File formats/Images - Revision history

AngelHerraez: /* Saving animated images */

2016-10-12T13:45:32Z

‎Saving animated images

AngelHerraez: /* Saving animated images */

2016-10-12T13:27:57Z

‎Saving animated images

AngelHerraez: saving animated images

2016-10-12T12:07:36Z

saving animated images

AngelHerraez: use scriptingdoc template

2010-02-06T12:34:26Z

use scriptingdoc template

AngelHerraez: moving POV-Ray information to a new subpage

2010-02-06T12:32:35Z

moving POV-Ray information to a new subpage

AngelHerraez: update on exporting images

2010-02-02T13:30:13Z

update on exporting images

AngelHerraez: thumbnail and image size do not work + more snapshots

2009-04-25T12:43:26Z

thumbnail and image size do not work + more snapshots

AngelHerraez: /* Saving images from Jmol application */

2009-04-25T12:24:50Z

‎Saving images from Jmol application

AngelHerraez: /* Saving images from Jmol application */

2009-04-25T12:22:34Z

‎Saving images from Jmol application

AngelHerraez: fill content brought from File formats page

2009-04-25T10:36:58Z

fill content brought from File formats page

@@ Line 126: / Line 126: @@
 == Saving animated images ==
 Animated images showing the model in rotation may be produced using the <code>capture</code> command, also available via the popup menu in both the Jmol application and the JSmol object (note, however, that producing these from the HTML5 modality of JSmol embedded in a webpage will take considerable time).
 These formats may be generated:
-* one animated {{file|gif}} file
+* one animated {{file|gif}} file  ''(examples displayed to the right)''
 * a series of static {{file|gif}} files (which may be combined into an animated image using external software)
 * a series of static {{file|png}} files (which may be combined into an animated image using external software)

@@ Line 126: / Line 126: @@
 == Saving animated images ==
-Animated images showing the model in rotation may be produced using the <code>capture</code> command, also available via the popup menu in both Jmol application and the JSmol object (note, however, that producing these from the HTML5 modality of JSmol embedded in a webpage will take considerable time).
+Animated images showing the model in rotation may be produced using the <code>capture</code> command, also available via the popup menu in both the Jmol application and the JSmol object (note, however, that producing these from the HTML5 modality of JSmol embedded in a webpage will take considerable time).
 These formats may be generated:
@@ Line 140: / Line 140: @@
   capture transparent "filename.gif" spin X
   capture transparent "filename.gif" rock X 20
-Y may be used instead of X (meaning the axis around which the rotation is performed)
+<code>Y</code> may be used instead of <code>X</code> (meaning the axis around which the rotation is performed),
-and 20 (the amplitude or rocking) may be changed to another angle
+and <code>20</code> (the amplitude of rocking) may be changed to another angle.
 = See also =

← Older revision		Revision as of 12:07, 12 October 2016
Line 124:		Line 124:
	Example and downloadable kit:		Example and downloadable kit:
	http://biomodel.uah.es/Jmol/export-image/		http://biomodel.uah.es/Jmol/export-image/
		+
		+	== Saving animated images ==
		+	Animated images showing the model in rotation may be produced using the <code>capture</code> command, also available via the popup menu in both Jmol application and the JSmol object (note, however, that producing these from the HTML5 modality of JSmol embedded in a webpage will take considerable time).
		+
		+	These formats may be generated:
		+	* one animated {{file\|gif}} file
		+	* a series of static {{file\|gif}} files (which may be combined into an animated image using external software)
		+	* a series of static {{file\|png}} files (which may be combined into an animated image using external software)
		+	See the [{{ScriptingDoc}}#capture scripting documentation] for details.
		+
		+	Here are some straightforward recipes:
		+	# For a continuously spinning model (360° rotation), the number of frames produced is 12 × the value of <code>spinFPS</code>; therefore you need to adjust <code>spinFPS</code> to nFrames/12, or 30/degreesPerFrame
		+	# For a rocking motion, the number of frames produced is 4 × the value of <code>spinFPS</code>; therefore you need to adjust <code>spinFPS</code> to nFrames/4, irrespective of the amplitude of rocking (degrees).
		+	# After that, you will use the <code>capture</code> command like this:
		+	capture transparent "filename.gif" spin X
		+	capture transparent "filename.gif" rock X 20
		+	Y may be used instead of X (meaning the axis around which the rotation is performed)
		+	and 20 (the amplitude or rocking) may be changed to another angle

