leonarski_fandClaude Opus 5.5
7c23b4befe
The .geom parser now takes the masking information the format defines: - mask arrays: mask/mask_file/mask_good/mask_bad (mask 0) and maskN_data/maskN_file/maskN_goodbits/ maskN_badbits for N = 0..7; global keys hold for the panels after them, a panel may override. A mask that is the same on every panel is one whole-frame mask, otherwise one per panel, applied on that panel's pixels only. - a relative mask_file is looked for in the working directory (as CrystFEL does), then beside the .geom. - bad regions (bad*): a lab-plane box (min_x..max_y) or a fs/ss range on a panel (or, old syntax, on the whole frame); mask_edge_pixels and no_index. JFJochXFELReader already had the static pixel mask and the per-frame mask path for these; the masks go through them unchanged. A mask whose path holds % (one per shot group) is applied frame by frame like a 3D one. Where the geometry names mask arrays, the data file's own Cheetah masks (CXI mask_shared and per-shot mask with Cheetah's generic bad bits, /metadata/pixelmask) are not added: the geometry says which bits matter (e.g. an AGIPD mask_bad that includes bit 32). --mask-good / --mask-bad still add their masks to these. Tests: [CrystFELGeometry] (new keys, per-panel override, relative mask file), JFJochXFELReader_* (new GeometryMasks case on a synthetic CXI + .geom), [JFJochMultiReader], JFJochXTCReader*. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
79 lines
3.2 KiB
C++
79 lines
3.2 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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// Where the panels of a stills detector lie and what their pixels are worth, as the XFEL readers
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// gather it from a file's own metadata (or, while it is still read, a CrystFEL geometry file): the
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// panels with their pixel ranges in the stored frame, fast/slow-scan directions and corners, the camera
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// length, the pixel size, the gain and the regions to leave out. The conventions are CrystFEL's - a
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// corner is the very corner of the panel's first pixel, x and y in pixels in the detector plane.
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//
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// Lengths are in pixels, except the camera length, which is held in metres. A value taken from the
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// image files (a camera length or photon energy stated per shot) is kept as its path, with the factor
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// that turns the stored number into the unit held here.
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namespace xfel {
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// A number stated in the layout, or a path to it in the image file, times scale.
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struct Value {
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std::string path; // empty: value holds the number
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double value = 0;
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double scale = 1; // what one stored unit at path is worth
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};
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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::optional<Value> clen; // metres
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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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int64_t mask_edge_pixels = 0;
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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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// A mask array: a pixel is bad where it has any of bad's bits set, or lacks any of good's - or, with
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// nonzero_good, where the array is zero.
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struct Mask {
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std::string data; // HDF5 path; a % in it stands for the shot group, as in the data path
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std::string file; // file holding it, or empty for the image file itself
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uint32_t good = 0, bad = 0;
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bool nonzero_good = false;
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std::string panel; // empty: every panel; otherwise only this panel's pixels
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bool operator==(const Mask &) const = default;
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[[nodiscard]] bool Bad(uint32_t v) const {
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return (bad != 0 && (v & bad) != 0) || (good != 0 && (v & good) != good) || (nonzero_good && v == 0);
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}
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};
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struct Layout {
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std::vector<Panel> panels;
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std::vector<BadRegion> bad;
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std::vector<Mask> masks;
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std::string data = "/data/data";
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std::optional<Value> photon_energy; // eV
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std::optional<Value> wavelength; // Angstrom; used where no photon_energy is stated
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};
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} // namespace xfel
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