Newer
Older
SpectrumView
============
.. contents:: Table of Contents
:local:
Overview
--------
The 2.2 release of MantidPlot includes the "SpectrumView" data viewer, a viewer
that quickly displays a large collection of spectra as an image. The viewer can
be started from the right-click menu of a matrix workspace by selecting ''Show
Spectrum Viewer''. Each row of the image represents one spectrum.
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
If the user points at a location on the image the data from that spectrum are
displayed on a graph across the bottom of the image, and the data from the
different spectra for that column are displayed on a graph at the left side of
the image. Basic information about that point on the image is shown in the
Image Info table. Similarly information about a position pointed at by the user
in a graph is displayed in the table associated
with that graph.
Example
-------
For example, the figure shows the spectra from slightly more than three LPSDs on
the ARCS instrument at the SNS. The four horizontal dark lines across the image
are due to there being no data from pixels at the ends of the LPSDs.The image
quickly shows several interesting aspects of the data, includingpowder lines,
single crystal peaks and a dead-time of the LPSDs for
approximately 200 micro-seconds following particularly strong SCD peaks.
.. figure:: /images/SpectrumViewer.jpg
Interactive Rebinning
---------------------
The spectra displayed are initially binned in 2000 uniform steps.
They can be quickly rebinned for the viewer by specifying new values for X Min,
X Max and a new Step size.
If the step size is positive, it specifies the size of the uniform bin width to
use across the selected X range. If the step size is negative, its absolute
value specifies the fractional increase for each bin boundary in a "log" scale.
The effect of rebinning with a large number of small bins is most useful in
combination with the horizontal scroll bar, described below.
Scrolling
---------
If there are more spectra than can be displayed at one time, the image can
be scrolled up and down using the vertical scroll bar at the right side of the
image. In this way, all spectra from an instrument with hundreds of
thousands of detector pixels can be examined quickly. The View menu includes
a control to turn off the vertical scroll bar. If the vertical scroll bar
is turned off, then the number of spectra displayed is limited to the number of
rows in the displayed image. For example, if there are 500 rows in the
image, but there are 5,000 spectra to display, then the image will be formed
by using every 10th spectrum. While this can be useful in some cases, this
subsampling of the available spectra can also miss important features and
can suffer from various "aliasing" effects. For this reason the vertical
scroll bar is turned on by default.
The view menu also has a control to turn on a horizontal scroll bar to
scroll the image left and right. This will only be useful when the spectra
are binned using more bins than the number of image columns. In this case,
the horizontal scroll bar will allow scrolling the image and associated
graph left and right to examine other portions of the spectra. If the
horizontal scroll bar is turned off, and the binning controls specify more
bins than can be displayed, the binning is adjusted to match the number
of displayable columns before the image is created.
Information Readout
-------------------
The user can use the left mouse button to point at features on the image
or graphs. This will initiate a full size crosshair cursor for comparing
features and will show information about the selected point in the table
associated with the image or graph in use. The information is for the
selected spectrum and X location. The "Value" shown is the value of
the spectrum in the selected bin, using the current binning.
Intensity to Color Mapping
--------------------------
A pseudo-log intensity scale is used to help see lower intensity features
in the same image as high intensity peaks. The relative intensity of low
intensity features to high intensity features is controlled by the intensity
slider.
When the slider is fully to the left, the mapping from
data value to color index is linear. As the slider is moved to the right
low intensity features are increasingly emphasized, relative to the
maximum intensity in the displayed image.
The selected color scale is always fully used. If the image is scrolled
to display a different portion of the image, the mapping is adjusted so
that the largest positive value present in the image is mapped to the
largest color index.
The color scale in use is displayed in a color bar on the right side of
the viewer. This color scale is "two-sided" in that separate color
scales are used for negative and for positive values in the data. In
the example shown, values greater than or equal to zero are mapped to
colors ranging from black to red, orange and then white. Negative
values range from black through shades of gray. The pseudo-log
intensity scaling is actually applied to the absolute value of the
data intensity, before mapping to a color. This allows small negative
as well as small positive values to be seen and distinguished in the
presence of large peaks. This can be useful when dealing with data
that was obtained by subtracting two workspaces, such as when
background is subtracted, since due to errors in the data, this often
introduces negative "intensities".
Graphs
------
The displayed graphs are just cuts through the displayed image.
That is, the graph of a spectrum across the bottom of the window
is obtained from the corresponding row of the image data. Consequently,
the graph shows that spectrum as rebinned for the image display.
Similarly, the graph at the left side of the window is obtained
from the corresponding column of the image data, so it shows values
from whatever spectra formed the image, at the selected bin.
The graphs are both "auto-scaling" and adapt to the range of values
in the selected portion of the data. The Graph Max control allows
the user to see lower level features in the data by reducing the
portion of the range of values that are displayed. When the control
is at the right limit, 100% of the total range is displayed. When
the control is in the middle, only 50% of the total range is
displayed. When the control is at the far left, only 1% of the
total range is displayed.
Each of the graphs is in a separate pane that can be collapsed
to zero size, if not needed. The "control" for this is a small
graphical "handle" on a divider between the graph and image.
The graph size can be altered by grabbing the handle with the
left mouse button pressed. The size can be increased or decreased
to a minimum size. If the handle is moved substantially below
the minimum size, the graph will collapse to zero size.