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| .. algorithm:: | ||
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| .. summary:: | ||
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| .. alias:: | ||
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| .. properties:: | ||
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| Description | ||
| ----------- | ||
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| The algorithm reads the pixel information defined in an ``.sqw`` file produced | ||
| by the `Horace <http://horace.isis.rl.ac.uk/Main_Page>`_ program and stores | ||
| it in a `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_. | ||
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| SQW objects in Horace can be split into 4 sections (see below for more detail): | ||
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| - *main\_header*: global information on the file | ||
| - *header(s)*: metadata for each ``.spe`` file that contributed to the final file | ||
| - *detpar*: detector parameters describing the instrument | ||
| - *data*: data section containing the pixel & projection information | ||
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| They can then come in two flavours: | ||
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| - sqw-type: all sections are filled in | ||
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| - dnd-type: *main\_header*, *header*, *detpar* are empty structures & ``data.urange`` and ``data.pix`` do not exist. | ||
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| DND-type objects can not be currently read or understood by Mantid. | ||
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| SQW File Structure | ||
| ################## | ||
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| Here we describe all of the fields of the ``.sqw`` file along with remarks regarding how they are treated within Mantid. | ||
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| :: | ||
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| Preamble: | ||
| % appname Name of the application that wrote the file (not stored) | ||
| % appversion Version of the application used to write the file (not stored) | ||
| % sqw_type Flag indicating object type (not stored) | ||
| % ndims Number of dimensions of the SQW file (ignored, always assumed to be 4) | ||
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| Main_header: | ||
| % main_headerfilename Name of sqw file that is being read, excluding path (ignored) | ||
| % main_headerfilepath Path to sqw file that is being read, including terminating file separator (ignored) | ||
| % main_headertitle Title of sqw data structure | ||
| % main_headernfiles Number of spe files that contribute to the sqw object | ||
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| Header: (scalar structure, or cellarray of scalar structures if more than one spe file) | ||
| % header{i}.filename Name of sqw file excluding path | ||
| % header{i}.filepath Path to sqw file including terminating file separator | ||
| % header{i}.efix Fixed energy (ei or ef depending on emode) | ||
| % header{i}.emode Emode=1 direct geometry, =2 indirect geometry, =0 if diffraction ''' Only emode 1 have ever been tried ''' | ||
| % header{i}.alatt Lattice parameters (Angstroms) | ||
| % header{i}.angdeg Lattice angles (deg) | ||
| % header{i}.cu First vector defining scattering plane (r.l.u.) | ||
| % header{i}.cv Second vector defining scattering plane (r.l.u.) | ||
| % header{i}.psi Orientation angle (rad) | ||
| % header{i}.omega --| | ||
| % header{i}.dpsi | Crystal misorientation description (rad) | ||
| % header{i}.gl | (See notes elsewhere e.g. Tobyfit manual | ||
| % header{i}.gs --| | ||
| % header{i}.en Energy bin boundaries (meV) in the input spe file [column vector] | ||
| % header{i}.uoffset Offset of origin of pixel projection axes in r.l.u. and energy i.e. [h; k; l; en] [column vector] | ||
| % header{i}.u_to_rlu Matrix (4x4) of pixel projection axes in hkle representation | ||
| % u(:,1) first vector - u(1:3,1) r.l.u., u(4,1) energy etc. | ||
| % header{i}.ulen Length of pixel projection axes vectors in Ang^-1 or meV [row vector] | ||
| % header{i}.ulabel Labels of the pixel projection axes [1x4 cell array of character strings] | ||
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| The pixel projection axes ``u1``, ``u2``, ``u3`` define the coordinate frame in which | ||
| the pixel coordinates are stored in ``data.pix``. They are defined such that: | ||
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| * ``u1`` is parallel to the vector ``u``, specified when generating the sqw file, defining the beam direction (so :math:`u_1||k_i`) | ||
| * ``u2`` is perpendicular to ``u1`` and in the scattering plane defined by the vectors ``u`` and ``v`` given when generating the sqw file | ||
| * ``u3`` is the cross-product of ``u1`` and ``u2``. | ||
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| Units are :math:`\AA^{-1}` for all 3 axes. | ||
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| :: | ||
