Diagnose - Revision history

Dickon Champion at 16:07, 30 January 2008

2008-01-30T16:07:38Z

Dickon Champion at 16:01, 30 January 2008

2008-01-30T16:01:33Z

Dickon Champion at 15:56, 30 January 2008

2008-01-30T15:56:14Z

Dickon Champion at 15:43, 30 January 2008

2008-01-30T15:43:59Z

Dickon Champion at 15:43, 30 January 2008

2008-01-30T15:43:24Z

Dickon Champion at 15:41, 30 January 2008

2008-01-30T15:41:14Z

Dickon Champion at 15:40, 30 January 2008

2008-01-30T15:40:21Z

Dickon Champion at 15:39, 30 January 2008

2008-01-30T15:39:43Z

Dickon Champion at 15:38, 30 January 2008

2008-01-30T15:38:14Z

Dickon Champion at 15:37, 30 January 2008

2008-01-30T15:37:30Z

@@ Line 1: / Line 1: @@
-The main diagnostic tool for homer is the diagnose function (analogous to the VMS DIAG function). It creates an [IXTmask] object with optional file output (nexus or ascii) for a given monochromatic run, using the data from a white beam vanadium integral [IXTrunfile]. It also outputs a matlab structure 'cause' detailing information on which files contributed to the exclusion of which spectra and the reason for their exclusion, and if appropriate the value which failed the test applied.
+The main diagnostic tool for homer is the diagnose function (analogous to the VMS DIAG function). It creates an [IXTmask] object with optional file output (nexus or ascii) for a given monochromatic run, using the data from a white beam vanadium integral [IXTrunfile].
-diagnose will optionally load a hard mask file, an [IXTmask] object or file (nexus or ascii), that is a list of spectra that are to be masked regardless of any diagnostic operations. Sometimes it is desirable to consider banks of spectra separately such as those connected to psd and non-psd detectors. If this is the case then an [IXTmap] object or file (nexus or ascii) may be supplied as an argument to the diagnose routine, defining these groups of spectra.
+*It also outputs a matlab structure 'cause' detailing information on which files contributed to the exclusion of which spectra and the reason for their exclusion, and if appropriate the value which failed the test applied.
 An simple example function call to <b>DIAG</b> might be as follows:
@@ Line 11: / Line 12: @@
 >> maps_bank=IXTmap({[1:17280],[17281:18432],[18433:32256],[32257:41472]});
 >> monosam=read_nxs('monosam.nxs',IXTrunfile,'mono_sam');
->> ~[mask,cause]=diagnose(dso, run_no,run_no,'wbrf.nxs','rf_v1_entry','whitebeam','bank',maps_bank,'hardmask','4to1_022.msk','nomess');
+>> [mask,cause]=diagnose(dso, run_no,run_no,'wbrf.nxs','rf_v1_entry','whitebeam','bank',maps_bank,'hardmask','4to1_022.msk','nomess');
 </pre>

@@ Line 1: / Line 1: @@
 The main diagnostic tool for homer is the diagnose function (analogous to the VMS DIAG function). It creates an [IXTmask] object with optional file output (nexus or ascii) for a given monochromatic run, using the data from a white beam vanadium integral [IXTrunfile]. It also outputs a matlab structure 'cause' detailing information on which files contributed to the exclusion of which spectra and the reason for their exclusion, and if appropriate the value which failed the test applied.
@@ Line 33: / Line 32: @@
 | 'bank'   || '{file}.map', '{map}.nxs' or [[IXTmap]] || file (nexus or ascii) or [[IXTmap]] object defining the spectra banks of the instrument [default: empty object with false validity]
 |-
-|  's_zero'|| real|| /ZERO_BKGD from VMS DIAG
+|  's_zero'|| real|| /ZERO_BKGD from VMS DIAG - will remove spectra with zero integrated signal in the range between bmin and bmax of the '''sample''' run[default: false]
 |-
 | 's_out_lo'|| real|| low outlier limit for monochromatic sample background integral
@@ Line 45: / Line 44: @@
 | 'sv_sig'   || real|| desc
 |-
-|  'v_zero'|| real|| desc
+|  'v_zero'|| real|| - will remove spectra with zero integrated signal in the range between bmin and bmax of the '''vanadium''' runs[default: true]
 |-
 | 'v_out_lo'|| real|| low outlier limit for vanadium integral

