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Merged
toastisme merged 2 commits into from
Aug 13, 2025
Merged

Add tof_helpers.InstrumentDefinitionReader #842

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ef7ab81
Add tof_helpers.InstrumentDefinitionReader to read instrument informa…
toastisme Aug 13, 2025
57c8ca6
Rename newsfragments/XXX.misc to newsfragments/842.misc
DiamondLightSource-build-server Aug 13, 2025
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1 change: 1 addition & 0 deletions newsfragments/842.misc
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Add `tof_helpers.InstrumentDefinitionReader` to read instrument information directly from xml data, and update FormatMANDI to use this by default.
209 changes: 31 additions & 178 deletions src/dxtbx/format/FormatMANDI.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
from __future__ import annotations

import xml
import xml.etree.ElementTree as ET
from multiprocessing import Pool, cpu_count
from os.path import join
from sys import argv
Expand All @@ -16,6 +18,7 @@
from dxtbx.model.beam import BeamFactory, PolychromaticBeam, Probe
from dxtbx.model.goniometer import Goniometer, GoniometerFactory
from dxtbx.model.scan import Scan, ScanFactory
from dxtbx.model.tof_helpers import InstrumentDefinitionReader


class FormatMANDI(FormatHDF5):
Expand All @@ -33,13 +36,21 @@ def __init__(self, image_file: str, **kwargs) -> None:
self._base_entry = self.get_base_entry_name(self.nxs_file)
self.detector = None
self.raw_data = None
self.xml_reader = InstrumentDefinitionReader()
self.xml_file = self.get_xml_file()

def open_file(self, image_file_path: str) -> h5py.File:
return h5py.File(image_file_path, "r")

def get_base_entry_name(self, nxs_file: h5py.File) -> str:
return list(nxs_file.keys())[0]

def get_xml_file(self) -> xml.etree.ElementTree.Element:
xml_string = self.nxs_file[self._base_entry]["instrument/instrument_xml/data"][
0
].decode()
return ET.fromstring(xml_string)

@staticmethod
def understand(image_file: str) -> bool:
try:
Expand All @@ -63,6 +74,20 @@ def get_name(image_file: str) -> str:

return get_name(image_file) == "MANDI"

def get_instrument_name(self) -> str:
return self.nxs_file[self._base_entry]["instrument/name"][0].decode()

def get_experiment_title(self) -> str:
return self.nxs_file[self._base_entry]["title"][0].decode()

def get_experiment_run_number(self) -> str:
return str(self.nxs_file[self._base_entry]["run_number"][0].decode())

def get_experiment_description(self) -> str:
title = self.get_experiment_title()
run_number = self.get_experiment_run_number()
return f"{title} ({run_number})"

def get_raw_data(self, index: int) -> tuple[flex.int]:
raw_data = []
panel_size = self._get_image_size()
Expand All @@ -84,9 +109,9 @@ def get_detector(self, index: int = None) -> Detector:
image_size = self._get_image_size()
trusted_range = self._get_panel_trusted_range()
pixel_size = self._get_pixel_size()
fast_axes = self._get_panel_fast_axes()
slow_axes = self._get_panel_slow_axes()
panel_origins = self._get_panel_origins()
panel_origins, fast_axes, slow_axes = (
self.xml_reader.get_dials_detector_geometry(self.xml_file)
)
gain = self._get_panel_gain()
panel_projections = self._get_panel_projections_2d()
detector = Detector()
Expand Down Expand Up @@ -125,190 +150,17 @@ def _get_sample_to_source_direction(self) -> tuple[float, float, float]:
return (0, 0, -1)

def _get_num_panels(self) -> int:
return 40
return self.xml_reader.get_num_panels(self.xml_file)

def _get_panel_names(self) -> tuple[str]:
return (
"bank1",
"bank2",
"bank3",
"bank5",
"bank7",
"bank8",
"bank11",
"bank12",
"bank13",
"bank17",
"bank18",
"bank19",
"bank20",
"bank21",
"bank22",
"bank23",
"bank26",
"bank27",
"bank28",
"bank29",
"bank31",
"bank32",
"bank33",
"bank37",
"bank39",
"bank40",
"bank41",
"bank42",
"bank43",
"bank46",
"bank47",
"bank48",
"bank49",
"bank50",
"bank51",
"bank52",
"bank53",
"bank57",
"bank58",
"bank59",
)
return self.xml_reader.get_panel_names(self.xml_file)

def _get_panel_gain(self) -> float:
return 1.0

def _get_panel_trusted_range(self) -> tuple[int, int]:
return (-1, 100000)

