From 943fed8b702b80dad720a285679efd837c257f7b Mon Sep 17 00:00:00 2001 From: "Daniel M. 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cannot share the environment and doctrees with the others -I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . - -.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " dirhtml to make HTML files named index.html in directories" - @echo " singlehtml to make a single large HTML file" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " qthelp to make HTML files and a qthelp project" - @echo " devhelp to make HTML files and a Devhelp project" - @echo " epub to make an epub" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " latexpdf to make LaTeX files and run them through pdflatex" - @echo " text to make text files" - @echo " man to make manual pages" - @echo " 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When it is not found, a full rebuild will be done. -config: 613726d7ead289eb5bc59a5d50e806e0 -tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/python/docSRC/_build/html/ASTRAProjector.html b/python/docSRC/_build/html/ASTRAProjector.html deleted file mode 100644 index 61c6a2f..0000000 --- a/python/docSRC/_build/html/ASTRAProjector.html +++ /dev/null @@ -1,235 +0,0 @@ - - - - - - - - Helper class: the ASTRAProjector module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
-

Navigation

- -
- -
-
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-
- -
-

Helper class: the ASTRAProjector module

-
-
-class astra.ASTRAProjector.ASTRAProjector2D(proj_geom, vol_geom, proj_type, useCUDA=False)[source]
-

Bases: builtins.object

-

Helps with various common ASTRA Toolbox 2D operations.

-

This class can perform several often used toolbox operations, such as:

-
    -
  • Forward projecting
    • -
  • Back projecting
    • -
  • Reconstructing
    • -
-

Note that this class has a some computational overhead, because it -copies a lot of data. If you use many repeated operations, directly -using the PyAstraToolbox methods directly is faster.

-

You can use this class as an abstracted weight matrix \(W\): multiplying an instance -proj of this class by an image results in a forward projection of the image, and multiplying -proj.T by a sinogram results in a backprojection of the sinogram:

-
proj = ASTRAProjector2D(...)
-fp = proj*image
-bp = proj.T*sinogram
-
-
- --- - - - -
Parameters:
    -
  • proj_geom (dict) – The projection geometry.
    • -
  • vol_geom (dict) – The volume geometry.
    • -
  • proj_type (string) – Projector type, such as 'line', 'linear', ...
    • -
  • useCUDA (bool) – If True, use CUDA for calculations, when possible.
    • -
-
-
-
-backProject(data)[source]
-

Backproject a sinogram.

- --- - - - - - -
Parameters:data (numpy.ndarray or int) – The sinogram data or ID.
Returns:numpy.ndarray – The backprojection.
-
- -
-
-forwardProject(data)[source]
-

Forward project an image.

- --- - - - - - -
Parameters:data (numpy.ndarray or int) – The image data or ID.
Returns:numpy.ndarray – The forward projection.
-
- -
-
-reconstruct(data, method, **kwargs)[source]
-

Reconstruct an image from a sinogram.

- --- - - - - - -
Parameters: -
Returns:

numpy.ndarray – The reconstruction.

-
-

Example of a SIRT reconstruction using CUDA:

-
proj = ASTRAProjector2D(...)
-rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)
-
-
-
- -
- -
-
-class astra.ASTRAProjector.ASTRAProjector2DTranspose(parentProj)[source]
-

Bases: builtins.object

-

Implements the proj.T functionality.

-

Do not use directly, since it can be accessed as member .T of -an ASTRAProjector2D object.

-
- -
- - -
-
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-
-
-

Previous topic

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Additional functions: the functions module

-

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MATLAB compatibility interface: the matlab module

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- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html deleted file mode 100644 index 08789f2..0000000 --- a/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - - - astra.ASTRAProjector — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
-

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Source code for astra.ASTRAProjector

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-
-import math
-from . import creators as ac
-from . import data2d
-
-
-
[docs]class ASTRAProjector2DTranspose():
-    """Implements the ``proj.T`` functionality.
-
-    Do not use directly, since it can be accessed as member ``.T`` of
-    an :class:`ASTRAProjector2D` object.
-
-    """
-    def __init__(self, parentProj):
-        self.parentProj = parentProj
-
-    def __mul__(self, data):
-        return self.parentProj.backProject(data)
-
-

-
[docs]class ASTRAProjector2D(object):
-    """Helps with various common ASTRA Toolbox 2D operations.
-
-    This class can perform several often used toolbox operations, such as:
-
-    * Forward projecting
-    * Back projecting
-    * Reconstructing
-
-    Note that this class has a some computational overhead, because it
-    copies a lot of data. If you use many repeated operations, directly
-    using the PyAstraToolbox methods directly is faster.
-
-    You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance
-    ``proj`` of this class by an image results in a forward projection of the image, and multiplying
-    ``proj.T`` by a sinogram results in a backprojection of the sinogram::
-
-        proj = ASTRAProjector2D(...)
-        fp = proj*image
-        bp = proj.T*sinogram
-
-    :param proj_geom: The projection geometry.
-    :type proj_geom: :class:`dict`
-    :param vol_geom: The volume geometry.
-    :type vol_geom: :class:`dict`
-    :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...
-    :type proj_type: :class:`string`
-    :param useCUDA: If ``True``, use CUDA for calculations, when possible.
-    :type useCUDA: :class:`bool`
-    """
-
-    def __init__(self, proj_geom, vol_geom, proj_type, useCUDA=False):
-        self.vol_geom = vol_geom
-        self.recSize = vol_geom['GridColCount']
-        self.angles = proj_geom['ProjectionAngles']
-        self.nDet = proj_geom['DetectorCount']
-        nexpow = int(pow(2, math.ceil(math.log(2 * self.nDet, 2))))
-        self.filterSize = nexpow / 2 + 1
-        self.nProj = self.angles.shape[0]
-        self.proj_geom = proj_geom
-        self.proj_id = ac.create_projector(proj_type, proj_geom, vol_geom)
-        self.useCUDA = useCUDA
-        self.T = ASTRAProjector2DTranspose(self)
-
-
[docs]    def backProject(self, data):
-        """Backproject a sinogram.
-
-        :param data: The sinogram data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :returns: :class:`numpy.ndarray` -- The backprojection.
-
-        """
-        vol_id, vol = ac.create_backprojection(
-            data, self.proj_id, useCUDA=self.useCUDA, returnData=True)
-        data2d.delete(vol_id)
-        return vol
-

-
[docs]    def forwardProject(self, data):
-        """Forward project an image.
-
-        :param data: The image data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :returns: :class:`numpy.ndarray` -- The forward projection.
-
-        """
-        sin_id, sino = ac.create_sino(data, self.proj_id, useCUDA=self.useCUDA, returnData=True)
-        data2d.delete(sin_id)
-        return sino
-

-
[docs]    def reconstruct(self, data, method, **kwargs):
-        """Reconstruct an image from a sinogram.
-
-        :param data: The sinogram data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :param method: Name of the reconstruction algorithm.
-        :type method: :class:`string`
-        :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`.
-        :returns: :class:`numpy.ndarray` -- The reconstruction.
-
-        Example of a SIRT reconstruction using CUDA::
-
-            proj = ASTRAProjector2D(...)
-            rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)
-
-        """
-        kwargs['returnData'] = True
-        rec_id, rec = ac.create_reconstruction(
-            method, self.proj_id, data, **kwargs)
-        data2d.delete(rec_id)
-        return rec
-

-    def __mul__(self, data):
-        return self.forwardProject(data)

-
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Source code for astra.algorithm

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-
-from . import algorithm_c as a
-
-
[docs]def create(config):
-    """Create algorithm object.
-    
-    :param config: Algorithm options.
-    :type config: :class:`dict`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return a.create(config)
-

-
[docs]def run(i, iterations=1):
-    """Run an algorithm.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :param iterations: Number of iterations to run.
-    :type iterations: :class:`int`
-    
-    """
-    return a.run(i,iterations)
-

-
[docs]def get_res_norm(i):
-    """Get residual norm of algorithm.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`float` -- The residual norm.
-    
-    """
-    
-    return a.get_res_norm(i)
-    

-
[docs]def delete(ids):
-    """Delete a matrix object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return a.delete(ids)
-

-
[docs]def clear():
-    """Clear all matrix objects."""
-    return a.clear()
-

-
[docs]def info():
-    """Print info on matrix objects in memory."""
-    return a.info()

-
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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/astra.html b/python/docSRC/_build/html/_modules/astra/astra.html deleted file mode 100644 index 53fac8e..0000000 --- a/python/docSRC/_build/html/_modules/astra/astra.html +++ /dev/null @@ -1,163 +0,0 @@ - - - - - - - - astra.astra — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.astra

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-
-from . import astra_c as a
-
-
[docs]def credits():
-    """Print credits of the ASTRA Toolbox."""
-    return a.credits()
-
-

-
[docs]def use_cuda():
-    """Test if CUDA is enabled.
-    
-    :returns: :class:`bool` -- ``True`` if CUDA is enabled.
-    """
-    return a.use_cuda()
-
-

-
[docs]def version(printToScreen=False):
-    """Check version of the ASTRA Toolbox.
-    
-    :param printToScreen: If ``True``, print version string. If ``False``, return version integer.
-    :type printToScreen: :class:`bool`
-    :returns: :class:`string` or :class:`int` -- The version string or integer.
-    
-    """
-    return a.version(printToScreen)
-

-
[docs]def set_gpu_index(idx):
-    """Set default GPU index to use.
-    
-    :param idx: GPU index
-    :type idx: :class:`int`
-    """
-    a.set_gpu_index(idx)

-
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Source code for astra.creators

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-
-import six
-import numpy as np
-import math
-from . import data2d
-from . import data3d
-from . import projector
-from . import algorithm
-
-
[docs]def astra_dict(intype):
-    """Creates a dict to use with the ASTRA Toolbox.
-    
-    :param intype: Type of the ASTRA object.
-    :type intype: :class:`string`
-    :returns: :class:`dict` -- An ASTRA dict of type ``intype``.
-    
-    """
-    if intype == 'SIRT_CUDA2':
-        intype = 'SIRT_CUDA'
-        six.print_('SIRT_CUDA2 has been deprecated. Use SIRT_CUDA instead.')
-    elif intype == 'FP_CUDA2':
-        intype = 'FP_CUDA'
-        six.print_('FP_CUDA2 has been deprecated. Use FP_CUDA instead.')
-    return {'type': intype}
-

-
[docs]def create_vol_geom(*varargin):
-    """Create a volume geometry structure.
-
-This method can be called in a number of ways:
-
-``create_vol_geom(N)``:
-    :returns: A 2D volume geometry of size :math:`N \\times N`.
-
-``create_vol_geom((M, N))``:
-    :returns: A 2D volume geometry of size :math:`M \\times N`.
-
-``create_vol_geom(M, N)``:
-    :returns: A 2D volume geometry of size :math:`M \\times N`.
-
-``create_vol_geom(M, N, minx, maxx, miny, maxy)``:
-    :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`.
-
-``create_vol_geom((M, N, Z))``:
-    :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.
-
-``create_vol_geom(M, N, Z)``:
-    :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.
-
-"""
-    vol_geom = {'option': {}}
-    # astra_create_vol_geom(row_count)
-    if len(varargin) == 1 and isinstance(varargin[0], int) == 1:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[0]
-        vol_geom['option']['WindowMinX'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0] / 2.
-    # astra_create_vol_geom([row_count col_count])
-    elif len(varargin) == 1 and len(varargin[0]) == 2:
-        vol_geom['GridRowCount'] = varargin[0][0]
-        vol_geom['GridColCount'] = varargin[0][1]
-        vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2.
-    # astra_create_vol_geom([row_count col_count slice_count])
-    elif len(varargin) == 1 and len(varargin[0]) == 3:
-        vol_geom['GridRowCount'] = varargin[0][0]
-        vol_geom['GridColCount'] = varargin[0][1]
-        vol_geom['GridSliceCount'] = varargin[0][2]
-        vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2.
-        vol_geom['option']['WindowMinZ'] = -varargin[0][2] / 2.
-        vol_geom['option']['WindowMaxZ'] = varargin[0][2] / 2.
-    # astra_create_vol_geom(row_count, col_count)
-    elif len(varargin) == 2:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[1]
-        vol_geom['option']['WindowMinX'] = -varargin[1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0] / 2.
-    # astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y)
-    elif len(varargin) == 6:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[1]
-        vol_geom['option']['WindowMinX'] = varargin[2]
-        vol_geom['option']['WindowMaxX'] = varargin[3]
-        vol_geom['option']['WindowMinY'] = varargin[4]
-        vol_geom['option']['WindowMaxY'] = varargin[5]
-    # astra_create_vol_geom(row_count, col_count, slice_count)
-    elif len(varargin) == 3:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[1]
-        vol_geom['GridSliceCount'] = varargin[2]
-    return vol_geom
-
-

