Index: /trunk/doc/ipptools/dettool.txt =================================================================== --- /trunk/doc/ipptools/dettool.txt (revision 9049) +++ /trunk/doc/ipptools/dettool.txt (revision 9050) @@ -60,5 +60,5 @@ to detProcessedImfiles: - dettool -addprocessed -det_id -exp_id -class_id -uri -recip -proc_bg -proc_bg_stdev -proc_bg_mean_stdev -b1_uri -b2_uri + dettool -addprocessed -det_id -exp_id -class_id -uri -recip -bg -bg_stdev -bg_mean_stdev -b1_uri -b2_uri In practise, the above "ppImage" and "dettool -addprocessed" commands @@ -85,5 +85,5 @@ the imfile statistics) is added into the database for the exposure: - dettool -addprocessedexp -exp_id -proc_bg -proc_bg_stdev -proc_bg_mean_stdev -uri -jpeg_uri + dettool -addprocessedexp -exp_id -bg -bg_stdev -bg_mean_stdev -uri -jpeg_uri In practise, the above "dettool -processed", "ppImage" and "dettool @@ -125,14 +125,7 @@ Once the stack has been completed, "dettool -addstacked" adds a -stacked class_id and and optionally marks it for normalization: - - dettool -addstacked [-pleasenormalize] -det_id -iter -class_id -recip -uri -norm_bg -norm_bg_stdev -norm_bg_mean_stdev - -The "-pleasenormalize" flag indicates that the normalisation steps are -to be performed (in the case of flat-fields); if this flag is missing, -then the normalisation steps are to be skipped and the stacked imfiles -are inserted in table of normalised imfiles. The statistics fields -have "norm" since these statistics will be used to determine the -normalisations. +stacked class_id: + + dettool -addstacked -det_id -iter -class_id -recip -uri -bg -bg_stdev -bg_mean_stdev In practise, the above three commands ("dettool -processed", "ppMerge" @@ -155,6 +148,6 @@ This returns the complete list of processed imfiles for the specified -det_id, providing exposure id, class id, statistic, which we use in -the normalisation: +det_id, providing exposure id, class id, statistic, detrend type, +which we use in the normalisation: ppNormCalc INPUT.mdc @@ -175,4 +168,8 @@ "ppNorm" and "dettool -addnormstat") will be performed by a Perl script, "detrend_norm_calc.pl". + +If the detrend type is not suitable for normalisation, then +normalisation values of unity will be generated without solving the +matrix with ppNormCalc. *** To do: possible upgrade path is to have "dettool -addnormstat" @@ -193,11 +190,12 @@ detNormalizedImfile. -For each imfile, we apply the normalisation: - - ppArith -file1 -operation * -constant -out +For each imfile, we apply the normalisation, generate binned images +and statistics: + + ppNormApply -file -norm -stat The normalised imfile is then inserted into detNormalizedImfile: - dettool -addnormalizedimfile -det_id -iter -class_id -uri + dettool -addnormalizedimfile -det_id -iter -class_id -uri -b1_uri -b2_uri -bg -bg_stdev -bg_mean_stdev In practise, the above two commands ("ppArith" and "dettool @@ -208,34 +206,7 @@ -------------------------------------------------------------------------------- -<<< Normalisation has completed. The skip introduced >>> -<<< by leaving out -pleasenormalize lands here. >>> - --------------------------------------------------------------------------------- - -Pan-Tasks regularly runs: - - dettool -stackedimfile - -which returns a list of stack imfiles which have been normalised (or -had normalisation skipped). This includes the exposure id, class id -and uri. - -For each imfile, we measure statistics and bin the images: - - ppImage -file -recipe PPIMAGE PPIMAGE_BIN -stat - -The resultant statistics and the binned images are pushed into the database: - - dettool -addstackimfilesummary -exp_id -class_id -b1_uri -b2_uri -stack_bg -stack_bg_stdev -stack_bg_mean_stdev - -In practise, the above commands ("ppImage" and "dettool --addnormimfilesummary") will be performed by a Perl script, -"detrend_poststack_imfile.pl". - --------------------------------------------------------------------------------- - -Pan-Tasks regularly runs: - - dettool -normalizedexp +Pan-Tasks regularly runs: + + dettool -normexp which returns a list of stack exposures which have had normalised @@ -244,5 +215,5 @@ For each exposure, we get the list of component imfiles: - dettool -stackimfile -exp_id + dettool -normimfile -exp_id This includes the statistics (bg, bg_stdev, bg_mean_stdev) and the @@ -254,9 +225,9 @@ The statistics and JPEG uri are pushed into the database: - dettool -addstackexpsummary -exp_id -jpeg1_uri -jpeg2_uri -norm_bg -norm_bg_stdev -norm_bg_mean_stdev + dettool -addnormexp -exp_id -j1_uri -j2_uri -bg -bg_stdev -bg_mean_stdev In practise, the above three commands ("dettool -stackimfile", -"ppImage" and "dettool -addnormexpsummary") will be performed by a -Perl script, "detrend_poststack_exp.pl". +"ppImage" and "dettool -addnormexp") will be performed by a +Perl script, "detrend_norm_exp.pl". -------------------------------------------------------------------------------- @@ -278,5 +249,5 @@ The residual is then inserted into the database: - dettool -addresidimfile -det_id -exp_id -class_id -recip -resid_bg -resid_bg_stdev -resid_bg_mean_stdev -b1_uri -b2_uri + dettool -addresidimfile -det_id -exp_id -class_id -recip -bg -bg_stdev -bg_mean_stdev -b1_uri -b2_uri In practise, the above two commands ("ppImage" and "dettool @@ -313,5 +284,5 @@ problems; these could be removed by other means): - dettool -addresidexp -det_id -iter -exp_id -recip -b1_uri -b2_uri -resid_bg -resid_bg_stdev -resid_bg_mean_stdev [-reject] + dettool -addresidexp -det_id -iter -exp_id -recip -j1_uri -j2_uri -bg -bg_stdev -bg_mean_stdev [-reject] where the "-reject" flag indicates that the exposure is not to be @@ -350,5 +321,5 @@ iteration as a whole we can run: - dettool -adddetrunsummary -det_id -iter -det_bg -det_bg_stdev -det_bg_mean_stdev [-accept] + dettool -adddetrunsummary -det_id -iter -bg -bg_stdev -bg_mean_stdev [-accept] Which allows per detrend run iteration summary statics to be