John W. Campbell
The JdlView objects basically fall into two categories. These are the
general purpose JdlView objects which are written without any particular
application in mind (e.g the menu area object or the I/O window
JdlView object) and those which are written with a particular application
or group of applications in mind (e.g. the image view-object)
For applications written using the JdlView manager object,
a number of the JdlView objects will be displayed with an 'active strip'
area at the top (see below for details) which indicates whether or not
the application program is currently ready to receive input from the
JdlView object in question. The JdlView objects can however be used
independently of any such manager, in which case no active strip will
appear.
Many of the JdlView objects use items such as buttons, sliders and
choice items which are also part of the JdlView package. These are
described in the section entitled 'JdlView Panel Items' below.
List of sections:
The 'Active Strip' Area
The Base Frame JdlView Object
The Menu Area JdlView Object
The Parameter Table JdlView Object
The I/O Window JdlView Object
The Text Table JdlView Object
The Cell Window JdlView Object
The Graphics Window JdlView Object
The Split List JdlView Object
The Progress Bar JdlView Object
The Blank Object JdlView Object
The PXImage JdlView Object
The PX Simulation JdlView Object
The Show Unique Coverage JdlView Object
JdlView Panel Items
If running under the JdlView manager, JdlView objects which can return
data to the program, will normally contain an 'active strip' area.
This indicates whether or not the program is waiting for the JdlView object
to return data (e.g. a menu selection, text string, spot position etc.)
to the program. The active strip consists of a diamond shaped item
at the left hand side and a rectangle at the right hand side, usually
stretching across the width of the JdlView object. When
the program is ready to receive input from the JdlView object, then the
diamond is displayed in a cyan colour and a message is displayed in
the rectangle. When the program is not waiting to receive input
then both parts of the active strip are cleared. A program may be
waiting to receive input from more than one JdlView object at a time and
from different JdlView objects at different times and hence the reason
for indicating to the user the current 'active/inactive' state of any
particular JdlView object.
Figure 1: An Active Strip in it's Active State
This is just an empty 'top level' window on which other JdlView objects may
be laid out. The window manager will usually add a frame of some kind
round such a window and its exact appearance will therefore depend on
the system on which the program is being run. Frequently the added frame
will display a title which has been supplied by the application
programmer. Any operations on the base frame (e.g. moving it or
resizing it) are functions of the particular window manager which is running.
The menu area JdlView object provides an area containing a menu from which
items may be selected by the user by means of the mouse. Typically, an
application will use the same menu area for a series of different
menus. The menu area has an optional title. It also has an optional extra
menu item situated below the other menu items and separated from them.
This item is typically used either as a 'Quit' item or as an item
which will instruct the program to return to the previously displayed
menu. The menu area also has an 'active strip' at the top of the area
when used in conjunction with the JdlView manager. When the program is
waiting for a menu item to be selected then this will display a
message e.g. (by default) 'Input Mode'.
Figure 2: Example of a Menu Area JdlView Object
When the menu area is in its 'active' state and the mouse pointer
is is within the boundary of a menu item, then
that item will be highlighted by displaying the item name in
bold print. A menu item is selected by pointing to the item and clicking
Button1 of the mouse.
The parameter table JdlView object provides an area containing an
editable table of parameter values. The parameter table has an
optional title. The table itself consists of one or more columns,
each with a number of rows containing a parameter name and a
parameter value. (These parameter items are 'Value Items' whose operation
is also described in the section on 'JdlView Panel Items below')
The parameter table has an 'active strip' at the top
when used in conjunction with the JdlView manager to indicate
when the entries may be edited; when the program is prepared to
service parameter value edits, then a message e.g. (by default)
'Input Mode' is displayed in the active strip. Optionally, a
Parameter Table object may be set up to display multiple tables of
parameters; in such a case, there will be a coloured oblong indicator displayed
at the right hand side of the title area. This is split into
segments with one segment for each of the alternative parameter sets. The
segment for the currently displayed parameter set is coloured green
and the other segments are coloured orange. The alternative parameter
sets are selected by clicking the mouse (Button1) on the required
segment of the indicator.
An example (with alternative parameter sets) is shown below.
Figure 3: Example of a Parameter Table JdlView Object
When the parameter table is in 'active' mode and the mouse pointer points
at an item in the table, then the parameter value for the
item may be changed by clicking Button1 of the mouse in the value area
of the item. The value string is cleared and a flashing cursor is displayed.
The user types in the new value and inputs it to the program by
pressing the 'Return' or 'Enter' or key. While a value string is being
input, incorrect characters may be deleted using the the 'Delete'
or 'Backspace' key. A value string selected/copied on another window may be
pasted in by pressing Button2 when the value input is awaited.
The user may abandon the input of the new value by
pressing the 'Escape' key, in which case, the old value will be
restored. If a new value is input, then it will normally be checked
by the application program which will decide what course of action
is taken. Usually, if an invalid input was given, the program will
use the function which causes an Error Dialogue to be displayed. This
will contain an error message and the message '** Old value will be
replaced **'. To proceed, the user must select the 'OK' box in the
dialogue; the old value will then be restored.
When inputting a new parameter value, the parameter table window
must have the keyboard focus. It will automatically gain the
keyboard focus when the mouse Button1 is clicked to change a
parameter value. If required, the keyboard focus may be restored to
the window by pointing to the value area and
clicking Button1 of the mouse. When the parameter table has the keyboard
focus, the cursor in the value area will flash rapidly (at 0.4 second
intevals); when it does not have the keyboard focus, the cursor will flash more
slowly (at 1.5 second intervals).
Parameter values longer than the displayed value field may be used.
In this case the value field may be scrolled by pointing to the value,
holding down Button2 and moving it to the left or right within the value
field. Moving the pointer to the left will move towards the start of the
value string and moving it to the right will move it towards the end
of the value string. Button2 is released to finish the scrolling.
When the value string extends beyond the displayed field, this is indicated by
an arrow mark at the appropriate end or ends. The maximum allowed length
for the value string is set under program control.
In some cases, parameter values may be displayed as 'toggle' values.
These are either a 'Yes/No' toggle or an 'On/Off' toggle. The toggle
value is displayed enclosed in a box. When an item with a toggle
value has been highlighted and when Button1 of the mouse is clicked,
then the value will switch to its alternative, 'Yes' to 'No' or vice versa
or 'On' to 'Off' or vice versa.
Alternatively, some items in the parameter table may have drop down
menus associated with them. These have an arrow menu button at the right
hand side of the parameter value field. To select a value from the
menu, click on the menu button and then click on the required menu
item.
A third special type of item may have a step button associated with
them. This is indicated by a small pair of up and down arrow buttons.
Clicking these buttons enables the user to step up and down through
a list of options or values (the exact details depend obviously on
the requirement of the program using the option).
Sometimes, the application may choose to emphasise certain items by
displaying them in a bold font, perhaps to bring particularly important
items to the attention of the user. These emphasised items are treated
in exactly the same way as the items in the normal font.
Also, sometimes the application may choose, in certain conditions, to
disallow (or freeze) the changing of selected parameter values.
There is also an option to have labels in the parameter table, perhaps
introducing a related group of items. These have a name but no value
and cannot therefore be selected.
The I/O window JdlView object provides an area for the output of
text from the program and input of text strings by the user when
required (e.g. for a question and answer sequence). The I/O window has
an 'active strip' at the top when used in conjunction with the
JdlView manager to indicate whether or not the program is waiting for
a reply string to be input by the user; when the program is waiting
for input, then a message ('Input mode' by default) is displayed in
the active strip.
