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| """CHEM-156 Bruker X4 POSEIDON benchtop micro-CT / 3D X-ray microscope, reflection-source configuration with the 7 MP flat-panel detector | |
| (essential configuration: standard rotation stage, single detector mount, fixed scan geometry, automated 7-position filter changer): | |
| runtime (SI units). | |
| Physics owned by the host clock (``step`` is the only entry that advances time): | |
| * power and safety: mains switch, boot with homing of the stage and the filter changer, motorized lead-glass door with the X-ray interlock | |
| and the safety light curtain, emergency stop (latched until released and acknowledged), multi-function status light; | |
| * X-ray source (tungsten reflection target, sealed): kV / current set points limited to 100 kV and 20 W, ramp and a warm-up program | |
| after each power-up, focal spot growing with the target power (< 5 um at 4 W), Kramers thick-target bremsstrahlung with the tungsten | |
| self-absorption of a reflection target, W K and L lines, beryllium exit window, 7-position filter changer and air path (NIST SRD 126 | |
| attenuation coefficients from the template library); | |
| * geometry: cone beam, fixed source-detector distance, the sample on a rotation stage carried along the beam axis (source-object distance | |
| = geometric magnification) and lifted vertically; exact constant-speed motion with event cuts; collision guard against the source window, | |
| the filter changer and the detector cover; hidden rotation-axis offset (geometry calibration and post-alignment); | |
| * flat-panel detector (CsI:Tl scintillator on a CMOS sensor, 2800 x 2400 pixels): absorbed energy per photon from mu and mu_en, conversion | |
| gain, compound-Poisson quantum noise, read noise, dark offset and dark current, 16-bit saturation, binning, exposure, frame averaging, | |
| fixed-pattern gain non-uniformity corrected by the dark / bright field calibration (stale after changing kV, current, filter, binning or | |
| exposure), optional random detector movement against ring artifacts, injected defective columns; | |
| * samples: analytic phantoms (cylinder with horizontal layers of library materials or volume mixtures, spherical pores and inclusions, | |
| planar cracks, optional container tube and mounting pin, calibration phantom with steel balls, tungsten edge for radiographic resolution); | |
| projections by exact ray tracing (chord lengths per material) and polychromatic Beer-Lambert transmission in energy groups (beam | |
| hardening follows), focal-spot penumbra and scintillator blur; exact truth (porosity, pores, cracks) for the evaluator; | |
| * reconstruction: Feldkamp (FDK) cone-beam filtered back-projection (Ram-Lak / Shepp-Logan / Hann), Parker weights for 180 deg + fan scans, | |
| beam-hardening linearisation for a named material, ring correction, post-alignment (manual or automatic), Gaussian smoothing, volume of | |
| interest; analysis: porosity (total, open, closed, pore sizes), crack detection (planar components), attenuation statistics, slices; | |
| * fault injection (evaluator): tube arc, defective detector columns, rotation stage stall, door interlock sensor, light curtain blocked; | |
| * ledgers: electrical energy into the tube, X-ray energy emitted and where it goes (target self-absorption, window, filter, air, sample | |
| absorbed and scattered, detector absorbed and passed, shielding), dose to the sample, projections, frames, stage travel. | |
| """ | |
| from __future__ import annotations | |
| import copy | |
| import functools | |
| import hashlib | |
| import json | |
| import math | |
| import random | |
| from pathlib import Path | |
| import numpy as np | |
| class ActionRejected(ValueError): | |
| pass | |
| # ---------------------------------------------------------------- schema helpers | |
| def number(unit='1', lo=None, hi=None): | |
| s = {'type': 'number', 'x-unit': unit} | |
| if lo is not None: | |
| s['minimum'] = lo | |
| if hi is not None: | |
| s['maximum'] = hi | |
| return s | |
| def obj(properties): | |
| return dict(type='object', properties=properties, required=list(properties), additionalProperties=False) | |
| def nullable(s): | |
| return {'anyOf': [s, {'type': 'null'}]} | |
| def array(s, minimum=0, maximum=4096): | |
| return dict(type='array', items=s, minItems=minimum, maxItems=maximum) | |
| def enum(items): | |
| return {'type': 'string', 'enum': list(items)} | |
| BOOL = {'type': 'boolean'} | |
| TEXT = {'type': 'string'} | |
| INT = {'type': 'integer', 'x-unit': '1'} | |
| def integer(lo, hi): | |
| return {'type': 'integer', 'x-unit': '1', 'minimum': lo, 'maximum': hi} | |
| def validate(s, v): | |
| if 'anyOf' in s: | |
| for o in s['anyOf']: | |
| try: | |
| validate(o, v) | |
| return | |
| except ActionRejected: | |
| pass | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| k = s.get('type') | |
| if k in ('number', 'integer'): | |
| if isinstance(v, bool) or not isinstance(v, (int, float)) or not math.isfinite(v) or (k == 'integer' and not float(v).is_integer()): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| if not s.get('minimum', -math.inf) <= v <= s.get('maximum', math.inf): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| elif k == 'object': | |
| if not isinstance(v, dict): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| if 'properties' in s: | |
| if set(v) != set(s['properties']): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| for key, value in v.items(): | |
| validate(s['properties'][key], value) | |
| elif k == 'array': | |
| if not isinstance(v, list) or not s.get('minItems', 0) <= len(v) <= s.get('maxItems', math.inf): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| for x in v: | |
| validate(s['items'], x) | |
| elif k == 'boolean' and type(v) is not bool: | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| elif k == 'string': | |
| if not isinstance(v, str) or len(v) > s.get('maxLength', 10 ** 6) or len(v) < s.get('minLength', 0): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| if 'pattern' in s: | |
| import re | |
| if not re.fullmatch(s['pattern'], v): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| elif k == 'null' and v is not None: | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| if 'enum' in s and v not in s['enum']: | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| # ---------------------------------------------------------------- identity, paths | |
| PROTOCOL_VERSION = '1.0.0' | |
| SLUG = 'bruker_x4poseidon' | |
| ASSET_TYPE_ID = 'instrument.' + SLUG | |
| CATALOG_ID = 'CHEM-156' | |
| ROOT = Path(__file__).resolve().parents[2] | |
| ASSET = ROOT / 'assets/expansion_batch04/t3_analytical' / SLUG | |
| LIBRARY_PATH = ASSET / 'xray_attenuation_library.json' | |
| LIBRARY_REL = str(LIBRARY_PATH.relative_to(ROOT)) | |
| # ---------------------------------------------------------------- documented (Bruker X4 POSEIDON product page, brochure, configurator) | |
| XRAY_KV_MAX_V = 100.0e3 # reflection source: up to 100 kV | |
| XRAY_POWER_MAX_W = 20.0 # reflection source: 20 W | |
| SPOT_AT_4W_M = 5.0e-6 # reflection source: < 5 um spot at 4 W | |
| DETECTOR_PIXELS = (2800, 2400) # 7 MP flat panel, 2800 x 2400 pixels | |
| SAMPLE_MAX_DIAMETER_M = 0.110 # object size up to 110 mm in diameter | |
| SAMPLE_MAX_HEIGHT_M = 0.300 # object size up to 300 mm in height | |
| FILTER_POSITIONS = 7 # automated 7-position filter changer (standard with both sources; configurator) | |
| DETAIL_DETECTABILITY_M = 5.0e-6 # reflection source: detail detectability down to 5 um (configurator) | |
| BODY_DIMENSIONS_M = (1.250, 0.604, 0.690) # W 1250 x D 604 x H 690 mm (specification table) | |
| MASS_KG = 350.0 # weight 350 kg | |
| MAINS_V = (100.0, 240.0) # 100 - 240 V AC, 50 - 60 Hz, 3 A max | |
| MAINS_A_MAX = 3.0 | |
| # ---------------------------------------------------------------- engineering values (not published; used for the process model) | |
| XRAY_KV_MIN_V = 20.0e3 | |
| XRAY_CURRENT_MAX_A = 0.5e-3 # tube current limit besides the 20 W power limit | |
| KV_RAMP_V_S = 10.0e3 # high-voltage ramp | |
| CURRENT_RAMP_A_S = 100.0e-6 # emission-current ramp | |
| WARMUP_S = 180.0 # conditioning program after every power-up of the tube (first enable after a boot) | |
| SPOT_GROWTH_EXP = 1.0 # focal spot = 5 um x max(1, P / 4 W)^exp (constant power density above 4 W) | |
| TAKEOFF_RAD = math.radians(20.0) # take-off angle of the reflection target | |
| BE_WINDOW_M = 0.25e-3 # beryllium exit window | |
| KRAMERS_K_PER_V = 1.1e-9 # bremsstrahlung efficiency eta = K Z V (thick target) | |
| K_LINE_FRACTION_100KV = 0.08 # W K lines: fraction of the emitted X-ray energy at 100 kV, scaling (U - 1)^1.63 | |
| L_LINE_FRACTION_50KV = 0.04 # W L lines: fraction at 50 kV, scaling (U_L - 1)^1.63 | |
| W_K_LINES_KEV = ((59.32, 0.46), (57.98, 0.27), (67.24, 0.19), (69.10, 0.08)) # energy (keV), relative intensity | |
| W_L_LINES_KEV = ((8.40, 0.55), (9.67, 0.35), (11.29, 0.10)) | |
| W_K_EDGE_KEV, W_L3_EDGE_KEV = 69.525, 10.207 | |
| CONE_HALF_ANGLE_RAD = math.radians(20.0) # emission cone of the source used for the shielding share of the ledger | |
| SDD_M = 0.450 # source-detector distance (fixed scan geometry) | |
| SOD_RANGE_M = (0.015, 0.395) # source-object distance (sample carriage on the beam rail) | |
| CHUCK_Z_RANGE_M = (0.160, 0.399) # chuck top height above the bench (sample lift; limited by the rotation stage below it) | |
| ENCLOSURE_X_M = 0.310 # enclosure centre in the asset frame (the workstation stands on its left) | |
| SOURCE_XYZ_M = (ENCLOSURE_X_M - 0.180, 0.020, 0.400) # focal spot in the asset frame (beam along +X at this height) | |
| WINDOW_OFFSET_M = 0.008 # exit window face from the focal spot | |
| FILTER_OFFSET_M = 0.010 # filter plane from the focal spot | |
| FILTER_CLEAR_M = 0.014 # front face of the filter changer from the focal spot (collision guard) | |
| DETECTOR_COVER_M = 0.012 # detector entrance cover in front of the active area (collision guard) | |
| COLLISION_MARGIN_M = 0.002 | |
| SOURCE_KEEPOUT_DZ = (-0.050, 0.050) # source head block (the filter slide moves laterally at beam height): nothing closer than FILTER_CLEAR | |
| DETECTOR_KEEPOUT_DZ = (-0.090, 0.090) # detector housing below / above the beam | |
| CHUCK_R_M, CHUCK_H_M = 0.012, 0.015 # brass chuck below the chuck top | |
| STAGE_R_M, STAGE_H_M = 0.0566, 0.050 # 80 x 80 mm rotation-stage housing and platter below the chuck (circumscribed radius, conservative) | |
| CHAMBER_CEILING_M = 0.640 # inner ceiling height of the enclosure above the bench | |
| PIXEL_PITCH_M = 49.5e-6 # flat-panel pixel pitch (2800 x 49.5 um = 138.6 mm) | |
| CSI_THICKNESS_M = 0.20e-3 # CsI:Tl scintillator | |
| ADU_PER_KEV = 0.8 # conversion gain (energy deposited in the scintillator -> ADU) | |
| READ_NOISE_ADU = 4.0 | |
| DARK_OFFSET_ADU = 100.0 | |
| DARK_CURRENT_ADU_S = 10.0 | |
| FULL_SCALE_ADU = 65535.0 | |
| DETECTOR_PSF_PX = 0.8 # scintillator light spread, sigma in detector pixels | |
| EXPOSURE_RANGE_S = (0.02, 10.0) | |
| AVERAGING_RANGE = (1, 16) | |
| BINNINGS = (1, 2, 4) | |
| FRAME_OVERHEAD_S = 0.03 # read-out per frame | |
| STEP_OVERHEAD_S = 0.20 # rotation step and settle per projection (step and shoot) | |
| ROTATION_SPEED_RAD_S = math.radians(60.0) | |
| CARRIAGE_SPEED_M_S = 0.020 | |
| LIFT_SPEED_M_S = 0.010 | |
| DOOR_TRAVEL_M = 0.400 # the door slides to the left behind the front panel (direction: photo estimate) | |
| DOOR_SPEED_M_S = 0.100 | |
| FILTER_PITCH_M = 0.012 # lateral filter slide pitch between positions (slide moves along -Y at beam height) | |
| FILTER_S_PER_STEP = 0.5 | |
| BOOT_S = 60.0 | |
| FLAT_FIELD_FRAMES = 20 # bright frames (and as many dark frames) of the calibration | |
| AXIS_OFFSET_SD_M = 40.0e-6 # hidden lateral offset of the rotation axis (1 sigma, at the axis) | |
| RECON_RATE_VOXEL_PROJ_S = 5.0e10 # reconstruction throughput of the workstation (voxel x projection per s) | |
| RECON_OVERHEAD_S = 5.0 | |
| SIM_DETECTOR = (175, 150) # simulated detector grid: 16 x 16 native pixels per simulated pixel | |
| SIM_MAX_PROJECTIONS = 200 # simulated projections (evenly spaced subset of the nominal ones, dose-equivalent) | |
| ENERGY_GROUPS = 24 | |
| RECON_GRIDS = (48, 64, 80, 96, 128) | |
| MAX_RECORDS = 60 | |
| MAX_EVENTS = 400 | |
| MAX_SAMPLES = 12 | |
| MAX_PORES = 400 | |
| MAX_CRACKS = 6 | |
| MAX_INCLUSIONS = 12 | |
| FILTERS = [ # position: id, label, layers (library material id, thickness m) | |
| dict(position=0, id='none', label='无滤片', layers=[]), | |
| dict(position=1, id='al_0p25', label='Al 0.25 mm', layers=[('al', 0.25e-3)]), | |
| dict(position=2, id='al_0p5', label='Al 0.5 mm', layers=[('al', 0.5e-3)]), | |
| dict(position=3, id='al_1p0', label='Al 1.0 mm', layers=[('al', 1.0e-3)]), | |
| dict(position=4, id='cu_0p1', label='Cu 0.1 mm', layers=[('cu', 0.1e-3)]), | |
| dict(position=5, id='cu_0p25', label='Cu 0.25 mm', layers=[('cu', 0.25e-3)]), | |
| dict(position=6, id='al_1p0_cu_0p1', label='Al 1.0 mm + Cu 0.1 mm', layers=[('al', 1.0e-3), ('cu', 0.1e-3)]), | |
| ] | |
| LIBRARY_MATERIALS_USED = ['w', 'be', 'al', 'cu', 'nist_air', 'nist_cesium', 'fe', 'nist_pmma'] | |
| KEV = 1.602176634e-16 # J per keV | |
| def filter_of(position): | |
| return FILTERS[position] | |
| # ---------------------------------------------------------------- template library (NIST SRD 126 mass attenuation coefficients) | |
| _LIB = [None] | |
| def library(): | |
| if _LIB[0] is None: | |
| raw = LIBRARY_PATH.read_bytes() | |
| d = json.loads(raw) | |
| d['subs'] = {s['substance_id']: s for s in d['substances']} | |
| d['sha256'] = hashlib.sha256(raw).hexdigest() | |
| _LIB[0] = d | |
| return _LIB[0] | |
| def substance(sid): | |
| s = library()['subs'].get(sid) | |
| if s is None: | |
| raise ActionRejected('UNKNOWN_SUBSTANCE') | |
| return s | |
| def _segments(sid): | |
| """Edge-free segments of a tabulated material: (log E, log mu/rho, log mu_en/rho) per segment (energies in keV, coefficients in m2/kg).""" | |
| s = substance(sid) | |
| e = np.array(s['energy_MeV']) * 1e3 | |
| mu = np.array(s['mu_rho_cm2_g']) * 0.1 | |
| men = np.array(s['mu_en_rho_cm2_g']) * 0.1 | |
| cut = np.where(np.diff(e) <= 0)[0] + 1 | |
| return [(np.log(e[i]), np.log(mu[i]), np.log(men[i]), e[i[0]], e[i[-1]]) for i in np.split(np.arange(len(e)), cut)] | |
| def mass_coefficients(sid, e_kev): | |
| """mu/rho and mu_en/rho (m2/kg) at the photon energies e_kev: log-log interpolation inside the edge-free segment containing each energy | |
| (an energy exactly at an edge takes the value above the edge).""" | |
| e_kev = np.atleast_1d(np.asarray(e_kev, float)) | |
| mu = np.empty_like(e_kev) | |
| men = np.empty_like(e_kev) | |
| segs = _segments(sid) | |
| for k, (le, lm, ln, lo, hi) in enumerate(segs): | |
| last = k == len(segs) - 1 | |
| m = (e_kev >= lo) & ((e_kev < segs[k + 1][3]) if not last else np.ones_like(e_kev, bool)) | |
| if k == 0: | |
| m |= e_kev < lo | |
| if m.any(): | |
| x = np.log(np.clip(e_kev[m], 1e-3, None)) | |
| mu[m] = np.exp(np.interp(x, le, lm)) | |
| men[m] = np.exp(np.interp(x, le, ln)) | |
| return mu, men | |
| def density(sid): | |
| return float(substance(sid)['density_kg_m3']) | |
| def linear_mu(sid, e_kev, rho=None): | |
| """Linear attenuation and energy-absorption coefficients (1/m) of a library material at its tabulated density (or rho).""" | |
| mu, men = mass_coefficients(sid, e_kev) | |
| r = density(sid) if rho is None else rho | |
| return mu * r, men * r | |
| def mixture_mu(parts, e_kev): | |
| """Linear coefficients of a volume mixture [(material id, volume fraction)], each constituent at its tabulated density.""" | |
| mu = np.zeros(np.atleast_1d(e_kev).shape) | |
| men = np.zeros_like(mu) | |
| for sid, f in parts: | |
| a, b = linear_mu(sid, e_kev) | |
| mu += f * a | |
| men += f * b | |
| return mu, men | |
| def mixture_density(parts): | |
| return sum(f * density(sid) for sid, f in parts) | |
| # ---------------------------------------------------------------- source spectrum, filters, detector response | |
| E_GRID_KEV = np.arange(1.0, 100.5, 0.5) # fine grid of the spectrum model | |
| def focal_spot_m(power_w): | |
| return SPOT_AT_4W_M * max(1.0, power_w / 4.0) ** SPOT_GROWTH_EXP | |
| def kanaya_range_m(e0_kev): | |
| """Kanaya-Okayama electron range in tungsten (A = 183.84, Z = 74, rho = 19.3 g/cm3).""" | |
| return 0.0276 * 183.84 * e0_kev ** 1.67 / (74 ** 0.889 * 19.3) * 1e-6 | |
| def emitted_spectrum(kv_v): | |
| """Photon energy spectrum emitted per electron per steradian at the anode, after the tungsten self-absorption of the reflection target, | |
| before the window: (E keV grid, photons / (sr keV electron)). Kramers intensity I(E) ~ Z (E0 - E) normalised so that the energy emitted | |
| into 4 pi equals eta V with eta = K Z V (V in volts); characteristic W K and L lines added as fractions of the emitted energy.""" | |
| e0 = kv_v / 1e3 | |
| e = E_GRID_KEV[E_GRID_KEV < e0] | |
| de = 0.5 | |
| intensity = np.clip(e0 - e, 0.0, None) # energy per keV (arbitrary units) | |
| eta = KRAMERS_K_PER_V * 74 * kv_v | |
| energy_per_electron_j = eta * kv_v * 1.602176634e-19 # emitted X-ray energy per electron (J) | |
| brems_frac = 1.0 | |
| lines = [] | |
| if e0 > W_K_EDGE_KEV: | |
| fk = K_LINE_FRACTION_100KV * ((e0 / W_K_EDGE_KEV - 1) / (100.0 / W_K_EDGE_KEV - 1)) ** 1.63 | |
| lines += [(E, fk * w) for E, w in W_K_LINES_KEV] | |
| brems_frac -= fk | |
| if e0 > W_L3_EDGE_KEV: | |
| fl = L_LINE_FRACTION_50KV * ((e0 / W_L3_EDGE_KEV - 1) / (50.0 / W_L3_EDGE_KEV - 1)) ** 1.63 | |
| fl = min(fl, 0.08) | |
| inc = [(E, fl * w) for E, w in W_L_LINES_KEV if E < e0] # a line above the tube voltage is not excited | |
| lines += inc | |
| brems_frac -= sum(f for _, f in inc) | |
| photons = np.zeros_like(e) | |
| ib = intensity * de | |
| photons += ib / ib.sum() * brems_frac * energy_per_electron_j / (e * KEV) # bremsstrahlung photons per bin | |
| for E, f in lines: | |
| j = int(np.argmin(np.abs(e - E))) | |
| photons[j] += f * energy_per_electron_j / (e[j] * KEV) # line in its 0.5 keV bin: energy kept exact | |
| photons /= (4 * math.pi) * de # per steradian and keV | |
| depth = kanaya_range_m(e0) / 3.0 / math.sin(TAKEOFF_RAD) # mean emission depth along the exit path | |
| mu_w, _ = linear_mu('w', e) | |
| return e, photons * np.exp(-mu_w * depth) | |
| def unabsorbed_spectrum(kv_v): | |
| """Same spectrum without the target self-absorption (for the energy ledger).""" | |
| e0 = kv_v / 1e3 | |
| e, ph = emitted_spectrum(kv_v) | |
| depth = kanaya_range_m(e0) / 3.0 / math.sin(TAKEOFF_RAD) | |
| mu_w, _ = linear_mu('w', e) | |
| return e, ph * np.exp(mu_w * depth) | |
| def beam_spectrum(kv_v, filter_position): | |
| """Photons / (sr keV electron) behind the beryllium window and the selected filter, before the air path.""" | |
| e, ph = emitted_spectrum(kv_v) | |
| mu_be, _ = linear_mu('be', e) | |
| t = np.exp(-mu_be * BE_WINDOW_M) | |
| for sid, th in filter_of(filter_position)['layers']: | |
| mu, _ = linear_mu(sid, e) | |
| t = t * np.exp(-mu * th) | |
| return e, ph * t | |
| def air_transmission(e_kev, length_m): | |
| mu, _ = linear_mu('nist_air', e_kev) | |
| return np.exp(-mu * length_m) | |
| def detector_response(e_key): | |
| """Per incident photon of energy E: probability of interaction in the CsI layer and the mean energy deposited (keV) = E (1 - e^-mu t) | |
| mu_en / mu (the local-deposition share of the interaction; fluorescence and Compton escape leave).""" | |
| e = np.array(e_key) | |
| mu, men = linear_mu('nist_cesium', e) | |
| p = 1.0 - np.exp(-mu * CSI_THICKNESS_M) | |
| return p, e * p * men / mu | |
| def energy_groups(e, w, edges_kev=(), n=ENERGY_GROUPS): | |
| """Group the fine spectrum into n groups of equal weight (weight w = detected energy per bin), forcing boundaries at the given edges; | |
| returns (group index per bin, group count).""" | |
| c = np.cumsum(w) | |
| c = c / c[-1] if c[-1] > 0 else np.linspace(0, 1, len(w)) | |
| b = set(np.searchsorted(c, np.linspace(0, 1, n + 1)[1:-1]).tolist()) | |
| for ed in edges_kev: | |
| j = int(np.searchsorted(e, ed)) | |
| if 0 < j < len(e): | |
| b.add(j) | |
| b = sorted(x for x in b if 0 < x < len(e)) | |
| idx = np.zeros(len(e), int) | |
| for k, j in enumerate(b): | |
| idx[j:] = k + 1 | |
| return idx, len(b) + 1 | |
| # ---------------------------------------------------------------- sample phantoms (sample frame: origin at the bottom centre of the sample | |
| # body on its own axis, +Z up; a mounting pin stands below it on the chuck) | |
| SAMPLE_KINDS = ['cylinder', 'calibration_phantom', 'edge_phantom'] | |
| CAL_BALLS = 8 # steel balls of the geometry calibration phantom (helix in a PMMA cylinder) | |
| CAL_BALL_RADIUS_M = 0.5e-3 | |
| EDGE_THICKNESS_M = 0.2e-3 # tungsten plate of the edge phantom (beam along its thickness at angle 0) | |
| def _layer_bounds(s): | |
| z = [0.0] | |
| for L in s['layers']: | |
| z.append(z[-1] + L['thickness_m']) | |
| return z | |
| def _materials(s): | |
| """All library materials of a sample (matrix constituents, inclusions, container, pin, phantom materials).""" | |
| ids = [] | |
| if s['kind'] == 'cylinder': | |
| for L in s['layers']: | |
| ids += [m['substance_id'] for m in L['materials']] | |
| ids += [i['substance_id'] for i in s['inclusions']] | |
| elif s['kind'] == 'calibration_phantom': | |
| ids += ['nist_pmma', 'fe'] | |
| else: | |
| ids += ['w'] | |
| if s['container']: | |
| ids.append(s['container']['substance_id']) | |
| if s['pin']: | |
| ids.append(s['pin']['substance_id']) | |
| return list(dict.fromkeys(ids)) | |
| def generate_pores(s): | |
| """Deterministic non-overlapping spherical pores (log-normal radii) fully inside the given layer of a cylinder sample; raises | |
| INVALID_SAMPLE when they cannot be placed.""" | |
| p = s['pores'] | |
| if s['kind'] != 'cylinder' or p['count'] == 0: | |
| return [] | |
| zb = _layer_bounds(s) | |
| lay = p['layer'] | |
| if lay >= len(s['layers']): | |
| raise ActionRejected('INVALID_SAMPLE') | |
| z0, z1 = zb[lay], zb[lay + 1] | |
| R = s['diameter_m'] / 2 | |
| rng = np.random.default_rng(int(hashlib.sha256(f"{s['sample_id']}|{p['seed']}".encode()).hexdigest()[:12], 16)) | |
| radii = np.sort(p['median_radius_m'] * np.exp(p['sigma_ln'] * rng.standard_normal(p['count'])))[::-1] | |
| out = [] | |
| for r in radii: | |
| if 2 * r >= min(R, (z1 - z0) / 2): | |
| raise ActionRejected('INVALID_SAMPLE') | |
| for _ in range(4000): | |
| rho = (R - r - 1e-6) * math.sqrt(rng.random()) | |
| ph = 2 * math.pi * rng.random() | |
| c = np.array([rho * math.cos(ph), rho * math.sin(ph), z0 + r + 1e-6 + (z1 - z0 - 2 * r - 2e-6) * rng.random()]) | |
| if all(np.linalg.norm(c - q[0]) > r + q[1] + 1e-6 for q in out) and not _hits_inclusion(s, c, r): | |
| out.append((c, float(r))) | |
| break | |
| else: | |
| raise ActionRejected('INVALID_SAMPLE') # too dense for non-overlapping pores | |
| return [dict(center_m=[float(v) for v in c], radius_m=r) for c, r in out] | |
| def _hits_inclusion(s, c, r): | |
| return any(np.linalg.norm(c - np.array(i['center_m'])) < r + i['radius_m'] + 1e-6 for i in s['inclusions']) | |
| def calibration_balls(s): | |
| """Steel balls of the geometry phantom on a helix (radius 0.35 D, one turn over 0.8 H).""" | |
| R, H = s['diameter_m'] / 2, s['height_m'] | |
| return [dict(center_m=[0.35 * 2 * R * math.cos(2 * math.pi * k / CAL_BALLS), 0.35 * 2 * R * math.sin(2 * math.pi * k / CAL_BALLS), | |
| 0.1 * H + 0.8 * H * k / (CAL_BALLS - 1)], radius_m=CAL_BALL_RADIUS_M) for k in range(CAL_BALLS)] | |
| def sample_truth(s): | |
| """Exact geometric truth of a phantom: volumes per material, porosity per layer and of the whole body, pores and cracks.""" | |
| R = s['diameter_m'] / 2 | |
| zb = _layer_bounds(s) if s['kind'] == 'cylinder' else [0.0, s['height_m']] | |
| body = math.pi * R * R * s['height_m'] if s['kind'] != 'edge_phantom' else s['diameter_m'] * EDGE_THICKNESS_M * s['height_m'] | |
| pores = s.get('_pores', []) | |
| pv = sum(4 / 3 * math.pi * p['radius_m'] ** 3 for p in pores) | |
| cv = sum(math.pi * c['radius_m'] ** 2 * c['aperture_m'] for c in s['cracks']) if s['kind'] == 'cylinder' else 0.0 | |
| iv = sum(4 / 3 * math.pi * i['radius_m'] ** 3 for i in s['inclusions']) if s['kind'] == 'cylinder' else 0.0 | |
| layers = [] | |
| if s['kind'] == 'cylinder': | |
| for k in range(len(s['layers'])): | |
| v = math.pi * R * R * (zb[k + 1] - zb[k]) | |
| pk = sum(4 / 3 * math.pi * p['radius_m'] ** 3 for p in pores if zb[k] <= p['center_m'][2] < zb[k + 1]) | |
| ck = sum(math.pi * c['radius_m'] ** 2 * c['aperture_m'] for c in s['cracks'] if zb[k] <= c['center_m'][2] < zb[k + 1]) | |
| layers.append(dict(layer=k, volume_m3=v, pore_volume_m3=pk, crack_volume_m3=ck, porosity=(pk + ck) / v)) | |
| return dict(body_volume_m3=body, pore_volume_m3=pv, crack_volume_m3=cv, inclusion_volume_m3=iv, porosity=(pv + cv) / body if body else 0.0, | |
| pore_count=len(pores), pore_equivalent_diameters_m=sorted(2 * p['radius_m'] for p in pores), | |
| cracks=[dict(area_m2=math.pi * c['radius_m'] ** 2, aperture_m=c['aperture_m'], radius_m=c['radius_m'], normal=list(c['normal']), | |
| center_m=list(c['center_m'])) for c in s['cracks']], layers=layers) | |
| def sample_height_total(s): | |
| return s['height_m'] + (s['pin']['length_m'] if s['pin'] else 0.0) | |
| def sample_radius_total(s): | |
| """Radius of the rotation envelope about the sample axis (container included).""" | |
| if s['kind'] == 'edge_phantom': | |
| return math.hypot(s['diameter_m'], EDGE_THICKNESS_M / 2) | |
| return s['diameter_m'] / 2 + (s['container']['wall_m'] if s['container'] else 0.0) | |
| def sample_mass_kg(s): | |
| """Mass of the sample body, consistent with the ray-traced geometry: layer matrices minus pores, cracks and inclusions, plus the | |
| inclusions at their own densities (container and pin are not part of the sample).""" | |
| R = s['diameter_m'] / 2 | |
| m = 0.0 | |
| if s['kind'] == 'cylinder': | |
| zb = _layer_bounds(s) | |
| rho = [mixture_density([(x['substance_id'], x['volume_fraction']) for x in L['materials']]) for L in s['layers']] | |
| def layer_of(z): | |
| return next((k for k in range(len(s['layers'])) if zb[k] <= z < zb[k + 1]), len(s['layers']) - 1) | |
| for k in range(len(s['layers'])): | |
| m += math.pi * R * R * (zb[k + 1] - zb[k]) * rho[k] | |
| for p in s.get('_pores', []): | |
| m -= 4 / 3 * math.pi * p['radius_m'] ** 3 * rho[s['pores']['layer']] | |
| for c in s['cracks']: | |
| m -= math.pi * c['radius_m'] ** 2 * c['aperture_m'] * rho[layer_of(c['center_m'][2])] | |
| for i in s['inclusions']: | |
| m += 4 / 3 * math.pi * i['radius_m'] ** 3 * (density(i['substance_id']) - rho[layer_of(i['center_m'][2])]) | |
| elif s['kind'] == 'calibration_phantom': | |
| m = math.pi * R * R * s['height_m'] * density('nist_pmma') + CAL_BALLS * 4 / 3 * math.pi * CAL_BALL_RADIUS_M ** 3 * (density('fe') - density('nist_pmma')) | |
| else: | |
| m = s['diameter_m'] * EDGE_THICKNESS_M * s['height_m'] * density('w') | |
| return m | |
| # ---------------------------------------------------------------- ray tracing (rays from the focal spot; lab frame: +X along the beam, +Y | |
| # across (asset +Y), +Z up, origin at the focal spot) | |
| def _slab(S, D, lo, hi, axis): | |
| """Parameter interval of the rays inside lo <= x_axis <= hi.""" | |
| d = D[:, axis] | |
| s = S[axis] if S.ndim == 1 else S[:, axis] | |
| with np.errstate(divide='ignore', invalid='ignore'): | |
| t1 = (lo - s) / d | |
| t2 = (hi - s) / d | |
| tl = np.where(np.abs(d) < 1e-15, np.where((s >= lo) & (s <= hi), -np.inf, np.inf), np.minimum(t1, t2)) | |
| th = np.where(np.abs(d) < 1e-15, np.where((s >= lo) & (s <= hi), np.inf, -np.inf), np.maximum(t1, t2)) | |
| return tl, th | |
| def _cyl(S, D, R, cx=0.0, cy=0.0): | |