-
[docs]def create_proj_geom(intype, *args):
-    """Create a projection geometry.
-
-This method can be called in a number of ways:
-
-``create_proj_geom('parallel', detector_spacing, det_count, angles)``:
-
-:param detector_spacing: Distance between two adjacent detector pixels.
-:type detector_spacing: :class:`float`
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:returns: A parallel projection geometry.
-
-
-``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``:
-
-:param det_width: Size of a detector pixel.
-:type det_width: :class:`float`
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:param source_origin: Position of the source.
-:param source_det: Position of the detector
-:returns: A fan-beam projection geometry.
-
-``create_proj_geom('fanflat_vec', det_count, V)``:
-
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param V: Vector array.
-:type V: :class:`numpy.ndarray`
-:returns: A fan-beam projection geometry.
-
-``create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)``:
-
-:param detector_spacing_*: Distance between two adjacent detector pixels.
-:type detector_spacing_*: :class:`float`
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:returns: A parallel projection geometry.
-
-``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``:
-
-:param detector_spacing_*: Distance between two adjacent detector pixels.
-:type detector_spacing_*: :class:`float`
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:param source_origin: Distance between point source and origin.
-:type source_origin: :class:`float`
-:param source_det: Distance between the detector and origin.
-:type source_det: :class:`float`
-:returns: A cone-beam projection geometry.
-
-``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``:
-
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param V: Vector array.
-:type V: :class:`numpy.ndarray`
-:returns: A cone-beam projection geometry.
-
-``create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V)``:
-
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param V: Vector array.
-:type V: :class:`numpy.ndarray`
-:returns: A parallel projection geometry.
-
-``create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id)``:
-
-:param det_width: Size of a detector pixel.
-:type det_width: :class:`float`
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:param matrix_id: ID of the sparse matrix.
-:type matrix_id: :class:`int`
-:returns: A projection geometry based on a sparse matrix.
-
-"""
-    if intype == 'parallel':
-        if len(args) < 3:
-            raise Exception(
-                'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)')
-        return {'type': 'parallel', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2]}
-    elif intype == 'fanflat':
-        if len(args) < 5:
-            raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)')
-        return {'type': 'fanflat', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'DistanceOriginSource': args[3], 'DistanceOriginDetector': args[4]}
-    elif intype == 'fanflat_vec':
-        if len(args) < 2:
-            raise Exception('not enough variables: astra_create_proj_geom(fanflat_vec, det_count, V)')
-        if not args[1].shape[1] == 6:
-            raise Exception('V should be a Nx6 matrix, with N the number of projections')
-        return {'type':'fanflat_vec', 'DetectorCount':args[0], 'Vectors':args[1]}
-    elif intype == 'parallel3d':
-        if len(args) < 5:
-            raise Exception('not enough variables: astra_create_proj_geom(parallel3d, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)')
-        return {'type':'parallel3d', 'DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2], 'DetectorColCount':args[3],'ProjectionAngles':args[4]}
-    elif intype == 'cone':
-        if len(args) < 7:
-            raise Exception('not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)')
-        return {'type':	'cone','DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2],'DetectorColCount':args[3],'ProjectionAngles':args[4],'DistanceOriginSource':	args[5],'DistanceOriginDetector':args[6]}
-    elif intype == 'cone_vec':
-        if len(args) < 3:
-            raise Exception('not enough variables: astra_create_proj_geom(cone_vec, det_row_count, det_col_count, V)')
-        if not args[2].shape[1] == 12:
-            raise Exception('V should be a Nx12 matrix, with N the number of projections')
-        return {'type': 'cone_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]}
-    elif intype == 'parallel3d_vec':
-        if len(args) < 3:
-            raise Exception('not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)')
-        if not args[2].shape[1] == 12:
-            raise Exception('V should be a Nx12 matrix, with N the number of projections')
-        return {'type': 'parallel3d_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]}    
-    elif intype == 'sparse_matrix':
-        if len(args) < 4:
-            raise Exception(
-                'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)')
-        return {'type': 'sparse_matrix', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'MatrixID': args[3]}
-    else:
-        raise Exception('Error: unknown type ' + intype) 
-
-

-
[docs]def create_backprojection(data, proj_id, useCUDA=False, returnData=True):
-    """Create a backprojection of a sinogram (2D).
-
-:param data: Sinogram data or ID.
-:type data: :class:`numpy.ndarray` or :class:`int`
-:param proj_id: ID of the projector to use.
-:type proj_id: :class:`int`
-:param useCUDA: If ``True``, use CUDA for the calculation.
-:type useCUDA: :class:`bool`
-:param returnData: If False, only return the ID of the backprojection.
-:type returnData: :class:`bool`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.
-
-"""
-    proj_geom = projector.projection_geometry(proj_id)
-    vol_geom = projector.volume_geometry(proj_id)
-    if isinstance(data, np.ndarray):
-        sino_id = data2d.create('-sino', proj_geom, data)
-    else:
-        sino_id = data
-    vol_id = data2d.create('-vol', vol_geom, 0)
-
-    algString = 'BP'
-    if useCUDA:
-        algString = algString + '_CUDA'
-
-    cfg = astra_dict(algString)
-    if not useCUDA:
-        cfg['ProjectorId'] = proj_id
-    cfg['ProjectionDataId'] = sino_id
-    cfg['ReconstructionDataId'] = vol_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data2d.delete(sino_id)
-
-    if returnData:
-        return vol_id, data2d.get(vol_id)
-    else:
-        return vol_id
-

-
[docs]def create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True):
-    """Create a backprojection of a sinogram (3D) using CUDA.
-
-:param data: Sinogram data or ID.
-:type data: :class:`numpy.ndarray` or :class:`int`
-:param proj_geom: Projection geometry.
-:type proj_geom: :class:`dict`
-:param vol_geom: Volume geometry.
-:type vol_geom: :class:`dict`
-:param returnData: If False, only return the ID of the backprojection.
-:type returnData: :class:`bool`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.
-
-"""
-    if isinstance(data, np.ndarray):
-        sino_id = data3d.create('-sino', proj_geom, data)
-    else:
-        sino_id = data
-
-    vol_id = data3d.create('-vol', vol_geom, 0)
-
-    cfg = astra_dict('BP3D_CUDA')
-    cfg['ProjectionDataId'] = sino_id
-    cfg['ReconstructionDataId'] = vol_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data3d.delete(sino_id)
-
-    if returnData:
-        return vol_id, data3d.get(vol_id)
-    else:
-        return vol_id
-
-

-
[docs]def create_sino(data, proj_id=None, proj_geom=None, vol_geom=None,
-                useCUDA=False, returnData=True, gpuIndex=None):
-    """Create a forward projection of an image (2D).
-
-    :param data: Image data or ID.
-    :type data: :class:`numpy.ndarray` or :class:`int`
-    :param proj_id: ID of the projector to use.
-    :type proj_id: :class:`int`
-    :param proj_geom: Projection geometry.
-    :type proj_geom: :class:`dict`
-    :param vol_geom: Volume geometry.
-    :type vol_geom: :class:`dict`
-    :param useCUDA: If ``True``, use CUDA for the calculation.
-    :type useCUDA: :class:`bool`
-    :param returnData: If False, only return the ID of the forward projection.
-    :type returnData: :class:`bool`
-    :param gpuIndex: Optional GPU index.
-    :type gpuIndex: :class:`int`
-    :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`)
-
-    If ``returnData=False``, returns the ID of the forward
-    projection. Otherwise, returns a tuple containing the ID of the
-    forward projection and the forward projection itself, in that
-    order.
-
-    The geometry of setup is defined by ``proj_id`` or with
-    ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then
-    ``proj_geom`` and ``vol_geom`` must be None and vice versa.
-"""
-    if proj_id is not None:
-        proj_geom = projector.projection_geometry(proj_id)
-        vol_geom = projector.volume_geometry(proj_id)
-    elif proj_geom is not None and vol_geom is not None:
-        if not useCUDA:
-            # We need more parameters to create projector.
-            raise ValueError(
-                """A ``proj_id`` is needed when CUDA is not used.""")
-    else:
-        raise Exception("""The geometry setup is not defined.
-        The geometry of setup is defined by ``proj_id`` or with
-        ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then
-        ``proj_geom`` and ``vol_geom`` must be None and vice versa.""")
-
-    if isinstance(data, np.ndarray):
-        volume_id = data2d.create('-vol', vol_geom, data)
-    else:
-        volume_id = data
-    sino_id = data2d.create('-sino', proj_geom, 0)
-    algString = 'FP'
-    if useCUDA:
-        algString = algString + '_CUDA'
-    cfg = astra_dict(algString)
-    if not useCUDA:
-        cfg['ProjectorId'] = proj_id
-    if gpuIndex is not None:
-        cfg['option'] = {'GPUindex': gpuIndex}
-    cfg['ProjectionDataId'] = sino_id
-    cfg['VolumeDataId'] = volume_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data2d.delete(volume_id)
-    if returnData:
-        return sino_id, data2d.get(sino_id)
-    else:
-        return sino_id
-
-
-

-
[docs]def create_sino3d_gpu(data, proj_geom, vol_geom, returnData=True, gpuIndex=None):
-    """Create a forward projection of an image (3D).
-
-:param data: Image data or ID.
-:type data: :class:`numpy.ndarray` or :class:`int`
-:param proj_geom: Projection geometry.
-:type proj_geom: :class:`dict`
-:param vol_geom: Volume geometry.
-:type vol_geom: :class:`dict`
-:param returnData: If False, only return the ID of the forward projection.
-:type returnData: :class:`bool`
-:param gpuIndex: Optional GPU index.
-:type gpuIndex: :class:`int`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.
-
-"""
-
-    if isinstance(data, np.ndarray):
-        volume_id = data3d.create('-vol', vol_geom, data)
-    else:
-        volume_id = data
-    sino_id = data3d.create('-sino', proj_geom, 0)
-    algString = 'FP3D_CUDA'
-    cfg = astra_dict(algString)
-    if not gpuIndex==None:
-        cfg['option']={'GPUindex':gpuIndex}
-    cfg['ProjectionDataId'] = sino_id
-    cfg['VolumeDataId'] = volume_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data3d.delete(volume_id)
-    if returnData:
-        return sino_id, data3d.get(sino_id)
-    else:
-        return sino_id
-
-

