Final PMT analysis scripts

README.md

@@ -1,25 +1,18 @@
 # mint-analysis
-Collection of scripts for MINT tests
+A framework to analysis p-one PMT data.
 
+The MINT analysis package processes data recorded by the Andromeda package (e.g., PMT or acoustic data) and applies advanced analysis routines that lie outside Andromeda’s scope.
 
-## Installation
-
-Clone the repo
-
-To install packages I recommend using uv [https://docs.astral.sh/uv/], which
-is a fast modern python package handler that also handles virtual environments.
-
-You'll need to install this first which is shown here [https://docs.astral.sh/uv/getting-started/installation/].
+For PMT data, two analysis frameworks are planned:
+- Pygama – Modern, Python-based, fast-turnaround DSP toolkit for time-series data.
+Status: Implemented.
+- IceTray – The classical IceCube framework and future default for P-ONE data.
+Status: Not yet implemented.
 
-Once you have it installed go to the cloned repo and inside you should see a pyproject.toml file
-this contains all the info on the packages needed.
+Detailed unboarding instructions can be found [on confluence](https://p-one.atlassian.net/wiki/spaces/PONE/pages/1797849089/MINT+Analysis+User+Onboarding).
 
-To install the packages simply run `uv sync`and they should all install.
-
-Then to open a jupyter notebook: `uv run --with jupyter jupyter notebook`. (In fact you don't even need the `uv sync` and can
-simply do the run, uv will handle the rest). This will run a jupyter notebook instance inside the virtual environment.
-
-Some packages may cause issues such as h5py which may need to be installed separately via brew.
+## Installation
 
-All new instances you make are completely independent so can use different package/python versions as
-specified in the pyproject.toml file.
+Clone the repo
+cd into repo
+`pip install .`

analysis.log

@@ -0,0 +1,16 @@
+[2025-12-15 15:05:54,438] [PESpectrum - main] [INFO] collected measurement results
+[2025-12-15 15:05:54,438] [PESpectrum - main] [INFO] collected PMT info
+[2025-12-15 15:05:54,439] [PESpectrum - main] [INFO] collected environment info
+[2025-12-15 15:05:54,439] [PESpectrum - main] [INFO] collected software info
+[2025-12-15 15:05:58,512] [PESpectrum - _connect_tunnel] [INFO] [info] SSH tunnel established: 127.0.0.1:43307 -> 127.0.0.1:27017 via production.pacific-neutrino.org
+[2025-12-15 15:05:58,620] [PESpectrum - _connect_client] [INFO] [info] Connected to MongoDB at 127.0.0.1:43307 with user p-one
+[2025-12-15 15:05:58,753] [PESpectrum - main] [INFO] Build data object
+[2025-12-15 15:05:58,753] [PESpectrum - main] [INFO] The following dict would be uploaded to the DB: {'measurement_type': 'dcr', 'measurement_location': 'MINT', 'devices_used': ['p-1-1-pmt-unit-KM56674_275', 'p-1-1-om-hs-01'], 'result': 26463.90079865678, 'result_unc': 30.15089782382669, 'units': 'Hz', 'pmt_info': {'v10_in_volt': 85.09310150146484, 'di10_in_mA': 2.9245901107788086, 'frac': 0.877996027469635}, 'env_info': {'temperature_in_celsius': 29.11357307688087, 'pressure_in_hpa': 1011.6844068085361, 'humidity_in_percent': 23.183785204174583, 'measurement_duration_in_s': 29.110747814178467}, 'software_info': {'framework': 'mint-xyz', 'pe_reconstruction': 'NNLS', 'sftp_path': '/mint/mint-data/p-1-1-om-hs-01/PMT', 'run_tags': '2025_12_13_03_31_52'}, 'mapping': None}
+[2025-12-15 15:05:58,753] [PESpectrum - main] [INFO] collected measurement results
+[2025-12-15 15:05:58,754] [PESpectrum - main] [INFO] collected PMT info
+[2025-12-15 15:05:58,754] [PESpectrum - main] [INFO] collected environment info
+[2025-12-15 15:05:58,754] [PESpectrum - main] [INFO] collected software info
+[2025-12-15 15:05:59,167] [PESpectrum - _connect_tunnel] [INFO] [info] SSH tunnel established: 127.0.0.1:38145 -> 127.0.0.1:27017 via production.pacific-neutrino.org
+[2025-12-15 15:05:59,242] [PESpectrum - _connect_client] [INFO] [info] Connected to MongoDB at 127.0.0.1:38145 with user p-one
+[2025-12-15 15:05:59,379] [PESpectrum - main] [INFO] Build data object
+[2025-12-15 15:05:59,380] [PESpectrum - main] [INFO] The following dict would be uploaded to the DB: {'measurement_type': 'dcr', 'measurement_location': 'MINT', 'devices_used': ['p-1-1-pmt-unit-KM54356_23', 'p-1-1-om-hs-01'], 'result': 26326.463667634333, 'result_unc': 30.07250335177778, 'units': 'Hz', 'pmt_info': {'v10_in_volt': 87.58090209960938, 'di10_in_mA': 1.8282999992370605, 'frac': 0.8174149990081787}, 'env_info': {'temperature_in_celsius': 29.11357307688087, 'pressure_in_hpa': 1011.6844068085361, 'humidity_in_percent': 23.183785204174583, 'measurement_duration_in_s': 29.110747814178467}, 'software_info': {'framework': 'mint-xyz', 'pe_reconstruction': 'NNLS', 'sftp_path': '/mint/mint-data/p-1-1-om-hs-01/PMT', 'run_tags': '2025_12_13_03_31_52'}, 'mapping': None}