Figure 4: Example of an i/o window JdlView Object
When the program is waiting for the input of a text string, then a
text cursor will be displayed at the point where the next character
is to be input. The input of a text string is completed by pressing the
'Return' or 'Enter' key. While a text string is being input, it may be
edited using the cursor left/right keys or the mouse to set a new
cursor position, followed by insertion or addition of characters and/or
deletion of characters using the 'Delete' or 'Backspace' keys.
Long text strings will wrap around onto successive lines as needed and
the text will scroll up when the bottom of the window is reached.
When inputting the characters of a text string, the I/O window
must have the keyboard focus. It will automatically gain the
keyboard focus when the text string input is first requested. If
required, the keyboard focus may be restored to the window by pointing
to the window and clicking Button1 of the mouse. When the I/O window
has the keyboard focus, the cursor will flash rapidly (at 0.4 second
intevals); when it does not have the keyboard focus, the cursor will flash more
slowly (at 1.5 second intervals); also, the message in the active
strip, if present, will be be in black if the window has got the keyboard
focus or blue if it has not.
When input is requested, previous commands may be recalled by pressing the
Up arrow (cursor) key; each press of the key goes one futher back in the
previous commands list. Pressing the Down arrow (cursor) key moves forward
through the list. The latest 100 commands are stored.
When a reply is to be input, text which has been 'selected' on another
or the same window, may be pasted into the reply field by clicking
Button2. Note that if the selected text contains more than one line,
then only the text up to the first newline character will be pasted in.
Text may be 'selected' by pointing to the first character of the
text to be selected, holding down Button1, dragging the pointer to the
last character of the text to be selected and then releasing Button1.
The selected text will be highlighted.
The I/O window object has a scroll bar at the right hand side of the
window so that previous contents of the window can be seen after they have
scrolled off at the top of the window.
The text table window JdlView object provides an area for the simple output of
text from the program, particularly for tabular data. There is no scrolling.
The text may be in bold or normal print in a variety of colours. The program
may output text at any character position within the window and areas of
the window may be cleared and redrawn as required. A limited series of symbols
are also available. There is an option to create a text table with
'active' cells defining areas of text which may be highlighted and,
when required, selected using the mouse. In the example figure, the
cell highlighting feature has been used to display additional details
relating to a selected item from the table.
Figure 5: Example of a Text Table JdlView Object
It may be noted that the text table uses a fixed width character font.
The cell window window JdlView object is basically an extended version
of the text table JdlView object described above. The additional
features are as follows:
- The window is scrollable.
- There is a fixed size overlay window which may be used for
example for some fixed position buttons to be output in front of the
scrollable area.
- Images (based on a cell size grid) may be output to the
window.
- There is special provision for the output of selectable opaque
icons/buttons to be output to the window.
- There is an option to output a command line at the bottom of the
window to enable the output of a prompt and input of a reply.
Figure 6: Example of a Cell Window JdlView Object
When the command line, if present, has the keyboard focus, the cursor
will flash rapidly (at 0.4 second intevals); when it does not have the
keyboard focus, the cursor will flash more slowly (at 1.5 second
intervals); also, the message in the active strip, if present, will be
be in black if the window has got the keyboard focus or blue if it has
not.
It may be noted that the cell window object uses a fixed width character
font. The functions of this object basically include all those of the
text table object but there is a difference in that the cell size used
in the text table depends on the size of the fixed font used (and can
therefore use a large character size if required) whereas the
characters in the cell window object are always fitted into a cell
which is eight pixels wide and sixteen pixels deep.
The functions of this object are basically a subset of a further developed
object, the JdlView graphics object which has, in addition, options
for graphical output and also for printer (/file) output.
The graphics window JdlView object incorporates all the functions of
the JdlView cell window object described above. In addition, the main
scrolling area may be used for the output of graphics. A number of
methods are supplied to give access to a basic set of line plotting
functions including drawing of rectangles, polygons
and arcs. Filled areas may also be drawn. Symbol, polysymbol and text
plotting functions are also available. In addition to the 'cell based'
text output as available in the cell window object, text strings may be output
using a variety of fonts (not all fixed width) and may be drawn at an
angle to the horizontal if required. For plotting graphs, there are
two simple axis drawing routines. The object has an optional printer
output facility.
Figure 7: Graphics Window Example with a Graph
Figure 8: Graphics Window Example for Music Input
In addition to responding to mouse clicks on 'active' cells
and/or buttons/icons, the program may accept input from the mouse when
it is outside these areas or from the keyboard.
When used for outputting graphics, a number of options are available
for defining the mapping of the user coordinates onto the window and for
handling possible re-sizing of the graphics window.
The command line, if present, may be positioned at either the top or
the bottom of the window.
A printer icon button will be displayed when the printing option is
available. This will be positioned to the right of
the command line, if present, or otherwise at the right hand side
of the active strip; If no command line or active strip is present,
then the printer icon button will be positioned at the right hand
side of a blank strip at the top of the window.
When the printer icon button is selected a dialogue window will be
displayed allowing various options to be selected.
Figure 9: Print Dialogue
The following choices may be made:
- Output in Landscape or Portrait format.
- Output the Full graphics area or just the Displayed area.
- Output the Main window and/or the Overlay window.
- Fill or do not fill the output plot with the background
colour.
This class provides a titled list which may be split into vertical columns
with movable boundaries. The list has a title line and is vertically
scrollable. One or more items may be selected from the list as
required. The Split List object may have an 'active strip' at the top
when used in conjunction with the JdlView manager to indicate whether
or not the program is waiting for items to be selected by the user;
when the program is waiting for input, then a message ('Input mode'
by default) is displayed in the active strip. An example is shown
below:
Figure 10: Example of a Split List JdlView Object
When the columns overlap, the right hand columns overlap those to the
left. A column boundary is moved by pointing to the boundary line
between the columns in the title area. When the cursor has changed, to
a form with a pair of vertical lines and arrows pointing to left and
right, the boundary may be moved by clicking and dragging with Button1
of the mouse. Columns to the right of the boundary being moved will
move with the selected boundary.
A single item may be selected by clicking on its line in the table
with Button1 of the mouse. A contiguous set of lines may be selected
by clicking on the first required line with the mouse, then holding
down the SHIFT key and clicking on the final line of the set of lines
to be selected. A non-contiguous set of lines may be selected by
holding down the CTRL key while selecting the required individual
lines using the mouse. Note that the selection modes actually made
available are under program control.
A scrollbar at the right hand side of the split list object enables
scrolling up and down the list when it is too long to be shown
complete within the window.
Optionally, a horizontal scrollbar may also be displayed at the bottom
of the split list object. Drag and drop and copy and paste options may
also be used. Drag and drop between split lists should normally only
be used between lists with the same number of columns if a transfer in
both directions is required.
The progress bar object is used to indicate the progress of a
time consuming operation e.g. reading in of a large file or performing
a lengthy calculation. The progress bar is a window containing a title
and the bar itself. The bar starts as an empty rectangle which is gradually
filled in colour as the operation proceeds. The program needs to be
able to pass the current degree of progress to the object at
reasonably frequent intervals for its use to be effective.
Figure 11: Example of a Progress Bar JdlView Object
This is merely a window with a surrounding border similar to that used
in other JdlView objects which may be output on a display for aesthetic
reasons to indicate the position on a layout which will be
occupied by another JdlView object at a later stage.
