Papaya viewer - command to view next slice - dicom

I am using papaya to view DICOM images. http://ric.uthscsa.edu/mango/papaya.html
I wanted to know how can I move to the next slice using the keyboard keys.
Since all the command is embedded on the javascript file, is there a specific function I should be looking for ?
Please help.

See the incrementAxial(), incrementCoronal(), and incrementSagittal() functions in viewer.js:
papaya.viewer.Viewer.prototype.incrementAxial
papaya.viewer.Viewer.prototype.incrementCoronal
papaya.viewer.Viewer.prototype.incrementSagittal
They take one argument, a boolean to indicate whether to increment (true) or decrement (false).
In order to know which one to increment, you need to know which slice direction is the main slice. See below for an example of how that it is handled:
if (this.mainImage.sliceDirection === papaya.viewer.ScreenSlice.DIRECTION_AXIAL) {
this.incrementAxial(false);
} else if (this.mainImage.sliceDirection === papaya.viewer.ScreenSlice.DIRECTION_CORONAL) {
this.incrementCoronal(false);
} else if (this.mainImage.sliceDirection === papaya.viewer.ScreenSlice.DIRECTION_SAGITTAL) {
this.incrementSagittal(true);
}

Related

Gremlin graph traversal backtracking

I have some code that generates gremlin traversals dynamically based on a query graph that a user supplies. It generates gremlin that relies heavily on backtracking. I've found some edge cases that are generating gremlin that doesn't do what I expected it to, but I also can't find anything online about the rules surrounding the usage of some of these pipes (like 'as' and 'back' in this case). An example of one of these edge cases:
g.V("id", "some id").as('1').inE("edgetype").outV.has("#class", "vertextype").as('2').inE("edgetype").outV.has("#class", "vertextype").filter{(it.getProperty("name") == "Bob")}.outE("edgetype").as('target').inV.has("id", "some id").back('2').outE("edgetype").inV.has("id", "some other id").back('target')
The goal of the traversal is to return the edges that were 'as'd as 'target'. When I run this against my orientdb database it encounters a null exception. I narrowed down the exception to the final pipe in the traversal: back('target'). I'm guessing that the order of the 'as's and 'back's matters and that the as('target') went 'out of scope' as soon as back('2') was executed. So a few questions:
Is my understanding (that 'target' goes out of scope because I backtracked to before it was 'as'd) correct?
Is there anywhere I can learn the rules surrounding backtracking without having to reverse engineer the gremlin source?
edit:
I found the relevant source code:
public static List<Pipe> removePreviousPipes(final Pipeline pipeline, final String namedStep) {
final List<Pipe> previousPipes = new ArrayList<Pipe>();
for (int i = pipeline.size() - 1; i >= 0; i--) {
final Pipe pipe = pipeline.get(i);
if (pipe instanceof AsPipe && ((AsPipe) pipe).getName().equals(namedStep)) {
break;
} else {
previousPipes.add(0, pipe);
}
}
for (int i = 0; i < previousPipes.size(); i++) {
pipeline.remove(pipeline.size() - 1);
}
if (pipeline.size() == 1)
pipeline.setStarts(pipeline.getStarts());
return previousPipes;
}
It looks like the BackFilterPipe does not remove any of the aspipes between the back pipe and the named as pipe, but they must not be visible to pipes outside the BackFilterPipe. I guess my algorithm for generating the code is going to have to be smarter about detecting when the target is within a meta pipe.
Turns out the way I was using 'as' and 'back' made no sense. When you consider that everything between the 'back('2')' and the 'as('2')' is contained within the BackFilterPipe's inner pipeline, it becomes clear that meta pipes can't be overlapped like this: as('2'), as('target'), back('2'), back('target').

Get cell types when reading and parsing excel files

I am trying to read and parse and excel and some unclear things come into play as usual for me.
Here is what i have:
while (true)
{
comVariantCell1 = cells.item(row, 1).value().variantType();
comVariantCell2 = cells.item(row, 2).value().variantType();
//if an empty cell is found, processing will stop and user will get an error message in order to solve the inconsistency.
if (comVariantCell1 != COMVariantType::VT_EMPTY && comVariantCell2 != COMVariantType::VT_EMPTY)
{
//both cells have values, check their types.
importedLine = conNull();
progress1.setText(strfmt("Importing row %1", row));
if (cells.item(row, 1).value().variantType() == COMVariantType::VT_BSTR)
{
importedLine += cells.item(row, 1).value().bStr();
}
else
{
importedLine += cells.item(row, 1).value().double();
}
importedLine += cells.item(row, 2).value().double();
importedLinesCollection += [importedLine]; //conIns(importedLinesCollection, row - 1, (importedLine));
row++;
}
else
{
info (strFmt("Empty cell found at line %1 - import will not continue and no records were saved.", row));
break;
}
}
Excel format:
Item number Transfer Qty
a100 50.5
a101 10
a102 25
This worked well to check if the cell type is string: COMVariantType::VT_BSTR
but what should i use to check for a real or integer value ?
I am pretty sure in this case, the quantity will be not contain real values but anyway, it could be useful in the future to make the difference between these two types.
I have to mention that, even if i have an int value and I use cells.item(row, 1).value().int() it won't work. I can't see why.
Why do i want to make the difference? Because if it's forbidden to have real values in the quantity column ( at least in my case ), i want to check that and give the user the opportunity to put a correct value in that place and maybe further investigate why that happened to be there.
Take a look on how it is done in \Classes\SysDataExcelCOM\readRow.
It is basically using switch to test the type. This is really boring!
Also take a look on ExcelIO, a class I made some years ago. It reads Excel and returns each row as a container. This is a more high-level approach.
As a last resort you could save the Excel as a tab separated file. Then use TextIO to read the content. This will be at least 10 times faster than using Excel!

