leonarski_fandClaude Opus 5.5
ce528f3a14
A CrystFEL .geom (current and old syntax) is parsed for panels (pixel ranges, fs/ss, corners), clen/coffset (a number, or an HDF5 path read as mm), res, adu_per_eV/adu_per_photon, max_adu, no_index, bad regions (panel, whole-frame or lab-plane) and the HDF5 mask (mask/mask_file, mask_good/mask_bad). JFJochCrystFELReader reads the frames the geometry's data path names - a 3D stack (Cheetah CXI), one 2D frame per file, or one group per shot (/%/data) - from a file or a directory, puts the panels on one flat image at their rounded positions with gaps and bad regions masked, and converts to photons where a gain is stated (otherwise the pre-scan measures it). One wavelength and one camera length per run: values taken from the files are averaged over the first file. Panel positions are used as given. Frames stored as one deflate(+shuffle) chunk are read raw under the HDF5 lock and decoded outside it. Replaces the MPCCD-specific reader of the previous commit. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
58 lines
2.2 KiB
C++
58 lines
2.2 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <cstdint>
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#include <optional>
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#include <string>
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#include <vector>
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// A CrystFEL detector geometry file (.geom), as far as it places pixels and says what they are worth:
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// the panels with their pixel ranges in the stored frame, fast/slow-scan directions and corners, the
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// camera length, the pixel size, the gain and the regions to leave out. Both the current syntax and
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// the older one - global keys that only take effect for the panels that follow them, bad regions
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// stated in whole-frame coordinates - are read.
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//
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// Every length is in pixels except clen and coffset, which are in metres. A value CrystFEL takes from
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// the image file instead (clen = /path, photon_energy = /path) is kept as that path, for the reader
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// to resolve.
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namespace crystfel {
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struct Panel {
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std::string name;
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int64_t min_fs = 0, max_fs = 0, min_ss = 0, max_ss = 0; // inclusive, in the stored frame
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double fs_x = 1, fs_y = 0, ss_x = 0, ss_y = 1;
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double corner_x = 0, corner_y = 0;
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double res = 0; // pixels per metre
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std::string clen; // metres, or an HDF5 path
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double coffset = 0; // metres
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std::optional<double> adu_per_eV;
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std::optional<double> adu_per_photon;
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std::optional<double> max_adu;
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bool no_index = false;
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};
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// A region to leave out: either a pixel range on one panel (or, in the old syntax, on the whole
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// frame), or a box in the laboratory plane, in pixels.
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struct BadRegion {
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std::string panel; // empty: fs/ss are whole-frame coordinates
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bool in_lab = false;
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double min_x = 0, max_x = 0, min_y = 0, max_y = 0;
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int64_t min_fs = 0, max_fs = 0, min_ss = 0, max_ss = 0;
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};
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struct Geometry {
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std::vector<Panel> panels;
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std::vector<BadRegion> bad;
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std::string data = "/data/data";
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std::string photon_energy; // eV, or an HDF5 path
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std::string mask; // HDF5 path, or empty
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std::string mask_file; // file holding it, or empty for the image file itself
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uint32_t mask_good = 0, mask_bad = 0;
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};
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Geometry Read(const std::string &filename);
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} // namespace crystfel
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