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From: <and...@us...> - 2006-11-22 21:35:47
|
Revision: 428
http://svn.sourceforge.net/fable/?rev=428&view=rev
Author: andy_gotz
Date: 2006-11-22 13:35:47 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
removed unused imports
Modified Paths:
--------------
gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/EurothermAction.java
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jpw...@us...> - 2006-11-22 21:27:40
|
Revision: 427
http://svn.sourceforge.net/fable/?rev=427&view=rev
Author: jpwright
Date: 2006-11-22 13:21:18 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
Update docs - trying to prepare incremental release
Modified Paths:
--------------
ImageD11/trunk/ImageD11/doc/ImageD11.blobcorrector.html
ImageD11/trunk/ImageD11/doc/ImageD11.connectedpixels.html
ImageD11/trunk/ImageD11/doc/ImageD11.hist.html
ImageD11/trunk/ImageD11/doc/ImageD11.html
ImageD11/trunk/ImageD11/doc/ImageD11.license.html
ImageD11/trunk/ImageD11/doc/ImageD11.opendata.html
ImageD11/trunk/ImageD11/doc/ImageD11.parameters.html
ImageD11/trunk/ImageD11/doc/ImageD11.plot3d.html
ImageD11/trunk/ImageD11/doc/ImageD11.refinegrains.html
ImageD11/trunk/ImageD11/doc/ImageD11.transform.html
ImageD11/trunk/ImageD11/doc/ImageD11.unitcell.html
ImageD11/trunk/ImageD11/doc/makedocs.py
Added Paths:
-----------
ImageD11/trunk/ImageD11/doc/ImageD11.scale.html
ImageD11/trunk/ImageD11/doc/index.html
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.blobcorrector.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.blobcorrector.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.blobcorrector.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -33,6 +33,7 @@
<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="ImageD11.blobcorrector.html#correctorclass">correctorclass</a>
+</font></dt><dt><font face="helvetica, arial"><a href="ImageD11.blobcorrector.html#perfect">perfect</a>
</font></dt></dl>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
@@ -44,7 +45,7 @@
<td colspan=2><tt>Applies a spatial distortion to a peak position using a fit2d splinefile<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
-<dl><dt><a name="correctorclass-__init__"><strong>__init__</strong></a>(self, splinefile)</dt><dd><tt>Argument is the name of a fit2d spline file</tt></dd></dl>
+<dl><dt><a name="correctorclass-__init__"><strong>__init__</strong></a>(self, splinefile, orientation<font color="#909090">='edf'</font>)</dt><dd><tt>Argument is the name of a fit2d spline file</tt></dd></dl>
<dl><dt><a name="correctorclass-correct"><strong>correct</strong></a>(self, x, y)</dt><dd><tt>Transform x,y in raw image coordinates into x,y of an<br>
idealised image. Returns a tuple (x,y), expects a<br>
@@ -55,6 +56,14 @@
<br>
Iterative algorithm...</tt></dd></dl>
+<dl><dt><a name="correctorclass-make_pixel_lut"><strong>make_pixel_lut</strong></a>(self, dims)</dt><dd><tt>Generate an x and y image which maps the array indices into<br>
+floating point array indices (to be corrected for pixel size later)<br>
+ <br>
+returns (FIXME - get them the right way around!)</tt></dd></dl>
+
+<dl><dt><a name="correctorclass-make_pos_lut"><strong>make_pos_lut</strong></a>(self, dims)</dt><dd><tt>Generate a look up table of pixel positions in microns<br>
+returns ...</tt></dd></dl>
+
<dl><dt><a name="correctorclass-readfit2dfloats"><strong>readfit2dfloats</strong></a>(self, fp, n, debug<font color="#909090">=0</font>)</dt><dd><tt>Interprets a 5E14.7 formatted fortran line</tt></dd></dl>
<dl><dt><a name="correctorclass-readfit2dspline"><strong>readfit2dspline</strong></a>(self, name)</dt><dd><tt>Reads a fit2d spline file into a scipy/fitpack tuple, tck<br>
@@ -63,6 +72,26 @@
<dl><dt><a name="correctorclass-test"><strong>test</strong></a>(self, x, y)</dt><dd><tt>Checks that the correct and distort functions are indeed<br>
inversely related to each other</tt></dd></dl>
+</td></tr></table> <p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#ffc8d8">
+<td colspan=3 valign=bottom> <br>
+<font color="#000000" face="helvetica, arial"><a name="perfect">class <strong>perfect</strong></a></font></td></tr>
+
+<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
+<td colspan=2><tt>To use on previously corrected images<br> </tt></td></tr>
+<tr><td> </td>
+<td width="100%">Methods defined here:<br>
+<dl><dt><a name="perfect-correct"><strong>correct</strong></a>(x, y)</dt></dl>
+
+<hr>
+Data and other attributes defined here:<br>
+<dl><dt><strong>splinefile</strong> = 'NO_CORRECTION_APPLIED'</dl>
+
+<dl><dt><strong>xsize</strong> = 'UNKNOWN'</dl>
+
+<dl><dt><strong>ysize</strong> = 'UNKNOWN'</dl>
+
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.connectedpixels.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.connectedpixels.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.connectedpixels.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -9,7 +9,7 @@
<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong><a href="ImageD11.html"><font color="#ffffff">ImageD11</font></a>.connectedpixels</strong></big></big></font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:///C|/python24/lib/site-packages/imaged11/connectedpixels.pyd">c:\python24\lib\site-packages\imaged11\connectedpixels.pyd</a></font></td></tr></table>
- <p></p>
+ <p><tt>C extensions for image analysis, part of ImageD11</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
@@ -17,8 +17,44 @@
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
-<td width="100%"><dl><dt><a name="-blobproperties"><strong>blobproperties</strong></a>(...)</dt><dd><tt>Computes various properties of a blob image (created by connectedpixels)</tt></dd></dl>
- <dl><dt><a name="-connectedpixels"><strong>connectedpixels</strong></a>(...)</dt><dd><tt>Assign connected pixels in image (first arg) above threshold (float second arg) to return image of peak number.Optional arguement verbose!=0 prints some info as it runs</tt></dd></dl>
- <dl><dt><a name="-roisum"><strong>roisum</strong></a>(...)</dt><dd><tt>Computes average in roi</tt></dd></dl>
+<td width="100%"><dl><dt><a name="-bloboverlaps"><strong>bloboverlaps</strong></a>(...)</dt><dd><tt>res = bloboverlaps ( Numeric.array(blob1, 2D, Int), n1 , <br>
+ Numeric.array(blob2, 2D, Int), n2 , verbose=0) <br>
+ <br>
+returns a disjoint set making the overlaps between blob1 and blob2 <br>
+res[0->n1] = peaks in image 1 <br>
+res[n2->n2+n1+1] = peaks in image 2</tt></dd></dl>
+ <dl><dt><a name="-blobproperties"><strong>blobproperties</strong></a>(...)</dt><dd><tt>res = blobproperties ( Numeric.array(data, 2D) , <br>
+ Numeric.array(blob, 2D, Int) ,<br>
+ Int np , <br>
+ Int verbose )<br>
+ <br>
+Computes various properties of a blob image (created by connectedpixels)<br>
+data = image data <br>
+blob = integer peak assignments from connectedpixels <br>
+np = number of peaks to treat <br>
+verbose - flag about whether to print<br>
+ <br>
+res = tuple (npix , sum , sumsq , com0 , com1 , com00 , com01 , com11 ) <br>
+...where fval = intensity in pixel and sum over pixels in blob of<br>
+ anpix[peak] =anpix[peak] + 1 ; // # of pixels<br>
+ asum[peak] =asum[peak] + fval; // total intensity<br>
+ asumsq[peak] =asumsq[peak] +fval*fval; // total intensity^2<br>
+ acom0[peak] =acom0[peak] + i*fval; // etc<br>
+ acom1[peak] =acom1[peak] + j*fval;<br>
+ acom00[peak] =acom00[peak] + i*i*fval;<br>
+ acom01[peak] =acom01[peak] + i*j*fval;<br>
+ acom11[peak] =acom11[peak] + j*j*fval;</tt></dd></dl>
+ <dl><dt><a name="-connectedpixels"><strong>connectedpixels</strong></a>(...)</dt><dd><tt>nblobs = connectedpixels ( Numeric.array(data, 2D) , <br>
+ Numeric.array(blob, 2D, Int) ,<br>
+ float threshold ,<br>
+ Int verbose )<br>
+data is normally an image <br>
+blob is an array to receive pixel -> blob assignments<br>
+threshold is the value above which a pixel is considered to be in a blob<br>
+verbose flags printing on stdout</tt></dd></dl>
+ <dl><dt><a name="-roisum"><strong>roisum</strong></a>(...)</dt><dd><tt>(float) roisum ( Numeric.array(2D), xl , xh , yl , yh , verbose=0 ) <br>
+sum( array[xl:xh , yl:yh] ) where x,y refer to SLOW/FAST indices <br>
+... NOT Numeric indices, but slow/fast <br>
+Unsure why this was written - can be done with Numeric anyway</tt></dd></dl>
</td></tr></table>
</body></html>
\ No newline at end of file
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.hist.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.hist.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.hist.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -33,5 +33,6 @@
<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
<td width="100%"><dl><dt><a name="-hist"><strong>hist</strong></a>(data, verbose<font color="#909090">=0</font>)</dt><dd><tt>Wrapper to ImageD11 histogram generators (c functions)<br>
returns histogram if data is a 2D Numeric.UInt16 array</tt></dd></dl>
+ <dl><dt><a name="-test_dvhist"><strong>test_dvhist</strong></a>()</dt></dl>
</td></tr></table>
</body></html>
\ No newline at end of file
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -42,6 +42,7 @@
<a href="ImageD11.data.html">data</a><br>
<a href="ImageD11.factors.html">factors</a><br>