This object is designed specifically for displaying X-ray diffraction
images used in Protein Crystallography. It may be used for measuring
spot positions and has facilities for overlaying symbols, boxes, other vectors
or text on top of the displayed image. A magnifying window within the
JdlView object shows a magnified version of a
portion of the image from the main
image display area. The image may also be zoomed in various ways.
A control panel allows for a series of adjustments to the display,
display of help information, initiation of hard copy (/file) output and
access to additional options which may be made available by the
calling program.
Figure 12: Example of JdlView PXImage Object
The object has an 'active strip' at the top when used in conjunction with the
JdlView manager to indicate whether or not the program is waiting for
user input (e.g. selecting a spot); when the program is waiting
for input, then a message ('Input mode' by default) is displayed in
the active strip.
The main image display area at the bottom of the object displays the
image using a gray or colour scale palette. It may
also be overlayed by symbols when the program requires it e.g. to mark
the image centre position or to display a predicted spot
pattern. There are scrollbars to the left and right of the image
display and at the bottom of the display. The left hand scrollbar is
used to zoom the image (other zoom options are also available). The
bottom scrollbar may be used to re-position the view of a zoomed image
in a horizontal direction and the right hand scrollbar may be used
to re-position the view of a zoomed image in a vertical direcion.
The magnifying window area (top left) shows an
enlarged section from a small part of the image in the main display
area (magnification may be changed by a Control Panel option - see
below). The portion of the image magnified normally follows the cursor
position on the main image display area though its position may be
frozen (fixed) when required. There is an option for doubling the size of the
magnifying window (see Mouse Buttons below). When this is done the
magifying window overlays the top left hand corner of the main
image display area.
The control panel area is situated at the top right of the object
to the right of the magnifying window.
The control panel contains the following panel items:-
- A label indicating the cursor position and pixel intensity.
- A slider to control the contrast in the displayed image.
- Two value items for minimum and maximum scaling thresholds.
- An icon button to select mouse options.
- An icon button to select the image display colour options.
- An icon buttonA drop down menu to select the magnification
for the magnifying window.
- An icon button to select overlaying options.
- An icon button to select the background handling options.
- An icon button to request printer (/file) output of the displayed
image.
- An icon button to request help information.
- An icon button to access additional options including any
additional options provided by the calling program.
The PXImage object makes use of a three button mouse (though a single
button mouse may be used if necessary - see mouse selection icon
button below). The three buttons are used as follows:
- Button1
-
- General Use
- Use with buttons, scrollbars etc.
- User Input
-
These are basically program dependent but would typically be:
- Selection of spot positions on main or magnifying window.
- Selection of an image area.
- Button2
- This button is used for the control of the magnifying window:
- Cursor in main image - freeze/un-freeze (alternately) the image
area displayed in the magnifying window. When frozen, a light blue
square on the main image display shows the position and approximate
size of the frozen area displayed in the magnifying window.
- Cursor in magnifgying window - toggle between small and large
size of magnifying window.
- Button3
- Image zooming
- Single click to re-centre on selected pixel.
- Select an area (point to one corner, hold down button, drag to
other corner and release button). The zoom factor will be the nearest
available value possible and the aspect ratio of the displayed portion
of the image will remain unchanged.
- Double click will restore the image to its original (un-zoomed)
state.
- When the image is zommed, hold down the SHIFT key and press
Button3 to show the un-zoomed image with the zoomed area marked.
Releasing the button returns to the zoomed image display.
Thus the image may be zoomed and the position of the zoomed section
selected either using the scrollbars or using Button3 of the mouse
as described above. When the image is sufficiently zoomed, the pixel
intensities will be shown on the image display (for greyscale images).
When the mouse pointer is within the main image display area or
within the magnifying window, a special cursor is displayed. This
is designed for selecting spot/symbol positions and for visibility
either on images with a light or dark background. It consists of
a cross made up of dashed lines with alternating black and white
segments. The centre of the cross is 'transparent' allowing the
underlying image to show through. Two sizes of cursor may be
used depending on the capability of the display device.
The label at the top of the control panel displays the current cursor
position as a pixel position within the full image as contained in
the image data file. The displayed image will frequently have several
pixels from the original image compressed into one and may possibly
only represent a section of the complete image. When the cursor is
outside the main image display area and the magnifying window area,
the label displays the message 'Cursor Position'. When an image has
been compressed before display then the pixel position is calculated
as the one which would be closest to the centre of the pixel selected
by the cursor position. The pixel intensity is also shown in brackets
following the pixel position.
It may be noted that, when symbols have been overlayed on the main
image display area, they will also appear on the magnifying window
though they will not be magnified in size. Any other overlayed vectors
will be magnified without any thickening of the lines.
If a rectangular area from the main image display is to be selected
(under program control), the user points to one corner of the
rectangle, presses and holds down Button1 of the
mouse and drags it to the opposite corner of the required rectangle.
Button1 is then released and the selected rectangle will be returned
to the calling program. During the selection, the current state of
the rectangle will be outlined on the display. If the user is not happy
with the rectangle being selected then the selection can be dismissed by
clicking on Button2 before Button1 has been released. Button1 is then
released and a new selection may be made.
Control Panel Options
The following paragraphs describe the options which may be selected
via the control panel.
-
Contrast Slider
This slider controls the contrast on the displayed image from minimum
at the left to maximum at the right hand side of the slider bar. The
position is ignored if a user defined colour display has
been selected via the colour choice icon button.
-
Minimum and Maximum Threshold Values
Editable minimum and maximum threshold
values, for scaling the displayed image, are shown in value
items (labels 'Min:' and 'Max:') on the control panel. The range of
pixel values between the minimum and maximum values is divided into
255 equal parts for display using the 255 gray or colour levels
selected. Pixel values lower than the minimum value are displayed
as for the minimum value and pixel values greater than the maximum
value are displayed as for the maximum value. The program ensures that
the maximum threshold value is at least one greater than the minimum
threshold value and also that the minimum and maximum threshold values
are within the range of pixel values in the image. Incorrect input
values will be reset by the program.
-
Mouse Options Icon Button
The normal operation of the PXImage object is based on the use
of a three button mouse. However, if needed, the object may be
controlled using a single button by using the mouse options icon
button to enable Button1 of the mouse to be used as either
Button1, Button2 or Button3. The user will obviously need to
switch between these options as required for a particular
function.
-
Colour Choice Icon Button
This enables the selection of a number of options for the colouring of
the image display. The following choices are available:
- Black on white
- This gives a 255 level gray scale with
increasing blackness as the pixel values increase.
- White on black
- This gives a 255 level gray scale with
increasing whiteness as the pixel values increase.
- User defined
- The program may set a user defined colour
map of 255 colours. This may be changed
under program control as needed. The
object has a default colour scheme if none has
been defined via the calling program.
-
--->
Magnification Icon Button
This enables the selection of the magnifying
factor to be used for the magnifying window. The values are
from 2 to 8.
-
Overlay Icon Button
This enables the selection of a number of options for the display of
overlays (symbols drawn on the image) when present.
Two different sets options may be presented (under program control).
The five icons shown are for the following cases:
- Overlays On (Overlay option types 1 and 2).
- Overlays Of (Overlay option types 1 and 2).
- Overlays Offset (Overlay option type 1).
- Overlay 1 Only (Overlay option type 2).
- Overlay 2 Only (Overlay option type 2).
For the first type, the following choices are available:
- on
- The overlayed symbols are displayed on the
main image display and on the magnifying window.
