nmma 0.2.1__tar.gz → 0.2.2__tar.gz

{nmma-0.2.1 → nmma-0.2.2}/.github/workflows/continous_integration.yml

@@ -111,7 +111,7 @@ jobs:
         if: matrix.os == 'macos-latest'
         run: |
           conda install -c conda-forge pyfftw c-compiler ligo-segments python-ligo-lw
-          echo "FC=$(which gfortran-11)" >> $GITHUB_ENV
+          echo "FC=$(which gfortran-14)" >> $GITHUB_ENV
           echo "CC=$(which gcc)" >> $GITHUB_ENV
           echo "CXX=$(which g++)" >> $GITHUB_ENV
 
@@ -119,7 +119,8 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt-get install -y texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super
+          sudo apt-get install -y texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super python3-mpi4py
+          
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade git+https://github.com/bitranox/wrapt_timeout_decorator.git

{nmma-0.2.1 → nmma-0.2.2}/.github/workflows/dependency-installation.yml

@@ -48,7 +48,7 @@ jobs:
 
       - name: Install NMMA (base)
         run: |
-          python -m pip install 'nmma @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install nmma
 
       - name: Verify base NMMA installation
         run: |
@@ -56,30 +56,30 @@ jobs:
 
       - name: Install and verify NMMA [grb]
         run: |
-          python -m pip install 'nmma[grb] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install 'nmma[grb]'
           python -c "import nmma, afterglowpy; print(f'Successfully imported {nmma.__name__}, {afterglowpy.__name__}')"
 
       - name: Install and verify NMMA [production]
         run: |
-          python -m pip install 'nmma[production] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install 'nmma[production]'
           python -c "import nmma, parallel_bilby, nestcheck, mpi4py; print(f'Successfully imported {nmma.__name__}, {parallel_bilby.__name__}, {nestcheck.__name__}, {mpi4py.__name__}')"
 
       - name: Install and verify NMMA [neuralnet]
         run: |
-          python -m pip install 'nmma[neuralnet] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install 'nmma[neuralnet]'
           python -c "import nmma, torch, nflows, torchvision; print(f'Successfully imported {nmma.__name__}, {torch.__name__}, {nflows.__name__}, {torchvision.__name__}')"
 
       - name: Install and verify NMMA [tf]
         run: |
-          python -m pip install 'nmma[tf] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install 'nmma[tf]'
           python -c "import nmma, tensorflow; print(f'Successfully imported {nmma.__name__}, {tensorflow.__name__}')"
 
       - name: Install and verify NMMA [sklearn]
         run: |
-          python -m pip install 'nmma[sklearn] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install 'nmma[sklearn]'
           python -c "import nmma, sklearn; print(f'Successfully imported {nmma.__name__}, {sklearn.__name__}')"
 
       - name: Install and verify NMMA [sampler]
         run: |
-          python -m pip install 'nmma[sampler] @ git+https://github.com/sahiljhawar/nmma.git@dependencies'
+          python -m pip install 'nmma[sampler]'
           python -c "import nmma, ultranest; print(f'Successfully imported {nmma.__name__}, {ultranest.__name__}')"

{nmma-0.2.1/nmma.egg-info → nmma-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmma
-Version: 0.2.1
+Version: 0.2.2
 Summary: A nuclear physics multi-messenger Bayesian inference library
 Author-email: "Peter Tsun Ho Pang, Michael Coughlin, Tim Dietrich, Ingo Tews" <nuclear_multimessenger_astronomy@googlegroups.com>
 License: GPLv3
@@ -35,7 +35,7 @@ Requires-Dist: numpy>=1.9
 Requires-Dist: matplotlib<3.8,>=2.0
 Requires-Dist: scipy>=1.10
 Requires-Dist: pandas<2.0,>=1.3.4
-Requires-Dist: astropy>=4.3.1
+Requires-Dist: astropy>=5.3.4
 Requires-Dist: pymultinest
 Requires-Dist: sncosmo
 Requires-Dist: dust_extinction
@@ -133,6 +133,18 @@ When utilizing this code for a publication, kindly make a reference to the packa
       url={https://doi.org/10.1038/s41467-023-43932-6}
 }
 ```
+If you are using the systematics error, please also cite the paper [A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties](https://arxiv.org/abs/2410.21978). The BibTeX entry for the paper is:
+```bibtex
+@article{Jhawar:2024ezm,
+    author = "Jhawar, Sahil and Wouters, Thibeau and Pang, Peter T. H. and Bulla, Mattia and Coughlin, Michael W. and Dietrich, Tim",
+    title = "{A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties}",
+    eprint = "2410.21978",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    month = "10",
+    year = "2024"
+}
+```
 
 ### Acknowledgments
 If you benefited from participating in our community, we ask that you please acknowledge the Nuclear Multi-Messenger Astronomy collaboration, and particular individuals who helped you, in any publications.

{nmma-0.2.1 → nmma-0.2.2}/README.md

@@ -54,6 +54,18 @@ When utilizing this code for a publication, kindly make a reference to the packa
       url={https://doi.org/10.1038/s41467-023-43932-6}
 }
 ```
+If you are using the systematics error, please also cite the paper [A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties](https://arxiv.org/abs/2410.21978). The BibTeX entry for the paper is:
+```bibtex
+@article{Jhawar:2024ezm,
+    author = "Jhawar, Sahil and Wouters, Thibeau and Pang, Peter T. H. and Bulla, Mattia and Coughlin, Michael W. and Dietrich, Tim",
+    title = "{A data-driven approach for modeling the temporal and spectral evolution of kilonova systematic uncertainties}",
+    eprint = "2410.21978",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    month = "10",
+    year = "2024"
+}
+```
 
