From f69d9f6bc1704560518da3c30c46e495c0228aac Mon Sep 17 00:00:00 2001 From: Daan Pelt Date: Thu, 30 Apr 2015 11:02:50 +0200 Subject: Check data size when using 'link' function in Python --- python/astra/data2d_c.pyx | 16 ++++++++++++ python/astra/data3d_c.pyx | 17 ++++++++++++ python/astra/functions.py | 25 ++---------------- python/astra/pythonutils.py | 63 +++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 98 insertions(+), 23 deletions(-) create mode 100644 python/astra/pythonutils.py diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index ac54898..29548b5 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -47,6 +47,12 @@ from .PyIncludes cimport * cimport utils from .utils import wrap_from_bytes +from .pythonutils import geom_size + +import operator + +from six.moves import reduce + cdef CData2DManager * man2d = PyData2DManager.getSingletonPtr() cdef extern from "CFloat32CustomPython.h": @@ -71,6 +77,16 @@ def create(datatype, geometry, data=None, link=False): cdef CProjectionGeometry2D * ppGeometry cdef CFloat32Data2D * pDataObject2D cdef CFloat32CustomMemory * pCustom + + if link: + geomSize = geom_size(geometry) + if len(data.shape)==1: + if data.size!=reduce(operator.mul,geomSize): + raise Exception("The dimensions of the data do not match those specified in the geometry.") + else: + if data.shape!=geomSize: + raise Exception("The dimensions of the data do not match those specified in the geometry.") + if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry2D() diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 84472c1..30745b4 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -45,6 +45,13 @@ from .PyXMLDocument cimport XMLDocument cimport utils from .utils import wrap_from_bytes +from .pythonutils import geom_size + +import operator + +from six.moves import reduce + + cdef CData3DManager * man3d = PyData3DManager.getSingletonPtr() cdef extern from *: @@ -61,6 +68,16 @@ def create(datatype,geometry,data=None, link=False): cdef CFloat32Data3DMemory * pDataObject3D cdef CConeProjectionGeometry3D* pppGeometry cdef CFloat32CustomMemory * pCustom + + if link: + geomSize = geom_size(geometry) + if len(data.shape)==1: + if data.size!=reduce(operator.mul,geomSize): + raise Exception("The dimensions of the data do not match those specified in the geometry.") + else: + if data.shape!=geomSize: + raise Exception("The dimensions of the data do not match those specified in the geometry.") + if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry3D() diff --git a/python/astra/functions.py b/python/astra/functions.py index 4025468..b826b86 100644 --- a/python/astra/functions.py +++ b/python/astra/functions.py @@ -38,6 +38,7 @@ from . import data2d from . import data3d from . import projector from . import algorithm +from . import pythonutils @@ -158,29 +159,7 @@ def geom_size(geom, dim=None): :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 + return pythonutils.geom_size(geom,dim) def geom_2vec(proj_geom): diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py new file mode 100644 index 0000000..8ea4af5 --- /dev/null +++ b/python/astra/pythonutils.py @@ -0,0 +1,63 @@ +#----------------------------------------------------------------------- +# 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 . +# +#----------------------------------------------------------------------- +"""Additional purely Python functions for PyAstraToolbox. + +.. moduleauthor:: Daniel M. Pelt + + +""" + +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 -- cgit v1.2.3 From f730efe78367e8fe8e589c2b43fb0886d384f5c8 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 7 May 2015 11:34:37 +0200 Subject: Do not allow 1D input in Python link method --- python/astra/data2d_c.pyx | 10 ++-------- python/astra/data3d_c.pyx | 10 ++-------- 2 files changed, 4 insertions(+), 16 deletions(-) diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index 29548b5..4919bf2 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -78,14 +78,8 @@ def create(datatype, geometry, data=None, link=False): cdef CFloat32Data2D * pDataObject2D cdef CFloat32CustomMemory * pCustom - if link: - geomSize = geom_size(geometry) - if len(data.shape)==1: - if data.size!=reduce(operator.mul,geomSize): - raise Exception("The dimensions of the data do not match those specified in the geometry.") - else: - if data.shape!=geomSize: - raise Exception("The dimensions of the data do not match those specified in the geometry.") + if link and data.shape!=geom_size(geometry): + raise Exception("The dimensions of the data do not match those specified in the geometry.") if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 30745b4..3b27ab7 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -69,14 +69,8 @@ def create(datatype,geometry,data=None, link=False): cdef CConeProjectionGeometry3D* pppGeometry cdef CFloat32CustomMemory * pCustom - if link: - geomSize = geom_size(geometry) - if len(data.shape)==1: - if data.size!=reduce(operator.mul,geomSize): - raise Exception("The dimensions of the data do not match those specified in the geometry.") - else: - if data.shape!=geomSize: - raise Exception("The dimensions of the data do not match those specified in the geometry.") + if link and data.shape!=geom_size(geometry): + raise Exception("The dimensions of the data do not match those specified in the geometry.") if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) -- cgit v1.2.3