From e5e7b58d206649bad8794622c13eea46c9ab3755 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Wed, 7 Oct 2026 20:37:02 +0200 Subject: [PATCH 01/10] mctest: add %Scan: tests (one row per scan), per-point scan seeds in mcrun %Scan: header lines describe a parameter scan test, using the mcrun scan syntax unchanged (so every mcrun scan form works), followed by one target detector value per scan point in a {}-enclosed list that may span lines: * %Scan: mcrun SE_example.instr dBz=-0.0001,0.0001 -N41 -n1e5 Detector: detector_I={ * 86.04,101.892,... * 85.406 } mctest: - %Scan: lines become tests like %Example: (own testnb, dir, JSON with "scan": true and list-valued targetval/testval) - "mcrun" and "*.instr" tokens on %Example:/%Scan: lines are ignored; a scan's own -n is used, else at most 1e5 per point - scans run with --scan_split=auto unless MPI is used, timeout scales with the number of points, mcdisplay runs at the first scan point - values are read from the scan's mccode.dat (McCode and NeXus formats); a scan passes when all points are within 20% of target - new --noscans option to skip scans mcviewtest: one cell per scan ("scan, 41/41 pts (41/41 pts OK)"), with a per-point test/target/percent hover tooltip. mcdoc: %Scan: lines are shown like %Example: lines, as "Scan: ...", with the target value list shortened to "{N values}". mcrun: - --scan_split=auto (alias for the existing 0): number of cores minus one - --scan_split is only overridden by an explicit multi-process --mpi (--mpi defaults to 1), with a warning when that happens - each scan point i now uses seed base+i*1024 in both the serial and the --scan_split scanner (previously only the latter), so serial and split scans give identical, reproducible results for a given --seed; without --seed the base is taken from the current time and logged; --seeds scans use the scanned seeds unchanged SE_example gets a 41-point %Scan: test (targets from -s 1000). Co-Authored-By: Claude Opus 5.5 --- .../SE_example/SE_example.instr | 6 + tools/Python/mccodelib/utils.py | 16 +- tools/Python/mcrun.md | 4 +- tools/Python/mcrun/mcrun.py | 20 ++- tools/Python/mcrun/optimisation.py | 34 +++- tools/Python/mctest.md | 12 ++ tools/Python/mctest/main.template | 4 +- tools/Python/mctest/mctest.py | 151 +++++++++++++++--- tools/Python/mctest/mcviewtest.py | 33 +++- 9 files changed, 222 insertions(+), 58 deletions(-) diff --git a/mcstas-comps/examples/Tests_polarization/SE_example/SE_example.instr b/mcstas-comps/examples/Tests_polarization/SE_example/SE_example.instr index 1a9a1190d4..8d743001ac 100644 --- a/mcstas-comps/examples/Tests_polarization/SE_example/SE_example.instr +++ b/mcstas-comps/examples/Tests_polarization/SE_example/SE_example.instr @@ -19,6 +19,12 @@ * MeanPolLambda_montior is used to monitor beam polarisation. * * Example: mcrun SE_example.instr dBz=-0.0001,0.0001 -N41 -n1e5 +* %Scan: mcrun SE_example.instr dBz=-0.0001,0.0001 -N41 -n1e5 Detector: detector_I={ +* 86.04,101.892,108.731,94.7348,89.0012,85.6308,108.935,102.351,69.0694,92.3323, +* 136.083,64.8421,57.8734,158.608,99.3713,18.8129,133.474,164.129,20.9553,74.1501, +* 193.637,76.1058,20.3687,168.351,133.934,18.4337,110.268,161.186,59.7896,65.6851, +* 141.567,96.8757,64.2307,106.846,110.065,90.8057,100.937,92.2149,106.729,106.231, +* 85.406 } * * %Parameters * POL_ANGLE: [deg] Reflection angle of polarizer/analyzer diff --git a/tools/Python/mccodelib/utils.py b/tools/Python/mccodelib/utils.py index 8dccbd4344..0d00fdf29c 100644 --- a/tools/Python/mccodelib/utils.py +++ b/tools/Python/mccodelib/utils.py @@ -395,7 +395,9 @@ def parse_header(text): tag_E=2 tag_P=3 tag_L=4 - lst = [text.find('%I'), text.find('%D'), text.find('%Ex'), text.find('%P'), text.find('%L')] + # %Scan: lines are tests too, so the test section starts at the first %Example or %Scan + tag_E_pos = min([p for p in (text.find('%Ex'), text.find('%Scan:')) if p != -1], default=-1) + lst = [text.find('%I'), text.find('%D'), tag_E_pos, text.find('%P'), text.find('%L')] # missing %Example tag if lst[tag_E] == -1: lst[tag_E] = lst[tag_P] @@ -493,9 +495,9 @@ def format_examples(test_text): ''' Splits the raw %Example header text (as stored in InstrCompHeaderInfo.test) into an ordered list of (line, is_example) - tuples. Lines starting with the '%Example:' tag have the leading - '%Example:' tag replaced with 'Test:' (so they render as - 'Test: ...') and are flagged True so that doc writers can highlight + tuples. Lines starting with the '%Example:' (or '%Scan:') tag have the + leading tag replaced with 'Test:' (or 'Scan:') (so they render as + 'Test: ...' / 'Scan: ...') and are flagged True so that doc writers can highlight them (e.g. in bold); all other lines are passed through unchanged and flagged False. Order is preserved even when %Example: lines are interspersed with other text. @@ -503,10 +505,12 @@ def format_examples(test_text): lines = [] if not test_text: return lines + # a %Scan: {...} list of target values may span several lines, show it as "{N values}" + test_text = re.sub(r'\{([-0-9.+eE,\s]*)\}', lambda m: '{%d values}' % len([v for v in m.group(1).split(',') if v.strip()]), test_text) for l in test_text.splitlines(): - m = re.match(r'%Example:\s*(.*)', l) + m = re.match(r'%(Example|Scan):\s*(.*)', l) if m: - lines.append(('Test: ' + m.group(1), True)) + lines.append((('Test: ' if m.group(1) == 'Example' else 'Scan: ') + m.group(2), True)) else: lines.append((l, False)) return lines diff --git a/tools/Python/mcrun.md b/tools/Python/mcrun.md index fc72515ecc..96d0420acf 100644 --- a/tools/Python/mcrun.md +++ b/tools/Python/mcrun.md @@ -34,7 +34,7 @@ in help text, and the McStas-only `-g`/`--gravitation` flag, differ). | `-N NP`, `--numpoints NP` | Set number of scan points. Two input modes available: 1) A single integer applies the same point count to every scanned parameter (default, and only valid form without -M) 2) Together with -M/--multi, a comma-separated list (e.g. -N=5,10,20) gives each scanned parameter its own point count, in the order in which parameters are listed on the command line. If a parameter is given as par="min:delta:max" the point count is instead computed from the requested bin width. | | `-L`, `--list` | Use list-mode scanning. Multiple input modes available: 1) If multiple lists (of identical length) are given (and -M is not requested) the lists are scanned together in lockstep. 2) Combined with -M/--multi, the cartesian product of each parameter's own list is used to set up a multidimensional 'grid' scan (lists may have different lengths) 3) Any parameter given as "min:delta:max" is expanded into its own explicit list of equidistant points and may be freely mixed with other, explicitly-listed parameters (e.g. a list of filenames) under -L. | | `-M`, `--multi` | Run a multi-dimensional scan (cartesian product of every scanned parameter's points, rather than a co-linear scan). Combine with -L/--list or give -N as a comma-separated list (see -N/--numpoints). | -| `--scan_split scan_split` | Scan by parallelising steps as individual cpu threads. Initialise by number of wanted threads (e.g. your number of cores). | +| `--scan_split scan_split` | Scan by parallelising steps as individual cpu threads. Initialise by number of wanted threads (e.g. your number of cores), or "auto" (or 0) for the number of cores minus one. | | `--seeds SEEDS` | Set range of seeds to scan (each must be: SEED != 0) | | `--optimize` | Optimize instrument variable parameters to maximize monitors | | `--optimize-maxiter optimize_maxiter` | Maximum number of optimization iterations to perform. Default=1000 | @@ -60,7 +60,7 @@ in help text, and the McStas-only `-g`/`--gravitation` flag, differ). | `--vecsize VECSIZE` | vector length in OpenACC parallel scenarios | | `--numgangs NUMGANGS` | number of 'gangs' in OpenACC parallel scenarios | | `--gpu_innerloop INNERLOOP` | Maximum particles in an OpenACC kernel run. (If INNERLOOP is smaller than ncount we repeat) | -| `-s SEED`, `--seed SEED` | Set random seed (must be: SEED != 0) | +| `-s SEED`, `--seed SEED` | Set random seed (must be: SEED != 0). In a scan, point i uses SEED+i*1024 (without --seed, the base seed is taken from the current time and logged) | | `-n COUNT`, `--ncount COUNT` | Set number of neutrons to simulate | | `-t trace`, `--trace trace` | Enable trace of neutrons through instrument | | `--no-trace` | Disable trace of neutrons in instrument (combine with -c) | diff --git a/tools/Python/mcrun/mcrun.py b/tools/Python/mcrun/mcrun.py index cd5bb77583..a62cb694d4 100644 --- a/tools/Python/mcrun/mcrun.py +++ b/tools/Python/mcrun/mcrun.py @@ -143,9 +143,9 @@ def add_mcrun_adv_options(parser): '(see -N/--numpoints). ') add("--scan_split", - type=int, metavar="scan_split", - help='Scan by parallelising steps as individual cpu threads. Initialise by number of wanted threads (e.g. your number of cores).') + help='Scan by parallelising steps as individual cpu threads. Initialise by number of wanted threads (e.g. your number of cores), ' + 'or "auto" (or 0) for the number of cores minus one.') add('--seeds', metavar='SEEDS', @@ -323,7 +323,8 @@ def add_mcstas_options(parser): add('-s', '--seed', metavar='SEED', type=int, action='callback', callback=check_seed, - help='Set random seed (must be: SEED != 0)') + help='Set random seed (must be: SEED != 0). In a scan, point i uses SEED+i*1024 ' + '(without --seed, the base seed is taken from the current time and logged)') add('-n', '--ncount', metavar='COUNT', type=float, default=1000000, @@ -904,8 +905,12 @@ def main(): interval_points = LinearInterval.from_range(options.numpoints, intervals) - # Check that mpi and scan split are not both used. Default to mpi if they are - if options.scan_split is not None and options.mpi is not None: + # Check that mpi and scan split are not both used. Default to mpi if they are. + # --mpi defaults to 1 (compile with MPI, run single-process), so only an + # explicit multi-process --mpi request should override --scan_split + if options.scan_split is not None and options.mpi is not None and str(options.mpi) != '1': + LOG.warning('--mpi=%s given, ignoring --scan_split=%s (scan points run serially via MPI)', + options.mpi, options.scan_split) options.scan_split = None # Parameters for linear scanning present @@ -917,8 +922,9 @@ def main(): scanner.run() # in optimisation.py elif options.scan_split is not None: - if options.scan_split == 0: - options.scan_split = multiprocessing.cpu_count()-1 + if options.scan_split in ("auto", "0"): + options.scan_split = max(1, multiprocessing.cpu_count()-1) + options.scan_split = int(options.scan_split) split_scanner = Scanner_split(mcstas, intervals, options.scan_split) split_scanner.set_points(interval_points) if (not options.dir == ''): diff --git a/tools/Python/mcrun/optimisation.py b/tools/Python/mcrun/optimisation.py index b1556124da..0fc2fbea57 100644 --- a/tools/Python/mcrun/optimisation.py +++ b/tools/Python/mcrun/optimisation.py @@ -392,8 +392,26 @@ def from_list(intervals): class InvalidInterval(McRunException): pass +def point_seed(base, i): + """ Seed for scan point i: the base seed shifted by i*1024, so every point + gets its own random sequence, reproducibly (a seed of 0 is not allowed) """ + return (base + i*1024) or 1 + +def scan_base_seed(mcstas, intervals): + """ The base seed for point_seed(): --seed if given, else the current Unix + epoch (logged, so the scan can be reproduced). None when --seed is itself + scanned (--seeds), in which case the scanned seeds are used unchanged. """ + if '--seed' in intervals: + return None + if mcstas.options.seed is None: + mcstas.options.seed = int(datetime.now().timestamp()) + LOG.info('No incoming seed from cmdline, scan base seed set from current Unix epoch: %d' % mcstas.options.seed) + else: + LOG.info('Scan base seed: %d' % mcstas.options.seed) + return mcstas.options.seed + def _simulate_point(args): - i, point, intervals, mcstas_config, mcstas_dir = args + i, point, intervals, mcstas_config, mcstas_dir, base_seed = args from shutil import copyfile from os.path import join @@ -405,8 +423,8 @@ def _simulate_point(args): # Ensure we get a mccode.sim pr. thread subdir (e.g. for monitoring seed value mcstas.simfile = join(mcstas_dir, 'mccode.sim') - # Shift thread seed to avoid duplicate simulations / biasing - mcstas.options.seed = (i*1024)+mcstas.options.seed + if base_seed is not None: + mcstas.options.seed = point_seed(base_seed, i) for key in intervals: mcstas.set_parameter(key, point[key]) @@ -487,9 +505,12 @@ def run(self): points = list(self.points) header_written = False skipped = [] + base_seed = scan_base_seed(self.mcstas, self.intervals) with open(self.outfile, 'w') as outfile: for i, point in enumerate(points): + if base_seed is not None: + self.mcstas.options.seed = point_seed(base_seed, i) par_values = [] for key in self.intervals: self.mcstas.set_parameter(key, point[key]) @@ -637,14 +658,11 @@ def run(self): mcstas_dir = self.mcstas.options.dir or '.' - if self.mcstas.options.seed is None: - dt=datetime.now() - LOG.info('No incoming seed from cmdline, setting to current Unix epoch (%d)!' % dt.timestamp()) - self.mcstas.options.seed=dt.timestamp() + base_seed = scan_base_seed(self.mcstas, self.intervals) # Prepare data to pass into processes args_list = [ - (i, point, self.intervals, self.mcstas, mcstas_dir) + (i, point, self.intervals, self.mcstas, mcstas_dir, base_seed) for i, point in enumerate(self.points) ] diff --git a/tools/Python/mctest.md b/tools/Python/mctest.md index 6c8ff10c1f..c42da3ed7f 100644 --- a/tools/Python/mctest.md +++ b/tools/Python/mctest.md @@ -10,6 +10,17 @@ Runs every `%Example` test embedded in the instrument library, compiling, displaying (single-particle), and running each one, then compares the result against the target value recorded in the instrument header. +A `%Scan:` header line works the same way for a parameter scan. The +parameters use the `mcrun` scan syntax, followed by one target value per +scan point, e.g. + + %Scan: dBz=-0.0001,0.0001 -N41 -n1e5 Detector: detector_I=79.2,102.7,... + +`mcrun` and `*.instr` tokens on `%Example:`/`%Scan:` lines are ignored. A scan +uses its own `-n` if given, otherwise at most `1e5` per point, and runs its +points in parallel (`--scan_split=auto`) unless MPI is used. A scan passes when +every point is within 20% of its target. + | Option | Description | |---|---| | `--ncount N`, `-n N` | ncount sent to `mcrun` (default: `1e6`) | @@ -32,6 +43,7 @@ result against the target value recorded in the instrument header. | `--compilemax S` | max seconds allowed per compilation (default: 1800; x100 with `--lint`) | | `--runmax S` | max seconds allowed per test run (default: 3600) | | `--displaymax S` | max seconds allowed per test display run (default: 60) | +| `--noscans` | skip the `%Scan` tests, only run the `%Example` tests | | `--noplots` | do not generate plots (`01_overview.pdf`, `02_plots.html`) of the test output | | `--permissive` | exit 0 even if some tests fail | | `--strict` | let instruments without `%Example` line(s) fail immediately (cannot be combined with `--permissive`) | diff --git a/tools/Python/mctest/main.template b/tools/Python/mctest/main.template index 53c9555a8b..d893bd4052 100644 --- a/tools/Python/mctest/main.template +++ b/tools/Python/mctest/main.template @@ -47,7 +47,7 @@ a:visited { color: lightgrey; background-color: transparent; text-decoration: no {%- for c in row %} {%- if loop.index0 > 0 %} {%- if c.0 == 1 %} - C:{{ c.1 }}/R:{{ c.2 }}
I={{ c.3 }} ({{ c.4 }}) + C:{{ c.1 }}/R:{{ c.2 }}
I={{ c.3 }} ({{ c.4 }})
{{ c.6 }}
PLOTS: [Interactive HTML] [PDF overview] {%- if c.8 %} @@ -58,7 +58,7 @@ a:visited { color: lightgrey; background-color: transparent; text-decoration: no {%- endif %} {%- elif c.0 == 2 %} - C:{{ c.1 }}/R:{{ c.2 }}
I={{ c.3 }} ({{ c.4 }}) + C:{{ c.1 }}/R:{{ c.2 }}
I={{ c.3 }} ({{ c.4 }})
{{ c.6 }}
PLOTS: [Interactive HTML] [PDF overview] {%- if c.8 %} diff --git a/tools/Python/mctest/mctest.py b/tools/Python/mctest/mctest.py index e359a99595..837b82176d 100644 --- a/tools/Python/mctest/mctest.py +++ b/tools/Python/mctest/mctest.py @@ -42,30 +42,72 @@ def paths_overlap(a: pathlib.Path, b: pathlib.Path) -> bool: # Functionality # -def create_instr_test_objs(sourcefile, localfile, header): - ''' returns a list containing one initialized test object pr %Example within the instr file ''' +def split_test_line(line): + ''' Splits the parameter part of a %Example/%Scan line into (parvals, ncount). + "mcrun" and "*.instr" tokens are dropped, since the test setup defines those, + and a -n/--ncount is taken out of parvals and returned separately (or None). ''' + toks = line.split() + parvals = [] + ncount = None + i = 0 + while i < len(toks): + t = toks[i] + m = re.match(r"(-n|--ncount)=?(.*)$", t) + if m: + ncount = m.group(2) + if not ncount and i + 1 < len(toks): + i += 1 + ncount = toks[i] + elif t != "mcrun" and not t.endswith(".instr"): + parvals.append(t) + i += 1 + return " ".join(parvals), ncount + +def scan_first_point(parvals): + ''' parvals for a single run at the first point of a %Scan, e.g. for mcdisplay: + scan options (-N, -L, -M, ...) are dropped and each "par=a,b,..." or "par=a:delta:b" + is reduced to "par=a" ''' + out = [] + for t in parvals.split(): + if t.startswith("-") or "=" not in t: + continue + key, value = t.split("=", 1) + numeric = re.fullmatch(r"[0-9.eE+:,-]+", value) + out.append(key + "=" + re.split(r"[:,]" if numeric else r"(? 0: - testnb = 1 - for m in ms: - parvals = m[0].strip() - detector = m[1].strip() - targetval = float(m[2].strip()) - tests.append(InstrExampleTest(sourcefile, localfile, parvals, detector, targetval, testnb)) - testnb = testnb + 1 - else: + for m in re.findall(r"\%Example:([^\n]*)Detector\:([^\n]*)_I=([0-9.+-e]+)", header): + parvals, ncount = split_test_line(m[0]) + tests.append(InstrExampleTest(sourcefile, localfile, parvals, m[1].strip(), float(m[2].strip()), len(tests) + 1, ncount=ncount)) + if not noscans: + # the target values are a {}-enclosed, comma-separated list that may span several header lines + for m in re.findall(r"\%Scan:([^\n]*)Detector\:([^\n]*)_I=\{([^}]*)\}", header): + parvals, ncount = split_test_line(m[0]) + targetvals = [float(v) for v in m[2].replace("*", " ").split(",") if v.strip()] + tests.append(InstrExampleTest(sourcefile, localfile, parvals, m[1].strip(), targetvals, len(tests) + 1, scan=True, ncount=ncount)) + if not tests: tests.append(InstrExampleTest(sourcefile, localfile)) return tests class InstrExampleTest: - ''' instruent test house keeping object ''' - def __init__(self, sourcefile, localfile, parvals=None, detector=None, targetval=None, testnb=0): + ''' instruent test house keeping object, for a %Scan targetval and testval are lists ''' + def __init__(self, sourcefile, localfile, parvals=None, detector=None, targetval=None, testnb=0, scan=False, ncount=None): self.sourcefile = sourcefile self.localfile = localfile self.instrname = splitext(basename(sourcefile))[0] self.testnb = testnb - + self.scan = scan + self.ncount = ncount + self.parvals = parvals self.detector = detector self.targetval = targetval @@ -87,6 +129,8 @@ def get_json_repr(self): "localfile" : self.localfile, "instrname" : self.instrname, "testnb" : self.testnb, + "scan" : self.scan, + "ncount" : self.ncount, "parvals" : self.parvals, "detector" : self.detector, @@ -116,6 +160,8 @@ def load(self,testnb=0): self.localfile=obj['localfile'] self.instrname=obj['instrname'] self.testnb=obj['testnb'] + self.scan=obj.get('scan', False) + self.ncount=obj.get('ncount') self.parvals=obj['parvals'] self.detector=obj['detector'] self.targetval=obj['targetval'] @@ -208,6 +254,28 @@ def extract_testvals(datafolder, monitorname): return (I, I_err, N) break +def extract_scanvals(datafolder, monitorname): + ''' + Extract the list of monitor I values pr. scan point from the mccode.dat that mcrun + writes for a scan (in both the McCode and NeXus formats). + + Returns the list, or None if mccode.dat or the monitor column is missing. + ''' + datfile = join(datafolder, "mccode.dat") + if not os.path.isfile(datfile): + return None + column = None + vals = [] + for l in open(datfile).read().splitlines(): + if l.startswith("# variables:"): + variables = l.split(":", 1)[1].split() + if monitorname + "_I" not in variables: + return None + column = variables.index(monitorname + "_I") + elif l.strip() and not l.startswith("#") and column is not None: + vals.append(float(l.split()[column])) + return vals if column is not None else None + def parse_detector_I_value(resfile_path, detector_name): """ Return (value_float, success_bool, raw_value_str_or_None). @@ -283,7 +351,7 @@ def mccode_test(branchdir, testdir, limitinstrs=None, instrfilter=None, compfilt text = open(f, encoding='utf-8').read() f_new=str(pathlib.Path(join(instrdir,os.path.basename(f))).as_posix()) # create a test object for every test defined in the instrument header - instrtests = create_instr_test_objs(sourcefile=f, localfile=f_new, header=text) + instrtests = create_instr_test_objs(sourcefile=f, localfile=f_new, header=text, noscans=noscans) try: shutil.copytree(os.path.dirname(f),instrdir) tests = tests + instrtests @@ -384,7 +452,8 @@ def mccode_test(branchdir, testdir, limitinstrs=None, instrfilter=None, compfilt # Run mcdisplay (single particle only) t1 = time.time() if test.testnb>0: - cmd = mccode_config.configuration["MCDISPLAY"]+'-classic %s --nobrowse %s %s -n0 -d display > displaylog.txt 2>&1' % (mpiswitch, test.instrname+'.instr', test.parvals if test.parvals else '-y') + dispvals = scan_first_point(test.parvals) if test.scan else test.parvals + cmd = mccode_config.configuration["MCDISPLAY"]+'-classic %s --nobrowse %s %s -n0 -d display > displaylog.txt 2>&1' % (mpiswitch, test.instrname+'.instr', dispvals if dispvals else '-y') else: cmd = mccode_config.configuration["MCDISPLAY"]+'-classic %s --nobrowse %s -y -n0 -d display > displaylog.txt 2>&1' % (mpiswitch, test.instrname+'.instr') retcode = utils.run_subtool_noread(cmd, cwd=join(testdir, test.instrname), timeout=displaymax) @@ -460,6 +529,15 @@ def mccode_test(branchdir, testdir, limitinstrs=None, instrfilter=None, compfilt # told to use the default values (-y can not be combined with # parameter values, since the instrument then ignores those): parvals = test.parvals if test.parvals else "-y" + # A %Scan uses its own -n if given, else at most 1e5 pr. point, and runs + # its points in parallel unless MPI already does that within each point + testncount = ncount + timeout = runmax + if test.scan: + testncount = test.ncount or "%g" % min(float(ncount), 1e5) + timeout = runmax * len(test.targetval) + if mpi is None: + parvals = parvals + " --scan_split=auto" # Did test run already? if not os.path.exists(join(testdir, test.instrname, str(test.testnb))): if nexus: @@ -468,23 +546,25 @@ def mccode_test(branchdir, testdir, limitinstrs=None, instrfilter=None, compfilt if openacc is True: if configdir: cmd = cmd + " --override-config=" + configdir - cmd = cmd + " -s %s %s %s -n%s --openacc --mpi=%s -d%d > run_stdout_%d.txt 2>&1" % (seed, test.instrname, parvals, ncount, mpi, test.testnb, test.testnb) + cmd = cmd + " -s %s %s %s -n%s --openacc --mpi=%s -d%d > run_stdout_%d.txt 2>&1" % (seed, test.instrname, parvals, testncount, mpi, test.testnb, test.testnb) else: if configdir: cmd = cmd + " --override-config=" + configdir - cmd = cmd + " -s %s %s %s -n%s --mpi=%s -d%d > run_stdout_%d.txt 2>&1" % (seed, test.instrname, parvals, ncount, mpi, test.testnb, test.testnb) + cmd = cmd + " -s %s %s %s -n%s --mpi=%s -d%d > run_stdout_%d.txt 2>&1" % (seed, test.instrname, parvals, testncount, mpi, test.testnb, test.testnb) else: if configdir: cmd = cmd + " --no-mpi --override-config=" + configdir - cmd = cmd + " --no-mpi -s %s %s %s -n%s -d%d > run_stdout_%d.txt 2>&1" % (seed, test.instrname, parvals, ncount, test.testnb, test.testnb) + cmd = cmd + " --no-mpi -s %s %s %s -n%s -d%d > run_stdout_%d.txt 2>&1" % (seed, test.instrname, parvals, testncount, test.testnb, test.testnb) - retcode = utils.run_subtool_noread(cmd, cwd=join(testdir, test.instrname),timeout=runmax) + retcode = utils.run_subtool_noread(cmd, cwd=join(testdir, test.instrname),timeout=timeout) t2 = time.time() didwrite = os.path.exists(join(testdir, test.instrname, str(test.testnb), "mccode.sim")) didwrite_nexus = os.path.exists(join(testdir, test.instrname, str(test.testnb), "mccode.h5")) # retcode is a tuple: (returncode, timed_out) - test.didrun = retcode[0] == 0 and not retcode[1] and (didwrite or didwrite_nexus) + # a scan always writes mccode.dat, but not always a top-level mccode.sim/mccode.h5 (NeXus + --scan_split) + didwrite_scan = test.scan and os.path.exists(join(testdir, test.instrname, str(test.testnb), "mccode.dat")) + test.didrun = retcode[0] == 0 and not retcode[1] and (didwrite or didwrite_nexus or didwrite_scan) test.runtime = t2 - t1 else: suffix=" (cached)" @@ -506,7 +586,12 @@ def mccode_test(branchdir, testdir, limitinstrs=None, instrfilter=None, compfilt resbase="(No file)" # test value extraction - if not didwrite_nexus: + if test.scan: + test.testval = extract_scanvals(join(testdir, test.instrname, str(test.testnb)), test.detector) + if test.testval is None: + runfailed=True + resbase ="run_stdout_%d.txt" % (test.testnb) + elif not didwrite_nexus: extraction = extract_testvals(join(testdir, test.instrname, str(test.testnb)), test.detector) if type(extraction) is tuple: test.testval = extraction[0] @@ -535,7 +620,18 @@ def mccode_test(branchdir, testdir, limitinstrs=None, instrfilter=None, compfilt suffix += " + !! RUNTIME FAILURE - see %s !! " % (resbase) formatstr = "%-" + "%ds: " % (maxnamelen+1) + \ "{:3d}.".format(math.floor(test.runtime)) + str(test.runtime-int(test.runtime)).split('.')[1][:2] - if test.targetval!=0: # Normal situation, non-zero target value + if test.scan: + testvals = test.testval or [] + percents = [round(percent_of(t, r)) for t, r in zip(testvals, test.targetval)] + numoff = len([p for p in percents if p<80 or p>120]) + if len(testvals) != len(test.targetval) or numoff > 0: + suffix += " <--- BIG DISCREPANCY??" + num_valfail = num_valfail + 1 + anyfailed=True + worst = max(percents, key=lambda p: abs(p-100)) if percents else 0 + logging.info(formatstr % test.get_display_name() + " [scan: %d/%d points within 20%%, worst %d %%, %d/%d points run]" + % (len(percents)-numoff, len(test.targetval), worst, len(testvals), len(test.targetval)) + suffix) + elif test.targetval!=0: # Normal situation, non-zero target value percent=round(100.0*test.testval/test.targetval) if percent<80 or percent>120: suffix += " <--- BIG DISCREPANCY??" @@ -792,6 +888,7 @@ def get_config_files(configfltr): compilemax = None displaymax = None noplots = None +noscans = None def main(args): configfilter = args.config # test only config matching this label (default: as installed) @@ -849,7 +946,7 @@ def main(args): quit(1) logging.debug("") - global ncount, no_mpi, mpi, skipnontest, openacc, nexus, lint, permissive, runLocal, compilemax, displaymax, runmax, seed, strict, noplots + global ncount, no_mpi, mpi, skipnontest, openacc, nexus, lint, permissive, runLocal, compilemax, displaymax, runmax, seed, strict, noplots, noscans ncount = "1e6" no_mpi = False if args.ncount: @@ -968,6 +1065,9 @@ def main(args): logging.info("Strict mode, tool will report failure for instruments without %Example") noplots = args.noplots + noscans = args.noscans + if noscans: + logging.info("%Scan tests are skipped") if noplots: logging.info("No plots of the test output will be generated") @@ -1003,6 +1103,7 @@ def main(args): parser.add_argument('--permissive', action='store_true', help='Use zero return-value even if some tests fail. Useful for full test con systems that are only partially functional. Can not be combined with --strict.') parser.add_argument('--strict', action='store_true', help='Let instruments without %%Example line(s) instantly fail. Can not be combined with --permissive.') parser.add_argument('--noplots', action='store_true', help='Do not generate plots (01_overview.pdf and 02_plots.html) of the test output. Useful e.g. in CI, where the plots are not looked at, and can take long for instruments with many monitors.') + parser.add_argument('--noscans', action='store_true', help='Skip the %%Scan tests, only run the %%Example tests.') parser.add_argument('--local', help='Instruments to test are NOT picked up from MCCODE installation, instead from --local=DIR. Local path and --testdir can not overlap!') args = parser.parse_args() diff --git a/tools/Python/mctest/mcviewtest.py b/tools/Python/mctest/mcviewtest.py index dfe010a913..5befec6573 100644 --- a/tools/Python/mctest/mcviewtest.py +++ b/tools/Python/mctest/mcviewtest.py @@ -17,6 +17,12 @@ sys.path.append(os.path.join(os.path.dirname(__file__), '..')) from mccodelib import utils, mccode_config +def percent_of(testval, targetval): + ''' testval in percent of targetval, a 0 target counts as 100% only for a 0 testval ''' + if targetval == 0: + return 100 if testval == 0 else 0 + return 100.0 * testval / targetval + def scantree(path): """Recursively yield DirEntry objects for given directory.""" for entry in os.scandir(path): @@ -249,6 +255,24 @@ def get_cell_tuple(cellobj, refval=None, refcellobj=None, row=None, col_idx=None compiletime = "" state = 2 return (state, compiletime, runtime, testval, "", url, display, displayurl) + elif cellobj.get("scan"): + # one cell pr. %Scan, per-point details in the hover tooltip + runtime = "%.2f s" % cellobj["runtime"] + compiletime = "%.2f s" % cellobj["compiletime"] if cellobj["testnb"] <= 1 else "" + testvals = cellobj["testval"] + refvals = cellobj["targetval"] + percents = [percent_of(t, r) for t, r in zip(testvals, refvals)] + numok = len([p for p in percents if abs(p-100) <= ERROR_PERCENT_THRESSHOLD_ACCEPT]) + state = 1 if numok == len(percents) == len(refvals) else 2 + testval = "scan, %d/%d pts" % (len(testvals), len(refvals)) + refp = "%d/%d pts OK" % (numok, len(refvals)) + tooltip = "\n".join("%d: %.4g / %.4g = %.0f%%" % (i, t, r, p) for i, (t, r, p) in enumerate(zip(testvals, refvals, percents))) + diffurl = None + coplotUrl = None + if diffall or state == 2: + diffurl = plan_diff_link(refcellobj, url, label, row, col_idx) + coplotUrl = plan_coplot_link(refcellobj, url, label, row, col_idx) + return (state, compiletime, runtime, testval, refp, url, display, displayurl, diffurl, coplotUrl, tooltip) else: testval = "%.2g" % float(cellobj["testval"]) runtime = "%.2f s" % cellobj["runtime"] @@ -259,14 +283,7 @@ def get_cell_tuple(cellobj, refval=None, refcellobj=None, row=None, col_idx=None # Always use embedded target value refval = float(cellobj["targetval"]) testval = float(cellobj["testval"]) - # Special case, target test value is 0 explicitly: - if refval==0: - if testval==0: - refp=100 - else: - refp=0 - else: # Standard case, target test value is non-zero - refp = abs(testval/refval*100) + refp = abs(percent_of(testval, refval)) if abs(refp-100) > ERROR_PERCENT_THRESSHOLD_ACCEPT: state = 2 else: From 39a8eaf240283a22948abdf3ebc01b2b6bfbcaf6 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Wed, 7 Oct 2026 20:38:31 +0200 Subject: [PATCH 02/10] mcplot-html/mccoplot-html/mcplotdiff-html: fix plotting of mcrun scan dirs Scan curves loaded from mccode.dat had an empty filepath and all shared filename 'mccode.dat', while the html frontends derive output file names from those fields: - mcplot-html wrote every curve to '.html'/'_log.html' in the cwd, and its parallel jobs raced on exists()/remove() of that shared file (FileNotFoundError). - mccoplot-html wrote every pane to 'coplot_mccode.html', so all panes showed the last detector. - mcplotdiff-html crashed: scan curves have no 'values' triplet, no (I, ERR) yvar pair and no N column. Fixes: - mcplotloader: give each scan curve a unique filepath / (e.g. scan/detector_I), so mcplot-html writes scan/detector_I.html. - mcplot-html: drop the racy exists()/remove() before writing; open('w') already truncates. - mcplotdiffloader: add monitor_basename() (basename of filepath, else filename) and use it to key and match monitors and to name the diff .dat files and the mccode.sim entries. Ordinary monitors keep their old names (e.g. PSD.dat). Make the diff and the .dat writer handle scan curves: % diff from summed curves when 'values' is empty, a derived _ERR yvar, and N=0 rows when there is no N column. - mccoplot-html/mcplotdiff-html: use monitor_basename() for page names and for locating existing mcplot-html pages to link to. Verified with an SE_example scan (-N41): mcplot-html, mccoplot-html and mcplotdiff-html produce one page per scan curve; the diff output dir reopens with mcplot-html; single step-dir diff/coplot output names are unchanged; matplotlib mcplot/mccoplot still work. Co-Authored-By: Claude Opus 5.5 --- tools/Python/mccodelib/mcplotdiffloader.py | 41 ++++++++++++++++------ tools/Python/mccodelib/mcplotloader.py | 4 +++ tools/Python/mcplot/html/mccoplot.py | 6 ++-- tools/Python/mcplot/html/mcplot.py | 3 -- tools/Python/mcplot/html/mcplotdiff.py | 8 ++--- 5 files changed, 42 insertions(+), 20 deletions(-) diff --git a/tools/Python/mccodelib/mcplotdiffloader.py b/tools/Python/mccodelib/mcplotdiffloader.py index 283255e667..45ce7ff59f 100644 --- a/tools/Python/mccodelib/mcplotdiffloader.py +++ b/tools/Python/mccodelib/mcplotdiffloader.py @@ -203,6 +203,24 @@ def resolve_simfile(path): return simfile, simdir +def monitor_basename(data): + """ Unique per-monitor file name: the monitor's own output file (e.g. + 'PSD.dat'), or for a scan curve - which all share filename + 'mccode.dat' - the per-curve name the loader gives it (e.g. + 'detector_I'), which is also what mcplot-html names its pages by. """ + return os.path.basename(data.filepath) if data.filepath else data.filename + + +def _dat_name(data, prefix): + name = prefix + monitor_basename(data) + return name if os.path.splitext(name)[1] else name + '.dat' + + +def _total(data): + """ Total intensity; scan curves carry no 'values' triplet, so sum the curve """ + return data.values[0] if data.values else float(np.sum(data.yvals)) + + def load_monitors(path): """ Loads a simulation (folder or single monitor file) and returns (monitors, directory), where monitors is a dict mapping a monitor @@ -227,7 +245,7 @@ def load_monitors(path): if not isinstance(data, (Data1D, Data2D)): # skip 0D / event-list / unknown monitors: nothing sensible to subtract continue - key = data.filename if data.filename else data.component + key = monitor_basename(data) or data.component if key in monitors: # extremely unlikely (duplicate filenames), disambiguate by component key = '%s__%s' % (key, data.component) @@ -301,7 +319,7 @@ def diff_1d(key, a, b, label_a, label_b): N = 0 d.values = (I, Ierr, N) d.statistics = '%s: %s\n%s: %s' % (label_a, a.statistics, label_b, b.statistics) - pct_str = _pct_diff_str(a.values[0], b.values[0]) + pct_str = _pct_diff_str(_total(a), _total(b)) d.diff_pct_str = pct_str d.title = ' - Diff (A - B), with:\n \nA=%s\nB=%s\nDiff: %s\n \n%s' % (label_a, label_b, pct_str, a.title) @@ -536,8 +554,7 @@ def _common_header_lines(data): def _write_1d_dat(data, outdir, prefix): - filename = prefix + data.filename - filepath = os.path.join(outdir, filename) + filepath = os.path.join(outdir, _dat_name(data, prefix)) lines = _common_header_lines(data) # Required: mcplotloader.py's _load_monitor() reads this line to decide @@ -548,9 +565,13 @@ def _write_1d_dat(data, outdir, prefix): lines.append('# xlabel: %s' % _sanitize(data.xlabel)) lines.append('# ylabel: %s' % _sanitize(data.ylabel)) lines.append('# xvar: %s' % _sanitize(data.xvar)) - lines.append('# yvar: (%s,%s)' % (data.yvar[0], data.yvar[1])) + yvar = data.yvar + if isinstance(yvar, str): + # scan curve: single 'detector_I' name rather than an (I, ERR) pair + yvar = (yvar, re.sub(r'_I$', '', yvar) + '_ERR') + lines.append('# yvar: (%s,%s)' % (yvar[0], yvar[1])) lines.append('# xlimits: %s %s' % (_fmt(data.xlimits[0]), _fmt(data.xlimits[1]))) - lines.append('# variables: %s %s %s N' % (data.xvar, data.yvar[0], data.yvar[1])) + lines.append('# variables: %s %s %s N' % (data.xvar, yvar[0], yvar[1])) lines.append('# values: %s %s %s' % (_fmt(data.values[0]), _fmt(data.values[1]), _fmt(data.values[2]))) # The standard "# statistics: X0=...; dX=...;" field is a # weighted centroid/width, which assumes a non-negative intensity @@ -565,15 +586,15 @@ def _write_1d_dat(data, outdir, prefix): with open(filepath, 'w') as f: f.write('\n'.join(lines) + '\n') - for x, y, yerr, n in zip(data.xvals, data.yvals, data.y_err_vals, data.Nvals): + Nvals = data.Nvals or [0] * len(data.xvals) # scan curves have no N column + for x, y, yerr, n in zip(data.xvals, data.yvals, data.y_err_vals, Nvals): f.write('%s %s %s %s\n' % (_fmt(x), _fmt(y), _fmt(yerr), _fmt(n))) return filepath def _write_2d_dat(data, outdir, prefix): - filename = prefix + data.filename - filepath = os.path.join(outdir, filename) + filepath = os.path.join(outdir, _dat_name(data, prefix)) lines = _common_header_lines(data) zshape = np.shape(data.zvals) if data.zvals else (0, 0) @@ -715,7 +736,7 @@ def write_mccode_sim(diffs, outdir, label_a=None, label_b=None, instrument='diff # This is the one line mcplotloader.py's _get_filenames_from_mccodesim() # actually looks for - it must match the real file written by # write_mccode_dat()/write_all_mccode_dat() with the same prefix. - lines.append(' filename: %s' % (prefix + data.filename)) + lines.append(' filename: %s' % _dat_name(data, prefix)) lines.append('end data') lines.append('') diff --git a/tools/Python/mccodelib/mcplotloader.py b/tools/Python/mccodelib/mcplotloader.py index 3033eff03a..d5ffc9adb7 100644 --- a/tools/Python/mccodelib/mcplotloader.py +++ b/tools/Python/mccodelib/mcplotloader.py @@ -483,6 +483,10 @@ def _load_multiplot_1D_lst(f_dat): data.yvar = yvars[2*i] data.title = '%s' % (data.yvar) data.component = data.title + # no per-curve file exists, so give each curve a unique path in + # the scan dir (frontends like mcplot-html derive output names + # from it; empty would make all curves collide on '.html') + data.filepath = join(dirname(f_dat), data.yvar) data.y_err_vals = yvals_err_lst[i] data_handle_lst.append(DataHandle(load_fct=None, data=data)) diff --git a/tools/Python/mcplot/html/mccoplot.py b/tools/Python/mcplot/html/mccoplot.py index 4c948cac87..164df71f3a 100644 --- a/tools/Python/mcplot/html/mccoplot.py +++ b/tools/Python/mcplot/html/mccoplot.py @@ -42,7 +42,7 @@ from mccodelib import mccode_config from mccodelib.mcplotdiffloader import ( path_base_name, resolve_labels, resolve_colours, dirsafe_name, - load_monitors, find_original_plot, match_monitors_multi, DEFAULT_PALETTE, + load_monitors, find_original_plot, match_monitors_multi, DEFAULT_PALETTE, monitor_basename, ) # The bare html-plotter (mcplot-html itself, or mxplot-html under McXtrace), @@ -195,7 +195,7 @@ def coplot_single(key, datas, outdir, use_logscale, colours, dat_links, identiti global logscale logscale = use_logscale - basename = 'coplot_' + path_base_name(datas[0].filename) + basename = 'coplot_' + path_base_name(monitor_basename(datas[0])) fname = basename + ('_log.html' if use_logscale else '.html') f = os.path.join(outdir, fname) @@ -447,7 +447,7 @@ def main(args): # mcplotdiff.py does dat_links = [] for d, data in zip(dirs, datas): - lin, log = find_original_plot(d, data.filename) + lin, log = find_original_plot(d, monitor_basename(data)) dat_links.append(_relhref(lin, outdir)) f = coplot_single(key, datas, outdir, False, colours, dat_links, identities, diff --git a/tools/Python/mcplot/html/mcplot.py b/tools/Python/mcplot/html/mcplot.py index 0f453a7053..fdbd5a6226 100644 --- a/tools/Python/mcplot/html/mcplot.py +++ b/tools/Python/mcplot/html/mcplot.py @@ -374,9 +374,6 @@ def plotfunc_single(data, f = None, use_logscale=False): else: f = data.filepath + ".html" - if os.path.exists(f): - os.remove(f) - # create 1D html if type(data) is Data1D: text = get_html('template_1d.html', get_params_str_1D(data), os.path.basename(data.filename), use_logscale) diff --git a/tools/Python/mcplot/html/mcplotdiff.py b/tools/Python/mcplot/html/mcplotdiff.py index 59ce193f13..3d9d3a0cf9 100644 --- a/tools/Python/mcplot/html/mcplotdiff.py +++ b/tools/Python/mcplot/html/mcplotdiff.py @@ -36,7 +36,7 @@ from mccodelib import mcplotdiffloader as diffloader from mccodelib.mcplotdiffloader import ( path_base_name, default_labels, dirsafe_name, load_monitors, compute_diffs, find_original_plot, - write_mccode_dat, write_mccode_sim, + write_mccode_dat, write_mccode_sim, monitor_basename, ) global WIDTH, HEIGHT @@ -280,7 +280,7 @@ def plot_diff_single(data, outdir, use_logscale, dat_basename=None): global logscale logscale = use_logscale - basename = 'diff_' + path_base_name(data.filename) + basename = 'diff_' + path_base_name(monitor_basename(data)) fname = basename + ('_log.html' if use_logscale else '.html') f = os.path.join(outdir, fname) @@ -522,8 +522,8 @@ def main(args): # locate any pre-existing mcplot-html plots for this monitor, so # we can link to the original a/b data alongside the diff plot - a_lin, a_log = find_original_plot(dir_a, data.filename) - b_lin, b_log = find_original_plot(dir_b, data.filename) + a_lin, a_log = find_original_plot(dir_a, monitor_basename(data)) + b_lin, b_log = find_original_plot(dir_b, monitor_basename(data)) if not (a_lin or a_log): print("Note: no existing mcplot-html output found for '%s' in '%s'" % (data.filename, args.a)) if not (b_lin or b_log): From a0f97e1436b60f0416e14b8cd31dc35c27b1b2f0 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 15:01:06 +0200 Subject: [PATCH 03/10] Add %Scan: tests to 13 McStas/McXtrace example instruments Scan examples that were written as plain "Example:"/"mcrun ..."/"mxrun ..." header lines are turned into %Scan: tests, with reference values generated the way mctest runs them (--no-mpi -s 1000 --scan_split=auto). Ranges, point counts and ncount are adjusted so every point has at most ~8% statistical error, keeping the 20% per-point tolerance meaningful: McStas: - SE_example2: dBz scan, 41 pts (as SE_example) - Tomography: omega=0,340 -N18; drops the stale offfile=bunny.off (the instrument has no such parameter, so every point failed) - SESANS_Delft: By=0,0.0468 -N31 -n1e6 - Test_PowderN_Res: radius=0.001,0.021 -N21 - Test_Magnon_bcc_TAS: hw=0,1 -N21 -n1e6 on e_monitor (e_monitor1 was up to 100% noisy and zero for most hw) - Test_Dispersion_relation_TAS: -M -N 5,5 (was 21,21 = 441 pts) - Samples_Incoherent: SAMPLE=1,5 -N5 STOP=1 (prose examples kept) - LLB_6T2: C60 200 rocking curve over the peak, phi=9.27,10.37 -N12 -n1e7 (was -N31 -n1e8 with --mpi); moved out of %Parameters McXtrace: - SSRL_bl_11_2_white_src / _not_white_src: Etohit=6900,7500 -N31 -n1e6 (was -N601) - SOLEIL_DISCO: x_screw=20,103 -N21 scan=1 on the Wavelength monitor - SOLEIL_ROCK: Cu edge E0=8.5,9.5 -N21 -n1e6 on fluo_monitor - Czerny_Turner: x_screw=20,103 -N21 -n1e6 scan=1 on Wavelength %Scan: lines are placed before any following descriptive text, so mcdoc keeps that text in the description. mctest: also ignore an "mxrun" token on %Example:/%Scan: lines. Verified: mctest and mxtest --local on all 13 pass with every point at 100% (macOS arm64); together they add ~2.5 min on 12 cores. Co-Authored-By: Claude Opus 5.5 --- mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr | 8 +++++--- .../examples/TUDelft/SESANS_Delft/SESANS_Delft.instr | 6 +++++- .../examples/Templates/Tomography/Tomography.instr | 5 ++++- .../Tests_polarization/SE_example2/SE_example2.instr | 8 +++++++- .../Samples_Incoherent/Samples_Incoherent.instr | 2 ++ .../Test_Dispersion_relation_TAS.instr | 7 +++++-- .../Test_Magnon_bcc_TAS/Test_Magnon_bcc_TAS.instr | 5 ++++- .../Tests_samples/Test_PowderN_Res/Test_PowderN_Res.instr | 5 ++++- .../examples/BARC/Czerny_Turner/Czerny_Turner.instr | 4 ++++ .../examples/SOLEIL/SOLEIL_DISCO/SOLEIL_DISCO.instr | 5 ++++- .../examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr | 6 +++++- .../SSRL_bl_11_2_not_white_src.instr | 6 +++++- .../SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr | 6 +++++- tools/Python/mctest/mctest.py | 4 ++-- 14 files changed, 61 insertions(+), 16 deletions(-) diff --git a/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr b/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr index 79fbe3c557..e524452721 100644 --- a/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr +++ b/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr @@ -25,6 +25,11 @@ * PG 002 DM=3.355 AA (Highly Oriented Pyrolythic Graphite) * Cu 220 DM=1.278 AA * +* Example of a C60 200 rocking curve scan: +* %Scan: mcrun LLB_6T2.instr -N12 lambda=2.4 phi=9.27,10.37 gamma=19.74 nu=0 monok=0 samp_f=C60.lau -n1e7 Detector: Mon_out_I={ +* 495.535,1014.3,1265.26,1449.65,1783.28,2217.03,2013.63,2151.44, +* 1934.61,1586.15,837.108,866.069 } +* * %Parameters * lambda: [AA] wavelength * phi: [Deg] sample rotation along the vertical axis @@ -33,9 +38,6 @@ * monok: [1] monochromator to use (0: PG, 1: Cu, 5: test mode) * samp_f: [str] LAU file describing sample * -* Example of a C60 200 rocking curve scan: -* mcrun LLB_6T2.instr --mpi=NUM_CORES -N31 lambda=2.4 phi=8.37,11.37 gamma=19.74 nu=0 monok=0 samp_f="C60.lau" -n 1e8 -d C60_200 -* * %End *******************************************************************************/ DEFINE INSTRUMENT LLB_6T2(lambda=1.0, phi=0, gamma=0, nu=0, monok=0, string samp_f="C60.lau") diff --git a/mcstas-comps/examples/TUDelft/SESANS_Delft/SESANS_Delft.instr b/mcstas-comps/examples/TUDelft/SESANS_Delft/SESANS_Delft.instr index a78758bd02..11b97b4657 100644 --- a/mcstas-comps/examples/TUDelft/SESANS_Delft/SESANS_Delft.instr +++ b/mcstas-comps/examples/TUDelft/SESANS_Delft/SESANS_Delft.instr @@ -24,7 +24,11 @@ * * %Example: -y Detector: det_I=2.2537e-07 * -* Scan Example: SESANS_Delft -n 1000000 -N 31 L0=2.165 DL=0.02 By=0,0.0468 +* %Scan: mcrun SESANS_Delft.instr L0=2.165 DL=0.02 By=0,0.0468 -N31 -n1e6 Detector: det_I={ +* 2.35556e-07,2.35296e-07,2.30432e-07,2.25294e-07,2.20061e-07,2.13707e-07,2.11276e-07,2.05654e-07, +* 2.03486e-07,2.00872e-07,1.99138e-07,2.00791e-07,1.99118e-07,1.98852e-07,1.98976e-07,1.99064e-07, +* 1.98964e-07,1.99602e-07,1.98235e-07,2.00064e-07,1.99617e-07,1.99683e-07,1.98427e-07,1.98624e-07, +* 1.97647e-07,1.98342e-07,1.98835e-07,1.99153e-07,1.99708e-07,1.99172e-07,1.98348e-07 } * * %P * : [] diff --git a/mcstas-comps/examples/Templates/Tomography/Tomography.instr b/mcstas-comps/examples/Templates/Tomography/Tomography.instr index 4d00b1c1b6..f917aed306 100644 --- a/mcstas-comps/examples/Templates/Tomography/Tomography.instr +++ b/mcstas-comps/examples/Templates/Tomography/Tomography.instr @@ -14,7 +14,10 @@ * %Description * Instrument to study tomographic imaging by means of the feature of OFF shape samples. * -* Example: mcrun Tomography.instr offfile=bunny.off -n1e4 -N18 omega=0,340 -d TomoScan +* %Scan: mcrun Tomography.instr omega=0,340 -N18 -n1e4 Detector: monitor_I={ +* 2.23321e-09,2.18277e-09,2.18764e-09,2.18301e-09,2.19154e-09,2.19422e-09,2.18277e-09,2.18521e-09, +* 2.19178e-09,2.23662e-09,2.19154e-09,2.18374e-09,2.18935e-09,2.18325e-09,2.20397e-09,2.17789e-09, +* 2.18033e-09,2.18691e-09 } * (Note that to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts * are needed) * diff --git a/mcstas-comps/examples/Tests_polarization/SE_example2/SE_example2.instr b/mcstas-comps/examples/Tests_polarization/SE_example2/SE_example2.instr index 6103e207ee..070ec58a08 100644 --- a/mcstas-comps/examples/Tests_polarization/SE_example2/SE_example2.instr +++ b/mcstas-comps/examples/Tests_polarization/SE_example2/SE_example2.instr @@ -18,7 +18,13 @@ * Pol_FieldBox is used to define guidefields and flippers. * MeanPolLambda_montior is used to monitor beam