 ### Acknowledgments
 If you benefited from participating in our community, we ask that you please acknowledge the Nuclear Multi-Messenger Astronomy collaboration, and particular individuals who helped you, in any publications.

{nmma-0.2.1 → nmma-0.2.2}/doc/index.rst

@@ -485,6 +485,7 @@ User Guide
    models
    training
    data_inj_obs
+   systematics
    fitting
    lfi_analysis
    gw_inference

nmma-0.2.2/doc/systematics.rst

@@ -0,0 +1,87 @@
+
+Systematics Uncertainties
+=========================
+
+NMMA currently uses ``--error-budget`` to specify the constant systematic uncertainties to be added to the likelihood quadrature.
+
+However, it is now possible to use systematic error (:math:`\sigma_{sys}`) prior  in form of a freely sampled parameter, time dependent and/or filter dependent systematic error. This can done by specifying the file path using the ``--systematics-file`` in ``lightcurve-analysis`` command.
+
+For more information on systematics error, please refer to the `paper <https://arxiv.org/abs/2410.21978>`__.
+
+The following are the examples of the systematics file:
+
+Example 1: Freely sampled (time independent) systematic error
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this case the systematic error is freely sampled and is not dependent on time or filter.
+
+.. code:: yaml
+
+  config:
+    withTime:
+      value: false
+      filters:
+        - null
+      time_nodes: 4
+      type: Uniform
+      minimum: 0
+      maximum: 2
+    withoutTime:
+      value: true
+      type: Uniform
+      minimum: 0
+      maximum: 2
+
+Example 2: Time dependent systematic error
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this configuration, a single systematic error is applied across all filters.
+
+.. code:: yaml
+
+    config:
+      withTime:
+        value: true
+        filters:
+          - null
+        time_nodes: 4
+        type: Uniform
+        minimum: 0
+        maximum: 2
+      withoutTime:
+        value: false
+        type: Uniform
+        minimum: 0
+        maximum: 2
+
+
+Example 3: Time and filter dependent systematic error
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this configuration, the ``sdssu`` and ``ztfr`` filters are sampled together for systematic errors, while the ``2massks`` filter is sampled independently. All other filters are grouped and sampled together
+
+.. code:: yaml
+
+    config:
+      withTime:
+        value: true
+        filters:
+          - [sdssu, ztfr]
+          - [2massks]
+          - null
+        time_nodes: 4
+        type: Uniform
+        minimum: 0
+        maximum: 2
+      withoutTime:
+        value: false
+        type: Uniform
+        minimum: 0
+        maximum: 2
+  
+
+Distribution types
+==================
+
+Distribution can be of any of the ``analytical`` prior from `bilby <https://git.ligo.org/lscsoft/bilby>`__.
+Please refer to bilby documentation for more information on the available distribution type and their usage. Only positional arguments are required for any of the distrbutions.

