Add detector geometries: Lake Geneva, KM3NeT-ORCA, ND280, SINE, UNDINE by austinschneider · Pull Request #101 · Harvard-Neutrino/SIREN

austinschneider · 2026-04-28T04:28:52Z

Stack: PR 3 of 14

This PR is part of a 14-PR stack decomposing dev/HNL_DIS into reviewable chunks.

Base: chore/ci-and-packaging
Head: feat/detectors-resources

Merge order: chore/ci-and-packaging should land before this PR.

Squashed contents

Squashed diff for paths:

resources/detectors
resources/examples
resources/fluxes/T2K_Kaons
python/_util.py

Source commits on dev/HNL_DIS_clean that contributed:
088b1cd (Nicholas Kamp): move around the HNL DIS fits files
23fa85c (Nicholas Kamp): Allow underscores in model names
eb78b84 (Nicholas Kamp): _util bug fixes and KM3Net renaming

Notes

This branch is the squashed cumulative diff of the listed source commits. Per-commit history is browsable on dev/HNL_DIS_clean.
Large .fits data files have been removed from the branch and are packaged separately.

Squashed diff for paths: - resources/detectors - resources/examples - resources/fluxes/T2K_Kaons - python/_util.py Source commits on dev/HNL_DIS_clean that contributed: 088b1cd (Nicholas Kamp): move around the HNL DIS fits files 23fa85c (Nicholas Kamp): Allow underscores in model names eb78b84 (Nicholas Kamp): _util bug fixes and KM3Net renaming Additional source commit: bea39f9 (Ming-Shau Liu): SIREN ND280+ MODULE ADDITION (#73) Co-authored-by: Ming-Shau Liu <123968200+mingshauliu@users.noreply.github.com>

Copilot

Pull request overview

Note

Copilot was unable to run its full agentic suite in this review.

Adds new detector geometry/material resources and tabulated flux resources (T2K kaons), plus small utility updates to support model naming and on-demand flux file generation.

Changes:

Add detector geometry/material resource files for SINE, UNDINE, ND280, and KM3NeT-ORCA; extend IceCube geometry with DeepCore and an enlarged fiducial shell.
Add T2K kaon flux resource data and a FluxCalculator.py to generate particle-specific flux files.
Update Python utilities to allow underscores in model names and to load/generate tabulated flux files from resources.

Reviewed changes

Copilot reviewed 18 out of 20 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/test.ipynb	Notebook used to generate/inspect flux ratios and plots.
resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/ratio.dat	Tabulated ratio data used for _bar scaling.
resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/kaon-flux-data.dat	Input kaon flux data (log-scale values).
resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/TOT_PLUS_NUMU.dat	Source flux table used to compute ratio data.
resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/TOT_MINUS_NUMUBAR.dat	Source flux table used to compute ratio data.
resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/FluxCalculator.py	Adds code to generate derived tabulated flux files from packaged data.
resources/examples/example2/PaperPlots.ipynb	Formatting/metadata cleanup in plotting notebook.
resources/examples/additional_paper_plots/PaperPlots.ipynb	Updates cross-section plotting/reweighting workflow and adds extra rate/diagnostic cells.
resources/detectors/UNDINE/UNDINE-v1/materials.dat	Adds material composition definitions for UNDINE resources.
resources/detectors/UNDINE/UNDINE-v1/densities.dat	Adds UNDINE geometry (air/rock/lake + cylinder detector) with densities.
resources/detectors/SINE/SINE-v1/materials.dat	Adds material composition definitions for SINE resources.
resources/detectors/SINE/SINE-v1/densities.dat	Adds SINE geometry (container panels) with densities.
resources/detectors/ND280/ND280-v1/materials.dat	Adds ND280 materials definitions for detailed detector composition.
resources/detectors/ND280/ND280-v1/densities.dat	Adds ND280 geometry layout with densities and fiducial definition.
resources/detectors/KM3NeTORCA/KM3NeTORCA-v1/materials.dat	Adds ORCA material definitions (water/rock/mantle/core/air).
resources/detectors/KM3NeTORCA/KM3NeTORCA-v1/densities.dat	Adds ORCA PREM-based geometry and cylindrical detector.
resources/detectors/IceCube/IceCube-v1/densities.dat	Adds DeepCore + enlarged shell and switches fiducial to enlarged shell.
python/_util.py	Allows underscores in model names; adds helpers to locate/generate tabulated flux files via `FluxCalculator.py`.