- off
- The overlayed symbols are not displayed.
- offset
- The overlayed symbols are displayed on the
main image display and on the magnifying
window but the symbols of the overlay set 1
are offset by a constant amount
from the actual positions to which they
refer. This may sometimes be useful when,
for example, a predicted pattern is displayed
as an overlay. In such a case the predicted
pattern symbols would be assigned to overlay
set 1 and any symbols marking observed spot
positions would be assigned to overlay set 2.
By default the offset is to the
left and down by 4 pixels in each direction
on the main image display area though some
programs may set other offsets.
For the second type , the following choices are available:
- on
- The overlayed symbols are displayed on the
main image display and on the magnifying window.
- off
- The overlayed symbols are not displayed.
- overlay 1 symbols on
- Only the symbols belonging to the overlay set 1 are displayed.
- overlay 2 symbols on
- Only the symbols belonging to the overlay set 2 are displayed.
-
Background Options Icon Button
The background image options will only be available if a
background image has been calculated. The options are
as follows:
the image JdlView object. The following choices are available:
- background image included
- The image is presented without any background subtraction being
performed.
- background image subtracted
- The background subtracted image is displayed.
- background image only
- The backgound image is displayed on its own.
-
Print Icon Button
This icon button initiates the process of either printing the
displayed image (with selected annotation) on the printer or
outputting the displayed image to a PNG or JPEG file. When
the button is selected a dialogue window is displayed.
Figure 13: Print Dialogue
This dialogue box enables the following items/options to be set:
- Title
- The title, if given, will be printed underneath the image.
- Width
- This is the required width of the image plot in cms.
The valid range is 0.5 to 18.0 cms.
- Header
- If selected, there will be a header line with the
words "Image Plot: " followed by the date.
- Key
- If selected, a key will be printed at the bottom of the
page containing details about the image section including its
size, orientation, maximum pixel value and scaling thresholds.
- Comment
- If present, the comment text will be output under the
title line (centred on the page). It may be split
into more than one line if it is too long to fit
into a single line.
The alternative file output may be selected via the JPEG File or
PNG File buttons depending on the format required. When one of
these is selected, the dialogue box will appear as follows:
Figure 14: File Output Dialogue
The required output file name may then be given.
Note that the printer and/or file output options will not work
when the PXImage object is used in an applet unless the
appropriate security permissions are in place. This is a
general feature of the use of Java Applets.
-
Help Icon Button
This icon button displays a scrollable window which gives 'Help'
information on how to use the PXImage object. A brief summary is
given on how to use the mouse buttons, how to zoom the image and
the functions of the control panel icon buttons is given.
-
Menu Icon Button
This icon button displays a drop down menu which gives
access to additional functions. There is one built in
function to calculate a background image (see below
for details). Other 'User Supplied Options...' are those, if any, which
have implemented by the calling program.
The object includes an option to calculate a background image which
may then be used for the background subtracted or background image
only displays. It is accessed via the menu option icon button followed
by the selection of the 'Calculate Background Image' item from the displayed
menu. The following dialogue box is then displayed enabling a few
parameters to be set before calculating the background image.
Figure 15: Dialogue Box for Background Image Calculation
The method used assumes an image with spots over a fairly slowly
changing background. The procedure calculates the background
at a pixel by taking the average of the lowest pixel values in a box
surrounding the pixel such that the number of such values is a requested
percentage of the total number of pixels in the box. To optimise the
calculation, the box is walked through the image moving a pixel at a time
starting at the top left. It then repeats the process of left from to right,
then one pixel down, then from right to left, and then one pixel down etc.
until the image has been covered. (In this description the slow moving image
index is visualised as being from top to bottom and the fast one from left
to right). The methods will cope with a maximum background level up to
around 65000. To speed up the calculation the image is normally based
on a compressed image. The following values may be selected for the
calculation:
- Background image compression factor
- Compress (sample) this number of pixels into 1 pixel in each
direction for background image.
- Box size (pixels - compressed image)
- Size, in pixels, of box (after compression of the image)
for each background calculation - preferably an odd number.
- Percentage of pixels for background
- Percentage of pixels within a box to treat as background.
If minus the required percentage value is given is given,
then pixel values of zero will be omitted from the calculation.
The overlay symbols are either vertical crosses, diagonal crosses or
squares which may be drawn in a range of different sizes using up to
six different colours. Options are also available for overlaying boxes and
other vectors on the image using the same six colours.
Facilities are available within the PXImage object and related
software to enable input of image data in any of the eight possible
orders and to display it with the axes again in any of the eight
possible combinations. When several pixels are combined into one then,
under program control, the contributing pixels may either be averaged
or just sampled.
This JdlView object was written for a specific use relating to Protein
Crystallography. It is used for displaying simulations of
monochromatic rotation image X-ray diffraction patterns, Weissenberg
patterns or Laue Diffraction patterns. Laue images may also be
displayed as Gnomonic projections. There two modes of display, a
standard mode and an interactive mode, both of which use colour codings
to represent different classes of spots. In each mode there is a
display area for the simulation, an area to list details of a selected
spot, a control panel area where various options may be selected. The
selection of Rotation/Weissenberg/Laue options is under program
control (e.g. Depending on the value of the diffraction type parameter
in the program PXSim). The following links show some examples:
Figure 16: Example of a Standard Colour Rotation Simulation
Figure 17: Example of an Interactive Rotation Simulation
Figure 18: Example of a Standard Colour Laue Simulation
Figure 19: Example of an Interactive Laue Simulation
Figure 20: Example of a Laue Gronomic Projection Simulation
As far as using the PX Simulation JdlView Object is concerned, the
Rotation and Weissenberg options are identical.
Before describing the detailed options for the various cases, some
features, common to all cases, are described:
- Mouse Buttons
-
The PX Simulation object assumes the use of a three button mouse
(though a single button mouse may be used if necessary - see mouse
selection icon button below). Button2 is not currently used.
The buttons are used as follows:
- Button1
-
- General Use
- Use with buttons, scrollbars etc.
- Spot Selection
- Click on a spot for which details are to be listed. Click away
from the spot to remove the selection.
- Spot labelling
- For interactive colour plots only. To label a spot do the following:
- Point to spot and hold down Button1
- Drag away from spot to required label position
- Release Button1
- Move Label
- (For interactive colour plots only) To move a label hold down
Button1 on the label, drag the label to the new position and release
Button1.
- Remove Label
- (For interactive colour plots only) Double click Button1 on
the label.
- Button3
- Image zooming
- Single click to re-centre on selected pixel.
- Select an area (point to one corner, hold down button, drag to
other corner and release button). The zoom factor will be the nearest
available value possible and the aspect ratio of the displayed portion
of the image will remain unchanged.
- Double click will restore the image to its original (un-zoomed)
state
- When the image is zommed, hold down the SHIFT key and press
Button3 to show the un-zoomed image with the zoomed area marked.
Releasing the button returns to the zoomed image display.
- Control Panel
-
The common items on the control panel are as follows:
-
Mode Button
This button toggles between the standard colour display and
the interactive colour display. (For Laue simulations, where
gnomonic projections have been calculated, the mode button will step
through the standard and interactive simulations first for the
normal pattern and then for the gnomonic projection).
-
Mouse Options Icon Button
The normal operation of the PX Simulations object is based on the use
of a three button mouse. However, if needed, the object may be
controlled using a single button by using the mouse options icon
button to enable Button1 of the mouse to be used as either
Button1, or Button3 (Button2 not currently used).