nmma-0.2.2/example_files/multi_config_analysis/config.yaml

@@ -0,0 +1,75 @@
+Me2017_1:
+  model: Me2017
+  outdir: outdir_1
+  label: injection
+  prior: ../../priors/Me2017.prior
+  tmin: 0.1
+  tmax: 20
+  dt: 0.5
+  error-budget: 1
+  nlive: 40
+  Ebv-max: 0
+  injection: ./injection.json
+  injection-num: 0
+  injection-outfile: outdir_1/lc.csv
+  generation-seed: 42
+  filters: ztfg,ztfr,ztfi
+  remove-nondetections: True
+  #process-per-config: 4
+
+Me2017_2:
+  model: Me2017
+  outdir: outdir_2
+  label: injection
+  prior: ../../priors/Me2017.prior
+  tmin: 0.1
+  tmax: 20
+  dt: 0.5
+  error-budget: 1
+  nlive: 40
+  Ebv-max: 0
+  injection: ./injection.json
+  injection-num: 0
+  injection-outfile: outdir_2/lc.csv
+  generation-seed: 42
+  filters: ztfg,ztfr,ztfi
+  remove-nondetections: True
+  #process-per-config: 5
+
+Me2017_3:
+  model: Me2017
+  outdir: outdir_3
+  label: injection
+  prior: ../../priors/Me2017.prior
+  tmin: 0.1
+  tmax: 20
+  dt: 0.5
+  error-budget: 1
+  nlive: 40
+  Ebv-max: 0
+  injection: ./injection.json
+  injection-num: 0
+  injection-outfile: outdir_3/lc.csv
+  generation-seed: 42
+  filters: ztfg,ztfr,ztfi
+  remove-nondetections: True
+  #process-per-config: 6
+
+Me2017_4:
+  model: Me2017
+  outdir: outdir_4
+  label: injection
+  prior: ../../priors/Me2017.prior
+  tmin: 0.1
+  tmax: 20
+  dt: 0.5
+  error-budget: 1
+  nlive: 40
+  Ebv-max: 0
+  injection: ./injection.json
+  injection-num: 0
+  injection-outfile: outdir_4/lc.csv
+  generation-seed: 42
+  filters: ztfg,ztfr,ztfi
+  remove-nondetections: True
+  #process-per-config: 7

nmma-0.2.2/example_files/multi_config_analysis/injection.json

@@ -0,0 +1,31 @@
+{
+    "injections": {
+        "__dataframe__": true,
+        "content": {
+            "simulation_id": [
+                0
+            ],
+            "luminosity_distance": [
+                152.52372678074587
+            ],
+            "beta": [
+                3.1674793717549354
+            ],
+            "log10_kappa_r": [
+                1.9033736926068743
+            ],
+            "timeshift": [
+                -1.640734750742769
+            ],
+            "log10_vej": [
+                -1.0471069387482033
+            ],
+            "log10_mej": [
+                -2.9158814967880233
+            ],
+            "geocent_time": [
+                0.09662692256248354
+            ]
+        }
+    }
+}

nmma-0.2.2/nmma/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.2.2"

{nmma-0.2.1 → nmma-0.2.2}/nmma/em/analysis.py

@@ -24,26 +24,6 @@ from .prior import create_prior_from_args
 from .utils import getFilteredMag, dataProcess
 from .io import loadEvent
 
-# import functions
-from ..mlmodel.dataprocessing import gen_prepend_filler, gen_append_filler, pad_the_data
-from ..mlmodel.resnet import ResNet
-from ..mlmodel.embedding import SimilarityEmbedding
-from ..mlmodel.normalizingflows import normflow_params
-from ..mlmodel.inference import cast_as_bilby_result
-
-# need to add these packages:
-import torch
-import torch.nn as nn
-from torch.utils.data import Dataset, DataLoader, TensorDataset, random_split
-import torch.nn.functional as F
-from nflows.nn.nets.resnet import ResidualNet
-from nflows import transforms, distributions, flows
-from nflows.distributions import StandardNormal
-from nflows.flows import Flow
-from nflows.transforms.autoregressive import MaskedAffineAutoregressiveTransform
-from nflows.transforms import CompositeTransform, RandomPermutation
-import nflows.utils as torchutils
-
 matplotlib.use("agg")
 
 
@@ -440,6 +420,12 @@ def get_parser(**kwargs):
         action="store_true",
         default=False,
     )
+    parser.add_argument(
+        "--systematics-file",
+        metavar="PATH",
+        help="Path to systematics configuration file",
+        default=None,
+    )
 
     return parser
 
@@ -791,6 +777,7 @@ def analysis(args):
         error_budget=error_budget,
         verbose=args.verbose,
         detection_limit=args.detection_limit,
+        systematics_file=args.systematics_file
     )
 
     likelihood = OpticalLightCurve(**likelihood_kwargs)
@@ -1175,6 +1162,26 @@ def analysis(args):
 
 def nnanalysis(args):
 
