From 1b4a05ce294d94f16b64e00879cdb6124d2b05b4 Mon Sep 17 00:00:00 2001
From: Martyn Gigg <martyn.gigg@stfc.ac.uk>
Date: Thu, 5 Jan 2012 21:09:41 +0000
Subject: [PATCH] Refs #4200. Diag should now match libisis.
Additional parameters were required to better match the granularity
of the libisis testsx
---
Code/Mantid/instrument/ARCS_Parameters.xml | 75 +++-
Code/Mantid/instrument/CNCS_Parameters.xml | 73 +++-
Code/Mantid/instrument/HYSPEC_Parameters.xml | 73 +++-
Code/Mantid/instrument/LET_Parameters.xml | 110 ++++-
Code/Mantid/instrument/MAPS_Parameters.xml | 105 ++++-
Code/Mantid/instrument/MARI_Parameters.xml | 98 ++++-
Code/Mantid/instrument/MERLIN_Parameters.xml | 111 ++++-
Code/Mantid/instrument/SEQUOIA_Parameters.xml | 73 +++-
.../Inelastic/DirectEnergyConversion.py | 197 ++++++---
Code/Mantid/scripts/Inelastic/diagnostics.py | 398 +++++++-----------
10 files changed, 895 insertions(+), 418 deletions(-)
diff --git a/Code/Mantid/instrument/ARCS_Parameters.xml b/Code/Mantid/instrument/ARCS_Parameters.xml
index 0f868a5cf40..5697452ec58 100644
--- a/Code/Mantid/instrument/ARCS_Parameters.xml
+++ b/Code/Mantid/instrument/ARCS_Parameters.xml
@@ -50,6 +50,74 @@
<!-- Diagnostic test defaults -->
+ <!-- Absolute lo threshold for vanadium diag (tiny) -->
+ <parameter name="diag_tiny">
+ <value val="1e-10"/>
+ </parameter>
+
+ <!-- Absolute hi threshold for vanadium diag (huge) -->
+ <parameter name="diag_huge">
+ <value val="1e10"/>
+ </parameter>
+
+ <!-- Remove zeroes in background (s_zero)-->
+ <parameter name="diag_samp_zero">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+ <parameter name="diag_samp_lo">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+ <parameter name="diag_samp_hi">
+ <value val="5.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+ <parameter name="diag_samp_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+ <parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+ </parameter>
+
+ <!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+ <parameter name="diag_van_out_hi">
+ <value val="100."/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+ <parameter name="diag_van_lo">
+ <value val="0.1"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+ <parameter name="diag_van_hi">
+ <value val="3.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+ <parameter name="diag_van_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- True if background is to be checked -->
+ <parameter name="check_background">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- True if the bleed tests should be run -->
+ <parameter name="diag_bleed_test">
+ <value val="0.0"/>
+ </parameter>
+
+
+ <!-- TO BE REMOVED Diagnostic test defaults -->
+
<parameter name="remove_zero">
<value val="1.0" />
</parameter>
@@ -87,6 +155,7 @@
</parameter>
<!-- -->
+
<!-- Absolute units conversion average -->
<parameter name="monovan_lo_bound">
@@ -106,12 +175,6 @@
</parameter>
<!-- -->
- <!-- PSD bleed test -->
-
- <parameter name="bleed_test">
- <value val="0.0" />
- </parameter>
-
<!-- All the following parameters are taken directly from the MARI definition
and are WRONG! They are only here for now to get things working -->
diff --git a/Code/Mantid/instrument/CNCS_Parameters.xml b/Code/Mantid/instrument/CNCS_Parameters.xml
index 4c3054e6479..af3a868ea1c 100644
--- a/Code/Mantid/instrument/CNCS_Parameters.xml
+++ b/Code/Mantid/instrument/CNCS_Parameters.xml
@@ -50,6 +50,73 @@
<!-- Diagnostic test defaults -->
+ <!-- Absolute lo threshold for vanadium diag (tiny) -->
+ <parameter name="diag_tiny">
+ <value val="1e-10"/>
+ </parameter>
+
+ <!-- Absolute hi threshold for vanadium diag (huge) -->
+ <parameter name="diag_huge">
+ <value val="1e10"/>
+ </parameter>
+
+ <!-- Remove zeroes in background (s_zero)-->
+ <parameter name="diag_samp_zero">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+ <parameter name="diag_samp_lo">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+ <parameter name="diag_samp_hi">
+ <value val="5.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+ <parameter name="diag_samp_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+ <parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+ </parameter>
+
+ <!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+ <parameter name="diag_van_out_hi">
+ <value val="100."/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+ <parameter name="diag_van_lo">
+ <value val="0.1"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+ <parameter name="diag_van_hi">
+ <value val="3.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+ <parameter name="diag_van_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- True if background is to be checked -->
+ <parameter name="check_background">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- True if the bleed tests should be run -->
+ <parameter name="diag_bleed_test">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- TO BE REMOVED Diagnostic test defaults -->
+
<parameter name="remove_zero">
<value val="1.0" />
</parameter>
@@ -104,12 +171,6 @@
<value val="1.2" />
</parameter>
- <!-- PSD bleed test -->
-
- <parameter name="bleed_test">
- <value val="0.0" />
- </parameter>
-
<!-- All the following parameters are taken directly from the MARI definition
and are WRONG! They are only here for now to get things working -->
diff --git a/Code/Mantid/instrument/HYSPEC_Parameters.xml b/Code/Mantid/instrument/HYSPEC_Parameters.xml
index f58e45f309f..5bf54fe1c1c 100644
--- a/Code/Mantid/instrument/HYSPEC_Parameters.xml
+++ b/Code/Mantid/instrument/HYSPEC_Parameters.xml
@@ -50,6 +50,73 @@
<!-- Diagnostic test defaults -->
+ <!-- Absolute lo threshold for vanadium diag (tiny) -->
+ <parameter name="diag_tiny">
+ <value val="1e-10"/>
+ </parameter>
+
+ <!-- Absolute hi threshold for vanadium diag (huge) -->
+ <parameter name="diag_huge">
+ <value val="1e10"/>
+ </parameter>
+
+ <!-- Remove zeroes in background (s_zero)-->
+ <parameter name="diag_samp_zero">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+ <parameter name="diag_samp_lo">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+ <parameter name="diag_samp_hi">
+ <value val="5.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+ <parameter name="diag_samp_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+ <parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+ </parameter>
+
+ <!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+ <parameter name="diag_van_out_hi">
+ <value val="100."/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+ <parameter name="diag_van_lo">
+ <value val="0.1"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+ <parameter name="diag_van_hi">
+ <value val="3.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+ <parameter name="diag_van_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- True if background is to be checked -->
