From 8f99dad3c42ab08d631b1ac02b195b33944c7240 Mon Sep 17 00:00:00 2001 From: Yaroslav Gevorkov Date: Thu, 24 May 2018 10:07:11 +0200 Subject: Add "peakfinder9" --- doc/man/indexamajig.1 | 30 +++++++++++++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) (limited to 'doc/man/indexamajig.1') diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index c0fe8277..bdcb7aa3 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -51,6 +51,8 @@ If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search aft If you instead use \fB--peaks=peakfinder8\fR, indexamajig will use the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Note that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored. +If you instead use \fB--peaks=peakfinder9\fR, indexamajig will user the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--window-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--sig-fac-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--sig-fac-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. + You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero. @@ -254,7 +256,33 @@ Set the square of the gradient threshold for peak detection using \fB--peaks=zae .PD 0 .IP \fB--min-snr=\fR\fIsnr\fR .PD -Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR or \fB--peaks=peakfinder8\fR. The default is \fB--min-snr=5\fR. + +Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB--peaks=peakfinder8\fR or \fB--peaks=peakfinder9\fR. The default is \fB--min-snr=5\fR for \fB--peaks=zaef\fR and \fB--peaks=peakfinder8\fR, \fB--min-snr=9\fR for \fB--peaks=peakfinder9\fR. + +.PD 0 +.IP \fB--window-radius=\fR +.PD +(peakFinder9 only) defines the radius in which the local background is estimated. Should be > max radius of peak. Default is 3. + +.PD 0 +.IP \fB--sig-fac-biggest-pix=\fR +.PD +(peakFinder9 only) min snr of the biggest pixel in the peak, given as a factor of the standard deviation. Default is 7.0. + +.PD 0 +.IP \fB--sig-fac-peak-pix=\fR +.PD +(peakFinder9 only) min snr of a peak pixel, given as a factor of the standard deviation. Should be smaller or equal to sig_fac_biggest_pix. Default is 6.0. + +.PD 0 +.IP \fB--min-sig=\fR +.PD +(peakFinder9 only) minimum standard deviation of the background. Prevents finding of peaks in erroneous or highly shadowed unmasked regions. Default is 11.0. + +.PD 0 +.IP \fB--min-peak-over-neighbour=\fR +.PD +(peakFinder9 only) just for speed. Biggest pixel must be n higher than the pixels in window_radius distance to be a candidate for the biggest pixel in a peak. Should be chosen as a small positive number, a few times smaller than the weakest expected peak. Can be set to -INFINITY to turn of speedup and search with max precision! Default is -INFINITY. .PD 0 .IP \fB--min-pix-count=\fR\fIcnt\fR -- cgit v1.2.3 From 44e55c27562ca655d9439a2fd885440f8995b3ff Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 24 May 2018 10:31:09 +0200 Subject: Tweak wording in manual --- doc/man/indexamajig.1 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'doc/man/indexamajig.1') diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index bdcb7aa3..10def01c 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -51,7 +51,7 @@ If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search aft If you instead use \fB--peaks=peakfinder8\fR, indexamajig will use the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Note that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored. -If you instead use \fB--peaks=peakfinder9\fR, indexamajig will user the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--window-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--sig-fac-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--sig-fac-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. +If you instead use \fB--peaks=peakfinder9\fR, indexamajig will use the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--window-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--sig-fac-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--sig-fac-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero. @@ -282,7 +282,7 @@ Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB .PD 0 .IP \fB--min-peak-over-neighbour=\fR .PD -(peakFinder9 only) just for speed. Biggest pixel must be n higher than the pixels in window_radius distance to be a candidate for the biggest pixel in a peak. Should be chosen as a small positive number, a few times smaller than the weakest expected peak. Can be set to -INFINITY to turn of speedup and search with max precision! Default is -INFINITY. +(peakFinder9 only) just for speed. Biggest pixel must be n higher than the pixels in window_radius distance to be a candidate for the biggest pixel in a peak. Should be chosen as a small positive number, a few times smaller than the weakest expected peak. The default is -INFINITY, which turns off the speedup and searches with maximum precision. .PD 0 .IP \fB--min-pix-count=\fR\fIcnt\fR -- cgit v1.2.3 From 4f087e3954699ba96d2915af8d82fa10ebd53280 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 24 May 2018 10:31:53 +0200 Subject: Update authorship and copyright dates --- doc/man/indexamajig.1 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'doc/man/indexamajig.1') diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 10def01c..de75f7e4 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -523,7 +523,7 @@ For a full explanation of how the internal layout of the data file can be descr You can use \fBlist_events\fR to prepare a list of each event in one or more input files. Note that you only need to do this if you need to perform some sorting or filtering on this list. If you want to process every