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-rw-r--r--libcrystfel/CMakeLists.txt2
-rw-r--r--libcrystfel/doc/index.md1
-rw-r--r--libcrystfel/src/datatemplate.c163
-rw-r--r--libcrystfel/src/datatemplate.h60
-rw-r--r--libcrystfel/src/detgeom.h275
5 files changed, 501 insertions, 0 deletions
diff --git a/libcrystfel/CMakeLists.txt b/libcrystfel/CMakeLists.txt
index 9f79b0c4..15d4ba19 100644
--- a/libcrystfel/CMakeLists.txt
+++ b/libcrystfel/CMakeLists.txt
@@ -75,6 +75,7 @@ set(LIBCRYSTFEL_SOURCES
src/pinkindexer.c
src/rational.c
src/spectrum.c
+ src/datatemplate.c
${BISON_symopp_OUTPUTS}
${FLEX_symopl_OUTPUTS}
)
@@ -117,6 +118,7 @@ set(LIBCRYSTFEL_HEADERS
src/pinkindexer.h
src/rational.h
src/spectrum.h
+ src/datatemplate.h
)
if (DOXYGEN_FOUND)
diff --git a/libcrystfel/doc/index.md b/libcrystfel/doc/index.md
index a14e62db..f1c72ed4 100644
--- a/libcrystfel/doc/index.md
+++ b/libcrystfel/doc/index.md
@@ -49,6 +49,7 @@ API documentation
* \ref felix.h "Felix indexer interface"
* \ref predict-refine.h "Prediction refinement"
* \ref integration.h "Integration of reflections"
+* \ref datatemplate.h "Contents of geometry files"
* \ref detector.h "Detector geometry descriptions"
* \ref spectrum.h "Radiation spectrum object"
* \ref hdf5-file.h "HDF5 file interface"
diff --git a/libcrystfel/src/datatemplate.c b/libcrystfel/src/datatemplate.c
new file mode 100644
index 00000000..22bad02c
--- /dev/null
+++ b/libcrystfel/src/datatemplate.c
@@ -0,0 +1,163 @@
+/*
+ * datatemplate.c
+ *
+ * Data template structure
+ *
+ * Copyright © 2019 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2019 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <stdlib.h>
+
+#include "datatemplate.h"
+
+
+/**
+ * \file datatemplate.h
+ */
+
+enum adu_per_unit
+{
+ ADU_PER_PHOTON,
+ ADU_PER_EV
+};
+
+
+/**
+ * Represents one panel of a detector
+ */
+struct panel_template
+{
+ /** Text name for panel (fixed length array) */
+ char name[1024];
+
+ /** \name Location of corner in units of the pixel size of this panel */
+ /**@{*/
+ double cnx;
+ double cny;
+ /**@}*/
+
+ /** Location to get \ref cnz from, e.g. from HDF5 file */
+ char *cnz_from;
+
+ /** The offset to be applied from \ref clen */
+ double coffset;
+
+ /** Location of mask data */
+ char *mask;
+
+ /** Filename for mask data */
+ char *mask_file;
+
+ /** Location of per-pixel saturation map */
+ char *satmap;
+
+ /** Filename for saturation map */
+ char *satmap_file;
+
+ /** Resolution in pixels per metre */
+ double pixel_pitch;
+
+ /** Readout direction (for filtering out clusters of peaks)
+ * ('x' or 'y') */
+ char badrow;
+
+ /** Number of detector intensity units per photon, or eV */
+ double adu_scale;
+ enum adu_per_unit adu_scale_unit;
+
+ /** Treat pixel as unreliable if higher than this */
+ double max_adu;
+
+ /** Location of data in file */
+ char *data;
+
+ /** Dimension structure */
+ struct dim_structure *dim_structure;
+
+ /** \name Transformation matrix from pixel coordinates to lab frame */
+ /*@{*/
+ double fsx;
+ double fsy;
+ double fsz;
+ double ssx;
+ double ssy;
+ double ssz;
+ /*@}*/
+
+ /** \name Rail direction */
+ /*@{*/
+ double rail_x;
+ double rail_y;
+ double rail_z;
+ /*@}*/
+
+ /* Value of clen (without coffset) at which beam is centered */
+ double clen_for_centering;
+
+ /** \name Position of the panel in the data block in the file. */
+ /*@{*/
+ int orig_min_fs;
+ int orig_max_fs;
+ int orig_min_ss;
+ int orig_max_ss;
+ /*@}*/
+};
+
+
+struct _datatemplate
+{
+ struct panel_template *panels;
+ int n_panels;
+
+ struct badregion *bad;
+ int n_bad;
+
+ unsigned int mask_bad;
+ unsigned int mask_good;
+
+ struct rigid_group **rigid_groups;
+ int n_rigid_groups;