+ <parameter name="check_background">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- True if the bleed tests should be run -->
+ <parameter name="diag_bleed_test">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- TO BE REMOVED Diagnostic test defaults -->
+
<parameter name="remove_zero">
<value val="1.0" />
</parameter>
@@ -104,12 +171,6 @@
<value val="1.2" />
</parameter>
- <!-- PSD bleed test -->
-
- <parameter name="bleed_test">
- <value val="0.0" />
- </parameter>
-
<!-- All the following parameters are taken directly from the MARI definition
and are WRONG! They are only here for now to get things working -->
diff --git a/Code/Mantid/instrument/LET_Parameters.xml b/Code/Mantid/instrument/LET_Parameters.xml
index af6cd303cc4..bbc34e406a0 100644
--- a/Code/Mantid/instrument/LET_Parameters.xml
+++ b/Code/Mantid/instrument/LET_Parameters.xml
@@ -72,42 +72,81 @@
<value val="50.9415"/>
</parameter>
-<!-- Diagnostic test defaults -->
-
-<parameter name="remove_zero">
- <value val="1.0"/>
-</parameter>
+<!-- Diagnostic defaults -->
-<parameter name="tiny">
+<!-- Absolute lo threshold for vanadium diag (tiny) -->
+<parameter name="diag_tiny">
<value val="1e-10"/>
</parameter>
-<parameter name="large">
+<!-- Absolute hi threshold for vanadium diag (huge) -->
+<parameter name="diag_huge">
<value val="1e10"/>
</parameter>
-<parameter name="median_lo">
- <value val="0.1"/>
+<!-- Remove zeroes in background (s_zero)-->
+<parameter name="diag_samp_zero">
+ <value val="0.0"/>
</parameter>
-<parameter name="median_hi">
- <value val="3.0"/>
+<!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+<parameter name="diag_samp_lo">
+ <value val="0.0"/>
</parameter>
-<parameter name="signif">
+<!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+<parameter name="diag_samp_hi">
+ <value val="1.5"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+<parameter name="diag_samp_sig">
<value val="3.3"/>
</parameter>
+<!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+<parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+</parameter>
+
+<!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+<parameter name="diag_van_out_hi">
+ <value val="100."/>
+</parameter>
+
+<!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+<parameter name="diag_van_lo">
+ <value val="0.1"/>
+</parameter>
+
+<!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+<parameter name="diag_van_hi">
+ <value val="2.0"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+<parameter name="diag_van_sig">
+ <value val="0.0"/>
+</parameter>
+
+<!-- True if background is to be checked -->
<parameter name="check_background">
<value val="1.0"/>
</parameter>
-<parameter name="bkgd_threshold">
- <value val="5.0"/>
+<!-- True if the bleed tests should be run -->
+<parameter name="diag_bleed_test">
+ <value val="1.0"/>
</parameter>
-<parameter name="variation">
- <value val="1.1"/>
+<!-- The maximum framerate to allow in a tube -->
+<parameter name="diag_bleed_maxrate">
+ <value val="0.01"/>
+</parameter>
+
+<!-- The number of pixels to ignore around the centre of the tube -->
+<parameter name="diag_bleed_pixels">
+ <value val="80"/>
</parameter>
<!-- -->
@@ -130,19 +169,44 @@
</parameter>
<!-- -->
-<!-- PSD bleed test -->
-<!-- PSD bleed test -->
-<parameter name="bleed_test">
+<!-- To be removed -->
+<!-- Diagnostic test defaults -->
+
+<parameter name="remove_zero">
<value val="1.0"/>
</parameter>
-<parameter name="bleed_max_framerate">
- <value val="0.01"/>
+<parameter name="tiny">
+ <value val="1e-10"/>
</parameter>
-<parameter name="bleed_ignored_pixels">
- <value val="80"/>
+<parameter name="large">
+ <value val="1e10"/>
+</parameter>
+
+<parameter name="median_lo">
+ <value val="0.1"/>
+</parameter>
+
+<parameter name="median_hi">
+ <value val="3.0"/>
+</parameter>
+
+<parameter name="signif">
+ <value val="3.3"/>
+</parameter>
+
+<parameter name="check_background">
+ <value val="1.0"/>
+</parameter>
+
+<parameter name="bkgd_threshold">
+ <value val="5.0"/>
+</parameter>
+
+<parameter name="variation">
+ <value val="1.1"/>
</parameter>
</component-link>
diff --git a/Code/Mantid/instrument/MAPS_Parameters.xml b/Code/Mantid/instrument/MAPS_Parameters.xml
index 7c032442ec3..513843b00fe 100644
--- a/Code/Mantid/instrument/MAPS_Parameters.xml
+++ b/Code/Mantid/instrument/MAPS_Parameters.xml
@@ -73,45 +73,80 @@
<value val="50.9415"/>
</parameter>
-<!-- Diagnostic test defaults -->
+<!-- Diagnostic defaults -->
-<parameter name="remove_zero">
- <value val="1.0"/>
+<!-- Perform diag by bank. These are the spectrum numbers -->
+<parameter name="diag_spectra" type="string">
+ <value val="(1,17280);(17281,18432);(18433,32256);(32257,41472)"/>
</parameter>
-<parameter name="tiny">
+<!-- Absolute lo threshold for vanadium diag (tiny) -->
+<parameter name="diag_tiny">
<value val="1e-10"/>
</parameter>
-<parameter name="large">
+<!-- Absolute hi threshold for vanadium diag (huge) -->
+<parameter name="diag_huge">
<value val="1e10"/>
</parameter>
-<parameter name="median_lo">
- <value val="0.1"/>
+<!-- Remove zeroes in background (s_zero)-->
+<parameter name="diag_samp_zero">
+ <value val="0.0"/>
</parameter>
-<parameter name="median_hi">
- <value val="3.0"/>
+<!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+<parameter name="diag_samp_lo">
+ <value val="0.0"/>
</parameter>
-<parameter name="signif">
+<!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+<parameter name="diag_samp_hi">
+ <value val="1.5"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+<parameter name="diag_samp_sig">
<value val="3.3"/>
</parameter>
-<parameter name="check_background">
- <value val="1.0"/>
+<!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+<parameter name="diag_van_out_lo">
+ <value val="0.01"/>
</parameter>
-<parameter name="bkgd_threshold">
- <value val="5.0"/>
+<!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+<parameter name="diag_van_out_hi">
+ <value val="100."/>
</parameter>
-<parameter name="variation">
- <value val="1.1"/>
+<!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+<parameter name="diag_van_lo">
+ <value val="0.1"/>
+</parameter>
+
+<!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+<parameter name="diag_van_hi">
+ <value val="2.0"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+<parameter name="diag_van_sig">
+ <value val="0.0"/>
+</parameter>
+
+<!-- True if background is to be checked -->
+<parameter name="check_background">
+ <value val="1.0"/>
+</parameter>
+
+<!-- True if the bleed tests should be run -->
+<parameter name="diag_bleed_test">
+ <value val="0.0"/>
</parameter>
<!-- -->
+
<!-- Absolute units conversion average -->
<parameter name="monovan_lo_bound">
@@ -130,12 +165,40 @@
<value val="1.2"/>
</parameter>
-<!-- -->
-<!-- PSD bleed test -->
-<!-- PSD bleed test -->
+<!-- -->
-<parameter name="bleed_test">
- <value val="0.0"/>