pyproject.toml

@@ -1,10 +1,14 @@
 [build-system]
-requires = [
-    "setuptools>=61.2",
-    "setuptools_scm[toml]>=7"
-]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools_scm]
+write_to = "src/mintanalysis/_version.py"
+# 'node-and-date' or 'node-and-timestamp' appends the short hash
+local_scheme = "node-and-date"
+# 'guess-next-dev' ensures versions like 1.0.1.dev1+gabc123
+version_scheme = "guess-next-dev"
+
 [tool.setuptools]
 include-package-data = true
 zip-safe = false
@@ -20,9 +24,6 @@ py-modules = []
 where = ["src"]
 
 
-[tool.setuptools_scm]
-write_to = "src/mintanalysis/_version.py"
-
 [project.urls]
 Homepage = "https://github.com/pone-software/mint-analysis"
 Issues = "https://github.com/pone-software/mint-analysis/issues"
@@ -58,6 +59,7 @@ dependencies = [
 "iminuit",
 "pymongo",
 "PyYAML",
+"pint",
 "sshtunnel",
 "pygama>=2.0.0",
 "legend-daq2lh5>=1.2.1",
@@ -66,6 +68,7 @@ dependencies = [
 "numba>0.52",
 "pandas",
 "matplotlib",
+"uncertainties",
 "scipy>=1.14",
 "jupyter",
 "ipython",
@@ -74,8 +77,6 @@ dependencies = [
 "dspeed==2.0.2",
 ]
 
-#"dspeed @ file:///${PROJECT_ROOT}/dspeed",
-
 [project.optional-dependencies]
 test = [
   "pytest >=6",
@@ -93,6 +94,8 @@ docs = [
 
 [project.scripts]
 # Format: <cli_command_name> = "<module_path>:<function_name>"
+build_ana = "mintanalysis.pmt.ana.peSpectrumAnalyzer:main"
+upload_ana = "mintanalysis.pmt.ana.uploadToDB:main"
 build_dsp = "mintanalysis.pmt.dsp.build_dsp:build_dsp_cli"
 build_nnls_db = "mintanalysis.pmt.dsp.build_nnls_database:build_nnls_database_cli"
 

src/mintanalysis/pmt/ana/__init__.py

@@ -0,0 +1,8 @@
+"""
+Routines for the final analysis of PMT data
+"""
+
+from . import uploadToDB
+from .peSpectrumAnalyzer import PESpectrumAnalyzer
+
+__all__ = ["PESpectrumAnalyzer", "uploadToDB"]