Comments suppressed due to low confidence (1)

resources/fluxes/T2K_Kaons/T2K_Kaons-v1.0/test.ipynb:1

This notebook is committed with execution counts and a large embedded PNG output, which bloats the repo and produces noisy diffs. Consider clearing outputs (execution_count: null, empty outputs) before committing and using an output-stripping tool (e.g., pre-commit nbstripout) to keep resources lightweight.

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Copilot · 2026-04-28T04:38:38Z

+        abs_flux_dir = get_tabulated_flux_model_path(model_name,must_exist=must_exist)
+        # require existence of FluxCalculator.py
+        FluxCalculatorFile = os.path.join(abs_flux_dir,"FluxCalculator.py")
+        assert(os.path.isfile(FluxCalculatorFile))
+        spec = importlib.util.spec_from_file_location("FluxCalculator", FluxCalculatorFile)
+        FluxCalculator = importlib.util.module_from_spec(spec)
+        sys.modules["FluxCalculator"] = FluxCalculator
+        spec.loader.exec_module(FluxCalculator)
+        flux_file = FluxCalculator.MakeFluxFile(tag,abs_flux_dir)
+        del sys.modules["FluxCalculator"] # remove flux directory from the system
+        return flux_file


The function body is over-indented (8 spaces) relative to the def line, which will raise an IndentationError (or create unintended nesting depending on surrounding code). Re-indent the body to a single level (4 spaces) and ensure consistent formatting with the rest of the module.

Suggested change

abs_flux_dir = get_tabulated_flux_model_path(model_name,must_exist=must_exist)

# require existence of FluxCalculator.py

FluxCalculatorFile = os.path.join(abs_flux_dir,"FluxCalculator.py")

assert(os.path.isfile(FluxCalculatorFile))

spec = importlib.util.spec_from_file_location("FluxCalculator", FluxCalculatorFile)

FluxCalculator = importlib.util.module_from_spec(spec)

sys.modules["FluxCalculator"] = FluxCalculator

spec.loader.exec_module(FluxCalculator)

flux_file = FluxCalculator.MakeFluxFile(tag,abs_flux_dir)

del sys.modules["FluxCalculator"] # remove flux directory from the system

return flux_file

abs_flux_dir = get_tabulated_flux_model_path(model_name,must_exist=must_exist)

# require existence of FluxCalculator.py

FluxCalculatorFile = os.path.join(abs_flux_dir,"FluxCalculator.py")

assert(os.path.isfile(FluxCalculatorFile))

spec = importlib.util.spec_from_file_location("FluxCalculator", FluxCalculatorFile)

FluxCalculator = importlib.util.module_from_spec(spec)

sys.modules["FluxCalculator"] = FluxCalculator

spec.loader.exec_module(FluxCalculator)

flux_file = FluxCalculator.MakeFluxFile(tag,abs_flux_dir)

del sys.modules["FluxCalculator"] # remove flux directory from the system

return flux_file

Copilot · 2026-04-28T04:38:39Z

+def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=25):
+
+
+    # Energy in GeV
+    m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)
+
+    extended_m_n = np.arange(m_n_min, m_n_max + m_n_step, m_n_step)


np.arange(m_n_min, m_n_max + m_n_step, m_n_step) with the default m_n_step=25 and m_n_max=0.4 produces an array with (effectively) a single point, so bar_scale(...) becomes nearly constant and the scaling will be wrong. Use a step size consistent with the ratio.dat domain resolution (or rename the parameter to reflect it), e.g., a small float step, or derive the extended grid from the input m_n spacing.