<a href="ImageD11.findreflections.html">findreflections</a><br>
+<a href="ImageD11.fitgrainxy.html">fitgrainxy</a><br>
</td><td width="25%" valign=top><a href="ImageD11.grain.html">grain</a><br>
<a href="ImageD11.guicommand.html">guicommand</a><br>
<a href="ImageD11.guifactors.html">guifactors</a><br>
@@ -51,8 +52,8 @@
<a href="ImageD11.guitransformer.html">guitransformer</a><br>
<a href="ImageD11.hist.html">hist</a><br>
<a href="ImageD11.indexing.html">indexing</a><br>
-</td><td width="25%" valign=top><a href="ImageD11.license.html">license</a><br>
-<a href="ImageD11.listdialog.html">listdialog</a><br>
+<a href="ImageD11.license.html">license</a><br>
+</td><td width="25%" valign=top><a href="ImageD11.listdialog.html">listdialog</a><br>
<a href="ImageD11.oldstuff.html"><strong>oldstuff</strong> (package)</a><br>
<a href="ImageD11.opendata.html">opendata</a><br>
<a href="ImageD11.parameters.html">parameters</a><br>
@@ -60,10 +61,12 @@
<a href="ImageD11.peakmerge_old.html">peakmerge_old</a><br>
<a href="ImageD11.plot3d.html">plot3d</a><br>
<a href="ImageD11.rebin2d.html">rebin2d</a><br>
-</td><td width="25%" valign=top><a href="ImageD11.refinegrains.html">refinegrains</a><br>
-<a href="ImageD11.simplex.html">simplex</a><br>
+<a href="ImageD11.refinegrains.html">refinegrains</a><br>
+<a href="ImageD11.scale.html">scale</a><br>
+</td><td width="25%" valign=top><a href="ImageD11.simplex.html">simplex</a><br>
<a href="ImageD11.test_transform.html">test_transform</a><br>
<a href="ImageD11.transform.html">transform</a><br>
+<a href="ImageD11.twod2threed.html">twod2threed</a><br>
<a href="ImageD11.twodplot.html">twodplot</a><br>
<a href="ImageD11.ubitool.html">ubitool</a><br>
<a href="ImageD11.unitcell.html">unitcell</a><br>
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.license.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.license.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.license.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -17,5 +17,5 @@
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
<tr><td bgcolor="#55aa55"><tt> </tt></td><td> </td>
-<td width="100%"><strong>license</strong> = '<font color="#c040c0">\n\n</font> GNU GENERAL PUBLIC L...icense instead of this License.<font color="#c040c0">\n\n</font> '</td></tr></table>
+<td width="100%"><strong>license</strong> = '<font color="#c040c0">\n</font> GNU GENERAL PUBLIC LI...License instead of this License.<font color="#c040c0">\n</font> '</td></tr></table>
</body></html>
\ No newline at end of file
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.opendata.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.opendata.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.opendata.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -68,5 +68,9 @@
TODO : Read in regions of interest<br>
<br>
PLEASE LEAVE THE STRANGE INTERFACE ALONE - IT IS USEFUL FOR THE BRUKER FORMAT</tt></dd></dl>
+ <dl><dt><a name="-writebruker"><strong>writebruker</strong></a>(filename, dataobject)</dt><dd><tt>Writes 16-bit + overflow bruker images based on the headerstring<br>
+Assumes you've got a good bruker headerstring in the data<br>
+object</tt></dd></dl>
+ <dl><dt><a name="-writedata"><strong>writedata</strong></a>(filename, dataobject)</dt></dl>
</td></tr></table>
</body></html>
\ No newline at end of file
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.parameters.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.parameters.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.parameters.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -33,7 +33,7 @@
<dl><dt><a name="parameters-dumbtypecheck"><strong>dumbtypecheck</strong></a>(self)</dt><dd><tt>Eventually parameter types (and units and fixed/varied to be<br>
specifieable<br>
-For now it just tries to coerce to int, then float, then does nothing</tt></dd></dl>
+For now it just tries to coerce to float, then does nothing</tt></dd></dl>
<dl><dt><a name="parameters-get_parameters"><strong>get_parameters</strong></a>(self)</dt><dd><tt>Returns a dictionary of <a href="#parameters">parameters</a></tt></dd></dl>
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.plot3d.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.plot3d.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.plot3d.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -6,7 +6,7 @@
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom> <br>
-<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong><a href="ImageD11.html"><font color="#ffffff">ImageD11</font></a>.plot3d</strong></big></big> (version 1.5, 2006/06/14 13:36:45)</font></td
+<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong><a href="ImageD11.html"><font color="#ffffff">ImageD11</font></a>.plot3d</strong></big></big> (version 1.6, 2006/06/25 10:05:10)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:///C|/python24/lib/site-packages/imaged11/plot3d.py">c:\python24\lib\site-packages\imaged11\plot3d.py</a></font></td></tr></table>
<p><tt>from example by Tarn Weisner Burton <twb...@us...> in pyopengl</tt></p>
@@ -851,8 +851,8 @@
<tr><td bgcolor="#55aa55"><tt> </tt></td><td> </td>
<td width="100%"><strong>__author__</strong> = 'Jon Wright <jpw...@us...> from...n Weisner Burton <twb...@us...>'<br>
-<strong>__date__</strong> = '2006/06/14 13:36:45'<br>
-<strong>__version__</strong> = '1.5'</td></tr></table><p>
+<strong>__date__</strong> = '2006/06/25 10:05:10'<br>
+<strong>__version__</strong> = '1.6'</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom> <br>
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.refinegrains.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.refinegrains.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.refinegrains.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -81,7 +81,7 @@
<hr>
Data and other attributes defined here:<br>
-<dl><dt><strong>stepsizes</strong> = {'chi': 0.00017453292519943296, 'distance': 0.10000000000000001, 'tilt-y': 0.0017453292519943296, 'tilt-z': 0.0017453292519943296, 'translation': 0.10000000000000001, 'wavelength': 0.001, 'wedge': 0.00017453292519943296, 'y-center': 0.10000000000000001, 'z-center': 0.10000000000000001}</dl>
+<dl><dt><strong>stepsizes</strong> = {'chi': 0.0017453292519943296, 'distance': 0.10000000000000001, 'tilt-y': 0.0017453292519943296, 'tilt-z': 0.0017453292519943296, 'translation': 0.10000000000000001, 'wavelength': 0.001, 'wedge': 0.0017453292519943296, 'y-center': 0.10000000000000001, 'z-center': 0.10000000000000001}</dl>
</td></tr></table></td></tr></table>
</body></html>
\ No newline at end of file
Added: ImageD11/trunk/ImageD11/doc/ImageD11.scale.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.scale.html (rev 0)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.scale.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -0,0 +1,80 @@
+
+<!doctype html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head><title>Python: module ImageD11.scale</title>
+</head><body bgcolor="#f0f0f8">
+
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
+<tr bgcolor="#7799ee">
+<td valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong><a href="ImageD11.html"><font color="#ffffff">ImageD11</font></a>.scale</strong></big></big></font></td
+><td align=right valign=bottom
+><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:///C|/python24/lib/site-packages/imaged11/scale.py">c:\python24\lib\site-packages\imaged11\scale.py</a></font></td></tr></table>
+ <p><tt>Class for scaling images with respect to each other due to moco<br>
+style instabilities.<br>
+ <br>
+Depends on there being a large background contribution to work with<br>
+ <br>
+ <br>
+Mathematically:<br>
+ y = a * x + b<br>
+ dy/da = x<br>
+ dy/db = 1<br>
+ Least squares problem with:<br>
+ matrix = ( dy/da*dy/da , dy/da*dy/db)<br>
+ ( dy/da*dy/db , dy/db*dy/db)<br>
+ rhs = ( dy/da*y )<br>
+ ( dy/db*y )<br>
+ <br>
+Has the option to use only pixels in the image to <a href="#scale">scale</a> to which<br>
+are above a threshold (eg the central circle on the bruker)</tt></p>
+<p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#aa55cc">
+<td colspan=3 valign=bottom> <br>
+<font color="#fffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
+
+<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
+<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="LinearAlgebra.html">LinearAlgebra</a><br>
+</td><td width="25%" valign=top><a href="Numeric.html">Numeric</a><br>
+</td><td width="25%" valign=top><a href="ImageD11.opendata.html">ImageD11.opendata</a><br>
+</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#ee77aa">
+<td colspan=3 valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
+
+<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
+<td width="100%"><dl>
+<dt><font face="helvetica, arial"><a href="ImageD11.scale.html#scale">scale</a>
+</font></dt></dl>
+ <p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#ffc8d8">
+<td colspan=3 valign=bottom> <br>
+<font color="#000000" face="helvetica, arial"><a name="scale">class <strong>scale</strong></a></font></td></tr>
+
+<tr><td bgcolor="#ffc8d8"><tt> </tt></td><td> </td>
+<td width="100%">Methods defined here:<br>