"Down arrow" moves cursor to end of line - how to turn it off

In IPython Notebook / Jupyter, arrow up/down keystrokes within a cell are handled by CodeMirror (as far as I can tell). I use these actions a lot (re-bound to control-p / control-n) to move between cells; but at the end of every cell, the cursor moves to end of line first before jumping to the next cell. This is counter-intuitive and, to me, rather distracting.
Is there any way to configure CodeMirror to make this move down to be just that - a move down?
Thanks!
The moving-to-next-cell behavior is defined by IPython wrapper code, which probably checks whether the cursor is at the end of the current cell, and overrides the default CodeMirror behavior in that case. You'll have to find that handler and somehow replace it with one that checks whether the cursor is on the last line. (I don't know much about IPython, only about CodeMirror, so I can't point you at the proper way to find and override the relevant code. They might have bound the Down key, or they might have overridden the goLineDown command.)
Knowing that I wasn't alone in wanting to skip the "going to end of line" behavior when going down from the last line of a code cell, I investigated that behavior and found out that:
it's CodeMirror that goes to the end of line when you type down in the last line of a code cell (file: codemirror.js ; "methods": findPosV and moveV)
and it's IPython that decides what to do with the "down" event after it has been handled by CodeMirror (file: cell.js ; class: Cell ; method: handle_codemirror_keyevent) ; looking at the code, I saw that IPython ignores the event when not at the last character of the last line.
This essentially confirms Marijin's answer.
The primary goal being to jump to the next cell, I think there's no need to prevent CodeMirror from going to the end of that line. The point is to force IPython to handle the event anyway.
My solution was to change the code from Cell.prototype.handle_codemirror_keyevent to this:
Cell.prototype.handle_codemirror_keyevent = function (editor, event) {
var shortcuts = this.keyboard_manager.edit_shortcuts;
var cur = editor.getCursor();
if((cur.line !== 0) && event.keyCode === 38){
// going up, but not from the first line
// don't do anything more with the event
event._ipkmIgnore = true;
}
var nLastLine = editor.lastLine();
if ((event.keyCode === 40) &&
((cur.line !== nLastLine))
) {
// going down, but not from the last line
// don't do anything more with the event
event._ipkmIgnore = true;
}
// if this is an edit_shortcuts shortcut, the global keyboard/shortcut
// manager will handle it
if (shortcuts.handles(event)) {
return true;
}
return false;
};
This code provides the desired behavior for the "down-arrow" key (almost: the cursor still goes to the end of the line, except that we don't see it, as we're already in another cell at that point), and also handles the "up-arrow" key similarly.
To modify the handle_codemirror_keyevent prototype, you have two possibilities:
You edit the cell.js file and change the code of the prototype to the code I gave above. The file is in <python>/Lib/site-packages/IPython/html/static/notebook/js or something similar depending on you distro
Much better, after the page is loaded, you change that prototype dynamically by doing this:
IPython.Cell.prototype.handle_codemirror_keyevent = function (editor, event) {
<same code as above>
};
You can do that in your custom.js for example, or create an extension to do it (that's what I did).