-
[docs]def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='no', mask=np.array([]), use_minc='no', minc=0, use_maxc='no', maxc=255, returnData=True, filterType=None, filterData=None):
-    """Create a reconstruction of a sinogram (2D).
-
-:param rec_type: Name of the reconstruction algorithm.
-:type rec_type: :class:`string`
-:param proj_id: ID of the projector to use.
-:type proj_id: :class:`int`
-:param sinogram: Sinogram data or ID.
-:type sinogram: :class:`numpy.ndarray` or :class:`int`
-:param iterations: Number of iterations to run.
-:type iterations: :class:`int`
-:param use_mask: Whether to use a mask.
-:type use_mask: ``'yes'`` or ``'no'``
-:param mask: Mask data or ID
-:type mask: :class:`numpy.ndarray` or :class:`int`
-:param use_minc: Whether to force a minimum value on the reconstruction pixels.
-:type use_minc: ``'yes'`` or ``'no'``
-:param minc: Minimum value to use.
-:type minc: :class:`float`
-:param use_maxc: Whether to force a maximum value on the reconstruction pixels.
-:type use_maxc: ``'yes'`` or ``'no'``
-:param maxc: Maximum value to use.
-:type maxc: :class:`float`
-:param returnData: If False, only return the ID of the reconstruction.
-:type returnData: :class:`bool`
-:param filterType: Which type of filter to use for filter-based methods.
-:type filterType: :class:`string`
-:param filterData: Optional filter data for filter-based methods.
-:type filterData: :class:`numpy.ndarray`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.
-
-"""
-    proj_geom = projector.projection_geometry(proj_id)
-    if isinstance(sinogram, np.ndarray):
-        sino_id = data2d.create('-sino', proj_geom, sinogram)
-    else:
-        sino_id = sinogram
-    vol_geom = projector.volume_geometry(proj_id)
-    recon_id = data2d.create('-vol', vol_geom, 0)
-    cfg = astra_dict(rec_type)
-    if not 'CUDA' in rec_type:
-        cfg['ProjectorId'] = proj_id
-    cfg['ProjectionDataId'] = sino_id
-    cfg['ReconstructionDataId'] = recon_id
-    cfg['options'] = {}
-    if use_mask == 'yes':
-        if isinstance(mask, np.ndarray):
-            mask_id = data2d.create('-vol', vol_geom, mask)
-        else:
-            mask_id = mask
-        cfg['options']['ReconstructionMaskId'] = mask_id
-    if not filterType == None:
-        cfg['FilterType'] = filterType
-    if not filterData == None:
-        if isinstance(filterData, np.ndarray):
-            nexpow = int(
-                pow(2, math.ceil(math.log(2 * proj_geom['DetectorCount'], 2))))
-            filtSize = nexpow / 2 + 1
-            filt_proj_geom = create_proj_geom(
-                'parallel', 1.0, filtSize, proj_geom['ProjectionAngles'])
-            filt_id = data2d.create('-sino', filt_proj_geom, filterData)
-        else:
-            filt_id = filterData
-        cfg['FilterSinogramId'] = filt_id
-    cfg['options']['UseMinConstraint'] = use_minc
-    cfg['options']['MinConstraintValue'] = minc
-    cfg['options']['UseMaxConstraint'] = use_maxc
-    cfg['options']['MaxConstraintValue'] = maxc
-    cfg['options']['ProjectionOrder'] = 'random'
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id, iterations)
-
-    algorithm.delete(alg_id)
-
-    if isinstance(sinogram, np.ndarray):
-        data2d.delete(sino_id)
-    if use_mask == 'yes' and isinstance(mask, np.ndarray):
-        data2d.delete(mask_id)
-    if not filterData == None:
-        if isinstance(filterData, np.ndarray):
-            data2d.delete(filt_id)
-    if returnData:
-        return recon_id, data2d.get(recon_id)
-    else:
-        return recon_id
-
-

-
[docs]def create_projector(proj_type, proj_geom, vol_geom):
-    """Create a 2D projector.
-
-:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...
-:type proj_type: :class:`string`
-:param proj_geom: Projection geometry.
-:type proj_geom: :class:`dict`
-:param vol_geom: Volume geometry.
-:type vol_geom: :class:`dict`
-:returns: :class:`int` -- The ID of the projector.
-
-"""
-    if proj_type == 'blob':
-        raise Exception('Blob type not yet implemented')
-    cfg = astra_dict(proj_type)
-    cfg['ProjectionGeometry'] = proj_geom
-    cfg['VolumeGeometry'] = vol_geom
-    return projector.create(cfg)

-
- -
-
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-

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- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data2d.html b/python/docSRC/_build/html/_modules/astra/data2d.html deleted file mode 100644 index d77cddd..0000000 --- a/python/docSRC/_build/html/_modules/astra/data2d.html +++ /dev/null @@ -1,225 +0,0 @@ - - - - - - - - astra.data2d — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.data2d

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-from . import data2d_c as d
-
-
[docs]def clear():
-    """Clear all 2D data objects."""
-    return d.clear()
-

-
[docs]def delete(ids):
-    """Delete a 2D object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return d.delete(ids)
-

-
[docs]def create(datatype, geometry, data=None):
-    """Create a 2D object.
-        
-    :param datatype: Data object type, '-vol' or '-sino'.
-    :type datatype: :class:`string`
-    :param geometry: Volume or projection geometry.
-    :type geometry: :class:`dict`
-    :param data: Data to fill the constructed object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return d.create(datatype,geometry,data)
-

-
[docs]def store(i, data):
-    """Fill existing 2D object with data.
-    
-    :param i: ID of object to fill.
-    :type i: :class:`int`
-    :param data: Data to fill the object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    
-    """
-    return d.store(i, data)
-    

-
[docs]def get_geometry(i):
-    """Get the geometry of a 2D object.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`dict` -- The geometry of object with ID ``i``.
-    
-    """
-    return d.get_geometry(i)
-

-
[docs]def change_geometry(i, geom):
-    """Change the geometry of a 2D object.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :param geom: new geometry.
-    :type geom: :class:`dict`
-    
-    """
-    return d.change_geometry(i, geom)
-    

-
[docs]def get(i):
-    """Get a 2D object.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get(i)
-

-
[docs]def get_shared(i):
-    """Get a 2D object with memory shared between the ASTRA toolbox and numpy array.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get_shared(i)
-
-

-
[docs]def get_single(i):
-    """Get a 2D object in single precision.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get_single(i)
-

-
[docs]def info():
-    """Print info on 2D objects in memory."""
-    return d.info()

-
- -
-
-
-
-
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-
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-
-
-

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- -
- -
- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data3d.html b/python/docSRC/_build/html/_modules/astra/data3d.html deleted file mode 100644 index 674d6d1..0000000 --- a/python/docSRC/_build/html/_modules/astra/data3d.html +++ /dev/null @@ -1,213 +0,0 @@ - - - - - - - - astra.data3d — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
-

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Source code for astra.data3d

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-from . import data3d_c as d
-
-
[docs]def create(datatype,geometry,data=None):
-    """Create a 3D object.
-        
-    :param datatype: Data object type, '-vol' or '-sino'.
-    :type datatype: :class:`string`
-    :param geometry: Volume or projection geometry.
-    :type geometry: :class:`dict`
-    :param data: Data to fill the constructed object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return d.create(datatype,geometry,data)
-

-
[docs]def get(i):
-    """Get a 3D object.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get(i)
-

-
[docs]def get_shared(i):
-    """Get a 3D object with memory shared between the ASTRA toolbox and numpy array.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get_shared(i)
-

-
[docs]def get_single(i):
-    """Get a 3D object in single precision.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return g.get_single(i)
-

-
[docs]def store(i,data):
-    """Fill existing 3D object with data.
-    
-    :param i: ID of object to fill.
-    :type i: :class:`int`
-    :param data: Data to fill the object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    
-    """
-    return d.store(i,data)
-

-
[docs]def dimensions(i):
-    """Get dimensions of a 3D object.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`tuple` -- dimensions of object with ID ``i``.
-    
-    """
-    return d.dimensions(i)
-

-
[docs]def delete(ids):
-    """Delete a 2D object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return d.delete(ids)
-

-
[docs]def clear():
-    """Clear all 3D data objects."""
-    return d.clear()
-

-
[docs]def info():
-    """Print info on 3D objects in memory."""
-    return d.info()

-
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-
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-
-
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-

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- -
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- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/functions.html b/python/docSRC/_build/html/_modules/astra/functions.html deleted file mode 100644 index 336431f..0000000 --- a/python/docSRC/_build/html/_modules/astra/functions.html +++ /dev/null @@ -1,375 +0,0 @@ - - - - - - - - astra.functions — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
-

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Source code for astra.functions

-#-----------------------------------------------------------------------
-# Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-# Author: Daniel M. Pelt
-# Contact: D.M.Pelt@cwi.nl
-# Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-# This file is part of the Python interface to the
-# All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-# The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-# The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-"""Additional functions for PyAstraToolbox.
-
-.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl>
-
-
-"""
-
-from . import creators as ac
-import numpy as np
-from six.moves import range
-
-from . import data2d
-from . import data3d
-from . import projector
-from . import algorithm
-
-
-
-
[docs]def clear():
-    """Clears all used memory of the ASTRA Toolbox.
-
-    .. note::
-        This is irreversible.
-
-    """
-    data2d.clear()
-    data3d.clear()
-    projector.clear()
-    algorithm.clear()
-
-

-
[docs]def data_op(op, data, scalar, gpu_core, mask=None):
-    """Perform data operation on data.
-
-    :param op: Operation to perform.
-    :param data: Data to perform operation on.
-    :param scalar: Scalar argument to data operation.
-    :param gpu_core: GPU core to perform operation on.
-    :param mask: Optional mask.
-
-    """
-
-    cfg = ac.astra_dict('DataOperation_CUDA')
-    cfg['Operation'] = op
-    cfg['Scalar'] = scalar
-    cfg['DataId'] = data
-    if not mask == None:
-        cfg['MaskId'] = mask
-    cfg['option']['GPUindex'] = gpu_core
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-

-
[docs]def add_noise_to_sino(sinogram_in, I0, seed=None):
-    """Adds Poisson noise to a sinogram.
-
-    :param sinogram_in: Sinogram to add noise to.
-    :type sinogram_in: :class:`numpy.ndarray`
-    :param I0: Background intensity. Lower values lead to higher noise.
-    :type I0: :class:`float`
-    :returns:  :class:`numpy.ndarray` -- the sinogram with added noise.
-
-    """
-
-    if not seed==None:
-        curstate = np.random.get_state()
-        np.random.seed(seed)
-
-    if isinstance(sinogram_in, np.ndarray):
-        sinogramRaw = sinogram_in
-    else:
-        sinogramRaw = data2d.get(sinogram_in)
-    max_sinogramRaw = sinogramRaw.max()
-    sinogramRawScaled = sinogramRaw / max_sinogramRaw
-    # to detector count
-    sinogramCT = I0 * np.exp(-sinogramRawScaled)
-    # add poison noise
-    sinogramCT_C = np.zeros_like(sinogramCT)
-    for i in range(sinogramCT_C.shape[0]):
-        for j in range(sinogramCT_C.shape[1]):
-            sinogramCT_C[i, j] = np.random.poisson(sinogramCT[i, j])
-    # to density
-    sinogramCT_D = sinogramCT_C / I0
-    sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D)
-
-    if not isinstance(sinogram_in, np.ndarray):
-        at.data2d.store(sinogram_in, sinogram_out)
-
-    if not seed==None:
-        np.random.set_state(curstate)
-
-    return sinogram_out
-