polarisation. * -* Example: mcrun SE_example2.instr dBz=-0.0001,0.0001 -N41 -n1e5 +* %Scan: mcrun SE_example2.instr dBz=-0.0001,0.0001 -N41 -n1e5 Detector: detector_I={ +* 131.576,155.634,159.227,142.21,139.368,130.51,165.979,155.359, +* 99.6514,142.272,209.645,95.7382,90.1825,237.694,146.859,28.2776, +* 199.631,244.785,32.2439,112.725,277.63,115.369,29.3693,243.049, +* 201.203,28.3267,163.182,240.944,90.531,95.7656,212.13,145.286, +* 93.5099,161.98,164.791,134.604,147.311,143.726,153.511,155.375, +* 129.977 } * * %Parameters * POL_ANGLE: [deg] Reflection angle of polarizer/analyzer diff --git a/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr b/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr index 78eeb42a07..696e03d74c 100644 --- a/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr +++ b/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr @@ -59,6 +59,8 @@ * %Example: SAMPLE=8 STOP=1 -n 1e5 Detector: PSD_Sphere_4pi_I=1.3233e+06 * %Example: SAMPLE=9 STOP=1 -n 1e5 Detector: PSD_Sphere_4pi_I=1.3239e+06 * %Example: SAMPLE=10 STOP=1 -n 1e5 Detector: PSD_Sphere_4pi_I=1.28905e+06 +* %Scan: mcrun Samples_Incoherent.instr SAMPLE=1,5 -N5 STOP=1 Detector: PSD_Sphere_4pi_I={ +* 1326220.0,1245050.0,1322310.0,1321210.0,1326550.0 } * * %Parameters * L_min: [AA] Minimum wavelength of neutrons diff --git a/mcstas-comps/examples/Tests_samples/Test_Dispersion_relation_TAS/Test_Dispersion_relation_TAS.instr b/mcstas-comps/examples/Tests_samples/Test_Dispersion_relation_TAS/Test_Dispersion_relation_TAS.instr index 05873c9444..46b4fe57ad 100644 --- a/mcstas-comps/examples/Tests_samples/Test_Dispersion_relation_TAS/Test_Dispersion_relation_TAS.instr +++ b/mcstas-comps/examples/Tests_samples/Test_Dispersion_relation_TAS/Test_Dispersion_relation_TAS.instr @@ -43,8 +43,6 @@ * along x, y, z for both samples), and (h, l) = (1, 0) is the magnetic zone * centre MnF2 (1 0 0). * -* Example: mcrun Test_Dispersion_relation_TAS.instr -M -N 21,21 -n 2e5 h=0.6,1.4 l=0.6,1.4 dE=5 sample_choice=0 -* * The dispersion files are written by the SHELL command below when the * instrument is compiled, if they do not exist yet, by * generate_dispersion_files.py (Python with numpy). @@ -54,6 +52,11 @@ * %Example: h=1.2 l=1 dE=5 sample_choice=0 primitive_cell=1 Detector: detector_I=1.46e-11 * %Example: h=1.15 l=0 dE=3 T=2 sample_choice=2 Detector: detector_I=8.91e-10 * %Example: h=1.15 l=0 dE=3 T=2 sample_choice=3 Detector: detector_I=9.41e-10 +* %Scan: mcrun Test_Dispersion_relation_TAS.instr -M -N 5,5 -n 2e5 h=0.6,1.4 l=0.6,1.4 dE=5 sample_choice=0 Detector: detector_I={ +* 0.0,0.0,0.0,0.0,0.0,0.0,1.2167e-12,3.52579e-11, +* 2.26406e-12,0.0,0.0,1.17383e-11,0.0,1.39525e-11,0.0,0.0, +* 6.10596e-12,1.00579e-11,8.66923e-12,0.0,0.0,0.0,0.0,0.0, +* 0.0 } * * %Parameters * h: [r.l.u.] Scattering vector component along a* (sample x axis) diff --git a/mcstas-comps/examples/Tests_samples/Test_Magnon_bcc_TAS/Test_Magnon_bcc_TAS.instr b/mcstas-comps/examples/Tests_samples/Test_Magnon_bcc_TAS/Test_Magnon_bcc_TAS.instr index d0e034c658..5e079410c0 100644 --- a/mcstas-comps/examples/Tests_samples/Test_Magnon_bcc_TAS/Test_Magnon_bcc_TAS.instr +++ b/mcstas-comps/examples/Tests_samples/Test_Magnon_bcc_TAS/Test_Magnon_bcc_TAS.instr @@ -13,7 +13,10 @@ * Generic TAS instrument for test of samples with dispersions. Modeled over the RITA-2 instrument at PSI (one analyzer only). The instrument is able to position in q-space at q=(h 0 0) and fixed Ei and Ef. This can be used to longitudinal constant-E scans or constant-q scans. In addition, transverse constant-E scans can be made by scanning the sample orientation A3. * * %Example: Test_Magnon_bcc_TAS.instr hw=0.5 Detector: e_monitor1_I=460000 -* Example: Test_Magnon_bcc_TAS.instr hw=0,1 -N21 +* %Scan: mcrun Test_Magnon_bcc_TAS.instr hw=0,1 -N21 -n1e6 Detector: e_monitor_I={ +* 5541440.0,5681320.0,4956300.0,4947280.0,4886770.0,4370310.0,3596940.0,3900100.0, +* 3656700.0,3712310.0,3128430.0,3254960.0,2708640.0,2961760.0,2536780.0,2524220.0, +* 2570960.0,2493820.0,2173830.0,2275870.0,2174740.0 } * * %P * hw: [meV] Neutron energy transfer diff --git a/mcstas-comps/examples/Tests_samples/Test_PowderN_Res/Test_PowderN_Res.instr b/mcstas-comps/examples/Tests_samples/Test_PowderN_Res/Test_PowderN_Res.instr index f1ec2cbe7e..a29e9f8c3c 100644 --- a/mcstas-comps/examples/Tests_samples/Test_PowderN_Res/Test_PowderN_Res.instr +++ b/mcstas-comps/examples/Tests_samples/Test_PowderN_Res/Test_PowderN_Res.instr @@ -18,7 +18,10 @@ * * By default, absorption in the sample is effectively suppressed. * -* Example: Lambda0=2.5667 dLambda=0.01 radius=0.001,0.021 TT=71.8 D_PHI=6 SPLITS=117 Distance=30 sig_abs=1e-09 -N21 +* %Scan: mcrun Test_PowderN_Res.instr Lambda0=2.5667 dLambda=0.01 radius=0.001,0.021 TT=71.8 D_PHI=6 SPLITS=117 Distance=30 sig_abs=1e-09 -N21 Detector: DetectorSmall_I={ +* 3.86698,15.1625,33.2541,57.6607,85.9154,119.618,158.827,201.183, +* 243.131,289.07,340.294,393.375,443.613,498.612,549.899,612.472, +* 671.715,723.508,778.461,837.07,895.16 } * %Example: Lambda0=2.5667 dLambda=0.01 radius=0.01 TT=71.8 D_PHI=6 SPLITS=117 Distance=30 sig_abs=1e-09 Detector: DetectorSmall_I=288.57 * * %Parameters diff --git a/mcxtrace-comps/examples/BARC/Czerny_Turner/Czerny_Turner.instr b/mcxtrace-comps/examples/BARC/Czerny_Turner/Czerny_Turner.instr index 6eb10defa4..5ceec336f9 100644 --- a/mcxtrace-comps/examples/BARC/Czerny_Turner/Czerny_Turner.instr +++ b/mcxtrace-comps/examples/BARC/Czerny_Turner/Czerny_Turner.instr @@ -20,6 +20,10 @@ * Example: Do a scan (scan parameter =1) from x_screw=20 to 103 mm. The calculated monitor "Wavelength(Ang) as a function of x_screw(mm)" will be a linear function. The monochromator functions properly. * * %Example: x_screw=60 Detector: w_monitor_I=1.10881e-06 +* %Scan: mxrun Czerny_Turner.instr -N21 x_screw=20,103 scan=1 -n1e6 Detector: Wavelength_I={ +* 2007.08,2406.85,2820.95,3242.17,3659.02,4075.98,4485.76,4901.23, +* 5324.84,5733.95,6156.24,6569.68,6979.66,7395.58,7805.61,8222.2, +* 8637.53,9053.14,9467.18,9882.52,10288.8 } * * %Parameters * x_screw: [mm] Displacement perpendicular to initial position of the lever (sine drive mechanism) diff --git a/mcxtrace-comps/examples/SOLEIL/SOLEIL_DISCO/SOLEIL_DISCO.instr b/mcxtrace-comps/examples/SOLEIL/SOLEIL_DISCO/SOLEIL_DISCO.instr index 588dc6b6cc..e4918a1750 100644 --- a/mcxtrace-comps/examples/SOLEIL/SOLEIL_DISCO/SOLEIL_DISCO.instr +++ b/mcxtrace-comps/examples/SOLEIL/SOLEIL_DISCO/SOLEIL_DISCO.instr @@ -13,7 +13,10 @@ * %Description * DISCO beamline description here: https://hal.archives-ouvertes.fr/hal-01479318/document * You may scan the grating monochromator with e.g.: -* mxrun -n 1e5 SOLEIL_DISCO.instr -N84 x_screw=20,103 scan=1 +* %Scan: mxrun SOLEIL_DISCO.instr -N21 x_screw=20,103 scan=1 Detector: Wavelength_I={ +* 2019.39,2365.97,2837.41,3242.59,3655.92,4070.23,4487.58,4921.15, +* 5306.77,5738.39,6151.91,6565.99,6979.47,7395.13,7786.17,8199.52, +* 8631.53,9051.46,9483.21,9913.98,10299.5 } * * %Example: grazing_angle_one=22.5 -n 1e5 Detector: second_HFP_I=2.08292e+11 * diff --git a/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr b/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr index 8cf7a10932..2c4245c907 100644 --- a/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr +++ b/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr @@ -40,7 +40,11 @@ * 32.44 | Sample * * Examples: -* Copper scan: mxrun SOLEIL_ROCK.instr E0=8.500,9.500 scan=1 cc=2 -N100 +* Copper scan: +* %Scan: mxrun SOLEIL_ROCK.instr E0=8.5,9.5 scan=1 cc=2 -N21 -n1e6 Detector: fluo_monitor_I={ +* 6512950000.0,6125570000.0,5973110000.0,6294990000.0,6219240000.0,6483710000.0,7090310000.0,5406090000.0, +* 6658460000.0,5907690000.0,7892760000.0,6702680000.0,7044170000.0,6930370000.0,8491040000.0,8899820000.0, +* 7356430000.0,6853240000.0,7013240000.0,7102780000.0,7068470000.0 } * Manganese and chrome scan: mxrun SOLEIL_ROCK.instr E0=5.700,6.800 scan=1 sample_file=MnCr cc=2 -N100 * Pretty energy repartition monitor result: mxrun SOLEIL_ROCK.instr E0=17.000 cc=2 -n1e8 * diff --git a/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_not_white_src/SSRL_bl_11_2_not_white_src.instr b/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_not_white_src/SSRL_bl_11_2_not_white_src.instr index a3b1eef5ca..88fc158472 100644 --- a/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_not_white_src/SSRL_bl_11_2_not_white_src.instr +++ b/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_not_white_src/SSRL_bl_11_2_not_white_src.instr @@ -19,7 +19,11 @@ * Documentation and results of the .instr here: https://gitlab.synchrotron-soleil.fr/grades/beamlines/-/tree/main/glitches * A jupyter notebook will soon be available regrouping everything. * You may scan like so for example: -* mxrun -n 1e7 SSRL_bl_11_2_not_white_src.instr -N601 Etohit=6900,7500 +* %Scan: mxrun SSRL_bl_11_2_not_white_src.instr -N31 Etohit=6900,7500 -n1e6 Detector: EnergyMonitor_first_I={ +* 13328900000.0,13634200000.0,14541900000.0,13884900000.0,13898100000.0,13682000000.0,13694000000.0,14507100000.0, +* 13206900000.0,13610500000.0,13946900000.0,15010800000.0,14594000000.0,15530700000.0,14609000000.0,13841600000.0, +* 14696400000.0,14927300000.0,15831200000.0,15905500000.0,16147000000.0,16044900000.0,16097800000.0,15847300000.0, +* 15588300000.0,16880100000.0,16423800000.0,18149700000.0,17975600000.0,17924000000.0,18274500000.0 } * * Example: Etohit=6900 Detector: EnergyMonitor_first_I=1.3e+10 * diff --git a/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr b/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr index 9dbc2eacd2..6274905c4b 100644 --- a/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr +++ b/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr @@ -18,7 +18,11 @@ * Documentation and results of the .instr here: https://gitlab.synchrotron-soleil.fr/grades/beamlines/-/tree/main/glitches * A jupyter notebook will soon be available regrouping everything. * You may scan like so for example: -* mxrun -n 1e7 SSRL_bl_11_2_white_src.instr -N601 Etohit=6900,7500 detuning_percentage=40 +* %Scan: mxrun SSRL_bl_11_2_white_src.instr -N31 Etohit=6900,7500 detuning_percentage=40 -n1e6 Detector: EnergyMonitor_first_I={ +* 10046700.0,10650900.0,8528260.0,8296880.0,7986510.0,22446400.0,24820300.0,25166000.0, +* 22197000.0,25054900.0,23876500.0,25019400.0,25330900.0,25429200.0,24424900.0,23806600.0, +* 23187200.0,21946700.0,23304900.0,19717000.0,18597400.0,21596200.0,21184500.0,15963900.0, +* 18022700.0,15979900.0,16987000.0,17278100.0,16956200.0,16034000.0,15923600.0 } * * %Example: Etohit=6900 Detector: EnergyMonitor_first_I=4.24366e+07 * diff --git a/tools/Python/mctest/mctest.py b/tools/Python/mctest/mctest.py index 837b82176d..6bc4c6f5af 100644 --- a/tools/Python/mctest/mctest.py +++ b/tools/Python/mctest/mctest.py @@ -44,7 +44,7 @@ def paths_overlap(a: pathlib.Path, b: pathlib.Path) -> bool: def split_test_line(line): ''' Splits the parameter part of a %Example/%Scan line into (parvals, ncount). - "mcrun" and "*.instr" tokens are dropped, since the test setup defines those, + "mcrun"/"mxrun" and "*.instr" tokens are dropped, since the test setup defines those, and a -n/--ncount is taken out of parvals and returned separately (or None). ''' toks = line.split() parvals = [] @@ -58,7 +58,7 @@ def split_test_line(line): if not ncount and i + 1 < len(toks): i += 1 ncount = toks[i] - elif t != "mcrun" and not t.endswith(".instr"): + elif t not in ("mcrun", "mxrun") and not t.endswith(".instr"): parvals.append(t) i += 1 return " ".join(parvals), ncount From aa47fecc24370bd743f3ced93c77a58cb72142e8 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 17:53:22 +0200 Subject: [PATCH 04/10] Add %Scan: tests to Risoe TAS1 instruments, 2nd scans for ROCK/Samples_Incoherent Reference values generated as mctest runs them (--no-mpi -s 1000 --scan_split=auto), ranges trimmed to the curve after trial scans so every point has at most ~6% statistical