+<dl><dt><a name="scale-__init__"><strong>__init__</strong></a>(self, im1, threshold<font color="#909090">=None</font>)</dt><dd><tt>Determines <a href="#scale">scale</a> and offset values for images<br>
+with respect to each other<br>
+im1 = a * im2 + b<br>
+returns a, b</tt></dd></dl>
+
+<dl><dt><a name="scale-scale"><strong>scale</strong></a>(self, im2)</dt><dd><tt>Fill out RHS and solve<br>
+returns the <a href="#scale">scale</a> to apply to the image stored in the class<br>
+ <br>
+You probably want the <a href="#scale">scale</a> to apply to the image you supply<br>
+...use <a href="#scale">scale</a> image for that</tt></dd></dl>
+
+<dl><dt><a name="scale-scaleimage"><strong>scaleimage</strong></a>(self, im2)</dt><dd><tt>Return a copy of the image scaled to match the class</tt></dd></dl>
+
+</td></tr></table></td></tr></table><p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#eeaa77">
+<td colspan=3 valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
+
+<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
+<td width="100%"><dl><dt><a name="-testscaleimage"><strong>testscaleimage</strong></a>()</dt></dl>
+</td></tr></table>
+</body></html>
\ No newline at end of file
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.transform.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.transform.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.transform.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -56,15 +56,15 @@
Just like range() except it returns an array whose type can be<br>
specified by the keyword argument typecode.</tt></dd></dl>
<dl><dt><a name="-choose"><strong>choose</strong></a>(...)</dt><dd><tt><a href="#-choose">choose</a>(a, (b1,b2,...))</tt></dd></dl>
- <dl><dt><a name="-compute_g_vectors"><strong>compute_g_vectors</strong></a>(tth, eta, omega, wavelength, wedge<font color="#909090">=0.0</font>)</dt><dd><tt>Generates spot positions in reciprocal space from twotheta, wavelength, omega and eta<br>
+ <dl><dt><a name="-compute_g_vectors"><strong>compute_g_vectors</strong></a>(tth, eta, omega, wavelength, wedge<font color="#909090">=0.0</font>, chi<font color="#909090">=0.0</font>)</dt><dd><tt>Generates spot positions in reciprocal space from twotheta, wavelength, omega and eta<br>
Assumes single axis vertical<br>
... unless a wedge angle is specified</tt></dd></dl>
- <dl><dt><a name="-compute_lorentz_factors"><strong>compute_lorentz_factors</strong></a>(args)</dt><dd><tt>From Kabsch 1988 J. Appl. Cryst. 21 619<br>
+ <dl><dt><a name="-compute_lorentz_factors"><strong>compute_lorentz_factors</strong></a>(tth, eta, omega, wavelength, wedge<font color="#909090">=0.0</font>, chi<font color="#909090">=0.0</font>)</dt><dd><tt>From Kabsch 1988 J. Appl. Cryst. 21 619<br>
<br>
Multiply the intensities by:<br>
-Lorentz = | S.(u x S_0)| / |S|.|S_0|<br>
+Lorentz = | S.(u x So)| / |S|.|So|<br>
S = scattered vector<br>
-S_0 = incident vector<br>
+So = incident vector<br>
u = unit vector along rotation axis</tt></dd></dl>
<dl><dt><a name="-compute_polarisation_factors"><strong>compute_polarisation_factors</strong></a>(args)</dt><dd><tt>From Kabsch 1988 J. Appl. Cryst. 21 619<br>
<br>
@@ -75,7 +75,11 @@
or "probability of finding electric field vector in plane having normal, n"<br>
S = scattered vector<br>
S_0 = incident vector<br>
-n = normal to polarisation plane, typically perpendicular to S_0</tt></dd></dl>
+n = normal to polarisation plane, typically perpendicular to S_0<br>
+ <br>
+In ImageD11 we normally expect to find:<br>
+x axis along the beam<br>
+z axis being up, and parallel to the normal n mentioned above</tt></dd></dl>
<dl><dt><a name="-compute_tth_eta"><strong>compute_tth_eta</strong></a>(peaks, yc, ys, ty, zc, zs, tz, dist, detector_orientation<font color="#909090">=((1, 0), (0, 1))</font>, crystal_translation<font color="#909090">=None</font>, omega<font color="#909090">=None</font>, axis_orientation1<font color="#909090">=0.0</font>, axis_orientation2<font color="#909090">=0.0</font>)</dt><dd><tt>Peaks is a 2 d array of x,y<br>
yc is the centre in y<br>
ys is the y pixel size<br>
@@ -95,6 +99,7 @@
z with respect to beam height, z centre<br>
omega data needed if crystal translations used</tt></dd></dl>
<dl><dt><a name="-cross_correlate"><strong>cross_correlate</strong></a>(...)</dt><dd><tt><a href="#-cross_correlate">cross_correlate</a>(a,v, mode=0)</tt></dd></dl>
+ <dl><dt><a name="-cross_product"><strong>cross_product</strong></a>(a, b)</dt></dl>
<dl><dt><a name="-degrees"><strong>degrees</strong></a>(x)</dt><dd><tt>Convenience function</tt></dd></dl>
<dl><dt><a name="-empty"><strong>empty</strong></a>(...)</dt><dd><tt><a href="#-empty">empty</a>((d1,...,dn),typecode='l',savespace=0) will return a new array<br>
of shape (d1,...,dn) and given type with all its entries uninitialized. If savespace is<br>
@@ -106,7 +111,7 @@
<dl><dt><a name="-reshape"><strong>reshape</strong></a>(...)</dt><dd><tt><a href="#-reshape">reshape</a>(a, (d1, d2, ..., dn)). Change the shape of a to be an n-dimensional array with dimensions given by d1...dn. Note: the size specified for the new array must be exactly equal to the size of the old one or an error will occur.</tt></dd></dl>
<dl><dt><a name="-searchsorted"><strong>searchsorted</strong></a> = binarysearch(...)</dt><dd><tt>binarysearch(a,v)</tt></dd></dl>
<dl><dt><a name="-take"><strong>take</strong></a>(...)</dt><dd><tt><a href="#-take">take</a>(a, indices, axis=0). Selects the elements in indices from array a along the given axis.</tt></dd></dl>
- <dl><dt><a name="-uncompute_g_vectors"><strong>uncompute_g_vectors</strong></a>(g, wavelength, wedge<font color="#909090">=0.0</font>)</dt><dd><tt>Given g-vectors compute tth,eta,omega<br>
+ <dl><dt><a name="-uncompute_g_vectors"><strong>uncompute_g_vectors</strong></a>(g, wavelength, wedge<font color="#909090">=0.0</font>, chi<font color="#909090">=0.0</font>)</dt><dd><tt>Given g-vectors compute tth,eta,omega<br>
assert <a href="#-uncompute_g_vectors">uncompute_g_vectors</a>(compute_g_vector(tth,eta,omega))==tth,eta,omega</tt></dd></dl>
<dl><dt><a name="-uncompute_one_g_vector"><strong>uncompute_one_g_vector</strong></a>(gv, wavelength, wedge<font color="#909090">=0.0</font>)</dt><dd><tt>Given g-vectors compute tth,eta,omega<br>
assert <a href="#-uncompute_g_vectors">uncompute_g_vectors</a>(compute_g_vector(tth,eta,omega))==tth,eta,omega</tt></dd></dl>
Modified: ImageD11/trunk/ImageD11/doc/ImageD11.unitcell.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/ImageD11.unitcell.html 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/ImageD11.unitcell.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -64,7 +64,7 @@
Argument dsmax is the d* limit (eg 1/d)<br>
Default of zero gives only the (000) reflection<br>
<br>
-assumes [h|k|l] < 20</tt></dd></dl>
+assumes [h|k|l] < 200</tt></dd></dl>
<dl><dt><a name="unitcell-makerings"><strong>makerings</strong></a>(self, limit, tol<font color="#909090">=0.001</font>)</dt><dd><tt>Makes a list of computed powder rings<br>
The tolerance is the difference in d* to decide<br>
Added: ImageD11/trunk/ImageD11/doc/index.html
===================================================================
--- ImageD11/trunk/ImageD11/doc/index.html (rev 0)
+++ ImageD11/trunk/ImageD11/doc/index.html 2006-11-22 21:21:18 UTC (rev 427)
@@ -0,0 +1,91 @@
+
+<!doctype html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head><title>Python: package ImageD11</title>
+</head><body bgcolor="#f0f0f8">
+
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
+<tr bgcolor="#7799ee">
+<td valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong>ImageD11</strong></big></big> (version 0.6.1)</font></td
+><td align=right valign=bottom
+><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:///C|/python24/lib/site-packages/imaged11/__init__.py">c:\python24\lib\site-packages\imaged11\__init__.py</a></font></td></tr></table>
+ <p><tt>ImageD11 - image analysis software for beamline ID11 at the ESRF<br>
+ <br>
+Copyright (C) 2005 Jon Wright<br>
+ <br>
+This program is free software; you can redistribute it and/or modify<br>
+it under the terms of the GNU General Public License as published by<br>
+the Free Software Foundation; either version 2 of the License, or<br>
+(at your option) any later version.<br>
+ <br>
+This program is distributed in the hope that it will be useful,<br>
+but WITHOUT ANY WARRANTY; without even the implied warranty of<br>
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the<br>
+GNU General Public License for more details.<br>
+ <br>
+You should have received a copy of the GNU General Public License<br>
+along with this program; if not, write to the Free Software<br>
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</tt></p>
+<p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#aa55cc">
+<td colspan=3 valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"><big><strong>Package Contents</strong></big></font></td></tr>
+
+<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
+<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="ImageD11._hist.html">_hist</a><br>
+<a href="ImageD11._splines.html">_splines</a><br>
+<a href="ImageD11.bisplev.html">bisplev</a><br>
+<a href="ImageD11.blobcorrector.html">blobcorrector</a><br>