@@ Line 23: / Line 23: @@
 The pop-up menu also allows in these cases (not in the normal, unsigned applet) to save a snapshot of the model, in <code>JPEG</code>, <code>PNG</code>, <code>GIF</code> or [[File_formats/Ray_Tracing|ray tracing]] formats. Open the pop-up menu (right-click, or Ctrl+click, or click on Jmol frank) and choose <code>File > Save</code> (or directly <code>Save</code> in older versions). After choosing a format, a dialog will open to choose the location and filename.
-You can also export images using a script (e.g. from the console) with the <code>write</code> command (see the [http://chemapps.stolaf.edu/jmol/docs/#writeimage,frames scripting documentation]).
+You can also export images using a script (e.g. from the console) with the <code>write</code> command (see the [{{ScriptingDoc}}#writeimage,frames scripting documentation]).
 == Saving images from Jmol applet ==

@@ Line 3: / Line 3: @@
 == Saving images from Jmol application ==
 Images (snapshots) of Jmol's viewport, including the model in the current rendering, can be saved by using the application's top menu bar:
-<code>File > Export > Export Image</code>. A dialog will open to allow choosing the location and filename, as well as the format in the <code>Image Type</code> drop-down list; choose among <code>JPEG</code>, <code>PNG</code>, <code>PPM</code> or <code>GIF</code> formats. There is also <code>PDF</code> format (one page with the captured image in the center).
+<br />
-:''Note: GIF format is only available in recent versions of Jmol.''
+<code>File > Export > Export Image</code>
-The menu also has <code>File > Export > Render in POV-Ray</code>, which produces images that can be displayed and edited in this raytracing program (using a dialog with options).
+Information on these [[:en:Graphics_file_format|image formats]] on Wikipedia.
-[[Image:ExportImageDialog-2.png|Image export dialog]]
+:''Note: GIF format is only available in recent versions of Jmol.''
-Information on these [[:en:Graphics_file_format|image formats]] and [[:en:POV-Ray|POV-Ray]] on Wikipedia.
+It is also possible to produce images that can be displayed and edited in ray tracing programs (see [[File_formats/Ray_Tracing]]).
 == Saving images from Jmol application and signed applet ==
-The pop-up menu also allows in these cases (not in the normal, unsigned applet) to save a snapshot of the model, in <code>JPEG</code>, <code>PNG</code>, <code>GIF</code> or <code>POV-Ray</code> (raytracing) formats. Open the pop-up menu (right-click, or Ctrl+click, or click on Jmol frank) and choose <code>File > Save</code> (or directly <code>Save</code> in older versions). After choosing a format, a dialog will open to choose the location and filename.
+The pop-up menu also allows in these cases (not in the normal, unsigned applet) to save a snapshot of the model, in <code>JPEG</code>, <code>PNG</code>, <code>GIF</code> or [[File_formats/Ray_Tracing|ray tracing]] formats. Open the pop-up menu (right-click, or Ctrl+click, or click on Jmol frank) and choose <code>File > Save</code> (or directly <code>Save</code> in older versions). After choosing a format, a dialog will open to choose the location and filename.
 You can also export images using a script (e.g. from the console) with the <code>write</code> command (see the [http://chemapps.stolaf.edu/jmol/docs/#writeimage,frames scripting documentation]).
@@ Line 122: / Line 127: @@
 = See also =
-[[File_formats/3D_Objects]] to export to POV-Ray, VRML, X3D, Maya, OBJ, IDTF, U3D.
+[[File_formats/3D_Objects]] to export to VRML, X3D, Maya, OBJ, IDTF, U3D.