Suggested change

def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=25):

# Energy in GeV

m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)

extended_m_n = np.arange(m_n_min, m_n_max + m_n_step, m_n_step)

def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=None):

# Energy in GeV

m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)

if m_n_step is None:

m_n_diffs = np.diff(m_n)

positive_diffs = m_n_diffs[m_n_diffs > 0]

if positive_diffs.size > 0:

m_n_step = positive_diffs.min()

else:

m_n_step = max(m_n_max - m_n_min, np.finfo(float).eps)

else:

m_n_step = float(m_n_step)

if m_n_step <= 0:

raise ValueError("m_n_step must be positive")

extended_m_n = np.arange(m_n_min, m_n_max + m_n_step * 0.5, m_n_step)

Copilot · 2026-04-28T04:38:39Z

+def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=25):
+
+
+    # Energy in GeV
+    m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)


np.arange(m_n_min, m_n_max + m_n_step, m_n_step) with the default m_n_step=25 and m_n_max=0.4 produces an array with (effectively) a single point, so bar_scale(...) becomes nearly constant and the scaling will be wrong. Use a step size consistent with the ratio.dat domain resolution (or rename the parameter to reflect it), e.g., a small float step, or derive the extended grid from the input m_n spacing.

Suggested change

def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=25):

# Energy in GeV

m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)

def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=None):

# Energy in GeV

m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)

if m_n.size < 2:

raise ValueError("ratio.dat must contain at least two mass points to build bar scaling")

if m_n_step is None:

m_n_diffs = np.diff(m_n)

positive_diffs = m_n_diffs[m_n_diffs > 0]

if positive_diffs.size == 0:

raise ValueError("ratio.dat must contain increasing mass values to derive m_n_step")

m_n_step = np.min(positive_diffs)

Copilot · 2026-04-28T04:38:39Z

+        print(f'Enhance tag "{tag}" is invalid')
+        exit(0)
+
+    if particle not in ["numu", "numubar"]:
+        print("%s particle specified in tag %s is not valid"%(particle))
+        exit(0)


Calling exit(0) inside a library-style helper can terminate the entire host process (including downstream tools/tests) and makes failures hard to handle. Prefer raising a typed exception (e.g., ValueError) with a clear message so callers (like python/_util.py) can catch and report it.

Suggested change

print(f'Enhance tag "{tag}" is invalid')

exit(0)

if particle not in ["numu", "numubar"]:

print("%s particle specified in tag %s is not valid"%(particle))

exit(0)

raise ValueError(f'Enhance tag "{tag}" is invalid')

if particle not in ["numu", "numubar"]:

raise ValueError('%s particle specified in tag %s is not valid' % (particle, tag))

Copilot · 2026-04-28T04:38:40Z



+def get_tabulated_flux_model_path(model_name, must_exist=True):
+    return _get_model_path(model_name,prefix="Fluxes", is_file=False, must_exist=must_exist)


The resources path shown in this PR is resources/fluxes/... (lowercase), but this helper uses prefix=\"Fluxes\". On case-sensitive filesystems this can prevent locating flux models. Align the prefix argument with the actual on-disk directory naming/convention used by _get_base_directory (e.g., \"fluxes\" if it maps directly to resources/fluxes).

Suggested change

return _get_model_path(model_name,prefix="Fluxes", is_file=False, must_exist=must_exist)

return _get_model_path(model_name,prefix="fluxes", is_file=False, must_exist=must_exist)

Copilot · 2026-04-28T04:38:41Z

@@ -0,0 +1,25 @@
+# Material model file
+# Detector: LakeGeneva


The header says Detector: LakeGeneva, but this file sits under resources/detectors/UNDINE/.... This looks like a copy/paste header mismatch and can confuse downstream users auditing detector configs. Update the header detector name to UNDINE (and similarly audit other headers in this PR for correct detector naming).

Suggested change

# Detector: LakeGeneva

# Detector: UNDINE

Copilot · 2026-04-28T04:38:41Z

@@ -0,0 +1,25 @@
+# Material model file
+# Detector: SurfaceGeneva


The header says Detector: SurfaceGeneva, but this file is under resources/detectors/SINE/.... If this is intended to be the SINE detector, update the header to match SINE to avoid ambiguity when these resources are consumed.

Suggested change

# Detector: SurfaceGeneva

# Detector: SINE

Copilot · 2026-04-28T04:38:41Z

+# Detector: UNDINE (UNDerwater Integrated Neutrino Detector)
+# Version: v1
+# Material model file: UNDINE_LHCb_North-v1.dat
+# Date: 2024-10-3


Date formatting is inconsistent (2024-10-3 vs YYYY-MM-DD used elsewhere). For consistency and easier parsing/validation, use zero-padded dates (e.g., 2024-10-03).