+<a href="ImageD11.closest.html">closest</a><br>
+<a href="ImageD11.connectedpixels.html">connectedpixels</a><br>
+<a href="ImageD11.data.html">data</a><br>
+<a href="ImageD11.factors.html">factors</a><br>
+<a href="ImageD11.findreflections.html">findreflections</a><br>
+<a href="ImageD11.fitgrainxy.html">fitgrainxy</a><br>
+</td><td width="25%" valign=top><a href="ImageD11.grain.html">grain</a><br>
+<a href="ImageD11.guicommand.html">guicommand</a><br>
+<a href="ImageD11.guifactors.html">guifactors</a><br>
+<a href="ImageD11.guiindexer.html">guiindexer</a><br>
+<a href="ImageD11.guimaker.html">guimaker</a><br>
+<a href="ImageD11.guipeaksearch.html">guipeaksearch</a><br>
+<a href="ImageD11.guitransformer.html">guitransformer</a><br>
+<a href="ImageD11.hist.html">hist</a><br>
+<a href="ImageD11.indexing.html">indexing</a><br>
+<a href="ImageD11.license.html">license</a><br>
+</td><td width="25%" valign=top><a href="ImageD11.listdialog.html">listdialog</a><br>
+<a href="ImageD11.oldstuff.html"><strong>oldstuff</strong> (package)</a><br>
+<a href="ImageD11.opendata.html">opendata</a><br>
+<a href="ImageD11.parameters.html">parameters</a><br>
+<a href="ImageD11.peakmerge.html">peakmerge</a><br>
+<a href="ImageD11.peakmerge_old.html">peakmerge_old</a><br>
+<a href="ImageD11.plot3d.html">plot3d</a><br>
+<a href="ImageD11.rebin2d.html">rebin2d</a><br>
+<a href="ImageD11.refinegrains.html">refinegrains</a><br>
+<a href="ImageD11.scale.html">scale</a><br>
+</td><td width="25%" valign=top><a href="ImageD11.simplex.html">simplex</a><br>
+<a href="ImageD11.test_transform.html">test_transform</a><br>
+<a href="ImageD11.transform.html">transform</a><br>
+<a href="ImageD11.twod2threed.html">twod2threed</a><br>
+<a href="ImageD11.twodplot.html">twodplot</a><br>
+<a href="ImageD11.ubitool.html">ubitool</a><br>
+<a href="ImageD11.unitcell.html">unitcell</a><br>
+<a href="ImageD11.write_graindex_gv.html">write_graindex_gv</a><br>
+</td></tr></table></td></tr></table><p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#55aa55">
+<td colspan=3 valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
+
+<tr><td bgcolor="#55aa55"><tt> </tt></td><td> </td>
+<td width="100%"><strong>__author__</strong> = ('Jon Wright',)<br>
+<strong>__author_email__</strong> = 'wr...@es...'<br>
+<strong>__version__</strong> = '0.6.1'</td></tr></table><p>
+<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
+<tr bgcolor="#7799ee">
+<td colspan=3 valign=bottom> <br>
+<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
+
+<tr><td bgcolor="#7799ee"><tt> </tt></td><td> </td>
+<td width="100%">('Jon Wright',)</td></tr></table>
+</body></html>
\ No newline at end of file
Modified: ImageD11/trunk/ImageD11/doc/makedocs.py
===================================================================
--- ImageD11/trunk/ImageD11/doc/makedocs.py 2006-11-22 21:06:49 UTC (rev 426)
+++ ImageD11/trunk/ImageD11/doc/makedocs.py 2006-11-22 21:21:18 UTC (rev 427)
@@ -2,6 +2,7 @@
import pydoc, os, ImageD11,inspect
pydoc.writedoc("ImageD11")
+os.system("copy ImageD11.html index.html")
done=[None]
for file in os.listdir(ImageD11.__path__[0]):
path = os.path.join(ImageD11.__path__[0], file)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <and...@us...> - 2006-11-22 21:06:50
|
Revision: 426
http://svn.sourceforge.net/fable/?rev=426&view=rev
Author: andy_gotz
Date: 2006-11-22 13:06:49 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
remvoed unused imports
Modified Paths:
--------------
gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/BeamlineStatusView.java
Modified: gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/BeamlineStatusView.java
===================================================================
--- gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/BeamlineStatusView.java 2006-11-22 20:59:02 UTC (rev 425)
+++ gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/BeamlineStatusView.java 2006-11-22 21:06:49 UTC (rev 426)
@@ -1,11 +1,7 @@
package fable.beamline.rcp;
-import org.eclipse.ui.forms.widgets.Form;
-import org.eclipse.ui.forms.widgets.FormToolkit;
-import org.eclipse.ui.forms.widgets.ScrolledForm;
import org.eclipse.ui.part.ViewPart;
import org.eclipse.ui.preferences.ScopedPreferenceStore;
-
import org.eclipse.core.runtime.preferences.ConfigurationScope;
import org.eclipse.jface.resource.ImageDescriptor;
import org.eclipse.swt.widgets.Button;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jpw...@us...> - 2006-11-22 20:59:06
|
Revision: 425
http://svn.sourceforge.net/fable/?rev=425&view=rev
Author: jpwright
Date: 2006-11-22 12:59:02 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
Merge CVS changes and add 3D peaksearching
Modified Paths:
--------------
ImageD11/trunk/ImageD11/blobcorrector.py
ImageD11/trunk/ImageD11/opendata.py
ImageD11/trunk/ImageD11/refinegrains.py
ImageD11/trunk/ImageD11/transform.py
ImageD11/trunk/ImageD11/unitcell.py
ImageD11/trunk/MANIFEST
ImageD11/trunk/scripts/fit2dcake.py
ImageD11/trunk/scripts/peaksearch.py
ImageD11/trunk/scripts/rubber.py
ImageD11/trunk/setup.py
ImageD11/trunk/src/connectedpixels.c
Added Paths:
-----------
ImageD11/trunk/scripts/ImageD11_2_shelx.py
Modified: ImageD11/trunk/ImageD11/blobcorrector.py
===================================================================
--- ImageD11/trunk/ImageD11/blobcorrector.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/ImageD11/blobcorrector.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -30,6 +30,18 @@
import Numeric as n
import bisplev, math
+
+class perfect:
+ """
+ To use on previously corrected images
+ """
+ splinefile = "NO_CORRECTION_APPLIED"
+ xsize = "UNKNOWN"
+ ysize = "UNKNOWN"
+ def correct(x,y):
+ return x, y
+
+
class correctorclass:
"""
Applies a spatial distortion to a peak position using a fit2d splinefile
Modified: ImageD11/trunk/ImageD11/opendata.py
===================================================================
--- ImageD11/trunk/ImageD11/opendata.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/ImageD11/opendata.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -153,6 +153,7 @@
else:
ar=Numeric.array(Numeric.reshape(
Numeric.fromstring(f.read(len),tin) ,(x,y)),typeout)
+ ar.savespace(1)
if(opened):f.close()
return(ar)
@@ -365,6 +366,7 @@
ar=Numeric.reshape(
Numeric.fromstring(datastring,numerictype).byteswapped(),
(hd["columns"],hd["rows"]) )
+ ar.savespace(1)
return data(ar,hd)
Modified: ImageD11/trunk/ImageD11/refinegrains.py
===================================================================
--- ImageD11/trunk/ImageD11/refinegrains.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/ImageD11/refinegrains.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -142,7 +142,13 @@
omega = om,
axis_orientation1 = self.parameters['wedge'],
axis_orientation2 = self.parameters['chi'])
- self.gv = transform.compute_g_vectors(tth,eta,om,float(self.parameters['wavelength']),
+ try:
+ sign = self.parameters['omegasign']
+ except:
+ sign = 1.0
+ # print "Using omegasign=",sign
+ self.gv = transform.compute_g_vectors(tth,eta,om*sign,
+ float(self.parameters['wavelength']),
self.parameters['wedge'],
self.parameters['chi'])
self.gv = Numeric.transpose(self.gv)
@@ -151,11 +157,12 @@
def refine(self,ubi,quiet=True):
from ImageD11 import closest
mat=ubi.copy()
+ #print self.tolerance
npks = closest.score_and_refine(mat, self.gv, self.tolerance)
if not quiet:
print npks
- #mat = indexing.refine(ubi,self.gv,self.tolerance,quiet=quiet)
- #print ubi, testmatrix,ubi-testmatrix,mat-testmatrix
+ #tm = indexing.refine(ubi,self.gv,self.tolerance,quiet=quiet)
+ #print ubi, tm,ubi-tm,mat-tm
return mat
def gof(self,args):
@@ -269,7 +276,7 @@
self.printresult(newguess)
def refineubis(self,quiet=True):
-
+ #print quiet
for key in self.grains.keys():
g = self.grains[key]
grainname = key[0]
Modified: ImageD11/trunk/ImageD11/transform.py
===================================================================
--- ImageD11/trunk/ImageD11/transform.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/ImageD11/transform.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -424,18 +424,59 @@
-def compute_lorentz_factors(args):
+def compute_lorentz_factors(tth,eta,omega,wavelength,wedge=0.,chi=0.):
"""
From Kabsch 1988 J. Appl. Cryst. 21 619
Multiply the intensities by:
- Lorentz = | S.(u x S_0)| / |S|.|S_0|
+ Lorentz = | S.(u x So)| / |S|.|So|
S = scattered vector
- S_0 = incident vector
+ So = incident vector
u = unit vector along rotation axis
"""
- pass
+ # So is along +x, the incident beam defines the co-ordinates in ImageD11
+ # length is in reciprocal space units, 1/lambda
+ So = [1./wavelength,0,0]
+ #
+ # u vector along rotation axis
+ # starts as along z
+ u = [0,0,1]
+ # rotate by
+ # g = R . W . k where:
+ # R = ( cos(omega) , sin(omega), 0 )
+ # (-sin(omega) , cos(omega), 0 )
+ # ( 0 , 0 , 1 )
+ #
+ W = [[ cos(wedge) , 0 , sin(wedge) ],
+ [ 0 , 1 , 0 ],
+ [-sin(wedge) , 0 , cos(wedge) ]]
+ #
+ C = [[ 1 , 0 , 0 ],
+ [ 0 , cos(chi) , sin(chi) ],
+ [ 0 , -sin(chi) , cos(chi) ]]
+ u = matrixmultiply(C,matrixmultiply(W,u))
+ u_x_So = cross_product(u,So)
+ # if DEBUG: print "axis orientation",u
+ #
+ # S = scattered vectors. Length 1/lambda.