The user will obviously need to switch between these options as
required for a particular function.
-
Help Icon Button
This icon button displays a scrollable window which gives 'Help'
information on how to use the PX Simulations object. A brief summary is
given on how to use the mouse buttons, how to zoom the image and
the functions of the control panel icon buttons is given.
-
Print Icon Button
This icon button initiates the process of either printing the
displayed simulation (with selected annotation) on the printer or
outputting the displayed pattern to a PNG or JPEG file. When
the button is selected a dialogue window is displayed.
Figure 21: Print Dialogue
This dialogue box enables the following items/options to be set:
- Title
- The title, if given, will be printed underneath the
simulated pattern.
- Width
- This is the required width of the simulated pattern plot in cms.
The valid range is 0.5 to 18.0 cms.
- Header
- If selected, there will be a header line showing the type of
plot followed by the date.
- Key
- If selected, a key will be printed at the bottom of the
page containing details about the parameters on which the
predicted simulation was based.
- Black bg
- If selected, the page will be printed with a black
background with any text required being output in a light
colour.
- Comment
- If present, the comment text will be output under the
title line (centred on the page). It may be split
into more than one line if it is too long to fit
into a single line.
The alternative file output may be selected via the JPEG File or
PNG File buttons depending on the format required. When one of
these is selected, the dialogue box will appear as follows:
Figure 22: File Output Dialogue
The required output file name may then be given. Note that, with these
type of plots with sharp features and a limited number of colours, the
PNG files provide a higher quality output than JPEG files.
Note that the printer and/or file output options will not work
when the PXImage object is used in an applet unless the
appropriate security permissions are in place. This is a
general feature of the use of Java Applets.
- Scrollbars
- There are scrollbars to the left and right of the simulated pattern
display and at the bottom of the display. The left hand scrollbar is
used to zoom the pattern (other zoom options are also available). The
bottom scrollbar may be used to re-position the view of a zoomed pattern
in a horizontal direction and the right hand scrollbar may be used
to re-position the view of a zoomed pattern in a vertical
direcion.
- Zooming
- The two methods for zooming in on the pattern have already been
described. These are the use of the scrollbars and the use of Button3
of the mouse.
Rotation and Weissenberg Simulations
- Control Panel Items
- Standard Colour Display
When this option is selected, the Rotation/Weissenberg simulation
is displayed as coloured spots displayed on a black
background. Various display options are available:
- Colour Coding
- Various colour codings are available. The display is qualified by the
settings of other control panel items. The options available are:
- Fulls/partials
- The spots are split into three categories, fulls partials
and those which are on the edge of the cusp region and
are partly visible. They are colour coded as follows:
- blue: fulls.
- cyan: partials (up to maximum used in
the prediction).
- red: cusp partials.
- Partiality 1
- The spots are colour coded by their partiality as
follows:
- blue: fulls.
- cyan: partial <=n as set in the
Partial 'n' panel item.
- yellow: partial >n and up to the
maximum used in the prediction.
- orange: wide partial (greater than the
maximum partiality used in the
prediction.
- red: cusp partial.
- Partiality 2
- The spots are colour coded by their partiality as follows:
- blue: fulls.
- cyan: partial =2.
- green: partial =3.
- yellow: partial >3 and up to the
maximum used in the prediction.
- orange: wide partial (greater than the
maximum partiality used in the
prediction).
- red: cusp partial.
- All the same
- All the recorded spots are displayed in the same (blue)
colour.
- Overlap status
- The spots are colour coded by whether or not they are spatially
overlapped. The colour coding is as follows:
- blue: not overlapped.
- yellow: spatially overlapped spot.
- Spot Types
- The types of spots to be displayed may be chosen from the
following three options:
- Display 'all' spots i.e. fulls and partials.
- Display fulls only.
- Display partials only.
- Spatials
- There are three options for the display of spatially
overlapped spots:
- Display all spots including spatially overlapped spots.
- Exclude spatially overlapped spots.
- Display the spatially overlapped spots only.
- Symbols
- The user may select one of four spot size options, small, medium,
large or actual size. For the last option, the size used is
calculated from the under program 'spot_size' parameter of the
Diffraction Data Module on which the display is based.
Note that when an image is zoomed, the displayed symbol size
remains unchanged for the first three options
but is scaled appropriately for the fourth option.
- Key
- The display, of a key at the top left of the display area showing the
colour coding, may be turned on or off via this choice item.
- Partial 'n'
- The partial 'n' value, used in deciding in which category a partial
spot is to be included for the Partiality 1 colour coding,
can be reset via this value item. The value must be
in the range of 2 to the maximum value used in the prediction.
- Interactive Colour Display
When this option is selected, the Rotation/Weissenberg simulation
is displayed in a similar manner to that for the standard colour
display but the details of the colour codings available are
different and there are also options to vary various parameters via
a slider and a spot labelling option is available using Button1
of the mouse. Because of the varying prediction parameters, spatial
overlaps are not calculated for the interactive colour displays.
Various display options are available:
- Colour Coding
- Various colour codings are available. The display is qualified by the
settings of other control panel items. The options available are:
- Fulls/partials
- The spots are split into three categories, fulls partials
and those which are on the edge of the cusp region and
are partly visible. They are colour coded as follows:
- blue: fulls.
- cyan: partials (up to maximum used in
the prediction).
- red: cusp partials.
- Partiality
- The spots are colour coded by their partiality as
follows:
- blue: fulls.
- cyan: partial <=n as set in the
Partial 'n' panel item.
- yellow: partial >n and up to the
maximum used in the prediction.
- orange: wide partial (greater than the
maximum partiality used in the
prediction.
- red: cusp partial.
- Labels
- Once labels have been drawn, this item enables the labels to
be displayed or not displayed as required.
- Slider
- This item selects the current prediction parameter which is to
be varied using the slider. The following parameters may be
chosen:
- Oscillation angle (degrees).
- Eta (mosaicity) (degrees).
- DeltaLambda/Lambda (x1000).
- Horizontal divergence (degrees).
- Correlated dispersion (degrees).
- Key
- The display, of a key at the top left of the display area showing the
colour coding, may be turned on or off via this choice item.
- Part-n
- The partial 'n' value, used in deciding in which category a partial
spot is to be included for the Partiality 1 colour coding
option a nodal, can be reset via this value item. The value must be
in the range of 2 to the maximum value used in the prediction.
- Listing Spot Details
When the mouse Button1 is pressed with the cursor on a spot position,
details of that spot will be listed in the spot details
area. The following information is listed:
- The indices
- The coordinates
- The detector xd, yd coordinates in millimetres
from the centre of the pattern.
- The partiality
- For a fully recorded spot the message 'fully recorded' is given.
For a partial the partiality is given and the offset from the current
image of the start image for the spot is indicated. 'Wide' or 'Cusp'
partials are flagged as such.
- The overlap status
- A symbol indicates whether or not the spot is spatially
overlapped. For a non-overlapped spot, the symbol is a grey disk
and for a spatially overlapped spot, the symbol is a grey disk
partly overlapped by a red disk. If the overlap status has not
been calculated, a grey circle overlayed with a red cross is
shown.
The selected spot is marked by a surrounding white circle on the display
area. The selection may be removed by clicking Button1 of the mouse
when the cursor is within the display area but not pointing to a
spot. When selecting a spot, the nearest spot to the cursor is
selected provided that the distance squared (pixels)
to the spot is no more than 18.