← Older revision		Revision as of 10:36, 25 April 2009
Line 1:		Line 1:
−	for ~~splitting~~ the ~~contents~~ of [[~~File~~ formats]] page	+	{{File_Formats}}
−	--to be ~~done~~	+	= File Formats for Images Exported from Jmol =
		+
		+	== Saving images from Jmol application ==
		+	Images (snapshots) of Jmol's viewport, including the model in the current rendering, can be saved by using the application's top menu bar:
		+	<code>File > Export > Export Image</code>. A dialog will open to allow choosing the location and filename, as well as the format in the <code>Image Type</code> drop-down list; choose among <code>JPEG</code>, <code>PNG</code>, <code>PPM</code> or <code>GIF</code> formats. The menu also has <code>File > Export > Render in POV-Ray</code>, which produces images that can be displayed and edited in this raytracing program.
		+	:''Note: GIF format is only available in recent versions of Jmol.''
		+
		+	Information on these [[:en:Graphics_file_format\|image formats]] and [[:en:POV-Ray\|POV-Ray]] on Wikipedia.
		+
		+	== Saving images from Jmol application and signed applet ==
		+
		+	The pop-up menu also allows in these cases (not in the normal, unsigned applet) to save a snapshot of the model, in <code>JPEG</code>, <code>PNG</code> or <code>POV-Ray</code> (raytracing) formats. Open the pop-up menu (right-click, or Ctrl+click, or click on Jmol frank) and choose <code>Save</code>. A dialog will open to choose the location and filename.
		+
		+	== Saving images from Jmol applet ==
		+	''These methods work for both signed and unsigned applet, but for the first the method above is more convenient.''
		+	=== Basic method ===
		+	<i>Note:</i> This only works for certain browsers, so it is not a general solution for the general user. In particular, it does not work in MSIE. In Firefox, it may fail for large applet sizes.
		+
		+	The command from the console or via JavaScript is
		+	<code>getProperty image</code>.
		+
		+	The result is a base-64 encoded JPEG image that looks like this:
		+	<pre>/9j/4AAQSkZJRgABAAAAAQABAAD//gBBSl...</pre>
		+
		+	Pop that into an <code><img></code> tag using Firefox or Opera (not MSIE), and you have
		+	an image that you can copy into your clipboard and do anything you would
		+	do with a JPG. The JavaScript required to create the tag looks like this:
		+	<pre>var myImage = jmolGetPropertyAsString("image")
		+	document.getElementById("someDiv").innerHTML =
		+	'<img src="data:image/jpeg;base64,' + myImage + '">'</pre>
		+
		+	Example:
		+	[{{ScriptingDoc}}examples-11/new.htm Bob Hanson's examples page] (Just under the applet, click on the word "image".)
		+
		+	=== General method, using Perl ===
		+	This works in any browser. The author must have access to the web server and be able to use a Perl script there.
		+
		+	It sends the "base64" encoded image (described above) to a perl
		+	script on the server. This script uses the <code>MIME::Base64</code> package to decode the image (<code>MIME::Base64::decode($data)</code>) and sends it back to the browser, embedded in an HTML page.
		+
		+	'''Example code:'''
		+
		+	''HTML file and Javascript (client side)'':
		+
		+	<pre><html>
		+	<head>
		+	<script type="text/javascript">
		+	function get_snapshot()
		+	{
		+	var BI = document.getElementById("bounce_image");
		+	var BI_D = document.getElementById("IMAGE_DATA");
		+	var BASE64 = jmolGetPropertyAsString("image");
		+	BI_D.value = BASE64;
		+	BI.submit();
		+	}
		+	</script>
		+	</head>
		+	<body>
		+	<script type="text/javascript">
		+	jmolInitialize("jmol/");
		+	jmolApplet(350,"load something.pdb");
		+	</script>
		+	<input type="button" id="snapshot" value="snapshot"
		+	onclick='get_snapshot()'>
		+	<form id="bounce_image"
		+	action="http://MY.SERVER.COM/cgi-bin/decode_snapshot.pl"
		+	method="post" target="_blank">
		+	<input type="hidden" id="IMAGE_DATA" name="IMAGE_DATA"
		+	value="empty">
		+	</form>
		+	</body>
		+	</html></pre>
		+
		+	''PERL script (server side) file 'decode_snapshot.pl''':
		+
		+	<pre>#!/usr/bin/perl
		+	use MIME::Base64;
		+	print "Content-type: image/jpeg\n\n";
		+	%postFields = ();
		+	read( STDIN, $tmpStr, $ENV{ "CONTENT_LENGTH" } );
		+	@parts = split( /\&/, $tmpStr );
		+	foreach (@parts) {
		+	s/%([0-9A-F][0-9A-F])/pack("c",hex($1))/ge;
		+	( $name, $value ) = split(/\=/);
		+	$postFields{ "$name" } = $value;
		+	}
		+	$decoded = decode_base64($postFields{"IMAGE_DATA"});
		+	open (MYFILE, '>path_to_file/jmol_snapshot.jpg');
		+	print MYFILE $decoded;
		+	close (MYFILE);
		+	print $decoded;
		+	exit;</pre>
		+
		+	It is also possible to add additional information to the page containing the generated image
		+	(like in the example below).
		+
		+	Example:
		+	http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh
		+	(click on the "snapshot" button in the "Graphics Window" section).
		+
		+	=== General method, using just HTML, and PHP if necessary ===
		+	This works in any browser. The server must support PHP, but no configuration is needed.
		+
		+	* No access to server configuration is needed (i.e., no need to install server-side scripts).
		+	* If the browser is MS Internet Explorer, it needs online access to a PHP-enabled server that will return the image using a php page which is part of this package.
		+	* If the browser is another, inline base64-encoded images will be used first (understood by Firefox and Opera, at least). This method works both online and off-line (e.g., from hard disk, USB disk or CDROM).
		+
		+	The image is opened in a new window, that fits the image size.
		+	It can then be copied to clipboard using the browser's pop-up menu on it. Some browsers also allow to save the image to disk, from the same pop-up menu.
		+
		+	Example and downloadable kit:
		+	http://biomodel.uah.es/Jmol/export-image/
		+
		+
		+	= See also =
		+	[[File_formats/3D_Objects]] to export to POV-Ray, VRML, Maya, or OBJ.