| """Parameter interval of the rays inside the infinite vertical cylinder of radius R about (cx, cy).""" | |
| sx, sy = S[0] - cx, S[1] - cy | |
| a = D[:, 0] ** 2 + D[:, 1] ** 2 | |
| b = 2 * (sx * D[:, 0] + sy * D[:, 1]) | |
| c = sx * sx + sy * sy - R * R | |
| disc = b * b - 4 * a * c | |
| ok = (disc > 0) & (a > 1e-30) | |
| sq = np.sqrt(np.where(ok, disc, 0.0)) | |
| with np.errstate(divide='ignore', invalid='ignore'): | |
| t1 = np.where(ok, (-b - sq) / (2 * a), np.inf) | |
| t2 = np.where(ok, (-b + sq) / (2 * a), -np.inf) | |
| return t1, t2 | |
| def _len(tl, th): | |
| return np.clip(th - tl, 0.0, None) | |
| def _add(out, sid, L): | |
| out[sid] = out[sid] + L if sid in out else L.copy() | |
| def body_paths(s, S, D): | |
| """Path lengths (m) of unit-direction rays S + t D (sample frame; S one point, D (n, 3)) through the materials of the sample body | |
| (layer matrices, pores, cracks, inclusions; phantom materials): {material id: array(n)}.""" | |
| n = D.shape[0] | |
| out = {} | |
| R = s['diameter_m'] / 2 | |
| if s['kind'] == 'edge_phantom': | |
| tl = np.full(n, -np.inf); th = np.full(n, np.inf) | |
| for ax, lo, hi in ((0, -EDGE_THICKNESS_M / 2, EDGE_THICKNESS_M / 2), (1, 0.0, s['diameter_m']), (2, 0.0, s['height_m'])): | |
| a, b = _slab(S, D, lo, hi, ax) | |
| tl, th = np.maximum(tl, a), np.minimum(th, b) | |
| _add(out, 'w', _len(tl, th)) | |
| return out | |
| c1, c2 = _cyl(S, D, R) | |
| if s['kind'] == 'calibration_phantom': | |
| zl, zh = _slab(S, D, 0.0, s['height_m'], 2) | |
| body = _len(np.maximum(c1, zl), np.minimum(c2, zh)) | |
| balls = sum_spheres(S, D, calibration_balls(s)) | |
| _add(out, 'nist_pmma', np.clip(body - balls, 0.0, None)) | |
| _add(out, 'fe', balls) | |
| return out | |
| zb = _layer_bounds(s) | |
| lay_pores = {} | |
| for p in s.get('_pores', []): | |
| lay_pores.setdefault(s['pores']['layer'], []).append(p) | |
| for k, L in enumerate(s['layers']): | |
| zl, zh = _slab(S, D, zb[k], zb[k + 1], 2) | |
| chord = _len(np.maximum(c1, zl), np.minimum(c2, zh)) | |
| if not chord.any(): | |
| continue | |
| void = sum_spheres(S, D, lay_pores.get(k, [])) | |
| inc_paths = {} | |
| for i in [i for i in s['inclusions'] if zb[k] <= i['center_m'][2] < zb[k + 1]]: | |
| inc_paths.setdefault(i['substance_id'], np.zeros(n)) | |
| inc_paths[i['substance_id']] += sum_spheres(S, D, [i]) | |
| crack = np.zeros(n) | |
| for c in s['cracks']: | |
| if zb[k] <= c['center_m'][2] < zb[k + 1]: | |
| crack += disc_path(S, D, c) | |
| matrix = np.clip(chord - void - crack - sum(inc_paths.values(), np.zeros(n)), 0.0, None) | |
| for m in L['materials']: | |
| _add(out, m['substance_id'], matrix * m['volume_fraction']) | |
| for sid, v in inc_paths.items(): | |
| _add(out, sid, v) | |
| return out | |
| def container_walls(s, S, D): | |
| """Path lengths through the container wall (open coaxial tube over the body height) before and after the inside of the tube along each | |
| ray: ({material: near}, {material: far}); a ray that misses the inside has all of its wall path in 'near'. A ray leaving the inside | |
| through the open top or bottom has no far part.""" | |
| if not s['container'] or s['kind'] == 'edge_phantom': | |
| return {}, {} | |
| R = s['diameter_m'] / 2 | |
| zl, zh = _slab(S, D, 0.0, s['height_m'], 2) | |
| o1, o2 = _cyl(S, D, R + s['container']['wall_m']) | |
| c1, c2 = _cyl(S, D, R) | |
| ol, oh = np.maximum(o1, zl), np.minimum(o2, zh) | |
| il, ih = np.maximum(c1, zl), np.minimum(c2, zh) | |
| inside = ih > il | |
| with np.errstate(invalid='ignore'): # rays missing a cylinder carry +-inf parameters | |
| near = np.where(inside, np.clip(il - ol, 0.0, None), _len(ol, oh)) | |
| far = np.where(inside, np.clip(oh - ih, 0.0, None), 0.0) | |
| near, far = np.where(np.isfinite(near), near, 0.0), np.where(np.isfinite(far), far, 0.0) | |
| sid = s['container']['substance_id'] | |
| return {sid: near}, {sid: far} | |
| def container_paths(s, S, D): | |
| """Path lengths through the container wall around the body (coaxial tube over the body height).""" | |
| near, far = container_walls(s, S, D) | |
| return {sid: near[sid] + far[sid] for sid in near} | |
| def pin_paths(s, S, D): | |
| """Path lengths through the mounting pin below the body.""" | |
| out = {} | |
| if s['pin']: | |
| zl, zh = _slab(S, D, -s['pin']['length_m'], 0.0, 2) | |
| p1, p2 = _cyl(S, D, s['pin']['diameter_m'] / 2) | |
| _add(out, s['pin']['substance_id'], _len(np.maximum(p1, zl), np.minimum(p2, zh))) | |
| return out | |
| def holder_paths(s, S, D): | |
| """Path lengths through the sample holder: the container around the body and the mounting pin below it.""" | |
| out = container_paths(s, S, D) | |
| for sid, L in pin_paths(s, S, D).items(): | |
| _add(out, sid, L) | |
| return out | |
| HARDWARE_MATERIALS = ('cu', 'al') # brass chuck (modelled as copper) and the aluminium rotation-stage housing with its platter | |
| STAGE_HOUSING_R_M = 0.0451 # 80 x 80 mm housing as the area-equivalent cylinder (it does not turn with the platter) | |
| def hardware_paths(S, D, ax, ay, z_top): | |
| """Path lengths through the stage hardware below the sample (sample frame): the chuck (r 12 mm, 15 mm high, modelled as copper) whose top | |
| is at z_top on the rotation axis (ax, ay), and below it the rotation-stage housing with the platter (aluminium, 50 mm high).""" | |
| out = {} | |
| for sid, r, z0, z1 in (('cu', CHUCK_R_M, z_top - CHUCK_H_M, z_top), ('al', STAGE_HOUSING_R_M, z_top - CHUCK_H_M - STAGE_H_M, z_top - CHUCK_H_M)): | |
| zl, zh = _slab(S, D, z0, z1, 2) | |
| c1, c2 = _cyl(S, D, r, ax, ay) | |
| L = _len(np.maximum(c1, zl), np.minimum(c2, zh)) | |
| if L.any(): | |
| _add(out, sid, L) | |
| return out | |
| def sample_paths(s, S, D): | |
| """Path lengths through every material of the sample body and its holder: {material id: array(n)}.""" | |
| out = body_paths(s, S, D) | |
| for sid, L in holder_paths(s, S, D).items(): | |
| _add(out, sid, L) | |
| return out | |
| def sum_spheres(S, D, spheres): | |
| """Sum of the chord lengths of the rays through the given spheres (exact; only rays within the sphere's angular footprint evaluated).""" | |
| n = D.shape[0] | |
| tot = np.zeros(n) | |
| if not spheres: | |
| return tot | |
| if n * len(spheres) <= 2_000_000: # small ray sets (energy ledger): all spheres at once, same formula | |
| C = np.array([sp['center_m'] for sp in spheres], float) | |
| r = np.array([sp['radius_m'] for sp in spheres], float) | |
| v = C - S | |
| dist = np.linalg.norm(v, axis=1) | |
| ok = dist > r | |
| if not ok.any(): | |
| return tot | |
| v, dist, r = v[ok], dist[ok], r[ok] | |
| cosmax = np.sqrt(np.clip(1 - (r / dist) ** 2, 0.0, None)) | |
| tc = D @ v.T # (rays, spheres) | |
| inside = tc / dist > cosmax - 1e-12 | |
| chord = 2 * np.sqrt(np.clip(r * r - (dist * dist - tc * tc), 0.0, None)) | |
| return (chord * inside).sum(1) | |
| for sp in spheres: | |
| C = np.asarray(sp['center_m'], float) | |
| r = sp['radius_m'] | |
| v = C - S | |
| dist = np.linalg.norm(v) | |
| if dist <= r: | |
| continue | |
| cosmax = math.sqrt(max(0.0, 1 - (r / dist) ** 2)) | |
| cand = np.where(D @ (v / dist) > cosmax - 1e-12)[0] | |
| if not len(cand): | |
| continue | |
| tc = D[cand] @ v | |
| d2 = dist * dist - tc * tc | |
| tot[cand] += 2 * np.sqrt(np.clip(r * r - d2, 0.0, None)) | |
| return tot | |
| def disc_path(S, D, c): | |
| """Path of the rays through a planar crack (disc of radius R and aperture a): a / |n.d| where the ray crosses the disc, at most 2 R.""" | |
| nrm = np.asarray(c['normal'], float) | |
| nrm = nrm / np.linalg.norm(nrm) | |
| C = np.asarray(c['center_m'], float) | |
| nd = D @ nrm | |
| with np.errstate(divide='ignore', invalid='ignore'): | |
| t = ((C - S) @ nrm) / nd | |
| P = S + t[:, None] * D | |
| inside = (np.abs(nd) > 1e-9) & (np.einsum('ij,ij->i', P - C, P - C) <= c['radius_m'] ** 2) | |
| return np.where(inside, np.minimum(c['aperture_m'] / np.maximum(np.abs(nd), 1e-12), 2 * c['radius_m']), 0.0) | |
| # ---------------------------------------------------------------- capabilities and state slots | |
| CAPS = {} | |
| def cap(k, s, o, e, c, meaning, visibility='agent', kind='device_command'): | |
| CAPS[k] = dict(input_schema=s, output_schema=o, example_arguments=e, component_ids=c, function_zh=meaning, visibility=visibility, kind=kind) | |
| SAMPLE_ID = dict(type='string', minLength=1, maxLength=40, pattern='^[A-Za-z0-9_.-]+$') | |
| SUB_ID = dict(type='string', minLength=1, maxLength=40) | |
| XYZ = array(number('m', -0.2, 0.2), 3, 3) | |
| FAULTS = ['xray_arc', 'detector_defects', 'rotation_stall', 'door_sensor', 'light_curtain_blocked'] | |
| FAULT_ERROR = {'xray_arc': 'XRAY_ARC', 'rotation_stall': 'STAGE_FAULT', 'door_sensor': 'INTERLOCK_FAULT'} | |
| PLANT_EXAMPLE = dict(room_k=295.15, mains_voltage_v=230.0, relative_humidity=0.45, noise_seed=1) | |
| PLANT = obj(dict(room_k=number('K', 283.15, 308.15), mains_voltage_v=number('V', 0.0, 264.0), relative_humidity=number('1', 0.0, 1.0), noise_seed=INT)) | |
| MIX = array(obj(dict(substance_id=SUB_ID, volume_fraction=number('1', 0.0, 1.0))), 1, 4) | |
| LAYER = obj(dict(thickness_m=number('m', 1.0e-5, SAMPLE_MAX_HEIGHT_M), materials=MIX)) | |
| PORES = obj(dict(count=integer(0, MAX_PORES), median_radius_m=number('m', 1.0e-6, 0.01), sigma_ln=number('1', 0.0, 1.5), layer=integer(0, 5), seed=INT)) | |
| CRACK = obj(dict(center_m=XYZ, normal=array(number('1', -1.0, 1.0), 3, 3), radius_m=number('m', 1.0e-4, 0.05), aperture_m=number('m', 1.0e-6, 1.0e-3))) | |
| INCLUSION = obj(dict(substance_id=SUB_ID, center_m=XYZ, radius_m=number('m', 1.0e-6, 0.02))) | |
| CONTAINER = nullable(obj(dict(substance_id=SUB_ID, wall_m=number('m', 1.0e-5, 5.0e-3)))) | |
| PIN = nullable(obj(dict(substance_id=SUB_ID, diameter_m=number('m', 5.0e-4, 0.02), length_m=number('m', 1.0e-3, 0.1)))) | |
| SAMPLE = obj(dict(sample_id=SAMPLE_ID, kind=enum(SAMPLE_KINDS), diameter_m=number('m', 5.0e-4, SAMPLE_MAX_DIAMETER_M), | |
| height_m=number('m', 5.0e-4, SAMPLE_MAX_HEIGHT_M), layers=array(LAYER, 0, 6), pores=PORES, cracks=array(CRACK, 0, MAX_CRACKS), | |
| inclusions=array(INCLUSION, 0, MAX_INCLUSIONS), container=CONTAINER, pin=PIN)) | |
| SAMPLE_EXAMPLE = dict(sample_id='alumina_pellet', kind='cylinder', diameter_m=0.006, height_m=0.006, | |
| layers=[dict(thickness_m=0.006, materials=[dict(substance_id='alumina', volume_fraction=1.0)])], | |
| pores=dict(count=120, median_radius_m=0.12e-3, sigma_ln=0.35, layer=0, seed=7), | |
| cracks=[dict(center_m=[0.0, 0.0, 0.003], normal=[1.0, 0.0, 0.0], radius_m=0.0018, aperture_m=30e-6)], inclusions=[], container=None, | |
| pin=dict(substance_id='al', diameter_m=0.003, length_m=0.035)) | |
| OPERATION = obj(dict(operation_id=TEXT)) | |
| STATUS = enum(['running', 'completed', 'failed', 'cancelled']) | |
| RANGES = ['180', '360'] | |
| SCAN = obj(dict(range_deg=enum(RANGES), step_rad=number('rad', math.radians(0.05), math.radians(2.0)), exposure_s=number('s', EXPOSURE_RANGE_S[0], EXPOSURE_RANGE_S[1]), | |
| averaging=integer(AVERAGING_RANGE[0], AVERAGING_RANGE[1]), binning=enum(['1x1', '2x2', '4x4']), random_movement=BOOL)) | |
| SCAN_EXAMPLE = dict(range_deg='180', step_rad=math.radians(0.4), exposure_s=0.3, averaging=2, binning='2x2', random_movement=True) | |
| FILTER_NAMES = ['none', 'hann', 'shepp_logan', 'ram_lak'] | |
| VOI = nullable(obj(dict(center_m=XYZ, size_m=array(number('m', 1.0e-4, 0.2), 3, 3)))) | |
| RECON = obj(dict(record_id=TEXT, grid=enum([str(g) for g in RECON_GRIDS]), filter=enum(FILTER_NAMES[1:]), beam_hardening=number('1', 0.0, 1.0), | |
| bh_material=nullable(SUB_ID), ring_correction=number('1', 0.0, 1.0), smoothing_vox=number('1', 0.0, 3.0), post_alignment=nullable(number('m', -0.005, 0.005)), | |
| auto_alignment=BOOL, voi=VOI)) | |
| RECON_EXAMPLE = dict(record_id='PJ0001', grid='80', filter='shepp_logan', beam_hardening=0.5, bh_material='alumina', ring_correction=0.5, smoothing_vox=0.0, | |
| post_alignment=None, auto_alignment=True, voi=None) | |
| PREVIEW = array(array(nullable(number('1')), 1, 128), 1, 128) | |
| XSET = obj(dict(voltage_v=number('V'), current_a=number('A'), power_w=number('W'), filter=TEXT, focal_spot_m=number('m'))) | |
| RECORD = obj(dict(record_id=TEXT, kind=enum(['flat_field', 'geometry_calibration', 'radiograph', 'projections', 'volume']), status=STATUS, started_s=number('s'), | |
| finished_s=nullable(number('s')), reason=nullable(TEXT), sample_id=nullable(TEXT), xray=nullable(XSET), scan=nullable(SCAN), | |
| sod_m=nullable(number('m')), sdd_m=number('m'), magnification=nullable(number('1')), voxel_size_nominal_m=nullable(number('m')), | |
| projections_nominal=INT, projections_simulated=INT, sim_detector=array(INT, 2, 2), sim_pixel_m=nullable(number('m')), transmission=nullable(obj(dict(min=number('1'), mean=number('1'), | |
| max=number('1')))), | |
| saturated_fraction=nullable(number('1', 0.0, 1.0)), dose_gy=nullable(number('Gy')), duration_s=number('s'), preview=nullable(PREVIEW), | |
| preview_unit=nullable(TEXT), source_record_id=nullable(TEXT), recon=nullable(obj({k: v for k, v in RECON['properties'].items() if k != 'record_id'})), | |
| volume=nullable(obj(dict(shape=array(INT, 3, 3), voxel_m=number('m'), origin_m=XYZ, mu_min_1_m=number('1/m'), mu_max_1_m=number('1/m'), | |
| histogram=array(INT, 0, 128), histogram_edges_1_m=array(number('1/m'), 0, 129), axis_offset_used_m=number('m')))), | |
| flat_field=nullable(obj(dict(frames=INT, mean_bright_adu=number('1'), dark_adu=number('1'), key=TEXT))), | |
| geometry=nullable(obj(dict(axis_offset_m=number('m'), residual_m=number('m'), balls=INT))), warnings=array(TEXT, 0, 16), | |
| template_source=obj(dict(library=TEXT, substances=array(TEXT, 0, 32))), note_zh=TEXT)) | |
| EVENT = obj(dict(time_s=number('s'), kind=enum(['power', 'door', 'xray', 'stage', 'filter', 'measurement', 'calibration', 'sample', 'error', 'fault', 'safety']), | |
| code=TEXT, message_zh=TEXT)) | |
| LEDGER_KEYS = ['xray_on_s', 'electrical_energy_j', 'xray_emitted_j', 'target_absorbed_j', 'window_absorbed_j', 'filter_absorbed_j', 'air_absorbed_j', | |
| 'sample_absorbed_j', 'holder_absorbed_j', 'sample_scattered_j', 'detector_absorbed_j', 'detector_passed_j', 'shielding_j', 'energy_residual_j', | |
| 'sample_dose_gy', | |
| 'projections', 'frames', 'rotation_rad', 'carriage_travel_m', 'lift_travel_m', 'door_cycles'] | |
| LEDGER = obj({k: number('J' if k.endswith('_j') else 's' if k.endswith('_s') else 'm' if k.endswith('_m') else 'rad' if k.endswith('_rad') else 'Gy' if k.endswith('_gy') | |
| else '1') for k in LEDGER_KEYS}) | |
| REGION = nullable(obj(dict(center_m=XYZ, radius_m=number('m', 1.0e-4, 0.06), z_min_m=number('m', -0.2, 0.2), z_max_m=number('m', -0.2, 0.2)))) | |
| POROSITY_OUT = obj(dict(record_id=TEXT, threshold_1_m=number('1/m'), method=TEXT, envelope_voxels=INT, pore_voxels=INT, porosity=number('1', 0.0, 1.0), | |
| open_porosity=number('1', 0.0, 1.0), closed_porosity=number('1', 0.0, 1.0), pore_count=INT, | |
| equivalent_diameter_m=obj(dict(mean=nullable(number('m')), d10=nullable(number('m')), d50=nullable(number('m')), d90=nullable(number('m')), | |
| max=nullable(number('m')))), voxel_m=number('m'), note_zh=TEXT)) | |
| CRACK_OUT = obj(dict(record_id=TEXT, threshold_1_m=number('1/m'), cracks=array(obj(dict(area_m2=number('m2'), aperture_m=number('m'), length_m=number('m'), | |
| normal=array(number('1'), 3, 3), center_m=XYZ, voxels=INT)), 0, 32), | |
| crack_count=INT, total_area_m2=number('m2'), note_zh=TEXT)) | |
| cap('plant.configure', PLANT, obj(dict(plant=PLANT)), PLANT_EXAMPLE, ['enclosure_base'], '宿主声明实验室条件(室温、电源电压、相对湿度、噪声种子)', 'evaluator', 'configuration') | |
| cap('sample.provide', SAMPLE, obj(dict(sample_id=TEXT, location=TEXT, mass_kg=number('kg'))), SAMPLE_EXAMPLE, ['sample_chuck'], | |
| '宿主在实验台上提供一个样品(圆柱体分层材料/体积混合物、球形孔、平面裂纹、夹杂、样品管、样品针;几何标定体模;钨刃边体模;材料来自X射线衰减模板库)', 'evaluator', | |
| 'configuration') | |
| cap('sample.place', obj(dict(sample_id=SAMPLE_ID, offset_x_m=number('m', -0.005, 0.005), offset_y_m=number('m', -0.005, 0.005))), | |
| obj(dict(sample_id=TEXT, offset_x_m=number('m'), offset_y_m=number('m'))), dict(sample_id='alumina_pellet', offset_x_m=0.0, offset_y_m=0.0), | |
| ['sample_chuck', 'sample_turntable', 'door_glass'], '门打开时把实验台上的样品装到旋转台样品夹上(宿主/机器人抽象;样品轴相对旋转轴的偏移)', 'agent', 'robot_skill') | |
| cap('sample.remove', obj(dict(sample_id=SAMPLE_ID)), obj(dict(sample_id=TEXT)), dict(sample_id='alumina_pellet'), ['sample_chuck', 'door_glass'], | |
| '门打开时把样品从样品夹取回实验台(宿主/机器人抽象)', 'agent', 'robot_skill') | |
| cap('power.set', obj(dict(enabled=BOOL)), obj(dict(enabled=BOOL, state=TEXT)), dict(enabled=True), ['button_mains', 'enclosure_base'], | |
| '系统电源(上电后60 s启动;各轴为绝对位置,保持断电时的位置,不回原点)') | |
| cap('power.press_button', obj({}), obj(dict(enabled=BOOL, state=TEXT)), {}, ['button_mains', 'enclosure_base'], | |
| '按右侧电源开关(按一次切换通断;与power.set同一上电/断电过程)') | |
| cap('emergency.stop', obj({}), obj(dict(stopped=BOOL)), {}, ['button_emergency_stop'], '按下正面红色安全按钮:立即关闭X射线、停止所有运动与门,锁存直到释放并确认') | |
| cap('emergency.release', obj({}), obj(dict(stopped=BOOL)), {}, ['button_emergency_stop'], '旋转释放安全按钮(之后用system.acknowledge确认错误)') | |
| cap('system.acknowledge', obj({}), obj(dict(cleared=nullable(TEXT))), {}, ['touchscreen'], '确认已排除原因的锁存错误') | |
| cap('fault.inject', obj(dict(fault=enum(FAULTS), active=BOOL)), obj(dict(faults=array(TEXT, 0, 8))), dict(fault='xray_arc', active=True), ['enclosure_base'], | |
| '注入或清除故障(评测者):X射线管打火、探测器坏列、旋转台卡滞、门联锁传感器故障、安全光幕被挡', 'evaluator', 'configuration') | |
| cap('door.open', obj({}), obj(dict(target_m=number('m'), duration_s=number('s'))), {}, ['door_glass'], '打开电动铅玻璃门(X射线开启时门锁住)') | |
| cap('door.close', obj({}), obj(dict(target_m=number('m'), duration_s=number('s'))), {}, ['door_glass'], '关闭电动铅玻璃门(安全光幕被挡时停止并重新打开)') | |
| cap('xray.set', obj(dict(voltage_v=number('V', XRAY_KV_MIN_V, XRAY_KV_MAX_V), current_a=number('A', 1.0e-6, XRAY_CURRENT_MAX_A))), | |
| obj(dict(voltage_v=number('V'), current_a=number('A'), power_w=number('W'), focal_spot_m=number('m'))), dict(voltage_v=60.0e3, current_a=150.0e-6), | |
| ['source_housing', 'source_head'], 'X射线管电压与电流设定(功率不超过20 W;束流开启时按斜率变化)', 'agent', 'configuration') | |
| cap('xray.enable', obj(dict(enabled=BOOL)), obj(dict(enabled=BOOL, warmup_s=number('s'), ramp_s=number('s'))), dict(enabled=True), ['source_housing', 'source_head'], | |
| '开关X射线(门关闭、联锁正常时;每次上电后首次开启先运行预热程序)') | |
| cap('filter.select', obj(dict(position=integer(0, FILTER_POSITIONS - 1))), obj(dict(filter=TEXT, duration_s=number('s'))), dict(position=3), | |
| ['filter_changer', 'filter_slide'], '电动7位滤片转换器选择滤片(无、Al 0.25/0.5/1.0 mm、Cu 0.1/0.25 mm、Al 1 mm+Cu 0.1 mm)') | |
| cap('stage.move', obj(dict(sod_m=number('m', SOD_RANGE_M[0], SOD_RANGE_M[1]), chuck_z_m=number('m', CHUCK_Z_RANGE_M[0], CHUCK_Z_RANGE_M[1]))), | |
| obj(dict(target=array(number('m'), 2, 2), duration_s=number('s'), magnification=number('1'))), dict(sod_m=0.045, chuck_z_m=0.362), | |
| ['sample_carriage', 'sample_lift'], '样品滑台沿光束轴移动(源-物距=几何放大)并升降样品夹(碰撞保护:源窗口、滤片转换器、探测器盖板、腔顶)') | |
| cap('stage.rotate', obj(dict(angle_rad=number('rad', 0.0, 2 * math.pi))), obj(dict(target_rad=number('rad'), duration_s=number('s'))), dict(angle_rad=math.pi / 2), | |
| ['sample_turntable', 'sample_lift'], '旋转台转到给定角度(沿最短方向;电机在升降支架上的旋转台壳体内)') | |
| cap('stage.go_to', obj(dict(position=enum(['load', 'center']))), obj(dict(target=array(number('m'), 2, 2), duration_s=number('s'))), dict(position='load'), | |
| ['sample_carriage', 'sample_lift'], '样品滑台移到命名位置(门口装样位、中间位)') | |
| cap('scan.configure', SCAN, obj(dict(settings=SCAN, projections=INT, duration_s=number('s'))), SCAN_EXAMPLE, ['touchscreen'], | |
| '扫描设置:角度范围180°(+锥角)/360°、旋转步长、曝光、帧平均、像素合并、随机移动(抑制环状伪影)', 'agent', 'configuration') | |
| cap('calibration.flat_field', obj({}), OPERATION, {}, ['detector_housing', 'source_head'], | |
| '探测器暗场与亮场校正(当前电压、电流、滤片、合并与曝光;光束中不能有样品)') | |
| cap('calibration.geometry', obj({}), OPERATION, {}, ['sample_turntable', 'detector_housing'], '几何标定:用钢球标定体模做36投影360°扫描,测出旋转轴横向偏移') | |
| cap('xray.radiograph', obj(dict(roi=nullable(obj(dict(center_u_m=number('m', -0.07, 0.07), center_v_m=number('m', -0.06, 0.06), size_px=integer(16, 256)))))), | |
| OPERATION, dict(roi=None), ['detector_housing', 'source_head', 'sample_turntable'], '单张投影(透视);可选探测器局部区域以合并后像素分辨率成像') | |
| cap('scan.start', obj({}), OPERATION, {}, ['source_head', 'sample_turntable', 'detector_housing', 'filter_slide'], '按扫描设置采集旋转投影序列') | |
| cap('recon.start', RECON, OPERATION, RECON_EXAMPLE, ['workstation_monitor'], | |
| 'FDK锥束重建(滤波器、束硬化校正、环状伪影校正、平滑、后对准(手动或自动)、感兴趣体积)', 'agent', 'analysis') | |
| cap('measurement.result', obj(dict(record_id=TEXT)), RECORD, dict(record_id='PJ0001'), ['workstation_monitor'], '读取记录(校正、透视、投影序列或体数据摘要)', 'agent', 'query') | |
| cap('data.porosity', obj(dict(record_id=TEXT, region=REGION, threshold_1_m=nullable(number('1/m', 0.0, 1.0e6)), min_pore_voxels=integer(1, 1000))), POROSITY_OUT, | |
| dict(record_id='VO0001', region=None, threshold_1_m=None, min_pore_voxels=2), ['workstation_monitor'], | |
| '孔隙率:样品包络内低衰减体素(阈值Otsu或给定)、连通孔(开孔/闭孔)、孔数与等效直径分布', 'agent', 'analysis') | |
| cap('data.cracks', obj(dict(record_id=TEXT, region=REGION, threshold_1_m=nullable(number('1/m', 0.0, 1.0e6)), min_voxels=integer(3, 10000))), CRACK_OUT, | |
| dict(record_id='VO0001', region=None, threshold_1_m=None, min_voxels=20), ['workstation_monitor'], | |
| '裂纹:低衰减连通体中的平面状部分(主成分最小/最大尺度比),面积、开口与方向', 'agent', 'analysis') | |
| cap('data.attenuation', obj(dict(record_id=TEXT, region=REGION)), | |
| obj(dict(record_id=TEXT, mean_1_m=number('1/m'), std_1_m=number('1/m'), median_1_m=number('1/m'), p05_1_m=number('1/m'), p95_1_m=number('1/m'), voxels=INT)), | |
| dict(record_id='VO0001', region=None), ['workstation_monitor'], '区域内线衰减系数统计(均值、标准差、分位数)', 'agent', 'analysis') | |
| cap('data.slice', obj(dict(record_id=TEXT, axis=enum(['x', 'y', 'z']), position_m=number('m', -0.2, 0.2), size_px=integer(16, 128))), | |
| obj(dict(record_id=TEXT, axis=TEXT, position_m=number('m'), pixel_m=number('m'), mu_1_m=PREVIEW)), dict(record_id='VO0001', axis='z', position_m=0.003, size_px=64), | |
| ['workstation_monitor'], '取体数据的一张切片(线衰减系数,重采样到给定像素数)', 'agent', 'analysis') | |
| cap('data.edge_resolution', obj(dict(record_id=TEXT)), obj(dict(record_id=TEXT, width_10_90_m=nullable(number('m')), width_detector_px=nullable(number('1')), | |
| edge_angle_rad=nullable(number('rad')), note_zh=TEXT)), dict(record_id='RG0001'), ['workstation_monitor'], | |
| '透视刃边法分辨率:刃边扩展函数10–90 %宽度(换算到样品平面)', 'agent', 'analysis') | |
| cap('records.list', obj({}), obj(dict(records=array(TEXT, 0, 200))), {}, ['workstation_monitor'], '列出记录', 'agent', 'query') | |
| cap('records.delete', obj(dict(record_id=TEXT)), obj(dict(record_id=TEXT, remaining=INT)), dict(record_id='RG0001'), ['workstation_monitor'], | |
| '删除一条记录及其缓存数据(记录数上限60;进行中的操作或正被重建的投影记录不能删除)', 'agent', 'configuration') | |
| cap('events.read', obj(dict(since_s=number('s', 0.0))), obj(dict(events=array(EVENT, 0, 500), dropped=INT)), dict(since_s=0.0), ['touchscreen'], '读取事件与报警', | |
| 'agent', 'query') | |
| cap('ledger.read', obj({}), LEDGER, {}, ['enclosure_base'], '能量与使用账本(X射线能量去向、样品剂量、投影与帧数、行程)', 'evaluator', 'query') | |
| cap('provenance.read', obj({}), obj(dict(library=TEXT, library_sha256=TEXT, substances=INT, license=TEXT)), {}, ['workstation_monitor'], '模板库来源', 'agent', 'query') | |
| cap('sim.step', obj(dict(dt_s=number('s', 0.0, 86400.0))), obj(dict(time_s=number('s'))), dict(dt_s=1.0), ['enclosure_base'], '宿主推进仿真时间', 'evaluator', 'simulation') | |
| UNSUPPORTED = { | |
| 'hardware.connect': '没有真实X4 POSEIDON硬件或3DxSUITE软件接口', | |
| 'robot.handle_sample': '机器人接触装样(抓取、插入样品夹)未建模;sample.place为宿主抽象', | |
| 'sample_changer.load': '15位样品转换器是选件,不在本配置', | |
| 'stage.micropositioning': '带微定位的高级旋转台是选件(本配置为标准旋转台)', | |
| 'detector.select_scmos': '16 MP sCMOS探测器与Multi-Vision双探测器是选件,不在本配置', | |
| 'source.transmission': '透射式X射线源(110 kV、16 W、<2 µm@2 W)是另一种源配置', | |
| 'geometry.best_scan': 'Best-Scan-Geometry(探测器连续移动)是选件(本配置为固定扫描几何)', | |
| 'scan.helical': '高级扫描模式(螺旋、HART+)是选件', | |
| 'stage.in_situ': '原位材料试验台(压缩4400 N、拉伸440 N)与加热/冷却台是选件', | |
| 'export.dataset': '3DxSUITE数据集导出(切片图像、网格、CAD比对)与相位恢复算法未建模', | |
| } | |
| for _k, _why in UNSUPPORTED.items(): | |
| cap(_k, obj({}), obj({}), {}, ['enclosure_base'], _why, 'agent', 'device_command') | |
| SLOTS = {} | |
| def slot(k, schema, unit, origin, component, meaning, visibility='agent', reference=None): | |
| SLOTS[k] = dict(schema=schema, unit=unit, origin=origin, component=component, meaning=meaning, visibility=visibility, reference=reference) | |
| XY = array(number('m'), 2, 2) | |
| slot('clock.time_s', number('s'), 's', 'derived', 'enclosure_base', '仿真时钟') | |
| slot('plant.configured', BOOL, '1', 'setpoint', 'enclosure_base', '已声明实验室条件') | |
| slot('power.enabled', BOOL, '1', 'setpoint', 'button_mains', '系统电源') | |
| slot('system.state', enum(['off', 'booting', 'ready']), '1', 'derived', 'touchscreen', '系统状态(断电/启动中/就绪)') | |
| slot('system.error_code', nullable(TEXT), '1', 'derived', 'touchscreen', '锁存的错误代码') | |
| slot('emergency.stopped', BOOL, '1', 'sensor', 'button_emergency_stop', '安全按钮被按下(锁存)') | |
| slot('door.position_m', number('m'), 'm', 'derived', 'door_glass', '铅玻璃门打开量(0为关闭,向左滑开;场景门关节镜像)') | |
| slot('door.target_m', number('m'), 'm', 'derived', 'door_glass', '门的目标位置') | |
| slot('door.moving', BOOL, '1', 'derived', 'door_glass', '门在移动') | |
| slot('door.closed', BOOL, '1', 'sensor', 'door_glass', '门关闭(联锁开关)') | |
| slot('light_curtain.blocked', BOOL, '1', 'sensor', 'door_frame', '门口安全光幕被挡') | |
| slot('interlock.ok', BOOL, '1', 'derived', 'door_frame', 'X射线联锁满足(门关闭、联锁传感器正常、安全按钮未按下)') | |
| slot('xray.voltage_set_v', number('V'), 'V', 'setpoint', 'source_head', '管电压设定') | |
| slot('xray.current_set_a', number('A'), 'A', 'setpoint', 'source_head', '管电流设定') | |
| slot('xray.enabled', BOOL, '1', 'setpoint', 'source_head', 'X射线开启命令') | |
| slot('xray.voltage_v', number('V'), 'V', 'sensor', 'source_head', '实际管电压(斜坡)') | |
| slot('xray.current_a', number('A'), 'A', 'sensor', 'source_head', '实际管电流(斜坡)') | |
| slot('xray.power_w', number('W'), 'W', 'derived', 'source_head', '靶功率=电压×电流') | |
| slot('xray.on', BOOL, '1', 'derived', 'source_head', 'X射线正在发射') | |
| slot('xray.ready', BOOL, '1', 'derived', 'source_head', 'X射线稳定在设定值且已预热') | |
| slot('xray.warmup_remaining_s', number('s', 0.0), 's', 'derived', 'source_head', '预热剩余时间') | |
| slot('xray.focal_spot_m', number('m'), 'm', 'derived', 'source_head', '焦点尺寸(随靶功率增大)') | |
| slot('filter.position', integer(0, FILTER_POSITIONS - 1), '1', 'setpoint', 'filter_slide', '滤片位置') | |
| slot('filter.label', TEXT, '1', 'derived', 'filter_slide', '滤片名称') | |
| slot('filter.slide_m', number('m'), 'm', 'derived', 'filter_slide', '滤片滑块位置(场景滑块关节镜像)') | |
| slot('filter.moving', BOOL, '1', 'derived', 'filter_slide', '滤片转换器在移动') | |
| slot('stage.sod_m', number('m'), 'm', 'derived', 'sample_carriage', '源-物距(焦点到旋转轴;场景滑台关节镜像)') | |
| slot('stage.sod_target_m', number('m'), 'm', 'derived', 'sample_carriage', '源-物距目标') | |
| slot('stage.chuck_z_m', number('m'), 'm', 'derived', 'sample_lift', '样品夹顶面高度(台面坐标;场景升降关节镜像)') | |
| slot('stage.chuck_z_target_m', number('m'), 'm', 'derived', 'sample_lift', '样品夹高度目标') | |
| slot('stage.rotation_rad', number('rad'), 'rad', 'derived', 'sample_turntable', '旋转台角度(场景旋转关节镜像)') | |
| slot('stage.rotation_target_rad', number('rad'), 'rad', 'derived', 'sample_turntable', '旋转台目标角度') | |
| slot('stage.moving', BOOL, '1', 'derived', 'sample_carriage', '滑台、升降或旋转台在移动') | |
| slot('stage.position_label', nullable(TEXT), '1', 'derived', 'sample_carriage', '命名位置(到位后)') | |
| slot('geometry.magnification', number('1'), '1', 'derived', 'sample_carriage', '几何放大倍数=源-探距/源-物距') | |
| slot('geometry.voxel_size_m', number('m'), 'm', 'derived', 'detector_housing', '名义体素尺寸=像素间距×合并/放大') | |
| slot('geometry.fov_m', XY, 'm', 'derived', 'detector_housing', '旋转轴处的视场宽×高') | |
| slot('scan.settings', SCAN, '1', 'setpoint', 'touchscreen', '扫描设置') | |