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| Detpar: | ||
| % detpar.filename Name of file excluding path | ||
| % detpar.filepath Path to file including terminating file separator | ||
| % detpar.group Row vector of detector group number | ||
| % detpar.x2 Row vector of secondary flightpaths (m) | ||
| % detpar.phi Row vector of scattering angles (deg) | ||
| % detpar.azim Row vector of azimuthal angles (deg) | ||
| % (West bank=0 deg, North bank=90 deg etc.) | ||
| % detpar.width Row vector of detector widths (m) | ||
| % detpar.height Row vector of detector heights (m) | ||
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| Data: | ||
| % data.filename Name of sqw file that is being read, excluding path | ||
| % data.filepath Path to sqw file that is being read, including terminating file separator | ||
| % data.title Title of sqw data structure | ||
| * data.alatt Lattice parameters for data field (Ang^-1) | ||
| * data.angdeg Lattice angles for data field (degrees) | ||
| % data.uoffset Offset of origin of projection axes in r.l.u. and energy ie. [h; k; l; en] [column vector] | ||
| % data.u_to_rlu Matrix (4x4) of projection axes in hkle representation | ||
| % u(:,1) first vector - u(1:3,1) r.l.u., u(4,1) energy etc. | ||
| % data.ulen Length of projection axes vectors in Ang^-1 or meV [row vector] | ||
| % data.ulabel Labels of the projection axes [1x4 cell array of character strings] | ||
| % data.iax Index of integration axes into the projection axes [row vector] | ||
| % Always in increasing numerical order | ||
| % e.g. if data is 2D, data.iax=[1,3] means summation has been performed along u1 and u3 axes | ||
| % data.iint Integration range along each of the integration axes. [iint(2,length(iax))] | ||
| % e.g. in 2D case above, is the matrix vector [u1_lo, u3_lo; u1_hi, u3_hi] | ||
| % data.pax Index of plot axes into the projection axes [row vector] | ||
| % Always in increasing numerical order | ||
| % e.g. if data is 3D, data.pax=[1,2,4] means u1, u2, u4 axes are x,y,z in any plotting | ||
| % 2D, data.pax=[2,4] " u2, u4, axes are x,y in any plotting | ||
| % data.p Call array containing bin boundaries along the plot axes [column vectors] | ||
| % i.e. row cell array {data.p{1}, data.p{2} ...} (for as many axes as length of data.pax) | ||
| % data.dax Index into data.pax of the axes for display purposes. For example we may have | ||
| % data.pax=[1,3,4] and data.dax=[3,1,2] This means that the first display axis is data.pax(3)=4, | ||
| % the second is data.pax(1)=1, the third is data.pax(2)=3. The reason for data.dax is to allow | ||
| % the display axes to be permuted but without the contents of the fields p, s,..pix needing to | ||
| % be reordered [row vector] | ||
| -----> Large data fields, data for MD image | ||
| % data.s Cumulative signal. [size(data.s)=(length(data.p1)-1, length(data.p2)-1, ...)] | ||
| % data.e Cumulative variance [size(data.e)=(length(data.p1)-1, length(data.p2)-1, ...)] | ||
| % data.npix No. contributing pixels to each bin of the plot axes. | ||
| % [size(data.pix)=(length(data.p1)-1, length(data.p2)-1, ...)] | ||
| -----> | ||
| * data.urange True range of the data along each axis [urange(2,4)] | ||
| ----> Pixels or events data | ||
| * data.pix Array containing data for each pixel: | ||
| * If npixtot=sum(npix), then pix(9,npixtot) contains: | ||
| * u1 -| | ||
| * u2 | Coordinates of pixel in the pixel projection axes | ||
| * u3 | | ||
| * u4 -| | ||
| * irun Run index in the header block from which pixel came | ||
| * idet Detector group number in the detector listing for the pixel | ||
| * ien Energy bin number for the pixel in the array in the (irun)th header | ||
| * signal Signal array | ||
| * err Error array (variance i.e. error bar squared) | ||
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| ``data.s`` is normalized by the number of pixels, as is the variance ``data.e``. | ||
| For those elements where ``data.npix==0``, ``data.s=0`` and ``data.e=0`` | ||
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| Assumptions | ||
| ########### | ||
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| Parts of the code were written with the idea of generalising | ||
| functionality at a later stage. However, we can now assume that: | ||
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| - the lattice parameters are all the same for all contributing spe files | ||
| - the energy offset is zero in cuts | ||
| - requires that all sqw files that are to be combined have | ||
| #. each been created from only one spe file | ||
| #. the same lattice parameters and pixel projection axes as held in the header block | ||
| #. the same projection axes and offsets, as held in the data block | ||
| #. the same plot and integration axes, with same bins and integration ranges | ||
| - the display axes will be taken from the first sqw object in the list to be combined | ||
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| .. categories:: | ||
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| .. sourcelink:: | ||
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