+
+ struct rg_collection **rigid_group_collections;
+ int n_rg_collections;
+
+ int path_dim;
+ int dim_dim;
+
+ struct panel_template defaults;
+};
+
+
+DataTemplate *data_template_new_from_file(const char *filename)
+{
+ return NULL;
+}
+
+
+void data_template_free(DataTemplate *dt)
+{
+}
diff --git a/libcrystfel/src/datatemplate.h b/libcrystfel/src/datatemplate.h
new file mode 100644
index 00000000..01292836
--- /dev/null
+++ b/libcrystfel/src/datatemplate.h
@@ -0,0 +1,60 @@
+/*
+ * datatemplate.h
+ *
+ * Template for loading data
+ *
+ * Copyright © 2019 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ *
+ * Authors:
+ * 2019 Thomas White <taw@physics.org>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef DATATEMPLATE_H
+#define DATATEMPLATE_H
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+/**
+ * \file datatemplate.h
+ * Template for loading data.
+ */
+
+/**
+ * This data structure is opaque. You must use the available accessor functions
+ * to read and write its contents.
+ **/
+typedef struct _datatemplate DataTemplate;
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern DataTemplate *data_template_new_from_file(const char *filename);
+extern void data_template_free(DataTemplate *dt);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* DATATEMPLATE_H */
diff --git a/libcrystfel/src/detgeom.h b/libcrystfel/src/detgeom.h
new file mode 100644
index 00000000..6b487c43
--- /dev/null
+++ b/libcrystfel/src/detgeom.h
@@ -0,0 +1,275 @@
+/*
+ * detector.h
+ *
+ * Detector properties
+ *
+ * Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
+ * a research centre of the Helmholtz Association.
+ * Copyright © 2012 Richard Kirian
+ *
+ * Authors:
+ * 2009-2019 Thomas White <taw@physics.org>
+ * 2011-2012 Richard Kirian <rkirian@asu.edu>
+ * 2014 Valerio Mariani
+ * 2011 Andrew Aquila
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#ifndef DETECTOR_H
+#define DETECTOR_H
+
+struct rigid_group;
+struct rg_collection;
+struct detector;
+struct panel;
+struct badregion;
+struct beam_params;
+struct hdfile;
+struct event;
+
+#include "hdf5-file.h"
+#include "image.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * \file detector.h
+ * Detector geometry structure and related functions.
+ */
+
+
+struct rigid_group
+{
+ char *name;
+ struct panel **panels;
+ int n_panels;
+};
+
+
+struct rg_collection
+{
+ char *name;
+ struct rigid_group **rigid_groups;
+ int n_rigid_groups;
+};
+
+
+/**
+ * Represents one panel of a detector
+ */
+struct panel
+{
+ /** Text name for panel */
+ const char *name;
+
+ /** \name Location of corner in units of the pixel size of this panel, \
+ * measured from the interaction point. */
+ /**@{*/
+ double cnx;
+ double cny;
+ double cnz;
+ /**@}*/
+
+ /** Pixel size in metres */
+ double pixel_pitch;
+
+ /** Readout direction (for filtering out clusters of peaks)
+ * ('x' or 'y') */
+ char badrow;
+
+ /** Number of detector intensity units per photon (or electron, etc) */
+ double adu_per_photon;
+
+ /** Treat pixel as unreliable if higher than this */
+ double max_adu;
+
+ /** \name Transformation matrix from pixel coordinates to lab frame */
+ /*@{*/
+ double fsx;
+ double fsy;
+ double fsz;
+ double ssx;
+ double ssy;
+ double ssz;
+ /*@}*/
+
+ /** \name Inverse of 2D part of transformation matrix */
+ /*@{*/
+ double xfs;
+ double yfs;
+ double xss;
+ double yss;
+ /*@}*/
+
+ /** \name Width and height of panel */
+ /*@{*/
+ int w;
+ int h;
+ /*@}*/
+};
+
+
+struct badregion
+{
+ char name[1024];
+ int is_fsss;
+ char *panel;
+
+ double min_x;
+ double max_x;
+ double min_y;
+ double max_y;
+
+ /* Specified INCLUSIVELY */
+ int min_fs;
+ int max_fs;
+ int min_ss;