| slot('scan.projections', INT, '1', 'derived', 'touchscreen', '扫描投影数(名义)') | |
| slot('scan.duration_s', number('s'), 's', 'derived', 'touchscreen', '扫描时间估计') | |
| slot('calibration.flat_field', obj(dict(valid=BOOL, key=nullable(TEXT), calibrated_s=nullable(number('s')))), '1', 'derived', 'detector_housing', | |
| '暗场/亮场校正是否与当前电压、电流、滤片、合并与曝光一致') | |
| slot('calibration.geometry', obj(dict(axis_offset_m=nullable(number('m')), calibrated_s=nullable(number('s')))), '1', 'derived', 'sample_turntable', | |
| '几何标定测得的旋转轴横向偏移') | |
| slot('measurement.id', nullable(TEXT), '1', 'derived', 'touchscreen', '进行中的记录ID') | |
| slot('measurement.kind', nullable(TEXT), '1', 'derived', 'touchscreen', '进行中的操作种类') | |
| slot('measurement.progress', nullable(number('1', 0.0, 1.0)), '1', 'derived', 'touchscreen', '进行中操作的进度') | |
| slot('measurement.remaining_s', nullable(number('s', 0.0)), 's', 'derived', 'touchscreen', '进行中操作的剩余时间') | |
| slot('measurement.started_by_other_agent', BOOL, '1', 'derived', 'touchscreen', '进行中的操作属于另一个agent') | |
| slot('recon.id', nullable(TEXT), '1', 'derived', 'workstation_monitor', '工作站上进行中的重建记录ID(与仪器采集并行)') | |
| slot('recon.remaining_s', nullable(number('s', 0.0)), 's', 'derived', 'workstation_monitor', '重建剩余时间') | |
| slot('result.last_record_id', nullable(TEXT), '1', 'derived', 'workstation_monitor', '最近完成的记录ID(agent只看到自己或宿主创建的记录)') | |
| slot('result.last_porosity', nullable(number('1', 0.0, 1.0)), '1', 'derived', 'workstation_monitor', '最近一次孔隙率分析的结果') | |
| slot('sample.bench_ids', array(TEXT, 0, MAX_SAMPLES), '1', 'derived', 'sample_chuck', '实验台上的样品') | |
| slot('sample.on_stage', nullable(obj(dict(sample_id=TEXT, offset_x_m=number('m'), offset_y_m=number('m')))), '1', 'derived', 'sample_chuck', '样品夹上的样品及偏移') | |
| slot('panel.status_green', BOOL, '1', 'derived', 'lamp_status_green', '状态灯绿(通电、无错误、X射线关)') | |
| slot('panel.status_orange', BOOL, '1', 'derived', 'lamp_status_orange', '状态灯橙(X射线开启)') | |
| slot('panel.status_red', BOOL, '1', 'derived', 'lamp_status_red', '状态灯红(错误或安全按钮按下)') | |
| slot('truth.axis_offset_m', number('m'), 'm', 'process_truth', 'sample_turntable', '旋转轴真实横向偏移', 'evaluator') | |
| slot('truth.samples', {'type': 'object'}, '1', 'process_truth', 'sample_chuck', '样品真实定义(含生成的孔)与真实孔隙率、裂纹', 'evaluator') | |
| slot('truth.faults', array(TEXT, 0, 8), '1', 'process_truth', 'enclosure_base', '注入的故障', 'evaluator') | |
| slot('truth.detector_defect_columns', array(INT, 0, 16), '1', 'process_truth', 'detector_housing', '注入的坏列(模拟探测器列号)', 'evaluator') | |
| class _Sum: | |
| """Neumaier-compensated running sum.""" | |
| def __init__(self): | |
| self.s = 0.0 | |
| self.c = 0.0 | |
| def add(self, x): | |
| t = self.s + x | |
| if abs(self.s) >= abs(x): | |
| self.c += (self.s - t) + x | |
| else: | |
| self.c += (x - t) + self.s | |
| self.s = t | |
| def value(self): | |
| return self.s + self.c | |
| def _axis_move(pos, target, speed, dt): | |
| """Linear move towards the target; arrives exactly (a remainder of rounding size snaps to the target).""" | |
| d = target - pos | |
| step = speed * dt | |
| return target if abs(d) <= step + 1e-12 else pos + math.copysign(step, d) | |
| def _rot_delta(a, b): | |
| """Shortest signed rotation from a to b (rad).""" | |
| return (b - a + math.pi) % (2 * math.pi) - math.pi | |
| def coerce(s, v): | |
| """Integral floats of 'integer' fields as int, recursively (the value was validated against s).""" | |
| if 'anyOf' in s: | |
| for o in s['anyOf']: | |
| try: | |
| validate(o, v) | |
| except ActionRejected: | |
| continue | |
| return coerce(o, v) | |
| return v | |
| k = s.get('type') | |
| if k == 'integer' and isinstance(v, float): | |
| return int(v) | |
| if k == 'object' and isinstance(v, dict) and 'properties' in s: | |
| return {key: coerce(s['properties'][key], val) if key in s['properties'] else val for key, val in v.items()} | |
| if k == 'array' and isinstance(v, list): | |
| return [coerce(s['items'], x) for x in v] | |
| return v | |
| def _segment_hits_box(p, q, box): | |
| """Does the segment p->q pass through the inside of the open axis-aligned rectangle ((x0, x1), (y0, y1)) (bounds may be infinite)?""" | |
| t0, t1 = 0.0, 1.0 | |
| for a, d, (lo, hi) in ((p[0], q[0] - p[0], box[0]), (p[1], q[1] - p[1], box[1])): | |
| if abs(d) < 1e-15: | |
| if not (lo < a < hi): | |
| return False | |
| continue | |
| ta, tb = (lo - a) / d, (hi - a) / d | |
| if ta > tb: | |
| ta, tb = tb, ta | |
| t0, t1 = max(t0, ta), min(t1, tb) | |
| if t0 >= t1: | |
| return False | |
| return t0 < t1 | |
| FAULT_PRIORITY = ('door_sensor', 'xray_arc', 'rotation_stall') # order of the latched errors after power-up / acknowledgement | |
| FLAT_MAX_SIGMA = 0.10 # a bright field whose binned-pixel relative error exceeds 10 % is not a usable calibration | |
| GEO_FIT_MAX_RESIDUAL_PX = 2.0 # ball-track fit accepted up to 2 window pixels (at the axis) rms, and at least ... | |
| GEO_FIT_MIN_LIMIT_M = 5.0e-6 # ... 5 um | |
| RATE_ROT_CELLS = 32 # energy-rate cells: the beam's energy flow is evaluated at the cell centre of the pose | |
| RATE_ROT_CELL_RAD = 2 * math.pi / RATE_ROT_CELLS | |
| RATE_POS_CELL_M = 0.25e-3 | |
| RATE_KV_CELL_V = 1.0e3 | |
| LEDGER_FINE_RAYS = 1024 # about this many rays over the projection of the sample body (energy ledger) | |
| LEDGER_RING_CELL_M = 0.008 # coarse ledger cells (detector plane) between the active area and the emission cone | |
| ENERGY_SINKS = ('target_absorbed_j', 'window_absorbed_j', 'filter_absorbed_j', 'air_absorbed_j', 'sample_absorbed_j', 'holder_absorbed_j', 'sample_scattered_j', | |
| 'detector_absorbed_j', 'detector_passed_j', 'shielding_j') | |
| def _to_boundary(x, w, cell): | |
| """Time until x moving at rate w (!= 0) crosses the next boundary of cells of width `cell` centred on integer multiples (boundaries at | |
| (k + 1/2) cell).""" | |
| if w > 0: | |
| b = (math.floor(x / cell - 0.5) + 1.5) * cell | |
| else: | |
| b = (math.ceil(x / cell - 0.5) - 0.5) * cell | |
| if (b - x) / w < 1e-9: # x sits on a boundary within rounding: the next one | |
| b += math.copysign(cell, w) | |
| return (b - x) / w | |
| def _mu_grid(sid, n): | |
| """Linear coefficients (1/m) of a library material on the first n energies of the fine spectrum grid (every tube voltage uses a prefix).""" | |
| return linear_mu(sid, E_GRID_KEV[:n]) | |
| def _cells(u0, u1, v0, v1, nu, nv): | |
| """Centres and sizes of an (nu x nv) grid of cells over the rectangle [u0, u1] x [v0, v1] of the detector plane.""" | |
| pu, pv = (u1 - u0) / nu, (v1 - v0) / nv | |
| U, V = np.meshgrid(u0 + (np.arange(nu) + 0.5) * pu, v1 - (np.arange(nv) + 0.5) * pv) | |
| return U.ravel(), V.ravel(), np.full(U.size, pu), np.full(U.size, pv) | |
| def _cell_rays(U, V, PU, PV): | |
| """Rays from the focal spot to cell centres of the detector plane: (unit directions, solid angles sr, focal-spot-to-plane distances, | |
| cell on the active area).""" | |
| P = np.stack([np.full(U.size, SDD_M), U, V], -1) | |
| r = np.linalg.norm(P, axis=1) | |
| hu, hv = DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2, DETECTOR_PIXELS[1] * PIXEL_PITCH_M / 2 | |
| return P / r[:, None], PU * PV * SDD_M / r ** 3, r, (np.abs(U) < hu) & (np.abs(V) < hv) | |
| def _ledger_grid(): | |
| """Coarse cells of the energy ledger over the emission cone: 35 x 30 on the active area and about 8 mm (detector plane) between it and | |
| the cone, so that no cell straddles the edge of the active area; a cell belongs to the cone when its centre does. Returns the cell | |
| centres and sizes (U, V, PU, PV) and their rays (directions, solid angles, distances, on the active area).""" | |
| c = SDD_M * math.tan(CONE_HALF_ANGLE_RAD) | |
| hu, hv = DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2, DETECTOR_PIXELS[1] * PIXEL_PITCH_M / 2 | |
| nu, nv = max(1, math.ceil((c - hu) / LEDGER_RING_CELL_M)), max(1, math.ceil((c - hv) / LEDGER_RING_CELL_M)) | |
| blocks = [_cells(u0, u1, v0, v1, a, b) for u0, u1, a in ((-c, -hu, nu), (-hu, hu, 35), (hu, c, nu)) | |
| for v0, v1, b in ((-c, -hv, nv), (-hv, hv, 30), (hv, c, nv))] | |
| U, V, PU, PV = (np.concatenate([bk[k] for bk in blocks]) for k in range(4)) | |
| keep = U * U + V * V <= c * c | |
| U, V, PU, PV = U[keep], V[keep], PU[keep], PV[keep] | |
| return (U, V, PU, PV) + _cell_rays(U, V, PU, PV) | |
| def _free_rays(kv_v, filter_position): | |
| """Energy per electron (J) of every coarse ledger ray that meets no object: absorbed in the air, deposited in and passing through the | |
| detector (rays on the active area), reaching the shielding (rays beside it).""" | |
| _, omega, r, det = _ledger_grid()[4:] | |
| e, ph = beam_spectrum(kv_v, filter_position) | |
| mu_air, _ = _mu_grid('nist_air', len(e)) | |
| inc = ph * np.exp(-np.multiply.outer(r, mu_air)) | |
| _, edep = detector_response(tuple(e)) | |
| f = 0.5 * KEV | |
| return (f * omega * (float(ph @ e) - inc @ e), np.where(det, f * omega * (inc @ edep), 0.0), | |
| np.where(det, f * omega * (inc @ (e - edep)), 0.0), np.where(det, 0.0, f * omega * (inc @ e))) | |
| DOOR_X_RANGE_M = (ENCLOSURE_X_M - 0.085, ENCLOSURE_X_M + 0.270) # door opening in the asset frame (the chuck is reachable when the axis lies inside) | |
| LOAD_POSITION = dict(sod=0.250, cz=0.250) | |
| CENTER_POSITION = dict(sod=0.200, cz=0.300) | |
| class BrukerX4PoseidonRuntime: | |
| """X4 POSEIDON (reflection source, flat panel, fixed geometry, standard rotation stage): power and safety, door, X-ray source, filter | |
| changer, sample carriage / lift / rotation, detector calibration, radiography, CT scans, FDK reconstruction and analysis (SI units).""" | |
| def __init__(self, instance_id='x4_poseidon_01'): | |
| self.instance_id = instance_id | |
| self.t = 0.0 | |
| self.revision = 0 | |
| self.plant = None | |
| self.power = False | |
| self.state = 'off' | |
| self.state_t0 = 0.0 | |
| self.error = None | |
| self.estop = False | |
| self.faults = set() | |
| self.door, self.door_target = 0.0, 0.0 | |
| self.xv_set, self.xi_set = 60.0e3, 150.0e-6 | |
| self.x_enabled = False | |
| self.xv, self.xi = 0.0, 0.0 | |
| self.warm_needed = True # first enable after every boot runs the warm-up program | |
| self.warm_v, self.warm_i = 0.0, 0.0 # end point of the running warm-up program (set point at its start) | |
| self.warm_end = None | |
| self.warm_from = None | |
| self.filter_pos, self.slide, self.slide_target = 0, 0.0, 0.0 | |
| self.sod, self.sod_target = LOAD_POSITION['sod'], LOAD_POSITION['sod'] | |
| self.cz, self.cz_target = LOAD_POSITION['cz'], LOAD_POSITION['cz'] | |
| self.rot, self.rot_target = 0.0, 0.0 | |
| self.position_label = 'load' | |
| self.scan_settings = dict(SCAN_EXAMPLE) | |
| self.flat = None # dict(key, t, bright, dark, frames) of the last dark / bright calibration | |
| self.geo_cal = dict(axis_offset_m=None, calibrated_s=None) | |
| self.samples = {} | |
| self.on_stage = None | |
| self.records = {} | |
| self._data = {} # record id -> simulated arrays (projections, volumes, images) | |
| self.seq = dict(ff=0, gc=0, rg=0, pj=0, vo=0, op=0) | |
| self.op = None # acquisition operation (flat field, geometry calibration, radiograph, scan) | |
| self.recon = None # reconstruction on the workstation (independent of the instrument) | |
| self.operations = {} | |
| self.events, self.events_dropped = [], 0 | |
| self.truth = dict(axis_offset=0.0, defects=[]) | |
| self.led = {k: _Sum() for k in LEDGER_KEYS} | |
| self.last_porosity = None | |
| self.last_porosity_rid = None | |
| self.used_substances = set() | |
| self._rate_cache = {} | |
| self._principals, self._requests, self._owners = {}, {}, {} | |
| self._porosity_owner = None # principal of the last porosity analysis (the session sets it) | |
| # ---------------------------------------------------------------- basics | |
| def time_s(self): | |
| return self.t | |
| def register_principal(self, name, visibility): | |
| if visibility not in ('agent', 'evaluator') or name in self._principals: | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| self._principals[name] = visibility | |
| def session(self, name): | |
| if name not in self._principals: | |
| raise ActionRejected('ACCESS_DENIED') | |
| return BrukerX4PoseidonSession(self, name) | |
| def _event(self, kind, code, message, rid=None, t=None): | |
| if len(self.events) >= MAX_EVENTS: | |
| self.events.pop(0) | |
| self.events_dropped += 1 | |
| self.events.append(dict(time_s=self.t if t is None else t, kind=kind, code=code, message_zh=message, _rid=rid)) | |
| def _seed(self): | |
| return self.plant['noise_seed'] if self.plant else 0 | |
| def _binning(self): | |
| return int(self.scan_settings['binning'][0]) | |
| def _magnification(self, sod=None): | |
| return SDD_M / (self.sod if sod is None else sod) | |
| def _voxel_nominal(self, sod=None): | |
| return PIXEL_PITCH_M * self._binning() / self._magnification(sod) | |
| def _fov(self, sod=None): | |
| m = self._magnification(sod) | |
| return [DETECTOR_PIXELS[0] * PIXEL_PITCH_M / m, DETECTOR_PIXELS[1] * PIXEL_PITCH_M / m] | |
| def _door_closed(self): | |
| return self.door <= 1e-9 and self.door_target <= 1e-9 | |
| def _door_moving(self): | |
| return abs(self.door - self.door_target) > 1e-12 | |
| def _interlock_ok(self): | |
| return self._door_closed() and 'door_sensor' not in self.faults and not self.estop | |
| def _xray_on(self): | |
| return self.power and self.xv > 0.0 and self.xi > 0.0 | |
| def _xray_ready(self): | |
| return (self._xray_on() and self.x_enabled and self.warm_end is None and abs(self.xv - self.xv_set) < 1e-6 and abs(self.xi - self.xi_set) < 1e-12) | |
| def _stage_moving(self): | |
| return abs(self.sod - self.sod_target) > 1e-12 or abs(self.cz - self.cz_target) > 1e-12 or abs(_rot_delta(self.rot, self.rot_target)) > 1e-12 | |
| def _filter_moving(self): | |
| return abs(self.slide - self.slide_target) > 1e-12 | |
| def _flat_key(self): | |
| s = self.scan_settings | |
| return f"{self.xv_set:.1f}|{self.xi_set * 1e9:.1f}|{self.filter_pos}|{s['binning']}|{s['exposure_s']:.6g}" | |
| def _flat_valid(self): | |
| return self.flat is not None and self.flat['key'] == self._flat_key() and self.flat.get('usable', True) | |
| def _nominal_projections(self, s=None): | |
| s = s or self.scan_settings | |
| span = self._scan_span(s) | |
| return int(math.floor(span / s['step_rad'] + 1e-9)) + (0 if s['range_deg'] == '360' else 1) | |
| def _scan_span(self, s=None): | |
| s = s or self.scan_settings | |
| if s['range_deg'] == '360': | |
| return 2 * math.pi | |
| half_fan = math.atan(DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2 / SDD_M) | |
| return math.pi + 2 * half_fan # 180 deg + fan angle (short scan) | |
| def _projection_time(self, s=None): | |
| s = s or self.scan_settings | |
| return s['averaging'] * (s['exposure_s'] + FRAME_OVERHEAD_S) + STEP_OVERHEAD_S | |
| def _scan_duration(self, s=None): | |
| return self._nominal_projections(s) * self._projection_time(s) | |
| # ---------------------------------------------------------------- read | |
| def read(self, visibility='agent'): | |
| o = self.op | |
| prog = rem = None | |
| if o is not None: | |
| prog = min(1.0, max(0.0, (self.t - o['t0']) / o['duration_s'])) if o['duration_s'] > 0 else 0.0 | |
| rem = max(0.0, o['t0'] + o['duration_s'] - self.t) | |
| err = self.error is not None or self.estop | |
| values = { | |
| 'clock.time_s': self.t, 'plant.configured': self.plant is not None, 'power.enabled': self.power, 'system.state': self.state, | |
| 'system.error_code': self.error, 'emergency.stopped': self.estop, 'door.position_m': self.door, 'door.target_m': self.door_target, | |
| 'door.moving': self._door_moving(), 'door.closed': self._door_closed(), 'light_curtain.blocked': 'light_curtain_blocked' in self.faults, | |
| 'interlock.ok': self._interlock_ok(), 'xray.voltage_set_v': self.xv_set, 'xray.current_set_a': self.xi_set, 'xray.enabled': self.x_enabled, | |
| 'xray.voltage_v': self.xv, 'xray.current_a': self.xi, 'xray.power_w': self.xv * self.xi, 'xray.on': self._xray_on(), 'xray.ready': self._xray_ready(), | |
| 'xray.warmup_remaining_s': max(0.0, self.warm_end - self.t) if self.warm_end is not None else 0.0, | |
| 'xray.focal_spot_m': focal_spot_m(self.xv * self.xi if self._xray_on() else self.xv_set * self.xi_set), | |
| 'filter.position': self.filter_pos, 'filter.label': filter_of(self.filter_pos)['label'], 'filter.slide_m': self.slide, 'filter.moving': self._filter_moving(), | |
| 'stage.sod_m': self.sod, 'stage.sod_target_m': self.sod_target, 'stage.chuck_z_m': self.cz, 'stage.chuck_z_target_m': self.cz_target, | |
| 'stage.rotation_rad': self.rot, 'stage.rotation_target_rad': self.rot_target, 'stage.moving': self._stage_moving(), 'stage.position_label': self.position_label, | |
| 'geometry.magnification': self._magnification(), 'geometry.voxel_size_m': self._voxel_nominal(), 'geometry.fov_m': self._fov(), | |
| 'scan.settings': dict(self.scan_settings), 'scan.projections': self._nominal_projections(), 'scan.duration_s': self._scan_duration(), | |
| 'calibration.flat_field': dict(valid=self._flat_valid(), key=self.flat['key'] if self.flat else None, calibrated_s=self.flat['t'] if self.flat else None), | |
| 'calibration.geometry': dict(self.geo_cal), 'measurement.id': o['record_id'] if o else None, 'measurement.kind': o['kind'] if o else None, | |
| 'measurement.progress': prog, 'measurement.remaining_s': rem, 'measurement.started_by_other_agent': False, | |
| 'recon.id': self.recon['record_id'] if self.recon else None, | |
| 'recon.remaining_s': max(0.0, self.recon['t0'] + self.recon['duration_s'] - self.t) if self.recon else None, | |
| 'result.last_record_id': self._last_record(), 'result.last_porosity': self.last_porosity, | |
| 'sample.bench_ids': sorted(k for k, s in self.samples.items() if s['location'] == 'bench'), | |
| 'sample.on_stage': (dict(sample_id=self.on_stage, offset_x_m=self.samples[self.on_stage]['offset_x_m'], offset_y_m=self.samples[self.on_stage]['offset_y_m']) | |
| if self.on_stage else None), | |
| 'panel.status_green': self.power and not err and not self._xray_on(), 'panel.status_orange': self.power and self._xray_on(), | |
| 'panel.status_red': self.power and err, | |
| 'truth.axis_offset_m': self.truth['axis_offset'], 'truth.samples': self._truth_samples(), 'truth.faults': sorted(self.faults), | |
| 'truth.detector_defect_columns': list(self.truth['defects']), | |
| } | |
| return {k: v for k, v in values.items() if SLOTS[k]['visibility'] == 'agent' or visibility == 'evaluator'} | |
| def _last_record(self, keep=None): | |
| done = [k for k, r in self.records.items() if r['status'] == 'completed' and (keep is None or keep(k))] | |
| return max(done, key=lambda k: (self.records[k]['finished_s'] or 0.0, k), default=None) | |
| def _truth_samples(self): | |
| out = {} | |
| for k, s in self.samples.items(): | |
| d = {kk: copy.deepcopy(vv) for kk, vv in s.items() if kk != '_pores'} | |
| d['pores_generated'] = copy.deepcopy(s.get('_pores', [])) | |
| d['truth'] = sample_truth(s) | |
| out[k] = d | |
| return out | |
| # ---------------------------------------------------------------- commands | |
| def invoke(self, capability_id, **a): | |
| if capability_id not in CAPS: | |
| raise ActionRejected('UNKNOWN_CAPABILITY') | |
| if capability_id in UNSUPPORTED: | |
| raise ActionRejected('UNSUPPORTED') | |
| validate(CAPS[capability_id]['input_schema'], a) | |
| a = coerce(CAPS[capability_id]['input_schema'], a) # integral floats of (nested) integer fields -> int | |
| fn = getattr(self, '_cmd_' + capability_id.replace('.', '_')) | |
| out = fn(**a) | |
| if CAPS[capability_id]['kind'] not in ('query', 'analysis', 'simulation'): | |
| self.revision += 1 | |
| return out | |
| def _need_plant(self): | |
| if self.plant is None: | |
| raise ActionRejected('PLANT_REQUIRED') | |
| def _need_power(self): | |
| self._need_plant() | |
| if not self.power: | |
| raise ActionRejected('POWER_OFF') | |
| def _need_ready(self, allow_error=False): | |
| self._need_power() | |
| if self.state != 'ready': | |
| raise ActionRejected('NOT_READY') | |
| if self.estop: | |
| raise ActionRejected('EMERGENCY_STOP') | |
| if self.error is not None and not allow_error: | |
| raise ActionRejected('ERROR_PENDING') | |
| def _need_idle(self): | |
| if self.op is not None: | |
| raise ActionRejected('MEASUREMENT_RUNNING') | |
| def _need_still(self): | |
| if self._stage_moving() or self._filter_moving() or self._door_moving(): | |
| raise ActionRejected('MOTION_IN_PROGRESS') | |
| # ---------------------------------------------------------------- setup, samples, power, safety, faults | |
| def _cmd_plant_configure(self, room_k, mains_voltage_v, relative_humidity, noise_seed): | |
| first = self.plant is None | |
| if not first and noise_seed != self.plant['noise_seed']: | |
| raise ActionRejected('SEED_FIXED') | |
| self.plant = dict(room_k=room_k, mains_voltage_v=mains_voltage_v, relative_humidity=relative_humidity, noise_seed=noise_seed) | |
| if first: | |
| rng = random.Random(noise_seed * 7919 + 17) | |
| self.truth['axis_offset'] = rng.gauss(0.0, AXIS_OFFSET_SD_M) | |
| if self.power and not (MAINS_V[0] * 0.9 <= mains_voltage_v <= MAINS_V[1] * 1.1): | |
| self._power_off('MAINS_FAULT') | |
| return dict(plant=dict(self.plant)) | |
| def _cmd_sample_provide(self, sample_id, kind, diameter_m, height_m, layers, pores, cracks, inclusions, container, pin): | |
| self._need_plant() | |
| if sample_id in self.samples: | |
| raise ActionRejected('SAMPLE_EXISTS') | |
| if len(self.samples) >= MAX_SAMPLES: | |
| raise ActionRejected('TOO_MANY_SAMPLES') | |
| s = dict(sample_id=sample_id, kind=kind, diameter_m=diameter_m, height_m=height_m, layers=copy.deepcopy(layers), pores=copy.deepcopy(pores), | |
| cracks=copy.deepcopy(cracks), inclusions=copy.deepcopy(inclusions), container=copy.deepcopy(container), pin=copy.deepcopy(pin), | |
| location='bench', offset_x_m=0.0, offset_y_m=0.0) | |
| R = diameter_m / 2 | |
| if kind == 'cylinder': | |
| if not layers or abs(sum(L['thickness_m'] for L in layers) - height_m) > 1e-9: | |
| raise ActionRejected('INVALID_SAMPLE') | |
| for L in layers: | |
| if abs(sum(m['volume_fraction'] for m in L['materials']) - 1.0) > 1e-6: | |
| raise ActionRejected('INVALID_SAMPLE') | |
| zb = _layer_bounds(s) | |
| for c in cracks: | |
| nrm = np.asarray(c['normal'], float) | |
| if np.linalg.norm(nrm) < 0.5 or math.hypot(c['center_m'][0], c['center_m'][1]) + c['radius_m'] > R or not any( | |
| zb[k] + c['radius_m'] <= c['center_m'][2] <= zb[k + 1] - c['radius_m'] for k in range(len(layers))): | |
| raise ActionRejected('INVALID_SAMPLE') | |
| for i in inclusions: | |
| if math.hypot(i['center_m'][0], i['center_m'][1]) + i['radius_m'] > R or not any( | |
| zb[k] + i['radius_m'] <= i['center_m'][2] <= zb[k + 1] - i['radius_m'] for k in range(len(layers))): | |
| raise ActionRejected('INVALID_SAMPLE') | |
| elif layers or pores['count'] or cracks or inclusions: | |
| raise ActionRejected('INVALID_SAMPLE') # phantoms have fixed materials and no pores / cracks / inclusions | |
| for sid in _materials(s): | |
| substance(sid) | |
| s['_pores'] = generate_pores(s) | |
| self.samples[sample_id] = s | |
| self.used_substances.update(_materials(s)) | |
| self._event('sample', 'SAMPLE_PROVIDED', f'样品{sample_id}放在实验台上') | |
| return dict(sample_id=sample_id, location='bench', mass_kg=sample_mass_kg(s)) | |
| def _envelope(self, s, ox, oy): | |
| return sample_radius_total(s) + math.hypot(ox, oy) | |
| def _geometry_ok(self, sod, cz, sample_id=None, ox=None, oy=None): | |
| sid = self.on_stage if sample_id is None else sample_id | |
| if sid is None: | |
| return self._clear(sod, cz, None) | |
| s = self.samples[sid] | |
| ox = s['offset_x_m'] if ox is None else ox | |
| oy = s['offset_y_m'] if oy is None else oy | |
| return self._clear(sod, cz, s, ox, oy) | |
| def _clear(self, sod, cz, s, ox=0.0, oy=0.0): | |
| """Keep-out check of the moving column (sample body, pin, chuck, rotation-stage housing; each a vertical cylinder about the rotation axis) | |
| against the source head / filter slide and the detector housing where their heights overlap, and against the chamber ceiling.""" | |
| bz = SOURCE_XYZ_M[2] | |
| segs = [(CHUCK_R_M, cz - CHUCK_H_M, cz), (STAGE_R_M, cz - CHUCK_H_M - STAGE_H_M, cz - CHUCK_H_M)] | |
| top = cz | |
| if s is not None: | |
| e = math.hypot(ox, oy) | |
| z0 = cz | |
| if s['pin']: | |
| segs.append((s['pin']['diameter_m'] / 2 + e, cz, cz + s['pin']['length_m'])) | |
| z0 = cz + s['pin']['length_m'] | |
| segs.append((sample_radius_total(s) + e, z0, z0 + s['height_m'])) | |
| top = z0 + s['height_m'] | |
| for r, za, zb_ in segs: | |
| if za < bz + SOURCE_KEEPOUT_DZ[1] and zb_ > bz + SOURCE_KEEPOUT_DZ[0] and sod - r < FILTER_CLEAR_M + COLLISION_MARGIN_M: | |
| return False | |
| if za < bz + DETECTOR_KEEPOUT_DZ[1] and zb_ > bz + DETECTOR_KEEPOUT_DZ[0] and SDD_M - DETECTOR_COVER_M - sod - r < COLLISION_MARGIN_M: | |
| return False | |
| return top <= CHAMBER_CEILING_M - COLLISION_MARGIN_M | |
| def _accessible(self): | |
| x_axis = SOURCE_XYZ_M[0] + self.sod | |
| return DOOR_X_RANGE_M[0] + 0.02 <= x_axis <= DOOR_X_RANGE_M[1] - 0.02 | |
| def _cmd_sample_place(self, sample_id, offset_x_m, offset_y_m): | |
| self._need_plant() | |
| s = self.samples.get(sample_id) | |
| if s is None: | |
| raise ActionRejected('UNKNOWN_SAMPLE') | |
| if s['location'] != 'bench': | |
| raise ActionRejected('SAMPLE_NOT_ON_BENCH') | |
| if self.on_stage is not None: | |
| raise ActionRejected('STAGE_OCCUPIED') | |
| self._need_idle() | |
| if self.door < DOOR_TRAVEL_M - 1e-9 or self._door_moving(): | |
| raise ActionRejected('DOOR_CLOSED') | |
| if self._stage_moving(): | |
| raise ActionRejected('MOTION_IN_PROGRESS') | |
| if not self._accessible(): | |
| raise ActionRejected('NOT_ACCESSIBLE') | |
| if not self._geometry_ok(self.sod, self.cz, sample_id, offset_x_m, offset_y_m): | |
| raise ActionRejected('COLLISION_RISK') | |
| s['location'], s['offset_x_m'], s['offset_y_m'] = 'stage', offset_x_m, offset_y_m | |
| self.on_stage = sample_id | |
| self._rate_cache.clear() | |
| self._event('sample', 'SAMPLE_PLACED', f'样品{sample_id}装到样品夹(偏移{offset_x_m * 1e3:.2f}, {offset_y_m * 1e3:.2f} mm)') | |
| return dict(sample_id=sample_id, offset_x_m=offset_x_m, offset_y_m=offset_y_m) | |
| def _cmd_sample_remove(self, sample_id): | |
| self._need_plant() | |
| if self.on_stage != sample_id: | |
| raise ActionRejected('SAMPLE_NOT_ON_STAGE') | |
| self._need_idle() | |
| if self.door < DOOR_TRAVEL_M - 1e-9 or self._door_moving(): | |
| raise ActionRejected('DOOR_CLOSED') | |
| if self._stage_moving(): | |
| raise ActionRejected('MOTION_IN_PROGRESS') | |
| if not self._accessible(): | |
| raise ActionRejected('NOT_ACCESSIBLE') | |
| s = self.samples[sample_id] | |
| s['location'], s['offset_x_m'], s['offset_y_m'] = 'bench', 0.0, 0.0 | |
| self.on_stage = None | |
| self._rate_cache.clear() | |
| self._event('sample', 'SAMPLE_REMOVED', f'样品{sample_id}取回实验台') | |
| return dict(sample_id=sample_id) | |
| def _cmd_fault_inject(self, fault, active): | |
| self._need_plant() | |
| if active: | |
| self.faults.add(fault) | |
| code = FAULT_ERROR.get(fault) | |
| if code and self.power: | |
| self._raise_error(code) | |
| if fault == 'detector_defects' and not self.truth['defects']: | |
| g = random.Random(self._seed() * 31 + 3) | |
| self.truth['defects'] = sorted(g.sample(range(20, SIM_DETECTOR[0] - 20), 3)) | |
| if fault == 'xray_arc': | |
| self._beam_off('XRAY_ARC') | |
| if fault == 'rotation_stall': | |
| self.rot_target = self.rot | |
| if self.op is not None and self.op['kind'] in ('projections', 'geometry_calibration'): | |
| self._fail_op('STAGE_FAULT') | |
| if fault == 'door_sensor': | |
| self._beam_off('INTERLOCK_FAULT') | |
| if fault == 'light_curtain_blocked' and self.door_target < self.door - 1e-12: | |
| self.door_target = DOOR_TRAVEL_M # closing door stops and reopens | |