def _get_panel_origins(self) -> tuple[tuple[float, float, float], ...]:
return (
(71.59649688799595, -407.9875271017446, 91.63277006330976),
(247.78726107849047, -370.86794223009696, 93.05022800601382),
(87.97790138773688, -409.33375923673844, -82.03599884101118),
(-85.64058504589039, -403.12747733399465, -97.65220987551567),
(-102.35072309461592, -404.43783650393084, 75.318849784288),
(-101.376307910567, -362.7034047105274, 249.52766339419702),
(188.46366913374928, -340.8394179451527, 264.04352540644584),
(304.0861943336393, -339.0817491399483, 97.69270882922524),
(306.2755999937922, -340.057049383876, -104.79738499213931),
(-317.25124354686346, -327.83699783860874, -104.13714348985233),
(-317.64898298095443, -328.5375200345585, 98.10329861513794),
(-199.4658588654215, -332.9638764406945, 263.6279591286127),
(114.10208135428759, -227.42718157198428, 359.56893399219473),
(303.4066657317839, -229.171259967358, 219.83460648731807),
(373.7935811124756, -229.42481664792578, -3.4456330231885866),
(307.8384913706013, -230.97676263539856, -228.302717512744),
(-312.1677269773796, -218.49351412060085, -227.8285640453776),
(-380.89278569326314, -215.05244003524544, -2.9178356187804786),
(-309.1414237681691, -217.46267271820048, 219.27597207117535),
(-121.94996995674012, -223.24489754625657, 361.1688851013957),
(233.5580884765005, -115.43121703586225, 320.63922658665984),
(378.45031177159586, -117.16549490064116, 120.41696423222004),
(372.89800332945197, -115.93989744162306, -124.92982019508003),
(-376.5169852579795, -102.17355196399106, -124.26626333114893),
(-234.11393874355227, -106.04709661250322, 316.95386906093717),
(137.13740529014822, 9.162292313720426, 417.1619791626718),
(357.2696434729768, 4.7468832636133955, 256.1368430867005),
(438.2478931969796, 3.3972037803596535, -3.291783715503191),
(361.08469499737765, 6.145340038510798, -263.82143408424554),
(-357.74327638098214, 18.735783076242843, -263.98028087869886),
(-439.2712284275042, 20.01853918185089, -2.3600188451399426),
(-355.6934447072983, 17.71984081232332, 255.6674822459931),
(-136.15700784634026, 13.793781420194758, 419.92464356648065),
(3.0211639276166506, 147.5028475462614, 442.29307467579065),
(264.40926501753853, 142.959186239358, 357.0786864461248),
(427.5813705436181, 141.24925820955698, 134.73307743251732),
(428.2623879171177, 143.0955989020943, -141.14258845564459),
(-418.3256035559564, 155.87101472044327, -139.2255203535932),
(-421.1137777088633, 156.31099046243813, 134.80694824067064),
(-259.44611581654755, 152.81413474372576, 357.96944889204525),
)

def _get_panel_fast_axes(self) -> tuple[tuple[float, float, float], ...]:
return (
(-0.9999583639962794, 0.004549995022478471, 0.007909982249012876),
(-0.9270112280582247, -0.36646049406596276, 0.07973010311615258),
(9.755968675898316e-17, 5.59387233726922e-17, 1.0),
(0.9999739794108949, -0.005200025869334086, 0.0050000232096750075),
(-0.0007900093059066182, -3.0005133535454756e-05, -0.9999996874924455),
(-0.09582968262311213, -0.39675869523887103, -0.9129070104236807),
(-0.3387401541674543, 0.6009102631780291, 0.7239903062623982),
(0.163969987359823, 0.5861999502774039, 0.7933999379505827),
(0.570700354137915, 0.6004903814689775, 0.5601003548919607),
(-0.13169977290772172, 0.6018189486770399, -0.7876986243667796),
(-0.5578201777633975, 0.6146602050286276, -0.5577001718075555),
(-0.7780136583020894, 0.6167928979211943, -0.1194205533791195),
(-0.6024392271286111, 0.6822191251868116, 0.41429946034966436),
(-0.26297968340353617, 0.6894191631846113, 0.6749391850758157),
(0.17966967519294516, 0.6836287651503686, 0.7073687293590546),
(0.5733071659167379, 0.6797166377204127, 0.45749774416337297),
(0.25794006072273956, 0.6797101771949186, -0.6866301770909884),
(-0.18668894896436913, 0.6831461280707687, -0.7060160083429384),
(-0.561269909625896, 0.6879698755373065, -0.4600799266450577),
(-0.7216806782398583, 0.6916006515467016, -0.02942001759747731),
(-0.5406021594612158, 0.7160628615705423, 0.44159176109306714),
(-0.22815117249667427, 0.7086036629348159, 0.667703445673118),
(0.24252895759587326, 0.7016769746800912, 0.669947108308748),
(0.23261954038002947, 0.7028586076557112, -0.6722186601677009),
(-0.5597197589436586, 0.717469677505232, -0.4146698123912455),
(-0.7199483374110611, 0.6930083967891861, 0.03759991274897956),
(-0.5756319823045508, 0.6837223456610776, 0.44852154350916884),
(-0.18817009429166837, 0.6803903231242386, 0.7082803285515974),
(0.25794006072273956, 0.6797101771949186, 0.6866301770909884),
(0.5733071659167379, 0.6797166377204127, -0.45749774416337297),
(0.20908971333938364, 0.6753790691234415, -0.7072090248049779),
(-0.24702047603368216, 0.6870212856103326, -0.6833612789282247),
(-0.5932592018008807, 0.6785590800586375, -0.43312941986034337),
(-0.7000908028386412, 0.5988306911020218, -0.38894044682318896),
(-0.7843286772076716, 0.6097189697574565, 0.11432980375899326),
(-0.5632010367672651, 0.6076211250557385, 0.5600010362225023),
(-0.14986972872339283, 0.5870889266408779, 0.7955285391662817),
(0.5752912394628964, 0.5971712830921335, -0.5589512039948916),
(0.1400298828594605, 0.605939509647955, -0.7830893579623988),
(-0.3374699569875644, 0.606049917647629, -0.720289889870817),
)