- Find hkl
Underneath the reflection details listing, there is a value
item which enables a set of indices to be input for a reflection
to be searched for. If found, a cross or circle will mark the
reflection position on the plot and the reflection details will
be listed. If the reflection is not found, the message 'Not found:'
followed by the indices will be displayed in the value area. For
a found reflection,a circle will be drawn for a standard colour
plot or for an interactive colour plot if the reflection is
currently displayed. When a reflection has been predicted for
an interactive plot, but is not currently displayed, the spot position
will be marked with a cross. When a reflection is selected from the
plot, its indices will be shown in the 'Find hkl' value area.
Laue Simulations
- Control Panel Items
- Standard Colour Display
When this option is selected, the Laue simulation (or gnomonic
projection) is displayed as coloured spots displayed on a black
background. Various display options are available:
- Colour Coding
- Various colour codings are available. The display is qualified by the
settings of other control panel items. The options available are:
- Wavelength
- The wavelength range is split into eight ranges
which are identified by eight different colours
on a scale running from blue (low wavelength)
to red (high wavelength). Multiple spots are
colour coded by their highest wavelength
component.
- Multiplicity
- The spots are colour coded by their multiplicity as
follows:
- blue: singles.
- cyan: doubles.
- yellow: triples.
- red: multiplicity > 3.
- Wavelength/Multiplicity
- The singles are colour coded by wavelength, The
wavelength range is split into eight ranges
which are identified by eight different colours
on a scale running from blue (low wavelength)
to red (high wavelength). The multiples are colour
coded white.
- Nodality
- The spots are colour coded by their nodalityity as follows:
- blue: non-nodal spot.
- yellow: nodal spot. The
nodal index may be set via the 'Nidx'
value item on the control panel and has
a default starting value of 4.
- Spot Types
- The types of spots to be displayed may be chosen from the
following three options:
- Display 'all' spots i.e. singles and multiples.
- Display singles only.
- Display multiples only.
- Spatials
- There are three options for the display of spatially
overlapped spots:
- Display all spots including spatially overlapped spots.
- Exclude spatially overlapped spots.
- Display the spatially overlapped spots only.
- Symbols
- The user may select one of four spot size options, small, medium,
large or actual size. For the last option, the size used is
calculated from the under program 'spot_size' parameter of the
Diffraction Data Module on which the display is based.
Note that when an image is zoomed, the displayed symbol size
remains unchanged for the first three options
but is scaled appropriately for the fourth option.
- Key
- The display, of a key at the top left of the display area showing the
colour coding, may be turned on or off via this choice item.
- Nidx
- The nodal index, used in deciding whether or not a spot is a nodal for
the plot colour coded by nodality, can be reset via the 'Nidx' value
item on the control panel. The value must be in the range 0
to 12.
- Interactive Colour Display
When this option is selected, the Laue simulation (or gnomonic projection)
is displayed in a similar manner to that for the standard colour
display but the details of the colour codings available are
different and there are also options to vary various parameters via
a slider and a spot labelling option is available using Button1
of the mouse. Because of the varying prediction parameters, spatial
overlaps are not calculated for the interactive colour displays.
Various display options are available:
- Colour Coding
- Various colour codings are available. The display is qualified by the
settings of other control panel items. The options available are:
- Wavelength
- The wavelength range is split into eight ranges
which are identified by eight different colours
on a scale running from blue (low wavelength)
to red (high wavelength). Multiple spots are
colour coded by their highest wavelength
component.
- Multiplicity
- The spots are colour coded by their multiplicity as
follows:
- blue: singles.
- cyan: doubles.
- yellow: triples.
- red: multiplicity > 3.
- Wavelength/Multiplicity
- The singles are colour coded by wavelength, The
wavelength range is split into eight ranges
which are identified by eight different colours
on a scale running from blue (low wavelength)
to red (high wavelength). The multiples are colour
coded white.
- Nodality
- The spots are colour coded by their nodalityity as follows:
- blue: non-nodal spot.
- yellow: nodal spot. The
nodal index may be set via the 'Nidx'
value item on the control panel and has
a default starting value of 4.
- Labels
- The following options are available for the labels' display:
- Labels off
- Minimum hkl - when a labelled spot is a multiple,
show the indices of the component with the lowest indices.
- Maximum hkl - when a labelled spot is a multiple,
show the indices of the component with the highest indices.
- Nodal hkl - show the nodal indices for the spot i.e. the
indices divided by their highest common factor.
- Slider
- This item selects the current prediction parameter which is to
be varied using the slider. The following parameters may be
chosen:
- Lambda-min (Angstroms).
- Lambda-max (Angstroms).
- Dmin (Angstroms).
- Key
- The display, of a key at the top left of the display area showing the
colour coding, may be turned on or off via this choice item.
- Nidx
- The nodal index, used in deciding whether or not a spot is a nodal for
the plot colour coded by nodality, can be reset via the 'Nidx' value
item on the control panel. The value must be in the range 0 to 12.
- Listing Spot Details
When the mouse Button1 is pressed with the cursor on a spot position,
details of that spot will be listed in the spot details
area. The following information is listed:
- The indices
- For a multiple spot these are for the lowest harmonic
present.
- The wavelength
- This is given in brackets following the indices (Angstroms).
For a multiple spot this is for the lowest harmonic present.
- The coordinates
- The detector xd, yd coordinates in millimetres
from the centre of the pattern.
- The multiplicity
- For a multiple spot, the multiplicity is followed by the range
of harmonics present.
- The overlap status
- A symbol indicates whether or not the spot is spatially
overlapped. For a non-overlapped spot, the symbol is a grey disk
and for a spatially overlapped spot, the symbol is a grey disk
partly overlapped by a red disk. If the overlap status has not
been calculated, a grey circle overlayed with a red cross is
shown.
The selected spot is marked by a surrounding white circle on the display
area. The selection may be removed by clicking Button1 of the mouse
when the cursor is within the display area but not pointing to a
spot. When selecting a spot, the nearest spot to the cursor is
selected provided that the distance squared (pixels)
to the spot is no more than 18.
- Find hkl
Underneath the reflection details listing, there is a value
item which enables a set of indices to be input for a spot
to be searched for. If found, a cross or circle will mark the
reflection position on the plot and the reflection details will
be listed. If the actual reflection is not found, but a spot with
the same nodal indices is present, details will be shown as before
but the reflection indices will be surrounded by [[ ]]
in the 'Find hkl' value area. If the reflection or harmonic
is not found, the message 'Not found:'
followed by the indices will be displayed in the value area. For
a found reflection,a circle will be drawn for a standard colour
plot or for an interactive colour plot if the reflection is
currently displayed. When a reflection has been predicted for
an interactive plot, but is not currently displayed, the spot position
will be marked with a cross. When a reflection is selected from the
plot, its indices will be shown in the 'Find hkl' value area.
This is a special purpose object for use within the field of Protein
crystallography. It is used to display, in pictorial or graphical
form, the coverage of the unique part of the reciprocal lattice by the
currently predicted and/or measured data. There are basically three
options:
- Display of Reciprocal Lattice Layers.
- Three Dimensional (Rotating) View.
- Histograms of Unique Coverage.
The object may be used to display unique data derived from either
Rotation or Laue data. In the former case reflections may be
categorized by whether or not they were fully recorded and in the
latter case whether they were single reflection spots or deconvoluted
from multiple spots.