+<!-- To be removed -->
+
+<parameter name="remove_zero">
+ <value val="1.0"/>
+</parameter>
+
+<parameter name="tiny">
+ <value val="1e-10"/>
+</parameter>
+
+<parameter name="large">
+ <value val="1e10"/>
+</parameter>
+
+<parameter name="median_lo">
+ <value val="0.1"/>
+</parameter>
+
+<parameter name="median_hi">
+ <value val="3.0"/>
+</parameter>
+
+<parameter name="signif">
+ <value val="3.3"/>
+</parameter>
+
+<parameter name="bkgd_threshold">
+ <value val="5.0"/>
+</parameter>
+
+<parameter name="variation">
+ <value val="1.1"/>
</parameter>
</component-link>
diff --git a/Code/Mantid/instrument/MARI_Parameters.xml b/Code/Mantid/instrument/MARI_Parameters.xml
index 3b5ff47f5f4..c325342fc20 100644
--- a/Code/Mantid/instrument/MARI_Parameters.xml
+++ b/Code/Mantid/instrument/MARI_Parameters.xml
@@ -72,42 +72,71 @@
<value val="50.9415"/>
</parameter>
-<!-- Diagnostic test defaults -->
+<!-- Diagnostic defaults -->
-<parameter name="remove_zero">
- <value val="1.0"/>
-</parameter>
-
-<parameter name="tiny">
+<!-- Absolute lo threshold for vanadium diag (tiny) -->
+<parameter name="diag_tiny">
<value val="1e-10"/>
</parameter>
-<parameter name="large">
+<!-- Absolute hi threshold for vanadium diag (huge) -->
+<parameter name="diag_huge">
<value val="1e10"/>
</parameter>
-<parameter name="median_lo">
+<!-- Remove zeroes in background (s_zero)-->
+<parameter name="diag_samp_zero">
+ <value val="0.0"/>
+</parameter>
+
+<!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+<parameter name="diag_samp_lo">
+ <value val="0.0"/>
+</parameter>
+
+<!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+<parameter name="diag_samp_hi">
+ <value val="2.0"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+<parameter name="diag_samp_sig">
+ <value val="3.3"/>
+</parameter>
+
+<!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+<parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+</parameter>
+
+<!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+<parameter name="diag_van_out_hi">
+ <value val="100."/>
+</parameter>
+
+<!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+<parameter name="diag_van_lo">
<value val="0.1"/>
</parameter>
-<parameter name="median_hi">
+<!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+<parameter name="diag_van_hi">
<value val="3.0"/>
</parameter>
-<parameter name="signif">
- <value val="3.3"/>
+<!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+<parameter name="diag_van_sig">
+ <value val="0.0"/>
</parameter>
+<!-- True if background is to be checked -->
<parameter name="check_background">
<value val="1.0"/>
</parameter>
-<parameter name="bkgd_threshold">
- <value val="5.0"/>
-</parameter>
-
-<parameter name="variation">
- <value val="1.1"/>
+<!-- True if the bleed tests should be run -->
+<parameter name="diag_bleed_test">
+ <value val="0.0"/>
</parameter>
<!-- -->
@@ -130,10 +159,39 @@
</parameter>
<!-- -->
-<!-- PSD bleed test -->
-<parameter name="bleed_test">
- <value val="0.0"/>
+<!-- To be removed -->
+
+<parameter name="remove_zero">
+ <value val="1.0"/>
+</parameter>
+
+<parameter name="large">
+ <value val="1e10"/>
+</parameter>
+
+<parameter name="median_lo">
+ <value val="0.1"/>
+</parameter>
+
+<parameter name="median_hi">
+ <value val="3.0"/>
+</parameter>
+
+<parameter name="signif">
+ <value val="3.3"/>
+</parameter>
+
+<parameter name="check_background">
+ <value val="1.0"/>
+</parameter>
+
+<parameter name="bkgd_threshold">
+ <value val="5.0"/>
+</parameter>
+
+<parameter name="variation">
+ <value val="1.1"/>
</parameter>
</component-link>
diff --git a/Code/Mantid/instrument/MERLIN_Parameters.xml b/Code/Mantid/instrument/MERLIN_Parameters.xml
index 31b46cfb72f..4cbb1d8bee3 100644
--- a/Code/Mantid/instrument/MERLIN_Parameters.xml
+++ b/Code/Mantid/instrument/MERLIN_Parameters.xml
@@ -73,42 +73,81 @@
<value val="50.9415"/>
</parameter>
-<!-- Diagnostic test defaults -->
-
-<parameter name="remove_zero">
- <value val="1.0"/>
-</parameter>
+<!-- Diagnostic defaults -->
-<parameter name="tiny">
+<!-- Absolute lo threshold for vanadium diag (tiny) -->
+<parameter name="diag_tiny">
<value val="1e-10"/>
</parameter>
-<parameter name="large">
+<!-- Absolute hi threshold for vanadium diag (huge) -->
+<parameter name="diag_huge">
<value val="1e10"/>
</parameter>
-<parameter name="median_lo">
- <value val="0.1"/>
+<!-- Remove zeroes in background (s_zero)-->
+<parameter name="diag_samp_zero">
+ <value val="0.0"/>
</parameter>
-<parameter name="median_hi">
- <value val="3.0"/>
+<!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+<parameter name="diag_samp_lo">
+ <value val="0.0"/>
</parameter>
-<parameter name="signif">
+<!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+<parameter name="diag_samp_hi">
+ <value val="1.5"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+<parameter name="diag_samp_sig">
<value val="3.3"/>
</parameter>
+<!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+<parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+</parameter>
+
+<!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+<parameter name="diag_van_out_hi">
+ <value val="100."/>
+</parameter>
+
+<!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+<parameter name="diag_van_lo">
+ <value val="0.1"/>
+</parameter>
+
+<!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+<parameter name="diag_van_hi">
+ <value val="2.0"/>
+</parameter>
+
+<!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+<parameter name="diag_van_sig">
+ <value val="0.0"/>
+</parameter>
+
+<!-- True if background is to be checked -->
<parameter name="check_background">
<value val="1.0"/>
</parameter>
-<parameter name="bkgd_threshold">
- <value val="5.0"/>
+<!-- True if the bleed tests should be run -->
+<parameter name="diag_bleed_test">
+ <value val="1.0"/>
</parameter>
-<parameter name="variation">
- <value val="1.1"/>
+<!-- The maximum framerate to allow in a tube -->
+<parameter name="diag_bleed_maxrate">
+ <value val="0.01"/>
+</parameter>
+
+<!-- The number of pixels to ignore around the centre of the tube -->
+<parameter name="diag_bleed_pixels">
+ <value val="80"/>
</parameter>
<!-- -->
@@ -131,20 +170,48 @@
</parameter>
<!-- -->
-<!-- PSD bleed test -->
-<parameter name="bleed_test">
+<!-- To be removed -->
+<!-- Diagnostic test defaults -->
+
+<parameter name="remove_zero">
<value val="1.0"/>
</parameter>
-<parameter name="bleed_max_framerate">
- <value val="0.01"/>
+<parameter name="tiny">
+ <value val="1e-10"/>
</parameter>
-<parameter name="bleed_ignored_pixels">
- <value val="80"/>
+<parameter name="large">
+ <value val="1e10"/>
</parameter>
+<parameter name="median_lo">
+ <value val="0.1"/>
+</parameter>
+
+<parameter name="median_hi">
+ <value val="3.0"/>
+</parameter>
+
+<parameter name="signif">
+ <value val="3.3"/>
+</parameter>
+
+<parameter name="check_background">
+ <value val="1.0"/>
+</parameter>