def _get_panel_slow_axes(self) -> tuple[tuple[float, float, float], ...]:
return (
(0.009080058381285394, 0.4099593618136086, 0.9120585914299427),
(-0.07844604621503816, 0.39736287118342395, 0.914302448010555),
(0.9135486805116207, 0.4067294043162809, -1.1187744674538443e-16),
(0.006681901394788637, 0.40642071283978043, -0.9136616202777456),
(-0.9000874338744042, 0.4357087607239177, 0.0006980041674738889),
(-0.9107931255862123, 0.40496046981334777, -0.08039216549795625),
(0.7862610251238533, 0.6034193349109014, -0.13296129747739685),
(0.5893302132278937, 0.5867709742995678, -0.555328482518501),
(0.14371018354248974, 0.598521065045708, -0.7881116150918823),
(-0.5542598612993068, 0.6140978131535265, 0.5618539686008542),
(-0.14408786300718987, 0.590035000756182, 0.7944163805062643),
(0.35367928103827984, 0.5871085430589494, 0.7281583102811113),
(0.7350692860342056, 0.6764910100824224, -0.04508944451672663),
(0.5937905665933713, 0.6670312021437351, -0.44998015333057373),
(0.23556951108705004, 0.6682489972510377, -0.7056559240303951),
(-0.2579398836750756, 0.6797104022878586, -0.6866300207763755),
(-0.5733092269127125, 0.6797160990021477, 0.4574959618335998),
(-0.18693934596038786, 0.680817634844769, 0.7081956149371988),
(0.24370146751944194, 0.6686329796911721, 0.7025236887096229),
(0.6312723758233735, 0.6749771526277607, 0.3819699346189881),
(0.5598433004196994, 0.6980113089477805, -0.446492655657609),
(0.2109292083765029, 0.7054769375484777, -0.6766174396517453),
(-0.21138055008498535, 0.712193415198309, -0.669401824313273),
(-0.20838062049588585, 0.7111470099447131, 0.671451746031272),
(0.5778286402826893, 0.696587990671485, 0.4252989933227231),
(0.6222313445360602, 0.6685195040380297, -0.4073202997612487),
(0.2748273430210124, 0.678368281303838, -0.6813856517779691),
(-0.15815963132467423, 0.6907582508433235, -0.705576764010207),
(-0.5733092269127125, 0.6797160990021477, -0.4574959618335998),
(-0.2579398836750756, 0.6797104022878586, 0.6866300207763755),
(0.20974959544136526, 0.6753887094166133, 0.7070043835824111),
(0.5889124037382343, 0.6664719408308167, 0.45716226091887696),
(0.7351718509309583, 0.6758902572003087, 0.0519105944913895),
(0.7138073326114943, 0.6012290545520337, -0.3591694807086639),
(0.3550890340368667, 0.5923840954415561, -0.7231824537242688),
(-0.13366751242833205, 0.6017868942416856, -0.7873915989138873),
(-0.5813390730622492, 0.598508802800182, -0.5512096652833816),
(0.14377848861475973, 0.5988879167456186, 0.7878204169655343),
(0.5985395808907364, 0.5782215084773593, 0.5544459010952365),
(0.8005222527712781, 0.587343547301513, 0.11912883891515713),
)

def get_num_images(self) -> int:
return len(self._get_time_of_flight())

Expand Down Expand Up @@ -365,6 +217,7 @@ def _get_panel_projections_2d(self) -> dict:
for j in range(5):
panel_pos[count] = ((1, 0, 0, 1), (p_h * i, p_w * j))
count += 1
panel_pos[count] = ((1, 0, 0, 1), (p_h * i, p_w * j))
return panel_pos

@staticmethod
Expand Down
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