plot2 module <extract>
This module extracts a 2-dimensional plane from an
n-dimensional data set.
- {parameter file} <parameter_file>
-
The parameters (e.g. dimension and sizes) of the data
set are required to be given in a 'par' (parameter) file.
These files are used and created by the processing programs.
- {select file...}
-
This pops up a file selection dialogue for the above.
- {data scale} <data_scale>
-
The data is scaled by this amount when extracted.
Usually, a data scale of 1 would be used.
- {name for plane} <plane_name>
-
Each extracted plane has its own name.
Use of a name for a second time deletes the previous one.
(The program asks to confirm that this is what you want.)
- {plane directions} <plane_directions>
-
The two dimensions (counting from 1) to be contoured.
The second dimension can be smaller than the first.
- {plane thickness} <plane_thickness>
-
The number of planes in each of the dimensions orthogonal
to the contour plane to be added together for the plot
(note that the result is not divided by the number of
planes used; to do this use an appropriate data scale).
The thickness can be specified either as (i) one number,
in which case the thickness is the same in each of the
dimensions orthogonal to the contour plane; or (ii) an
array of numbers, in which case the thickness in each
dimension is as specified. In case (ii), the array must
have an entry for all dimensions, but only the entries
in the slots orthogonal to the plane dimensions are used.
The slots of the plane dimensions do not have to have
numbers in them (see below for an example).
Usually, a plane thickness of 1 would be used.
- {plane point} <point_on_plane>
-
This must have an entry for all dimensions, but only the
entries in the slots orthogonal to the plane dimensions
are used. The slots of the plane dimensions do not have
to have numbers in them. Thus, for example, with a
3-dimensional data set, the (d1, d3) plane d2 = 12 can be
given by '- 12 -' or '0 12 0' or anything else like this.
The plane(s) closest to the point is (are) extracted.
- {points : ppm : Hz} <reference>
-
The plane point can be specified in points, ppm or Hz.
If specified in points, start counting at 1.
- {all of plane : chosen subset} <plane_subset>
-
Typically all of the plane would be extracted.
The idea behind a chosen subset is that the plane might
be so large (e.g. 2048 x 2048) that only some points
(e.g. every fourth) might need to be extracted in order
to have a first look (this speeds up the contouring).
- If a subset (i.e. not the whole plane) is extracted:
-
- {first points} <first_points>
-
The first points (numbers must be given for all dims.) of
the extracted plane. This must be specified in points.
- {last points} <last_points>
-
The last points (numbers must be given for all dims.) of
the extracted plane. This must be specified in points.
- {step through points} <steps_through_points>
-
The step size through the points (numbers must be given
for all of the dimensions) of the extracted plane. This
must be specified in points.
- {script file} <script_file>
-
The name of a plot2 script file.
- {select script...}
-
This pops up a file selection dialogue for the above.
- {run script} <run>
-
Run the specified script.
- {load} <load>
-
Extract (load from disk) the specified plane.
NOTE: the contours for an extracted plane are not
drawn until after an explicit command for doing so.
- {dismiss}
-
Close the module (the parameters are remembered).
- {help}
-
Display this message.
Azara help: plot2/extract / W. Boucher / azara@bioc.cam.ac.uk