+ S = [ cos(radians(tth)/2.)*sin(radians(eta))/wavelength,
+ cos(radians(tth)/2.)*cos(radians(eta))/wavelength,
+ sin(radians(tth)/2.)/wavelength]
+ S_dot_u_x_So = dot(S,u_x_So)
+ mod_S = sqrt(dot(S,S))
+ mod_So = sqrt(dot(So,So))
+ try:
+ lorentz = abs(S_dot_u_x_So)/mod_S/mod_So
+ except:
+ raise Exception("Please fix this div0 crap in lorentz")
+ return lorentz
+def cross_product(a,b):
+ assert len(a)==len(b)==3
+ return array([a[1]*b[2]-a[2]*b[1],
+ a[2]*b[0]-a[0]*b[2],
+ a[0]*b[1]-a[1]*b[0]])
+
def compute_polarisation_factors(args):
"""
From Kabsch 1988 J. Appl. Cryst. 21 619
@@ -448,8 +489,13 @@
S = scattered vector
S_0 = incident vector
n = normal to polarisation plane, typically perpendicular to S_0
+
+ In ImageD11 we normally expect to find:
+ x axis along the beam
+ z axis being up, and parallel to the normal n mentioned above
"""
- pass
+ n = [0,0,1]
+
if __name__=="__main__":
# from indexing import mod_360
Modified: ImageD11/trunk/ImageD11/unitcell.py
===================================================================
--- ImageD11/trunk/ImageD11/unitcell.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/ImageD11/unitcell.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -45,7 +45,12 @@
"""
Normalise vector a to unit length
"""
- return a/Numeric.sqrt(Numeric.dot(a,a))
+ try:
+ return a/Numeric.sqrt(Numeric.dot(a,a))
+ except:
+ l=Numeric.dot(a,a)
+ print "Length of a is",l
+ raise
@@ -178,7 +183,7 @@
Argument dsmax is the d* limit (eg 1/d)
Default of zero gives only the (000) reflection
- assumes [h|k|l] < 20
+ assumes [h|k|l] < 200
"""
if dsmax == self.limit and self.peaks!=None:
return self.peaks
@@ -187,9 +192,9 @@
hs=ks=ls=1
b=0
peaks=[]
- while abs(h)<20: # H
- while abs(k)<20: # K
- while abs(l)<20: #L
+ while abs(h)<200: # H
+ while abs(k)<200: # K
+ while abs(l)<200: #L
ds=self.ds([h,k,l])
if ds < dsmax:
if not self.absent(h,k,l):
Modified: ImageD11/trunk/MANIFEST
===================================================================
--- ImageD11/trunk/MANIFEST 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/MANIFEST 2006-11-22 20:59:02 UTC (rev 425)
@@ -5,6 +5,7 @@
ImageD11/data.py
ImageD11/factors.py
ImageD11/findreflections.py
+ImageD11/fitgrainxy.py
ImageD11/grain.py
ImageD11/guicommand.py
ImageD11/guifactors.py
@@ -36,12 +37,15 @@
scripts/edfheader.py
scripts/fit2dcake.py
scripts/peaksearch.py
+scripts/mar2bruker.py
scripts/plotedf.py
+scripts/rubber.py
scripts/powderimagetopeaks.py
scripts/recoveromega.py
scripts/rubber.py
scripts/scriptable_gui.py
src/bispev.c
+src/bispev.f
src/closest.c
src/connectedpixels.c
src/hist.c
Added: ImageD11/trunk/scripts/ImageD11_2_shelx.py
===================================================================
--- ImageD11/trunk/scripts/ImageD11_2_shelx.py (rev 0)
+++ ImageD11/trunk/scripts/ImageD11_2_shelx.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -0,0 +1,51 @@
+#!/bliss/users/blissadm/python/bliss_python/suse82/bin/python
+
+
+# ImageD11_v0.4 Software for beamline ID11
+# Copyright (C) 2005 Jon Wright
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+
+
+"""
+Script for getting integrated intensities from .flt + .ubi file
+from the command line
+"""
+
+
+
+
+
+if __name__=="__main__":
+ import sys
+ try:
+ flt = sys.argv[1]
+ ubi = sys.argv[2]
+ par = sys.argv[3]
+ out = sys.argv[4]
+ from ImageD11.refinegrains import refinegrains
+ o=refinegrains()
+ o.loadparameters(par)
+ o.loadfiltered(flt)
+ o.readubis(ubi)
+ o.generate_grains()
+ o.tolerance = 0.1 # to command line arg
+ o.refineubis(False)
+
+
+ except:
+ print "Usage: %s fltfile ubifile parfile outfile"
+ raise
Modified: ImageD11/trunk/scripts/fit2dcake.py
===================================================================
--- ImageD11/trunk/scripts/fit2dcake.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/scripts/fit2dcake.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -502,7 +502,7 @@
except:
os.environ["DISPLAY"]=":1"
array=str(self.mask_pars_values["DIM1_DATA"])+"x"+str(self.mask_pars_values["DIM2_DATA"])
- os.system("fit2d_12_081_i686_linux2.4.20 -dim%s -mac%s"%(array,tmpfilename))
+ os.system("/users/wright/bin/fit2d_12_081_i686_linux2.4.20 -dim%s -mac%s"%(array,tmpfilename))
os.system("rm -f %s"%(tmpfilename))
if show is None:
os.environ["DISPLAY"]=displaywas
Modified: ImageD11/trunk/scripts/peaksearch.py
===================================================================
--- ImageD11/trunk/scripts/peaksearch.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/scripts/peaksearch.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -16,7 +16,7 @@
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 0211-1307 USA
@@ -40,31 +40,284 @@
from ImageD11 import connectedpixels
import Numeric
-def peaksearch(filename, outputfile, corrector, blobim , thresholds,
+class labelimage:
+ def __init__(self,shape,fileout=sys.stdout,spatial=blobcorrector.perfect):
+ self.shape=shape
+ self.bl = Numeric.zeros(shape,Numeric.Int)
+ self.lastbl = Numeric.zeros(shape,Numeric.Int)
+ self.np = 0
+ self.res = (0,)*10
+ self.lastres = []
+ self.lastnp=-1
+ self.verbose=0
+ self.nprop = 9 # number of accumulating properties
+ self.corrector=corrfunc
+ self.closed =None
+ self.finalpeaks=[]
+ self.outfile=open(fileout,"w")
+ self.outfile.write("# xc yc omega npixels avg_intensity x_raw y_raw sigx sigy covxy\n")
+
+ def peaksearch(self,data,threshold):
+ """
+ # Call the c extension to do the peaksearch, on entry:
+ #
+ # picture = 2D Numeric UInt16 array (of your data)
+ # blobim = 2D Numeric Int array of same shape as data
+ # threshold = float - pixels above this number are put into objects
+ # verbose = 0/1 - whether or not to print anything
+ #
+ # One return - np is the number of peaks found (number of
+ # connnected objects) picture should be unchanged
+ # blobim should be overwritten with integers giving the peak number for
+ # that pixel
+ # or zero if the pixel was below the threshold
+ #
+
+ """
+ self.bl = Numeric.zeros(self.shape,Numeric.Int)
+ # print "labelimage.peaksearch",data[0,0],threshold
+ self.np = connectedpixels.connectedpixels(data, self.bl, threshold,
+ self.verbose)
+ return self.np
+
+ def properties(self,data,omega=0.):
+ """
+ # Now get the properties of the identified objects, on entry:
+ # picture = data, as before
+ # blobim = peak assignments
+ # np = the number of peaks to find
+ # verbose = 0/1 - whether to print or not
+ #
+ #
+ # This returns a series of 1D Numeric arrays:
+ # npi = Number of pixels in objects ... for each blob pixel
+ # sum 1
+ # isum = sum of intensity in blobs
+ # sum data[i][j]
+ # sumsq = sum of intensity squared
+ # sum data[i][j] * data[i][j]
+ # com0 = sum of intensity multiplied by fast index:
+ # sum i*data[i][j]
+ # com1 = sum of intensity multiplied by slow index:
+ # sum j*data[i][j]
+ # com00 = sum of intensity multiplied by fast index squared:
+ # sum i*i*data[i][j]
+ # com01 = sum of intensity multiplied by fast index and slow index:
+ # sum i*j*data[i][j]
+ # com00 = sum of intensity multiplied by slow index squared:
+ # sum j*j*data[i][j]
+ # com2 = sum of intensity multiplied by slowest index (normally rotation angle)
+ # = sum omega*isum
+ #
+
+ """
+ if self.np>0:
+ res = connectedpixels.blobproperties(data, self.bl, self.np, self.verbose)
+ try:
+ self.res = res + (Numeric.ones(res[1].shape[0],Numeric.Float)*omega * res[1],)
+ except:
+# print res,self.np
+ raise
+ else:
+ self.res = (0,)*10
+ return self.res
+
+ def mergelast(self):
+ """
+ Merge the last two images searched
+ """
+ if self.lastnp < 0:
+ # no previous to merge with, just save the current for next time
+ self.lastbl = self.bl
+ self.lastnp = self.np
+ self.lastres = self.res
+ return
+ # print "Calling bloboverlaps",self.verbose
+ ds = connectedpixels.bloboverlaps(self.bl, self.np, self.lastbl, self.lastnp, self.verbose)
+ # ds is a disjoint set.