event in a file, simply specify the filename in the input file. .SH AUTHOR -This page was written by Thomas White. +This page was written by Thomas White, Yaroslav Gevorkov and Valerio Mariani. .SH REPORTING BUGS Report bugs to , or visit . -- cgit v1.2.3 From 8c0fce3cc328c0edceb756821e1f498d4f0041d8 Mon Sep 17 00:00:00 2001 From: Yaroslav Gevorkov Date: Thu, 24 May 2018 16:01:17 +0200 Subject: Adapted doc to min-sig -> min-snr change --- doc/man/indexamajig.1 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'doc/man/indexamajig.1') diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index de75f7e4..495abfa2 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -51,7 +51,7 @@ If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search aft If you instead use \fB--peaks=peakfinder8\fR, indexamajig will use the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Note that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored. -If you instead use \fB--peaks=peakfinder9\fR, indexamajig will use the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--window-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--sig-fac-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--sig-fac-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. +If you instead use \fB--peaks=peakfinder9\fR, indexamajig will use the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--window-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--min-snr-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--min-snr-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero. @@ -265,12 +265,12 @@ Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB (peakFinder9 only) defines the radius in which the local background is estimated. Should be > max radius of peak. Default is 3. .PD 0 -.IP \fB--sig-fac-biggest-pix=\fR +.IP \fB--min-snr-biggest-pix=\fR .PD (peakFinder9 only) min snr of the biggest pixel in the peak, given as a factor of the standard deviation. Default is 7.0. .PD 0 -.IP \fB--sig-fac-peak-pix=\fR +.IP \fB--min-snr-peak-pix=\fR .PD (peakFinder9 only) min snr of a peak pixel, given as a factor of the standard deviation. Should be smaller or equal to sig_fac_biggest_pix. Default is 6.0. -- cgit v1.2.3 From d8f176d1902e6fb90747d4065c7e775b86476d5b Mon Sep 17 00:00:00 2001 From: Yaroslav Gevorkov Date: Thu, 24 May 2018 15:03:04 +0200 Subject: Changed parameter window-radius -> local-bg-radius --- doc/man/indexamajig.1 | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) (limited to 'doc/man/indexamajig.1') diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 495abfa2..1d19bfad 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -51,7 +51,7 @@ If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search aft If you instead use \fB--peaks=peakfinder8\fR, indexamajig will use the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Note that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored. -If you instead use \fB--peaks=peakfinder9\fR, indexamajig will use the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--window-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--min-snr-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--min-snr-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. +If you instead use \fB--peaks=peakfinder9\fR, indexamajig will use the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--local-bg-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--min-snr-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--min-snr-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted. You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero. @@ -259,11 +259,6 @@ Set the square of the gradient threshold for peak detection using \fB--peaks=zae Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB--peaks=peakfinder8\fR or \fB--peaks=peakfinder9\fR. The default is \fB--min-snr=5\fR for \fB--peaks=zaef\fR and \fB--peaks=peakfinder8\fR, \fB--min-snr=9\fR for \fB--peaks=peakfinder9\fR. -.PD 0 -.IP \fB--window-radius=\fR -.PD -(peakFinder9 only) defines the radius in which the local background is estimated. Should be > max radius of peak. Default is 3. - .PD 0 .IP \fB--min-snr-biggest-pix=\fR .PD @@ -297,7 +292,7 @@ Accepts peaks only if they include less than \fR\fIcnt\fR pixels, when using \fB .PD 0 .IP \fB--local-bg-radius=\fR\fIr\fR .PD -Radius (in pixels) used for the estimation of the local background when using \fB--peaks=peakfinder8\fR. The default is \fB--local-bg-radius=3\fR. +Radius (in pixels) used for the estimation of the local background when using \fB--peaks=peakfinder8 or --peaks=peakfinder9\fR. The default is \fB--local-bg-radius=3\fR. .PD 0 .IP \fB--min-res=\fR\fIpx\fR -- cgit v1.2.3 From aae5b9636a9efe1ece80a3b823956a75d4149dca Mon Sep 17 00:00:00 2001 From: Thomas White Date: Thu, 24 May 2018 16:26:39 +0200 Subject: Use only one min-snr option --- doc/man/indexamajig.1 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'doc/man/indexamajig.1') diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 1d19bfad..37e80801 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -256,8 +256,7 @@ Set the square of the gradient threshold for peak detection using \fB--peaks=zae .PD 0 .IP \fB--min-snr=\fR\fIsnr\fR .PD - -Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB--peaks=peakfinder8\fR or \fB--peaks=peakfinder9\fR. The default is \fB--min-snr=5\fR for \fB--peaks=zaef\fR and \fB--peaks=peakfinder8\fR, \fB--min-snr=9\fR for \fB--peaks=peakfinder9\fR. +Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB--peaks=peakfinder8\fR or \fB--peaks=peakfinder9\fR. The default is \fB--min-snr=5\fR. .PD 0 .IP \fB--min-snr-biggest-pix=\fR -- cgit v1.2.3