| self._event('safety', 'LIGHT_CURTAIN', '安全光幕被挡:门停止关闭并重新打开') | |
| else: | |
| self.faults.discard(fault) | |
| if fault == 'detector_defects': | |
| self.truth['defects'] = [] | |
| self._event('fault', 'FAULT_' + ('ON' if active else 'OFF'), fault) | |
| return dict(faults=sorted(self.faults)) | |
| def _raise_error(self, code): | |
| if self.error is None: | |
| self.error = code | |
| self._event('error', code, ERROR_ZH.get(code, code)) | |
| def _beam_off(self, code=None): | |
| """Switch the X-ray off at once (interlock, arc, emergency stop); a running exposure fails.""" | |
| was_on = self._xray_on() or self.x_enabled | |
| self.x_enabled = False | |
| self.xv = self.xi = 0.0 | |
| self.warm_end = None | |
| if self.op is not None and self.op['kind'] in ('flat_field', 'geometry_calibration', 'radiograph', 'projections'): | |
| self._fail_op(code or 'XRAY_OFF') | |
| if was_on: | |
| self._event('xray', 'XRAY_OFF', 'X射线关闭' + (f'({code})' if code else '')) | |
| def _cmd_power_press_button(self): | |
| return self._cmd_power_set(not self.power) | |
| def _cmd_power_set(self, enabled): | |
| self._need_plant() | |
| if enabled and not self.power: | |
| if not (MAINS_V[0] * 0.9 <= self.plant['mains_voltage_v'] <= MAINS_V[1] * 1.1): | |
| raise ActionRejected('MAINS_OUT_OF_RANGE') | |
| self.power, self.state, self.state_t0 = True, 'booting', self.t | |
| self.warm_needed = True | |
| if self.error == 'MAINS_FAULT': | |
| self.error = None | |
| self._latch_persisting_causes() | |
| self._event('power', 'POWER_ON', '系统通电,启动(各轴保持断电时的位置)') | |
| elif not enabled and self.power: | |
| self._power_off(None) | |
| return dict(enabled=self.power, state=self.state) | |
| def _power_off(self, code): | |
| self._beam_off('POWER_OFF') | |
| if self.op is not None: | |
| self._fail_op('POWER_OFF') | |
| self.power, self.state = False, 'off' | |
| self.sod_target, self.cz_target, self.rot_target = self.sod, self.cz, self.rot | |
| self.door_target = self.door | |
| self.slide_target = self.slide | |
| if code: | |
| if self.error is None: | |
| self.error = code | |
| self._event('error', code, ERROR_ZH.get(code, code)) | |
| self._event('power', 'POWER_OFF', '系统断电:X射线关闭,各轴停止') | |
| def _cmd_emergency_stop(self): | |
| self._need_plant() | |
| if not self.estop: | |
| self.estop = True | |
| self._beam_off('EMERGENCY_STOP') | |
| if self.op is not None: | |
| self._fail_op('EMERGENCY_STOP') | |
| self.sod_target, self.cz_target, self.rot_target = self.sod, self.cz, self.rot | |
| self.door_target = self.door | |
| self.slide_target = self.slide | |
| if self.power: | |
| self._raise_error('EMERGENCY_STOP') | |
| self._event('safety', 'EMERGENCY_STOP', '安全按钮按下:X射线关闭,所有运动停止') | |
| return dict(stopped=True) | |
| def _cmd_emergency_release(self): | |
| self._need_plant() | |
| if self.estop: | |
| self.estop = False | |
| self._event('safety', 'EMERGENCY_RELEASED', '安全按钮已释放(需确认错误)') | |
| return dict(stopped=False) | |
| def _cmd_system_acknowledge(self): | |
| self._need_power() | |
| if self.error is None: | |
| return dict(cleared=None) | |
| cause = {v: k for k, v in FAULT_ERROR.items()}.get(self.error) | |
| if cause in self.faults or (self.error == 'EMERGENCY_STOP' and self.estop) or \ | |
| (self.error == 'MAINS_FAULT' and not (MAINS_V[0] * 0.9 <= self.plant['mains_voltage_v'] <= MAINS_V[1] * 1.1)): | |
| raise ActionRejected('CAUSE_PERSISTS') | |
| cleared, self.error = self.error, None | |
| self._event('error', 'ACKNOWLEDGED', f'确认错误{cleared}') | |
| if self.power: | |
| self._latch_persisting_causes() # another cause still present latches its own error | |
| return dict(cleared=cleared) | |
| # ---------------------------------------------------------------- door, X-ray, filter, stage | |
| def _cmd_door_open(self): | |
| self._need_ready() | |
| self._need_idle() | |
| if self._xray_on() or self.x_enabled: | |
| raise ActionRejected('XRAY_ON') | |
| self.door_target = DOOR_TRAVEL_M | |
| return dict(target_m=DOOR_TRAVEL_M, duration_s=abs(DOOR_TRAVEL_M - self.door) / DOOR_SPEED_M_S) | |
| def _cmd_door_close(self): | |
| self._need_ready() | |
| if 'light_curtain_blocked' in self.faults: | |
| raise ActionRejected('LIGHT_CURTAIN_BLOCKED') | |
| self.door_target = 0.0 | |
| return dict(target_m=0.0, duration_s=self.door / DOOR_SPEED_M_S) | |
| def _cmd_xray_set(self, voltage_v, current_a): | |
| self._need_plant() | |
| if voltage_v * current_a > XRAY_POWER_MAX_W + 1e-9: | |
| raise ActionRejected('POWER_LIMIT') | |
| if self.op is not None and self.op['kind'] in ('flat_field', 'geometry_calibration', 'radiograph', 'projections'): | |
| raise ActionRejected('MEASUREMENT_RUNNING') | |
| self.xv_set, self.xi_set = voltage_v, current_a | |
| return dict(voltage_v=voltage_v, current_a=current_a, power_w=voltage_v * current_a, focal_spot_m=focal_spot_m(voltage_v * current_a)) | |
| def _cmd_xray_enable(self, enabled): | |
| if not enabled: | |
| self._need_plant() | |
| if self.op is not None and self.op['kind'] in ('flat_field', 'geometry_calibration', 'radiograph', 'projections'): | |
| raise ActionRejected('MEASUREMENT_RUNNING') | |
| self._beam_off(None) | |
| return dict(enabled=False, warmup_s=0.0, ramp_s=0.0) | |
| self._need_ready() | |
| if not self._door_closed(): | |
| raise ActionRejected('DOOR_OPEN') | |
| if not self._interlock_ok(): | |
| raise ActionRejected('INTERLOCK_OPEN') | |
| if 'xray_arc' in self.faults: | |
| raise ActionRejected('XRAY_ARC') | |
| if self.x_enabled: | |
| return dict(enabled=True, warmup_s=max(0.0, self.warm_end - self.t) if self.warm_end else 0.0, ramp_s=self._ramp_time()) | |
| self.x_enabled = True | |
| warm = 0.0 | |
| if self.warm_needed: | |
| self.warm_from, self.warm_end = self.t, self.t + WARMUP_S | |
| self.warm_v, self.warm_i = self.xv_set, self.xi_set | |
| warm = WARMUP_S | |
| self._event('xray', 'WARMUP', f'X射线预热程序{WARMUP_S:.0f} s') | |
| self._event('xray', 'XRAY_ON', 'X射线开启') | |
| self._rate_cache.clear() | |
| return dict(enabled=True, warmup_s=warm, ramp_s=0.0 if warm else self._ramp_time()) | |
| def _ramp_time(self): | |
| return max(abs(self.xv_set - self.xv) / KV_RAMP_V_S, abs(self.xi_set - self.xi) / CURRENT_RAMP_A_S) | |
| def _cmd_filter_select(self, position): | |
| self._need_ready() | |
| self._need_idle() | |
| self.filter_pos = position | |
| self.slide_target = position * FILTER_PITCH_M | |
| self._rate_cache.clear() | |
| return dict(filter=filter_of(position)['label'], duration_s=abs(self.slide_target - self.slide) / (FILTER_PITCH_M / FILTER_S_PER_STEP)) | |
| def _stage_checks(self): | |
| self._need_ready() | |
| if 'rotation_stall' in self.faults: | |
| raise ActionRejected('STAGE_FAULT') | |
| self._need_idle() | |
| def _latch_persisting_causes(self): | |
| """Latch the error of the highest-priority cause that is still present (fixed order: safety button, interlock sensor, tube arc, | |
| rotation stall).""" | |
| if self.estop: | |
| self._raise_error('EMERGENCY_STOP') | |
| for f in FAULT_PRIORITY: | |
| if f in self.faults and FAULT_ERROR.get(f): | |
| self._raise_error(FAULT_ERROR[f]) | |
| def _forbidden_boxes(self, s, ox, oy): | |
| """Open rectangles in the (SOD, chuck height) plane that the moving column must not enter (source head / filter slide and detector | |
| housing for each of its cylinders: stage housing, chuck, pin, sample) and the highest allowed chuck height (ceiling).""" | |
| bz = SOURCE_XYZ_M[2] | |
| segs = [(CHUCK_R_M, -CHUCK_H_M, 0.0), (STAGE_R_M, -CHUCK_H_M - STAGE_H_M, -CHUCK_H_M)] | |
| top = 0.0 | |
| if s is not None: | |
| ecc = math.hypot(ox, oy) | |
| z0 = 0.0 | |
| if s['pin']: | |
| segs.append((s['pin']['diameter_m'] / 2 + ecc, 0.0, s['pin']['length_m'])) | |
| z0 = s['pin']['length_m'] | |
| segs.append((sample_radius_total(s) + ecc, z0, z0 + s['height_m'])) | |
| top = z0 + s['height_m'] | |
| boxes = [] | |
| for r, a, b in segs: | |
| boxes.append(((-math.inf, FILTER_CLEAR_M + COLLISION_MARGIN_M + r), (bz + SOURCE_KEEPOUT_DZ[0] - b, bz + SOURCE_KEEPOUT_DZ[1] - a))) | |
| boxes.append(((SDD_M - DETECTOR_COVER_M - COLLISION_MARGIN_M - r, math.inf), (bz + DETECTOR_KEEPOUT_DZ[0] - b, bz + DETECTOR_KEEPOUT_DZ[1] - a))) | |
| return boxes, CHAMBER_CEILING_M - COLLISION_MARGIN_M - top | |
| def _path_ok(self, sod1, cz1): | |
| """Swept-path keep-out check: carriage and lift start together at their own speeds, so the column follows two straight segments in | |
| the (SOD, chuck height) plane; neither may cross a forbidden rectangle.""" | |
| s = self.samples[self.on_stage] if self.on_stage else None | |
| boxes, cz_max = self._forbidden_boxes(s, s['offset_x_m'] if s else 0.0, s['offset_y_m'] if s else 0.0) | |
| s0, c0 = self.sod, self.cz | |
| ts, tz = abs(sod1 - s0) / CARRIAGE_SPEED_M_S, abs(cz1 - c0) / LIFT_SPEED_M_S | |
| if ts <= tz: # the carriage arrives first: the corner lies exactly on its target | |
| mid = (sod1, c0 + math.copysign(LIFT_SPEED_M_S * ts, cz1 - c0) if tz > 0 else c0) | |
| else: | |
| mid = (s0 + math.copysign(CARRIAGE_SPEED_M_S * tz, sod1 - s0), cz1) | |
| pts = [(s0, c0), mid, (sod1, cz1)] | |
| if max(p[1] for p in pts) > cz_max + 1e-12: | |
| return False | |
| return not any(_segment_hits_box(pts[k], pts[k + 1], box) for k in range(2) for box in boxes) | |
| def _recon_region(self, data, axis): | |
| """Reconstructable region of an acquisition window (as in _fdk): radius about the axis and the height range at that radius, less the | |
| +-200 um the automatic alignment may shift the axis.""" | |
| w, sod = data['window'], data['sod'] | |
| us = (w['u0'] + (np.arange(w['nu']) + 0.5) * w['pitch'] - axis * SDD_M / sod) * sod / SDD_M | |
| vs = (w['v1'] - (np.arange(w['nv']) + 0.5) * w['pitch']) * sod / SDD_M | |
| fov_r = min(abs(us.min()), abs(us.max())) * sod / math.hypot(sod, abs(us).max()) - 200e-6 | |
| return fov_r, float(vs.min()) * (sod - fov_r) / sod, float(vs.max()) * (sod - fov_r) / sod | |
| def _move_stage(self, sod, cz, label=None): | |
| if not self._geometry_ok(sod, cz) or not self._path_ok(sod, cz): | |
| raise ActionRejected('COLLISION_RISK') | |
| self.sod_target, self.cz_target = sod, cz | |
| self.position_label = label | |
| d = max(abs(sod - self.sod) / CARRIAGE_SPEED_M_S, abs(cz - self.cz) / LIFT_SPEED_M_S) | |
| return dict(target=[sod, cz], duration_s=d, magnification=SDD_M / sod) | |
| def _cmd_stage_move(self, sod_m, chuck_z_m): | |
| self._stage_checks() | |
| out = self._move_stage(sod_m, chuck_z_m) | |
| return out | |
| def _cmd_stage_go_to(self, position): | |
| self._stage_checks() | |
| p = LOAD_POSITION if position == 'load' else CENTER_POSITION | |
| out = self._move_stage(p['sod'], p['cz'], position) | |
| return dict(target=out['target'], duration_s=out['duration_s']) | |
| def _cmd_stage_rotate(self, angle_rad): | |
| self._stage_checks() | |
| self.rot_target = angle_rad % (2 * math.pi) | |
| return dict(target_rad=self.rot_target, duration_s=abs(_rot_delta(self.rot, self.rot_target)) / ROTATION_SPEED_RAD_S) | |
| def _cmd_scan_configure(self, range_deg, step_rad, exposure_s, averaging, binning, random_movement): | |
| self._need_plant() | |
| self._need_idle() | |
| s = dict(range_deg=range_deg, step_rad=step_rad, exposure_s=exposure_s, averaging=averaging, binning=binning, random_movement=random_movement) | |
| n = self._nominal_projections(s) | |
| self.scan_settings = s | |
| return dict(settings=dict(s), projections=n, duration_s=self._scan_duration(s)) | |
| # ---------------------------------------------------------------- operations | |
| def _new_op(self, kind, rid=None): | |
| self.seq['op'] += 1 | |
| oid = f'op{self.seq["op"]:05d}' | |
| self.operations[oid] = dict(operation_id=oid, kind=kind, phase='running', record_id=rid, started_s=self.t, reason=None) | |
| return oid | |
| def _new_record_id(self, prefix, key): | |
| if len(self.records) >= MAX_RECORDS: | |
| raise ActionRejected('RECORDS_FULL') | |
| self.seq[key] += 1 | |
| return f'{prefix}{self.seq[key]:04d}' | |
| def _acq_checks(self, need_sample=True, need_flat=True): | |
| self._need_ready() | |
| self._need_idle() | |
| self._need_still() | |
| if not self._door_closed(): | |
| raise ActionRejected('DOOR_OPEN') | |
| if not self._xray_ready(): | |
| raise ActionRejected('XRAY_NOT_READY') | |
| if 'rotation_stall' in self.faults: | |
| raise ActionRejected('STAGE_FAULT') | |
| if need_sample and self.on_stage is None: | |
| raise ActionRejected('NO_SAMPLE') | |
| if need_flat and not self._flat_valid(): | |
| raise ActionRejected('FLAT_FIELD_REQUIRED') | |
| def _xsnap(self): | |
| return dict(voltage_v=self.xv_set, current_a=self.xi_set, power_w=self.xv_set * self.xi_set, filter=filter_of(self.filter_pos)['label'], | |
| focal_spot_m=focal_spot_m(self.xv_set * self.xi_set)) | |
| def _record_stub(self, rid, kind, ctx): | |
| r = dict(record_id=rid, kind=kind, status='running', started_s=self.t, finished_s=None, reason=None, sample_id=ctx.get('sample_id'), | |
| xray=self._xsnap() if kind != 'volume' else None, scan=dict(ctx['scan']) if ctx.get('scan') else None, sod_m=ctx.get('sod'), sdd_m=SDD_M, | |
| magnification=SDD_M / ctx['sod'] if ctx.get('sod') else None, | |
| voxel_size_nominal_m=PIXEL_PITCH_M * int(ctx['scan']['binning'][0]) * ctx['sod'] / SDD_M if ctx.get('scan') and ctx.get('sod') else None, | |
| projections_nominal=ctx.get('n_nom', 0), projections_simulated=ctx.get('n_sim', 0), sim_detector=list(SIM_DETECTOR), sim_pixel_m=None, transmission=None, | |
| saturated_fraction=None, dose_gy=None, duration_s=0.0, preview=None, preview_unit=None, source_record_id=ctx.get('source'), recon=None, volume=None, | |
| flat_field=None, geometry=None, warnings=[], template_source=dict(library=LIBRARY_REL, substances=sorted(ctx.get('materials', []))), note_zh='') | |
| self.records[rid] = r | |
| return r | |
| def _start_op(self, kind, record_id, items, ctx): | |
| oid = self._new_op(kind, record_id) | |
| t, ends = self.t, [] | |
| for it in items: | |
| t += it[1] | |
| ends.append(t) | |
| self.op = dict(kind=kind, op=oid, record_id=record_id, t0=self.t, duration_s=ends[-1] - self.t if ends else 0.0, items=items, ends=ends, i=-1, | |
| phase=None, ctx=ctx) | |
| self._next_item() | |
| return dict(operation_id=oid) | |
| def _next_item(self): | |
| o = self.op | |
| while o is not None: | |
| o['i'] += 1 | |
| if o['i'] >= len(o['items']): | |
| return | |
| it = o['items'][o['i']] | |
| o['phase'] = it[0] | |
| if it[0] == 'rotate': # scan rotation driven by the phase clock (a full turn returns to the start) | |
| o['rot0'], o['rot_amount'], o['rot_t0'], o['rot_dur'] = self.rot, it[2], self.t, it[1] | |
| elif it[0] == 'call': | |
| getattr(self, it[2])(*it[3:]) | |
| if self.op is not o: | |
| return | |
| if self.t < o['ends'][o['i']] - 1e-12: | |
| return | |
| def _ctx(self, kind, materials=None): | |
| s = self.samples.get(self.on_stage) if self.on_stage else None | |
| return dict(kind=kind, sample_id=self.on_stage, sod=self.sod, cz=self.cz, rot0=self.rot, scan=dict(self.scan_settings), kv=self.xv_set, ia=self.xi_set, | |
| filter=self.filter_pos, seed=self._op_seed(kind), axis=self.truth['axis_offset'], defects=list(self.truth['defects']), | |
| materials=_materials(s) if s else [], flat=self.flat, offset=(s['offset_x_m'], s['offset_y_m']) if s else (0.0, 0.0), | |
| axis_known=self.geo_cal['axis_offset_m']) | |
| def _op_seed(self, tag): | |
| self.seq[tag] = self.seq.get(tag, 0) + 1 | |
| return int(hashlib.sha256(f'{self._seed()}|{tag}|{self.seq[tag]}'.encode()).hexdigest()[:12], 16) | |
| def _cmd_calibration_flat_field(self): | |
| self._acq_checks(need_sample=False, need_flat=False) | |
| if self._anything_in_field(): | |
| raise ActionRejected('SAMPLE_IN_BEAM') | |
| rid = self._new_record_id('FF', 'ff') | |
| ctx = self._ctx('flat_field') | |
| self._record_stub(rid, 'flat_field', ctx) | |
| tf = FLAT_FIELD_FRAMES * (self.scan_settings['exposure_s'] + FRAME_OVERHEAD_S) | |
| items = [('dark', tf), ('bright', tf), ('call', 0.0, '_finish_flat_field')] | |
| return self._start_op('flat_field', rid, items, ctx) | |
| def _cyl_on_detector(self, r, zb, zt, full=False): | |
| """Does a vertical cylinder of radius r about the rotation axis between heights zb..zt above the beam project onto the detector | |
| (full=True: completely)?""" | |
| half_u, half_v = DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2, DETECTOR_PIXELS[1] * PIXEL_PITCH_M / 2 | |
| sod = self.sod | |
| near, far = sod - r, sod + r | |
| uc = SDD_M * self.truth['axis_offset'] / sod | |
| uh = SDD_M * r / math.sqrt(max(sod * sod - r * r, 1e-12)) | |
| vs = [SDD_M * z / d for z in (zb, zt) for d in (near, far)] | |
| if full: | |
| return abs(uc) + uh <= half_u and -half_v <= min(vs) and max(vs) <= half_v | |
| return abs(uc) - uh < half_u and max(vs) > -half_v and min(vs) < half_v | |
| def _sample_in_field(self): | |
| """Does the sample body (envelope cylinder, container included; not the mounting pin) project onto the detector?""" | |
| s = self.samples[self.on_stage] | |
| zb = self.cz - SOURCE_XYZ_M[2] + (s['pin']['length_m'] if s['pin'] else 0.0) | |
| return self._cyl_on_detector(self._envelope(s, s['offset_x_m'], s['offset_y_m']), zb, zb + s['height_m']) | |
| def _anything_in_field(self): | |
| """Sample, mounting pin, chuck or rotation-stage housing in the beam (a flat field must see the empty beam).""" | |
| z = self.cz - SOURCE_XYZ_M[2] | |
| if self._cyl_on_detector(STAGE_HOUSING_R_M, z - CHUCK_H_M - STAGE_H_M, z): | |
| return True | |
| if self.on_stage is None: | |
| return False | |
| s = self.samples[self.on_stage] | |
| return self._cyl_on_detector(self._envelope(s, s['offset_x_m'], s['offset_y_m']), z, z + sample_height_total(s)) | |
| def _cmd_calibration_geometry(self): | |
| self._acq_checks(need_sample=True) | |
| s = self.samples[self.on_stage] | |
| if s['kind'] != 'calibration_phantom': | |
| raise ActionRejected('PHANTOM_REQUIRED') | |
| zb = self.cz - SOURCE_XYZ_M[2] + (s['pin']['length_m'] if s['pin'] else 0.0) | |
| if not self._cyl_on_detector(self._envelope(s, s['offset_x_m'], s['offset_y_m']), zb, zb + s['height_m'], full=True): | |
| raise ActionRejected('PHANTOM_NOT_IN_FIELD') # every ball must stay on the detector at every angle | |
| rid = self._new_record_id('GC', 'gc') | |
| ctx = self._ctx('geometry_calibration') | |
| ctx['n_nom'] = ctx['n_sim'] = 36 | |
| self._record_stub(rid, 'geometry_calibration', ctx) | |
| tp = self._projection_time() | |
| items = [('rotate', 36 * tp, 2 * math.pi), ('call', 0.0, '_finish_geometry_calibration')] | |
| return self._start_op('geometry_calibration', rid, items, ctx) | |
| def _cmd_xray_radiograph(self, roi): | |
| self._acq_checks(need_sample=False) | |
| if roi is not None: | |
| half = roi['size_px'] / 2 * PIXEL_PITCH_M * self._binning() | |
| if abs(roi['center_u_m']) + half > DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2 + 1e-12 or \ | |
| abs(roi['center_v_m']) + half > DETECTOR_PIXELS[1] * PIXEL_PITCH_M / 2 + 1e-12: | |
| raise ActionRejected('ROI_OUTSIDE_DETECTOR') | |
| rid = self._new_record_id('RG', 'rg') | |
| ctx = self._ctx('radiograph') | |
| ctx['roi'] = copy.deepcopy(roi) | |
| ctx['n_nom'] = ctx['n_sim'] = 1 | |
| self._record_stub(rid, 'radiograph', ctx) | |
| s = self.scan_settings | |
| items = [('expose', s['averaging'] * (s['exposure_s'] + FRAME_OVERHEAD_S)), ('call', 0.0, '_finish_radiograph')] | |
| return self._start_op('radiograph', rid, items, ctx) | |
| def _cmd_scan_start(self): | |
| self._acq_checks(need_sample=True) | |
| if not self._sample_in_field(): | |
| raise ActionRejected('SAMPLE_NOT_IN_FIELD') | |
| rid = self._new_record_id('PJ', 'pj') | |
| ctx = self._ctx('projections') | |
| n = self._nominal_projections() | |
| ctx['n_nom'] = n | |
| ctx['n_sim'] = min(n, SIM_MAX_PROJECTIONS) | |
| ctx['span'] = self._scan_span() | |
| ctx['dose0'] = self.samples[self.on_stage].get('dose_gy', 0.0) | |
| self._record_stub(rid, 'projections', ctx) | |
| items = [('rotate', n * self._projection_time(), ctx['span']), ('call', 0.0, '_finish_scan')] | |
| return self._start_op('projections', rid, items, ctx) | |
| def _cmd_records_delete(self, record_id): | |
| self._need_plant() | |
| r = self.records.get(record_id) | |
| if r is None: | |
| raise ActionRejected('UNKNOWN_RECORD') | |
| if r['status'] == 'running' or (self.recon is not None and self.recon['ctx']['source'] == record_id): | |
| raise ActionRejected('RECORD_IN_USE') | |
| del self.records[record_id] | |
| self._data.pop(record_id, None) | |
| if self.last_porosity_rid == record_id: | |
| self.last_porosity = self.last_porosity_rid = None | |
| self._event('measurement', 'RECORD_DELETED', f'记录{record_id}已删除', rid=record_id) | |
| return dict(record_id=record_id, remaining=len(self.records)) | |
| def _cmd_recon_start(self, record_id, grid, filter, beam_hardening, bh_material, ring_correction, smoothing_vox, post_alignment, auto_alignment, voi): | |
| self._need_plant() | |
| src = self.records.get(record_id) | |
| if src is None: | |
| raise ActionRejected('UNKNOWN_RECORD') | |
| if src['kind'] != 'projections' or src['status'] != 'completed': | |
| raise ActionRejected('RECORD_NOT_SUITABLE') | |
| if bh_material is not None: | |
| substance(bh_material) | |
| if self.recon is not None: | |
| raise ActionRejected('RECON_BUSY') | |
| data = self._data.get(record_id) | |
| if data is None: | |
| raise ActionRejected('DATA_NOT_CACHED') | |
| voi_partial = False | |
| if voi is not None: | |
| fov_r, z_lo, z_hi = self._recon_region(data, self.geo_cal['axis_offset_m'] or 0.0) | |
| cx, cy, cz_ = voi['center_m'] | |
| sx, sy, sz = voi['size_m'] | |
| if math.hypot(cx, cy) > fov_r or not z_lo <= cz_ <= z_hi: | |
| raise ActionRejected('INVALID_VOI') # the centre must lie in the reconstructable region | |
| voi_partial = math.hypot(abs(cx) + sx / 2, abs(cy) + sy / 2) > fov_r + 1e-12 or cz_ - sz / 2 < z_lo or cz_ + sz / 2 > z_hi | |
| rid = self._new_record_id('VO', 'vo') | |
| n = int(grid) | |
| ctx = dict(kind='volume', source=record_id, sample_id=src['sample_id'], sod=src['sod_m'], scan=src['scan'], | |
| recon=dict(grid=grid, filter=filter, beam_hardening=beam_hardening, bh_material=bh_material, ring_correction=ring_correction, | |
| smoothing_vox=smoothing_vox, post_alignment=post_alignment, auto_alignment=auto_alignment, voi=copy.deepcopy(voi)), | |
| n_nom=src['projections_nominal'], n_sim=src['projections_simulated'], materials=src['template_source']['substances'], | |
| axis_cal=self.geo_cal['axis_offset_m'], voi_partial=voi_partial) | |
| r = self._record_stub(rid, 'volume', ctx) | |
| r['recon'] = dict(ctx['recon']) | |
| r['xray'] = copy.deepcopy(src['xray']) | |
| b = int(src['scan']['binning'][0]) | |
| frac = 1.0 if voi is None else min(1.0, float(np.prod(voi['size_m'])) / (self._fov(src['sod_m'])[0] ** 2 * self._fov(src['sod_m'])[1])) | |
| t = (DETECTOR_PIXELS[0] / b) ** 2 * (DETECTOR_PIXELS[1] / b) * frac * src['projections_nominal'] / RECON_RATE_VOXEL_PROJ_S + RECON_OVERHEAD_S | |
| oid = self._new_op('recon', rid) | |
| self.recon = dict(kind='recon', op=oid, record_id=rid, t0=self.t, duration_s=t, ctx=ctx) | |
| return dict(operation_id=oid) | |
| def _complete(self, o, r, dur=None): | |
| r.update(status='completed', finished_s=self.t, duration_s=self.t - r['started_s'] if dur is None else dur) | |
| self.operations[o['op']].update(phase='completed', finished_s=self.t) | |
| self._event('measurement', 'OP_DONE', f'操作{o["op"]}完成,记录{r["record_id"]}', rid=r['record_id']) | |
| if self.recon is o: | |
| self.recon = None | |
| else: | |
| self.op = None | |
| def _fail_op(self, code): | |
| o = self.op | |
| if o is None: | |
| return | |
| self.operations[o['op']].update(phase='failed', finished_s=self.t, reason=code) | |
| if o['record_id'] in self.records: | |
| r = self.records[o['record_id']] | |
| r.update(status='failed', finished_s=self.t, reason=code, duration_s=self.t - r['started_s']) | |
| self._event('measurement', 'OP_FAILED', f'操作{o["op"]}失败:{code}', rid=o['record_id']) | |
| self.op = None | |
| self.rot_target = self.rot | |
| def _cancel_op(self, op): | |
| if self.recon is not None and self.recon['op'] == op['operation_id']: | |
| o = self.recon | |
| self.operations[o['op']].update(phase='cancelled', finished_s=self.t, reason='USER_CANCEL') | |
| r = self.records[o['record_id']] | |
| r.update(status='cancelled', finished_s=self.t, reason='USER_CANCEL', duration_s=self.t - r['started_s']) | |
| self._event('measurement', 'OP_CANCELLED', f'重建{o["op"]}取消', rid=o['record_id']) | |
| self.recon = None | |
| return | |
| o = self.op | |
| if o is None or o['op'] != op['operation_id']: | |
| raise ActionRejected('NOT_RUNNING') | |
| self.operations[o['op']].update(phase='cancelled', finished_s=self.t, reason='USER_CANCEL') | |
| if o['record_id'] in self.records: | |
| r = self.records[o['record_id']] | |
| r.update(status='cancelled', finished_s=self.t, reason='USER_CANCEL', duration_s=self.t - r['started_s']) | |
| self._event('measurement', 'OP_CANCELLED', f'操作{o["op"]}取消', rid=o['record_id']) | |
| self.op = None | |
| self.rot_target = self.rot | |
| # ---------------------------------------------------------------- time | |
| def _cmd_sim_step(self, dt_s): | |
| self.step(dt_s) | |
| return dict(time_s=self.t) | |
| def step(self, dt_s): | |
| if not (isinstance(dt_s, (int, float)) and math.isfinite(dt_s) and dt_s >= 0): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| t_end = self.t + dt_s | |
| guard = 0 | |
| while self.t < t_end and guard < 1_000_000: | |
| guard += 1 | |
| h = min(t_end - self.t, self._next_event_dt()) | |
| self._advance(h) | |
| self.t = t_end if h >= t_end - self.t else self.t + h | |
| self._handle_events() | |
| self._handle_events() | |
| def _xray_targets(self): | |
| """Voltage and current the tube is driven towards now (warm-up program: linear from 0 to the set point over WARMUP_S).""" | |
| if not (self.power and self.x_enabled and self._interlock_ok()): | |
| return 0.0, 0.0 | |
| if self.warm_end is not None: | |
| f = min(1.0, max(0.0, (self.t - self.warm_from) / WARMUP_S)) | |
| return self.warm_v * f, self.warm_i * f | |
| return self.xv_set, self.xi_set | |
| def _next_event_dt(self): | |
| c = [math.inf] | |
| if self.state == 'booting': | |
| c.append(self.state_t0 + BOOT_S - self.t) | |
| if self.power: | |
| if self._door_moving(): | |
| c.append(abs(self.door_target - self.door) / DOOR_SPEED_M_S) | |
| if self._filter_moving(): | |
| c.append(abs(self.slide_target - self.slide) / (FILTER_PITCH_M / FILTER_S_PER_STEP)) | |
| if abs(self.sod - self.sod_target) > 1e-12: | |
| c.append(abs(self.sod_target - self.sod) / CARRIAGE_SPEED_M_S) | |
| if abs(self.cz - self.cz_target) > 1e-12: | |
| c.append(abs(self.cz_target - self.cz) / LIFT_SPEED_M_S) | |
| if not (self.op and self.op.get('phase') == 'rotate') and abs(_rot_delta(self.rot, self.rot_target)) > 1e-12: | |
| c.append(abs(_rot_delta(self.rot, self.rot_target)) / ROTATION_SPEED_RAD_S) | |
| if self.warm_end is not None: | |
| c.append(self.warm_end - self.t) | |
| elif self.x_enabled: | |
| tv, ti = self._xray_targets() | |
| if abs(self.xv - tv) > 1e-6: | |
| c.append(abs(tv - self.xv) / KV_RAMP_V_S) | |
| if abs(self.xi - ti) > 1e-12: | |
| c.append(abs(ti - self.xi) / CURRENT_RAMP_A_S) | |
| o = self.op | |
| if o is not None and 0 <= o['i'] < len(o['ends']): | |
| c.append(o['ends'][o['i']] - self.t) | |
| if self.recon is not None: | |
| c.append(self.recon['t0'] + self.recon['duration_s'] - self.t) | |
| if self._beam_live(): | |
| c += self._cell_boundary_dt() | |
| return max(0.0, min(c)) | |
| def _beam_live(self): | |
| """The tube emits now or starts to within the next sub-step (ramping up from zero).""" | |
| return self.power and (self._xray_on() or (self.x_enabled and self._interlock_ok())) | |
| def _cell_boundary_dt(self): | |
| """Times until a moving quantity crosses the next boundary of the energy-rate cells (rotation 2 pi / 32, carriage and lift 0.25 mm, | |