@@ Line 1: / Line 1: @@
-<b>DIAG</b> will optionally load a hard mask file, an [IXTmask] object or file (nexus or ascii), that is a list of spectra that are to be masked regardless of any diagnostic operations. Sometimes it is desirable to consider banks of spectra separately such as those connected to psd and non-psd detectors. If this is the case then an [IXTmap] object or file (nexus or ascii) may be supplied as an argument to the <b>DIAG</b> routine, defining these groups of spectra.
+The main diagnostic tool for homer is the diagnose function (analogous to the VMS DIAG function). It creates an [IXTmask] object with optional file output (nexus or ascii) for a given monochromatic run, using the data from a white beam vanadium integral [IXTrunfile]. It also outputs a matlab structure 'cause' detailing information on which files contributed to the exclusion of which spectra and the reason for their exclusion, and if appropriate the value which failed the test applied.
-There are also arguments to <b>DIAG</b> which set certain limits and tolerances in the diagnostic process of <b>DIAG</b>, all of which have default values. Some of these values bear relation to VMS DIAG input, in each case this has been defined below.
+diagnose will optionally load a hard mask file, an [IXTmask] object or file (nexus or ascii), that is a list of spectra that are to be masked regardless of any diagnostic operations. Sometimes it is desirable to consider banks of spectra separately such as those connected to psd and non-psd detectors. If this is the case then an [IXTmap] object or file (nexus or ascii) may be supplied as an argument to the diagnose routine, defining these groups of spectra.
 An simple example function call to <b>DIAG</b> might be as follows:
@@ Line 9: / Line 12: @@
 >> maps_bank=IXTmap({[1:17280],[17281:18432],[18433:32256],[32257:41472]});
 >> monosam=read_nxs('monosam.nxs',IXTrunfile,'mono_sam');
->> ~[mask,cause]=diagnose(monosam,'rf_v1','wbrf.nxs','rf_v1_entry','whitebeam','bank',maps_bank,'hmask','4to1_022.msk','nomess');
+>> ~[mask,cause]=diagnose(dso, run_no,run_no,'wbrf.nxs','rf_v1_entry','whitebeam','bank',maps_bank,'hardmask','4to1_022.msk','nomess');
 </pre>
@@ Line 17: / Line 20: @@
 !width="20%"|Parameter Type
 !width="70%"|Brief Description
 |-
 |  'rf_v1'|| '{file}.nxs' or [[IXTrunfile]] || white beam vanadium integral [[IXTrunfile]], can be loaded from a nexus file or a matlab object, /V1 argument from VMS DIAG
@@ Line 60: / Line 61: @@
 | 'r_sig'   || real|| desc
 |-
-|  'tiny'|| real|| exterme low outliers [default: 1e-10]
+|  'tiny'|| real|| extreme low outliers [default: 1e-10]
 |-
 |  'huge'|| real|| extreme high outliers [default: 1e10]

@@ Line 60: / Line 60: @@
 | 'r_sig'   || real|| desc
 |-
-|  'tiny'|| real|| exterme low outliers
+|  'tiny'|| real|| exterme low outliers [default: 1e-10]
 |-
-|  'huge'|| real|| extreme high outliers
+|  'huge'|| real|| extreme high outliers [default: 1e10]
 |-
 |  'rfile_entry'|| 'string' || nexus file entry_name for monochromatic sample background [default: ' ']

@@ Line 31: / Line 31: @@
 |-
 | 'bank'   || '{file}.map', '{map}.nxs' or [[IXTmap]] || file (nexus or ascii) or [[IXTmap]] object defining the spectra banks of the instrument [default: empty object with false validity]
 |-
 |  's_zero'|| real|| /ZERO_BKGD from VMS DIAG
@@ Line 63: / Line 59: @@
 |-
 | 'r_sig'   || real|| desc
 |-
 |  'rfile_entry'|| 'string' || nexus file entry_name for monochromatic sample background [default: ' ']