+ # print ds
+ # already filled out self.res, self.lastres
+ #
+ # Move counts in self.lastres forwards to self.res
+ # Once all checked move non-zeros in self.lastres to self.closed
+ three_d_debug=False
+ if three_d_debug:
+ print len(ds),self.np,self.lastnp,ds
+ print "np",self.np,"len(self.res[0])",len(self.res[0])
+ print "lastnp",self.lastnp,"len(self.lastres[0])",len(self.lastres[0])
+ for i in range(self.np+1,len(ds)):
+# print i
+# if ds[i]==i and i<self.np:
+# # this peak is on res and not overlapped, it will, eventually, move to lastres
+# continue
+ if ds[i]!=i:
+ if three_d_debug:
+ print "linking ds[i],i",ds[i],i,
+ assert ds[i] < self.np, "Link on the same image"
+ # propose to link these two spots...
+ # print "l",i,ds[i]," ",
+ # bring the stuff forwards from last
+ if three_d_debug:
+ peak1 = []
+ peak2 = []
+ for j in range(self.nprop): # loop over properties
+ if three_d_debug: # debug
+ peak1.append(self.res[j][ds[i]])
+ peak2.append(self.lastres[j][i-self.np])
+ try:
+ self.res[j][ds[i]]=self.res[j][ds[i]]+self.lastres[j][i-self.np]
+ except:
+ print j,i,ds[i]
+ print ds
+ raise Exception("You should not be seeing this error!!")
+ if three_d_debug:
+ print "Linking ds[i],[i-self.np]",i,ds[i],i-self.np
+ print self.to_string(peak1),
+ print self.to_string(peak2),
+ else: # this peak is no longer active so write it out
+ peak = []
+ for j in range(self.nprop): # loop over properties
+ # self.res[property][peak]
+ try:
+ peak.append(self.lastres[j][i-self.np])
+ except:
+ print "indices",j,i,i-self.np,self.lastres
+ raise
+ self.outputpeak(peak)
+ # Now get the overlaps on the current frame
+ #
+ for i in range(1,self.np):
+ if ds[i]!=i :
+ # propose to link these two spots on the current active frame
+ # print "linking on current not implemented",i,ds[i]
+ peak1=[]; peak2=[]
+ # write the correct number in the blob image
+ # ... expensive - could be done in C??
+ self.bl = Numeric.where(self.bl == i, ds[i], self.bl)
+ for j in range(self.nprop): # loop over properties
+ try:
+ self.res[j][ds[i]]=self.res[j][ds[i]]+self.res[j][i]
+ self.res[j][i]=0
+ except:
+ print j,i,ds[i]
+ print ds
+ raise Exception("You should not be seeing this error!!")
+ temp = self.lastbl
+ self.lastbl = self.bl
+ self.bl=temp
+ self.lastnp = self.np
+ self.lastres = self.res
+
+
+ def outputpeak(self,peak):
+ self.outfile.write(self.to_string(peak))
+
+ def to_string(self,peak):
+ """
+ Convert the accumulators to more meaningful things
+ self.outfile.write("# xc yc omega npixels avg_intensity x_raw y_raw sigx sigy covxy\n")
+ """
+ npi, isum, sumsq, com0, com1, com00, com01, com11, omisum = peak
+ if npi < 1:
+ return ""
+ else:
+ n = npi
+ # Average intensity
+ avg = isum/n
+ if n==1:
+ si = sqrt(sumsq - n*avg*avg)
+ else:
+ si = sqrt((sumsq - n*avg*avg)/(n-1.))
+ # Standard dev on intensity
+ c0 = com0/isum
+ # Centre of mass in index 0
+ c1 = com1/isum
+ # Centre of mass in index 1
+ # Covariances - try except to allow for zeros
+ try:
+ c00 = sqrt((com00/isum - c0*c0))
+ except:
+ c00 = 0. # this means a line of pixels and rounding errors
+ try:
+ c11 = sqrt((com11/isum - c1*c1))
+ except:
+ c11 = 0.
+ try:
+ c01 = (com01/isum - c0*c1)/c00/c11
+ except:
+ c01 = 0.
+ # Spatial corrections,
+ # c0c and c1c are the distortion corrected centre of mass :
+ c0c, c1c = self.corrector.correct(c0, c1)
+ om = omisum/isum
+ if False:# abs(c0c-1229)<2 and abs(c1c-1486)<2:
+ print "c0c,c1c",c0c,c1c
+ print peak
+ print "%f %f %f %d %f %f %f %f %f %f\n"%(c0c, c1c, om, n, avg, c0, c1, c00, c11, c01)
+ raise Exception("who are you??")