| filter slide one position pitch, voltage 1 kV): every sub-step with the beam on then lies inside one cell, so the booked energy does not | |
| depend on the host steps.""" | |
| c = [] | |
| o = self.op | |
| if o is not None and o.get('phase') == 'rotate' and o['rot_dur'] > 0: | |
| w = o['rot_amount'] / o['rot_dur'] | |
| else: | |
| d = _rot_delta(self.rot, self.rot_target) | |
| w = math.copysign(ROTATION_SPEED_RAD_S, d) if abs(d) > 1e-12 else 0.0 | |
| if w: | |
| c.append(_to_boundary(self.rot, w, RATE_ROT_CELL_RAD)) | |
| for x, tgt, v in ((self.sod, self.sod_target, CARRIAGE_SPEED_M_S), (self.cz, self.cz_target, LIFT_SPEED_M_S)): | |
| if abs(tgt - x) > 1e-12: | |
| c.append(_to_boundary(x, math.copysign(v, tgt - x), RATE_POS_CELL_M)) | |
| if abs(self.slide_target - self.slide) > 1e-12: | |
| c.append(_to_boundary(self.slide, math.copysign(FILTER_PITCH_M / FILTER_S_PER_STEP, self.slide_target - self.slide), FILTER_PITCH_M)) | |
| if self.warm_end is not None: | |
| rate = self.warm_v / WARMUP_S | |
| else: | |
| tv, _ = self._xray_targets() | |
| rate = math.copysign(KV_RAMP_V_S, tv - self.xv) if abs(tv - self.xv) > 1e-6 else 0.0 | |
| if rate: | |
| c.append(_to_boundary(self.xv, rate, RATE_KV_CELL_V)) | |
| return c | |
| def _advance(self, h): | |
| if h <= 0: | |
| return | |
| if self.power: | |
| v0, i0, rot0, sod0, cz0, sl0 = self.xv, self.xi, self.rot, self.sod, self.cz, self.slide | |
| was = self.door != self.door_target | |
| self.door = _axis_move(self.door, self.door_target, DOOR_SPEED_M_S, h) | |
| if was and self.door == self.door_target: | |
| self.led['door_cycles'].add(0.5) | |
| self._event('door', 'DOOR_' + ('OPEN' if self.door > 0 else 'CLOSED'), '门已打开' if self.door > 0 else '门已关闭', t=self.t + h) | |
| self.slide = _axis_move(self.slide, self.slide_target, FILTER_PITCH_M / FILTER_S_PER_STEP, h) | |
| new = _axis_move(self.sod, self.sod_target, CARRIAGE_SPEED_M_S, h) | |
| self.led['carriage_travel_m'].add(abs(new - self.sod)); self.sod = new | |
| new = _axis_move(self.cz, self.cz_target, LIFT_SPEED_M_S, h) | |
| self.led['lift_travel_m'].add(abs(new - self.cz)); self.cz = new | |
| o = self.op | |
| if o is not None and o.get('phase') == 'rotate': | |
| f = min(1.0, (self.t + h - o['rot_t0']) / o['rot_dur']) if o['rot_dur'] > 0 else 1.0 | |
| new = (o['rot0'] + o['rot_amount'] * f) % (2 * math.pi) | |
| self.led['rotation_rad'].add(abs(o['rot_amount']) * h / o['rot_dur'] if o['rot_dur'] > 0 else 0.0) | |
| self.rot = self.rot_target = new | |
| else: | |
| d = _rot_delta(self.rot, self.rot_target) | |
| step = min(abs(d), ROTATION_SPEED_RAD_S * h) | |
| self.led['rotation_rad'].add(step) | |
| self.rot = (self.rot + math.copysign(step, d)) % (2 * math.pi) if abs(d) > step else self.rot_target | |
| if self.warm_end is not None or self.x_enabled: | |
| tv, ti = self._xray_targets() | |
| if self.warm_end is not None: | |
| f = min(1.0, max(0.0, (self.t + h - self.warm_from) / WARMUP_S)) | |
| self.xv, self.xi = self.warm_v * f, self.warm_i * f | |
| else: | |
| self.xv = _axis_move(self.xv, tv, KV_RAMP_V_S, h) | |
| self.xi = _axis_move(self.xi, ti, CURRENT_RAMP_A_S, h) | |
| if (v0 > 0.0 and i0 > 0.0) or self._xray_on(): | |
| self.led['xray_on_s'].add(h) | |
| pose = dict(xv=0.5 * (v0 + self.xv), rot=(rot0 + 0.5 * _rot_delta(rot0, self.rot)) % (2 * math.pi), sod=0.5 * (sod0 + self.sod), | |
| cz=0.5 * (cz0 + self.cz), slide=0.5 * (sl0 + self.slide)) | |
| self._book_energy(h, v0, i0, self.xv, self.xi, pose) | |
| def _handle_events(self): | |
| for _ in range(10000): | |
| changed = False | |
| if self.state == 'booting' and self.t >= self.state_t0 + BOOT_S - 1e-9: | |
| self.state = 'ready' | |
| self._event('power', 'READY', '启动完成(各轴为绝对位置,保持断电时的位置)') | |
| changed = True | |
| if self.power: | |
| if abs(self.slide - self.slide_target) <= 1e-12: | |
| self.slide = self.slide_target | |
| for a, b in (('sod', 'sod_target'), ('cz', 'cz_target')): | |
| if abs(getattr(self, a) - getattr(self, b)) <= 1e-12: | |
| setattr(self, a, getattr(self, b)) | |
| if self.warm_end is not None and self.t >= self.warm_end - 1e-9: | |
| self.warm_end = self.warm_from = None | |
| self.warm_needed = False | |
| self.xv, self.xi = self.warm_v, self.warm_i # the program's end point; a newer set point follows with the ramp | |
| self._event('xray', 'WARMUP_DONE', '预热完成') | |
| changed = True | |
| o = self.op | |
| if o is not None and 0 <= o['i'] < len(o['ends']) and self.t >= o['ends'][o['i']] - 1e-9: | |
| it = o['items'][o['i']] | |
| if it[0] == 'rotate': | |
| self.rot = self.rot_target = (o['rot0'] + o['rot_amount']) % (2 * math.pi) | |
| self._next_item() | |
| changed = True | |
| rc = self.recon | |
| if rc is not None and self.t >= rc['t0'] + rc['duration_s'] - 1e-9: | |
| self._finish_recon(rc) | |
| changed = True | |
| if not changed: | |
| return | |
| # ---------------------------------------------------------------- energy ledger | |
| def _to_sample(self, s, D, sod, cz, rot, axis, ox, oy): | |
| c, sn = math.cos(-rot), math.sin(-rot) | |
| Rm = np.array([[c, -sn, 0.0], [sn, c, 0.0], [0.0, 0.0, 1.0]]) | |
| zb = cz - SOURCE_XYZ_M[2] + (s['pin']['length_m'] if s['pin'] else 0.0) | |
| S = Rm @ np.array([-sod, -axis, 0.0]) - np.array([ox, oy, zb]) | |
| return S, D @ Rm.T | |
| def _frame(self, s, D, sod, cz, rot, axis): | |
| """Sample frame of a pose (origin at the bottom centre of the sample body on its own axis; without a sample at the chuck top on the | |
| rotation axis): (S, directions, rotation axis x, y and chuck-top z in that frame).""" | |
| if s is not None: | |
| S, Ds = self._to_sample(s, D, sod, cz, rot, axis, s['offset_x_m'], s['offset_y_m']) | |
| return S, Ds, -s['offset_x_m'], -s['offset_y_m'], -(s['pin']['length_m'] if s['pin'] else 0.0) | |
| c, sn = math.cos(-rot), math.sin(-rot) | |
| Rm = np.array([[c, -sn, 0.0], [sn, c, 0.0], [0.0, 0.0, 1.0]]) | |
| S = Rm @ np.array([-sod, -axis, 0.0]) - np.array([0.0, 0.0, cz - SOURCE_XYZ_M[2]]) | |
| return S, D @ Rm.T, 0.0, 0.0, 0.0 | |
| def _book_energy(self, h, v0, i0, v1, i1, pose): | |
| """Energy of a sub-step inside one rate cell: the sinks scale with V^2 I (Kramers efficiency eta = K Z V times the power V I), the | |
| electrical energy with V I; V and I are linear in time within a sub-step (ramps and the warm-up program), so both integrals are exact.""" | |
| dv, di = v1 - v0, i1 - i0 | |
| vi = h * (v0 * i0 + 0.5 * (v0 * di + i0 * dv) + dv * di / 3.0) | |
| v2i = h * (v0 * v0 * i0 + 0.5 * (v0 * v0 * di + 2.0 * v0 * i0 * dv) + (2.0 * v0 * dv * di + i0 * dv * dv) / 3.0 + 0.25 * dv * dv * di) | |
| base, kv = self._base_rates(pose) | |
| f = v2i / (1.602176634e-19 * kv * kv) | |
| amt = {k: v * f for k, v in base.items()} | |
| amt['electrical_energy_j'] = vi | |
| amt['xray_emitted_j'] = KRAMERS_K_PER_V * 74 * v2i | |
| amt['energy_residual_j'] = amt['xray_emitted_j'] - sum(amt[k] for k in ENERGY_SINKS) | |
| for k, v in amt.items(): | |
| self.led[k].add(v) | |
| if self.on_stage is not None: | |
| s = self.samples[self.on_stage] | |
| dose = amt['sample_absorbed_j'] / max(sample_mass_kg(s), 1e-12) # energy absorbed in the sample body only | |
| s['dose_gy'] = s.get('dose_gy', 0.0) + dose | |
| self.led['sample_dose_gy'].add(dose) | |
| def _beam_filter(self, slide=None): | |
| """Filter position in the beam: the one nearest the slide (the spectrum changes while the slide passes, not at the command).""" | |
| return min(FILTER_POSITIONS - 1, max(0, int(round((self.slide if slide is None else slide) / FILTER_PITCH_M)))) | |
| def _rate_key(self, pose): | |
| """Cell of the pose: voltage (1 kV, at least 2 kV since the spectrum grid starts at 1 keV), filter in the beam, sample and its offsets, | |
| carriage and lift (0.25 mm), rotation (2 pi / 32).""" | |
| s = self.samples.get(self.on_stage) if self.on_stage else None | |
| return (max(2, int(round(pose['xv'] / RATE_KV_CELL_V))), self._beam_filter(pose.get('slide')), self.on_stage, (s['offset_x_m'], s['offset_y_m']) if s else None, | |
| int(round(pose['sod'] / RATE_POS_CELL_M)), int(round(pose['cz'] / RATE_POS_CELL_M)), | |
| int(round(pose['rot'] / RATE_ROT_CELL_RAD)) % RATE_ROT_CELLS) | |
| def _object_box(self, s, sod, cz, rot): | |
| """Rectangle of the detector plane holding the projection of the sample body with its container at the rotation angle of the rate | |
| cell (the cell's energy flow is evaluated at that pose): the tangents of the enclosing vertical cylinder about the sample's own axis | |
| and its height seen from the near and far side, clipped to the emission cone (the beam irradiates the sample beside the active area | |
| too); None when it misses the cone.""" | |
| c = SDD_M * math.tan(CONE_HALF_ANGLE_RAD) | |
| rt_ = sample_radius_total(s) | |
| ox, oy = s['offset_x_m'], s['offset_y_m'] | |
| xc = sod + ox * math.cos(rot) - oy * math.sin(rot) # sample axis in the source frame (beam along x) | |
| yc = self.truth['axis_offset'] + ox * math.sin(rot) + oy * math.cos(rot) | |
| rho = math.hypot(xc, yc) | |
| if rho <= rt_ or xc - rt_ <= 0.0: | |
| return -c, c, -c, c | |
| th, al = math.atan2(yc, xc), math.asin(rt_ / rho) | |
| us = [SDD_M * math.tan(th - al), SDD_M * math.tan(th + al)] | |
| z0 = cz - SOURCE_XYZ_M[2] + (s['pin']['length_m'] if s['pin'] else 0.0) | |
| vv = [SDD_M * z / (xc + sg * rt_) for z in (z0, z0 + s['height_m']) for sg in (-1, 1)] | |
| pu = 0.02 * (us[1] - us[0]) + 2 * PIXEL_PITCH_M | |
| pv = 0.02 * (max(vv) - min(vv)) + 2 * PIXEL_PITCH_M | |
| u0, u1 = max(us[0] - pu, -c), min(us[1] + pu, c) | |
| v0, v1 = max(min(vv) - pv, -c), min(max(vv) + pv, c) | |
| if u0 >= u1 or v0 >= v1: | |
| return None | |
| return u0, u1, v0, v1 | |
| def _ray_energy(self, e, ph_f, omega, r, det, up, mount, near, body, far): | |
| """Energy flow per electron (J) of a ray set through the objects in their order along each ray: the mount (stage housing, chuck and | |
| pin, stacked below the sample: first on rays going up, last on rays going down), the container wall before the inside of the tube, | |
| the sample body, the wall after it. Each object absorbs the mu_en / mu share of the energy it removes from the beam reaching it; | |
| returns air, holder (mount and container), body, scattered, detector deposited and passed (rays on the active area) and shielding | |
| (rays beside it). mount / near / body / far: {material: path lengths}.""" | |
| f, n = 0.5 * KEV, len(e) | |
| mu_air, _ = _mu_grid('nist_air', n) | |
| inc = ph_f * np.exp(-np.multiply.outer(r, mu_air)) # (rays, E) photons at the objects / detector plane | |
| W = inc * e | |
| out = dict(air=f * (float(omega.sum()) * float(ph_f @ e) - float(omega @ W.sum(1))), holder=0.0, body=0.0, scattered=0.0) | |
| def seg(paths): | |
| if not paths: | |
| return None | |
| mats = sorted(paths) | |
| L = np.stack([paths[m] for m in mats], 1) | |
| mt = L @ np.stack([_mu_grid(m, n)[0] for m in mats]) | |
| return mt, L @ np.stack([_mu_grid(m, n)[1] for m in mats]), np.exp(-mt) | |
| segs = [('holder', seg(mount)), ('holder', seg(near)), ('body', seg(body)), ('holder', seg(far))] | |
| T = [x[2] if x is not None else None for _, x in segs] | |
| def prod(ks): | |
| p = None | |
| for k in ks: | |
| if T[k] is not None: | |
| p = T[k] if p is None else p * T[k] | |
| return 1.0 if p is None else p | |
| before = [(prod([]), prod([1, 2, 3])), (prod([0]), prod([])), (prod([0, 1]), prod([1])), (prod([0, 1, 2]), prod([1, 2]))] # (up, down) | |
| u = up[:, None] | |
| for k, (g, x) in enumerate(segs): | |
| if x is None: | |
| continue | |
| mt, me, Tk = x | |
| bu, bd = before[k] | |
| R = W * (1.0 - Tk) * (np.where(u, bu, bd) if (np.ndim(bu) or np.ndim(bd)) else 1.0) | |
| A = np.divide(R * me, mt, out=np.zeros_like(R), where=mt > 0) | |
| ra, aa = f * float(omega @ R.sum(1)), f * float(omega @ A.sum(1)) | |
| out[g] += aa | |
| out['scattered'] += ra - aa | |
| at = inc * prod([0, 1, 2, 3]) | |
| _, edep = detector_response(tuple(e)) | |
| wd, ws = omega * det, omega * ~det | |
| out['dep'] = f * float(wd @ (at @ edep)) | |
| out['passed'] = f * float(wd @ (at @ (e - edep))) | |
| out['shield'] = f * float(ws @ (at @ e)) | |
| return out | |
| def _base_rates(self, pose): | |
| """Energy flow per electron (J) at the centre of the rate cell of the pose: the target absorbs the back half of the emission and the | |
| self-absorbed part of the front half (take-off path of the reflection target), the window and the filter their shares of the emission | |
| cone; the rays of the cone split into air, the sample body (absorbed: its dose), the holder and stage hardware (pin, container, chuck, | |
| housing), scattered, detector deposited and passed (rays on the active area) and shielding (rays beside it); the rest of the front | |
| half goes to the shielding. The coarse cells of the cone keep one ray each (rays meeting no object from a per-spectrum cache); the | |
| cells overlapping the projection box of the sample body (at the cell's angle) are cut at the box edges, the parts inside it split into | |
| sub-cells of a fine pitch (about LEDGER_FINE_RAYS rays over the box, at least 16 across either side), the parts beside it keep one | |
| ray; the pieces tile the cone, so every share is a sum of positive ray terms, and along each ray the objects absorb in their order | |
| (_ray_energy); returns (rates, cell voltage).""" | |
| key = self._rate_key(pose) | |
| kv = key[0] * RATE_KV_CELL_V | |
| base = self._rate_cache.get(key) | |
| if base is not None: | |
| return base, kv | |
| sod, cz, rot = key[4] * RATE_POS_CELL_M, key[5] * RATE_POS_CELL_M, key[6] * RATE_ROT_CELL_RAD | |
| fpos = key[1] | |
| s = self.samples.get(self.on_stage) if self.on_stage else None | |
| axis = self.truth['axis_offset'] | |
| e, ph_un = unabsorbed_spectrum(kv) | |
| _, ph_self = emitted_spectrum(kv) | |
| ph_win = ph_self * np.exp(-_mu_grid('be', len(e))[0] * BE_WINDOW_M) | |
| _, ph_f = beam_spectrum(kv, fpos) | |
| E = lambda ph: float((ph * e).sum() * 0.5 * KEV) # J per sr per electron | |
| omega_cone = 2 * math.pi * (1 - math.cos(CONE_HALF_ANGLE_RAD)) | |
| def objects(D, with_body): | |
| """(mount, near wall, body, far wall) paths of rays D; the sample frame keeps the vertical, so D[:, 2] > 0 is a ray going up.""" | |
| S, Ds, ax, ay, zt = self._frame(s, D, sod, cz, rot, axis) | |
| mount, near, bod, far = dict(hardware_paths(S, Ds, ax, ay, zt)), {}, {}, {} | |
| if s is not None: | |
| for sid, L in pin_paths(s, S, Ds).items(): | |
| _add(mount, sid, L) | |
| near, far = container_walls(s, S, Ds) | |
| if with_body: | |
| bod = body_paths(s, S, Ds) | |
| return mount, near, bod, far | |
| U, V, PU, PV, D, omega, r, det = _ledger_grid() | |
| box = self._object_box(s, sod, cz, rot) if s is not None else None | |
| sel = np.zeros(len(U), bool) | |
| if box is not None: | |
| u0, u1, v0, v1 = box | |
| sel = (U + PU / 2 > u0) & (U - PU / 2 < u1) & (V + PV / 2 > v0) & (V - PV / 2 < v1) | |
| tot = dict(air=0.0, dep=0.0, passed=0.0, shield=0.0, scattered=0.0, holder=0.0, body=0.0) | |
| c = np.flatnonzero(~sel) | |
| mount, near, _, far = objects(D[c], False) | |
| hit = np.zeros(len(c), bool) | |
| for L in list(mount.values()) + list(near.values()) + list(far.values()): | |
| hit |= L > 0 | |
| for k, a in zip(('air', 'dep', 'passed', 'shield'), _free_rays(kv, fpos)): | |
| tot[k] += float(a[c[~hit]].sum()) | |
| if hit.any(): | |
| ch = c[hit] | |
| o = self._ray_energy(e, ph_f, omega[ch], r[ch], det[ch], D[ch, 2] > 0, *({k: v[hit] for k, v in g.items()} for g in (mount, near, {}, far))) | |
| for k, v in o.items(): | |
| tot[k] += v | |
| w_used = float(omega[c].sum()) | |
| if sel.any(): | |
| u0, u1, v0, v1 = box | |
| nb = max(16, int(round(math.sqrt(LEDGER_FINE_RAYS * (u1 - u0) / (v1 - v0))))) # at least 16 rays across either side | |
| pu_f, pv_f = (u1 - u0) / nb, (v1 - v0) / max(16, int(round(LEDGER_FINE_RAYS / nb))) | |
| a0, a1, b0, b1 = U[sel] - PU[sel] / 2, U[sel] + PU[sel] / 2, V[sel] - PV[sel] / 2, V[sel] + PV[sel] / 2 | |
| ue = (a0, np.maximum(a0, u0), np.minimum(a1, u1), a1) # each cell cut at the box edges into 3 x 3 pieces | |
| ve = (b0, np.maximum(b0, v0), np.minimum(b1, v1), b1) | |
| pieces = [] | |
| for iu in range(3): | |
| for iv in range(3): | |
| lu, hu_, lv, hv_ = ue[iu], ue[iu + 1], ve[iv], ve[iv + 1] | |
| ok = (hu_ - lu > 1e-12) & (hv_ - lv > 1e-12) | |
| if iu == 1 and iv == 1: # inside the box: sub-cells of about the fine pitch | |
| nu_ = np.maximum(1, np.ceil((hu_ - lu) / pu_f - 1e-9)).astype(int) | |
| nv_ = np.maximum(1, np.ceil((hv_ - lv) / pv_f - 1e-9)).astype(int) | |
| else: # beside the box (no body at any angle): one ray | |
| nu_ = nv_ = np.ones(len(lu), int) | |
| pieces.append([x[ok] for x in (lu, hu_, lv, hv_, nu_, nv_)]) | |
| lu, hu_, lv, hv_, nu_, nv_ = (np.concatenate([p[k] for p in pieces]) for k in range(6)) | |
| cnt = nu_ * nv_ | |
| idx = np.repeat(np.arange(len(cnt)), cnt) | |
| j = np.arange(int(cnt.sum())) - np.repeat(np.cumsum(cnt) - cnt, cnt) | |
| wu, wv = (hu_ - lu) / nu_, (hv_ - lv) / nv_ | |
| Df, omf, rf, detf = _cell_rays(lu[idx] + (j % nu_[idx] + 0.5) * wu[idx], lv[idx] + (j // nu_[idx] + 0.5) * wv[idx], wu[idx], wv[idx]) | |
| o = self._ray_energy(e, ph_f, omf, rf, detf, Df[:, 2] > 0, *objects(Df, True)) | |
| for kk, v in o.items(): | |
| tot[kk] += v | |
| w_used += float(omf.sum()) | |
| out = dict(xray_emitted_j=4 * math.pi * E(ph_un), target_absorbed_j=2 * math.pi * E(ph_un) + 2 * math.pi * (E(ph_un) - E(ph_self)), | |
| window_absorbed_j=omega_cone * (E(ph_self) - E(ph_win)), filter_absorbed_j=omega_cone * (E(ph_win) - E(ph_f)), | |
| shielding_j=(2 * math.pi - omega_cone) * E(ph_self) + (omega_cone - w_used) * E(ph_f) + tot['shield'], | |
| air_absorbed_j=tot['air'], sample_absorbed_j=tot['body'], holder_absorbed_j=tot['holder'], | |
| sample_scattered_j=tot['scattered'], detector_absorbed_j=tot['dep'], detector_passed_j=tot['passed']) | |
| out = {k: float(v) for k, v in out.items()} | |
| if len(self._rate_cache) > 512: | |
| self._rate_cache.clear() | |
| self._rate_cache[key] = out | |
| return out, kv | |
| def _energy_rates(self): | |
| """Instantaneous energy flow (J/s) at the actual voltage, current and pose (for inspection; the ledger integrates _book_energy).""" | |
| pose = dict(xv=self.xv, rot=self.rot, sod=self.sod, cz=self.cz) | |
| base, kv = self._base_rates(pose) | |
| f = self.xv * self.xv * self.xi / (1.602176634e-19 * kv * kv) | |
| rates = {k: v * f for k, v in base.items()} | |
| rates['electrical_energy_j'] = self.xv * self.xi | |
| rates['xray_emitted_j'] = KRAMERS_K_PER_V * 74 * self.xv * self.xv * self.xi | |
| rates['energy_residual_j'] = rates['xray_emitted_j'] - sum(rates[k] for k in ENERGY_SINKS) | |
| return rates | |
| # ---------------------------------------------------------------- detector simulation | |
| def _groups(self, kv, fpos, materials): | |
| """Energy groups of the detected spectrum at the detector (central-ray air path): photons per sr per electron per group, mean deposited | |
| energy per incident photon (keV), second moment of the deposited energy (keV2 per incident photon) and group-mean linear attenuation | |
| coefficients of the materials (weighted by the detected energy).""" | |
| e, ph = beam_spectrum(kv, fpos) | |
| de = 0.5 | |
| ph = ph * air_transmission(e, SDD_M) * de | |
| p, edep = detector_response(tuple(e)) | |
| mu_c, men_c = linear_mu('nist_cesium', e) | |
| eps_int = e * men_c / mu_c | |
| w = ph * edep | |
| edges = [33.169, 35.985] | |
| for sid in materials: | |
| edges += [ed['energy_MeV'] * 1e3 for ed in substance(sid)['edges'] if ed['label'].endswith(' K') and 5.0 < ed['energy_MeV'] * 1e3 < kv / 1e3] | |
| idx, G = energy_groups(e, w, edges) | |
| n = np.array([ph[idx == g].sum() for g in range(G)]) | |
| keep = n > 0 | |
| eps = np.array([(ph * edep)[idx == g].sum() for g in range(G)]) | |
| m2 = np.array([(ph * p * eps_int ** 2)[idx == g].sum() for g in range(G)]) | |
| mus = {} | |
| for sid in materials: | |
| mu, _ = linear_mu(sid, e) | |
| mus[sid] = np.array([(w * mu)[idx == g].sum() / max(w[idx == g].sum(), 1e-300) for g in range(G)])[keep] | |
| return dict(n=n[keep], eps=eps[keep] / n[keep], m2=m2[keep] / n[keep], mu=mus, mean_e=float((w * e).sum() / w.sum())) | |
| def _window(self, ctx, s, roi=None): | |
| """Detector region simulated for an acquisition: the ROI of a radiograph (binned native pixels), the whole detector for a radiograph | |
| without sample, else the projected envelope of the sample over all angles (nominal geometry, calibrated axis offset, margins for the | |
| unknown offset), sampled with at most SIM_DETECTOR pixels but not finer than one binned native pixel.""" | |
| b = int(ctx['scan']['binning'][0]) | |
| nat = PIXEL_PITCH_M * b | |
| hu, hv = DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2, DETECTOR_PIXELS[1] * PIXEL_PITCH_M / 2 | |
| if roi is not None: | |
| n = roi['size_px'] | |
| return dict(u0=roi['center_u_m'] - n / 2 * nat, v1=roi['center_v_m'] + n / 2 * nat, pitch=nat, nu=n, nv=n, binning=b) | |
| if s is None or ctx.get('full_window'): | |
| u0, u1, v0, v1 = -hu, hu, -hv, hv | |
| else: | |
| r = self._envelope(s, *ctx['offset']) | |
| sod = ctx['sod'] | |
| a = ctx.get('axis_known') or 0.0 | |
| uh = SDD_M * r / math.sqrt(max(sod * sod - r * r, 1e-12)) | |
| uc = SDD_M * a / sod | |
| mu_ = 0.06 * uh + 4 * AXIS_OFFSET_SD_M * SDD_M / sod + 2 * nat | |
| u0, u1 = uc - uh - mu_, uc + uh + mu_ | |
| zb = ctx['cz'] - SOURCE_XYZ_M[2] + (s['pin']['length_m'] if s['pin'] else 0.0) # sample body only (not the mounting pin) | |
| zt = zb + s['height_m'] | |
| vv = [SDD_M * z / (sod + sg * r) for z in (zb, zt) for sg in (-1, 1)] | |
| mv = 0.04 * (max(vv) - min(vv)) + 2 * nat | |
| v0, v1 = min(vv) - mv, max(vv) + mv | |
| u0, u1, v0, v1 = max(u0, -hu), min(u1, hu), max(v0, -hv), min(v1, hv) | |
| p = max(math.sqrt((u1 - u0) * (v1 - v0) / (SIM_DETECTOR[0] * SIM_DETECTOR[1])), (u1 - u0) / 400, (v1 - v0) / 400, nat) # pixel budget | |
| return dict(u0=u0, v1=v1, pitch=p, nu=max(2, int(math.ceil((u1 - u0) / p - 1e-9))), nv=max(2, int(math.ceil((v1 - v0) / p - 1e-9))), binning=b) | |
| def _window_rays(self, w): | |
| u = w['u0'] + (np.arange(w['nu']) + 0.5) * w['pitch'] | |
| v = w['v1'] - (np.arange(w['nv']) + 0.5) * w['pitch'] | |
| U, V = np.meshgrid(u, v) | |
| P = np.stack([np.full(U.size, SDD_M), U.ravel(), V.ravel()], -1) | |
| r = np.linalg.norm(P, axis=1) | |
| return P / r[:, None], w['pitch'] ** 2 * (SDD_M / r) ** 3 / SDD_M ** 2, u, v | |
| def _flat_residual(self, flat, w): | |
| """Residual fixed pattern after the dark / bright correction on the window grid: the bright-field noise of each window pixel (the | |
| per-pixel gain itself is divided out), a field fixed for that calibration; dead columns of the injected defect fault.""" | |
| n_px = (w['pitch'] / (PIXEL_PITCH_M * w['binning'])) ** 2 | |
| sig = flat['sigma_binned'] / math.sqrt(n_px) | |
| key = int(hashlib.sha256(f"{flat['seed']}|{w['u0']:.9f}|{w['v1']:.9f}|{w['pitch']:.12f}|{w['nu']}|{w['nv']}".encode()).hexdigest()[:12], 16) | |
| xi = np.random.default_rng(key).standard_normal((w['nv'], w['nu'])) | |
| return 1.0 / (1.0 + sig * xi) | |
| def _dead_columns(self, ctx, w): | |
| """Window columns that fall into the injected dead detector columns (native column bands of 16 pixels).""" | |
| if not ctx['defects']: | |
| return np.zeros(w['nu'], bool) | |
| u = w['u0'] + (np.arange(w['nu']) + 0.5) * w['pitch'] | |
| band = DETECTOR_PIXELS[0] / SIM_DETECTOR[0] * PIXEL_PITCH_M | |
| col = np.floor((u + DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2) / band).astype(int) | |
| return np.isin(col, ctx['defects']) | |
| def _simulate(self, ctx, s, angles, shifts, frames, t_exp, w, rng=None, with_sample=True): | |
| """Normalised transmission images of the given rotation angles on the window w: exact paths, energy groups, focal-spot penumbra and | |
| scintillator blur, compound-Poisson quantum noise, read noise, 16-bit saturation, residual fixed pattern after the flat-field correction | |
| (random detector movement shifts it by 'shifts' window columns), dead columns.""" | |
| from scipy.ndimage import gaussian_filter | |
| mats = list(dict.fromkeys((_materials(s) if (s is not None and with_sample) else []) + list(HARDWARE_MATERIALS))) | |
| grp = self._groups(ctx['kv'], ctx['filter'], mats) | |
| electrons = ctx['ia'] / 1.602176634e-19 | |
| D, omega, _, _ = self._window_rays(w) | |
| n_bin = (w['pitch'] / (PIXEL_PITCH_M * w['binning'])) ** 2 # binned native pixels per simulated pixel | |
| spot = focal_spot_m(ctx['kv'] * ctx['ia']) | |
| M = SDD_M / ctx['sod'] | |
| sigma_px = math.hypot(spot / 2.355 * (M - 1) / w['pitch'], DETECTOR_PSF_PX * PIXEL_PITCH_M / w['pitch']) | |
| flat = ctx['flat'] | |
| resid0 = self._flat_residual(flat, w) | |
| dead = self._dead_columns(ctx, w) | |
| out, sat = [], 0.0 | |
| for k, beta in enumerate(angles): | |
| if s is not None and with_sample: | |
| S, Ds = self._to_sample(s, D, ctx['sod'], ctx['cz'], beta, ctx['axis'], ctx['offset'][0], ctx['offset'][1]) | |
| paths = sample_paths(s, S, Ds) | |
| ax, ay, zt = -ctx['offset'][0], -ctx['offset'][1], -(s['pin']['length_m'] if s['pin'] else 0.0) | |
| else: | |
| S, Ds, ax, ay, zt = self._frame(None, D, ctx['sod'], ctx['cz'], beta, ctx['axis']) | |
| paths = {} | |
| for sid, L in hardware_paths(S, Ds, ax, ay, zt).items(): # brass chuck and rotation-stage housing below the sample | |
| _add(paths, sid, L) | |
| att = np.zeros((D.shape[0], len(grp['n']))) | |
| for sid, L in paths.items(): | |
| att += np.outer(L, grp['mu'][sid]) | |
| T = np.exp(-att) | |
| ph = electrons * t_exp * frames * omega[:, None] * grp['n'][None, :] # incident photons per group and pixel | |
| mean_kev = (ph * T * grp['eps'][None, :]).sum(1) | |
| var_kev2 = (ph * T * grp['m2'][None, :]).sum(1) | |
| mean0 = (ph * grp['eps'][None, :]).sum(1) | |
| img = mean_kev.reshape(w['nv'], w['nu']) | |
| if sigma_px > 0.05: | |
| img = gaussian_filter(img, sigma_px, mode='nearest') | |
| sig = ADU_PER_KEV * img.ravel() | |
| var = ADU_PER_KEV ** 2 * var_kev2 + READ_NOISE_ADU ** 2 * n_bin * frames | |
| full = (FULL_SCALE_ADU - DARK_OFFSET_ADU - DARK_CURRENT_ADU_S * t_exp) * n_bin * frames | |
| meas = sig + np.sqrt(var) * rng.standard_normal(sig.shape) | |
| sat += float(np.mean(sig > full)) | |
| meas = np.minimum(meas, full) | |
| bright = np.minimum(ADU_PER_KEV * mean0, full) # the bright field clips at full scale too | |
| t = (meas / np.maximum(bright, 1e-30)).reshape(w['nv'], w['nu']) | |
| sh = shifts[k] if shifts is not None else 0 | |
| t = t * np.roll(resid0, sh, axis=1) | |
| if dead.any(): | |
| dk = np.roll(dead, sh) | |
| if flat['defects']: # dead columns in the bright field too: gain divided out, noise stays | |
| t[:, dk] = t[:, dk] + 0.15 * rng.standard_normal((w['nv'], int(dk.sum()))) | |
| else: | |
| t[:, dk] = t[:, dk] * 0.02 | |
| out.append(t) | |
| return out, sat / max(len(angles), 1), grp | |
| # ---------------------------------------------------------------- operation finishers | |
| def _finish_flat_field(self): | |
| o = self.op | |
| ctx = o['ctx'] | |
| r = self.records[o['record_id']] | |
| b = int(ctx['scan']['binning'][0]) | |
| grp = self._groups(ctx['kv'], ctx['filter'], []) | |
| electrons = ctx['ia'] / 1.602176634e-19 | |
| omega = (PIXEL_PITCH_M * b) ** 2 / SDD_M ** 2 # one binned pixel on the central ray | |
| texp = ctx['scan']['exposure_s'] | |
| m_b = ADU_PER_KEV * electrons * texp * omega * float((grp['n'] * grp['eps']).sum()) # ADU per binned pixel per frame | |
| v_b = ADU_PER_KEV ** 2 * electrons * texp * omega * float((grp['n'] * grp['m2']).sum()) | |
| nf = FLAT_FIELD_FRAMES | |
| sigma_binned = math.sqrt(v_b * nf + READ_NOISE_ADU ** 2 * nf * 2) / (m_b * nf) # relative bright-field error of one binned pixel | |
| level = m_b + DARK_OFFSET_ADU + DARK_CURRENT_ADU_S * texp | |