-
[docs]def move_vol_geom(geom, pos, is_relative=False):
-    """Moves center of volume geometry to new position.
-
-    :param geom: Input volume geometry
-    :type geom: :class:`dict`
-    :param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])
-    :type pos: :class:`tuple`
-    :param is_relative: Whether new position is relative to the old position
-    :type is_relative: :class:`bool`
-    :returns: :class:`dict` -- Volume geometry with the new center
-    """
-
-    ret_geom = geom.copy()
-    ret_geom['option'] = geom['option'].copy()
-
-    if not is_relative:
-        ret_geom['option']['WindowMinX'] = -geom['GridColCount']/2.
-        ret_geom['option']['WindowMaxX'] = geom['GridColCount']/2.
-        ret_geom['option']['WindowMinY'] = -geom['GridRowCount']/2.
-        ret_geom['option']['WindowMaxY'] = geom['GridRowCount']/2.
-        if len(pos)>2:
-            ret_geom['option']['WindowMinZ'] = -geom['GridSliceCount']/2.
-            ret_geom['option']['WindowMaxZ'] = geom['GridSliceCount']/2.
-    ret_geom['option']['WindowMinX'] += pos[0]
-    ret_geom['option']['WindowMaxX'] += pos[0]
-    ret_geom['option']['WindowMinY'] += pos[1]
-    ret_geom['option']['WindowMaxY'] += pos[1]
-    if len(pos)>2:
-        ret_geom['option']['WindowMinZ'] += pos[2]
-        ret_geom['option']['WindowMaxZ'] += pos[2]
-    return ret_geom
-
-

-
[docs]def geom_size(geom, dim=None):
-    """Returns the size of a volume or sinogram, based on the projection or volume geometry.
-
-    :param geom: Geometry to calculate size from
-    :type geometry: :class:`dict`
-    :param dim: Optional axis index to return
-    :type dim: :class:`int`
-    """
-
-    if 'GridSliceCount' in geom:
-        # 3D Volume geometry?
-        s = (geom['GridSliceCount'], geom[
-             'GridRowCount'], geom['GridColCount'])
-    elif 'GridColCount' in geom:
-        # 2D Volume geometry?
-        s = (geom['GridRowCount'], geom['GridColCount'])
-    elif geom['type'] == 'parallel' or geom['type'] == 'fanflat':
-        s = (len(geom['ProjectionAngles']), geom['DetectorCount'])
-    elif geom['type'] == 'parallel3d' or geom['type'] == 'cone':
-        s = (geom['DetectorRowCount'], len(
-            geom['ProjectionAngles']), geom['DetectorColCount'])
-    elif geom['type'] == 'fanflat_vec':
-        s = (geom['Vectors'].shape[0], geom['DetectorCount'])
-    elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec':
-        s = (geom['DetectorRowCount'], geom[
-             'Vectors'].shape[0], geom['DetectorColCount'])
-
-    if dim != None:
-        s = s[dim]
-
-    return s
-
-

-
[docs]def geom_2vec(proj_geom):
-    """Returns a vector-based projection geometry from a basic projection geometry.
-
-    :param proj_geom: Projection geometry to convert
-    :type proj_geom: :class:`dict`
-    """
-    if proj_geom['type'] == 'fanflat':
-        angles = proj_geom['ProjectionAngles']
-        vectors = np.zeros((len(angles), 6))
-        for i in range(len(angles)):
-
-            # source
-            vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource']
-            vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource']
-
-            # center of detector
-            vectors[i, 2] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector']
-            vectors[i, 3] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector']
-
-            # vector from detector pixel 0 to 1
-            vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth']
-            vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth']
-        proj_geom_out = ac.create_proj_geom(
-        'fanflat_vec', proj_geom['DetectorCount'], vectors)
-
-    elif proj_geom['type'] == 'cone':
-        angles = proj_geom['ProjectionAngles']
-        vectors = np.zeros((len(angles), 12))
-        for i in range(len(angles)):
-            # source
-            vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource']
-            vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource']
-            vectors[i, 2] = 0
-
-            # center of detector
-            vectors[i, 3] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector']
-            vectors[i, 4] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector']
-            vectors[i, 5] = 0
-
-            # vector from detector pixel (0,0) to (0,1)
-            vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 8] = 0
-
-            # vector from detector pixel (0,0) to (1,0)
-            vectors[i, 9] = 0
-            vectors[i, 10] = 0
-            vectors[i, 11] = proj_geom['DetectorSpacingY']
-
-        proj_geom_out = ac.create_proj_geom(
-        'cone_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors)
-
-    # PARALLEL
-    elif proj_geom['type'] == 'parallel3d':
-        angles = proj_geom['ProjectionAngles']
-        vectors = np.zeros((len(angles), 12))
-        for i in range(len(angles)):
-
-            # ray direction
-            vectors[i, 0] = np.sin(angles[i])
-            vectors[i, 1] = -np.cos(angles[i])
-            vectors[i, 2] = 0
-
-            # center of detector
-            vectors[i, 3] = 0
-            vectors[i, 4] = 0
-            vectors[i, 5] = 0
-
-            # vector from detector pixel (0,0) to (0,1)
-            vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 8] = 0
-
-            # vector from detector pixel (0,0) to (1,0)
-            vectors[i, 9] = 0
-            vectors[i, 10] = 0
-            vectors[i, 11] = proj_geom['DetectorSpacingY']
-
-        proj_geom_out = ac.create_proj_geom(
-        'parallel3d_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors)
-
-    else:
-        raise ValueError(
-        'No suitable vector geometry found for type: ' + proj_geom['type'])
-    return proj_geom_out

-
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Source code for astra.matlab

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-"""This module implements a MATLAB-like interface to the ASTRA Toolbox.
-
-Note that all functions are called with a :class:`string` as the first
-argument, specifying the operation to perform. This un-pythonic way
-is used to make transitioning from MATLAB code to Python code easier, as
-the MATLAB interface uses the same type of method calling.
-
-After an initial ``import astra``, these functions can be accessed in the
-``astra.m`` module.
-
-"""
-
-from . import astra_c
-from . import data2d_c
-from . import data3d_c
-from . import projector_c
-from . import algorithm_c
-from . import matrix_c
-import numpy as np
-
-
-
[docs]def astra(command, *args):
-    """MATLAB-like interface to the :mod:`astra.astra` module
-    
-    For example:
-    
-    ``astra.m.astra('use_cuda')`` -- Check if CUDA is enabled.
-    
-    """
-    return getattr(astra_c, command)(*args)
-
-

-
[docs]def data2d(command, *args):
-    """MATLAB-like interface to the :mod:`astra.data2d` module
-    
-    For example:
-    
-    ``astra.m.data2d('create',type,geometry,data)`` -- Create a 2D object.
-    
-    """
-    return getattr(data2d_c, command)(*args)
-
-

-
[docs]def data3d(command, *args):
-    """MATLAB-like interface to the :mod:`astra.data3d` module
-    
-    For example:
-    
-    ``astra.m.data3d('get',i)`` -- Get 3D object data.
-    
-    """
-    return getattr(data3d_c, command)(*args)
-
-

-
[docs]def projector(command, *args):
-    """MATLAB-like interface to the :mod:`astra.projector` module
-    
-    For example:
-    
-    ``astra.m.projector('volume_geometry',i)`` -- Get volume geometry.
-    
-    """
-    return getattr(projector_c, command)(*args)
-
-

-
[docs]def matrix(command, *args):
-    """MATLAB-like interface to the :mod:`astra.matrix` module
-    
-    For example:
-    
-    ``astra.m.matrix('delete',i)`` -- Delete a matrix.
-    
-    """
-    return getattr(matrix_c, command)(*args)
-
-

-
[docs]def algorithm(command, *args):
-    """MATLAB-like interface to the :mod:`astra.algorithm` module
-    
-    For example:
-    
-    ``astra.m.algorithm('run',i,1000)`` -- Run an algorithm with 1000 iterations.
-    
-    """
-    if command == 'iterate':
-        command = 'run'
-    return getattr(algorithm_c, command)(*args)

-
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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/matrix.html b/python/docSRC/_build/html/_modules/astra/matrix.html deleted file mode 100644 index 5f75455..0000000 --- a/python/docSRC/_build/html/_modules/astra/matrix.html +++ /dev/null @@ -1,191 +0,0 @@ - - - - - - - - astra.matrix — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.matrix

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-from . import matrix_c as m
-
-
[docs]def delete(ids):
-    """Delete a matrix object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return m.delete(ids)
-

-
[docs]def clear():
-    """Clear all matrix objects."""
-    return m.clear()
-

-
[docs]def create(data):
-    """Create matrix object with data.
-    
-    :param data: Data to fill the created object with.
-    :type data: :class:`scipy.sparse.csr_matrix`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return m.create(data)
-
-    

-
[docs]def store(i,data):
-    """Fill existing matrix object with data.
-    
-    :param i: ID of object to fill.
-    :type i: :class:`int`
-    :param data: Data to fill the object with.
-    :type data: :class:`scipy.sparse.csr_matrix`
-    
-    """
-    return m.store(i,data)
-

-
[docs]def get_size(i):
-    """Get matrix dimensions.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`tuple` -- matrix dimensions.
-    """
-    return m.get_size(i)
-    

-
[docs]def get(i):
-    """Get a matrix object.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`scipy.sparse.csr_matrix` --  The object data.
-    
-    """
-    return m.get(i)
-

-
[docs]def info():
-    """Print info on matrix objects in memory."""
-    return m.info()
-    
-        

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Source code for astra.projector

-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
-#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
-#
-#
-#This file is part of the Python interface to the
-#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
-#
-#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
-#it under the terms of the GNU General Public License as published by
-#the Free Software Foundation, either version 3 of the License, or
-#(at your option) any later version.
-#
-#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-#GNU General Public License for more details.
-#
-#You should have received a copy of the GNU General Public License
-#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
-#
-#-----------------------------------------------------------------------
-from . import projector_c as p
-
-
[docs]def create(config):
-    """Create projector object.
-    
-    :param config: Projector options.
-    :type config: :class:`dict`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return p.create(config)
-
-

-
[docs]def delete(ids):
-    """Delete a projector object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return p.delete(ids)
-
-

-
[docs]def clear():
-    """Clear all projector objects."""
-    return p.clear()
-
-

-
[docs]def info():
-    """Print info on projector objects in memory."""
-    return p.info()
-

-
[docs]def projection_geometry(i):
-    """Get projection geometry of a projector.
-    
-    :param i: ID of projector.
-    :type i: :class:`int`
-    :returns: :class:`dict` -- projection geometry
-    
-    """
-    return p.projection_geometry(i)
-
-

-
[docs]def volume_geometry(i):
-    """Get volume geometry of a projector.
-    
-    :param i: ID of projector.
-    :type i: :class:`int`
-    :returns: :class:`dict` -- volume geometry
-    
-    """
-    return p.volume_geometry(i)
-
-

-
[docs]def weights_single_ray(i, projection_index, detector_index):
-    return p.weights_single_ray(i, projection_index, detector_index)
-
-

-
[docs]def weights_projection(i, projection_index):
-    return p.weights_projection(i, projection_index)
-
-

-
[docs]def splat(i, row, col):
-    return p.splat(i, row, col)
-
-

-
[docs]def matrix(i):
-    """Get sparse matrix of a projector.
-    
-    :param i: ID of projector.
-    :type i: :class:`int`
-    :returns: :class:`int` -- ID of sparse matrix.
-    
-    """
-    return p.matrix(i)