+ return "%f %f %f %d %f %f %f %f %f %f\n"%(c0c, c1c, om, n, avg, c0, c1, c00, c11, c01)
+
+
+ def finalize(self):
+ """
+ Assume we finished the last image
+ """
+ # self.outfile.write("#final frame\n")
+ for i in range(len(self.lastres[0])): # loop over peaks
+ peak = []
+ for j in range(len(self.lastres)): # loop over properties
+ # self.res[property][peak]
+ try:
+ peak.append(self.lastres[j][i])
+ except:
+ print "indices",j,i,i-self.np,self.lastres
+ raise
+ self.outputpeak(peak)
+ self.outfile.close()
+
+class timer:
+ def __init__(self):
+ self.start = time.time()
+ self.now = self.start
+ def tick(self,msg=""):
+ now = time.time()
+ print msg,"%.2f/s"%(now-self.now),
+ self.now = now
+ def tock(self,msg=""):
+ self.tick(msg)
+ print "%.2f/s"%(self.now-self.start)
+
+def peaksearch(filename, outputfile, corrector, labims , thresholds,
dark=None, flood=None):
"""
Searches for peaks, arguments are:
filename : image filename to search for peaks in
outputfile : ascii file to receive results
corrector : ImageD11.blobcorrector object to correct peak positions
- blobim : Numeric.Int array of same shape as data image to hold blob
- assignments
+ labim : Numeric.Int array of same shape as data image to hold blob
+ assignments (dict[thresholds] of pairs)
thresholds : List of threshold values to use (use more than one if you are
not sure what to use), any iterable will do, not just list
"""
- t0 = time.time()
+ t = timer()
f = open(outputfile,"aq") # Open the output file for appending
# Assumes an edf file for now - TODO - should be independent
data_object = opendata.opendata(filename)
picture = data_object.data
# picture is (hopefully) a 2D Numeric array of type UInt16
+ # t.tick("read")
if dark != None:
# Slows down timing but avoid overflows
- picture = picture.astype(Numeric.Float32)-dark
+ # print "Subtracting dark,",picture[0,0]
+ # print picture.shape,picture.typecode(),dark.shape,dark.typecode()
+ picture.savespace(0) # avoid overflows - very slow and silly
+ picture = picture.astype(Numeric.Int)-dark
+ # print "Subtracted dark,",picture[0,0]
+ # t.tick("dark")
if flood != None:
picture = picture/flood
- print "%s" % (filename), # Progress indicator
- #
+ t.tick(filename+" io/cor") # Progress indicator
+ #print "datatype for searching", picture.typecode() #
# Transfer header information to output file
# Also information on spatial correction applied
f.write("\n\n# File %s\n" % (filename))
@@ -83,69 +336,39 @@
str(data_object.header[item]).replace("\n"," ")))
except KeyError:
pass
- # Check the blobim matches the data for shape
- if blobim.shape != data_object.data.shape:
- raise "Incompatible blobimage buffer for file %s" %(filename)
#
# Now peaksearch at each threshold level
for threshold in thresholds:
+ labelim = labims[threshold]
+ if labelim.shape != picture.shape:
+ raise "Incompatible blobimage buffer for file %s" %(filename)
#
npks = 0
#
- # Call the c extension to do the peaksearch, on entry:
+ # Do the peaksearch
+ np = labelim.peaksearch(picture,threshold)
#
- # picture = 2D Numeric UInt16 array (of your data)
- # blobim = 2D Numeric Int array of same shape as data
- # threshold = float - pixels above this number are put into objects
- # verbose = 0/1 - whether or not to print anything
- #
- np = connectedpixels.connectedpixels(picture, blobim, threshold,
- verbose=0)
- #
- # One return - np is the number of peaks found (number of
- # connnected objects) picture should be unchanged
- # blobim should be overwritten with integers giving the peak number for
- # that pixel
- # or zero if the pixel was below the threshold
- #
- # Now get the properties of the identified objects, on entry:
- # picture = data, as before
- # blobim = peak assignments
- # np = the number of peaks to find
- # verbose = 0/1 - whether to print or not
- #
- npi, isum, sumsq, com0, com1, com00, com01, com11 = \
- connectedpixels.blobproperties(picture, blobim, np, verbose=0)
- #
- # This returns a series of 1D Numeric arrays:
- # npi = Number of pixels in objects ... for each blob pixel
- # sum 1
- # isum = sum of intensity in blobs
- # sum data[i][j]
- # sumsq = sum of intensity squared
- # sum data[i][j] * data[i][j]
- # com0 = sum of intensity multiplied by fast index:
- # sum i*data[i][j]
- # com1 = sum of intensity multiplied by slow index:
- # sum j*data[i][j]
- # com00 = sum of intensity multiplied by fast index squared:
- # sum i*i*data[i][j]
- # com01 = sum of intensity multiplied by fast index and slow index:
- # sum i*j*data[i][j]
- # com00 = sum of intensity multiplied by slow index squared:
- # sum j*j*data[i][j]
- #
+ try:
+ omega = float(data_object.header["Omega"])
+ except: # Might have imagenumber or something??
+ omega = 0.
+ props = labelim.properties(picture,omega)
+ npi, isum, sumsq, com0, com1, com00, com01, com11, omisum = props
+ # omisum is omega * isum
# Now write results out for this threshold level
f.write("\n#Threshold level %f\n" % (threshold))
f.write( "# Number_of_pixels Average_counts x y xc yc sig_x sig_y cov_xy\n")
outstrfmt = "%d %f %f %f %f %f %f %f %f\n"
for i in range(len(npi)): # Loop over peaks
- if npi[i]>1: # Throw out one pixel peaks (div zero)
+ if npi[i]>=1: # Throw out one pixel peaks (div zero)
npks = npks+1
n = npi[i]
# Average intensity
avg = isum[i]/n
- si = sqrt((sumsq[i] - n*avg*avg)/(n-1.))
+ if n>2:
+ si = sqrt((sumsq[i] - n*avg*avg)/(n-1.))
+ else:
+ si = sqrt((sumsq[i] - n*avg*avg)/n)
# Standard dev on intensity
c0 = com0[i]/isum[i]
# Centre of mass in index 0
@@ -171,11 +394,12 @@
except:
c0c, c1c = c0, c1
f.write(outstrfmt % (n, avg, c0, c1, c0c, c1c, c00, c11, c01))
+ labelim.mergelast() # called here!!!
print "T=%-5d n=%-5d;" % (int(threshold),npks),
# Close the output file
f.close()
# Finish progress indicator for this file
- print " time %f/s" % (time.time()-t0)
+ t.tock()
sys.stdout.flush()
return npks # Number of peaks found
@@ -230,13 +454,8 @@
corrfunc = blobcorrector.correctorclass(options.spline)
else:
print "Avoiding spatial correction"
- class dummy:
- splinefile = "NO_CORRECTION_APPLIED"
- xsize = "UNKNOWN"
- ysize = "UNKNOWN"
- def correct(x,y):
- return x, y
- corrfunc = dummy()
+ corfunc = blobcorrector.perfect()
+
# List comprehension - convert remaining args to floats
thresholds_list = [float(t) for t in options.thresholds]
# Generate list of files to process
@@ -248,21 +467,27 @@
files = ["%s.%04d" % (stem,i) for i in range(first,last+1)]
corrfunc.orientation = "bruker"
if options.spline.find("spatial2k.spline")>0:
- if raw_input("Are you sure abuot the spline??")!="y":
+ if raw_input("Are you sure about the spline??")!="y":
sys.exit()
# Make a blobimage the same size as the first image to process
if len(files)==0:
raise "No files found for stem %s" % (stem)
- blobar=Numeric.zeros(opendata.opendata(files[0]).data.shape,Numeric.Int)
+ li_objs={} # label image objects, dict of
+ s = opendata.opendata(files[0]).data.shape # data array shape
+ # Create label images
+ for t in thresholds_list:
+ mergefile="%s_merge_t%d"%(options.outfile,t)
+ li_objs[t]=labelimage(shape=s,fileout=mergefile,spatial=corrfunc)
# Not sure why that was there (I think if glob was used)
# files.sort()
if options.dark!=None:
- darkimage=(opendata.opendata(options.dark).data - \
+ print "Using dark (background)",options.dark,"with added offset",options.darkoffset
+ darkimage= (opendata.opendata(options.dark).data.astype(Numeric.Int)-\
options.darkoffset).astype(Numeric.UInt16)
else:
darkimage=None
if options.flood!=None:
- floodimage=opendata.opendata(options.flood).data
+ floodimage=opendata.opendata(options.flood).data.astype(Numeric.Float32)
# Check flood normalisation
m1 = floodimage.shape[0]/6
m2 = floodimage.shape[1]/6
@@ -275,8 +500,10 @@
start = time.time()
print "File being treated in -> out, elapsed time"
for filein in files:
- peaksearch(filein, outfile, corrfunc, blobar, \
+ peaksearch(filein, outfile, corrfunc, li_objs, \
thresholds_list,dark=darkimage,flood=floodimage)
+ for t in thresholds_list:
+ li_objs[t].finalize()
except:
# print "Usage: %s filename outputfile first last spline threshold [threshold...]" % (sys.argv[0])
print
Modified: ImageD11/trunk/scripts/rubber.py
===================================================================
--- ImageD11/trunk/scripts/rubber.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/scripts/rubber.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -39,7 +39,11 @@
image[DEFAULT_HEIGHT-1-ys[x],len_x-x-1] = 0
image = transpose(image)
elif image.typecode() != 'b':
- image = 255 * (image - themin) / (themax-themin)
+ try:
+ image.savespace(0)
+ image = 255 * (image - themin) / (themax-themin)
+ except:
+ print "Exception",themax,themin
image = where(image<256,image,255)
image = where(image>0,image,0).astype('b')
@@ -77,7 +81,7 @@
class rubber(Frame):
- def __init__(self, datafile=None, master=None):
+ def __init__(self, datafile=None, bkgfile=None, master=None):
self.master=master
Frame.__init__(self, master)
if datafile==None:
@@ -94,7 +98,15 @@
if type(datafile)==type(array([10,11,12])):
self.data=datafile
self.datafile="unknown0000.edf"
+ self.data.savespace(0)
+ if type(bkgfile)==type("string"):
+ self.bkgfile=bkgfile
+ bkgobj=opendata(bkgfile)
+ self.bkg=bkgobj.data
+ self.data=self.data-self.bkg
+ print "Got your background from",bkgfile,self.bkg.shape
+
Pack.config(self,expand=1,fill=BOTH)
self.b=Frame(self)
Button(self.b,text="Quit",command=self.close).pack(side=RIGHT)
@@ -253,7 +265,13 @@
dataobj=opendata(self.datafile)
self.status.config(text=self.datafile)
self.data=dataobj.data
+ self.data.savespace(0)
try:
+ self.data=self.data-self.bkg
+ except:
+ print "Failed to subtract bkg",self.bkg.shape,self.data.shape
+ pass
+ try:
self.omega=float(dataobj.header["Omega"])
except:
self.omega = None
@@ -500,7 +518,9 @@
import sys
from ImageD11.opendata import opendata
-if len(sys.argv)>1:
+if len(sys.argv)>2:
+ test = rubber(sys.argv[1],bkgfile=sys.argv[2])
+elif len(sys.argv)>2:
test = rubber(sys.argv[1])
else:
test = rubber()
Modified: ImageD11/trunk/setup.py
===================================================================
--- ImageD11/trunk/setup.py 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/setup.py 2006-11-22 20:59:02 UTC (rev 425)