error: - TAS1_C1: monochromator rocking curve PHM=-38.077,-36.077 -N11 - TAS1_C1_Tilt: collimator tilt OMC1=-44.5,55.5 -N21 - TAS1_Diff_Slit: direct beam C1=30 TT=-0.6,0.6 -N13 - TAS1_Diff_Powder: powder line TT=32.92,34.32 -N15 - TAS1_Diff_Vana: flat incoherent background TT=31.52,35.52 -N21 - TAS1_Powder, TAS1_Vana: analyzer scan OMA=-19.45,-15.45 -N21; a note explains the transmission dip (with TTA=0 the detector looks straight through the analyzer) (all -n1e6) - SOLEIL_ROCK: Mn/Cr edge scan E0=5.7,6.8 sample_file=MnCr -N21 -n1e6 replaces its prose example line - Samples_Incoherent: the two beamstop-removed scans SAMPLE=2,5 -N4 STOP=0 (PSD_Sphere_4pi) and with DB=1 (Dirbeam) Doc fix: OMC1 is in arcmin (the code divides it by 60), not deg, in the six TAS1 instruments that have it. Verified: mctest/mxtest --local pass with every point at 100% (macOS arm64); together ~3.5 min, of which 74 s is the SOLEIL_ROCK Mn/Cr scan. Co-Authored-By: Claude Opus 5.5 --- mcstas-comps/examples/Risoe/TAS1_C1/TAS1_C1.instr | 3 +++ .../examples/Risoe/TAS1_C1_Tilt/TAS1_C1_Tilt.instr | 6 +++++- .../Risoe/TAS1_Diff_Powder/TAS1_Diff_Powder.instr | 5 ++++- .../examples/Risoe/TAS1_Diff_Slit/TAS1_Diff_Slit.instr | 5 ++++- .../examples/Risoe/TAS1_Diff_Vana/TAS1_Diff_Vana.instr | 6 +++++- mcstas-comps/examples/Risoe/TAS1_Powder/TAS1_Powder.instr | 8 +++++++- mcstas-comps/examples/Risoe/TAS1_Vana/TAS1_Vana.instr | 8 +++++++- .../Samples_Incoherent/Samples_Incoherent.instr | 4 ++++ .../examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr | 6 +++++- 9 files changed, 44 insertions(+), 7 deletions(-) diff --git a/mcstas-comps/examples/Risoe/TAS1_C1/TAS1_C1.instr b/mcstas-comps/examples/Risoe/TAS1_C1/TAS1_C1.instr index 807fe531c6..1d290d4335 100644 --- a/mcstas-comps/examples/Risoe/TAS1_C1/TAS1_C1.instr +++ b/mcstas-comps/examples/Risoe/TAS1_C1/TAS1_C1.instr @@ -26,6 +26,9 @@ * detector is at the sample position. * * %Example: PHM=-37.077 Detector: sng_I=0.000429426 +* %Scan: mcrun TAS1_C1.instr PHM=-38.077,-36.077 -N11 -n1e6 Detector: sng_I={ +* 1.7037e-05,5.77737e-05,0.000131759,0.000247282,0.00036353,0.000415802,0.000377557,0.000267179, +* 0.000149367,5.89201e-05,1.85848e-05 } * * %Parameters * PHM: [deg] Monochromator arm angle, aka A1 diff --git a/mcstas-comps/examples/Risoe/TAS1_C1_Tilt/TAS1_C1_Tilt.instr b/mcstas-comps/examples/Risoe/TAS1_C1_Tilt/TAS1_C1_Tilt.instr index a3a9b6e5cf..383263ca1d 100644 --- a/mcstas-comps/examples/Risoe/TAS1_C1_Tilt/TAS1_C1_Tilt.instr +++ b/mcstas-comps/examples/Risoe/TAS1_C1_Tilt/TAS1_C1_Tilt.instr @@ -26,12 +26,16 @@ * detector is at the sample position and there is no analyzer. * * %Example: TTM=-74 Detector: sng_I=0.000405056 +* %Scan: mcrun TAS1_C1_Tilt.instr OMC1=-44.5,55.5 -N21 -n1e6 Detector: sng_I={ +* 7.82478e-05,0.000118605,0.000165766,0.000222136,0.000277334,0.000324033,0.00036983,0.000407361, +* 0.000420118,0.000412682,0.000402763,0.000373695,0.000323706,0.000280374,0.000224993,0.000165908, +* 0.000121172,8.11465e-05,4.92901e-05,2.88144e-05,1.46245e-05 } * * %Parameters * PHM: [deg] Monochromator arm angle, aka A1 * TTM: [deg] Monochromator take-off angle, aka A2 * C1: [min] Collimator 1 aperture (mono-sample arm) -* OMC1: [deg] Tilt angle of the Collimator 1 +* OMC1: [arcmin] Tilt angle of the Collimator 1 * * %Link * The McStas User manual diff --git a/mcstas-comps/examples/Risoe/TAS1_Diff_Powder/TAS1_Diff_Powder.instr b/mcstas-comps/examples/Risoe/TAS1_Diff_Powder/TAS1_Diff_Powder.instr index 79907965c5..d59528a67f 100644 --- a/mcstas-comps/examples/Risoe/TAS1_Diff_Powder/TAS1_Diff_Powder.instr +++ b/mcstas-comps/examples/Risoe/TAS1_Diff_Powder/TAS1_Diff_Powder.instr @@ -27,6 +27,9 @@ * sample is a powder and there is no analyzer. * * %Example: PHM=-37.077 Detector: sng_I=4.50892e-07 +* %Scan: mcrun TAS1_Diff_Powder.instr TT=32.92,34.32 -N15 -n1e6 Detector: sng_I={ +* 3.44621e-09,1.42523e-08,3.66193e-08,9.83779e-08,1.88888e-07,3.09967e-07,4.32565e-07,5.50027e-07, +* 5.59591e-07,5.02795e-07,3.84587e-07,2.46907e-07,1.35535e-07,6.38448e-08,2.13895e-08 } * * %Parameters * PHM: [deg] Monochromator arm angle, aka A1 @@ -34,7 +37,7 @@ * TT: [deg] Take-off angle at the sample position, aka A4 * TTA: [deg] Take-off angle at the analyzer position, aka A6 * C1: [min] Collimator 1 aperture (mono-sample arm) -* OMC1: [deg] Tilt angle of the Collimator 1 +* OMC1: [arcmin] Tilt angle of the Collimator 1 * C2: [min] Collimator 2 aperture (sample-ana arm) * C3: [min] Collimator 3 aperture (ana-detector arm) * diff --git a/mcstas-comps/examples/Risoe/TAS1_Diff_Slit/TAS1_Diff_Slit.instr b/mcstas-comps/examples/Risoe/TAS1_Diff_Slit/TAS1_Diff_Slit.instr index a73f2c1adf..782b51d707 100644 --- a/mcstas-comps/examples/Risoe/TAS1_Diff_Slit/TAS1_Diff_Slit.instr +++ b/mcstas-comps/examples/Risoe/TAS1_Diff_Slit/TAS1_Diff_Slit.instr @@ -27,13 +27,16 @@ * sample is a slit and there is no analyzer. * * %Example: C1=30 TT=0 Detector: sng_I=2e-5 +* %Scan: mcrun TAS1_Diff_Slit.instr C1=30 TT=-0.6,0.6 -N13 -n1e6 Detector: sng_I={ +* 6.85677e-07,2.11237e-06,4.51499e-06,8.20823e-06,1.39162e-05,1.73145e-05,2.01992e-05,2.05377e-05, +* 1.71222e-05,1.22857e-05,8.94974e-06,5.09308e-06,2.51101e-06 } * * %Parameters * PHM: [deg] Monochromator arm angle, aka A1 * TTM: [deg] Monochromator take-off angle, aka A2 * TT: [deg] Take-off angle at the sample position, aka A4 * C1: [min] Collimator 1 aperture (mono-sample arm) -* OMC1: [deg] Tilt angle of the Collimator 1 +* OMC1: [arcmin] Tilt angle of the Collimator 1 * C2: [min] Collimator 2 aperture (sample-ana arm) * C3: [min] Collimator 3 aperture (ana-detector arm) * diff --git a/mcstas-comps/examples/Risoe/TAS1_Diff_Vana/TAS1_Diff_Vana.instr b/mcstas-comps/examples/Risoe/TAS1_Diff_Vana/TAS1_Diff_Vana.instr index ec11525698..10de482760 100644 --- a/mcstas-comps/examples/Risoe/TAS1_Diff_Vana/TAS1_Diff_Vana.instr +++ b/mcstas-comps/examples/Risoe/TAS1_Diff_Vana/TAS1_Diff_Vana.instr @@ -27,6 +27,10 @@ * sample is a vanadium cylinder and there is no analyzer. * * %Example: PHM=-37.077 Detector: sng_I=1.95173e-09 +* %Scan: mcrun TAS1_Diff_Vana.instr TT=31.52,35.52 -N21 -n1e6 Detector: sng_I={ +* 1.8001e-09,1.87932e-09,1.86258e-09,1.89395e-09,1.86904e-09,1.86482e-09,1.85878e-09,1.87728e-09, +* 1.81479e-09,1.84234e-09,1.91997e-09,1.89089e-09,1.82982e-09,1.9059e-09,1.88333e-09,1.775e-09, +* 1.80894e-09,1.99095e-09,1.89532e-09,1.94438e-09,1.94377e-09 } * * %Parameters * PHM: [deg] Monochromator arm angle, aka A1 @@ -34,7 +38,7 @@ * TT: [deg] Take-off angle at the sample position, aka A4 * TTA: [deg] Take-off angle at the analyzer position, aka A6 * C1: [min] Collimator 1 aperture (mono-sample arm) -* OMC1: [deg] Tilt angle of the Collimator 1 +* OMC1: [arcmin] Tilt angle of the Collimator 1 * C2: [min] Collimator 2 aperture (sample-ana arm) * C3: [min] Collimator 3 aperture (ana-detector arm) * diff --git a/mcstas-comps/examples/Risoe/TAS1_Powder/TAS1_Powder.instr b/mcstas-comps/examples/Risoe/TAS1_Powder/TAS1_Powder.instr index 22cd1cc7cb..fe207cdca8 100644 --- a/mcstas-comps/examples/Risoe/TAS1_Powder/TAS1_Powder.instr +++ b/mcstas-comps/examples/Risoe/TAS1_Powder/TAS1_Powder.instr @@ -25,6 +25,12 @@ * The sample is a powder and the analyzer is a single plate. * * %Example: PHM=-37.077 Detector: sng_I=2.26723e-07 +* With TTA=0 the detector looks straight through the analyzer, so an OMA scan shows +* a transmission dip where the analyzer is at its Bragg angle: +* %Scan: mcrun TAS1_Powder.instr OMA=-19.45,-15.45 -N21 -n1e6 Detector: sng_I={ +* 4.37937e-07,4.53735e-07,4.60594e-07,4.49352e-07,4.43857e-07,4.36457e-07,4.22756e-07,4.15322e-07, +* 3.49642e-07,2.82077e-07,2.31752e-07,2.48424e-07,3.1068e-07,3.96655e-07,4.27444e-07,4.42215e-07, +* 4.49148e-07,4.60529e-07,4.36828e-07,4.39458e-07,4.52569e-07 } * * %Parameters * PHM: [deg] Monochromator rotation angle, aka A1 @@ -33,7 +39,7 @@ * OMA: [deg] Analyzer rotation angle, aka A5 * TTA: [deg] Take-off angle at the analyzer position, aka A6 * C1: [min] Collimator 1 aperture (mono-sample arm) -* OMC1: [deg] Tilt angle of the Collimator 1 +* OMC1: [arcmin] Tilt angle of the Collimator 1 * C2: [min] Collimator 2 aperture (sample-ana arm) * C3: [min] Collimator 3 aperture (ana-detector arm) * diff --git a/mcstas-comps/examples/Risoe/TAS1_Vana/TAS1_Vana.instr b/mcstas-comps/examples/Risoe/TAS1_Vana/TAS1_Vana.instr index a63a3ae25e..53e8e737a1 100644 --- a/mcstas-comps/examples/Risoe/TAS1_Vana/TAS1_Vana.instr +++ b/mcstas-comps/examples/Risoe/TAS1_Vana/TAS1_Vana.instr @@ -25,6 +25,12 @@ * The sample is a vanadium and the analyzer is a single plate. * * %Example: PHM=-37.077 Detector: sng_I=1.11099e-09 +* With TTA=0 the detector looks straight through the analyzer, so an OMA scan shows +* a transmission dip where the analyzer is at its Bragg angle: +* %Scan: mcrun TAS1_Vana.instr OMA=-19.45,-15.45 -N21 -n1e6 Detector: sng_I={ +* 1.81292e-09,1.90855e-09,1.8668e-09,1.86678e-09,1.85029e-09,1.834e-09,1.76611e-09,1.60322e-09, +* 1.33626e-09,1.0796e-09,1.09548e-09,1.2646e-09,1.46433e-09,1.72966e-09,1.83299e-09,1.77587e-09, +* 1.82133e-09,1.94325e-09,1.88317e-09,1.89597e-09,1.94066e-09 } * * %Parameters * PHM: [deg] Monochromator rotation angle, aka A1 @@ -33,7 +39,7 @@ * OMA: [deg] Analyzer rotation angle, aka A5 * TTA: [deg] Take-off angle at the analyzer position, aka A6 * C1: [min] Collimator 1 aperture (mono-sample arm) -* OMC1: [deg] Tilt angle of the Collimator 1 +* OMC1: [arcmin] Tilt angle of the Collimator 1 * C2: [min] Collimator 2 aperture (sample-ana arm) * C3: [min] Collimator 3 aperture (ana-detector arm) * diff --git a/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr b/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr index 696e03d74c..8066109e48 100644 --- a/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr +++ b/mcstas-comps/examples/Tests_samples/Samples_Incoherent/Samples_Incoherent.instr @@ -61,6 +61,10 @@ * %Example: SAMPLE=10 STOP=1 -n 1e5 Detector: PSD_Sphere_4pi_I=1.28905e+06 * %Scan: mcrun Samples_Incoherent.instr SAMPLE=1,5 -N5 STOP=1 Detector: PSD_Sphere_4pi_I={ * 1326220.0,1245050.0,1322310.0,1321210.0,1326550.0 } +* %Scan: mcrun Samples_Incoherent.instr SAMPLE=2,5 -N4 STOP=0 Detector: PSD_Sphere_4pi_I={ +* 12415200.0,7154040.0,7759140.0,1327980.0 } +* %Scan: mcrun Samples_Incoherent.instr SAMPLE=2,5 -N4 STOP=0 DB=1 Detector: Dirbeam_I={ +* 11195400.0,5833780.0,6441470.0,5783.69 } * * %Parameters * L_min: [AA] Minimum wavelength of neutrons diff --git a/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr b/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr index 2c4245c907..371b9f5394 100644 --- a/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr +++ b/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr @@ -45,7 +45,11 @@ * 6512950000.0,6125570000.0,5973110000.0,6294990000.0,6219240000.0,6483710000.0,7090310000.0,5406090000.0, * 6658460000.0,5907690000.0,7892760000.0,6702680000.0,7044170000.0,6930370000.0,8491040000.0,8899820000.0, * 7356430000.0,6853240000.0,7013240000.0,7102780000.0,7068470000.0 } -* Manganese and chrome scan: mxrun SOLEIL_ROCK.instr E0=5.700,6.800 scan=1 sample_file=MnCr cc=2 -N100 +* Manganese and chrome scan: +* %Scan: mxrun SOLEIL_ROCK.instr E0=5.7,6.8 scan=1 sample_file=MnCr cc=2 -N21 -n1e6 Detector: fluo_monitor_I={ +* 3873570000.0,3543840000.0,3341540000.0,3925230000.0,3599480000.0,4314580000.0,5588890000.0,5427100000.0, +* 5606400000.0,5332170000.0,5525900000.0,5405550000.0,5510330000.0,6243680000.0,6657880000.0,6746670000.0, +* 5808630000.0,7117800000.0,4755990000.0,4941770000.0,5925960000.0 } * Pretty energy repartition monitor result: mxrun SOLEIL_ROCK.instr E0=17.000 cc=2 -n1e8 * * %Example: E0=15.918 Detector: fluo_monitor_I=2e+09 From efa2cc9d08417e42fd94140e435265a1af1a098c Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 17:55:28 +0200 Subject: [PATCH 05/10] mccode-git-diff-code: treat %Scan: lines as test definitions too %Scan: header lines are mctest test definitions like %Example: lines, so edits to