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- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_sources/ASTRAProjector.txt b/python/docSRC/_build/html/_sources/ASTRAProjector.txt deleted file mode 100644 index 1c267e3..0000000 --- a/python/docSRC/_build/html/_sources/ASTRAProjector.txt +++ /dev/null @@ -1,8 +0,0 @@ -Helper class: the :mod:`ASTRAProjector` module -============================================== - -.. automodule:: astra.ASTRAProjector - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/algorithm.txt b/python/docSRC/_build/html/_sources/algorithm.txt deleted file mode 100644 index 83752bd..0000000 --- a/python/docSRC/_build/html/_sources/algorithm.txt +++ /dev/null @@ -1,8 +0,0 @@ -Algorithms: the :mod:`algorithm` module -======================================= - -.. automodule:: astra.algorithm - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/astra.txt b/python/docSRC/_build/html/_sources/astra.txt deleted file mode 100644 index 5d5fdf0..0000000 --- a/python/docSRC/_build/html/_sources/astra.txt +++ /dev/null @@ -1,8 +0,0 @@ -Additional ASTRA methods: the :mod:`astra` module -======================================================== - -.. automodule:: astra.astra - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/creators.txt b/python/docSRC/_build/html/_sources/creators.txt deleted file mode 100644 index d6249c3..0000000 --- a/python/docSRC/_build/html/_sources/creators.txt +++ /dev/null @@ -1,8 +0,0 @@ -Creation of objects: the :mod:`creators` module -=============================================== - -.. automodule:: astra.creators - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/data2d.txt b/python/docSRC/_build/html/_sources/data2d.txt deleted file mode 100644 index 342cbec..0000000 --- a/python/docSRC/_build/html/_sources/data2d.txt +++ /dev/null @@ -1,8 +0,0 @@ -2D data objects: the :mod:`data2d` module -========================================= - -.. automodule:: astra.data2d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/data3d.txt b/python/docSRC/_build/html/_sources/data3d.txt deleted file mode 100644 index 5b7de23..0000000 --- a/python/docSRC/_build/html/_sources/data3d.txt +++ /dev/null @@ -1,8 +0,0 @@ -3D data objects: the :mod:`data3d` module -========================================= - -.. automodule:: astra.data3d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/functions.txt b/python/docSRC/_build/html/_sources/functions.txt deleted file mode 100644 index 749eb27..0000000 --- a/python/docSRC/_build/html/_sources/functions.txt +++ /dev/null @@ -1,8 +0,0 @@ -Additional functions: the :mod:`functions` module -================================================= - -.. automodule:: astra.functions - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/index.txt b/python/docSRC/_build/html/_sources/index.txt deleted file mode 100644 index 8d17a4a..0000000 --- a/python/docSRC/_build/html/_sources/index.txt +++ /dev/null @@ -1,34 +0,0 @@ -.. .. documentation master file, created by - sphinx-quickstart on Wed Mar 13 16:36:32 2013. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to PyASTRAToolbox's documentation! -========================================== - -Contents: - -.. toctree:: - :maxdepth: 4 - - data2d - data3d - projector - algorithm - matrix - creators - functions - ASTRAProjector - matlab - astra -.. astra -.. builder - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/python/docSRC/_build/html/_sources/matlab.txt b/python/docSRC/_build/html/_sources/matlab.txt deleted file mode 100644 index fb7033e..0000000 --- a/python/docSRC/_build/html/_sources/matlab.txt +++ /dev/null @@ -1,8 +0,0 @@ -MATLAB compatibility interface: the :mod:`matlab` module -======================================================== - -.. automodule:: astra.matlab - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/matrix.txt b/python/docSRC/_build/html/_sources/matrix.txt deleted file mode 100644 index 6f11d8a..0000000 --- a/python/docSRC/_build/html/_sources/matrix.txt +++ /dev/null @@ -1,8 +0,0 @@ -Sparse matrices: the :mod:`matrix` module -========================================= - -.. automodule:: astra.matrix - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/projector.txt b/python/docSRC/_build/html/_sources/projector.txt deleted file mode 100644 index b0854e8..0000000 --- a/python/docSRC/_build/html/_sources/projector.txt +++ /dev/null @@ -1,8 +0,0 @@ -Projector object: the :mod:`projector` module -============================================= - -.. automodule:: astra.projector - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_static/ajax-loader.gif b/python/docSRC/_build/html/_static/ajax-loader.gif deleted file mode 100644 index 61faf8c..0000000 Binary files a/python/docSRC/_build/html/_static/ajax-loader.gif and /dev/null differ diff --git a/python/docSRC/_build/html/_static/basic.css b/python/docSRC/_build/html/_static/basic.css deleted file mode 100644 index 967e36c..0000000 --- a/python/docSRC/_build/html/_static/basic.css +++ /dev/null @@ -1,537 +0,0 @@ -/* - * basic.css - 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'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' - }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } -} - - - -/** - * Simple result scoring code. - */ -var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [filename, title, anchor, descr, score] - // and returns the new score. - /* - score: function(result) { - return result[4]; - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: {0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5}, // used to be unimportantResults - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - // query found in terms - term: 5 -}; - - -/** - * Search Module - */ -var Search = { - - _index : null, - _queued_query : null, - _pulse_status : -1, - - init : function() { - var params = $.getQueryParameters(); - if (params.q) { - var query = params.q[0]; - $('input[name="q"]')[0].value = query; - this.performSearch(query); - } - }, - - loadIndex : function(url) { - $.ajax({type: "GET", url: url, data: null, - dataType: "script", cache: true, - complete: function(jqxhr, textstatus) { - if (textstatus != "success") { - document.getElementById("searchindexloader").src = url; - } - }}); - }, - - setIndex : function(index) { - var q; - this._index = index; - if ((q = this._queued_query) !== null) { - this._queued_query = null; - Search.query(q); - } - }, - - hasIndex : function() { - return this._index !== null; - }, - - deferQuery : function(query) { - this._queued_query = query; - }, - - stopPulse : function() { - this._pulse_status = 0; - }, - - startPulse : function() { - if (this._pulse_status >= 0) - return; - function pulse() { - var i; - Search._pulse_status = (Search._pulse_status + 1) % 4; - var dotString = ''; - for (i = 0; i < Search._pulse_status; i++) - dotString += '.'; - Search.dots.text(dotString); - if (Search._pulse_status > -1) - window.setTimeout(pulse, 500); - } - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch : function(query) { - // create the required interface elements - this.out = $('#search-results'); - this.title = $('

' + _('Searching') + '

').appendTo(this.out); - this.dots = $('').appendTo(this.title); - this.status = $('

').appendTo(this.out); - this.output = $('
'); - } - // Prettify the comment rating. - comment.pretty_rating = comment.rating + ' point' + - (comment.rating == 1 ? '' : 's'); - // Make a class (for displaying not yet moderated comments differently) - comment.css_class = comment.displayed ? '' : ' moderate'; - // Create a div for this comment. - var context = $.extend({}, opts, comment); - var div = $(renderTemplate(commentTemplate, context)); - - // If the user has voted on this comment, highlight the correct arrow. - if (comment.vote) { - var direction = (comment.vote == 1) ? 'u' : 'd'; - div.find('#' + direction + 'v' + comment.id).hide(); - div.find('#' + direction + 'u' + comment.id).show(); - } - - if (opts.moderator || comment.text != '[deleted]') { - div.find('a.reply').show(); - if (comment.proposal_diff) - div.find('#sp' + comment.id).show(); - if (opts.moderator && !comment.displayed) - div.find('#cm' + comment.id).show(); - if (opts.moderator || (opts.username == comment.username)) - div.find('#dc' + comment.id).show(); - } - return div; - } - - /** - * A simple template renderer. Placeholders such as <%id%> are replaced - * by context['id'] with items being escaped. Placeholders such as <#id#> - * are not escaped. - */ - function renderTemplate(template, context) { - var esc = $(document.createElement('div')); - - function handle(ph, escape) { - var cur = context; - $.each(ph.split('.'), function() { - cur = cur[this]; - }); - return escape ? esc.text(cur || "").html() : cur; - } - - return template.replace(/<([%#])([\w\.]*)\1>/g, function() { - return handle(arguments[2], arguments[1] == '%' ? true : false); - }); - } - - /** Flash an error message briefly. */ - function showError(message) { - $(document.createElement('div')).attr({'class': 'popup-error'}) - .append($(document.createElement('div')) - .attr({'class': 'error-message'}).text(message)) - .appendTo('body') - .fadeIn("slow") - .delay(2000) - .fadeOut("slow"); - } - - /** Add a link the user uses to open the comments popup. */ - $.fn.comment = function() { - return this.each(function() { - var id = $(this).attr('id').substring(1); - var count = COMMENT_METADATA[id]; - var title = count + ' comment' + (count == 1 ? '' : 's'); - var image = count > 0 ? opts.commentBrightImage : opts.commentImage; - var addcls = count == 0 ? ' nocomment' : ''; - $(this) - .append( - $(document.createElement('a')).attr({ - href: '#', - 'class': 'sphinx-comment-open' + addcls, - id: 'ao' + id - }) - .append($(document.createElement('img')).attr({ - src: image, - alt: 'comment', - title: title - })) - .click(function(event) { - event.preventDefault(); - show($(this).attr('id').substring(2)); - }) - ) - .append( - $(document.createElement('a')).attr({ - href: '#', - 'class': 'sphinx-comment-close hidden', - id: 'ah' + id - }) - .append($(document.createElement('img')).attr({ - src: opts.closeCommentImage, - alt: 'close', - title: 'close' - })) - .click(function(event) { - event.preventDefault(); - hide($(this).attr('id').substring(2)); - }) - ); - }); - }; - - var opts = { - processVoteURL: '/_process_vote', - addCommentURL: '/_add_comment', - getCommentsURL: '/_get_comments', - acceptCommentURL: '/_accept_comment', - deleteCommentURL: '/_delete_comment', - commentImage: '/static/_static/comment.png', - closeCommentImage: '/static/_static/comment-close.png', - loadingImage: '/static/_static/ajax-loader.gif', - commentBrightImage: '/static/_static/comment-bright.png', - upArrow: '/static/_static/up.png', - downArrow: '/static/_static/down.png', - upArrowPressed: '/static/_static/up-pressed.png', - downArrowPressed: '/static/_static/down-pressed.png', - voting: false, - moderator: false - }; - - if (typeof COMMENT_OPTIONS != "undefined") { - opts = jQuery.extend(opts, COMMENT_OPTIONS); - } - - var popupTemplate = '\ -
\ -

\ - Sort by:\ - best rated\ - newest\ - oldest\ -

\ -
Comments
\ -
\ - loading comments...
\ -
    \ -
    \ -

    Add a comment\ - (markup):

    \ -
    \ - reStructured text markup: *emph*, **strong**, \ - ``code``, \ - code blocks: :: and an indented block after blank line
    \ -
    \ - \ -

    \ - \ - Propose a change ▹\ - \ - \ - Propose a change ▿\ - \ -

    \ - \ - \ - \ - \ - \ -
    \ -
    '; - - var commentTemplate = '\ -
    \ -
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    \ - \ - \ - \ - \ - \ - \ -
    \ -
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    \ - <%username%>\ - <%pretty_rating%>\ - <%time.delta%>\ -

    \ -
    <#text#>
    \ -

    \ - \ - reply ▿\ - proposal ▹\ - proposal ▿\ - \ - \ -

    \ - 
    \
-<#proposal_diff#>\
-
    \ -
      \ -
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    • \ -
      \ -
      \ - \ - \ - \ - \ - \ - \ -
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      • '; - - $(document).ready(function() { - init(); - }); -})(jQuery); - -$(document).ready(function() { - // add comment anchors for all paragraphs that are commentable - $('.sphinx-has-comment').comment(); - - // highlight search words in search results - $("div.context").each(function() { - var params = $.getQueryParameters(); - var terms = (params.q) ? params.q[0].split(/\s+/) : []; - var result = $(this); - $.each(terms, function() { - result.highlightText(this.toLowerCase(), 'highlighted'); - }); - }); - - // directly open comment window if requested - var anchor = document.location.hash; - if (anchor.substring(0, 9) == '#comment-') { - $('#ao' + anchor.substring(9)).click(); - document.location.hash = '#s' + anchor.substring(9); - } -}); diff --git a/python/docSRC/_build/html/algorithm.html b/python/docSRC/_build/html/algorithm.html deleted file mode 100644 index bf4b90f..0000000 --- a/python/docSRC/_build/html/algorithm.html +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - - - Algorithms: the algorithm module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      Algorithms: the algorithm module

      -
      -
      -astra.algorithm.clear()[source]
      -

      Clear all matrix objects.