In each case, there is a main display area on which the data is
displayed and a control panel area at the top which enables various
options to be selected. On each control panel, there is a
'Mode' button which is used to step through the three types
of display. The three cases are described in detail below:
- Display of Reciprocal Lattice Layers
The main display area shows a single section of the reciprocal lattice
at a time showing which reflections are part of the unique area of the
reciprocal lattice and which of these reflections have been predicted
or observed. An example is shown below:
Figure 23: Unique Coverage - Layers
Different categories of reflections e.g. fulls, singles,
partials or deconvoluted multiples may be included in the plot and,
where appropriate, merged or unmerged anomalous data pairs may be indicated.
Spots predicted as spatial overlaps may be included or excluded as desired.
Spots which are classified as unknown full/partial/single/multiple
(e.g. derived from a merged dataset) are included in the display as
fully recorded or single (and non-spatially overlapped) spots. If
anomalous separated data is displayed then these spots may also be
of unknown sign (see below for colour coding). In all cases the
section axis is along 'l'. On the l=0 section the a* and b* axes are displayed.
The points on the unique part of the reciprocal lattice are marked by small
greenish dots for those spots which have not been predicted/measured.
The following options are available via the control panel (the case
for the Rotation data case is shown first with any variation for the
Laue case following in square brackets):
- Fulls [Singles]
- The options are for fulls [singles] to be included or excluded.
- Partials [Mults]
- For partials the options are as follows:
- none.
- partiality = 2 partials only included.
- partiality <= 3 partials only included.
- partiality <= nwmax partials included (nwmax is a parameter
from the Diffraction Data Module (DDM)).
[For deconvoluted multiples the options are as follows:
- none.
- deconvoluted from multiplicity = 2 only included.
- deconvoluted from multiplicity <= 3 only included.
- deconvoluted from any multiple.]
- Anom
- The options are as follows:
- merged.
- separate.
- both I+ and I- measurements made.
- I+ measurement made.
- I- measurement made.
For merged data, all measured reflections are shown as yellow
spots. For the other cases, the colour coding is as follows:
- yellow: Both an I+ and an I- reflection are
present.
- red: Only the I+ reflection is present.
- blue: Only the I- reflection is present.
- white : Unknown sign (i.e. both I+ and I- are
not present though I+ or I- may be
present in addition to measurements
flagged as being of unknown sign.
- Spatials
- Spatially overlapped spots may be either included or excluded.
- Up and Down buttons and Slider
- Clicking on one of these buttons moves up or down one layer of
the reciprocal lattice. The slider between the buttons enables
rapid access to the different layers though, if there are a
large number of layers, a final adjustment may be needed using
the Up/Down buttons to get to the exact layer required. The
current layer number is shown at the bottom left of the plot.
- Cycle button and Slider
- Clicking the Cycle button will start/stop automatically cycling
through the layers. The speed of the cycling may be adjusted
using the slider to the left of the Cycle button.
- Printer Icon Button
- This initiates the output of the plots to a printer or a file.
Details are given below.
- 3D Unique Coverage Plot
In this case, the main display area shows a three dimensional
perspective view of the unique section of the reciprocal lattice.
The picture indicates by colour coded dots which of these reflections
have been predicted or observed. This view may be rotated
automatically or its orientation changed by means of a slider. An
example is shown below:
Figure 24: Unique Coverage - 3D Plot
Different categories of reflections e.g. fulls, singles,
partials or deconvoluted multiples may be included in the plot and,
where appropriate, merged or unmerged anomalous data pairs may be indicated.
Spots predicted as spatial overlaps may be included or excluded as desired.
Spots which are classified as unknown full/partial/single/multiple
(e.g. derived from a merged dataset) are included in the display as
fully recorded or single (and non-spatially overlapped) spots. If
anomalous separated data is displayed then these spots may also be
of unknown sign (see below for colour coding). The a* and b* axes are
displayed in the horizontal plane an c* is in an upwards direction.
The points on the unique part of the reciprocal lattice are marked by small
greenish dots for those spots which have not been predicted/measured.
The following options are available via the control panel (the case
for the Rotation data case is shown first with any variation for the
Laue case following in square brackets):
- Fulls [Singles]
- The options are for fulls [singles] to be included or excluded.
- Partials [Mults]
- For partials the options are as follows:
- none.
- partiality = 2 partials only included.
- partiality <= 3 partials only included.
- partiality <= nwmax partials included (nwmax is a parameter
from the Diffraction Data Module (DDM)).
[For deconvoluted multiples the options are as follows:
- none.
- deconvoluted from multiplicity = 2 only included.
- deconvoluted from multiplicity <= 3 only included.
- deconvoluted from any multiple.]
- Anom
- The options are as follows:
- merged.
- separate.
- both I+ and I- measurements made.
- I+ measurement made.
- I- measurement made.
For merged data, all measured reflections are shown as yellow
spots. For the other cases, the colour coding is as follows:
- yellow: Both an I+ and an I- reflection are
present.
- red: Only the I+ reflection is present.
- blue: Only the I- reflection is present.
- white : Unknown sign (i.e. both I+ and I- are
not present though I+ or I- may be
present in addition to measurements
flagged as being of unknown sign.
- Spatials
- Spatially overlapped spots may be either included or excluded.
- Up and Down buttons and Slider
- Clicking on one of these buttons moves the viewing angle
of the three dimensional plot up or down 5 degrees
at a time up to a maximum view angle of plus or minus
45 degrees. The slider between the buttons enables the
3D plot to be rotated to any of the positions within
the possible 360 degrees of rotation.
- Cycle button and Slider
- Clicking the Cycle button will start/stop automatically rotating
the 3D view of the reciprocal lattice. The speed of the
rotation may be adjusted using the slider to the left of the Cycle button.
- Printer Icon Button
- This initiates the output of the plots to a printer or a file.
Details are given below.
- Unique Coverage Histograms
In this case, the main display area shows one of a series of
histograms. These are all plots against resolution. The requested
resolution range is divided into eight equal bins of
4.sin**2(theta)/lambda**2. An example is shown below:
Figure 25: Unique Coverage - 3D Plot
Different categories of reflections e.g. fulls, singles,
partials or deconvoluted multiples may be included in the plots.
The three types of histogram available are as follows:
:
- Unique Data
This plot shows the percentage of coverage of the unique data within
each resolution bin. Where partials [deconvoluted multiples] are
included two coloured bars are drawn, an orange one indicating the coverage
for the full [single] reflections and an additional green section
showing the coverage with the included partials [deconvoluted
multiples]. The overall percentage coverage for each of these cases
is given at the top of the plot. Where no partials [deconvoluted
multiples] are included, an orange bar shows the coverage for the
fulls [singles] data and the overall coverage by the fulls [singles]
data is given at the top of the plot.
- Acentric Pairs
This plot shows the percentage coverage of the unique acentric
data within each resolution bin. A reflection must be present for
each mate of a Bijvoet pair to be included. Where partials
[deconvoluted multiples] are included in the analysis, two coloured
bars are drawn, an orange one indicating the coverage
for the full [single] reflections and an additional green section
showing the coverage with the included partials [deconvoluted multiples].
The overall percentage coverage for each of these cases is given
at the top of the plot. Where no partials [deconvoluted multiples] are
included, an orange bar shows the coverage for the
fulls [singles] data and the overall coverage by the fulls [singles]
data is given at the top of the plot. Reflections of unknown sign are
excluded from the analyses of acentric pairs.