+
+<parameter name="bkgd_threshold">
+ <value val="5.0"/>
+</parameter>
+
+<parameter name="variation">
+ <value val="1.1"/>
+</parameter>
+
+
+
</component-link>
</parameter-file>
diff --git a/Code/Mantid/instrument/SEQUOIA_Parameters.xml b/Code/Mantid/instrument/SEQUOIA_Parameters.xml
index def201e0981..1dc31bdde0d 100644
--- a/Code/Mantid/instrument/SEQUOIA_Parameters.xml
+++ b/Code/Mantid/instrument/SEQUOIA_Parameters.xml
@@ -39,6 +39,73 @@
<!-- Diagnostic test defaults -->
+ <!-- Absolute lo threshold for vanadium diag (tiny) -->
+ <parameter name="diag_tiny">
+ <value val="1e-10"/>
+ </parameter>
+
+ <!-- Absolute hi threshold for vanadium diag (huge) -->
+ <parameter name="diag_huge">
+ <value val="1e10"/>
+ </parameter>
+
+ <!-- Remove zeroes in background (s_zero)-->
+ <parameter name="diag_samp_zero">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (sv_lo)-->
+ <parameter name="diag_samp_lo">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (sv_hi)-->
+ <parameter name="diag_samp_hi">
+ <value val="5.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (sv_sig) -->
+ <parameter name="diag_samp_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- Lower bound defining outliers as fraction of median value (v_out_lo)-->
+ <parameter name="diag_van_out_lo">
+ <value val="0.01"/>
+ </parameter>
+
+ <!-- Upper bound defining outliers as fraction of median value (v_out_hi)-->
+ <parameter name="diag_van_out_hi">
+ <value val="100."/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting low for the white beam diag (vv_lo)-->
+ <parameter name="diag_van_lo">
+ <value val="0.1"/>
+ </parameter>
+
+ <!-- Fraction of median to consider counting high for the white beam diag (vv_hi)-->
+ <parameter name="diag_van_hi">
+ <value val="3.0"/>
+ </parameter>
+
+ <!-- Error criterion as a multiple of error bar for background (vv_sig) -->
+ <parameter name="diag_van_sig">
+ <value val="3.3"/>
+ </parameter>
+
+ <!-- True if background is to be checked -->
+ <parameter name="check_background">
+ <value val="1.0"/>
+ </parameter>
+
+ <!-- True if the bleed tests should be run -->
+ <parameter name="diag_bleed_test">
+ <value val="0.0"/>
+ </parameter>
+
+ <!-- TO BE REMOVED Diagnostic test defaults -->
+
<parameter name="remove_zero">
<value val="1.0" />
</parameter>
@@ -95,12 +162,6 @@
</parameter>
<!-- -->
- <!-- PSD bleed test -->
-
- <parameter name="bleed_test">
- <value val="0.0" />
- </parameter>
-
<!-- All the following parameters are taken directly from the MARI definition
and are WRONG! They are only here for now to get things working -->
diff --git a/Code/Mantid/scripts/Inelastic/DirectEnergyConversion.py b/Code/Mantid/scripts/Inelastic/DirectEnergyConversion.py
index 815f0ffd1ec..f8ccd459ff8 100755
--- a/Code/Mantid/scripts/Inelastic/DirectEnergyConversion.py
+++ b/Code/Mantid/scripts/Inelastic/DirectEnergyConversion.py
@@ -44,7 +44,7 @@ def setup_reducer(inst_name):
"""
try:
return DirectEnergyConversion(inst_name)
- except RuntimeError:
+ except RuntimeError, exc:
raise RuntimeError('Unknown instrument "%s", cannot continue' % inst_name)
@@ -53,65 +53,123 @@ class DirectEnergyConversion(object):
Performs a convert to energy assuming the provided instrument is an elastic instrument
"""
- def diagnose(self, white_run, sample_run=None, other_white=None, remove_zero=None,
- tiny=None, large=None, median_lo=None, median_hi=None, signif=None,
- bkgd_threshold=None, bkgd_range=None, variation=None,
- bleed_test=False, bleed_maxrate=None, bleed_pixels=None,
- hard_mask=None, print_results=False):
+ def diagnose(self, white, **kwargs):
"""
- A pass through method to the 'real' one in diagnostics.py
-
- Run diagnostics on the provided run and white beam files.
-
- There are 4 possible tests, depending on the input given:
- White beam diagnosis
- Background tests
- Second white beam
- PSD bleed test
+ Run diagnostics on the provided workspaces.
- Required inputs:
-
- white_run - The run number or filepath of the white beam run
-
- Optional inputs:
- sample_run - The run number or filepath of the sample run for the background test (default = None)
- other_white - If provided an addional set of tests is performed on this file. (default = None)
- remove_zero - If true then zeroes in the data will count as failed (default = False)
- tiny - Minimum threshold for acceptance (default = 1e-10)
- large - Maximum threshold for acceptance (default = 1e10)
- median_lo - Fraction of median to consider counting low (default = 0.1)
- median_hi - Fraction of median to consider counting high (default = 3.0)
- signif - Counts within this number of multiples of the
- standard dev will be kept (default = 3.3)
- bkgd_threshold - High threshold for background removal in multiples of median (default = 5.0)
- bkgd_range - The background range as a list of 2 numbers: [min,max].
- If not present then they are taken from the parameter file. (default = None)
- variation - The number of medians the ratio of the first/second white beam can deviate from
- the average by (default=1.1)
- bleed_test - If true then the CreatePSDBleedMask algorithm is run
- bleed_maxrate - If the bleed test is on then this is the maximum framerate allowed in a tube
- bleed_pixels - If the bleed test is on then this is the number of pixels ignored within the
- bleed test diagnostic
- hard_mask - A file specifying those spectra that should be masked without testing
- print_results - If True then the results are printed to std out
- inst_name - The name of the instrument to perform the diagnosis.
- If it is not provided then the default instrument is used (default = None)
- """
+ This method does some additional processing before moving on to the diagnostics:
+ 1) Computes the white beam integrals, converting to energy
+ 2) Computes the background integral using the instrument defined range
+ 3) Computes a total count from the sample
+
+ These inputs are passed to the diagnostics functions
+
+ Required inputs:
+
+ white - A workspace, run number or filepath of a white beam run. A workspace is assumed to
+ have simple been loaded and nothing else.
+
+ Optional inputs:
+ sample - A workspace, run number or filepath of a sample run. A workspace is assumed to
+ have simple been loaded and nothing else. (default = None)
+ second_white - If provided an additional set of tests is performed on this. (default = None)
+ hard_mask - A file specifying those spectra that should be masked without testing (default=None)
+ tiny - Minimum threshold for acceptance (default = 1e-10)
+ huge - Maximum threshold for acceptance (default = 1e10)
+ bkgd_range - A list of two numbers indicating the background range (default=instrument defaults)
+ van_out_lo - Lower bound defining outliers as fraction of median value (default = 0.01)
+ van_out_hi - Upper bound defining outliers as fraction of median value (default = 100.)