Selectively removing node labels in D3 force directed diagram

Overall context: I have a db of cross-references among pages in a wiki space, and want an incrementally-growing visualization of links.
I have working code that shows clusters of labels as you mouseover. But when you move away, rather than hiding all the labels, I want to keep certain key labels (e.g. the centers of clusters).
I forked an existing example and got it roughly working.
info is at http://webseitz.fluxent.com/wiki/WikiGraphBrowser
near the bottom of that or any other page in that space, in the block that starts with "BackLinks:", at the end you'll find "Click here for WikiGraphBrowser" which will launch a window with the interface
equivalent static subset example visible at http://www.wikigraph.net/static/d3/cgmartin/WikiGraphBrowser/:
code for that example is at https://github.com/BillSeitz/WikiGraphBrowser/blob/master/js/wiki_graph.js
Code that works at removing all labels:
i = j = 0;
if (!bo) { //bo=False - from mouseout
//labels.select('text.label').remove();
labels.filter(function(o) {
return !(o.name in clicked_names);
})
.text(function(o) { return ""; });
j++;
}
Code attempting to leave behind some labels, which does not work:
labels.forEach(function(o) {
if (!(d.name in clicked_names)) {
d.text.label.remove();
}
I know I'm just not grokking the d3 model at all....
thx
The problem comes down to your use of in to search for a name in an array. The Javascript in keyword searches object keys not object values. For an array, the keys are the index values. So testing (d.name in clicked_names) will always return false.
Try
i = j = 0;
if (!bo) { //bo=False - from mouseout
//labels.select('text.label').remove();
labels.filter(function(o) {
return (clicked_names.indexOf(o.name) < 0);
})
.text(function(o) { return ""; });
j++;
}
The array .indexOf(object) method returns -1 if none of the elements in the array are equal (by triple-equals standards) to the parameter. Alternatively, if you are trying to support IE8 (I'm assuming not, since you're using SVG), you could use a .some(function) test.
By the way, there's a difference between removing a label and just setting it's text content to the empty string. Which one to use will depend on whether you want to show the text again later. Either way, just be sure you don't end up with a proliferation of empty labels clogging up your browser.

Keyboard code mapping in Adobe Flash/Flex for the browser

N.B. Keep in mind the difference between key code and character code. For example, the number 1 (one) and the character ! (bang) both have the same key code but different character codes. Likewise, the number 7 from the row of numbers and the number 7 from the numpad have different key codes but the same character codes.
I'm programming a music rhythm game in Adobe Flex and would like to bind keyboard keys. This isn't a problem, but I certainly would have a problem, say, setting the default keys to A, S, D, and F and telling the user that this is the case.
If you take a look at the documentation for flash.ui.Keyboard, you'll see that there are constants for keyboard keys to key codes. However, these are only available in Adobe AIR and not the browser. This makes sense since not all operating systems and keyboards are alike (or present!), so key codes can vary.
So, how can I assign default keys that have meaning instead of picking key codes and praying?
My only sane thought is to store the character codes for the key bindings and then provide an character code to String mapping so I can tell the user what to press. However, my gut tells me that this will break in subtle or not-so-subtle ways. Like CAPSLOCK.
Thanks.
Update: I am currently using radekg's answer, but I still think that this will break easily. I would feel more comfortable with some persuasion that this is correct.
according to Flash 8 documentation you can simply rely on ASCII codes. Take a look at these topics of the Flash 8 documentation:
http://livedocs.adobe.com/flash/mx2004/main_7_2/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Flash_MX_2004&file=00001113.html
http://livedocs.adobe.com/flash/mx2004/main_7_2/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Flash_MX_2004&file=00001115.html#71579
http://livedocs.adobe.com/flash/mx2004/main_7_2/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Flash_MX_2004&file=00001116.html#71709
http://livedocs.adobe.com/flash/mx2004/main_7_2/wwhelp/wwhimpl/common/html/wwhelp.htm?context=Flash_MX_2004&file=00001114.html#71525
As far as I'm aware of all modern operating systems use standard ASCII. These codes have not changed since Flash 5 era. To compare letters if you don't want to rely on ASCII codes:
private function compareChar(code:Number):void {
if ( "a" == String.fromCharCode( code ).toLowerCase() ) {
trace("A pressed");
} else {
trace("You pressed " + String.fromCharCode(code));
}
}
...
compareChar(65); // 65 is A
compareChar(96); // 96 is numpad 0
However I think you can rely on ASCII codes.
Hope this helps.
Radekg is mostly correct.
Flash has a built in Class flash.ui.KeyLocation with four static properties: LEFT, RIGHT, NUM_PAD, STANDARD. This means that you can have a definitive idea which key has been pressed, even if the keyboard has been remapped. If you this in combination with String.fromCharCode, you should be able to solve this problem rather neatly.
Your final code might look like:
import flash.ui.KeyLocation;
import flash.events.KeyboardEvent;
function handleKeyboardEvent( event:KeyboardEvent )
{
// This will work for a majority of the keys.
var key:String = String.fromCharCode( event.charCode ).toLowerCase();
// Use strict comparison
if( event.keyLocation !== KeyLocation.STANDARD )
{
// The key is a number, then it needs to be re-identified.
if( event.keyLocation == KeyLocation.RIGHT ) key = "r" + key;
if( event.keyLocation == KeyLocation.LEFT ) key = "l" + key;
if( event.keyLocation == KeyLocation.NUM_PAD) key = "n" + key;
}
switch( key )
{
case "r1":
// Do something with the one which is not on the keypad.
break;
case "n.":
// Do something with the number pad's period.
break;
case "n":
// Do something with the letter N.
break;
}
}
I will admit, I am not certain what will happen with String.fromCharCode and control keys (F1, Alt, Ctrl, etc), but the KeyboardEvent does support event.shiftKey, event.ctrlKey, event.altKey

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