+ int max_ss;
+
+};
+
+
+struct detector
+{
+ struct panel *panels;
+ int n_panels;
+
+ struct badregion *bad;
+ int n_bad;
+
+ unsigned int mask_bad;
+ unsigned int mask_good;
+
+ struct rigid_group **rigid_groups;
+ int n_rigid_groups;
+
+ struct rg_collection **rigid_group_collections;
+ int n_rg_collections;
+
+ /* Location of the pixel furthest away from the beam position, which
+ * will have the largest value of 2theta regardless of camera length
+ * and wavelength */
+ struct panel *furthest_out_panel;
+ double furthest_out_fs;
+ double furthest_out_ss;
+
+ /* As above, but for the smallest 2theta */
+ struct panel *furthest_in_panel;
+ double furthest_in_fs;
+ double furthest_in_ss;
+};
+
+
+extern struct rvec get_q_for_panel(struct panel *p, double fs, double ss,
+ double *ttp, double k);
+
+extern double get_tt(struct image *image, double xs, double ys, int *err);
+
+extern int in_bad_region(struct detector *det, struct panel *p,
+ double fs, double ss);
+
+extern void record_image(struct image *image, int do_poisson, double background,
+ gsl_rng *rng, double beam_radius, double nphotons);
+
+extern struct panel *find_orig_panel(struct detector *det,
+ double fs, double ss);
+
+extern signed int find_orig_panel_number(struct detector *det,
+ double fs, double ss);
+
+extern int panel_number(const struct detector *det, const struct panel *p);
+
+extern struct detector *get_detector_geometry(const char *filename,
+ struct beam_params *beam);
+
+extern struct detector *get_detector_geometry_2(const char *filename,
+ struct beam_params *beam,
+ char **hdf5_peak_path);
+
+extern struct detector *get_detector_geometry_from_string(const char *string,
+ struct beam_params *beam,
+ char **hdf5_peak_path);
+
+extern void free_detector_geometry(struct detector *det);
+
+extern struct detector *simple_geometry(const struct image *image, int w, int h);
+
+extern void get_pixel_extents(struct detector *det,
+ double *min_x, double *min_y,
+ double *max_x, double *max_y);
+
+extern void fill_in_adu(struct image *image);
+extern void adjust_centering_for_rail(struct panel *p);
+
+extern int panel_is_in_rigid_group(const struct rigid_group *rg,
+ struct panel *p);
+
+extern int rigid_group_is_in_collection(struct rg_collection *c,
+ struct rigid_group *rg);
+
+extern struct detector *copy_geom(const struct detector *in);
+
+extern int reverse_2d_mapping(double x, double y, struct detector *det,
+ struct panel **pp, double *pfs, double *pss);
+
+extern double largest_q(struct image *image);
+
+extern double smallest_q(struct image *image);
+
+extern struct panel *find_panel_by_name(struct detector *det, const char *name);
+
+extern int write_detector_geometry_2(const char *geometry_filename,
+ const char *output_filename,
+ struct detector *det,
+ const char *additional_comment,
+ int write_panel_coffset);
+
+extern int write_detector_geometry_3(const char *geometry_data,
+ const char *output_filename,
+ struct detector *det,
+ const char *additional_comment,
+ int write_panel_coffset);
+
+extern int write_detector_geometry(const char *geometry_filename,
+ const char *output_filename,
+ struct detector *det);
+
+extern void mark_resolution_range_as_bad(struct image *image,
+ double min, double max);
+
+
+extern int single_panel_data_source(struct detector *det, const char *element);
+
+struct rg_collection *find_rigid_group_collection_by_name(struct detector *det,
+ const char *name);
+
+extern int detector_has_clen_references(struct detector *det);
+
+extern int multi_event_geometry(struct detector *det);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* DETECTOR_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-29 05:48:07 +0000