Commit 98fbe586 authored by Pilar Cossio's avatar Pilar Cossio

Order doc inputparam

parent a9dcb7fb
......@@ -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
~~~~~~~~~~~~~
......
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