| usable = sigma_binned <= FLAT_MAX_SIGMA | |
| if level > FULL_SCALE_ADU: | |
| r['warnings'].append('亮场饱和:降低电流或曝光(亮区的透过率在满量程截止)') | |
| if not usable: | |
| r['warnings'].append(f'亮场信号不足:单个合并像素相对误差{sigma_binned * 100:.1f} %(上限{FLAT_MAX_SIGMA * 100:.0f} %),校正无效;提高电流、曝光或帧平均,或减少滤片') | |
| self.led['frames'].add(2 * nf) | |
| self.flat = dict(key=self._flat_key_of(ctx), t=self.t, seed=ctx['seed'], sigma_binned=sigma_binned, defects=bool(ctx['defects']), frames=nf, | |
| level_adu=level, usable=usable) | |
| r['flat_field'] = dict(frames=nf, mean_bright_adu=float(min(level, FULL_SCALE_ADU)), dark_adu=DARK_OFFSET_ADU + DARK_CURRENT_ADU_S * texp, key=self.flat['key']) | |
| _, omega_px, _, _ = self._window_rays(dict(u0=-DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2, v1=DETECTOR_PIXELS[1] * PIXEL_PITCH_M / 2, | |
| pitch=DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 88, nu=88, nv=75, binning=b)) | |
| prof = (omega_px / omega_px.max()).reshape(75, 88) * min(level, FULL_SCALE_ADU) / FULL_SCALE_ADU | |
| r['preview'] = [[float(x) for x in row] for row in prof] | |
| r['preview_unit'] = 'fraction of full scale (bright field, cos^3 fall-off)' | |
| r['note_zh'] = f'暗场与亮场各{nf}帧;亮场中心{level:.0f} ADU(满量程65535);单个合并像素亮场相对误差{sigma_binned * 100:.2f} %' | |
| self._complete(o, r) | |
| def _flat_key_of(self, ctx): | |
| s = ctx['scan'] | |
| return f"{ctx['kv']:.1f}|{ctx['ia'] * 1e9:.1f}|{ctx['filter']}|{s['binning']}|{s['exposure_s']:.6g}" | |
| def _finish_radiograph(self): | |
| o = self.op | |
| ctx = o['ctx'] | |
| r = self.records[o['record_id']] | |
| s = self.samples.get(ctx['sample_id']) if ctx['sample_id'] else None | |
| rng = np.random.default_rng(ctx['seed']) | |
| sc = ctx['scan'] | |
| w = self._window(dict(ctx, full_window=True), s, ctx['roi']) | |
| self.led['projections'].add(1); self.led['frames'].add(sc['averaging']) | |
| imgs, sat, grp = self._simulate(ctx, s, [ctx['rot0']], None, sc['averaging'], sc['exposure_s'], w, rng=rng) | |
| t = imgs[0] | |
| self._data[r['record_id']] = dict(image=t.astype(np.float32), roi=copy.deepcopy(ctx['roi']), sod=ctx['sod'], binning=int(sc['binning'][0]), window=w) | |
| r['sim_detector'], r['sim_pixel_m'] = [w['nu'], w['nv']], w['pitch'] | |
| r.update(transmission=dict(min=float(t.min()), mean=float(t.mean()), max=float(t.max())), saturated_fraction=sat) | |
| step = max(1, int(math.ceil(max(t.shape) / 88))) | |
| r['preview'] = [[float(x) for x in row] for row in t[::step, ::step][:128, :128]] | |
| r['preview_unit'] = 'transmission I/I0' | |
| r['note_zh'] = f'透视(平均探测能量{grp["mean_e"]:.1f} keV)' + (',局部区域' if ctx['roi'] else '') | |
| self._evict() | |
| self._complete(o, r) | |
| def _finish_geometry_calibration(self): | |
| o = self.op | |
| ctx = o['ctx'] | |
| r = self.records[o['record_id']] | |
| s = self.samples[ctx['sample_id']] | |
| rng = np.random.default_rng(ctx['seed']) | |
| angles = [ctx['rot0'] + 2 * math.pi * k / 36 for k in range(36)] | |
| sc = ctx['scan'] | |
| w = self._window(ctx, s) | |
| self.led['projections'].add(36); self.led['frames'].add(36 * sc['averaging']) | |
| imgs, sat, grp = self._simulate(ctx, s, angles, None, sc['averaging'], sc['exposure_s'], w, rng=rng) | |
| r['sim_detector'], r['sim_pixel_m'] = [w['nu'], w['nv']], w['pitch'] | |
| est = self._fit_axis(imgs, angles, ctx['sod'], w) | |
| if est is None: | |
| r['warnings'].append('标定球识别失败') | |
| r['note_zh'] = '钢球识别失败:检查标定体模是否完整在视场内' | |
| self._complete(o, r) | |
| return | |
| a, resid, n_balls = est | |
| r['geometry'] = dict(axis_offset_m=a, residual_m=resid, balls=n_balls) | |
| limit = max(GEO_FIT_MAX_RESIDUAL_PX * w['pitch'] * ctx['sod'] / SDD_M, GEO_FIT_MIN_LIMIT_M) | |
| if resid > limit or n_balls < CAL_BALLS - 1: | |
| r['warnings'].append(f'钢球轨迹拟合残差{resid * 1e6:.1f} µm超过{limit * 1e6:.1f} µm或识别的钢球不足({n_balls}个):标定未采用') | |
| r['note_zh'] = f'拟合失败:旋转轴横向偏移{a * 1e6:.1f} µm不可信(残差{resid * 1e6:.1f} µm),保留原标定' | |
| self._complete(o, r) | |
| return | |
| self.geo_cal = dict(axis_offset_m=a, calibrated_s=self.t) | |
| r['note_zh'] = f'旋转轴横向偏移{a * 1e6:.1f} µm({n_balls}个钢球,拟合残差{resid * 1e6:.2f} µm)' | |
| self._complete(o, r) | |
| def _fit_axis(self, imgs, angles, sod, w): | |
| """Track the steel balls in the 36 projections (blobs of high line integral) and fit the exact cone-beam trajectories | |
| u = SDD (a + r sin(b + phi)) / (SOD + r cos(b + phi)) jointly for the axis offset a.""" | |
| from scipy import ndimage, optimize | |
| pu = pv = w['pitch'] | |
| ball_px = 2 * CAL_BALL_RADIUS_M * SDD_M / sod / pu # projected ball diameter in window pixels | |
| se = max(9, 2 * int(round(2 * ball_px)) + 1) # top-hat element: about four ball diameters | |
| blobs = [] | |
| for k, t in enumerate(imgs): | |
| q = -np.log(np.clip(t, 1e-6, None)) | |
| d = ndimage.white_tophat(q, size=se) # balls stand out of the PMMA cylinder background | |
| lab, n = ndimage.label(d > 0.5 * max(d.max(), 1e-9)) | |
| found = [] | |
| for j in range(1, n + 1): | |
| wt = np.where(lab == j, d, 0.0) | |
| if wt.sum() <= 0 or (lab == j).sum() < 2: | |
| continue | |
| cy, cx = ndimage.center_of_mass(wt) | |
| found.append((w['u0'] + (cx + 0.5) * pu, w['v1'] - (cy + 0.5) * pv)) | |
| blobs.append(found) | |
| seed = max(range(len(blobs)), key=lambda k: len(blobs[k])) | |
| if len(blobs[seed]) < 3: | |
| return None | |
| means = sorted(v for _, v in blobs[seed]) | |
| tol = 0.45 * min(np.diff(means)) if len(means) > 1 else 10 * pv | |
| tracks = {i: [] for i in range(len(means))} | |
| for k, found in enumerate(blobs): # nearest track in v (cone-beam magnification makes v wobble) | |
| for u, v in found: | |
| i = int(np.argmin([abs(v - m) for m in means])) | |
| if abs(v - means[i]) < tol: | |
| tracks[i].append((angles[k], u)) | |
| balls = [np.array(v) for v in tracks.values() if len(v) >= 24] | |
| if len(balls) < 3: | |
| return None | |
| M = SDD_M / sod | |
| def res(p): | |
| a = p[0] | |
| out = [] | |
| for i, bl in enumerate(balls): | |
| rr, ph = p[1 + 2 * i], p[2 + 2 * i] | |
| out.append(SDD_M * (a + rr * np.sin(bl[:, 0] + ph)) / (sod + rr * np.cos(bl[:, 0] + ph)) - bl[:, 1]) | |
| return np.concatenate(out) | |
| p0 = [float(np.mean([bl[:, 1].mean() for bl in balls]) / M)] | |
| for bl in balls: | |
| amp = (bl[:, 1].max() - bl[:, 1].min()) / 2 / M | |
| k = int(np.argmax(bl[:, 1])) | |
| p0 += [max(amp, 1e-4), math.pi / 2 - bl[k, 0]] | |
| sol = optimize.least_squares(res, p0, method='lm') | |
| rms = float(np.sqrt(np.mean(sol.fun ** 2))) | |
| return float(sol.x[0]), rms / M, len(balls) | |
| def _finish_scan(self): | |
| o = self.op | |
| ctx = o['ctx'] | |
| r = self.records[o['record_id']] | |
| s = self.samples[ctx['sample_id']] | |
| rng = np.random.default_rng(ctx['seed']) | |
| sc = ctx['scan'] | |
| n_sim, n_nom = ctx['n_sim'], ctx['n_nom'] | |
| full = sc['range_deg'] == '360' | |
| angles = [ctx['rot0'] + ctx['span'] * k / (n_sim if full else max(n_sim - 1, 1)) for k in range(n_sim)] | |
| shifts = [int(x) for x in rng.integers(-4, 5, n_sim)] if sc['random_movement'] else None | |
| frames = sc['averaging'] * n_nom / n_sim # dose-equivalent aggregation of the skipped projections | |
| self.led['projections'].add(n_nom); self.led['frames'].add(n_nom * sc['averaging']) | |
| w = self._window(ctx, s) | |
| imgs, sat, grp = self._simulate(ctx, s, angles, shifts, frames, sc['exposure_s'], w, rng=rng) | |
| q = np.stack([-np.log(np.clip(t, 1e-6, None)) for t in imgs]).astype(np.float32) | |
| self._data[r['record_id']] = dict(q=q, angles=np.array(angles) - ctx['rot0'], full=full, sod=ctx['sod'], span=ctx['span'], grp=grp, | |
| materials=_materials(s), kv=ctx['kv'], filter=ctx['filter'], window=w) | |
| r['sim_detector'], r['sim_pixel_m'] = [w['nu'], w['nv']], w['pitch'] | |
| tt = np.stack(imgs) | |
| r.update(transmission=dict(min=float(tt.min()), mean=float(tt.mean()), max=float(tt.max())), saturated_fraction=sat, | |
| dose_gy=float(s.get('dose_gy', 0.0) - ctx.get('dose0', 0.0))) | |
| st = max(1, int(math.ceil(max(imgs[0].shape) / 96))) | |
| r['preview'] = [[float(x) for x in row] for row in imgs[0][::st, ::st][:128, :128]] | |
| r['preview_unit'] = 'transmission I/I0 (first projection, acquisition window)' | |
| if tt.min() < 0.02: | |
| r['warnings'].append('部分射线透过率低于2 %:提高电压或加滤片') | |
| if sat > 0.001: | |
| r['warnings'].append('探测器饱和:降低电流或曝光') | |
| r['note_zh'] = f'{n_nom}个名义投影(模拟{n_sim}个,剂量等效合并);平均探测能量{grp["mean_e"]:.1f} keV' | |
| self._evict() | |
| self._complete(o, r) | |
| def _evict(self): | |
| keep = sorted((k for k in self._data if self.records[k]['kind'] in ('projections', 'radiograph')), key=lambda k: self.records[k]['started_s']) | |
| for k in keep[:-8]: | |
| del self._data[k] | |
| # ---------------------------------------------------------------- reconstruction | |
| def _finish_recon(self, rc): | |
| ctx = rc['ctx'] | |
| r = self.records[rc['record_id']] | |
| data = self._data.get(ctx['source']) | |
| if data is None: | |
| self.operations[rc['op']].update(phase='failed', finished_s=self.t, reason='DATA_EVICTED') | |
| r.update(status='failed', finished_s=self.t, reason='DATA_EVICTED', duration_s=self.t - r['started_s']) | |
| self._event('measurement', 'OP_FAILED', f'重建{rc["op"]}失败:投影数据已被清除', rid=r['record_id']) | |
| self.recon = None | |
| return | |
| rs = ctx['recon'] | |
| q = data['q'].astype(np.float64) | |
| sod = data['sod'] | |
| M = SDD_M / sod | |
| w = data['window'] | |
| warnings = [] | |
| if rs['beam_hardening'] > 0 and rs['bh_material']: | |
| q = self._bh_linearise(q, data['grp'], data['kv'], data['filter'], rs['bh_material'], rs['beam_hardening']) | |
| if rs['ring_correction'] > 0: | |
| from scipy.ndimage import median_filter | |
| m = q.mean(axis=0) | |
| q = q - rs['ring_correction'] * (m - median_filter(m, size=(1, 9)))[None, :, :] | |
| axis = ctx['axis_cal'] if ctx['axis_cal'] is not None else 0.0 | |
| if rs['post_alignment'] is not None: | |
| axis += rs['post_alignment'] | |
| elif rs['auto_alignment']: | |
| d_axis = self._auto_align(q, data['angles'], data['full'], M, w, axis, sod, data['span']) | |
| if d_axis is None: | |
| warnings.append('中心平面(光束高度)没有可用的样品数据:自动对准未执行,使用几何标定值或0') | |
| else: | |
| axis += d_axis | |
| if ctx['axis_cal'] is None and rs['post_alignment'] is None and not rs['auto_alignment']: | |
| warnings.append('未做几何标定也未后对准:旋转轴偏移会造成伪影') | |
| if ctx.get('voi_partial'): | |
| warnings.append('感兴趣体积部分超出采集窗口可重建的区域:该部分体素不完整或为0') | |
| vol, origin, voxel = self._fdk(q, data['angles'], data['full'], data['span'], sod, w, axis, int(rs['grid']), rs['filter'], rs['voi']) | |
| if rs['smoothing_vox'] > 0: | |
| from scipy.ndimage import gaussian_filter | |
| vol = gaussian_filter(vol, rs['smoothing_vox']) | |
| vol = vol.astype(np.float32) | |
| self._data[r['record_id']] = dict(volume=vol, origin=origin, voxel=voxel, sod=sod, sample_id=ctx['sample_id']) | |
| hist, edges = np.histogram(vol, bins=64) | |
| r['volume'] = dict(shape=list(vol.shape), voxel_m=voxel, origin_m=[float(x) for x in origin], mu_min_1_m=float(vol.min()), mu_max_1_m=float(vol.max()), | |
| histogram=[int(x) for x in hist], histogram_edges_1_m=[float(x) for x in edges], axis_offset_used_m=float(axis)) | |
| zc = vol.shape[0] // 2 | |
| stepv = max(1, int(math.ceil(max(vol.shape[1:]) / 96))) | |
| r['preview'] = [[float(x) for x in row] for row in vol[zc, ::stepv, ::stepv][:128, :128]] | |
| r['preview_unit'] = 'linear attenuation coefficient 1/m (central axial slice)' | |
| r['warnings'] = warnings | |
| r['note_zh'] = f'FDK重建{vol.shape[2]}×{vol.shape[1]}×{vol.shape[0]}体素(模拟体素{voxel * 1e6:.1f} µm;名义体素{r["voxel_size_nominal_m"] * 1e6:.2f} µm)' | |
| o = rc | |
| self._complete(o, r) | |
| def _bh_linearise(self, q, grp, kv, fpos, material, strength): | |
| """Beam-hardening linearisation for one material: the polychromatic line integral q_poly(L) of the scan spectrum (detected-energy | |
| weights of the energy groups) is mapped to mu(E_eff) L with E_eff the detected mean energy of the unattenuated beam (a monochromatic | |
| equivalent); strength 0..1 blends the corrected and the measured line integrals.""" | |
| g = grp if material in grp['mu'] else self._groups(kv, fpos, [material]) | |
| mu = g['mu'][material] | |
| w = g['n'] * g['eps'] / (g['n'] * g['eps']).sum() | |
| mu_ref = float(linear_mu(material, [g['mean_e']])[0][0]) | |
| L = np.linspace(0.0, 30.0 / max(float((w * mu).sum()), 1e-9), 400) | |
| qp = -np.log((w[None, :] * np.exp(-np.outer(L, mu))).sum(1)) | |
| lin = np.interp(q, qp, L, right=L[-1]) * mu_ref | |
| return q + strength * (lin - q) | |
| def _auto_align(self, q, angles, full, M, w, axis0, sod=None, span=None): | |
| """Residual axis offset from the consistency of conjugate rays in the central plane (the detector row at the beam height is an exact | |
| fan-beam sinogram): a ray of view angle b1 and lab angle t1 = atan(u1 / SDD) lies at distance s = SOD sin t - a cos t from the axis | |
| and is measured again, reversed, at b2 = b1 - pi + 2 (alpha - t1), t2 = 2 alpha - t1 with alpha = atan(a / SOD). The candidate a | |
| (+-200 um around the starting offset, 5 um grid, parabolic vertex) that minimises the robust mean squared difference of all conjugate | |
| pairs inside the scanned range wins; short scans use their redundant end region, full scans every ray.""" | |
| sod = SDD_M / M if sod is None else sod | |
| span = (2 * math.pi if full else math.pi) if span is None else span | |
| nv = q.shape[1] | |
| vs = w['v1'] - (np.arange(nv) + 0.5) * w['pitch'] | |
| j = int(np.argmin(np.abs(vs))) | |
| if abs(vs[j]) > w['pitch']: | |
| return None # the acquisition window does not reach the central plane | |
| row = q[:, j, :].astype(np.float64) | |
| if float(np.mean(row > 0.05 * max(float(row.max()), 1e-9))) < 0.05: | |
| return None # no sample in the central plane | |
| us = w['u0'] + (np.arange(w['nu']) + 0.5) * w['pitch'] | |
| b = np.asarray(angles, float) | |
| n_p, nu = row.shape | |
| db = span / n_p if full else span / max(n_p - 1, 1) | |
| B1, T1 = np.meshgrid(b, np.arctan(us / SDD_M), indexing='ij') | |
| body = row > 0.02 * max(float(row.max()), 1e-9) | |
| def pairs(a): | |
| al = math.atan2(a, sod) | |
| B2 = B1 - math.pi + 2 * (al - T1) | |
| B2 = np.mod(B2, 2 * math.pi) | |
| fk = B2 / db | |
| fi = (SDD_M * np.tan(2 * al - T1) - us[0]) / w['pitch'] | |
| k0, i0 = np.floor(fk).astype(int), np.floor(fi).astype(int) | |
| ok = (i0 >= 0) & (i0 < nu - 1) & ((k0 >= 0) & (k0 < n_p) if full else (k0 >= 0) & (k0 < n_p - 1)) | |
| k0 = np.clip(k0, 0, n_p - 1) | |
| k1 = np.mod(k0 + 1, n_p) if full else np.clip(k0 + 1, 0, n_p - 1) | |
| i0 = np.clip(i0, 0, nu - 2) | |
| ak, ai = fk - np.floor(fk), np.clip(fi - i0, 0.0, 1.0) | |
| p2 = (1 - ak) * ((1 - ai) * row[k0, i0] + ai * row[k0, i0 + 1]) + ak * ((1 - ai) * row[k1, i0] + ai * row[k1, i0 + 1]) | |
| sel = ok & (body | (p2 > 0.02 * max(float(row.max()), 1e-9))) | |
| return row[sel] - p2[sel] | |
| d0 = pairs(axis0) | |
| if d0.size < 20: | |
| return None # no conjugate rays in the scanned range (keep the starting offset) | |
| c2 = (10.0 * max(float(np.median(np.abs(d0))), 1e-6)) ** 2 # robust: clip outliers (dead columns, noise spikes) | |
| def err(a): | |
| d = pairs(a) | |
| return float(np.mean(np.minimum(d * d, c2))) if d.size else math.inf | |
| cand = axis0 + np.linspace(-200e-6, 200e-6, 81) | |
| e = [err(a) for a in cand] | |
| k = int(np.argmin(e)) | |
| best = cand[k] | |
| if 0 < k < len(cand) - 1: | |
| dd = e[k - 1] - 2 * e[k] + e[k + 1] | |
| if dd > 0: | |
| best = cand[k] + 0.5 * (e[k - 1] - e[k + 1]) / dd * (cand[1] - cand[0]) | |
| return float(best - axis0) | |
| def _fdk(self, q, angles, full, span, sod, w, axis, n, filt, voi): | |
| """Feldkamp-Davis-Kress reconstruction of the projections q (line integrals) on an n-grid (whole field of view or a volume of | |
| interest); returns (volume [z, y, x] in 1/m, origin of voxel (0, 0, 0) in the rotating frame (axis at the beam height), voxel size).""" | |
| n_p, nv, nu = q.shape | |
| pu = pv = w['pitch'] | |
| us = (w['u0'] + (np.arange(nu) + 0.5) * pu - axis * SDD_M / sod) * sod / SDD_M # virtual detector at the axis, axis-centred | |
| vs = (w['v1'] - (np.arange(nv) + 0.5) * pv) * sod / SDD_M | |
| dus = pu * sod / SDD_M | |
| U, V = np.meshgrid(us, vs) | |
| pre = sod / np.sqrt(sod ** 2 + U ** 2 + V ** 2) | |
| npad = int(2 ** math.ceil(math.log2(2 * nu))) | |
| k = np.arange(npad) | |
| k = np.where(k <= npad // 2, k, k - npad) | |
| h = np.zeros(npad) | |
| h[0] = 1.0 / (4 * dus * dus) | |
| odd = (k % 2) != 0 | |
| h[odd] = -1.0 / (np.pi ** 2 * k[odd] ** 2 * dus * dus) | |
| H = np.real(np.fft.fft(h)) * dus | |
| f = np.abs(np.fft.fftfreq(npad, d=dus)) | |
| fmax = 0.5 / dus | |
| if filt == 'shepp_logan': | |
| H = H * np.sinc(f / (2 * fmax)) | |
| elif filt == 'hann': | |
| H = H * 0.5 * (1 + np.cos(np.pi * f / fmax)) | |
| gamma_m = math.atan(DETECTOR_PIXELS[0] * PIXEL_PITCH_M / 2 / SDD_M) # fan half-angle of the whole detector (Parker range) | |
| fov_r = min(abs(us.min()), abs(us.max())) * sod / math.hypot(sod, abs(us).max()) | |
| if voi is None: | |
| size = [2 * fov_r, 2 * fov_r, (vs.max() - vs.min()) * (sod - fov_r) / sod] | |
| center = [0.0, 0.0, 0.5 * (vs.max() + vs.min()) * (sod - fov_r) / sod] | |
| else: | |
| size, center = list(voi['size_m']), [voi['center_m'][0], voi['center_m'][1], voi['center_m'][2]] | |
| voxel = max(size) / n | |
| dims = [max(2, int(round(sz / voxel))) for sz in size] # x, y, z counts | |
| xs = center[0] + (np.arange(dims[0]) + 0.5 - dims[0] / 2) * voxel | |
| ys = center[1] + (np.arange(dims[1]) + 0.5 - dims[1] / 2) * voxel | |
| zs = center[2] + (np.arange(dims[2]) + 0.5 - dims[2] / 2) * voxel | |
| Z, Y, X = np.meshgrid(zs, ys, xs, indexing='ij') | |
| vol = np.zeros(X.shape) | |
| d_beta = span / (n_p if full else max(n_p - 1, 1)) | |
| if not full: | |
| gp = -np.arctan(us / sod) # Parker fan angle: the stage turns so that (b, g) and (b + pi - 2 g, -g) coincide | |
| def parker(bb): | |
| wp = np.ones_like(gp) | |
| wp = np.where(bb < 2 * (gamma_m - gp), np.sin(np.pi / 4 * bb / np.maximum(gamma_m - gp, 1e-12)) ** 2, wp) | |
| wp = np.where(bb > np.pi - 2 * gp, np.sin(np.pi / 4 * np.clip(np.pi + 2 * gamma_m - bb, 0.0, None) / np.maximum(gamma_m + gp, 1e-12)) ** 2, wp) | |
| return 2.0 * wp | |
| for kk in range(n_p): | |
| beta = angles[kk] | |
| proj = q[kk] * pre | |
| if not full: | |
| proj = proj * parker(beta)[None, :] | |
| pad = np.zeros((nv, npad)) | |
| pad[:, :nu] = proj | |
| filt_p = np.real(np.fft.ifft(np.fft.fft(pad, axis=1) * H[None, :], axis=1))[:, :nu] | |
| cb, sb = math.cos(beta), math.sin(beta) | |
| xr = X * cb - Y * sb | |
| yr = X * sb + Y * cb | |
| Uu = sod + xr | |
| up = sod * yr / Uu | |
| vp = sod * Z / Uu | |
| fi = (up - us[0]) / dus | |
| fj = (vs[0] - vp) / (dus * pv / pu) | |
| i0 = np.floor(fi).astype(int) | |
| j0 = np.floor(fj).astype(int) | |
| ok = (i0 >= 0) & (i0 < nu - 1) & (j0 >= 0) & (j0 < nv - 1) | |
| i0c, j0c = np.clip(i0, 0, nu - 2), np.clip(j0, 0, nv - 2) | |
| ai, aj = fi - i0c, fj - j0c | |
| val = ((1 - aj) * ((1 - ai) * filt_p[j0c, i0c] + ai * filt_p[j0c, i0c + 1]) + aj * ((1 - ai) * filt_p[j0c + 1, i0c] + ai * filt_p[j0c + 1, i0c + 1])) | |
| w = (sod / Uu) ** 2 | |
| vol += np.where(ok, w * val, 0.0) | |
| vol *= 0.5 * d_beta | |
| origin = [float(xs[0]), float(ys[0]), float(zs[0])] | |
| return vol, origin, voxel | |
| # ---------------------------------------------------------------- analysis | |
| def _vol(self, rid): | |
| r = self.records.get(rid) | |
| if r is None: | |
| raise ActionRejected('UNKNOWN_RECORD') | |
| if r['kind'] != 'volume' or r['status'] != 'completed': | |
| raise ActionRejected('RECORD_NOT_SUITABLE') | |
| return r, self._data[rid] | |
| def _grids(d): | |
| nz, ny, nx = d['volume'].shape | |
| x0, y0, z0 = d['origin'] | |
| v = d['voxel'] | |
| return x0 + np.arange(nx) * v, y0 + np.arange(ny) * v, z0 + np.arange(nz) * v | |
| def _region_mask(self, d, region): | |
| if region is None: | |
| return None | |
| if region['z_max_m'] <= region['z_min_m']: | |
| raise ActionRejected('INVALID_REGION') | |
| xs, ys, zs = self._grids(d) | |
| Z, Y, X = np.meshgrid(zs, ys, xs, indexing='ij') | |
| return ((X - region['center_m'][0]) ** 2 + (Y - region['center_m'][1]) ** 2 <= region['radius_m'] ** 2) & (Z >= region['z_min_m']) & (Z <= region['z_max_m']) | |
| def _otsu(x, bins=256): | |
| hist, edges = np.histogram(x, bins=bins) | |
| c = (edges[:-1] + edges[1:]) / 2 | |
| w0 = np.cumsum(hist) | |
| w1 = w0[-1] - w0 | |
| m0 = np.cumsum(hist * c) / np.maximum(w0, 1) | |
| m1 = ((hist * c).sum() - np.cumsum(hist * c)) / np.maximum(w1, 1) | |
| k = int(np.argmax(w0 * w1 * (m0 - m1) ** 2)) | |
| return float(c[k]) | |
| def _segment(self, d, region, threshold): | |
| """Sample envelope (Otsu between air and material, holes filled slice by slice and in 3D, one voxel eroded against the partial-volume | |
| shell, clipped to the region) and the pore threshold (ISO 50: midway between the air and the matrix levels, unless given).""" | |
| from scipy import ndimage | |
| vol = d['volume'] | |
| t_env = self._otsu(vol.ravel()) | |
| solid = vol > t_env | |
| env = np.stack([ndimage.binary_fill_holes(sl) for sl in solid]) | |
| env = ndimage.binary_fill_holes(env) | |
| env = ndimage.binary_erosion(env, iterations=1) | |
| mask = self._region_mask(d, region) | |
| if mask is not None: | |
| env &= mask | |
| outside = ~ndimage.binary_dilation(solid, iterations=2) | |
| mu_air = float(np.median(vol[outside])) if outside.any() else 0.0 | |
| mu_mat = float(np.median(vol[env])) if env.any() else t_env | |
| t = threshold if threshold is not None else 0.5 * (mu_air + mu_mat) | |
| return env, t, mu_air, mu_mat | |
| def _cmd_data_porosity(self, record_id, region, threshold_1_m, min_pore_voxels): | |
| from scipy import ndimage | |
| r, d = self._vol(record_id) | |
| env, t, mu_air, mu_mat = self._segment(d, region, threshold_1_m) | |
| n_env = int(env.sum()) | |
| v3 = d['voxel'] ** 3 | |
| empty = dict(mean=None, d10=None, d50=None, d90=None, max=None) | |
| if n_env < 27: | |
| return dict(record_id=record_id, threshold_1_m=t, method='iso50' if threshold_1_m is None else 'manual', envelope_voxels=n_env, pore_voxels=0, porosity=0.0, | |
| open_porosity=0.0, closed_porosity=0.0, pore_count=0, equivalent_diameter_m=empty, voxel_m=d['voxel'], note_zh='区域内没有足够的样品体素') | |
| pores = env & (d['volume'] < t) | |
| lab, n = ndimage.label(pores, structure=np.ones((3, 3, 3))) | |
| sizes = ndimage.sum(pores, lab, np.arange(1, n + 1)) if n else np.array([]) | |
| keep = np.where(sizes >= min_pore_voxels)[0] + 1 | |
| boundary = env & ~ndimage.binary_erosion(env) | |
| open_ids = set(np.unique(lab[boundary]).tolist()) - {0} | |
| vox = sizes[keep - 1] if len(keep) else np.array([]) | |
| n_open = float(sum(sizes[i - 1] for i in keep if i in open_ids)) | |
| eqd = np.sort((6 * vox * v3 / math.pi) ** (1 / 3)) if len(vox) else np.array([]) | |
| por = float(vox.sum() / n_env) | |
| stats = (dict(mean=float(eqd.mean()), d10=float(np.percentile(eqd, 10)), d50=float(np.percentile(eqd, 50)), d90=float(np.percentile(eqd, 90)), max=float(eqd.max())) | |
| if len(eqd) else empty) | |
| self.last_porosity, self.last_porosity_rid = por, record_id | |
| self._porosity_owner = None | |
| self.revision += 1 | |
| return dict(record_id=record_id, threshold_1_m=t, method='iso50' if threshold_1_m is None else 'manual', envelope_voxels=n_env, pore_voxels=int(vox.sum()), | |
| porosity=por, open_porosity=n_open / n_env, closed_porosity=por - n_open / n_env, pore_count=int(len(keep)), equivalent_diameter_m=stats, | |
| voxel_m=d['voxel'], note_zh=f'阈值{t:.1f} 1/m(空气{mu_air:.1f}、基体{mu_mat:.1f});体素{d["voxel"] * 1e6:.1f} µm,小于约2体素的孔无法分辨') | |
| def _cmd_data_cracks(self, record_id, region, threshold_1_m, min_voxels): | |
| from scipy import ndimage | |
| r, d = self._vol(record_id) | |
| env, t, mu_air, mu_mat = self._segment(d, region, threshold_1_m) | |
| xs, ys, zs = self._grids(d) | |
| low = env & (d['volume'] < t) | |
| lab, n = ndimage.label(low, structure=np.ones((3, 3, 3))) | |
| out = [] | |
| for j in range(1, n + 1): | |
| idx = np.argwhere(lab == j) | |
| if len(idx) < min_voxels: | |
| continue | |
| P = np.column_stack([xs[idx[:, 2]], ys[idx[:, 1]], zs[idx[:, 0]]]) | |
| c = P.mean(0) | |
| w, vec = np.linalg.eigh(np.cov((P - c).T) + np.eye(3) * (d['voxel'] ** 2 / 12)) | |
| l3, l2, l1 = w | |
| if math.sqrt(l3 / l1) < 0.3 and math.sqrt(l2 / l1) > 0.35: | |
| R1, R2 = 2 * math.sqrt(l1), 2 * math.sqrt(l2) | |
| area = math.pi * R1 * R2 | |
| out.append(dict(area_m2=area, aperture_m=len(idx) * d['voxel'] ** 3 / area, length_m=2 * R1, normal=[float(x) for x in vec[:, 0]], | |
| center_m=[float(x) for x in c], voxels=int(len(idx)))) | |
| out.sort(key=lambda x: -x['area_m2']) | |
| return dict(record_id=record_id, threshold_1_m=t, cracks=out[:32], crack_count=len(out), total_area_m2=float(sum(x['area_m2'] for x in out)), | |
| note_zh=f'平面状低衰减连通体(厚/长<0.3,宽/长>0.35);开口受体素{d["voxel"] * 1e6:.1f} µm限制(部分体积)') | |
| def _cmd_data_attenuation(self, record_id, region): | |
| r, d = self._vol(record_id) | |
| if region is None: | |
| env, _, _, _ = self._segment(d, None, None) | |
| m = env | |
| else: | |
| m = self._region_mask(d, region) | |
| if not m.any(): | |
| raise ActionRejected('INVALID_REGION') # the region holds no voxel of the volume | |
| x = d['volume'][m] if m.any() else d['volume'].ravel() | |
| return dict(record_id=record_id, mean_1_m=float(x.mean()), std_1_m=float(x.std()), median_1_m=float(np.median(x)), p05_1_m=float(np.percentile(x, 5)), | |
| p95_1_m=float(np.percentile(x, 95)), voxels=int(x.size)) | |
| def _cmd_data_slice(self, record_id, axis, position_m, size_px): | |
| from scipy.ndimage import map_coordinates | |
| r, d = self._vol(record_id) | |
| vol = d['volume'] | |
| xs, ys, zs = self._grids(d) | |
| g = dict(x=xs, y=ys, z=zs) | |
| if not g[axis][0] - 0.5 * d['voxel'] <= position_m <= g[axis][-1] + 0.5 * d['voxel']: | |
| raise ActionRejected('OUT_OF_VOLUME') | |
| other = [a for a in 'xyz' if a != axis] | |
| a0, a1 = g[other[0]], g[other[1]] | |
| ext = max(a0[-1] - a0[0], a1[-1] - a1[0]) + d['voxel'] | |
| pix = ext / size_px | |
| c0, c1 = (a0[0] + a0[-1]) / 2, (a1[0] + a1[-1]) / 2 | |
| p0 = c0 + (np.arange(size_px) + 0.5 - size_px / 2) * pix | |
| p1 = c1 + (np.arange(size_px) + 0.5 - size_px / 2) * pix | |
| B, A = np.meshgrid(p1, p0, indexing='ij') | |
| coord = {axis: np.full(A.shape, position_m), other[0]: A, other[1]: B} | |
| idx = [(coord[k] - g[k][0]) / d['voxel'] for k in ('z', 'y', 'x')] | |
| img = map_coordinates(vol, idx, order=1, mode='constant', cval=0.0) | |
| return dict(record_id=record_id, axis=axis, position_m=position_m, pixel_m=pix, mu_1_m=[[float(v) for v in row] for row in img]) | |
| def _cmd_data_edge_resolution(self, record_id): | |
| r = self.records.get(record_id) | |
| if r is None: | |
| raise ActionRejected('UNKNOWN_RECORD') | |
| if r['kind'] != 'radiograph' or r['status'] != 'completed' or record_id not in self._data: | |
| raise ActionRejected('RECORD_NOT_SUITABLE') | |
| d = self._data[record_id] | |
| t = d['image'].astype(float) | |
| q = -np.log(np.clip(t, 1e-6, None)) | |
| rows, cols = q.shape | |
| pitch = PIXEL_PITCH_M * d['binning'] if d['roi'] else DETECTOR_PIXELS[0] * PIXEL_PITCH_M / SIM_DETECTOR[0] | |
| M = SDD_M / d['sod'] | |
| lo, hi = np.percentile(q, 5), np.percentile(q, 95) | |
| if hi - lo < 0.05: | |
| return dict(record_id=record_id, width_10_90_m=None, width_detector_px=None, edge_angle_rad=None, note_zh='图像中没有足够对比度的刃边') | |
| mid = 0.5 * (lo + hi) | |
| xe, ye = [], [] | |
| for i in range(rows): | |
| p = q[i] | |
| s = np.where(np.diff(np.sign(p - mid)) != 0)[0] | |
| if len(s) == 1: | |
| j = s[0] | |
| xe.append(j + (mid - p[j]) / (p[j + 1] - p[j])); ye.append(i) | |
| if len(xe) < rows // 3: | |