@@ Line 28: / Line 28: @@
 | 'bmax'|| real || /BMAX argument from VMS DIAG
 |-
-|  'hardmask'|| '{file}.msk', '{mask}.nxs' or [[IXTmask]] || file (nexus or ascii) or [[IXTmask]] object defining the hard mask [default- empty object with false validity], /HARD argument from VMS DIAG
+|  'hardmask'|| '{file}.msk', '{mask}.nxs' or [[IXTmask]] || file (nexus or ascii) or [[IXTmask]] object defining the hard mask [default:empty object with false validity], /HARD argument from VMS DIAG
 |-
-| 'bank'   || '{file}.map', '{map}.nxs' or [[IXTmap]] || file (nexus or ascii) or [[IXTmap]] object defining the spectra banks of the instrument [default- empty object with false validity]
+| 'bank'   || '{file}.map', '{map}.nxs' or [[IXTmap]] || file (nexus or ascii) or [[IXTmap]] object defining the spectra banks of the instrument [default: empty object with false validity]
 |-
 |  'tiny'|| real|| desc
@@ Line 64: / Line 64: @@
 | 'r_sig'   || real|| desc
 |-
-|  'rfile_entry'|| 'string' || nexus file entry_name for monochromatic sample background [default- '']
+|  'rfile_entry'|| 'string' || nexus file entry_name for monochromatic sample background [default: ' ']
 |-
-|  'rf_v1_entry'|| 'string' || nexus file entry_name for first whitebeam vanadium integral [default- '']
+|  'rf_v1_entry'|| 'string' || nexus file entry_name for first whitebeam vanadium integral [default: ' ']
 |-
-|  'rf_v2_entry'|| 'string || nexus file entry_name for second whitebeam vanadium integral [default- '']
+|  'rf_v2_entry'|| 'string || nexus file entry_name for second whitebeam vanadium integral [default: ' ']
 |-
-|  'hmask_entry'|| 'string || nexus file entry_name for hard mask [default- '']
+|  'hmask_entry'|| 'string || nexus file entry_name for hard mask [default: ' ']
 |-
-|  'bank_entry'|| 'string || nexus file entry_name for bank specification [default- '']
+|  'bank_entry'|| 'string || nexus file entry_name for bank specification [default: ' ']
 |-
 |  ||   ||  '''Keyword arguments for DIAG output'''
 |-
-|  'out_nex'|| '{file}.nxs || nexus output mask filename specification [default- 'out.nxs']
+|  'out_nex'|| '{file}.nxs || nexus output mask filename specification [default: 'out.nxs']
 |-
-|  'out_nex_entry'|| 'string' || out nexus mask file entry_name  [default- '']
+|  'out_nex_entry'|| 'string' || out nexus mask file entry_name  [default: ' ']
 |-
-|  'out_asc'|| '{file}.msk' || ascii output mask filename specification [default:: 'out.msk']
+|  'out_asc'|| '{file}.msk' || ascii output mask filename specification [default: 'out.msk']
 |-
-|  'summary'|| logical || flag stipulating text output summary of reasons for spectrum exclusion [default- true]
+|  'summary'|| logical || flag stipulating text output summary of reasons for spectrum exclusion [default: true]
 |-
-|  'messages'|| logical || flag stipulating text output of numerical values calculated for spectrum exclusion [default- false]
+|  'messages'|| logical || flag stipulating text output of numerical values calculated for spectrum exclusion [default: false]
 |}

@@ Line 22: / Line 22: @@
 |  'rf_v1'|| '{file}.nxs' or [[IXTrunfile]] || white beam vanadium integral [[IXTrunfile]], can be loaded from a nexus file or a matlab object, /V1 argument from VMS DIAG
 |-
-|  'rf_v2'|| '{file}.nxs' or [[IXTrunfile]] || second white beam vanadium integral [[IXTrunfile]], can be loaded from a nexus file or a matlab object [default- empty object with false validity], /V2 argument from VMS DIAG
+|  'rf_v2'|| '{file}.nxs' or [[IXTrunfile]] || second white beam vanadium integral [[IXTrunfile]], can be loaded from a nexus file or a matlab object [default: empty object with false validity], /V2 argument from VMS DIAG
 |-
 | 'bmin'|| real || /BMIN argument from VMS DIAG