From 61565336125a999790fb4c36219e9c46c5eb30cc Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 3 Mar 2017 17:37:10 +0100 Subject: Allow indexing system to store its own data, independently of indexing methods Previously, the indexing system passed all the information on to the indexing engines and then forgot about it. That made it difficult to do things like check the indexing solution after prediction refinement, because the target unit cell was unavailable. Now, the indexing system itself can keep some information. Of course, that information includes the private pointers for the indexing engines themselves. I took the opportunity to streamline things a little bit. The caller can now set up the indexing system in one step, without having to separately parse the names of the indexing methods. The caller no longer has to keep track of a separate array of methods, instead just one structure which contains everything. --- src/process_image.h | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index d41c23f5..57be255c 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -61,8 +61,7 @@ struct index_args float min_snr; int check_hdf5_snr; struct detector *det; - IndexingMethod *indm; - IndexingPrivate **ipriv; + IndexingPrivate *ipriv; int peaks; /* Peak detection method */ float tols[4]; struct beam_params *beam; -- cgit v1.2.3 From 772ed44b99c2429ac9bcaab327583e92464e2fd5 Mon Sep 17 00:00:00 2001 From: Valerio Mariani Date: Fri, 10 Mar 2017 14:29:55 +0100 Subject: Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementation --- src/process_image.h | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index d41c23f5..4c5c5a96 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -3,12 +3,12 @@ * * The processing pipeline for one image * - * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY, + * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY, * a research centre of the Helmholtz Association. * * Authors: * 2010-2016 Thomas White - * 2014 Valerio Mariani + * 2014-2017 Valerio Mariani * * This file is part of CrystFEL. * @@ -42,6 +42,7 @@ struct index_args; enum { + PEAK_PEAKFINDER8, PEAK_ZAEF, PEAK_HDF5, PEAK_CXI, @@ -73,6 +74,13 @@ struct index_args float ir_inn; float ir_mid; float ir_out; + int iterations; + int min_res; + int max_res; + int max_n_peaks; + int min_pix_count; + int max_pix_count; + int local_bg_radius; struct copy_hdf5_field *copyme; int integrate_saturated; int use_saturated; -- cgit v1.2.3 From 173fe22faba8c101e723b5c865fa0c5dd822ce78 Mon Sep 17 00:00:00 2001 From: Valerio Mariani Date: Sat, 11 Mar 2017 02:00:56 +0100 Subject: Removed unused iarg --- src/process_image.h | 1 - 1 file changed, 1 deletion(-) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index 4c5c5a96..2ac48b83 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -74,7 +74,6 @@ struct index_args float ir_inn; float ir_mid; float ir_out; - int iterations; int min_res; int max_res; int max_n_peaks; -- cgit v1.2.3 From 3746b4dbed15569764ec6de473806468951748b8 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 31 Mar 2017 16:27:13 +0200 Subject: Offset peak locations from HDF5 or CXI files by 0.5,0.5 CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry. In contrast, Cheetah considers the peak locations to be pixel indices in the data array. Therefore, a half-pixel offset is needed when importing the peak lists. For users who need the old behaviour, this commit adds a new option indexamajig --no-half-pixel-shift to deactivate this offset. --- src/process_image.h | 1 + 1 file changed, 1 insertion(+) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index bc8b31fd..d63679cf 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -67,6 +67,7 @@ struct index_args float tols[4]; struct beam_params *beam; char *hdf5_peak_path; + int half_pixel_shift; float pk_inn; float pk_mid; float pk_out; -- cgit v1.2.3 From cb6389ae61e8f7e279ea16f8ab1a94969d6c0dc9 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Fri, 28 Apr 2017 17:15:13 +0200 Subject: Skeleton image file API --- src/process_image.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index d63679cf..14f90c78 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -80,7 +80,7 @@ struct index_args int min_pix_count; int max_pix_count; int local_bg_radius; - struct copy_hdf5_field *copyme; + struct imagefile_field_list *copyme; int integrate_saturated; int use_saturated; int no_revalidate; -- cgit v1.2.3 From 38c560f7fc99383883890d746e74bd774a0309c7 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Sat, 13 May 2017 12:04:47 +0200 Subject: indexamajig: Add --min-peaks (basic hitfinder functionality) --- src/process_image.h | 1 + 1 file changed, 1 insertion(+) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index 14f90c78..a668f1ba 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -80,6 +80,7 @@ struct index_args int min_pix_count; int max_pix_count; int local_bg_radius; + int min_peaks; struct imagefile_field_list *copyme; int integrate_saturated; int use_saturated; -- cgit v1.2.3 From 8672f2857f18841576dc54b9a64e25837730cddd Mon Sep 17 00:00:00 2001 From: Thomas White Date: Tue, 27 Jun 2017 15:14:50 +0200 Subject: indexamajig: Add --no-non-hits-in-stream --- src/process_image.h | 1 + 1 file changed, 1 insertion(+) (limited to 'src/process_image.h') diff --git a/src/process_image.h b/src/process_image.h index a668f1ba..ec51c188 100644 --- a/src/process_image.h +++ b/src/process_image.h @@ -87,6 +87,7 @@ struct index_args int no_revalidate; int stream_peaks; int stream_refls; + int stream_nonhits; IntegrationMethod int_meth; IntDiag int_diag; signed int int_diag_h; -- cgit v1.2.3