| return dict(record_id=record_id, width_10_90_m=None, width_detector_px=None, edge_angle_rad=None, note_zh='找不到单一直刃边(每行应只穿越一次)') | |
| k, b0 = np.polyfit(ye, xe, 1) | |
| Y, X = np.mgrid[0:rows, 0:cols] | |
| dist = (X - (k * Y + b0)) / math.sqrt(1 + k * k) | |
| order = np.argsort(dist.ravel()) | |
| ds, qs = dist.ravel()[order], q.ravel()[order] | |
| bins = np.arange(-12, 12.25, 0.25) | |
| prof = np.array([qs[(ds >= a) & (ds < a + 0.25)].mean() if np.any((ds >= a) & (ds < a + 0.25)) else np.nan for a in bins[:-1]]) | |
| xc = bins[:-1] + 0.125 | |
| ok = np.isfinite(prof) | |
| xc, prof = xc[ok], prof[ok] | |
| a, bnd = prof[:8].mean(), prof[-8:].mean() | |
| f = (prof - a) / (bnd - a) | |
| if f[-1] < f[0]: | |
| f = 1 - f | |
| f = np.maximum.accumulate(np.clip(f, 0, 1)) | |
| x10, x90 = float(np.interp(0.1, f, xc)), float(np.interp(0.9, f, xc)) | |
| w_px = x90 - x10 | |
| return dict(record_id=record_id, width_10_90_m=w_px * pitch / M, width_detector_px=w_px, edge_angle_rad=float(math.atan(k)), | |
| note_zh=f'刃边扩展函数10–90 %宽度{w_px:.2f}像素(探测器像素{pitch * 1e6:.1f} µm,放大{M:.2f})') | |
| # ---------------------------------------------------------------- queries | |
| def _out(r): | |
| return copy.deepcopy(r) | |
| def _cmd_measurement_result(self, record_id): | |
| r = self.records.get(record_id) | |
| if r is None: | |
| raise ActionRejected('UNKNOWN_RECORD') | |
| return self._out(r) | |
| def _cmd_records_list(self): | |
| return dict(records=sorted(self.records)) | |
| def _cmd_events_read(self, since_s): | |
| return dict(events=[{k: v for k, v in e.items() if k != '_rid'} for e in self.events if e['time_s'] >= since_s], dropped=self.events_dropped) | |
| def ledger(self): | |
| out = {k: v.value() for k, v in self.led.items()} | |
| return out | |
| def _cmd_ledger_read(self): | |
| return self.ledger() | |
| def _cmd_provenance_read(self): | |
| lib = library() | |
| return dict(library=LIBRARY_REL, library_sha256=lib['sha256'], substances=len(lib['substances']), license=lib['license_zh']) | |
| ASYNC = {'calibration.flat_field', 'calibration.geometry', 'xray.radiograph', 'scan.start', 'recon.start'} | |
| ACQUISITION = {'calibration.flat_field', 'calibration.geometry', 'xray.radiograph', 'scan.start'} | |
| _DATA_GUARDED = {'measurement.result', 'records.delete'} | |
| _RECORD_ARG = {'measurement.result': 'record_id', 'records.delete': 'record_id'} | |
| _ANALYSIS_RECORD_ARGS = {'recon.start': ['record_id'], 'data.porosity': ['record_id'], 'data.cracks': ['record_id'], 'data.attenuation': ['record_id'], | |
| 'data.slice': ['record_id'], 'data.edge_resolution': ['record_id']} | |
| _CONTROL_GUARDED = {k for k, v in CAPS.items() if v['visibility'] == 'agent' and v['kind'] in ('device_command', 'robot_skill') and k not in UNSUPPORTED} | |
| class BrukerX4PoseidonSession: | |
| def __init__(self, host, principal_id): | |
| self._host = host | |
| self._principal = principal_id | |
| def _role(self): | |
| return self._host._principals[self._principal] | |
| def _target(self, instance_id): | |
| if not isinstance(instance_id, str) or instance_id != self._host.instance_id: | |
| raise ActionRejected('UNKNOWN_INSTANCE') | |
| def describe(self, *, instance_id=None, asset_type_id=None): | |
| if (instance_id is None) == (asset_type_id is None): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| if instance_id is not None: | |
| self._target(instance_id) | |
| if asset_type_id is not None and asset_type_id != ASSET_TYPE_ID: | |
| raise ActionRejected('UNKNOWN_INSTANCE') | |
| meta = copy.deepcopy(export_bruker_x4poseidon_contract_metadata()) | |
| caps = {k: v for k, v in meta['capabilities'].items() if v['visibility'] == 'agent' or self._role != 'agent'} | |
| slots = {k: v for k, v in meta['state_slots'].items() if v['visibility'] == 'agent' or self._role != 'agent'} | |
| if self._role == 'agent': | |
| for c in caps.values(): | |
| c['state_effects'] = [e for e in c['state_effects'] if e['state_id'] in slots] | |
| c['observes'] = [x for x in c['observes'] if x in slots] | |
| for pre in c['preconditions']: | |
| pre['state_ids'] = [x for x in pre['state_ids'] if x in slots] | |
| c['execution']['completion_state_ids'] = [x for x in c['execution']['completion_state_ids'] if x in slots] | |
| for m in meta['mechanisms'].values(): | |
| m['state_ids'] = [x for x in m['state_ids'] if x in slots] | |
| return dict(protocol_version=PROTOCOL_VERSION, asset_type_id=ASSET_TYPE_ID, asset_version='1.0.0', capabilities=caps, state_slots=slots) | |
| def _foreign(self, object_id): | |
| owner = self._host._owners.get(object_id) | |
| return owner is not None and owner != self._principal and self._host._principals.get(owner) == 'agent' | |
| def _foreign_op(self): | |
| h = self._host | |
| return h.op is not None and self._foreign(h.op['op']) | |
| def read(self, *, instance_id, state_ids=None): | |
| self._target(instance_id) | |
| h = self._host | |
| values = h.read(self._role) | |
| foreign = self._role == 'agent' and self._foreign_op() | |
| values['measurement.started_by_other_agent'] = foreign | |
| if foreign: | |
| values['measurement.id'] = None | |
| if self._role == 'agent': | |
| if h.recon is not None and self._foreign(h.recon['op']): | |
| values['recon.id'] = None | |
| values['result.last_record_id'] = h._last_record(lambda k: not self._foreign(k)) | |
| if self._foreign(h.last_porosity_rid) or (h._porosity_owner not in (None, self._principal) and h._principals.get(h._porosity_owner) == 'agent'): | |
| values['result.last_porosity'] = None # another agent's analysis (or an analysis of its volume) | |
| ids = list(values) if state_ids is None else state_ids | |
| if not isinstance(ids, list) or any(not isinstance(k, str) for k in ids): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| if any(k not in values for k in ids): | |
| raise ActionRejected('ACCESS_DENIED') | |
| return dict(instance_id=instance_id, status='succeeded', state_revision=h.revision, clock={'domain': 'simulation', 'time_s': h.time_s}, | |
| observations={k: dict(value=copy.deepcopy(values[k]), unit=SLOTS[k]['unit'], | |
| quality='unavailable' if values[k] is None else 'estimated' if SLOTS[k]['origin'] in ('sensor', 'derived') else 'valid', | |
| sample_time_s=h.time_s, sample_window_s=None) for k in ids}) | |
| def _guard(self, capability_id, arguments): | |
| if self._role != 'agent': | |
| return | |
| h = self._host | |
| if capability_id in _CONTROL_GUARDED and self._foreign_op(): | |
| if capability_id in ('power.set', 'power.press_button') and not h.power: | |
| return | |
| if capability_id == 'emergency.stop': # the safety button always works | |
| return | |
| raise ActionRejected('ACCESS_DENIED') | |
| if capability_id in _DATA_GUARDED: | |
| rid = arguments.get(_RECORD_ARG[capability_id]) | |
| if self._foreign(rid): | |
| raise ActionRejected('ACCESS_DENIED') | |
| owner = h._owners.get(rid) | |
| if capability_id == 'records.delete' and owner is not None and owner != self._principal: | |
| raise ActionRejected('ACCESS_DENIED') # an agent deletes only its own records and those of the host | |
| for arg in _ANALYSIS_RECORD_ARGS.get(capability_id, []): | |
| if arguments.get(arg) is not None and self._foreign(arguments[arg]): | |
| raise ActionRejected('ACCESS_DENIED') | |
| def invoke(self, *, instance_id, capability_id, arguments, request_id): | |
| h = self._host | |
| key = digest = None | |
| try: | |
| self._target(instance_id) | |
| if not isinstance(request_id, str) or not request_id: | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| key = (self._principal, request_id) | |
| try: | |
| digest = json.dumps([capability_id, arguments], sort_keys=True, allow_nan=False) | |
| except (TypeError, ValueError): | |
| digest = None | |
| if key in h._requests: | |
| old, response = h._requests[key] | |
| if digest is None or old != digest or not isinstance(response, dict): | |
| raise ActionRejected('REQUEST_CONFLICT') | |
| return copy.deepcopy(response) | |
| if not isinstance(capability_id, str) or capability_id not in CAPS: | |
| raise ActionRejected('UNKNOWN_CAPABILITY') | |
| if self._role == 'agent' and CAPS[capability_id]['visibility'] != 'agent': | |
| raise ActionRejected('ACCESS_DENIED') | |
| if not isinstance(arguments, dict): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| validate(CAPS[capability_id]['input_schema'], arguments) | |
| self._guard(capability_id, arguments) | |
| result = h.invoke(capability_id, **arguments) | |
| if self._role == 'agent': | |
| if capability_id == 'records.list': | |
| result = dict(records=[r for r in result['records'] if not self._foreign(r)]) | |
| elif capability_id == 'events.read': | |
| result = dict(events=[{k: v for k, v in e.items() if k != '_rid'} for e in h.events | |
| if e['time_s'] >= arguments['since_s'] and not self._foreign(e.get('_rid')) and e['kind'] != 'fault'], dropped=h.events_dropped) | |
| elif capability_id == 'measurement.result': | |
| result = dict(result, template_source=dict(library=result['template_source']['library'], substances=[]), dose_gy=None) | |
| if capability_id == 'data.porosity': | |
| h._porosity_owner = self._principal | |
| operation = result.get('operation_id') if capability_id in ASYNC else None | |
| if operation: | |
| h._owners[operation] = self._principal | |
| rid = h.operations[operation].get('record_id') | |
| if rid: | |
| h._owners[rid] = self._principal | |
| response = dict(protocol_version=PROTOCOL_VERSION, instance_id=instance_id, request_id=request_id, operation_id=operation, | |
| status='accepted' if operation else 'succeeded', state_revision=h.revision, clock={'domain': 'simulation', 'time_s': h.time_s}, | |
| result=copy.deepcopy(result), observations={}, error=None) | |
| h._requests[key] = (digest, copy.deepcopy(response)) | |
| return response | |
| except ActionRejected as exc: | |
| response = dict(protocol_version=PROTOCOL_VERSION, instance_id=instance_id, request_id=request_id, operation_id=None, | |
| status='unsupported' if str(exc) == 'UNSUPPORTED' else 'rejected', state_revision=h.revision, | |
| clock={'domain': 'simulation', 'time_s': h.time_s}, result={}, observations={}, | |
| error=dict(code=str(exc), message=ERROR_ZH.get(str(exc), str(exc)), retryable=False, side_effects='none')) | |
| if key is not None and digest is not None and key not in h._requests: | |
| h._requests[key] = (digest, copy.deepcopy(response)) | |
| return response | |
| def write(self, *, instance_id, state_id, value, request_id): | |
| self._target(instance_id) | |
| raise ActionRejected('ACCESS_DENIED') # set points are written through capabilities | |
| def poll(self, operation_id): | |
| h = self._host | |
| if not isinstance(operation_id, str): | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| op = h.operations.get(operation_id) | |
| if op is None: | |
| raise ActionRejected('UNKNOWN_OPERATION') | |
| if h._owners.get(operation_id) != self._principal and self._role != 'evaluator': | |
| raise ActionRejected('ACCESS_DENIED') # evaluators observe every operation | |
| if op.get('record_id') in h.records: | |
| res = h._out(h.records[op['record_id']]) | |
| if self._role == 'agent': | |
| res['template_source'] = dict(library=res['template_source']['library'], substances=[]) | |
| res['dose_gy'] = None # absorbed dose follows the true sample mass: evaluator only | |
| else: | |
| res = {k: v for k, v in op.items() if k in ('phase', 'reason')} | |
| return dict(operation_id=operation_id, status=op['phase'], result=res) | |
| def cancel(self, operation_id, request_id): | |
| h = self._host | |
| if not isinstance(request_id, str) or not request_id: | |
| raise ActionRejected('INVALID_ARGUMENT') | |
| key = (self._principal, request_id) | |
| digest = json.dumps(['cancel', operation_id]) if isinstance(operation_id, str) else None | |
| if key in h._requests: | |
| old, response = h._requests[key] | |
| if digest is None or old != digest: | |
| raise ActionRejected('REQUEST_CONFLICT') | |
| if isinstance(response, str): | |
| raise ActionRejected(response) | |
| return copy.deepcopy(response) | |
| try: | |
| self.poll(operation_id) | |
| op = h.operations[operation_id] | |
| if op['phase'] != 'running': | |
| raise ActionRejected('NOT_RUNNING') | |
| h._cancel_op(op) | |
| except ActionRejected as exc: | |
| if digest is not None: | |
| h._requests[key] = (digest, str(exc)) | |
| raise | |
| h.revision += 1 | |
| response = dict(protocol_version=PROTOCOL_VERSION, instance_id=h.instance_id, request_id=request_id, operation_id=operation_id, status='succeeded', | |
| state_revision=h.revision, clock={'domain': 'simulation', 'time_s': h.time_s}, result=dict(phase=op['phase']), observations={}, error=None) | |
| h._requests[key] = (digest, copy.deepcopy(response)) | |
| return response | |
| ERROR_ZH = { | |
| 'INVALID_ARGUMENT': '参数不符合输入模式或取值范围', 'REQUEST_CONFLICT': '同一request_id对应不同的调用', 'UNKNOWN_INSTANCE': '实例不存在', | |
| 'UNKNOWN_CAPABILITY': '能力不存在', 'UNSUPPORTED': '本配置不支持该能力', 'ACCESS_DENIED': '无权访问(评测槽、另一个agent的记录或操作)', | |
| 'PLANT_REQUIRED': '尚未声明实验室条件', 'SEED_FIXED': '噪声种子只能在首次声明时设定', 'POWER_OFF': '系统未通电', 'NOT_READY': '系统启动中', | |
| 'ERROR_PENDING': '有未确认的错误', 'EMERGENCY_STOP': '安全按钮被按下(锁存)', 'CAUSE_PERSISTS': '错误原因仍存在,不能确认', | |
| 'MAINS_OUT_OF_RANGE': '电源电压超出100–240 VAC ±10 %', 'MAINS_FAULT': '供电电压超出范围,系统断电', 'UNKNOWN_SUBSTANCE': '模板库中没有该材料', | |
| 'SAMPLE_EXISTS': '样品ID已存在', 'TOO_MANY_SAMPLES': '样品数量超过上限', | |
| 'INVALID_SAMPLE': '样品定义不自洽(层厚之和须等于高度、体积分数之和为1、裂纹/夹杂须在所在层与圆柱内、孔过密无法不重叠放置、体模不能带层/孔/裂纹/夹杂)', | |
| 'UNKNOWN_SAMPLE': '样品不存在', 'SAMPLE_NOT_ON_BENCH': '样品不在实验台上', 'STAGE_OCCUPIED': '样品夹上已有样品', 'DOOR_CLOSED': '门没有完全打开', | |
| 'NOT_ACCESSIBLE': '样品夹不在门口范围(先stage.go_to load)', 'COLLISION_RISK': '目标位置或移动路径上样品、样品针、样品夹或旋转台会碰到滤片转换器/源头部、探测器外壳或腔顶(碰撞保护)', | |
| 'SAMPLE_NOT_ON_STAGE': '该样品不在样品夹上', 'MEASUREMENT_RUNNING': '有采集操作进行中', 'MOTION_IN_PROGRESS': '门、滤片或样品台在移动', | |
| 'XRAY_ON': 'X射线开启时门锁住', 'LIGHT_CURTAIN_BLOCKED': '门口安全光幕被挡,门不能关闭', 'POWER_LIMIT': '靶功率超过20 W', | |
| 'DOOR_OPEN': '门没有关闭', 'INTERLOCK_OPEN': 'X射线联锁未满足(门、联锁传感器或安全按钮)', 'XRAY_ARC': 'X射线管打火', | |
| 'INTERLOCK_FAULT': '门联锁传感器故障', 'STAGE_FAULT': '旋转台故障(卡滞)', | |
| 'RECORDS_FULL': '记录数已达上限', 'XRAY_NOT_READY': 'X射线未开启、未预热完成或未稳定在设定值', 'NO_SAMPLE': '样品夹上没有样品', | |
| 'FLAT_FIELD_REQUIRED': '当前电压、电流、滤片、合并与曝光没有有效的暗场/亮场校正', 'SAMPLE_IN_BEAM': '亮场校正时样品、样品针、样品夹或旋转台在光束中(先降低或移开)', | |
| 'PHANTOM_REQUIRED': '几何标定需要钢球标定体模', 'SAMPLE_NOT_IN_FIELD': '样品不在探测器视场内', 'UNKNOWN_RECORD': '记录不存在', | |
| 'RECORD_NOT_SUITABLE': '记录种类或状态不适用', 'RECON_BUSY': '工作站正在进行另一个重建', 'INVALID_VOI': '感兴趣体积的中心不在采集窗口可重建的区域内', | |
| 'INVALID_REGION': '分析区域无效(z上限须大于下限,区域须含体数据的体素)', 'OUT_OF_VOLUME': '切片位置不在体数据内', 'NOT_RUNNING': '操作不在进行中', | |
| 'ROI_OUTSIDE_DETECTOR': '局部区域超出探测器有效面', 'PHANTOM_NOT_IN_FIELD': '钢球标定体模须在所有角度完整位于视场内(降低放大或调整高度)', | |
| 'DATA_NOT_CACHED': '投影数据已不在缓存中(只保留最近8组投影/透视)', 'RECORD_IN_USE': '记录正在使用(进行中的操作或正被重建的投影)', | |
| 'UNKNOWN_OPERATION': '操作不存在', 'USER_CANCEL': '操作被取消', 'XRAY_OFF': '采集中X射线被关闭', 'DATA_EVICTED': '投影数据已从缓存中清除(只保留最近8组投影/透视)', | |
| } | |
| EFFECTS = { | |
| 'plant.configure': ['door.closed', 'door.moving', 'door.target_m', 'filter.moving', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', | |
| 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'panel.status_red', 'plant.configured', 'power.enabled', 'stage.chuck_z_target_m', | |
| 'stage.moving', 'stage.rotation_target_rad', 'stage.sod_target_m', 'system.error_code', 'system.state', 'truth.axis_offset_m', 'xray.current_a', 'xray.enabled', | |
| 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'sample.provide': ['sample.bench_ids', 'truth.samples'], | |
| 'sample.place': ['sample.bench_ids', 'sample.on_stage', 'truth.samples'], | |
| 'sample.remove': ['sample.bench_ids', 'sample.on_stage', 'truth.samples'], | |
| 'power.set': ['door.closed', 'door.moving', 'door.target_m', 'filter.moving', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', | |
| 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'panel.status_red', 'power.enabled', 'stage.chuck_z_target_m', 'stage.moving', | |
| 'stage.rotation_target_rad', 'stage.sod_target_m', 'system.error_code', 'system.state', 'xray.current_a', 'xray.enabled', 'xray.focal_spot_m', 'xray.on', | |
| 'xray.power_w', 'xray.ready', 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'power.press_button': ['door.closed', 'door.moving', 'door.target_m', 'filter.moving', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', | |
| 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'panel.status_red', 'power.enabled', 'stage.chuck_z_target_m', 'stage.moving', | |
| 'stage.rotation_target_rad', 'stage.sod_target_m', 'system.error_code', 'system.state', 'xray.current_a', 'xray.enabled', 'xray.focal_spot_m', 'xray.on', | |
| 'xray.power_w', 'xray.ready', 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'emergency.stop': ['door.closed', 'door.moving', 'door.target_m', 'emergency.stopped', 'filter.moving', 'interlock.ok', 'measurement.id', 'measurement.kind', | |
| 'measurement.progress', 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'panel.status_red', 'stage.chuck_z_target_m', 'stage.moving', | |
| 'stage.rotation_target_rad', 'stage.sod_target_m', 'system.error_code', 'xray.current_a', 'xray.enabled', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', | |
| 'xray.ready', 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'emergency.release': ['emergency.stopped', 'interlock.ok'], | |
| 'system.acknowledge': ['panel.status_green', 'panel.status_red', 'system.error_code'], | |
| 'fault.inject': ['door.target_m', 'interlock.ok', 'light_curtain.blocked', 'measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', | |
| 'panel.status_green', 'panel.status_orange', 'panel.status_red', 'stage.moving', 'stage.rotation_target_rad', 'system.error_code', | |
| 'truth.detector_defect_columns', 'truth.faults', 'xray.current_a', 'xray.enabled', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', | |
| 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'door.open': ['door.closed', 'door.moving', 'door.target_m', 'interlock.ok'], | |
| 'door.close': ['door.closed', 'door.moving', 'door.target_m', 'interlock.ok'], | |
| 'xray.set': ['calibration.flat_field', 'xray.current_set_a', 'xray.focal_spot_m', 'xray.ready', 'xray.voltage_set_v'], | |
| 'xray.enable': ['panel.status_green', 'panel.status_orange', 'xray.current_a', 'xray.enabled', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', | |
| 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'filter.select': ['calibration.flat_field', 'filter.label', 'filter.moving', 'filter.position'], | |
| 'stage.move': ['stage.chuck_z_target_m', 'stage.moving', 'stage.position_label', 'stage.sod_target_m'], | |
| 'stage.rotate': ['stage.moving', 'stage.rotation_target_rad'], | |
| 'stage.go_to': ['stage.chuck_z_target_m', 'stage.moving', 'stage.position_label', 'stage.sod_target_m'], | |
| 'scan.configure': ['calibration.flat_field', 'geometry.voxel_size_m', 'scan.duration_s', 'scan.projections', 'scan.settings'], | |
| 'calibration.flat_field': ['measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'measurement.started_by_other_agent'], | |
| 'calibration.geometry': ['measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'measurement.started_by_other_agent'], | |
| 'xray.radiograph': ['measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'measurement.started_by_other_agent'], | |
| 'scan.start': ['measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'measurement.started_by_other_agent'], | |
| 'recon.start': ['recon.id', 'recon.remaining_s'], | |
| 'data.porosity': ['result.last_porosity'], | |
| 'data.cracks': [], | |
| 'data.attenuation': [], | |
| 'data.slice': [], | |
| 'data.edge_resolution': [], | |
| 'records.delete': ['result.last_porosity', 'result.last_record_id'], | |
| } | |
| EFFECTS['sim.step'] = ['clock.time_s'] | |
| ON_STEP = { | |
| 'plant.configure': ['calibration.flat_field', 'calibration.geometry', 'door.closed', 'door.moving', 'door.position_m', 'filter.moving', 'filter.slide_m', | |
| 'geometry.fov_m', 'geometry.magnification', 'geometry.voxel_size_m', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', | |
| 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'result.last_record_id', 'stage.chuck_z_m', 'stage.moving', 'stage.rotation_rad', | |
| 'stage.rotation_target_rad', 'stage.sod_m', 'system.state', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', | |
| 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'power.set': ['calibration.flat_field', 'calibration.geometry', 'door.closed', 'door.moving', 'door.position_m', 'filter.moving', 'filter.slide_m', 'geometry.fov_m', | |
| 'geometry.magnification', 'geometry.voxel_size_m', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', | |
| 'panel.status_green', 'panel.status_orange', 'result.last_record_id', 'stage.chuck_z_m', 'stage.moving', 'stage.rotation_rad', 'stage.rotation_target_rad', | |
| 'stage.sod_m', 'system.state', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', 'xray.voltage_v', | |
| 'xray.warmup_remaining_s'], | |
| 'power.press_button': ['calibration.flat_field', 'calibration.geometry', 'door.closed', 'door.moving', 'door.position_m', 'filter.moving', 'filter.slide_m', | |
| 'geometry.fov_m', 'geometry.magnification', 'geometry.voxel_size_m', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', | |
| 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'result.last_record_id', 'stage.chuck_z_m', 'stage.moving', 'stage.rotation_rad', | |
| 'stage.rotation_target_rad', 'stage.sod_m', 'system.state', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', | |
| 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'emergency.stop': ['calibration.flat_field', 'calibration.geometry', 'door.closed', 'door.moving', 'door.position_m', 'filter.moving', 'filter.slide_m', | |
| 'geometry.fov_m', 'geometry.magnification', 'geometry.voxel_size_m', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', | |
| 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'result.last_record_id', 'stage.chuck_z_m', 'stage.moving', 'stage.rotation_rad', | |
| 'stage.rotation_target_rad', 'stage.sod_m', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', 'xray.voltage_v', | |
| 'xray.warmup_remaining_s'], | |
| 'fault.inject': ['calibration.flat_field', 'calibration.geometry', 'door.closed', 'door.moving', 'door.position_m', 'interlock.ok', 'measurement.id', | |
| 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'panel.status_green', 'panel.status_orange', 'result.last_record_id', 'stage.moving', | |
| 'stage.rotation_rad', 'stage.rotation_target_rad', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', | |
| 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'door.open': ['door.closed', 'door.moving', 'door.position_m', 'interlock.ok'], | |
| 'door.close': ['door.closed', 'door.moving', 'door.position_m', 'interlock.ok'], | |
| 'xray.set': ['truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.power_w', 'xray.ready', 'xray.voltage_v'], | |
| 'xray.enable': ['panel.status_green', 'panel.status_orange', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', 'xray.on', 'xray.power_w', 'xray.ready', | |
| 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| 'filter.select': ['filter.moving', 'filter.slide_m', 'truth.samples'], | |
| 'stage.move': ['geometry.fov_m', 'geometry.magnification', 'geometry.voxel_size_m', 'stage.chuck_z_m', 'stage.moving', 'stage.sod_m', 'truth.samples'], | |
| 'stage.rotate': ['stage.moving', 'stage.rotation_rad', 'truth.samples'], | |
| 'stage.go_to': ['geometry.fov_m', 'geometry.magnification', 'geometry.voxel_size_m', 'stage.chuck_z_m', 'stage.moving', 'stage.sod_m', 'truth.samples'], | |
| 'scan.configure': ['geometry.voxel_size_m'], | |
| 'calibration.flat_field': ['calibration.flat_field', 'measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', | |
| 'measurement.started_by_other_agent', 'result.last_record_id'], | |
| 'calibration.geometry': ['calibration.geometry', 'measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', | |
| 'measurement.started_by_other_agent', 'result.last_record_id', 'stage.rotation_rad', 'stage.rotation_target_rad', 'truth.samples'], | |
| 'xray.radiograph': ['measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'measurement.started_by_other_agent', | |
| 'result.last_record_id'], | |
| 'scan.start': ['measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', 'measurement.started_by_other_agent', | |
| 'result.last_record_id', 'stage.rotation_rad', 'stage.rotation_target_rad', 'truth.samples'], | |
| 'recon.start': ['recon.id', 'recon.remaining_s', 'result.last_record_id'], | |
| 'records.delete': ['result.last_record_id'], | |
| 'sim.step': ['calibration.flat_field', 'calibration.geometry', 'door.closed', 'door.moving', 'door.position_m', 'filter.moving', 'filter.slide_m', 'geometry.fov_m', | |
| 'geometry.magnification', 'geometry.voxel_size_m', 'interlock.ok', 'measurement.id', 'measurement.kind', 'measurement.progress', 'measurement.remaining_s', | |
| 'measurement.started_by_other_agent', 'panel.status_green', 'panel.status_orange', 'recon.id', 'recon.remaining_s', 'result.last_record_id', 'stage.chuck_z_m', | |
| 'stage.moving', 'stage.rotation_rad', 'stage.rotation_target_rad', 'stage.sod_m', 'system.state', 'truth.samples', 'xray.current_a', 'xray.focal_spot_m', | |
| 'xray.on', 'xray.power_w', 'xray.ready', 'xray.voltage_v', 'xray.warmup_remaining_s'], | |
| } | |
| ON_STEP_ZH = { | |
| 'power.set': '启动60 s后进入就绪(各轴保持位置);断电时各轴停止', 'power.press_button': '同power.set', 'door.open': '门以0.1 m/s滑开', 'door.close': '门以0.1 m/s关闭', | |
| 'xray.enable': '电压与电流按斜率(或上电后首次开启的180 s预热程序,升到开启时的设定值)升到设定值,X射线能量计入账本', | |
| 'xray.set': '束流开启时电压与电流按斜率变化到新设定值(预热中程序照旧,结束后再按斜率变化)', | |
| 'filter.select': '滤片滑块每档0.5 s(光束能谱随滑块经过的滤片变化)', 'stage.move': '滑台20 mm/s、升降10 mm/s', 'stage.go_to': '同stage.move', 'stage.rotate': '旋转60°/s', | |
| 'calibration.flat_field': '暗场与亮场各20帧后写入校正', 'calibration.geometry': '36个投影、旋转一周后写入标定', 'xray.radiograph': '曝光×帧平均后写入透视记录', | |
| 'scan.start': '按投影时间连续旋转,完成后写入投影记录', 'recon.start': '按工作站重建时间完成后写入体数据', 'sim.step': '推进全部运动、X射线斜坡、操作阶段与能量账', | |
| 'emergency.stop': '已停止(无后续演化)', 'fault.inject': '故障对进行中的操作与运动的影响', 'records.delete': '删除本身没有后续演化;之后完成的采集或重建写入新的最新记录号(有无删除都一样;按有/无调用的对比列为步进效应)', | |
| } | |
| _R = ['power.enabled', 'system.state', 'system.error_code', 'emergency.stopped'] | |
| _ACQ = _R + ['measurement.id', 'door.closed', 'xray.ready', 'stage.moving', 'filter.moving', 'door.moving'] | |
| PRECONDITIONS = { | |
| 'plant.configure': ('噪声种子只能在首次声明时设定', ['plant.configured']), | |
| 'sample.provide': ('已声明实验室条件;样品ID未用过;材料在模板库中;几何自洽(层厚之和等于高度、体积分数之和为1、裂纹/夹杂在所在层内)', ['plant.configured', 'sample.bench_ids']), | |
| 'sample.place': ('样品在实验台上、样品夹空;门完全打开且不在移动;无采集操作;样品台静止并在门口范围;样品包络与滤片转换器、探测器盖板、腔顶留有2 mm', | |
| ['sample.bench_ids', 'sample.on_stage', 'door.position_m', 'door.moving', 'measurement.id', 'stage.moving', 'stage.sod_m', 'stage.chuck_z_m']), | |
| 'sample.remove': ('样品在样品夹上;门完全打开;无采集操作;样品台静止并在门口范围', ['sample.on_stage', 'door.position_m', 'measurement.id', 'stage.moving', 'stage.sod_m']), | |
| 'power.set': ('已声明实验室条件;上电需电源电压在100–240 VAC ±10 %内;上电时仍存在的原因(安全按钮锁存、故障)按优先级锁存错误', ['plant.configured']), | |
| 'power.press_button': ('同power.set(按一次切换通断)', ['plant.configured', 'power.enabled']), | |
| 'emergency.stop': ('已声明实验室条件;任何时候可按', ['plant.configured']), 'emergency.release': ('已声明实验室条件', ['plant.configured', 'emergency.stopped']), | |
| 'system.acknowledge': ('已通电;错误原因已排除(故障已清除、安全按钮已释放、电源恢复)', ['power.enabled', 'system.error_code', 'emergency.stopped']), | |
| 'fault.inject': ('已声明实验室条件', ['plant.configured']), | |
| 'door.open': ('已就绪、无错误、安全按钮未按下;无采集操作;X射线关闭(门锁)', _R + ['measurement.id', 'xray.on', 'xray.enabled']), | |
| 'door.close': ('已就绪、无错误、安全按钮未按下;安全光幕未被挡', _R + ['light_curtain.blocked']), | |
| 'xray.set': ('已声明实验室条件;电压20–100 kV、电流≤0.5 mA且功率≤20 W;无采集操作', ['plant.configured', 'measurement.id']), | |