them must still list the .comp/.instr file. A %Scan: line runs on to the } closing its target values, which may span several header lines; the header's * prefixes inside the {} are ignored, so re-wrapping the values is not a change. The stderr reason is now %Example/%Scan. Checked on a0f97e143 and aa47fecc2: all 13 resp. 9 instruments with new %Scan: lines are listed (previously skipped as header-only edits). Co-Authored-By: Claude Opus 5.5 --- devel/bin/mccode-git-diff-code | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/devel/bin/mccode-git-diff-code b/devel/bin/mccode-git-diff-code index c2258ea3bf..1b92ca7dd3 100755 --- a/devel/bin/mccode-git-diff-code +++ b/devel/bin/mccode-git-diff-code @@ -6,14 +6,16 @@ Drop-in replacement for `git diff --name-only BASE [TARGET]` that leaves out A .comp/.instr file is listed only if its "code" differs between BASE and TARGET, where code means: - everything from the DEFINE COMPONENT / DEFINE INSTRUMENT line onward, and - - the %Example: lines of the header (mctest uses them as test definitions), - so a header edit that touches %Example: lines still triggers a test run. + - the %Example: and %Scan: lines of the header (mctest uses them as test + definitions), so a header edit that touches them still triggers a test run. + A %Scan: line includes its {}-enclosed target values, which may span + several header lines; re-wrapping those values is not a change. Other header edits (mcdoc text, %P parameter docs, typos, units) are ignored, and so are whitespace-only edits: indentation, blank lines, re-wrapped lines, spacing around operators. Whitespace between two words (int a vs inta) and the line break after a #-preprocessor line or a line with // are still significant. -For each listed .comp/.instr file, the reason (new, code, %Example) is written +For each listed .comp/.instr file, the reason (new, code, %Example/%Scan) is written to stderr; stdout carries only the file names. Added or renamed files are always listed; deleted files never are (nothing to @@ -27,7 +29,8 @@ import subprocess import sys DEFINE = re.compile(r'^[ \t]*DEFINE[ \t]+(COMPONENT|INSTRUMENT)\b', re.M) -EXAMPLE = re.compile(r'%Example:.*') +# a %Scan: line runs on to the } closing its target values, possibly over several lines +TESTLINE = re.compile(r'%(?:Example:[^\n]*|Scan:[^\n{]*(?:\{[^}]*\}[^\n]*)?)') def git(*args): @@ -65,11 +68,14 @@ def squash(text): def split(text): - ''' (%Example lines, code body) of a .comp/.instr file, whitespace-insensitive. ''' + ''' (%Example/%Scan lines, code body) of a .comp/.instr file, whitespace-insensitive. ''' m = DEFINE.search(text) if not m: return '', squash(text) # unrecognised layout: compare everything - return squash('\n'.join(EXAMPLE.findall(text[:m.start()]))), squash(text[m.start():]) + # the header's * line prefixes inside a multi-line {} value list are layout, not content + tests = [re.sub(r'\{[^}]*\}', lambda v: v.group(0).replace('*', ' '), t) + for t in TESTLINE.findall(text[:m.start()])] + return squash('\n'.join(tests)), squash(text[m.start():]) def main(argv): @@ -85,7 +91,7 @@ def main(argv): why = 'new' else: (ex0, body0), (ex1, body1) = split(old), split(new) - why = ', '.join(w for w, a, b in (('code', body0, body1), ('%Example', ex0, ex1)) if a != b) + why = ', '.join(w for w, a, b in (('code', body0, body1), ('%Example/%Scan', ex0, ex1)) if a != b) if not why: continue sys.stderr.write('mccode-git-diff-code: %s (%s)\n' % (path, why)) From c40616d8568ed3c1bf503e2d0dbff67b33c8173c Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 18:43:20 +0200 Subject: [PATCH 06/10] SPLIT 10 on mono and adjust scan range --- mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr b/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr index e524452721..2f494ed85d 100644 --- a/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr +++ b/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr @@ -26,9 +26,8 @@ * Cu 220 DM=1.278 AA * * Example of a C60 200 rocking curve scan: -* %Scan: mcrun LLB_6T2.instr -N12 lambda=2.4 phi=9.27,10.37 gamma=19.74 nu=0 monok=0 samp_f=C60.lau -n1e7 Detector: Mon_out_I={ -* 495.535,1014.3,1265.26,1449.65,1783.28,2217.03,2013.63,2151.44, -* 1934.61,1586.15,837.108,866.069 } +* %Scan: mcrun LLB_6T2.instr -N8 lambda=2.4 phi=9.47,10.17 gamma=19.74 nu=0 monok=0 samp_f=C60.lau -n1e7 Detector: Mon_out_I={ +* 1275.57,1550.07,1814.4,1908.03,1887.14,1956.2,1833.21,1501.39 } * * %Parameters * lambda: [AA] wavelength @@ -204,7 +203,7 @@ COMPONENT Pos_2 = Arm( AT (0,0,b2mon) RELATIVE Bar_out ROTATED (0,monoc_ang,0) ABSOLUTE -COMPONENT Monoc=Monochromator_curved( +SPLIT 10 COMPONENT Monoc=Monochromator_curved( zwidth=0.015, yheight=0.1, gap=0.0005, NH=7, NV=1, mosaich=25.0, mosaicv=25.0, reflect="HOPG.rfl", transmit="HOPG.trm", From 29bd4b0578f35359de11e6a71d389fe464c1e744 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 19:01:41 +0200 Subject: [PATCH 07/10] Disable %Scan: tests for LLB_6T2 and SOLEIL_ROCK for now Both scans failed outside the reference setup (other seeds / MPI rank layouts): the true seed-to-seed scatter is far larger than the reported error bars, because few independent histories get past the monochromator and the downstream SPLIT (sample / fluorescence) reuses them, so the errors are underestimated. E.g. LLB_6T2 at -n1e7: points moved up to 50% with +/-3% error bars; SOLEIL_ROCK Mn/Cr at -n1e6: 3 of 21 points >20% off, worst 50%, with +/-4% error bars. The header example lines are restored to their pre-%Scan text. LLB_6T2 keeps SPLIT 10 on Monoc, which halves the real scatter. Co-Authored-By: Claude Opus 5.5 --- mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr | 7 +++---- .../examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr | 12 ++---------- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr b/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr index 2f494ed85d..a4292ba4fa 100644 --- a/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr +++ b/mcstas-comps/examples/LLB/LLB_6T2/LLB_6T2.instr @@ -25,10 +25,6 @@ * PG 002 DM=3.355 AA (Highly Oriented Pyrolythic Graphite) * Cu 220 DM=1.278 AA * -* Example of a C60 200 rocking curve scan: -* %Scan: mcrun LLB_6T2.instr -N8 lambda=2.4 phi=9.47,10.17 gamma=19.74 nu=0 monok=0 samp_f=C60.lau -n1e7 Detector: Mon_out_I={ -* 1275.57,1550.07,1814.4,1908.03,1887.14,1956.2,1833.21,1501.39 } -* * %Parameters * lambda: [AA] wavelength * phi: [Deg] sample rotation along the vertical axis @@ -37,6 +33,9 @@ * monok: [1] monochromator to use (0: PG, 1: Cu, 5: test mode) * samp_f: [str] LAU file describing sample * +* Example of a C60 200 rocking curve scan: +* mcrun LLB_6T2.instr --mpi=NUM_CORES -N31 lambda=2.4 phi=8.37,11.37 gamma=19.74 nu=0 monok=0 samp_f="C60.lau" -n 1e8 -d C60_200 +* * %End *******************************************************************************/ DEFINE INSTRUMENT LLB_6T2(lambda=1.0, phi=0, gamma=0, nu=0, monok=0, string samp_f="C60.lau") diff --git a/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr b/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr index 371b9f5394..8cf7a10932 100644 --- a/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr +++ b/mcxtrace-comps/examples/SOLEIL/SOLEIL_ROCK/SOLEIL_ROCK.instr @@ -40,16 +40,8 @@ * 32.44 | Sample * * Examples: -* Copper scan: -* %Scan: mxrun SOLEIL_ROCK.instr E0=8.5,9.5 scan=1 cc=2 -N21 -n1e6 Detector: fluo_monitor_I={ -* 6512950000.0,6125570000.0,5973110000.0,6294990000.0,6219240000.0,6483710000.0,7090310000.0,5406090000.0, -* 6658460000.0,5907690000.0,7892760000.0,6702680000.0,7044170000.0,6930370000.0,8491040000.0,8899820000.0, -* 7356430000.0,6853240000.0,7013240000.0,7102780000.0,7068470000.0 } -* Manganese and chrome scan: -* %Scan: mxrun SOLEIL_ROCK.instr E0=5.7,6.8 scan=1 sample_file=MnCr cc=2 -N21 -n1e6 Detector: fluo_monitor_I={ -* 3873570000.0,3543840000.0,3341540000.0,3925230000.0,3599480000.0,4314580000.0,5588890000.0,5427100000.0, -* 5606400000.0,5332170000.0,5525900000.0,5405550000.0,5510330000.0,6243680000.0,6657880000.0,6746670000.0, -* 5808630000.0,7117800000.0,4755990000.0,4941770000.0,5925960000.0 } +* Copper scan: mxrun SOLEIL_ROCK.instr E0=8.500,9.500 scan=1 cc=2 -N100 +* Manganese and chrome scan: mxrun SOLEIL_ROCK.instr E0=5.700,6.800 scan=1 sample_file=MnCr cc=2 -N100 * Pretty energy repartition monitor result: mxrun SOLEIL_ROCK.instr E0=17.000 cc=2 -n1e8 * * %Example: E0=15.918 Detector: fluo_monitor_I=2e+09 From 2bdb2c06002e79eca6923944e95125ed6f0034e8 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 19:15:42 +0200 Subject: [PATCH 08/10] Tomography: Python tomographic reconstruction, %Scan: over a full rotation - tomo_recon.py: Python port (numpy + matplotlib) of the old Matlab tomo_recon.m. Filtered back-projection (ramp*Hann filter, as Matlab iradon's 'hann') of an mcrun omega scan, one sinogram per detector row from the I block of each step's x_y monitor file, using -log(I/I_max) as projection. Shows the 3 central slices; --save writes vol.npy. Usage: python tomo_recon.py [--save] - Tomography.instr / README.md: point to tomo_recon.py instead of the Matlab function (which needed the imaging toolbox, PGPLOT output and is no longer in tools/matlab). - %Scan: now a full rotation omega=0,350 -N36 -n1e6, with targets from that scan (error bars ~0.1%, no SPLIT in the instrument). Verified: mctest passes the scan (36/36 points at 100%, ~48 s); tomo_recon.py reconstructs an 80x80x40 volume from it. Co-Authored-By: Claude Opus 5.5 --- .../examples/Templates/Tomography/README.md | 5 +- .../Templates/Tomography/Tomography.instr | 15 ++-- .../Templates/Tomography/tomo_recon.py | 71 +++++++++++++++++++ 3 files changed, 81 insertions(+), 10 deletions(-) create mode 100644 mcstas-comps/examples/Templates/Tomography/tomo_recon.py diff --git a/mcstas-comps/examples/Templates/Tomography/README.md b/mcstas-comps/examples/Templates/Tomography/README.md index 98a2427c1d..b37939b663 100644 --- a/mcstas-comps/examples/Templates/Tomography/README.md +++ b/mcstas-comps/examples/Templates/Tomography/README.md @@ -18,9 +18,8 @@ Example: mcrun Tomography.instr offfile=bunny.off -n1e4 -N18 omega=0,340 -d Tomo (Note that to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts are needed) -Use the provided Matlab tomo_recon.m function (requires imaging toolbox, PGPLOT output data -and a Unix/Mac) in the tools/matlab folder to reconstruct a 3D volume of the object. Use e.g. -isosurface to do thresholding for extraction of the object surface. +Use the provided tomo_recon.py (numpy + matplotlib) in this folder to reconstruct a 3D +volume of the object from the scan directory: python tomo_recon.py TomoScan [--save] ``` ## Examples diff --git a/mcstas-comps/examples/Templates/Tomography/Tomography.instr b/mcstas-comps/examples/Templates/Tomography/Tomography.instr index f917aed306..a372df95f4 100644 --- a/mcstas-comps/examples/Templates/Tomography/Tomography.instr +++ b/mcstas-comps/examples/Templates/Tomography/Tomography.instr @@ -14,16 +14,17 @@ * %Description * Instrument to study tomographic imaging by means of the feature of OFF shape samples. * -* %Scan: mcrun Tomography.instr omega=0,340 -N18 -n1e4 Detector: monitor_I={ -* 2.23321e-09,2.18277e-09,2.18764e-09,2.18301e-09,2.19154e-09,2.19422e-09,2.18277e-09,2.18521e-09, -* 2.19178e-09,2.23662e-09,2.19154e-09,2.18374e-09,2.18935e-09,2.18325e-09,2.20397e-09,2.17789e-09, -* 2.18033e-09,2.18691e-09 } +* %Scan: mcrun Tomography.instr omega=0,350 -N36 -n1e6 Detector: monitor_I={ +* 2.23423e-09,2.20782e-09,2.18698e-09,2.17973e-09,2.18055e-09,2.17717e-09,2.17522e-09,2.18334e-09, +* 2.19383e-09,2.21727e-09,2.19529e-09,2.18096e-09,2.17704e-09,2.17798e-09,2.18358e-09,2.18236e-09, +* 2.18861e-09,2.20975e-09,2.23448e-09,2.20947e-09,2.18712e-09,2.18229e-09,2.1835e-09,2.17813e-09, +* 2.17685e-09,2.1831e-09,2.19357e-09,2.2165e-09,2.19268e-09,2.18099e-09,2.17494e-09,2.17799e-09, +* 2.18184e-09,2.18032e-09,2.18734e-09,2.20725e-09 } * (Note that to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts * are needed) * -* Use the provided Matlab tomo_recon.m function (requires imaging toolbox, PGPLOT output data -* and a Unix/Mac) in the tools/matlab folder to reconstruct a 3D volume of the object. Use e.g. -* isosurface to do thresholding for extraction of the object surface. +* Use the provided tomo_recon.py (numpy + matplotlib) in this folder to reconstruct a 3D +* volume of the object from the scan directory: python tomo_recon.py TomoScan [--save] * * %Example: omega=0 Detector: monitor_I=2.23492e-09 * diff --git a/mcstas-comps/examples/Templates/Tomography/tomo_recon.py b/mcstas-comps/examples/Templates/Tomography/tomo_recon.py new file mode 100644 index 0000000000..4cd7e06d93 --- /dev/null +++ b/mcstas-comps/examples/Templates/Tomography/tomo_recon.py @@ -0,0 +1,71 @@ +#!