      -
      - -
      -
      -astra.algorithm.create(config)[source]
      -

      Create algorithm object.

      -
      --- - - - - - -
      Parameters:config (dict) – Algorithm options.
      Returns:int – the ID of the constructed object.
      - - -
      -
      -astra.algorithm.delete(ids)[source]
      -

      Delete a matrix object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.algorithm.get_res_norm(i)[source]
      -

      Get residual norm of algorithm.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:float – The residual norm.
      -
      - -
      -
      -astra.algorithm.info()[source]
      -

      Print info on matrix objects in memory.

      -
      - -
      -
      -astra.algorithm.run(i, iterations=1)[source]
      -

      Run an algorithm.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object.
        • -
      • iterations (int) – Number of iterations to run.
        • -
      -
      -
      - - - - - - - -
      -
      -

      Previous topic

      -

      Projector object: the projector module

      -

      Next topic

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      Sparse matrices: the matrix module

      -

      This Page

      - - - -
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      -

      Navigation

      - -
      - -
      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/astra.html b/python/docSRC/_build/html/astra.html deleted file mode 100644 index 42d68b8..0000000 --- a/python/docSRC/_build/html/astra.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - - - - - Additional ASTRA methods: the astra module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      Additional ASTRA methods: the astra module

      -
      -
      -astra.astra.credits()[source]
      -

      Print credits of the ASTRA Toolbox.

      -
      - -
      -
      -astra.astra.set_gpu_index(idx)[source]
      -

      Set default GPU index to use.

      - --- - - - -
      Parameters:idx (int) – GPU index
      -
      - -
      -
      -astra.astra.use_cuda()[source]
      -

      Test if CUDA is enabled.

      - --- - - - -
      Returns:bool – True if CUDA is enabled.
      -
      - -
      -
      -astra.astra.version(printToScreen=False)[source]
      -

      Check version of the ASTRA Toolbox.

      - --- - - - - - -
      Parameters:printToScreen (bool) – If True, print version string. If False, return version integer.
      Returns:string or int – The version string or integer.
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      MATLAB compatibility interface: the matlab module

      -

      This Page

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      Navigation

      - -
      - -
      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/creators.html b/python/docSRC/_build/html/creators.html deleted file mode 100644 index 2f29232..0000000 --- a/python/docSRC/_build/html/creators.html +++ /dev/null @@ -1,520 +0,0 @@ - - - - - - - - Creation of objects: the creators module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      Creation of objects: the creators module

      -
      -
      -astra.creators.astra_dict(intype)[source]
      -

      Creates a dict to use with the ASTRA Toolbox.

      - --- - - - - - -
      Parameters:intype (string) – Type of the ASTRA object.
      Returns:dict – An ASTRA dict of type intype.
      -
      - -
      -
      -astra.creators.create_backprojection(data, proj_id, useCUDA=False, returnData=True)[source]
      -

      Create a backprojection of a sinogram (2D).

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Sinogram data or ID.
        • -
      • proj_id (int) – ID of the projector to use.
        • -
      • useCUDA (bool) – If True, use CUDA for the calculation.
        • -
      • returnData (bool) – If False, only return the ID of the backprojection.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True)[source]
      -

      Create a backprojection of a sinogram (3D) using CUDA.

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Sinogram data or ID.
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      • returnData (bool) – If False, only return the ID of the backprojection.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_proj_geom(intype, *args)[source]
      -

      Create a projection geometry.

      -

      This method can be called in a number of ways:

      -

      create_proj_geom('parallel', detector_spacing, det_count, angles):

      - --- - - - - - -
      Parameters:
        -
      • detector_spacing (float) – Distance between two adjacent detector pixels.
        • -
      • det_count (int) – Number of detector pixels.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      -
      Returns:

      A parallel projection geometry.

      -
      -

      create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det):

      - --- - - - - - -
      Parameters:
        -
      • det_width (float) – Size of a detector pixel.
        • -
      • det_count (int) – Number of detector pixels.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      • source_origin – Position of the source.
        • -
      • source_det – Position of the detector
        • -
      -
      Returns:

      A fan-beam projection geometry.

      -
      -

      create_proj_geom('fanflat_vec', det_count, V):

      - --- - - - - - -
      Parameters:
        -
      • det_count (int) – Number of detector pixels.
        • -
      • V (numpy.ndarray) – Vector array.
        • -
      -
      Returns:

      A fan-beam projection geometry.

      -
      -

      create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles):

      - --- - - - - - -
      Parameters:
        -
      • detector_spacing_* (float) – Distance between two adjacent detector pixels.
        • -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      -
      Returns:

      A parallel projection geometry.

      -
      -

      create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det):

      - --- - - - - - -
      Parameters:
        -
      • detector_spacing_* (float) – Distance between two adjacent detector pixels.
        • -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      • source_origin (float) – Distance between point source and origin.
        • -
      • source_det (float) – Distance between the detector and origin.
        • -
      -
      Returns:

      A cone-beam projection geometry.

      -
      -

      create_proj_geom('cone_vec', det_row_count, det_col_count, V):

      - --- - - - - - -
      Parameters:
        -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • V (numpy.ndarray) – Vector array.
        • -
      -
      Returns:

      A cone-beam projection geometry.

      -
      -

      create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V):

      - --- - - - - - -
      Parameters:
        -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • V (numpy.ndarray) – Vector array.
        • -
      -
      Returns:

      A parallel projection geometry.

      -
      -

      create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id):

      - --- - - - - - -
      Parameters:
        -
      • det_width (float) – Size of a detector pixel.
        • -
      • det_count (int) – Number of detector pixels.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      • matrix_id (int) – ID of the sparse matrix.
        • -
      -
      Returns:

      A projection geometry based on a sparse matrix.

      -
      -
      - -
      -
      -astra.creators.create_projector(proj_type, proj_geom, vol_geom)[source]
      -

      Create a 2D projector.

      - --- - - - - - -
      Parameters:
        -
      • proj_type (string) – Projector type, such as 'line', 'linear', ...
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      -
      Returns:

      int – The ID of the projector.

      -
      -
      - -
      -
      -astra.creators.create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='no', mask=array([], dtype=float64), use_minc='no', minc=0, use_maxc='no', maxc=255, returnData=True, filterType=None, filterData=None)[source]
      -

      Create a reconstruction of a sinogram (2D).

      - --- - - - - - -
      Parameters:
        -
      • rec_type (string) – Name of the reconstruction algorithm.
        • -
      • proj_id (int) – ID of the projector to use.
        • -
      • sinogram (numpy.ndarray or int) – Sinogram data or ID.
        • -
      • iterations (int) – Number of iterations to run.
        • -
      • use_mask ('yes' or 'no') – Whether to use a mask.
        • -
      • mask (numpy.ndarray or int) – Mask data or ID
        • -
      • use_minc ('yes' or 'no') – Whether to force a minimum value on the reconstruction pixels.
        • -
      • minc (float) – Minimum value to use.
        • -
      • use_maxc ('yes' or 'no') – Whether to force a maximum value on the reconstruction pixels.
        • -
      • maxc (float) – Maximum value to use.
        • -
      • returnData (bool) – If False, only return the ID of the reconstruction.
        • -
      • filterType (string) – Which type of filter to use for filter-based methods.
        • -
      • filterData (numpy.ndarray) – Optional filter data for filter-based methods.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_sino(data, proj_id=None, proj_geom=None, vol_geom=None, useCUDA=False, returnData=True, gpuIndex=None)[source]
      -

      Create a forward projection of an image (2D).

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Image data or ID.
        • -
      • proj_id (int) – ID of the projector to use.
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      • useCUDA (bool) – If True, use CUDA for the calculation.
        • -
      • returnData (bool) – If False, only return the ID of the forward projection.
        • -
      • gpuIndex (int) – Optional GPU index.
        • -
      -
      Returns:

      int or (int, numpy.ndarray)

      -
      -

      If returnData=False, returns the ID of the forward -projection. Otherwise, returns a tuple containing the ID of the -forward projection and the forward projection itself, in that -order.

      -

      The geometry of setup is defined by proj_id or with -proj_geom and vol_geom. If proj_id is given, then -proj_geom and vol_geom must be None and vice versa.

      -
      - -
      -
      -astra.creators.create_sino3d_gpu(data, proj_geom, vol_geom, returnData=True, gpuIndex=None)[source]
      -

      Create a forward projection of an image (3D).

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Image data or ID.
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      • returnData (bool) – If False, only return the ID of the forward projection.
        • -
      • gpuIndex (int) – Optional GPU index.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_vol_geom(*varargin)[source]
      -

      Create a volume geometry structure.

      -

      This method can be called in a number of ways:

      -
      -
      create_vol_geom(N):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(N \times N\).
      -
      -
      create_vol_geom((M, N)):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(M \times N\).
      -
      -
      create_vol_geom(M, N):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(M \times N\).
      -
      -
      create_vol_geom(M, N, minx, maxx, miny, maxy):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(M \times N\), windowed as \(minx \leq x \leq maxx\) and \(miny \leq y \leq maxy\).
      -
      -
      create_vol_geom((M, N, Z)):
      -
      --- - - - -
      returns:A 3D volume geometry of size \(M \times N \times Z\).
      -
      -
      create_vol_geom(M, N, Z):
      -
      --- - - - -
      returns:A 3D volume geometry of size \(M \times N \times Z\).
      -
      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      Sparse matrices: the matrix module

      -

      Next topic

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      Additional functions: the functions module

      -

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      Navigation

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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/data2d.html b/python/docSRC/_build/html/data2d.html deleted file mode 100644 index 6b01d41..0000000 --- a/python/docSRC/_build/html/data2d.html +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - - - 2D data objects: the data2d module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

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      - -
      -

      2D data objects: the data2d module

      -
      -
      -astra.data2d.change_geometry(i, geom)[source]
      -

      Change the geometry of a 2D object.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object.
        • -
      • geom (dict) – new geometry.
        • -
      -
      -
      - -
      -
      -astra.data2d.clear()[source]
      -

      Clear all 2D data objects.

      -
      - -
      -
      -astra.data2d.create(datatype, geometry, data=None)[source]
      -

      Create a 2D object.

      - --- - - - - - -
      Parameters:
        -
      • datatype (string) – Data object type, ‘-vol’ or ‘-sino’.
        • -
      • geometry (dict) – Volume or projection geometry.
        • -
      • data (float or numpy.ndarray) – Data to fill the constructed object with, either a scalar or array.
        • -
      -
      Returns:

      int – the ID of the constructed object.