+ van_lo - Fraction of median to consider counting low for the white beam diag (default = 0.1)
+ van_hi - Fraction of median to consider counting high for the white beam diag (default = 1.5)
+ van_sig - Error criterion as a multiple of error bar i.e. to fail the test, the magnitude of the\n"
+ "difference with respect to the median value must also exceed this number of error bars (default=0.0)
+ samp_zero - If true then zeroes in the vanadium data will count as failed (default = True)
+ samp_lo - Fraction of median to consider counting low for the white beam diag (default = 0)
+ samp_hi - Fraction of median to consider counting high for the white beam diag (default = 2.0)
+ samp_sig - Error criterion as a multiple of error bar i.e. to fail the test, the magnitude of the\n"
+ "difference with respect to the median value must also exceed this number of error bars (default=3.3)
+ variation - The number of medians the ratio of the first/second white beam can deviate from
+ the average by (default=1.1)
+ bleed_test - If true then the CreatePSDBleedMask algorithm is run
+ bleed_maxrate - If the bleed test is on then this is the maximum framerate allowed in a tube
+ bleed_pixels - If the bleed test is on then this is the number of pixels ignored within the
+ bleed test diagnostic
+ print_results - If True then the results are printed to the screen
+ """
+ if kwargs.get('second_white', None) is not None:
+ raise RuntimeError("Diagnostic does not support second white beam run yet")
+
lhs_names = lhs_info('names')
if len(lhs_names) > 0:
var_name = lhs_names[0]
else:
var_name = None
-
- __diagnostic_mask = diagnostics.diagnose(white_run, sample_run, other_white, remove_zero,
- tiny, large, median_lo, median_hi, signif,
- bkgd_threshold, bkgd_range, variation,
- bleed_test, bleed_maxrate, bleed_pixels,
- hard_mask, print_results, self.instr_name)
- if var_name is not None:
- result = RenameWorkspace(str(__diagnostic_mask), var_name).workspace()
+
+ # Check for any keywords that have not been supplied and put in the defaults
+ for par in self.diag_params:
+ arg = par.lstrip('diag_')
+ if arg not in kwargs:
+ kwargs[arg] = getattr(self, par)
+
+ # Get the white beam vanadium integrals
+ whiteintegrals = self.do_white(white, None, None) # No grouping yet
+ # Get the background/total counts from the sample if present
+ if 'sample' in kwargs:
+ sample = kwargs['sample']
+ del kwargs['sample']
+ # If the bleed test is requested then we need to pass in the sample_run as well
+ if kwargs.get('bleed_test', False):
+ kwargs['sample_run'] = sample
+
+ # Set up the background integrals
+ result_ws = common.load_runs(sample)
+ self.normalise(result_ws, result_ws, self.normalise_method)
+ if 'bkgd_range' in kwargs:
+ bkgd_range = kwargs['bkgd_range']
+ del kwargs['bkgd_range']
+ else:
+ bkgd_range = self.background_range
+ background_int = Integration(result_ws, OutputWorkspace='background_int',\
+ RangeLower=bkgd_range[0],RangeUpper=bkgd_range[1], \
+ IncludePartialBins=True).workspace()
+ total_counts = Integration(result_ws, OutputWorkspace='total_counts', IncludePartialBins=True).workspace()
+ background_int = ConvertUnits(background_int, background_int, "Energy", AlignBins=0).workspace()
+ background_int *= 1.7016e8
+ background_int /= whiteintegrals
+ kwargs['background_int'] = background_int
+ kwargs['sample_counts'] = total_counts
+
+ # Check how we should run diag
+ if self.diag_spectra is None:
+ # Do the whole lot at once
+ diagnostics.diagnose(whiteintegrals, **kwargs)
+ else:
+ banks = self.diag_spectra.split(";")
+ bank_spectra = []
+ for b in banks:
+ token = b.split(",") # b = "(,)"
+ if len(token) != 2:
+ raise ValueError("Invalid bank spectra specification in diag %s" % self.diag_spectra)
+ start = int(token[0].lstrip('('))
+ end = int(token[1].rstrip(')'))
+ bank_spectra.append((start,end))
+
+ for index, bank in enumerate(bank_spectra):
+ kwargs['start_index'] = bank[0] - 1
+ kwargs['end_index'] = bank[1] - 1
+ diagnostics.diagnose(whiteintegrals, **kwargs)
+
+ if 'sample' in kwargs:
+ DeleteWorkspace('background_int')
+ DeleteWorkspace('total_counts')
+ # Return a mask workspace
+ diag_mask = ExtractMasking(whiteintegrals, OutputWorkspace='diag_mask').workspace()
+ DeleteWorkspace(whiteintegrals)
+
+ if var_name is not None and var_name != str(diag_mask):
+ result = RenameWorkspace(str(diag_mask), var_name).workspace()
else:
- result = __diagnostic_mask
+ result = diag_mask
self.spectra_masks = result
return result
@@ -495,13 +553,13 @@ class DirectEnergyConversion(object):
ConvertToMatrixWorkspace(data_ws, data_ws)
- min_value = self.tiny
- max_value = self.large
+ min_value = self.diag_tiny
+ max_value = self.diag_huge
median_lbound = self.monovan_lo_bound
median_ubound = self.monovan_hi_bound
median_frac_low = self.monovan_lo_frac
median_frac_hi = self.monovan_hi_frac
- median_sig = self.signif
+ median_sig = self.diag_samp_sig
self.mask_detectors_outside_range(data_ws, min_value, max_value, median_lbound,
median_ubound, median_frac_low, median_frac_hi, median_sig)
@@ -728,13 +786,34 @@ class DirectEnergyConversion(object):
self.van_mass = self.get_default_parameter("vanadium-mass")
self.van_rmm = self.get_default_parameter("vanadium-rmm")
- self.tiny = self.get_default_parameter('tiny')
- self.large = self.get_default_parameter('large')
+ # Diag
+ self.diag_params = ['diag_tiny', 'diag_huge', 'diag_samp_zero', 'diag_samp_lo', 'diag_samp_hi','diag_samp_sig',\
+ 'diag_van_out_lo', 'diag_van_out_hi', 'diag_van_lo', 'diag_van_hi', 'diag_van_sig']
+ # Add an attribute for each of them
+ for par in self.diag_params:
+ setattr(self, par, self.get_default_parameter(par))
+
+ # Bleed options
+ try:
+ self.diag_bleed_test = self.get_default_parameter('diag_bleed_test')
+ self.diag_bleed_maxrate = self.get_default_parameter('diag_bleed_maxrate')
+ self.diag_bleed_pixels = self.get_default_parameter('diag_bleed_pixels')
+ self.diag_params.extend(['diag_bleed_maxrate','diag_bleed_pixels'])
+ except ValueError:
+ self.diag_bleed_test = False
+ self.diag_params.append('diag_bleed_test')
+
+ # Do we have specified spectra to diag over
+ try:
+ self.diag_spectra = self.instrument.getStringParameter("diag_spectra")[0]
+ except Exception:
+ self.diag_spectra = None
+
+ # Absolute units
self.monovan_lo_bound = self.get_default_parameter('monovan_lo_bound')
self.monovan_hi_bound = self.get_default_parameter('monovan_hi_bound')
self.monovan_lo_frac = self.get_default_parameter('monovan_lo_frac')
self.monovan_hi_frac = self.get_default_parameter('monovan_hi_frac')
- self.signif = self.get_default_parameter('signif')
# Mark IDF files as read
self._idf_values_read = True
@@ -755,4 +834,4 @@ class DirectEnergyConversion(object):
if self._log_to_mantid:
mtd.sendLogMessage(msg)
-#-----------------------------------------------------------------
\ No newline at end of file
+#-----------------------------------------------------------------
diff --git a/Code/Mantid/scripts/Inelastic/diagnostics.py b/Code/Mantid/scripts/Inelastic/diagnostics.py
index 13e82bade91..b1c1bb03176 100644
--- a/Code/Mantid/scripts/Inelastic/diagnostics.py
+++ b/Code/Mantid/scripts/Inelastic/diagnostics.py
@@ -11,200 +11,173 @@ masking and also passed to MaskDetectors to match masking there.
