+   Number of grid points used in the integration over
+   :math:`\cos(\beta) \in [-1,1]`.
+
+-  :inpar:`USE_QUATERNIONS`: (Integration of Orientations) If using
+   quaternions to the describe the orientations. *Recommended* for
+   uniformly sampling of :math:`SO3` with the quaternions lists
+   available in the **Quaternions** directory.
+
+-  :inpar:`GRIDPOINTS_QUATERNION` ``(int)``: (Integration of
+   Orientations) For a hypercubic grid quaternion sampling. Each
+   quaternion is within :math:`[-1,1]`. ``(int)`` is the number of
+   grid points per dimension.
+
+-  :inpar:`ELECTRON_WAVELENGTH` ``(float)``: To change the default
+   value of the electron wavelength ``(float)`` used to calculate the
+   CTF phase with the defocus. Default 0.019688 :math:`\AA`.
+
+-  :inpar:`PRIOR_MODEL` ``(float)``: Prior probability of
+   model. **Default** 1.
+
+-  :inpar:`PRIOR_ANGLES`: To read the prior of each orientation in the input
+   file of orientations.
+
+-  :inpar:`SIGMA_PRIOR_B_CTF` ``(float)``: To change the Gaussian width
+   of the prior probability of the CTF envelope parameter :math:`b`
+   (section :ref:`priorsec`). **Default** 100 Å.
+
+-  :inpar:`SIGMA_PRIOR_DEFOCUS` ``(float)``: To change the Gaussian
+   width of the prior of the defocus :math:`\sigma_{\Delta f}`
+   (section :ref:`priorsec`).  **Default** 1 :math:`\mu` m.
+
+-  :inpar:`PRIOR_DEFOCUS_CENTER` ``(float)``: To change the Gaussian
+   center of the prior of the defocus :math:`\Delta f_c` (section
+   :ref:`priorsec`).  **Default** 3 :math:`\mu` m.
+
+-  :inpar:`SIGMA_PRIOR_AMP_CTF` ``(float)``: To change the Gaussian
+   width of the prior of the amplitude :math:`\sigma_{A}` (section
+   :ref:`priorsec`).  **Default** 0.3.
+
+-  :inpar:`PRIOR_AMP_CTF_CENTER` ``(float)``: To change the Gaussian
+   center of the prior of the amplitude :math:`A_c` (section
+   :ref:`priorsec`).  **Default** 0.
+
+-  :inpar:`NO_MAP_NORM`: Condition to not normalize to zero mean and unit
+   variance the input maps.
+
+-  :inpar:`WRITE_PROB_ANGLES` ``(int)``: To write out the posterior as
+   a function of the best ``(int)`` orientation.
+
+.. _anaout:
+
 File Formats
 ------------
 
@@ -939,103 +1037,6 @@ orientations file is described in the following:
    end of each line an extra column (of format “%12.6f”) that indicates
    the value of the prior probability for each orientation.
 