      -
      -
      - -
      -
      -astra.data2d.delete(ids)[source]
      -

      Delete a 2D object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.data2d.get(i)[source]
      -

      Get a 2D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data2d.get_geometry(i)[source]
      -

      Get the geometry of a 2D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:dict – The geometry of object with ID i.
      -
      - -
      -
      -astra.data2d.get_shared(i)[source]
      -

      Get a 2D object with memory shared between the ASTRA toolbox and numpy array.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data2d.get_single(i)[source]
      -

      Get a 2D object in single precision.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data2d.info()[source]
      -

      Print info on 2D objects in memory.

      -
      - -
      -
      -astra.data2d.store(i, data)[source]
      -

      Fill existing 2D object with data.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object to fill.
        • -
      • data (float or numpy.ndarray) – Data to fill the object with, either a scalar or array.
        • -
      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      Welcome to PyASTRAToolbox’s documentation!

      -

      Next topic

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      3D data objects: the data3d module

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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/data3d.html b/python/docSRC/_build/html/data3d.html deleted file mode 100644 index 926bd6e..0000000 --- a/python/docSRC/_build/html/data3d.html +++ /dev/null @@ -1,259 +0,0 @@ - - - - - - - - 3D data objects: the data3d module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
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      Navigation

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      - -
      -

      3D data objects: the data3d module

      -
      -
      -astra.data3d.clear()[source]
      -

      Clear all 3D data objects.

      -
      - -
      -
      -astra.data3d.create(datatype, geometry, data=None)[source]
      -

      Create a 3D object.

      - --- - - - - - -
      Parameters:
        -
      • datatype (string) – Data object type, ‘-vol’ or ‘-sino’.
        • -
      • geometry (dict) – Volume or projection geometry.
        • -
      • data (float or numpy.ndarray) – Data to fill the constructed object with, either a scalar or array.
        • -
      -
      Returns:

      int – the ID of the constructed object.

      -
      -
      - -
      -
      -astra.data3d.delete(ids)[source]
      -

      Delete a 2D object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.data3d.dimensions(i)[source]
      -

      Get dimensions of a 3D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:tuple – dimensions of object with ID i.
      -
      - -
      -
      -astra.data3d.get(i)[source]
      -

      Get a 3D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data3d.get_shared(i)[source]
      -

      Get a 3D object with memory shared between the ASTRA toolbox and numpy array.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data3d.get_single(i)[source]
      -

      Get a 3D object in single precision.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data3d.info()[source]
      -

      Print info on 3D objects in memory.

      -
      - -
      -
      -astra.data3d.store(i, data)[source]
      -

      Fill existing 3D object with data.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object to fill.
        • -
      • data (float or numpy.ndarray) – Data to fill the object with, either a scalar or array.
        • -
      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      2D data objects: the data2d module

      -

      Next topic

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      Projector object: the projector module

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      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/functions.html b/python/docSRC/_build/html/functions.html deleted file mode 100644 index 7ec397e..0000000 --- a/python/docSRC/_build/html/functions.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - Additional functions: the functions module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
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      -
      -
      - -
      -

      Additional functions: the functions module

      -

      Additional functions for PyAstraToolbox.

      -
      -
      -astra.functions.add_noise_to_sino(sinogram_in, I0, seed=None)[source]
      -

      Adds Poisson noise to a sinogram.

      - --- - - - - - -
      Parameters:
        -
      • sinogram_in (numpy.ndarray) – Sinogram to add noise to.
        • -
      • I0 (float) – Background intensity. Lower values lead to higher noise.
        • -
      -
      Returns:

      numpy.ndarray – the sinogram with added noise.

      -
      -
      - -
      -
      -astra.functions.clear()[source]
      -

      Clears all used memory of the ASTRA Toolbox.

      -
      -

      Note

      -

      This is irreversible.

      -
      -
      - -
      -
      -astra.functions.data_op(op, data, scalar, gpu_core, mask=None)[source]
      -

      Perform data operation on data.

      - --- - - - -
      Parameters:
        -
      • op – Operation to perform.
        • -
      • data – Data to perform operation on.
        • -
      • scalar – Scalar argument to data operation.
        • -
      • gpu_core – GPU core to perform operation on.
        • -
      • mask – Optional mask.
        • -
      -
      -
      - -
      -
      -astra.functions.geom_2vec(proj_geom)[source]
      -

      Returns a vector-based projection geometry from a basic projection geometry.

      - --- - - - -
      Parameters:proj_geom (dict) – Projection geometry to convert
      -
      - -
      -
      -astra.functions.geom_size(geom, dim=None)[source]
      -

      Returns the size of a volume or sinogram, based on the projection or volume geometry.

      - --- - - - -
      Parameters:
        -
      • geom – Geometry to calculate size from
        • -
      • dim (int) – Optional axis index to return
        • -
      -
      -
      - -
      -
      -astra.functions.move_vol_geom(geom, pos, is_relative=False)[source]
      -

      Moves center of volume geometry to new position.

      - --- - - - - - -
      Parameters:
        -
      • geom (dict) – Input volume geometry
        • -
      • pos (tuple) – Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])
        • -
      • is_relative (bool) – Whether new position is relative to the old position
        • -
      -
      Returns:

      dict – Volume geometry with the new center

      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      Creation of objects: the creators module

      -

      Next topic

      -

      Helper class: the ASTRAProjector module

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      Navigation

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      -

      Navigation

      - -
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      -
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      - - -

      Index

      - -
      - A - | B - | C - | D - | F - | G - | I - | M - | P - | R - | S - | U - | V - | W - -
      -

      A

      - - - -
      - -
      add_noise_to_sino() (in module astra.functions) -
      - - -
      algorithm() (in module astra.matlab) -
      - - -
      astra() (in module astra.matlab) -
      - - -
      astra.algorithm (module) -
      - - -
      astra.astra (module) -
      - - -
      astra.ASTRAProjector (module) -
      - - -
      astra.creators (module) -
      - - -
      astra.data2d (module) -
      - -
      - -
      astra.data3d (module) -
      - - -
      astra.functions (module) -
      - - -
      astra.matlab (module) -
      - - -
      astra.matrix (module) -
      - - -
      astra.projector (module) -
      - - -
      astra_dict() (in module astra.creators) -
      - - -
      ASTRAProjector2D (class in astra.ASTRAProjector) -
      - - -
      ASTRAProjector2DTranspose (class in astra.ASTRAProjector) -
      - -
      - -

      B

      - - -
      - -
      backProject() (astra.ASTRAProjector.ASTRAProjector2D method) -
      - -
      - -

      C

      - - - -
      - -
      change_geometry() (in module astra.data2d) -
      - - -
      clear() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.functions) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      - -
      create() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      - -
      create_backprojection() (in module astra.creators) -
      - - -
      create_backprojection3d_gpu() (in module astra.creators) -
      - - -
      create_proj_geom() (in module astra.creators) -
      - -
      - -
      create_projector() (in module astra.creators) -
      - - -
      create_reconstruction() (in module astra.creators) -
      - - -
      create_sino() (in module astra.creators) -
      - - -
      create_sino3d_gpu() (in module astra.creators) -
      - - -
      create_vol_geom() (in module astra.creators) -
      - - -
      credits() (in module astra.astra) -
      - -
      - -

      D

      - - - -
      - -
      data2d() (in module astra.matlab) -
      - - -
      data3d() (in module astra.matlab) -
      - - -
      data_op() (in module astra.functions) -
      - -
      - -
      delete() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      - -
      dimensions() (in module astra.data3d) -
      - -
      - -

      F

      - - -
      - -
      forwardProject() (astra.ASTRAProjector.ASTRAProjector2D method) -
      - -
      - -

      G

      - - - -
      - -
      geom_2vec() (in module astra.functions) -
      - - -
      geom_size() (in module astra.functions) -
      - - -
      get() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - -
      - -
      get_geometry() (in module astra.data2d) -
      - -
      - -
      get_res_norm() (in module astra.algorithm) -
      - - -
      get_shared() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - -
      - -
      get_single() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - -
      - -
      get_size() (in module astra.matrix) -
      - -
      - -

      I

      - - -
      - -
      info() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      -
      - -

      M

      - - - -
      - -
      matrix() (in module astra.matlab) -
      - -
      - -
      (in module astra.projector) -
      - -
      -
      - -
      move_vol_geom() (in module astra.functions) -
      - -
      - -

      P

      - - - -
      - -
      projection_geometry() (in module astra.projector) -
      - -
      - -
      projector() (in module astra.matlab) -
      - -
      - -

      R

      - - - -
      - -
      reconstruct() (astra.ASTRAProjector.ASTRAProjector2D method) -
      - -
      - -
      run() (in module astra.algorithm) -
      - -
      - -

      S

      - - - -
      - -
      set_gpu_index() (in module astra.astra) -
      - - -
      splat() (in module astra.projector) -
      - -
      - -
      store() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - -
      -
      - -

      U

      - - -
      - -
      use_cuda() (in module astra.astra) -
      - -
      - -

      V

      - - - -
      - -
      version() (in module astra.astra) -
      - -
      - -
      volume_geometry() (in module astra.projector) -
      - -
      - -

      W

      - - - -
      - -
      weights_projection() (in module astra.projector) -
      - -
      - -
      weights_single_ray() (in module astra.projector) -
      - -
      - - - -
      -
      -
      -
      -
      - - - - - -
      -
      -
      -
      -
      -

      Navigation

      - -
      - -
      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/index.html b/python/docSRC/_build/html/index.html deleted file mode 100644 index 817e07f..0000000 --- a/python/docSRC/_build/html/index.html +++ /dev/null @@ -1,148 +0,0 @@ - - - - - - - - Welcome to PyASTRAToolbox’s documentation! — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - - -
      -

      Indices and tables

      - -
      - - -
      -
      -
      -
      -
      -

      Table Of Contents

      - - -

      Next topic

      -

      2D data objects: the data2d module

      -

      This Page

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      Navigation

      - -
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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/matlab.html b/python/docSRC/_build/html/matlab.html deleted file mode 100644 index 8b4bf31..0000000 --- a/python/docSRC/_build/html/matlab.html +++ /dev/null @@ -1,184 +0,0 @@ - - - - - - - - MATLAB compatibility interface: the matlab module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
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      MATLAB compatibility interface: the matlab module

      -

      This module implements a MATLAB-like interface to the ASTRA Toolbox.

      -

      Note that all functions are called with a string as the first -argument, specifying the operation to perform. This un-pythonic way -is used to make transitioning from MATLAB code to Python code easier, as -the MATLAB interface uses the same type of method calling.

      -

      After an initial import astra, these functions can be accessed in the -astra.m module.

      -
      -
      -astra.matlab.algorithm(command, *args)[source]
      -

      MATLAB-like interface to the astra.algorithm module

      -

      For example:

      -

      astra.m.algorithm('run',i,1000) – Run an algorithm with 1000 iterations.

      -
      - -
      -
      -astra.matlab.astra(command, *args)[source]
      -

      MATLAB-like interface to the astra.astra module

      -

      For example:

      -

      astra.m.astra('use_cuda') – Check if CUDA is enabled.

      -
      - -
      -
      -astra.matlab.data2d(command, *args)[source]
      -

      MATLAB-like interface to the astra.data2d module

      -

      For example:

      -

      astra.m.data2d('create',type,geometry,data) – Create a 2D object.

      -
      - -
      -
      -astra.matlab.data3d(command, *args)[source]
      -

      MATLAB-like interface to the astra.data3d module

      -

      For example:

      -

      astra.m.data3d('get',i) – Get 3D object data.

      -
      - -
      -
      -astra.matlab.matrix(command, *args)[source]
      -

      MATLAB-like interface to the astra.matrix module

      -

      For example:

      -

      astra.m.matrix('delete',i) – Delete a matrix.