- Multiplicity
This plot shows the average reflection measurement multiplicity
within each resolution bin. This refers to the number of times each
reflection was measured and not, in the case of Laue data, to the
multiplicity of individual spots (multiples). Where partials
[deconvoluted multiples]
are included, two coloured bars are drawn, an orange one indicating
the multiplicity for the full [single] reflections and an additional
green section showing the multiplicity with the included partials
[deconvoluted multiples]. Note: It can happen in some cases that the
multiplicity in a resolution bin decreases when partials [deconvoluted
multiples] data are included as there will be additional reflections
which could have any multiplicities; in such cases, a green line
will be drawn through the orange bar at the appropriate height.
The overall average multiplicity for each
of these cases is given at the top of the plot. Where no partials
[deconvoluted multiples] are included, an orange bar shows the
multiplicity for the fulls [singles] data and the average multiplicity
for the fulls [singles] data is given at the top of the plot.
The following options are available via the control panel (the case
for the Rotation data case is shown first with any variation for the
Laue case following in square brackets):
- Fulls [Singles]
- The options are for fulls [singles] to be included or excluded.
- Partials [Mults]
- For partials the options are as follows:
- none.
- partiality = 2 partials only included.
- partiality <= 3 partials only included.
- partiality <= nwmax partials included (nwmax is a parameter
from the Diffraction Data Module (DDM)).
[For deconvoluted multiples the options are as follows:
- none.
- deconvoluted from multiplicity = 2 only included.
- deconvoluted from multiplicity <= 3 only included.
- deconvoluted from any multiple.]
- Type
- This selects the type of histogram to be displayed.The options
are as follows:
- Unique.
- Acentric Data.
- Multiplicity.
- Spatials
- Spatially overlapped spots may be either included or excluded.
- Printer Icon Button
- This initiates the output of the plots to a printer or a file.
Details are given below.
Printer/File Output
When the printer icon button is selected a dialogue window is
displayed, for example as follows:
Figure 26: Print Dialogue
The 'Multiple' check box is only present for the first type of unique
data coverage plot (Reciprocal Lattice Layers). In general, the
dialogue box enables the following items/options to be set:
- Title
- The title, if given, will be printed underneath the displayed plot.
- Width
- This is the required width of the simulated pattern plot in cms.
The valid range is 0.5 to 18.0 cms.
- Header
- If selected, there will be a header line showing the type of
plot followed by the date.
- Multiple
- This is only present for the Reciprocal Lattice Layers type
of plot. If selected, this enables the output of a plot with
a whole series of layers shown (up to 9 per page). The
dialogue changes in that the 'Header' and 'Width' options
are removed but there is instead a 'Layers or All' option.
In this, the user may give a list of layer numbers and/or
ranges of layers (e.g. 1, 2, 3, 10-20, 25) or the code 'All'
(the initial default) for all layers.
- Black bg
- If selected, the page will be printed with a black
background with any text required being output in a light colour.
- Comment
- If present, the comment text will be output under the
title line (centred on the page). It may be split
into more than one line if it is too long to fit
into a single line.
The alternative file output may be selected via the JPEG File or
PNG File buttons depending on the format required. When one of
these is selected, the dialogue box will appear as follows:
Figure 27: File Output Dialogue
The required output file name may then be given. Note that, with these
type of plots with sharp features and a limited number of colours, the
PNG files provide a higher quality output than JPEG files.
Note that the printer and/or file output options will not work
when the PXImage object is used in an applet unless the
appropriate security permissions are in place. This is a
general feature of the use of Java Applets.
The panel items are objects which are used in the coding of the higher
level JdlView objects to provide items like labels, buttons, sliders
etc. Not all of them require user input, but for those that do, their
use is described in this section.
The following figure shows the available panel items (though not all
variations are shown):
Figure 28: JdlView Panel Items
These are used as follows:
- Labels
These may be used to output text or labels with an image or drawn picture.
They have no user input.
- Buttons
There are buttons of various shapes and an up-down arrow pair button.
All respond to a mouse Button 1 click though the diamond button, for example,
can be used as an indicator by a program (using its in and out states), in
which case it does not accept user input.
- Value Item
The basic value item (a) displays a parameter name (label) at the left hand
side and a value field at the right hand side. When the value field has
been selected (click on it with Button 1 of the mouse), a new value may
be input. A cursor in the value field indicates that value input is
in progress. The value field must have the keyboard focus to receive
input; this is automatically requested when the value field is first
selected and if it is lost the user needs to click Button 1 on the value
field again. When the value field has the keyboard focus, the cursor flashes
on and off at 400 ms intervals which increase to intervals of 1.5 seconds
when the focus is lost. Selected text may be pasted in to the value field using
by clicking Button 2 of the mouse when the selected value field has
the keyboard focus. Pressing the Return or Enter keys on the keyboard
completes the input of the new value. If the Escape key
on the keyboard is pressed, the value input will be aborted and the
previous value restored. If a value is too long to be displayed then
a scroll arrow will be shown at one end of the value field. Dragging
the mouse Button 2 along the field will let the user scan the full
value string (to the left moves the view towards the start of the
string and to the right moves the view towards the end of the string).
A version (b) with a drop down menu may also be used. If the arrow button
is selected (Button 1 click) a pop-up menu will be displayed with a choice
of values. A value is selected from this menu by clicking Button 1 on the
required item. If Button 1 is clicked with the pointer not on the menu,
the menu will be removed without any change to the value. Normally, when
a value item has a menu option available, a new value may be input as
for the standard case described above; however, there is an option to
allow only value changes via the menu and in this case the button will be
highlighted in blue if an attempt is made to change the value by selecting
the value field.
A version (c) with an up/down button pair is also available. This enables
the user to step up and down though a series of values as implemented
by the calling program. When this option is available, a new value may
still be input as for the standard case described above.
A version (d) may be used for parameters which toggle between on/off values
or yes/no values. In this case, selecting the value field will change the
value to its opposite value.
Occasionally a value item may be used, without a value field, as a label.
This may be used, for example, in the parameter table object. When in this
state, there is no user input.
- Slider
The slider enables a value to be selected from a value range. The value
is changed by pointing to the slider grip, holding down Button 1 of the
mouse and dragging it to the left or right as required and then
releasing the mouse button when the required position is reached.
Note that the program using the slider may choose to make continuous
adjustments while the slider grip is being dragged or may wait until
the grip is released before responding to the new value
- Separator
This is just used to separate items on a display. There is no user input.
- Scrollbar
The scroll bar item may be used to scroll though a window or as another
form of slider. The slider is moved by dragging the grip as for the
slider item described above. In addition, the program can respond to
clicking Button 1 on an end arrow of the scrollbar item (usually to
make a minimum increment in the scrolled value) or on 'empty space'
between the grip and an end arrow to make (usually to make a larger
increment in the scrolled value). As for the slider, the program may
choose to respond continuously to the movement of the grip or to
respond only when the grip is released.
To make it clear when the mouse pointer is on a scrollbar, it is
changed to a special form as shown to the right of the scrollbar
in the figure.
- Command Line
This allows for the output of a prompt followed by the input of a
text string (all on a single line. When input is expected, a text
cursor will be displayed. The input field must have the keyboard focus
to receive input; this is automatically requested when the input is
first requested and if it is lost the user needs to click Button 1 on
the input field again. When the input field has the keyboard focus,
the cursor flashes on and off at 400 ms intervals which increase
to intervals of 1.5 seconds when the focus is lost. Selected text
may be pasted in to the value field using by clicking Button 2 of
the mouse when the input field has the keyboard focus.
⇑ Up 2
⇑ Up 1
⇑ Top of this