/usr/bin/env python3 +"""Reconstruct a volume from a Tomography.instr omega scan, e.g. + + mcrun Tomography.instr omega=0,350 -N36 -n1e7 -d TomoScan + python tomo_recon.py TomoScan + +Filtered back-projection (ramp*Hann filter, like Matlab iradon's 'hann'), +one sinogram per detector row. Shows 3 central slices; --save writes vol.npy. +Python port of tools/matlab/tomo_recon.m (PW, 20080620). +""" +import glob, os, sys +import numpy as np +import matplotlib.pyplot as plt + + +def header(path, key): + for line in open(path): + if line.startswith('# ' + key): + return line[len(key) + 2:].strip() + + +def iradon(sino, theta): + """sino: (nbins, nproj), theta in degrees -> (nbins, nbins) slice.""" + n = sino.shape[0] + pad = 1 << int(np.ceil(np.log2(2 * n))) + f = np.fft.fftfreq(pad) + h = 2 * np.abs(f) * (1 + np.cos(2 * np.pi * f)) / 2 + filt = np.fft.ifft(np.fft.fft(sino, pad, axis=0) * h[:, None], axis=0).real[:n] + x = np.arange(n) - (n - 1) / 2 + X, Y = np.meshgrid(x, -x) + img = np.zeros((n, n)) + for p, t in zip(filt.T, np.deg2rad(theta)): + img += np.interp(X * np.cos(t) + Y * np.sin(t), x, p, left=0, right=0) + return img * np.pi / (2 * len(theta)) + + +def main(datadir, save=False): + dat = os.path.join(datadir, 'mccode.dat') + nproj = int(header(dat, 'Numpoints:')) + lo, hi = map(float, header(dat, 'xlimits:').split()) + theta = np.linspace(lo, hi, nproj) + + mons = [] + for j in range(nproj): + f = glob.glob(os.path.join(datadir, str(j), '*.x_y'))[0] + I = np.loadtxt(f) + mons.append(I[:len(I) // 3]) # I block only, rows = y slices + geometry = header(f, 'Param: geometry=') + mons = np.array(mons) # (nproj, nslice, nbins) + pos = mons[mons > 0] + mons = np.maximum(mons, pos.min() if pos.size else 1) # avoid log(0) + + vol = np.stack([iradon(np.log(m.max() / m).T, theta) + for m in mons.transpose(1, 0, 2)], axis=2) # (x, z, y) + if save: + np.save(os.path.join(datadir, 'vol.npy'), vol) + + title = 'slice from %s, Hann filtered' % geometry + c = [s // 2 for s in vol.shape] + fig, ax = plt.subplots(1, 3, figsize=(15, 5)) + for a, img, name in zip(ax, (vol[c[0]].T, vol[:, c[1]].T, vol[:, :, c[2]]), 'xyz'): + a.imshow(img, origin='lower') + a.set_title('Central %s %s' % (name, title)) + plt.show() + return vol + + +if __name__ == '__main__': + if len(sys.argv) < 2 or not os.path.isdir(sys.argv[1]): + sys.exit('usage: tomo_recon.py [--save]') + main(sys.argv[1], '--save' in sys.argv) From e5117f93e4abe0bb13bea90536bcd885059051c9 Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 20:13:00 +0200 Subject: [PATCH 09/10] Tomography: real-world description, smaller/finer detector, 5 deg scan - Description says what the instrument does (OFF sample rotated by omega around y, transmitted beam on a 2D detector) and gives a working tomography command (omega=0,355 -N72 -n1e7 -d TomoScan), replacing the stale example with the non-existent offfile= parameter and the unshipped bunny.off. - %Scan: moved after %Example so mcdoc keeps the description intact; now a full rotation in 5 deg steps, omega=0,355 -N72 -n1e6, targets generated as mctest runs it (-s 1000 --scan_split=auto). - Defaults det_w=0.25, det_h=0.15, opts="x bins=128 y bins=64"; %Example: target updated for the smaller detector (9.37708e-10). - README.md regenerated with mcdoc's Markdown writer. Verified: mctest passes the %Example (100%) and the scan (72/72 points at 100%, ~82 s). Co-Authored-By: Claude Opus 5.5 --- .../examples/Templates/Tomography/README.md | 16 +++++++----- .../Templates/Tomography/Tomography.instr | 26 ++++++++++++------- 2 files changed, 27 insertions(+), 15 deletions(-) diff --git a/mcstas-comps/examples/Templates/Tomography/README.md b/mcstas-comps/examples/Templates/Tomography/README.md index b37939b663..1d1688ce36 100644 --- a/mcstas-comps/examples/Templates/Tomography/README.md +++ b/mcstas-comps/examples/Templates/Tomography/README.md @@ -13,9 +13,12 @@ ```text Instrument to study tomographic imaging by means of the feature of OFF shape samples. +The sample (geometry, an OFF file, default socket.off) is rotated by omega around the +vertical axis, and the transmitted beam is recorded on a 2D detector (monitor). -Example: mcrun Tomography.instr offfile=bunny.off -n1e4 -N18 omega=0,340 -d TomoScan -(Note that to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts +A tomography is a scan of omega over a full rotation, e.g. +mcrun Tomography.instr omega=0,355 -N72 -n1e7 -d TomoScan +(to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts are needed) Use the provided tomo_recon.py (numpy + matplotlib) in this folder to reconstruct a 3D @@ -24,7 +27,8 @@ volume of the object from the scan directory: python tomo_recon.py TomoScan [--s ## Examples -- **Test: omega=0 Detector: monitor_I=2.23492e-09** +- **Test: omega=0 Detector: monitor_I=9.37708e-10** +- **Scan: mcrun Tomography.instr omega=0,355 -N72 -n1e6 Detector: monitor_I={72 values}** ## Input parameters @@ -40,9 +44,9 @@ Parameters in **boldface** are required; the others are optional. | div_h | deg | Source horisontal divergence (angular width) | 1e-4 | | source_w | m | Source width | 0.4 | | source_h | m | Source height | 0.2 | -| det_w | m | Detector width | 0.4 | -| det_h | m | Detector height | 0.2 | -| opts | string | Monitor_nD options string | "x bins=80 y bins=40" | +| det_w | m | Detector width | 0.25 | +| det_h | m | Detector height | 0.15 | +| opts | string | Monitor_nD options string | "x bins=128 y bins=64" | ## Links diff --git a/mcstas-comps/examples/Templates/Tomography/Tomography.instr b/mcstas-comps/examples/Templates/Tomography/Tomography.instr index a372df95f4..f43d44c0a9 100644 --- a/mcstas-comps/examples/Templates/Tomography/Tomography.instr +++ b/mcstas-comps/examples/Templates/Tomography/Tomography.instr @@ -13,20 +13,28 @@ * * %Description * Instrument to study tomographic imaging by means of the feature of OFF shape samples. +* The sample (geometry, an OFF file, default socket.off) is rotated by omega around the +* vertical axis, and the transmitted beam is recorded on a 2D detector (monitor). * -* %Scan: mcrun Tomography.instr omega=0,350 -N36 -n1e6 Detector: monitor_I={ -* 2.23423e-09,2.20782e-09,2.18698e-09,2.17973e-09,2.18055e-09,2.17717e-09,2.17522e-09,2.18334e-09, -* 2.19383e-09,2.21727e-09,2.19529e-09,2.18096e-09,2.17704e-09,2.17798e-09,2.18358e-09,2.18236e-09, -* 2.18861e-09,2.20975e-09,2.23448e-09,2.20947e-09,2.18712e-09,2.18229e-09,2.1835e-09,2.17813e-09, -* 2.17685e-09,2.1831e-09,2.19357e-09,2.2165e-09,2.19268e-09,2.18099e-09,2.17494e-09,2.17799e-09, -* 2.18184e-09,2.18032e-09,2.18734e-09,2.20725e-09 } -* (Note that to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts +* A tomography is a scan of omega over a full rotation, e.g. +* mcrun Tomography.instr omega=0,355 -N72 -n1e7 -d TomoScan +* (to achieve proper statistics for tomographic reconstruction, MUCH higher ncounts * are needed) * * Use the provided tomo_recon.py (numpy + matplotlib) in this folder to reconstruct a 3D * volume of the object from the scan directory: python tomo_recon.py TomoScan [--save] * -* %Example: omega=0 Detector: monitor_I=2.23492e-09 +* %Example: omega=0 Detector: monitor_I=9.37708e-10 +* %Scan: mcrun Tomography.instr omega=0,355 -N72 -n1e6 Detector: monitor_I={ +* 9.42128e-10,9.25881e-10,9.14476e-10,9.04288e-10,8.94769e-10,8.8652e-10,8.84254e-10,8.86881e-10, +* 8.87397e-10,8.86793e-10,8.80893e-10,8.80094e-10,8.82899e-10,8.84653e-10,8.8854e-10,8.9252e-10, +* 9.01629e-10,9.10865e-10,9.22842e-10,9.09788e-10,8.99241e-10,8.92795e-10,8.87909e-10,8.83615e-10, +* 8.80372e-10,8.81549e-10,8.8362e-10,8.86581e-10,8.88443e-10,8.89103e-10,8.85436e-10,8.86795e-10, +* 8.92286e-10,9.02972e-10,9.15912e-10,9.25596e-10,9.39192e-10,9.28645e-10,9.15208e-10,9.03769e-10, +* 8.93097e-10,8.87378e-10,8.87768e-10,8.88077e-10,8.88221e-10,8.88865e-10,8.84663e-10,8.81642e-10, +* 8.83464e-10,8.85594e-10,8.8875e-10,8.90938e-10,8.98263e-10,9.09941e-10,9.22377e-10,9.11957e-10, +* 8.98938e-10,8.90529e-10,8.85399e-10,8.83245e-10,8.80727e-10,8.78931e-10,8.82134e-10,8.84583e-10, +* 8.84924e-10,8.87263e-10,8.88867e-10,8.87931e-10,8.92295e-10,9.00247e-10,9.15281e-10,9.26476e-10 } * * %Parameters * geometry: [string] Name of the OFF file describing the sample shape @@ -46,7 +54,7 @@ * * %End *******************************************************************************/ -DEFINE INSTRUMENT Tomography(string geometry="socket.off", omega=0, sigma_abs=100, frac_scatt=0, div_v=1e-4, div_h=1e-4, source_w=0.4, source_h=0.2, det_w=0.4, det_h=0.2, string opts="x bins=80 y bins=40") +DEFINE INSTRUMENT Tomography(string geometry="socket.off", omega=0, sigma_abs=100, frac_scatt=0, div_v=1e-4, div_h=1e-4, source_w=0.4, source_h=0.2, det_w=0.25, det_h=0.15, string opts="x bins=128 y bins=64") DEPENDENCY " -DUSE_OFF " TRACE From b7201d7bfea13c3a5417a8c3f98a5dabaf347fcd Mon Sep 17 00:00:00 2001 From: Peter Willendrup Date: Thu, 8 Oct 2026 20:41:45 +0200 Subject: [PATCH 10/10] SSRL_bl_11_2_white_src: %Scan: at -n1e7 with a 3-seed mean reference The scan failed on Windows CI (mxtest --mpi=auto, 29/31 points, worst 125%): the two SPLIT 10 Bragg crystals reuse each history up to 100x, so at 1e6 the real seed-to-seed scatter was 8-12% per point against 3-5% error bars. At 1e7 the typical scatter is ~2%. Targets are the mean of seeds 1000/2000/3000 (all within 8% of it). Verified: mxtest --seed 5000 (31/31, worst 92%, 50 s) and --mpi=auto (31/31, worst 106%, 92 s) on macOS arm64. Expect ~15 min on Windows CI. Co-Authored-By: Claude Opus 5.5 --- .../SSRL_bl_11_2_white_src.instr | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr b/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr index 6274905c4b..7faea4ec76 100644 --- a/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr +++ b/mcxtrace-comps/examples/SSRL/SSRL_bl_11_2_white_src/SSRL_bl_11_2_white_src.instr @@ -18,11 +18,11 @@ * Documentation and results of the .instr here: https://gitlab.synchrotron-soleil.fr/grades/beamlines/-/tree/main/glitches * A jupyter notebook will soon be available regrouping everything. * You may scan like so for example: -* %Scan: mxrun SSRL_bl_11_2_white_src.instr -N31 Etohit=6900,7500 detuning_percentage=40 -n1e6 Detector: EnergyMonitor_first_I={ -* 10046700.0,10650900.0,8528260.0,8296880.0,7986510.0,22446400.0,24820300.0,25166000.0, -* 22197000.0,25054900.0,23876500.0,25019400.0,25330900.0,25429200.0,24424900.0,23806600.0, -* 23187200.0,21946700.0,23304900.0,19717000.0,18597400.0,21596200.0,21184500.0,15963900.0, -* 18022700.0,15979900.0,16987000.0,17278100.0,16956200.0,16034000.0,15923600.0 } +* %Scan: mxrun SSRL_bl_11_2_white_src.instr -N31 Etohit=6900,7500 detuning_percentage=40 -n1e7 Detector: EnergyMonitor_first_I={ +* 9.6608e+06,9.36768e+06,8.8759e+06,8.45813e+06,8.60571e+06,2.19181e+07,2.5781e+07,2.47468e+07, +* 2.33347e+07,2.36432e+07,2.44606e+07,2.54374e+07,2.50395e+07,2.47904e+07,2.48351e+07,2.48054e+07, +* 2.25687e+07,2.16413e+07,2.15756e+07,2.08025e+07,2.13743e+07,2.14039e+07,2.09034e+07,1.55632e+07, +* 1.75271e+07,1.73956e+07,1.73963e+07,1.72547e+07,1.72151e+07,1.74949e+07,1.71321e+07 } * * %Example: Etohit=6900 Detector: EnergyMonitor_first_I=4.24366e+07 *