      -
      - -
      -
      -astra.matlab.projector(command, *args)[source]
      -

      MATLAB-like interface to the astra.projector module

      -

      For example:

      -

      astra.m.projector('volume_geometry',i) – Get volume geometry.

      -
      - -
      - - -
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      Previous topic

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      Helper class: the ASTRAProjector module

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      Additional ASTRA methods: the astra module

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      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/matrix.html b/python/docSRC/_build/html/matrix.html deleted file mode 100644 index 1df4c30..0000000 --- a/python/docSRC/_build/html/matrix.html +++ /dev/null @@ -1,221 +0,0 @@ - - - - - - - - Sparse matrices: the matrix module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
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      Sparse matrices: the matrix module

      -
      -
      -astra.matrix.clear()[source]
      -

      Clear all matrix objects.

      -
      - -
      -
      -astra.matrix.create(data)[source]
      -

      Create matrix object with data.

      - --- - - - - - -
      Parameters:data (scipy.sparse.csr_matrix) – Data to fill the created object with.
      Returns:int – the ID of the constructed object.
      -
      - -
      -
      -astra.matrix.delete(ids)[source]
      -

      Delete a matrix object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.matrix.get(i)[source]
      -

      Get a matrix object.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:scipy.sparse.csr_matrix – The object data.
      -
      - -
      -
      -astra.matrix.get_size(i)[source]
      -

      Get matrix dimensions.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:tuple – matrix dimensions.
      -
      - -
      -
      -astra.matrix.info()[source]
      -

      Print info on matrix objects in memory.

      -
      - -
      -
      -astra.matrix.store(i, data)[source]
      -

      Fill existing matrix object with data.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object to fill.
        • -
      • data (scipy.sparse.csr_matrix) – Data to fill the object with.
        • -
      -
      -
      - -
      - - -
      -
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      Previous topic

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      Algorithms: the algorithm module

      -

      Next topic

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      Creation of objects: the creators module

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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/objects.inv b/python/docSRC/_build/html/objects.inv deleted file mode 100644 index 54bab0b..0000000 Binary files a/python/docSRC/_build/html/objects.inv and /dev/null differ diff --git a/python/docSRC/_build/html/projector.html b/python/docSRC/_build/html/projector.html deleted file mode 100644 index 9df5d0b..0000000 --- a/python/docSRC/_build/html/projector.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - - - Projector object: the projector module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
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      - -
      -

      Projector object: the projector module

      -
      -
      -astra.projector.clear()[source]
      -

      Clear all projector objects.

      -
      - -
      -
      -astra.projector.create(config)[source]
      -

      Create projector object.

      - --- - - - - - -
      Parameters:config (dict) – Projector options.
      Returns:int – the ID of the constructed object.
      -
      - -
      -
      -astra.projector.delete(ids)[source]
      -

      Delete a projector object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.projector.info()[source]
      -

      Print info on projector objects in memory.

      -
      - -
      -
      -astra.projector.matrix(i)[source]
      -

      Get sparse matrix of a projector.

      - --- - - - - - -
      Parameters:i (int) – ID of projector.
      Returns:int – ID of sparse matrix.
      -
      - -
      -
      -astra.projector.projection_geometry(i)[source]
      -

      Get projection geometry of a projector.

      - --- - - - - - -
      Parameters:i (int) – ID of projector.
      Returns:dict – projection geometry
      -
      - -
      -
      -astra.projector.splat(i, row, col)[source]
      -
      - -
      -
      -astra.projector.volume_geometry(i)[source]
      -

      Get volume geometry of a projector.

      - --- - - - - - -
      Parameters:i (int) – ID of projector.
      Returns:dict – volume geometry
      -
      - -
      -
      -astra.projector.weights_projection(i, projection_index)[source]
      -
      - -
      -
      -astra.projector.weights_single_ray(i, projection_index, detector_index)[source]
      -
      - -
      - - -
      -
      -
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      Previous topic

      -

      3D data objects: the data3d module

      -

      Next topic

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      Algorithms: the algorithm module

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      Python Module Index

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      - a
      - astra -
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\ No newline at end of file diff --git a/python/docSRC/_templates/layout.html b/python/docSRC/_templates/layout.html deleted file mode 100644 index f30df11..0000000 --- a/python/docSRC/_templates/layout.html +++ /dev/null @@ -1,15 +0,0 @@ -{% extends "!layout.html" %} - -{% block footer %} -{{ super() }} - -{% endblock %} diff --git a/python/docSRC/algorithm.rst b/python/docSRC/algorithm.rst deleted file mode 100644 index 83752bd..0000000 --- a/python/docSRC/algorithm.rst +++ /dev/null @@ -1,8 +0,0 @@ -Algorithms: the :mod:`algorithm` module -======================================= - -.. automodule:: astra.algorithm - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/astra.rst b/python/docSRC/astra.rst deleted file mode 100644 index 5d5fdf0..0000000 --- a/python/docSRC/astra.rst +++ /dev/null @@ -1,8 +0,0 @@ -Additional ASTRA methods: the :mod:`astra` module -======================================================== - -.. automodule:: astra.astra - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py deleted file mode 100644 index 78f7d42..0000000 --- a/python/docSRC/conf.py +++ /dev/null @@ -1,287 +0,0 @@ -# -*- coding: utf-8 -*- -# -# .. documentation build configuration file, created by -# sphinx-quickstart on Wed Mar 13 16:36:32 2013. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import sys, os - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) - -# -- General configuration ----------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode','sphinx.ext.mathjax','sphinx.ext.intersphinx'] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix of source filenames. -source_suffix = '.rst' - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'PyASTRAToolbox' -copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '1.7.1' -# The full version, including alpha/beta/rc tags. -release = '1.7.1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -#language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -#add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] - - -# -- Options for HTML output --------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = 'default' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -#html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -#html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -#html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -#html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'doc' - - -# -- Options for LaTeX output -------------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ('index', '.tex', u'.. Documentation', - u'Author', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output -------------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', '', u'.. Documentation', - [u'Author'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------------ - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', '', u'.. Documentation', - u'Author', '', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - - -# -- Options for Epub output --------------------------------------------------- - -# Bibliographic Dublin Core info. -epub_title = u'..' -epub_author = u'Author' -epub_publisher = u'Author' -epub_copyright = u'2013, Author' - -# The language of the text. It defaults to the language option -# or en if the language is not set. -#epub_language = '' - -# The scheme of the identifier. Typical schemes are ISBN or URL. -#epub_scheme = '' - -# The unique identifier of the text. This can be a ISBN number -# or the project homepage. -#epub_identifier = '' - -# A unique identification for the text. -#epub_uid = '' - -# A tuple containing the cover image and cover page html template filenames. -#epub_cover = () - -# HTML files that should be inserted before the pages created by sphinx. -# The format is a list of tuples containing the path and title. -#epub_pre_files = [] - -# HTML files shat should be inserted after the pages created by sphinx. -# The format is a list of tuples containing the path and title. -#epub_post_files = [] - -# A list of files that should not be packed into the epub file. -#epub_exclude_files = [] - -# The depth of the table of contents in toc.ncx. -#epub_tocdepth = 3 - -# Allow duplicate toc entries. -#epub_tocdup = True - -intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'numpy':('http://docs.scipy.org/doc/numpy/',None)} diff --git a/python/docSRC/creators.rst b/python/docSRC/creators.rst deleted file mode 100644 index d6249c3..0000000 --- a/python/docSRC/creators.rst +++ /dev/null @@ -1,8 +0,0 @@ -Creation of objects: the :mod:`creators` module -=============================================== - -.. automodule:: astra.creators - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/data2d.rst b/python/docSRC/data2d.rst deleted file mode 100644 index 342cbec..0000000 --- a/python/docSRC/data2d.rst +++ /dev/null @@ -1,8 +0,0 @@ -2D data objects: the :mod:`data2d` module -========================================= - -.. automodule:: astra.data2d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/data3d.rst b/python/docSRC/data3d.rst deleted file mode 100644 index 5b7de23..0000000 --- a/python/docSRC/data3d.rst +++ /dev/null @@ -1,8 +0,0 @@ -3D data objects: the :mod:`data3d` module -========================================= - -.. automodule:: astra.data3d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/functions.rst b/python/docSRC/functions.rst deleted file mode 100644 index 749eb27..0000000 --- a/python/docSRC/functions.rst +++ /dev/null @@ -1,8 +0,0 @@ -Additional functions: the :mod:`functions` module -================================================= - -.. automodule:: astra.functions - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst deleted file mode 100644 index dcc6590..0000000 --- a/python/docSRC/index.rst +++ /dev/null @@ -1,35 +0,0 @@ -.. .. documentation master file, created by - sphinx-quickstart on Wed Mar 13 16:36:32 2013. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to PyASTRAToolbox's documentation! -========================================== - -Contents: - -.. toctree:: - :maxdepth: 4 - - data2d - data3d - projector - algorithm - matrix - creators - functions - operator - plugins - matlab - astra -.. astra -.. builder - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/python/docSRC/make.bat b/python/docSRC/make.bat deleted file mode 100644 index d70c604..0000000 --- a/python/docSRC/make.bat +++ /dev/null @@ -1,190 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. - goto end -) - -if "%1" == "pickle" ( - %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the pickle files. - goto end -) - -if "%1" == "json" ( - %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the JSON files. - goto end -) - -if "%1" == "htmlhelp" ( - %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run HTML Help Workshop with the ^ -.hhp project file in %BUILDDIR%/htmlhelp. - goto end -) - -if "%1" == "qthelp" ( - %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run "qcollectiongenerator" with the ^ -.qhcp project file in %BUILDDIR%/qthelp, like this: - echo.^> qcollectiongenerator %BUILDDIR%\qthelp\.qhcp - echo.To view the help file: - echo.^> assistant -collectionFile %BUILDDIR%\qthelp\.ghc - goto end -) - -if "%1" == "devhelp" ( - %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. - goto end -) - -if "%1" == "epub" ( - %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -:end diff --git a/python/docSRC/matlab.rst b/python/docSRC/matlab.rst deleted file mode 100644 index fb7033e..0000000 --- a/python/docSRC/matlab.rst +++ /dev/null @@ -1,8 +0,0 @@ -MATLAB compatibility interface: the :mod:`matlab` module -======================================================== - -.. automodule:: astra.matlab - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/matrix.rst b/python/docSRC/matrix.rst deleted file mode 100644 index 6f11d8a..0000000 --- a/python/docSRC/matrix.rst +++ /dev/null @@ -1,8 +0,0 @@ -Sparse matrices: the :mod:`matrix` module -========================================= - -.. automodule:: astra.matrix - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/operator.rst b/python/docSRC/operator.rst deleted file mode 100644 index fe500ba..0000000 --- a/python/docSRC/operator.rst +++ /dev/null @@ -1,8 +0,0 @@ -OpTomo class: the :mod:`optomo` module -============================================== - -.. automodule:: astra.optomo - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/plugins.rst b/python/docSRC/plugins.rst deleted file mode 100644 index dc7c607..0000000 --- a/python/docSRC/plugins.rst +++ /dev/null @@ -1,8 +0,0 @@ -Plugins: the :mod:`plugin` module -========================================= - -.. automodule:: astra.plugin - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/projector.rst b/python/docSRC/projector.rst deleted file mode 100644 index b0854e8..0000000 --- a/python/docSRC/projector.rst +++ /dev/null @@ -1,8 +0,0 @@ -Projector object: the :mod:`projector` module -============================================= - -.. automodule:: astra.projector - :members: - :undoc-members: - :show-inheritance: - -- cgit v1.2.3