Suggested change

# Date: 2024-10-3

# Date: 2024-10-03

Copilot · 2026-04-28T04:38:41Z

+LEAD 3
+1000822080  0.77528090       # Pb208
+1000260560  0.20224719       # Fe56
+1000240520  0.02247191       # Fe56


Line 93's isotope code 1000240520 corresponds to Z=24 (Cr), but the comment says Fe56. Either the isotope code or the comment is wrong; please correct this to avoid incorrect interpretation of the material composition (and to prevent accidental physics mistakes if someone later updates values based on comments).

Suggested change

1000240520 0.02247191 # Fe56

1000240520 0.02247191 # Cr52

Copilot · 2026-04-28T04:38:42Z

-    "    primary_type = numubar if \"bar\" in k else numu\n",
-    "    plt.plot(erange,[primary_xs[k].GetCrossSectionsForTarget(target_type)[0].TotalCrossSection(primary_type,e) for e in erange],label=labels[k])\n",
+    "si_xsfiledir = siren.utilities.get_cross_section_model_path(cross_section_model)\n",
+    "li_xsfiledir = \"/cvmfs/icecube.opensciencegrid.org/data/neutrino-generator/cross_section_data/csms_differential_v1.0/\"\n",


li_xsfiledir is defined but never used (the loop iterates only over [si_xsfiledir]). If the intent is to compare SIREN-packaged vs CVMFS tables, consider including li_xsfiledir in the loop or removing it to avoid dead code in the example notebook.

Suggested change

"li_xsfiledir = \"/cvmfs/icecube.opensciencegrid.org/data/neutrino-generator/cross_section_data/csms_differential_v1.0/\"\n",

austinschneider · 2026-04-28T15:31:36Z

Closing to reopen from the commit author's account so they can be added as a reviewer. Branch unchanged; will be re-linked from the new PR shortly.

Copilot AI review requested due to automatic review settings April 28, 2026 04:28

austinschneider force-pushed the chore/ci-and-packaging branch from d00f148 to f15cfc2 Compare April 28, 2026 04:34

austinschneider force-pushed the feat/detectors-resources branch from da5daf5 to 4112bfa Compare April 28, 2026 04:34

Copilot AI reviewed Apr 28, 2026

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austinschneider force-pushed the feat/detectors-resources branch from 4112bfa to 4a7e297 Compare April 28, 2026 05:09

Copilot started reviewing on behalf of austinschneider April 28, 2026 10:12 View session

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austinschneider force-pushed the feat/detectors-resources branch from 4a7e297 to e68be1a Compare April 28, 2026 13:26

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Add detector geometries: Lake Geneva, KM3NeT-ORCA, ND280, SINE, UNDINE#101

Add detector geometries: Lake Geneva, KM3NeT-ORCA, ND280, SINE, UNDINE#101
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-def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=25):
-    # Energy in GeV
-    m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)
-    extended_m_n = np.arange(m_n_min, m_n_max + m_n_step, m_n_step)
+def bar_scaling(abs_flux_dir, m_n_min=0.002, m_n_max=0.4, m_n_step=None):
+    # Energy in GeV
+    m_n, ratio = np.loadtxt(os.path.join(abs_flux_dir,'ratio.dat'), usecols=(0, 1), unpack=True)
+    if m_n_step is None:
+        m_n_diffs = np.diff(m_n)
+        positive_diffs = m_n_diffs[m_n_diffs > 0]
+        if positive_diffs.size > 0:
+            m_n_step = positive_diffs.min()
+        else:
+            m_n_step = max(m_n_max - m_n_min, np.finfo(float).eps)
+    else:
+        m_n_step = float(m_n_step)
+        if m_n_step <= 0:
+            raise ValueError("m_n_step must be positive")
+    extended_m_n = np.arange(m_n_min, m_n_max + m_n_step * 0.5, m_n_step)



		def get_tabulated_flux_model_path(model_name, must_exist=True):
		return _get_model_path(model_name,prefix="Fluxes", is_file=False, must_exist=must_exist)

		@@ -0,0 +1,25 @@
		# Material model file
		# Detector: SurfaceGeneva

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austinschneider commented Apr 28, 2026

Stack: PR 3 of 14

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