-Keywords for the input-parameter file
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-In the following, we provide a list of the possible keywords read from
-the input-parameter.
-
-BioEM posterior probability computation:
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
--  :inpar:`PIXEL_SIZE` ``(float)``: Micrograph pixel size in Å.
-
--  :inpar:`NUMBER_PIXELS` ``(int)``: Assuming a square particle-image,
-   it is the number of pixels along an axis. This should coincide with
-   the number of pixels read from the micrograph.
-
--  :inpar:`CTF_DEFOCUS` ``(float) (float) (int)``: (CTF integration)
-   Grid sampling of CTF defocus, :math:`\Delta f`. Units of
-   micro-meters.  ``(float) (float)`` are the starting and ending
-   limits, respectively, and ``(int)`` is the number of grid points.
-
--  :inpar:`CTF_B_ENV` ``(float) (float) (int)``: (CTF integration)
-   Grid sampling of envelope parameter :math:`b`. Units of Å\
-   :math:`^2`.  ``(float) (float)`` are the starting and ending
-   limits, respectively, and ``(int)`` is the number of grid points.
-
--  :inpar:`CTF_AMPLITUDE` ``(float) (float) (int)``: (CTF integration)
-   Grid sampling of the CTF amplitude, :math:`A` (adimensional
-   :math:`\in [0,1]`). ``(float) (float)`` are the starting and ending
-   limits, respectively, and ``(int)`` is the number of grid points.
-
--  :inpar:`DISPLACE_CENTER` ``(int) (int)``: (Integration of particle
-   center displacement) Sampling within a square grid. Units of
-   pixels.  ``(int) (int)`` are the maximum displacement from the
-   center in both directions, and the grid spacing, respectively.
-
-Optional keywords:
-^^^^^^^^^^^^^^^^^^
-
--  :inpar:`GRIDPOINTS_ALPHA` ``(int)``: (Integration of orientations,
-   mandatory if quaterionions or `--ReadOrientation` are not used)
-   Number of grid points used in the integration over Euler angle
-   :math:`\alpha \in [-\pi,\pi]`. Here a cubic grid in Euler angle
-   space is performed. The integral over Euler angle :math:`\gamma` is
-   identical to that of :math:`\alpha`.
-
--  :inpar:`GRIDPOINTS_BETA` ``(int)``: (Integration of orientations,
-   mandatory if quaterionions or `--ReadOrientation` are not used)
-   Number of grid points used in the integration over
-   :math:`\cos(\beta) \in [-1,1]`.
-
--  :inpar:`USE_QUATERNIONS`: (Integration of Orientations) If using
-   quaternions to the describe the orientations. *Recommended* for
-   uniformly sampling of :math:`SO3` with the quaternions lists
-   available in the **Quaternions** directory.
-
--  :inpar:`GRIDPOINTS_QUATERNION` ``(int)``: (Integration of
-   Orientations) For a hypercubic grid quaternion sampling. Each
-   quaternion is within :math:`[-1,1]`. ``(int)`` is the number of
-   grid points per dimension.
-
--  :inpar:`ELECTRON_WAVELENGTH` ``(float)``: To change the default
-   value of the electron wavelength ``(float)`` used to calculate the
-   CTF phase with the defocus. Default 0.019688 :math:`\AA`.
-
--  :inpar:`PRIOR_MODEL` ``(float)``: Prior probability of
-   model. **Default** 1.
-
--  :inpar:`PRIOR_ANGLES`: To read the prior of each orientation in the input
-   file of orientations.
-
--  :inpar:`SIGMA_PRIOR_B_CTF` ``(float)``: To change the Gaussian width
-   of the prior probability of the CTF envelope parameter :math:`b`
-   (section :ref:`priorsec`). **Default** 100 Å.
-
--  :inpar:`SIGMA_PRIOR_DEFOCUS` ``(float)``: To change the Gaussian
-   width of the prior of the defocus :math:`\sigma_{\Delta f}`
-   (section :ref:`priorsec`).  **Default** 1 :math:`\mu` m.
-
--  :inpar:`PRIOR_DEFOCUS_CENTER` ``(float)``: To change the Gaussian
-   center of the prior of the defocus :math:`\Delta f_c` (section
-   :ref:`priorsec`).  **Default** 3 :math:`\mu` m.
-
--  :inpar:`SIGMA_PRIOR_AMP_CTF` ``(float)``: To change the Gaussian
-   width of the prior of the amplitude :math:`\sigma_{A}` (section
-   :ref:`priorsec`).  **Default** 0.3.
-
--  :inpar:`PRIOR_AMP_CTF_CENTER` ``(float)``: To change the Gaussian
-   center of the prior of the amplitude :math:`A_c` (section
-   :ref:`priorsec`).  **Default** 0.
-
--  :inpar:`NO_MAP_NORM`: Condition to not normalize to zero mean and unit
-   variance the input maps.
-
--  :inpar:`WRITE_PROB_ANGLES` ``(int)``: To write out the posterior as
-   a function of the best ``(int)`` orientation.
-
-.. _anaout:
 
 Output format
 ~~~~~~~~~~~~~