+    # import functions
+    from ..mlmodel.dataprocessing import gen_prepend_filler, gen_append_filler, pad_the_data
+    from ..mlmodel.resnet import ResNet
+    from ..mlmodel.embedding import SimilarityEmbedding
+    from ..mlmodel.normalizingflows import normflow_params
+    from ..mlmodel.inference import cast_as_bilby_result
+
+    # need to add these packages:
+    import torch
+    import torch.nn as nn
+    from torch.utils.data import Dataset, DataLoader, TensorDataset, random_split
+    import torch.nn.functional as F
+    from nflows.nn.nets.resnet import ResidualNet
+    from nflows import transforms, distributions, flows
+    from nflows.distributions import StandardNormal
+    from nflows.flows import Flow
+    from nflows.transforms.autoregressive import MaskedAffineAutoregressiveTransform
+    from nflows.transforms import CompositeTransform, RandomPermutation
+    import nflows.utils as torchutils
+
     # only continue if the Kasen model is selected
     if args.model != "Ka2017":
         print(

{nmma-0.2.1 → nmma-0.2.2}/nmma/em/analysis_lbol.py

@@ -222,6 +222,13 @@ def get_parser(**kwargs):
         action="store_true",
         default=False,
     )
+    parser.add_argument( #no use in this script
+        "--systematics-file",
+        metavar="PATH",
+        help="Path to systematics configuration file",
+        default=None,
+    )
+
     return parser
 
 

{nmma-0.2.1 → nmma-0.2.2}/nmma/em/likelihood.py

@@ -4,10 +4,12 @@ import numpy as np
 import scipy.stats
 from scipy.interpolate import interp1d
 from scipy.stats import truncnorm
+from pathlib import Path
+import yaml
 
-from bilby.core.likelihood import Likelihood
-from . import utils
 
+from bilby.core.likelihood import Likelihood
+from . import utils, systematics
 
 def truncated_gaussian(m_det, m_err, m_est, lim):
 
@@ -55,6 +57,7 @@ class OpticalLightCurve(Likelihood):
         filters,
         light_curve_data,
         trigger_time,
+        systematics_file,
         detection_limit=None,
         error_budget=1.0,
         tmin=0.0,
@@ -81,6 +84,7 @@ class OpticalLightCurve(Likelihood):
             light_curve_data, self.filters, self.trigger_time, self.tmin, self.tmax
         )
         self.light_curve_data = processedData
+        self.systematics_file = systematics_file
 
         self.detection_limit = {}
         if detection_limit:
@@ -144,6 +148,40 @@ class OpticalLightCurve(Likelihood):
                     bounds_error=False,
                 )
 
+        if self.systematics_file is not None:
+            yaml_dict = yaml.safe_load(Path(self.systematics_file).read_text())
+            systematics.validate_only_one_true(yaml_dict)
+
+            if yaml_dict["config"]["withTime"]["value"]:
+                n = yaml_dict["config"]["withTime"]["time_nodes"]
+                time_array = np.round(np.linspace(self.tmin, self.tmax, n), 2)
+                yaml_filters = yaml_dict["config"]["withTime"]["filters"]
+                systematics.validate_filters(yaml_filters)
+
+                for filter_group in yaml_filters:
+                    if isinstance(filter_group, list):
+                        filt = "___".join(filter_group)
+                    elif filter_group is None:
+                        filt = "all"
+                    else:
+                        filt = filter_group
+
+                    globals()[f"sys_err_{filt}_array"] = np.array([])
+
+                    for i in range(1, n + 1):
+                        value = self.parameters.get(f"sys_err_{filt}{i}")
+                        globals()[f"sys_err_{filt}_array"] = np.append(globals()[f"sys_err_{filt}_array"], value)
+
+                for filter_group in yaml_dict["config"]["withTime"]["filters"]:
+                    if isinstance(filter_group, list):
+                        filt = "___".join(filter_group)
+                    elif filter_group is None:
+                        filt = "all"
+                    else:
+                        filt = filter_group
+                    globals()[f"sys_err_{filt}_interped"] = interp1d(time_array, globals()[f"sys_err_{filt}_array"], fill_value="extrapolate", bounds_error=False)
+        
+
         # compare the estimated light curve and the measured data
         minus_chisquare_total = 0.0
         gaussprob_total = 0.0
@@ -153,9 +191,31 @@ class OpticalLightCurve(Likelihood):
             data_mag = self.light_curve_data[filt][:, 1]
             data_sigma = self.light_curve_data[filt][:, 2]
 