from mantidsimple import *
import CommonFunctions as common
-def diagnose(white_run, sample_run=None, other_white=None, remove_zero=None,
- tiny=None, large=None, median_lo=None, median_hi=None, signif=None,
- bkgd_threshold=None, bkgd_range=None, variation=None,
- bleed_test=False, bleed_maxrate=None, bleed_pixels=None,
- hard_mask=None, print_results=False, inst_name=None):
- """
- Run diagnostics on the provided run and white beam files.
-
- There are 4 possible tests, depending on the input given:
- White beam diagnosis
- Background tests
- Second white beam
- Bleed test
-
- Required inputs:
+class ArgumentParser(object):
- white_run - The run number or filepath of the white beam run
-
- Optional inputs:
- sample_run - The run number or filepath of the sample run for the background test (default = None)
- other_white - If provided an addional set of tests is performed on this file. (default = None)
- remove_zero - If true then zeroes in the data will count as failed (default = False)
- tiny - Minimum threshold for acceptance (default = 1e-10)
- large - Maximum threshold for acceptance (default = 1e10)
- median_lo - Fraction of median to consider counting low (default = 0.1)
- median_hi - Fraction of median to consider counting high (default = 3.0)
- signif - Counts within this number of multiples of the
- standard dev will be kept (default = 3.3)
- bkgd_threshold - High threshold for background removal in multiples of median (default = 5.0)
- bkgd_range - The background range as a list of 2 numbers: [min,max].
- If not present then they are taken from the parameter file. (default = None)
- variation - The number of medians the ratio of the first/second white beam can deviate from
- the average by (default=1.1)
- bleed_test - If true then the CreatePSDBleedMask algorithm is run
- bleed_maxrate - If the bleed test is on then this is the maximum framerate allowed in a tube
- bleed_pixels - If the bleed test is on then this is the number of pixels ignored within the
- bleed test diagnostic
- hard_mask - A file specifying those spectra that should be masked without testing
- print_results - If True then the results are printed to std out
- inst_name - The name of the instrument to perform the diagnosis.
- If it is not provided then the default instrument is used (default = None)
+ def __init__(self, keywords):
+ self.start_index = None # Make this more general for anything that is missing!
+ self.end_index = None
+ for key, value in keywords.iteritems():
+ setattr(self, key, value)
+
+
+
+def diagnose(white_int, **kwargs):
"""
- # Set the default instrument so that Mantid can search for the runs correctly,
- # but switch it back at the end
- def_inst = mtd.settings["default.instrument"]
- if inst_name == None:
- inst_name = def_inst
- elif inst_name != def_inst:
- mtd.settings["default.instrument"] = inst_name
- else: pass
+ Run diagnostics on the provided workspaces.
+ Required inputs:
+
+ white_int - A workspace, run number or filepath of a white beam run. If a run/file is given it
+ simply loaded and integrated. A workspace is assumed to be prepared in it's integrated form
+
+ Optional inputs:
+ start_index - The index to start the diag
+ end_index - The index to finish the diag
+ background_int - A workspace, run number or filepath of a sample run that has been integrated over the background region.
+ If a run/file is given it simply loaded and integrated across the whole range
+ sample_counts - A workspace containing the total integrated counts from a sample run
+ second_white - If provided an additional set of tests is performed on this.
+ hard_mask - A file specifying those spectra that should be masked without testing
+ tiny - Minimum threshold for acceptance
+ huge - Maximum threshold for acceptance
+ van_out_lo - Lower bound defining outliers as fraction of median value
+ van_out_hi - Upper bound defining outliers as fraction of median value
+ van_lo - Fraction of median to consider counting low for the white beam diag
+ van_hi - Fraction of median to consider counting high for the white beam diag
+ van_sig - Error criterion as a multiple of error bar i.e. to fail the test, the magnitude of the
+ difference with respect to the median value must also exceed this number of error bars
+ samp_zero - If true then zeroes in background are masked also
+ samp_lo - Fraction of median to consider counting low for the background diag
+ samp_hi - Fraction of median to consider counting high for the background diag
+ samp_sig - Error criterion as a multiple of error bar i.e. to fail the test, the magnitude of the\n"
+ "difference with respect to the median value must also exceed this number of error bars
+ variation - The number of medians the ratio of the first/second white beam can deviate from
+ the average by
+ bleed_test - If true then the CreatePSDBleedMask algorithm is run
+ bleed_maxrate - If the bleed test is on then this is the maximum framerate allowed in a tube
+ bleed_pixels - If the bleed test is on then this is the number of pixels ignored within the
+ bleed test diagnostic
+ print_results - If True then the results are printed to the screen
+ """
+ # Grab the arguments
+ parser = ArgumentParser(kwargs)
+ start_index = parser.start_index
+ end_index = parser.end_index
+
# Load the hard mask file if necessary
hard_mask_spectra = ''
- if hard_mask is not None:
+ if kwargs.get('hard_mask', None) is not None:
hard_mask_spectra = common.load_mask(hard_mask)
# Map the test number to the results
# Each element is the mask workspace name then the number of failures
test_results = [ [None, None], [None, None], [None, None], [None, None]]
-
- ##
- ## Accumulate the masking on this workspace
- ##
- # What shall we call the output
- lhs_names = lhs_info('names')
- if len(lhs_names) > 0:
- diag_total_mask = lhs_names[0]
- else:
- diag_total_mask = 'diag_total_mask'
+
##
## White beam Test
##
white_counts = None
- if white_run is not None and str(white_run) != '':
- # Load and integrate
- data_ws = common.load_run(white_run)
- # Make sure we have a matrix workspace otherwise Integration() returns all zeros.
- ConvertToMatrixWorkspace(data_ws, data_ws)
- white_counts = Integration(data_ws, "__counts_white-beam").workspace()
- MaskDetectors(white_counts, SpectraList=hard_mask_spectra)
+ if white_int is not None and str(white_int) != '':
+ # Hard mask
+ MaskDetectors(white_int, SpectraList=hard_mask_spectra)
# Run first white beam tests
- __white_masks, num_failed = \
- _do_white_test(white_counts, tiny, large, median_lo, median_hi, signif)
+ __white_masks, num_failed = _do_white_test(white_int, parser.tiny, parser.huge,
+ parser.van_out_lo, parser.van_out_hi,
+ parser.van_lo, parser.van_hi,
+ parser.van_sig, start_index, end_index)
test_results[0] = [str(__white_masks), num_failed]
- diag_total_mask = CloneWorkspace(__white_masks, diag_total_mask).workspace()
+ _add_masking(white_int, __white_masks, start_index, end_index)
+ DeleteWorkspace(__white_masks)
else:
raise RuntimeError('Invalid input for white run "%s"' % str(white_run))
- ##
- ## Second white beam Test
- ##
- second_white_counts = None
- if other_white is not None and str(other_white) != '':
- # Load and integrate
- data_ws = common.load_run(other_white)
- second_white_counts = Integration(data_ws, "__counts_white-beam2").workspace()
- MaskDetectors(white_counts, SpectraList=hard_mask_spectra)
- # Run tests
- __second_white_masks, num_failed = \
- _do_second_white_test(white_counts, second_white_counts,
- tiny, large, median_lo, median_hi,
- signif,variation)
- test_results[1] = [str(__second_white_masks), num_failed]
- # Accumulate
- diag_total_mask += __second_white_masks
-
- ##
- ## Tests on the sample(s)
- ##
- if sample_run is not None and sample_run != '':
- if type(sample_run) != list:
- sample_run = [sample_run]
- __bkgd_masks = None
- __bleed_masks = None
- bkgd_failures = 0
- bleed_failures = 0
- for sample in sample_run:
- ## Background test
- __bkgd_masks_i, failures = _do_background_test(sample, white_counts, second_white_counts,
- bkgd_range, bkgd_threshold, remove_zero, signif,
- hard_mask_spectra)
- bkgd_failures += failures
- __bkgd_masks = _accumulate(__bkgd_masks,__bkgd_masks_i)
-
- ## PSD Bleed Test
- if type(bleed_test) == bool and bleed_test == True:
- __bleed_masks_i, failures = _do_bleed_test(sample, bleed_maxrate, bleed_pixels)
- bleed_failures += failures
- __bleed_masks = _accumulate(__bleed_masks, __bleed_masks_i)
-
- ## End of sample loop
- test_results[2] = [str(__bkgd_masks), bkgd_failures]
- diag_total_mask += __bkgd_masks
- if __bleed_masks is not None:
- test_results[3] = [str(__bleed_masks), bleed_failures]
- diag_total_mask += __bleed_masks
-
- ## End of background test
-
- # Remove temporary workspaces
- mtd.deleteWorkspace(str(white_counts))
- if second_white_counts is not None:
- mtd.deleteWorkspace(str(second_white_counts))
+ #
+ # Zero total count check for sample counts
+ #
+ if hasattr(parser, 'sample_counts'):
+ _add_masking(parser.sample_counts, white_int)
+ maskZero = FindDetectorsOutsideLimits(InputWorkspace=parser.sample_counts, OutputWorkspace='maskZero',
+ StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index,
+ LowThreshold=1e-10, HighThreshold=1e100).workspace()
+ _add_masking(white_int, maskZero, start_index, end_index)
+ DeleteWorkspace(maskZero)
+
+ #
+ # Background check
+ #
+ if hasattr(parser, 'background_int'):
+ _add_masking(parser.background_int, white_int)
+ __bkgd_mask, failures = _do_background_test(parser.background_int, parser.samp_lo,
+ parser.samp_hi, parser.samp_sig, parser.samp_zero, start_index, end_index)
+ _add_masking(white_int, __bkgd_mask, start_index, end_index)
+ DeleteWorkspace(__bkgd_mask)
- # Revert our default instrument changes if necessary
- if inst_name != def_inst:
- mtd.settings["default.instrument"] = def_inst
-
- if print_results:
- print_test_summary(test_results)
+ #
+ # Bleed test
+ #
+ if hasattr(parser, 'bleed_test') and parser.bleed_test:
+ if not hasattr(parser, 'sample_run'):
+ raise RuntimeError("Bleed test requested but the sample_run keyword has not been provided")
+ _bleed_masks, failures = _do_bleed_test(parser.sample_run, parser.bleed_maxrate, parser.bleed_pixels)
+ _add_masking(white_int, __bleed_masks)
+ DeleteWorkspace(_bleed_masks)
- # This will be a MaskWorkspace which contains the accumulation of all of the masks
- return diag_total_mask
+ if hasattr(parser, 'print_results') and parser.print_results:
+ print_test_summary(test_results)
#-------------------------------------------------------------------------------
-def _do_white_test(white_counts, tiny, large, median_lo, median_hi, signif):
+def _add_masking(input_ws, mask_ws, start_index=None, end_index=None):
+ """
+ Mask the Detectors on the input workspace that are masked
+ on the mask_ws. Avoids a current bug in using MaskDetectors with a MaskedWorkspace in a loop
+ """
+ #MaskDetectors(input_ws, MaskedWorkspace=mask_ws, StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index)
+ masked = ExtractMasking(mask_ws, '__tmp')
+ MaskDetectors(input_ws, DetectorList=masked.getPropertyValue("DetectorList"))
+ DeleteWorkspace(masked.workspace())
+
+#-------------------------------------------------------------------------------
+
+def _do_white_test(white_int, tiny, large, out_lo, out_hi, median_lo, median_hi, sigma,
+ start_index=None, end_index=None):
"""
Run the diagnostic tests on the integrated white beam run
Required inputs:
- white_counts - A workspace containing the integrated counts from a
- white beam vanadium run
- tiny - Minimum threshold for acceptance
- large - Maximum threshold for acceptance
- median_lo - Fraction of median to consider counting low
- median_hi - Fraction of median to consider counting high
- signif - Counts within this number of multiples of the
- standard dev will be kept (default = 3.3)
+ white_int - An integrated workspace
+ tiny - Minimum threshold for acceptance
+ large - Maximum threshold for acceptance
+ out_lo - Lower bound defining outliers as fraction of median value (default = 0.01)
+ out_hi - Upper bound defining outliers as fraction of median value (default = 100.)