@@ -68,7 +68,7 @@
# See the distutils docs...
setup(name='ImageD11',
- version='0.6.1',
+ version='0.7.1',
author='Jon Wright',
author_email='wr...@es...',
description='ImageD11',
@@ -77,6 +77,7 @@
ext_modules = [cl,cp,bl,ch],
packages = ["ImageD11"],
scripts = ["scripts/peaksearch.py",
+ "scripts/ImageD11_2_shelx.py",
"scripts/fit2dcake.py",
"scripts/edfheader.py",
"scripts/recoveromega.py",
Modified: ImageD11/trunk/src/connectedpixels.c
===================================================================
--- ImageD11/trunk/src/connectedpixels.c 2006-11-22 20:49:16 UTC (rev 424)
+++ ImageD11/trunk/src/connectedpixels.c 2006-11-22 20:59:02 UTC (rev 425)
@@ -405,7 +405,7 @@
/* return PyArray_Return(results); */
/* Py_DECREF(results);*/
/* Py_DECREF(dataarray);*/
- return Py_BuildValue("i", np);
+ return Py_BuildValue("i", np+1);/* why the plus one?? */
}
@@ -571,13 +571,130 @@
}
+static char bloboverlaps_doc[] =\
+" res = bloboverlaps ( Numeric.array(blob1, 2D, Int), n1 , \n"\
+" Numeric.array(blob2, 2D, Int), n2 , verbose=0) \n"\
+" \n"\
+" returns a disjoint set making the overlaps between blob1 and blob2 \n"\
+" res[0->n1] = peaks in image 1 \n"\
+" res[n2->n2+n1+1] = peaks in image 2 \n";
+
+
+static PyObject * bloboverlaps (PyObject *self, PyObject *args, PyObject *keywds)
+{
+ PyArrayObject *b1=NULL,*b2=NULL, *res=NULL; /* in (not modified) */
+ int i,j,s,f, verbose ; /* loop vars, flag */
+ int p1,p2,n1,n2; /* peak num and npeaks in each */
+ int *link , percent, safelyneed;
+ static char *kwlist[] = {"blob1","n1","blob2","n2","verbose", NULL};
+ if(!PyArg_ParseTupleAndKeywords(args,keywds, "O!iO!i|i",kwlist,
+ &PyArray_Type, &b1, /* blobs */
+ &n1,
+ &PyArray_Type, &b2, /* blobs */
+ &n2,
+ &verbose)) /* threshold and optional verbosity */
+ return NULL;
+ if(verbose!=0)printf("Welcome to bloboverlaps\n");
+
+ /* Check array is two dimensional and int - results from connectedpixels above */
+
+ if(b1->nd != 2 && b1->descr->type_num != PyArray_INT){
+ PyErr_SetString(PyExc_ValueError,
+ "Blob1 array must be 2d and integer, first arg problem");
+ return NULL;
+ }
+ if(b2->nd != 2 && b2->descr->type_num != PyArray_INT){
+ PyErr_SetString(PyExc_ValueError,"Blob2 array must be 2d and integer, second arg problem");
+ return NULL;
+ }
+ if (b1->strides[0]!=b2->strides[0] ||
+ b1->strides[1]!=b2->strides[1] ||
+ b1->dimensions[0]!=b2->dimensions[0] ||
+ b1->dimensions[1]!=b2->dimensions[1] ){
+ PyErr_SetString(PyExc_ValueError,
+ "Blob1 and Blob2 array be similar (dims & strides)");
+ return NULL;
+ }
+ /* Decide on fast/slow loop - inner versus outer */
+ if(b1->strides[0] > b1->strides[1]) {
+ f=1; s=0;}
+ else {
+ f=0; s=1;
+ }
+ if (verbose!=0){
+ printf("Fast index is %d, slow index is %d, ",f,s);
+ printf("strides[0]=%d, strides[1]=%d\n",b1->strides[0],b2->strides[1]);
+ }
+ /* Initialise a disjoint set in link
+ * image 1 has peak[i]=i ; i=1->n1
+ * image 2 has peak[i]=i+n1 ; i=1->n2
+ * link to hold 0->n1-1 ; n1->n2+n2-1 */
+ safelyneed=n1+n2+1;
+ res = (PyArrayObject *)PyArray_FromDims(1,&safelyneed,PyArray_INT);
+ link = (int *) res->data;
+ if(!res){ /* max length */
+ PyErr_SetString(PyExc_ValueError,
+ "Failed to malloc link array");
+ return NULL;
+ }
+
+ for(i=0;i<n1+n2+1;i++){link[i]=i;} /* first image */
+ /* flag the start of image number 2 */
+ link[n1]=-99999; /* Should never be touched by anyone */
+
+ /* results lists of pairs of numbers */
+ if(verbose!=0){
+ printf("Scanning image, n1=%d n2=%d\n",n1,n2);
+ }
+ percent = b1->dimensions[s] / 100.;
+ for( i = 0 ; i <= (b1->dimensions[s]-1) ; i++ ){ /* i,j is looping along the indices data array */
+ if(verbose!=0 && (i%percent == 0) )printf(".");
+ for( j = 0 ; j <= (b1->dimensions[f]-1) ; j++ ){
+ p1=* (int *) (b1->data + i*b1->strides[s] + j*b1->strides[f]);
+ if (p1==0){ continue; }
+ p2=* (int *) (b2->data + i*b2->strides[s] + j*b2->strides[f]);
+ if (p2==0){ continue; }
+ /* Link contains the peak that this peak is */
+ if(link[p1]<0 || link[p2+n1]<0){
+ printf("Whoops p1=%d p2=%d p2+n1=%d link[p1]=%d link[p2+n1]=%d",p1,p2,p2+n1,link[p1],link[p2+n1]);
+ return NULL;
+ }
+ /* printf("link[60]=%d %d %d ",link[60],p1,p2+n1);*/
+ dset_makeunion(link,p1,p2+n1);
+ /* printf("link[60]=%d ",link[60]); */
+ if(verbose>2)printf("link[p1=%d]=%d link[p2+n1=%d]=%d\n",p1,link[p1],p2+n1,link[p2+n1]);
+ } /* j */
+ } /* i */
+ if(verbose!=0){
+ printf("\n");
+ for(i=0;i<n1+n2;i++){
+ if(i!=link[i]){
+ printf("Link found!! %d %d\n",i,link[i]);
+ }
+ }
+ }
+ return Py_BuildValue("O", PyArray_Return(res));
+}
+
+
+
+
+
+
+
+
+
+
+
static PyMethodDef connectedpixelsMethods[] = {
{"connectedpixels", (PyCFunction) connectedpixels, METH_VARARGS | METH_KEYWORDS,
connectedpixels_doc},
{"blobproperties", (PyCFunction) blobproperties, METH_VARARGS | METH_KEYWORDS,
blobproperties_doc},
+ {"bloboverlaps", (PyCFunction) bloboverlaps, METH_VARARGS | METH_KEYWORDS,
+ bloboverlaps_doc},
{"roisum", (PyCFunction) roisum, METH_VARARGS | METH_KEYWORDS,
roisum_doc},
{NULL, NULL, 0, NULL} /* setinel */
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|
|
From: <and...@us...> - 2006-11-22 20:49:16
|
Revision: 424
http://svn.sourceforge.net/fable/?rev=424&view=rev
Author: andy_gotz
Date: 2006-11-22 12:49:16 -0800 (Wed, 22 Nov 2006)
Log Message:
-----------
removed unused imports
Modified Paths:
--------------
gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/DiodemuxView.java
Modified: gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/DiodemuxView.java
===================================================================
--- gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/DiodemuxView.java 2006-11-22 10:22:46 UTC (rev 423)
+++ gui/trunk/fable.beamline.rcp/src/fable/beamline/rcp/DiodemuxView.java 2006-11-22 20:49:16 UTC (rev 424)
@@ -1,19 +1,17 @@
package fable.beamline.rcp;
import org.eclipse.jface.preference.IPreferenceStore;
-import org.eclipse.jface.window.ApplicationWindow;
import org.eclipse.swt.SWT;
import org.eclipse.swt.layout.FillLayout;
import org.eclipse.swt.layout.GridData;
import org.eclipse.swt.layout.GridLayout;
-import org.eclipse.swt.layout.RowLayout;
+
import org.eclipse.swt.widgets.Button;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Event;
import org.eclipse.swt.widgets.Group;
import org.eclipse.swt.widgets.Label;
-import org.eclipse.swt.widgets.Layout;
import org.eclipse.swt.widgets.Listener;
import org.eclipse.ui.part.ViewPart;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: Andy G. <and...@es...> - 2006-11-22 16:22:35
|
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