| 'xray.enable': ('开启:已就绪、无错误、安全按钮未按下、门关闭、联锁正常、无打火;关闭:无采集操作', _R + ['door.closed', 'interlock.ok', 'measurement.id']), | |
| 'filter.select': ('已就绪、无错误;无采集操作', _R + ['measurement.id']), | |
| 'stage.move': ('已就绪、无错误;旋转台无故障;无采集操作;目标位置与滑台/升降同时运动的路径上样品、样品针、样品夹与旋转台都不进入禁入区', _R + ['measurement.id', 'sample.on_stage', 'stage.sod_m', 'stage.chuck_z_m']), | |
| 'stage.go_to': ('已就绪、无错误;旋转台无故障;无采集操作;从当前位置到装样位或中心位、滑台(20 mm/s)与升降(10 mm/s)同时运动的路径上样品、样品针、样品夹与旋转台' | |
| '都不进入禁入区(路径从当前位置开始,贴近禁入区时先用stage.move分步移开)', _R + ['measurement.id', 'sample.on_stage', 'stage.sod_m', 'stage.chuck_z_m']), 'stage.rotate': ('已就绪、无错误;旋转台无故障;无采集操作', _R + ['measurement.id']), | |
| 'scan.configure': ('已声明实验室条件;无采集操作', ['plant.configured', 'measurement.id']), | |
| 'calibration.flat_field': ('已就绪、无错误;无采集操作与运动;门关闭;X射线就绪;样品、样品针、样品夹与旋转台都不在光束中', _ACQ + ['sample.on_stage', 'stage.sod_m', 'stage.chuck_z_m']), | |
| 'calibration.geometry': ('同扫描;样品夹上为钢球标定体模且在所有角度完整位于视场内;有效的暗场/亮场校正', _ACQ + ['sample.on_stage', 'calibration.flat_field', 'stage.sod_m', 'stage.chuck_z_m']), | |
| 'xray.radiograph': ('已就绪、无错误;无采集操作与运动;门关闭;X射线就绪;有效的暗场/亮场校正;局部区域在探测器有效面内', _ACQ + ['calibration.flat_field']), | |
| 'scan.start': ('同透视;样品夹上有样品且样品本体在视场内', _ACQ + ['sample.on_stage', 'calibration.flat_field', 'stage.sod_m', 'stage.chuck_z_m']), | |
| 'recon.start': ('投影记录已完成且投影数据仍在缓存;工作站没有另一个重建;感兴趣体积的中心在采集窗口可重建的区域内(留出自动对准±200 µm;超出部分给出警告)', ['recon.id']), | |
| 'records.delete': ('记录存在且不在使用中(进行中的操作、正被重建的投影记录);agent只能删除自己或宿主的记录', ['result.last_record_id', 'recon.id', 'measurement.id']), | |
| } | |
| _COMMON_ERRORS = ['INVALID_ARGUMENT', 'REQUEST_CONFLICT', 'UNKNOWN_INSTANCE'] | |
| _RE = ['PLANT_REQUIRED', 'POWER_OFF', 'NOT_READY', 'EMERGENCY_STOP', 'ERROR_PENDING'] | |
| _ACQ_ERR = _RE + ['MEASUREMENT_RUNNING', 'MOTION_IN_PROGRESS', 'DOOR_OPEN', 'XRAY_NOT_READY', 'STAGE_FAULT', 'RECORDS_FULL'] | |
| _ACQ_FAIL = ['POWER_OFF', 'EMERGENCY_STOP', 'XRAY_ARC', 'INTERLOCK_FAULT', 'USER_CANCEL'] | |
| CAP_ERRORS = { | |
| 'plant.configure': ['SEED_FIXED'], 'sample.provide': ['PLANT_REQUIRED', 'SAMPLE_EXISTS', 'TOO_MANY_SAMPLES', 'INVALID_SAMPLE', 'UNKNOWN_SUBSTANCE'], | |
| 'sample.place': ['PLANT_REQUIRED', 'UNKNOWN_SAMPLE', 'SAMPLE_NOT_ON_BENCH', 'STAGE_OCCUPIED', 'MEASUREMENT_RUNNING', 'DOOR_CLOSED', 'MOTION_IN_PROGRESS', | |
| 'NOT_ACCESSIBLE', 'COLLISION_RISK'], | |
| 'sample.remove': ['PLANT_REQUIRED', 'SAMPLE_NOT_ON_STAGE', 'MEASUREMENT_RUNNING', 'DOOR_CLOSED', 'MOTION_IN_PROGRESS', 'NOT_ACCESSIBLE'], | |
| 'power.set': ['PLANT_REQUIRED', 'MAINS_OUT_OF_RANGE'], 'power.press_button': ['PLANT_REQUIRED', 'MAINS_OUT_OF_RANGE'], | |
| 'emergency.stop': ['PLANT_REQUIRED'], 'emergency.release': ['PLANT_REQUIRED'], 'system.acknowledge': ['PLANT_REQUIRED', 'POWER_OFF', 'CAUSE_PERSISTS'], | |
| 'fault.inject': ['PLANT_REQUIRED'], 'door.open': _RE + ['MEASUREMENT_RUNNING', 'XRAY_ON'], 'door.close': _RE + ['LIGHT_CURTAIN_BLOCKED'], | |
| 'xray.set': ['PLANT_REQUIRED', 'POWER_LIMIT', 'MEASUREMENT_RUNNING'], | |
| 'xray.enable': _RE + ['DOOR_OPEN', 'INTERLOCK_OPEN', 'XRAY_ARC', 'MEASUREMENT_RUNNING'], 'filter.select': _RE + ['MEASUREMENT_RUNNING'], | |
| 'stage.move': _RE + ['STAGE_FAULT', 'MEASUREMENT_RUNNING', 'COLLISION_RISK'], 'stage.go_to': _RE + ['STAGE_FAULT', 'MEASUREMENT_RUNNING', 'COLLISION_RISK'], | |
| 'stage.rotate': _RE + ['STAGE_FAULT', 'MEASUREMENT_RUNNING'], 'scan.configure': ['PLANT_REQUIRED', 'MEASUREMENT_RUNNING'], | |
| 'calibration.flat_field': _ACQ_ERR + ['SAMPLE_IN_BEAM'] + _ACQ_FAIL, | |
| 'calibration.geometry': _ACQ_ERR + ['NO_SAMPLE', 'FLAT_FIELD_REQUIRED', 'PHANTOM_REQUIRED', 'PHANTOM_NOT_IN_FIELD'] + _ACQ_FAIL, | |
| 'xray.radiograph': _ACQ_ERR + ['FLAT_FIELD_REQUIRED', 'ROI_OUTSIDE_DETECTOR'] + _ACQ_FAIL, | |
| 'scan.start': _ACQ_ERR + ['NO_SAMPLE', 'FLAT_FIELD_REQUIRED', 'SAMPLE_NOT_IN_FIELD'] + _ACQ_FAIL, | |
| 'recon.start': ['PLANT_REQUIRED', 'UNKNOWN_RECORD', 'RECORD_NOT_SUITABLE', 'UNKNOWN_SUBSTANCE', 'RECON_BUSY', 'DATA_NOT_CACHED', 'INVALID_VOI', 'RECORDS_FULL', | |
| 'DATA_EVICTED', 'USER_CANCEL'], | |
| 'records.delete': ['PLANT_REQUIRED', 'UNKNOWN_RECORD', 'RECORD_IN_USE'], | |
| 'measurement.result': ['UNKNOWN_RECORD'], 'data.porosity': ['UNKNOWN_RECORD', 'RECORD_NOT_SUITABLE', 'INVALID_REGION'], | |
| 'data.cracks': ['UNKNOWN_RECORD', 'RECORD_NOT_SUITABLE', 'INVALID_REGION'], 'data.attenuation': ['UNKNOWN_RECORD', 'RECORD_NOT_SUITABLE', 'INVALID_REGION'], | |
| 'data.slice': ['UNKNOWN_RECORD', 'RECORD_NOT_SUITABLE', 'OUT_OF_VOLUME'], 'data.edge_resolution': ['UNKNOWN_RECORD', 'RECORD_NOT_SUITABLE'], | |
| } | |
| _PARTIAL = {'USER_CANCEL', 'POWER_OFF', 'EMERGENCY_STOP', 'XRAY_ARC', 'INTERLOCK_FAULT', 'DATA_EVICTED'} | |
| CAP_ERROR_ZH = {('scan.start', 'POWER_OFF'): '未通电;或扫描中断电(记录以failed结束,不保留部分投影)', | |
| ('scan.start', 'STAGE_FAULT'): '旋转台故障;或扫描中旋转台卡滞(记录以failed结束)', | |
| ('scan.start', 'XRAY_ARC'): '扫描中X射线管打火:X射线关闭,记录以failed结束', | |
| ('recon.start', 'DATA_EVICTED'): '重建完成前投影数据已从缓存清除:记录以failed结束'} | |
| MODEL_NONE_ZH = { | |
| 'plant.configure': '实验室条件没有可见模型', 'sample.provide': '样品在实验台上,场景中没有样品几何', 'sample.place': '样品在场景中没有几何(运行层状态)', | |
| 'sample.remove': '样品在场景中没有几何', 'fault.inject': '注入故障本身没有可见变化', 'system.acknowledge': '只清除错误状态(状态灯随之变化)', | |
| 'xray.set': '只写设定(束流开启时电压电流读数随之变化)', 'scan.configure': '只写设置', 'recon.start': '工作站计算,仪器没有可见变化', | |
| 'emergency.release': '只释放锁存(错误确认后状态灯变化)', 'records.delete': '只删除工作站上的记录,仪器与显示没有变化', | |
| } | |
| SCENE_MIRRORED = {'door.position_m', 'filter.slide_m', 'stage.sod_m', 'stage.chuck_z_m', 'stage.rotation_rad', 'xray.voltage_v', 'xray.current_a', | |
| 'measurement.remaining_s', 'result.last_porosity', 'panel.status_green', 'panel.status_orange', 'panel.status_red'} | |
| def _model_effects(k, un): | |
| if un: | |
| return dict(mode='none', description_zh='不支持:不实现,没有模型变化', binding_ids=[]) | |
| seen = sorted((set(EFFECTS.get(k, [])) | set(ON_STEP.get(k, []))) & SCENE_MIRRORED) | |
| if seen: | |
| return dict(mode='host_required', binding_ids=[], | |
| description_zh='状态经宿主桥(Matterix)镜像到场景关节、触摸屏读数或状态灯(' + '、'.join(seen) + ';绑定见合同model_bindings),运行层本身不驱动模型' | |
| + (';' + MODEL_NONE_ZH[k] if k in MODEL_NONE_ZH else '')) | |
| return dict(mode='none', description_zh=MODEL_NONE_ZH.get(k, '没有镜像到场景的状态变化'), binding_ids=[]) | |
| EXEC_TEXT = { # asynchronous capabilities: completion criterion, partial failure | |
| 'calibration.flat_field': ('暗场与亮场各20帧(每帧曝光+0.03 s读出)完成后写入校正与记录', '取消或失败(断电、安全按钮、打火、联锁)时不写入校正,旧校正保持;没有运动。'), | |
| 'calibration.geometry': ('旋转一周36个投影完成后拟合钢球轨迹并写入旋转轴偏移', '取消或失败(断电、安全按钮、打火、联锁、旋转台卡滞)时不写入标定;旋转台停在当时角度。'), | |
| 'xray.radiograph': ('曝光×帧平均完成后写入透视记录', '取消或失败时不写入图像;没有运动。'), | |
| 'scan.start': ('按投影时间旋转完扫描范围后写入投影记录(投影在完成时计算)', '取消或失败(断电、安全按钮、打火、联锁、旋转台卡滞)时记录以cancelled/failed结束,不保留部分投影;旋转台停在当时角度。'), | |
| 'recon.start': ('按工作站重建时间完成后计算体数据并写入记录', '取消时不写入体数据;源投影记录不变;投影数据已被清除时以failed结束。'), | |
| } | |
| RESOURCES = {'calibration.flat_field': ['xray_source', 'detector', 'host_clock'], 'calibration.geometry': ['xray_source', 'detector', 'rotation_stage', 'host_clock'], | |
| 'xray.radiograph': ['xray_source', 'detector', 'host_clock'], 'scan.start': ['xray_source', 'detector', 'rotation_stage', 'host_clock'], | |
| 'recon.start': ['workstation', 'host_clock'], 'door.open': ['door'], 'door.close': ['door'], 'xray.set': ['xray_source'], 'xray.enable': ['xray_source'], | |
| 'filter.select': ['filter_changer'], 'stage.move': ['sample_carriage', 'sample_lift'], 'stage.go_to': ['sample_carriage', 'sample_lift'], | |
| 'stage.rotate': ['rotation_stage'], 'power.set': ['mains'], 'power.press_button': ['mains'], 'emergency.stop': ['safety_circuit'], | |
| 'emergency.release': ['safety_circuit'], 'plant.configure': ['room', 'mains'], 'sample.provide': ['bench'], 'sample.place': ['bench', 'sample_chuck'], | |
| 'sample.remove': ['bench', 'sample_chuck'], 'fault.inject': ['evaluator'], 'sim.step': ['host_clock'], 'system.acknowledge': ['controller'], | |
| 'scan.configure': ['controller'], 'records.delete': ['workstation']} | |
| OBSERVES = { | |
| 'power.set': ['power.enabled', 'system.state', 'panel.status_green'], 'power.press_button': ['power.enabled', 'system.state', 'panel.status_green'], | |
| 'emergency.stop': ['emergency.stopped', 'panel.status_red'], 'emergency.release': ['emergency.stopped'], 'system.acknowledge': ['system.error_code'], | |
| 'door.open': ['door.position_m', 'door.closed'], 'door.close': ['door.position_m', 'door.closed', 'light_curtain.blocked'], | |
| 'xray.set': ['xray.voltage_set_v', 'xray.current_set_a', 'xray.focal_spot_m'], 'xray.enable': ['xray.on', 'xray.ready', 'xray.warmup_remaining_s', 'panel.status_orange'], | |
| 'filter.select': ['filter.position', 'filter.label'], 'stage.move': ['stage.sod_m', 'stage.chuck_z_m', 'geometry.magnification', 'geometry.voxel_size_m'], | |
| 'stage.go_to': ['stage.position_label', 'stage.sod_m'], 'stage.rotate': ['stage.rotation_rad'], 'scan.configure': ['scan.settings', 'scan.projections', 'scan.duration_s'], | |
| 'calibration.flat_field': ['measurement.id', 'calibration.flat_field'], 'calibration.geometry': ['measurement.id', 'calibration.geometry'], | |
| 'xray.radiograph': ['measurement.id', 'result.last_record_id'], 'scan.start': ['measurement.id', 'measurement.progress', 'result.last_record_id'], | |
| 'recon.start': ['recon.id', 'recon.remaining_s', 'result.last_record_id'], 'data.porosity': ['result.last_porosity'], | |
| 'sample.place': ['sample.on_stage'], 'sample.remove': ['sample.bench_ids'], 'records.delete': ['result.last_record_id', 'result.last_porosity'], | |
| } | |
| _SPEC = 'manufacturer_primary' | |
| _BRO = 'manufacturer_brochures' | |
| _BRL = 'manufacturer_brochures' | |
| _CFG = 'manufacturer_configurator' | |
| _PHOTO = 'product_photos' | |
| _NIST = 'nist_srd126' | |
| _PUB = 'pubchem_densities' | |
| _LIBS = 'xray_attenuation_library' | |
| _PHYS = 'physics_literature' | |
| _SIM = 'simulation_assumption' | |
| _WB = 'user_workbook' | |
| CAP_SOURCES = { | |
| 'plant.configure': [_SPEC, _SIM], 'sample.provide': [_LIBS, _NIST, _PUB, _WB, _SPEC], 'sample.place': [_SPEC, _BRO, _SIM], 'sample.remove': [_SIM], | |
| 'power.set': [_SPEC, _SIM], 'power.press_button': [_SPEC, _PHOTO, _SIM], 'emergency.stop': [_BRO, _PHOTO, _SIM], 'emergency.release': [_SIM], | |
| 'system.acknowledge': [_SIM], 'fault.inject': [_SIM], 'door.open': [_BRO, _PHOTO, _SIM], 'door.close': [_BRO, _SIM], 'xray.set': [_SPEC, _BRO, _WB], | |
| 'xray.enable': [_SPEC, _BRO, _SIM, _PHYS], 'filter.select': [_BRO, _CFG, _SIM], 'stage.move': [_BRO, _SPEC, _SIM], 'stage.go_to': [_SIM], | |
| 'stage.rotate': [_BRO, _CFG, _SIM], 'scan.configure': [_SPEC, _WB, _SIM], 'calibration.flat_field': [_SPEC, _SIM, _PHYS], | |
| 'calibration.geometry': [_BRO, _SIM, _PHYS], 'xray.radiograph': [_SPEC, _WB, _LIBS, _NIST, _PHYS], 'scan.start': [_SPEC, _WB, _BRO, _LIBS, _NIST, _PHYS, _SIM], | |
| 'recon.start': [_BRO, _WB, _PHYS], 'measurement.result': [_WB], 'data.porosity': [_WB, _PHYS], 'data.cracks': [_WB, _PHYS], 'data.attenuation': [_PHYS], | |
| 'data.slice': [_WB], 'data.edge_resolution': [_BRO, _CFG, _PHYS], 'records.list': [_SIM], 'records.delete': [_SIM], 'events.read': [_SIM], | |
| 'ledger.read': [_SIM, _PHYS, _NIST], | |
| 'provenance.read': [_LIBS, _NIST, _PUB], 'sim.step': [_SIM], **{k: [_SPEC, _BRO, _CFG] for k in UNSUPPORTED}} | |
| PARAM_ZH = {'room_k': '实验室室温(记录用;X射线计算的空气密度取NIST表列值,与室温无关)', 'mains_voltage_v': '供电电压(厂家100–240 VAC)', | |
| 'relative_humidity': '相对湿度(记录用;不影响X射线计算)', 'noise_seed': '噪声种子(首次声明后固定)'} | |
| _DEFAULT_LIMIT = '过程层实现;机器人与硬件层未实现;整体模型边界见mechanisms.x4_poseidon_ct.limitations。' | |
| CAP_LIMITS = { | |
| 'sample.provide': ['样品为解析体模:竖直圆柱(最多6层,每层为模板库材料的体积混合,各组分按表列密度)、球形孔(对数正态半径、互不重叠、在指定层内)、平面圆盘裂纹、球形夹杂、' | |
| '样品管与样品针;另有钢球几何标定体模与钨刃边体模。多孔材料的孔径小于模拟体素时看不到;样品在场景中没有几何。'], | |
| 'sample.place': ['宿主/机器人抽象:门完全打开、样品夹在门口范围时装样;样品轴相对旋转轴的偏移≤5 mm;机器人接触与夹持未建模。'], | |
| 'xray.set': ['管电压20–100 kV(下限为工程值)、电流≤0.5 mA(工程值)且功率≤20 W(厂家);焦点=5 µm×max(1, P/4 W)(厂家给出4 W时<5 µm,增长规律为工程假设)。'], | |
| 'xray.enable': ['每次上电后首次开启运行180 s预热程序(工程值),之后电压10 kV/s、电流100 µA/s斜坡(工程值);门、联锁传感器与安全按钮任一不满足即立即关闭。' | |
| '钨反射靶谱:Kramers厚靶轫致辐射(效率K·Z·V,K=1.1e-9 /V)、Kanaya-Okayama射程1/3深度按20°出射角的自吸收、W K与L线(能量份额为工程值)、' | |
| '0.25 mm铍窗;衰减系数来自NIST SRD 126模板库。'], | |
| 'filter.select': ['7位滤片转换器为厂家标准配置;各位置的滤片(无、Al 0.25/0.5/1.0 mm、Cu 0.1/0.25 mm、Al 1.0 mm+Cu 0.1 mm)为工程选择。'], | |
| 'stage.move': ['源-探距固定0.450 m、源-物距0.015–0.395 m、光束高度0.400 m、样品夹高度0.160–0.399 m与速度为工程值(厂家未公布);碰撞保护:样品本体、样品针、样品夹与旋转台外壳(各为绕旋转轴的竖直圆柱)在高度重叠处不得进入源头部/滤片滑块与探测器外壳的禁入区,并低于腔顶;目标位置与路径都检查(滑台20 mm/s与升降10 mm/s同时启动,路径为(源-物距,高度)平面上的两段直线),路径穿过禁入区时拒绝(COLLISION_RISK),须分两步移动;' | |
| '300 mm高的样品放得进样品腔(腔顶0.640 m),升降行程加低放大视场可覆盖到距其底部约290 mm。'], | |
| 'door.open': ['门的运动方向(向左滑入前面板后)为照片估计,行程0.40 m、速度0.1 m/s为工程值;X射线开启时门锁住。'], | |
| 'door.close': ['安全光幕被挡时门不能关闭,关闭中被挡则停止并重新打开(工程逻辑,按厂家“安全光幕”功能)。'], | |
| 'scan.configure': ['扫描范围180°(+锥角,Parker加权)或360°;步长0.05–2°;曝光0.02–10 s;帧平均1–16;合并1×1/2×2/4×4;随机移动(探测器每投影随机平移±4模拟列)。'], | |
| 'calibration.flat_field': ['暗场与亮场各20帧(工程值);校正对应电压、电流、滤片、合并与曝光,任一改变即失效;亮场噪声使固定图案残留(环状伪影来源之一);' | |
| '亮场饱和时亮区透过率在满量程截止;单个合并像素亮场相对误差超过10 %时校正无效(信号不足);像素增益不均由亮场除去,不单独模拟。'], | |
| 'calibration.geometry': ['钢球体模36投影360°扫描;按精确锥束轨迹u=SDD(a+r sin(β+φ))/(SOD+r cos(β+φ))联合最小二乘求旋转轴横向偏移a;源-物距与源-探距视为已知;' | |
| '体模须在所有角度完整位于视场内(否则拒绝);拟合残差超过2个窗口像素(旋转轴处,至少5 µm)或识别的钢球少于7个时不采用。'], | |
| 'xray.radiograph': ['整幅为175×150模拟像素(每模拟像素16×16原生像素);局部区域以合并后原生像素成像(≤256×256,须在探测器有效面内);平场校正后的固定图案残留按窗口像素计。'], | |
| 'scan.start': ['采集窗口=样品本体在所有角度的投影包络(按名义几何、已标定的轴偏移,加6 %及未知轴偏移的余量),最多175×150模拟像素且不细于一个合并后的原生像素;' | |
| '投影最多模拟200个(均匀子集),光子数按名义投影数与帧数剂量等效合并;连续旋转近似步进采集;' | |
| '能量分24组(强制K边分界);复合泊松量子噪声、读出噪声、16位饱和、焦点半影与闪烁体模糊;未建模散射、相位衬度、探测器余辉、射线管漂移与热漂移。'], | |
| 'recon.start': ['FDK滤波反投影(Ram-Lak/Shepp-Logan/Hann),180°+锥角扫描用Parker权重;束硬化线性化:按指定材料与扫描能谱的多色衰减曲线把线积分映射为μ(E_eff)·L' | |
| '(E_eff=未衰减束的探测能量加权平均能量);环状伪影校正=减去投影平均列剖面的高频部分;自动后对准=中心平面共轭射线一致性(±200 µm内5 µm网格加抛物线顶点),' | |
| '中心平面(光束高度)没有样品数据时不执行并给出警告;手动后对准为给定值,否则用几何标定值;180°+锥角短扫描的Parker权重按本旋转方向的共轭射线(β+π−2γ)在滤波前加权;' | |
| '投影数据须仍在缓存中(只保留最近8组投影/透视);感兴趣体积的中心须在采集窗口可重建的区域内(超出部分给出警告);重建网格48–128(模拟体素远大于名义体素);' | |
| '工作站重建时间按名义体素×投影数/5e10每秒估计(工程值)。'], | |
| 'data.porosity': ['包络=Otsu阈值实体区逐层与三维填孔后腐蚀1体素;孔阈值默认ISO50(空气与基体中值的中点);26连通;开孔=接触包络边界;等效直径=(6V/π)^(1/3);小于约2体素的孔无法分辨。'], | |
| 'data.cracks': ['低衰减连通体主成分分析:厚/长<0.3且宽/长>0.35判为裂纹;面积=π·R1·R2(R=2√λ)、开口=体积/面积、长度=2R1;开口小于体素时部分体积使对比度下降,可能检测不到或开口偏大。'], | |
| 'data.edge_resolution': ['刃边法:逐行找刃边位置并直线拟合,按到刃边距离的0.25像素分箱平均得刃边扩展函数,10–90 %宽度按探测器像素与放大换算到样品平面。'], | |
| 'ledger.read': ['能量流在旋转2π/32、滑台与升降0.25 mm、电压1 kV、滤片位置(按滑块经过的位置)的格点中心计算(每个格内恒定,跨格时步进在格边界切分),电压与电流的斜坡与' | |
| '预热按V²·I精确积分,账本与宿主步长无关;去向:靶(向靶内一侧的半球全部、出射半球沿出射路径的自吸收)、铍窗与滤片(有用发射锥内)、空气、样品本体吸收(μen/μ;' | |
| '剂量=样品本体吸收÷本体质量)、样品架与台架吸收(样品针、样品管、样品夹、旋转台)、散射、探测器沉积/穿透、屏蔽(出射半球其余部分与锥内探测器以外的射线),残差为舍入误差;' | |
| '发射锥(半角20°)内的射线全部计入(样品伸出探测器视野的部分同样受照):锥用格子铺满(探测器上35×30格、其外约8 mm格,格不跨探测器边缘),' | |
| '与样品本体(含样品管)在该格转角下的投影框相交的格沿框边切开,框内按细步距再分(框上约1000条射线,任一方向至少16条),各去向都是正的射线项之和;' | |
| '每条射线按穿过的先后吸收:样品台壳体、样品夹与样品针(位于样品下方:向上的射线先经过,向下的射线最后经过)、样品管在管内之前的壁、样品本体、管内之后的壁(从开口端离开的射线没有这一段)。'], | |
| 'records.delete': ['删除记录及其缓存数据;进行中的操作或正被重建的投影记录不能删除;agent只能删除自己或宿主创建的记录;删除后该记录的结果不再可查。'], | |
| 'measurement.result': ['记录中的样品剂量dose_gy取决于样品真实质量与组成,只对评测者可见(agent为null)。'], | |
| } | |
| LIMITATIONS = [ | |
| '选定配置:X4 POSEIDON基本配置(反射式X射线源、7 MP平板探测器、标准旋转台、单探测器支架、固定扫描几何、7位滤片转换器);透射源、sCMOS、Multi-Vision、Best-Scan-Geometry、' | |
| '样品转换器、原位试验台与高级扫描模式为不支持的选件。', | |
| '源-探距、源-物距范围、光束高度、像素间距、闪烁体、增益与噪声、斜坡与预热、门与各轴的速度、滤片组成为工程假设(厂家未公布);电压、功率、焦点、探测器像素数、样品尺寸、' | |
| '外形与质量为厂家值。', | |
| 'X射线物理:NIST SRD 126衰减系数(模板库145种物质)、多组能量Beer-Lambert、闪烁体能量沉积与复合泊松噪声;未建模康普顿散射到探测器、相位衬度、射线管漂移、探测器余辉。', | |
| '模拟网格:探测器175×150、投影≤200、重建网格≤128,名义体素只在记录中给出;分辨率与噪声按剂量等效合并近似。', | |
| '台架:黄铜样品夹按铜(8.96 g/cm³)、旋转台壳体与转盘按等面积铝圆柱(半径45.1 mm、高50 mm)参与衰减;室温与湿度只作记录,空气密度取NIST表列值。', | |
| '上电后各轴保持断电时的位置(绝对位置,工程假设;厂家未说明回原点行为)。', | |
| '没有真实X4 POSEIDON硬件与3DxSUITE软件接口;机器人装样没有接触验证。', | |
| ] | |
| def _sampling_text(k): | |
| if k in ('door.position_m', 'filter.slide_m', 'stage.sod_m', 'stage.chuck_z_m', 'stage.rotation_rad', 'xray.voltage_v', 'xray.current_a', 'xray.power_w', | |
| 'clock.time_s', 'measurement.progress', 'measurement.remaining_s', 'recon.remaining_s', 'xray.warmup_remaining_s'): | |
| return 'Instantaneous value at the read time: constant-speed motions, voltage / current ramps and operation phases are integrated exactly and cut at every event.' | |
| return 'Changes when a command is accepted or at an event of the operation (phase ends, record completion); no other time dynamics.' | |
| def _errors_of(k): | |
| if k in UNSUPPORTED: | |
| return ['UNSUPPORTED'] + _COMMON_ERRORS | |
| extra = ['ACCESS_DENIED'] if (k in _CONTROL_GUARDED or k in _DATA_GUARDED or k in _ANALYSIS_RECORD_ARGS or CAPS[k]['visibility'] != 'agent') else [] | |
| return list(dict.fromkeys(CAP_ERRORS.get(k, []) + _COMMON_ERRORS + extra)) | |
| def _foreign_text(k): | |
| if k == 'emergency.stop': | |
| return ';安全按钮不受另一个agent的操作限制' | |
| return ';另一个agent的采集操作进行中时,agent调用被拒(ACCESS_DENIED;未通电时开机除外)' if k in _CONTROL_GUARDED else '' | |
| def export_bruker_x4poseidon_contract_metadata(): | |
| slots, caps = {}, {} | |
| for k, v in SLOTS.items(): | |
| slots[k] = dict(meaning_zh=v['meaning'], component_ids=[v['component']], value_schema=copy.deepcopy(v['schema']), unit=v['unit'], | |
| reference_conditions=v['reference'], origin=v['origin'], visibility=v['visibility'], access='read_only', | |
| read_binding=dict(backend='host', artifact_id='runtime', accessor=f'BrukerX4PoseidonSession.read(state_ids=[{k!r}])'), write_via=None, | |
| sampling=dict(mode='instant', time_domain='simulation', window_description=_sampling_text(k)), source_ids=['simulation_assumption']) | |
| for k, v in CAPS.items(): | |
| un = k in UNSUPPORTED | |
| async_ = k in ASYNC | |
| c = {key: copy.deepcopy(v[key]) for key in ['input_schema', 'output_schema', 'component_ids', 'function_zh', 'kind', 'visibility', 'example_arguments']} | |
| c.update(availability='unsupported' if un else 'implemented', | |
| implementation={layer: 'absent' if un or layer in ('scene', 'robot', 'hardware') else 'implemented' for layer in ['process', 'scene', 'robot', 'hardware', 'host']}, | |
| binding=None if un else dict(backend='host', artifact_id='runtime', entrypoint='asset_runtime.bruker_x4poseidon.BrukerX4PoseidonSession.invoke', | |
| invocation=f'session.invoke(instance_id="x4_poseidon_01",capability_id={k!r},arguments={v["example_arguments"]!r},request_id="unique")'), | |
| preconditions=[] if un or k not in PRECONDITIONS else [dict(description_zh=PRECONDITIONS[k][0] + _foreign_text(k) + ';被拒时状态不变。', | |
| state_ids=list(PRECONDITIONS[k][1]) + (['measurement.started_by_other_agent'] if k in _CONTROL_GUARDED else []), | |
| enforced_by='runtime', check='BrukerX4PoseidonRuntime.invoke / BrukerX4PoseidonSession._guard')], | |
| state_effects=[dict(state_id=s, timing='on_step' if k == 'sim.step' else 'immediate', | |
| description_zh='设定、目标、状态标志或立即改变的派生量;位置、斜坡与操作进度只随step推进') for s in EFFECTS.get(k, [])], | |
| observes=[] if un else list(OBSERVES.get(k, [])), | |
| model_effects=_model_effects(k, un), | |
| execution=dict(mode='asynchronous' if async_ else 'synchronous', time_domain='simulation', | |
| completion_criterion=EXEC_TEXT[k][0] if k in EXEC_TEXT else '原子设定、配置、分析或查询;运动由step推进', | |
| completion_state_ids=(['measurement.id', 'measurement.progress', 'result.last_record_id'] if k in ACQUISITION | |
| else ['recon.id', 'result.last_record_id'] if k == 'recon.start' else []), | |
| timeout_s=None, cancellation='supported' if async_ else 'unsupported', retry='same_request_id', resources=list(RESOURCES.get(k, [])), | |
| partial_failure_zh=(EXEC_TEXT[k][1] if k in EXEC_TEXT else | |
| ('不支持:不执行,状态不变' if un else '同步原子操作:成功时一次写入全部效果(运动目标),被拒时状态不变'))), | |
| errors=[dict(code=e, meaning_zh=CAP_ERROR_ZH.get((k, e), ERROR_ZH.get(e, e)), side_effects='partial' if async_ and e in _PARTIAL else 'none') for e in _errors_of(k)], | |
| verification=[], limitations=[UNSUPPORTED[k]] if un else list(CAP_LIMITS.get(k, [_DEFAULT_LIMIT])), source_ids=list(CAP_SOURCES[k])) | |
| if k in ON_STEP: | |
| c['state_effects'] += [dict(state_id=s, timing='on_step', description_zh=ON_STEP_ZH.get(k, '随step演化')) for s in ON_STEP[k] | |
| if not (k == 'sim.step' and s in EFFECTS.get(k, []))] | |
| caps[k] = c | |
| params = {} | |
| for name, (val, unit, meaning, src) in { | |
| 'xray_kv_max_v': (XRAY_KV_MAX_V, 'V', '反射源最高100 kV(厂家、调研表)', [_SPEC, _BRO, _WB]), | |
| 'xray_power_max_w': (XRAY_POWER_MAX_W, 'W', '反射源20 W(厂家、调研表)', [_SPEC, _BRO, _WB]), | |
| 'spot_at_4w_m': (SPOT_AT_4W_M, 'm', '反射源焦点<5 µm@4 W(厂家、调研表;取上限)', [_SPEC, _WB]), | |
| 'detector_pixels': (list(DETECTOR_PIXELS), '1', '7 MP平板探测器2800×2400像素(厂家、调研表)', [_SPEC, _WB, _CFG]), | |
| 'sample_max_diameter_m': (SAMPLE_MAX_DIAMETER_M, 'm', '样品直径最大110 mm(厂家、调研表)', [_SPEC, _WB]), | |
| 'sample_max_height_m': (SAMPLE_MAX_HEIGHT_M, 'm', '样品高度最大300 mm(厂家、调研表)', [_SPEC, _WB]), | |
| 'filter_positions': (FILTER_POSITIONS, '1', '自动7位滤片转换器为标准配置(厂家配置器)', [_CFG]), | |
| 'detail_detectability_m': (DETAIL_DETECTABILITY_M, 'm', '反射源细节可检测度低至5 µm(厂家配置器)', [_CFG]), | |
| 'body_dimensions_m': (list(BODY_DIMENSIONS_M), 'm', '外形W 1250×D 604×H 690 mm(厂家规格表、调研表)', [_SPEC, _WB]), | |
| 'mass_kg': (MASS_KG, 'kg', '重量350 kg(厂家、调研表)', [_SPEC, _BRO, _WB]), | |
| 'mains_voltage_v': (list(MAINS_V), 'V', '电源100–240 VAC 50–60 Hz(厂家)', [_SPEC]), 'mains_current_max_a': (MAINS_A_MAX, 'A', '最大3 A(厂家)', [_SPEC])}.items(): | |
| params[name] = dict(value=val, unit=unit, meaning_zh=meaning, evidence='documented', source_ids=list(src), uncertainty=None) | |
| for name, (val, unit, meaning) in { | |
| 'xray_kv_min_v': (XRAY_KV_MIN_V, 'V', '管电压下限'), 'xray_current_max_a': (XRAY_CURRENT_MAX_A, 'A', '管电流上限(另受20 W限制)'), | |
| 'kv_ramp_v_s': (KV_RAMP_V_S, 'V/s', '电压斜坡'), 'current_ramp_a_s': (CURRENT_RAMP_A_S, 'A/s', '电流斜坡'), 'warmup_s': (WARMUP_S, 's', '上电后首次开启的预热程序'), | |
| 'spot_growth_exp': (SPOT_GROWTH_EXP, '1', '焦点随功率增长的指数(4 W以上)'), 'takeoff_rad': (TAKEOFF_RAD, 'rad', '反射靶出射角'), | |
| 'be_window_m': (BE_WINDOW_M, 'm', '铍窗厚度'), 'kramers_k_per_v': (KRAMERS_K_PER_V, '1/V', 'Kramers效率常数(η=K·Z·V;文献值)'), | |
| 'k_line_fraction_100kv': (K_LINE_FRACTION_100KV, '1', '100 kV时W K线能量份额'), 'l_line_fraction_50kv': (L_LINE_FRACTION_50KV, '1', '50 kV时W L线能量份额'), | |
| 'cone_half_angle_rad': (CONE_HALF_ANGLE_RAD, 'rad', '源发射锥半角(账本中屏蔽份额)'), 'sdd_m': (SDD_M, 'm', '源-探距(固定扫描几何)'), | |
| 'sod_range_m': (list(SOD_RANGE_M), 'm', '源-物距范围'), 'chuck_z_range_m': (list(CHUCK_Z_RANGE_M), 'm', '样品夹高度范围'), | |
| 'source_xyz_m': (list(SOURCE_XYZ_M), 'm', '焦点在资产坐标中的位置(光束沿+X)'), 'filter_clear_m': (FILTER_CLEAR_M, 'm', '滤片转换器前表面到焦点距离'), | |
| 'detector_cover_m': (DETECTOR_COVER_M, 'm', '探测器盖板到有效面距离'), 'chamber_ceiling_m': (CHAMBER_CEILING_M, 'm', '腔顶高度'), | |
| 'source_keepout_dz_m': (list(SOURCE_KEEPOUT_DZ), 'm', '源头部与滤片滑块禁入区相对光束的高度范围'), | |
| 'detector_keepout_dz_m': (list(DETECTOR_KEEPOUT_DZ), 'm', '探测器外壳禁入区相对光束的高度范围'), | |
| 'chuck_r_m': (CHUCK_R_M, 'm', '样品夹半径'), 'stage_r_m': (STAGE_R_M, 'm', '旋转台壳体外接圆半径(保守包络)'), | |
| 'pixel_pitch_m': (PIXEL_PITCH_M, 'm', '平板像素间距'), 'csi_thickness_m': (CSI_THICKNESS_M, 'm', 'CsI:Tl闪烁体厚度'), | |
| 'adu_per_j': (ADU_PER_KEV / KEV, '1/J', '闪烁体沉积能量到ADU的转换增益(0.8 ADU/keV)'), 'read_noise_adu': (READ_NOISE_ADU, '1', '读出噪声(ADU)'), | |
| 'dark_offset_adu': (DARK_OFFSET_ADU, '1', '暗电平(ADU)'), 'dark_current_adu_s': (DARK_CURRENT_ADU_S, '1/s', '暗电流(ADU/s)'), | |
| 'flat_max_sigma': (FLAT_MAX_SIGMA, '1', '可用亮场的合并像素相对误差上限'), 'detector_psf_px': (DETECTOR_PSF_PX, '1', '闪烁体光扩散σ(原生像素)'), | |
| 'step_overhead_s': (STEP_OVERHEAD_S, 's', '每投影旋转与稳定时间'), 'frame_overhead_s': (FRAME_OVERHEAD_S, 's', '每帧读出'), | |
| 'rotation_speed_rad_s': (ROTATION_SPEED_RAD_S, 'rad/s', '旋转台定位速度'), 'carriage_speed_m_s': (CARRIAGE_SPEED_M_S, 'm/s', '样品滑台速度'), | |
| 'lift_speed_m_s': (LIFT_SPEED_M_S, 'm/s', '升降速度'), 'door_travel_m': (DOOR_TRAVEL_M, 'm', '门行程'), 'door_speed_m_s': (DOOR_SPEED_M_S, 'm/s', '门速度'), | |
| 'filter_s_per_step': (FILTER_S_PER_STEP, 's', '滤片每档时间'), 'boot_s': (BOOT_S, 's', '启动与回原点时间'), | |
| 'flat_field_frames': (FLAT_FIELD_FRAMES, '1', '暗场/亮场帧数'), 'axis_offset_sd_m': (AXIS_OFFSET_SD_M, 'm', '隐藏旋转轴横向偏移(1σ)'), | |
| 'recon_rate_voxel_proj_s': (RECON_RATE_VOXEL_PROJ_S, '1/s', '工作站重建吞吐(体素×投影/秒)'), 'sim_detector_px': (list(SIM_DETECTOR), '1', '模拟探测器网格'), | |
| 'sim_max_projections': (SIM_MAX_PROJECTIONS, '1', '模拟投影数上限'), 'energy_groups': (ENERGY_GROUPS, '1', '能量分组数')}.items(): | |
| params[name] = dict(value=val, unit=unit, meaning_zh=meaning, evidence='assumption', source_ids=[_SIM], uncertainty='工程值') | |
| mechanism = dict( | |
| component_ids=['source_housing', 'source_head', 'source_window', 'filter_changer', 'filter_slide', 'sample_carriage', 'sample_lift', 'sample_turntable', | |
| 'sample_chuck', 'detector_housing', 'detector_window', 'door_glass', 'button_emergency_stop', 'enclosure_base', 'workstation_monitor'], | |
| state_ids=list(slots), implementation='lumped', | |
| meaning_zh='X4 POSEIDON台式显微CT:钨反射源谱、滤片、锥束几何与样品旋转、平板探测器响应与噪声、暗场/亮场与几何标定、FDK重建、孔隙率与裂纹分析、安全联锁与能量账', | |
| equations=['Kramers: I(E) dE ~ Z i (E0 - E) dE, eta = K Z V (K = 1.1e-9 /V); self-absorption exp(-mu_W(E) R_KO(E0) / (3 sin(takeoff)))', | |
| 'beam: N(E) = N0(E) exp(-mu_Be t_Be - sum_f mu_f t_f - mu_air SDD / cos(alpha)); omega_pixel = A cos^3(alpha) / SDD^2', | |
| 'transmission: T_g = exp(-sum_m mu_m,g L_m) (energy groups, mu weighted by the detected energy); L_m exact chord lengths of the phantom', | |
| 'detector: E_dep(E) = E (1 - exp(-mu_CsI t)) mu_en/mu; S = G sum_g n_g T_g <E_dep>_g; Var = G^2 sum_g n_g T_g <p eps^2>_g + sigma_read^2 n_reads', | |
| 'flat field: t = (S - D) / (F - D); q = -ln t; magnification M = SDD/SOD; voxel = pitch x binning / M; penumbra sigma = spot/2.355 (M - 1)', | |
| 'FDK: f(x) = 1/2 sum_beta (SOD/U)^2 [ (SOD/sqrt(SOD^2+u^2+v^2) q) * h_ramp ](u(x), v(x)) d_beta, U = SOD + x cos b - y sin b; Parker w for pi + 2 gamma_m', | |
| 'Parker (short scan pi + 2 gamma_m, this stage: conjugate (b, g) ~ (b + pi - 2 g, -g)): w(b, g) with g -> -g applied to the projections before the ramp filter', | |
| 'beam hardening: q -> q + s (mu_m(E_eff) L(q) - q), L(q) inverse of q_poly(L) = -ln sum_g w_g exp(-mu_m,g L), E_eff = detected-energy mean of the unattenuated beam; porosity = N_pore / N_envelope (ISO 50 threshold)', | |
| 'geometry calibration: u_i(b) = SDD (a + r_i sin(b + phi_i)) / (SOD + r_i cos(b + phi_i)), joint least squares over the tracked steel balls for the axis offset a', | |
| 'auto alignment (central row): a* = argmin_a mean min((p(b, u) - p(b - pi + 2 (alpha - t), SDD tan(2 alpha - t)))^2, c^2), alpha = atan(a / SOD), t = atan(u / SDD)', | |
| 'energy: E_emitted = 4 pi E_un = target (2 pi E_un + 2 pi (E_un - E_self)) + window + filter (cone) + air + sample body absorbed (mu_en/mu) + holder / stage absorbed + scattered + detector deposited + passed + shielding', | |
| 'ledger per sub-step inside one rate cell: E_sink = base_sink(cell) int V^2 I dt / (e V_c^2), E_electrical = int V I dt (V, I linear in the sub-step); dose = E_sample_body / m_body'], | |
| parameters=params, source_ids=[_SIM, _LIBS, _NIST, _PUB, _SPEC, _BRO, _CFG, _PHYS, _WB], limitations=list(LIMITATIONS)) | |
| import importlib.util | |
| spec = importlib.util.spec_from_file_location('_x4poseidon_local_annotations', ROOT / 'scripts/asset_runtime/_annotations.py') | |
| ann = importlib.util.module_from_spec(spec) | |
| spec.loader.exec_module(ann) | |
| ann.KEY_ZH.update({k: v['meaning'] for k, v in SLOTS.items()}) | |
| ann.PARAM_ZH.update(PARAM_ZH) | |
| ann.annotate_export(SLUG, caps, slots, {'x4_poseidon_ct': mechanism}, inputs={'plant.configure': (PLANT, PLANT_EXAMPLE)}) | |
| for k, v in SLOTS.items(): | |
| slots[k]['meaning_zh'] = v['meaning'] | |
| if v['reference']: | |
| slots[k]['reference_conditions'] = v['reference'] | |
| return dict(asset_type_id=ASSET_TYPE_ID, catalog_id=CATALOG_ID, capabilities=caps, state_slots=slots, mechanisms={'x4_poseidon_ct': mechanism}) | |