+ median_lo - Fraction of median to consider counting low
+ median_hi - Fraction of median to consider counting high
+ sigma - Error criterion as a multiple of error bar
+
"""
mtd.sendLogMessage('Running first white beam test')
- # What shall we call the output
- lhs_names = lhs_info('names')
- if len(lhs_names) > 0:
- ws_name = lhs_names[0]
- else:
- ws_name = '__do_white_test'
-
# Make sure we are a MatrixWorkspace
- ConvertToMatrixWorkspace(white_counts, white_counts)
+ ConvertToMatrixWorkspace(white_int, white_int)
# The output workspace will have the failed detectors masked
- range_check = FindDetectorsOutsideLimits(white_counts, ws_name, HighThreshold=large, LowThreshold=tiny)
- median_test = MedianDetectorTest(white_counts, ws_name, SignificanceTest=signif,
- LowThreshold=median_lo, HighThreshold=median_hi)
-
- num_failed = range_check['NumberOfFailures'].value + median_test['NumberOfFailures'].value
-
- maskWS = median_test.workspace()
- MaskDetectors(white_counts, MaskedWorkspace=maskWS)
- return maskWS, num_failed
+ white_masks = FindDetectorsOutsideLimits(white_int, OutputWorkspace='white_masks', StartWorkspaceIndex=start_index,
+ EndWorkspaceIndex=end_index,
+ HighThreshold=large, LowThreshold=tiny)
+ MaskDetectors(white_int, MaskedWorkspace=white_masks.workspace(),StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index)
+ num_failed = white_masks['NumberOfFailures'].value
+ DeleteWorkspace(white_masks.workspace())
+
+ white_masks = MedianDetectorTest(white_int, OutputWorkspace='white_masks', StartWorkspaceIndex=start_index,
+ EndWorkspaceIndex=end_index, SignificanceTest=sigma,
+ LowThreshold=median_lo, HighThreshold=median_hi,
+ LowOutlier=out_lo, HighOutlier=out_hi, ExcludeZeroesFromMedian=False)
+ MaskDetectors(white_int, MaskedWorkspace=white_masks.workspace(), StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index)
+ num_failed += white_masks['NumberOfFailures'].value
+
+ return white_masks.workspace(), num_failed
#-------------------------------------------------------------------------------
@@ -259,75 +232,24 @@ def _do_second_white_test(white_counts, comp_white_counts, tiny, large, median_l
#------------------------------------------------------------------------------
-def _do_background_test(sample_run, white_counts, comp_white_counts, bkgd_range,
- bkgd_threshold, remove_zero, signif, hard_mask_spectra):
+def _do_background_test(background_int, median_lo, median_hi, sigma, mask_zero,
+ start_index=None, end_index=None):
"""
- Run the background tests on the integrated sample run normalised by an
- integrated white beam run
+ Run the background tests
Required inputs:
-
- sample_run - The run number or filepath of the sample run
- white_counts - A workspace containing the integrated counts from a
- white beam vanadium run
- comp_white_counts - A second workspace containing the integrated counts from a
- different white beam vanadium run
- bkgd_range - The background range as a list of 2 numbers: [min,max].
- If not present then they are taken from the parameter file.
- bkgd_threshold - High threshold for background removal in multiples of median
- remove_zero - If true then zeroes in the data will count as failed (default = False)
- signif - Counts within this number of multiples of the
- standard dev will be kept (default = 3.3)
- prev_ma sks - If present then this masking is applied to the sample run before the
- test is applied. It is expected as a MaskWorkspace
+ background_int - An integrated workspace
+ median_lo - Fraction of median to consider counting low
+ median_hi - Fraction of median to consider counting high
+ sigma - Error criterion as a multiple of error bar
+ mask_zero - If True, zero background counts will be considered a fail
+
"""
mtd.sendLogMessage('Running background count test')
- # Load and integrate the sample using the defined background range. If none is given use the
- # instrument defaults
- data_ws = common.load_runs(sample_run)
- instrument = data_ws.getInstrument()
- if bkgd_range is None:
- min_value = float(instrument.getNumberParameter('bkgd-range-min')[0])
- max_value = float(instrument.getNumberParameter('bkgd-range-max')[0])
- elif len(bkgd_range) != 2:
- raise ValueError("The provided background range is incorrect. A list of 2 numbers is required.")
- else:
- min_value = bkgd_range[0]
- if min_value is None:
- float(instrument.getNumberParameter('bkgd-range-min')[0])
- max_value = bkgd_range[1]
- if max_value is None:
- float(instrument.getNumberParameter('bkgd-range-max')[0])
-
- # Get the total counts
- sample_counts = Integration(data_ws, '__counts_mono-sample', RangeLower=min_value, \
- RangeUpper=max_value).workspace()
-
- # Apply hard mask spectra and previous masking first
- MaskDetectors(sample_counts, SpectraList=hard_mask_spectra, MaskedWorkspace=white_counts)
-
- # If we have another white beam then compute the harmonic mean of the counts
- # The harmonic mean: 1/av = (1/Iwbv1 + 1/Iwbv2)/2
- # We'll resuse the comp_white_counts workspace as we don't need it anymore
- white_count_mean = white_counts
- if comp_white_counts is not None:
- MaskDetectors(sample_counts, MaskedWorkspace=comp_white_counts)
- white_count_mean = (comp_white_counts * white_counts)/(comp_white_counts + white_counts)
-
- # Make sure we have matrix workspaces before this division
- ConvertToMatrixWorkspace(white_count_mean, white_count_mean)
- ConvertToMatrixWorkspace(sample_counts, sample_counts)
-
- # Normalise the sample run
- sample_counts = Divide(sample_counts, white_count_mean, sample_counts).workspace()
- if comp_white_counts is not None:
- mtd.deleteWorkspace(str(white_count_mean))
# If we need to remove zeroes as well then set the the low threshold to a tiny positive number
- if remove_zero:
- low_threshold = 1e-40
- else:
- low_threshold = -1.0
+ if mask_zero:
+ median_lo = 1e-40
# What shall we call the output
lhs_names = lhs_info('names')
@@ -336,13 +258,13 @@ def _do_background_test(sample_run, white_counts, comp_white_counts, bkgd_range,
else:
ws_name = '__do_background_test'
- median_test = MedianDetectorTest(sample_counts, ws_name, SignificanceTest=signif,\
- LowThreshold=low_threshold, HighThreshold=bkgd_threshold)
- # Remove temporary
- mtd.deleteWorkspace(str(sample_counts))
+ mask_bkgd = MedianDetectorTest(InputWorkspace=background_int, OutputWorkspace='mask_bkgd',
+ StartWorkspaceIndex=start_index, EndWorkspaceIndex=end_index,
+ SignificanceTest=sigma,
+ LowThreshold=median_lo, HighThreshold=median_hi,
+ LowOutlier=0.0, HighOutlier=1e100, ExcludeZeroesFromMedian=True)
- num_failed = median_test['NumberOfFailures'].value
- return median_test.workspace(), num_failed
+ return mask_bkgd.workspace(), mask_bkgd['NumberOfFailures'].value
#-------------------------------------------------------------------------------
@@ -378,23 +300,6 @@ def _do_bleed_test(sample_run, max_framerate, ignored_pixels):
#-------------------------------------------------------------------------------
-def _accumulate(lhs, rhs):
- """Essentially performs lhs += rhs for workspaces
- but checks if the lhs is None first and just assigns the workspace over
- """
- if lhs is None:
- lhs_names = lhs_info('names')
- if len(lhs_names) == 0:
- raise RuntimeError('diagnostics._accumulate called without assignment of return value')
- lhs = RenameWorkspace(rhs, lhs_names[0]).workspace()
- else:
- lhs += rhs
- mtd.deleteWorkspace(str(rhs))
-
- return lhs
-
-#-------------------------------------------------------------------------------
-
def print_test_summary(test_results):
"""Print a summary of the failures per test run.
@@ -460,11 +365,6 @@ def get_failed_spectra_list(diag_workspace):
if type(diag_workspace) == str:
diag_workspace = mtd[diag_workspace]
- if hasattr(diag_workspace, "getAxis") == False:
- raise ValueError("Invalid input to get_failed_spectra_list. "
- "A workspace handle or name is expected")
-
- spectra_axis = diag_workspace.getAxis(1)
failed_spectra = []
for i in range(diag_workspace.getNumberHistograms()):
try:
@@ -472,6 +372,6 @@ def get_failed_spectra_list(diag_workspace):
except RuntimeError:
continue
if det.isMasked():
- failed_spectra.append(spectra_axis.spectraNumber(i))
+ failed_spectra.append(diag_workspace.getSpectrum(i).getSpectrumNo())
return failed_spectra
--
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