+            if self.systematics_file is not None:
+                if yaml_dict["config"]["withTime"]["value"]:
+                    yaml_filters = yaml_dict["config"]["withTime"]["filters"]
+
+                    filter_group_finite_idx_match = False
+
+                    if yaml_filters is not None and yaml_filters != []:
+                        for yaml_filt in yaml_filters:
+                            if yaml_filt is not None and filt in yaml_filt:
+                                if len(yaml_filt) == 1:
+                                    filters_to_use = yaml_filt[0]
+                                else:
+                                    filters_to_use = "___".join(yaml_filt)
+                                filter_group_finite_idx_match = True
+                                break
+                    if not filter_group_finite_idx_match:
+                        filters_to_use = "all"
+                    data_sigma = np.sqrt(data_sigma**2 + (globals()[f"sys_err_{filters_to_use}_interped"](data_time)) ** 2)
+                    
+                elif yaml_dict["config"]["withoutTime"]["value"]:
+                    data_sigma = np.sqrt(data_sigma**2 + self.parameters["sys_err"] ** 2)
+
             # include the error budget into calculation
-            if 'em_syserr' in self.parameters:
-                data_sigma = np.sqrt(data_sigma**2 + self.parameters['em_syserr']**2)
+            elif 'sys_err' in self.parameters:
+                data_sigma = np.sqrt(data_sigma**2 + self.parameters['sys_err']**2)
             else:
                 data_sigma = np.sqrt(data_sigma**2 + self.error_budget[filt]**2)
 
@@ -186,15 +246,36 @@ class OpticalLightCurve(Likelihood):
 
             # evaluate the data with infinite error
             if len(infIdx) > 0:
-                if 'em_syserr' in self.parameters:
-                    upperlim_sigma = self.parameters['em_syserr']
-                    gausslogsf = scipy.stats.norm.logsf(
-                        data_mag[infIdx], mag_est[infIdx], upperlim_sigma
-                    )
+                if self.systematics_file is not None:
+                    if yaml_dict["config"]["withTime"]["value"]:
+                        yaml_filters = yaml_dict["config"]["withTime"]["filters"]
+
+                        filter_group_infinite_idx_match = False
+
+                        if yaml_filters is not None and yaml_filters != []:
+                            for yaml_filt in yaml_filters:
+                                if yaml_filt is not None and filt in yaml_filt:
+                                    if len(yaml_filt) == 1:
+                                        upperlim_sigma = globals()[f"sys_err_{yaml_filt}_interped"](data_time)[infIdx]
+                                    else:
+                                        filters_to_use = "___".join(yaml_filt)
+                                        upperlim_sigma = globals()[f"sys_err_{filters_to_use}_interped"](data_time)[infIdx]
+                                    filter_group_infinite_idx_match = True
+                                    break
+                        if not filter_group_infinite_idx_match:
+                            filters_to_use = "all"
+                            upperlim_sigma = globals()[f"sys_err_{filters_to_use}_interped"](data_time)[infIdx]
+
+                        gausslogsf = scipy.stats.norm.logsf(data_mag[infIdx], mag_est[infIdx], upperlim_sigma)
+
+                    elif yaml_dict["config"]["withoutTime"]["value"]:
+                        upperlim_sigma = self.parameters["sys_err"]
+                        gausslogsf = scipy.stats.norm.logsf(data_mag[infIdx], mag_est[infIdx], upperlim_sigma)
+                elif 'sys_err' in self.parameters:
+                    upperlim_sigma = self.parameters['sys_err']
+                    gausslogsf = scipy.stats.norm.logsf(data_mag[infIdx], mag_est[infIdx], upperlim_sigma)
                 else:
-                    gausslogsf = scipy.stats.norm.logsf(
-                        data_mag[infIdx], mag_est[infIdx], self.error_budget[filt]
-                    )
+                    gausslogsf = scipy.stats.norm.logsf(data_mag[infIdx], mag_est[infIdx], self.error_budget[filt])
                 gaussprob_total += np.sum(gausslogsf)
 
         log_prob = minus_chisquare_total + gaussprob_total

{nmma-0.2.1 → nmma-0.2.2}/nmma/em/model.py

@@ -509,6 +509,11 @@ class GRBLightCurveModel(LightCurveMixin):
         grb_param_dict["epsilon_B"] = 10 ** new_parameters["log10_epsilon_B"]
         grb_param_dict["z"] = z
 
+        # make sure L0, q and ts are also passed
+        for param in ['L0', 'q', 'ts']:
+            if param in new_parameters:
+                grb_param_dict[param] = new_parameters[param]
+
         if "thetaWing" in new_parameters:
             grb_param_dict["thetaWing"] = new_parameters["thetaWing"]
             if new_parameters["thetaWing"] / new_parameters["thetaCore"] > self.resolution: