pz-rail-astro-tools 1.0.3__tar.gz → 1.0.4__tar.gz

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 1.0.3
+Version: 1.0.4
 Author-email: "LSST Dark Energy Science Collaboration (DESC)" <lsst-desc-rail-admin@slac.stanford.edu>
 License: MIT License
         

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/pz_rail_astro_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 1.0.3
+Version: 1.0.4
 Author-email: "LSST Dark Energy Science Collaboration (DESC)" <lsst-desc-rail-admin@slac.stanford.edu>
 License: MIT License
         

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/pz_rail_astro_tools.egg-info/SOURCES.txt

@@ -23,7 +23,6 @@ src/pz_rail_astro_tools.egg-info/top_level.txt
 src/rail/astro_tools/__init__.py
 src/rail/astro_tools/_version.py
 src/rail/creation/degraders/grid_selection.py
-src/rail/creation/degraders/lsst_error_model.py
 src/rail/creation/degraders/observing_condition_degrader.py
 src/rail/creation/degraders/photometric_errors.py
 src/rail/creation/degraders/spectroscopic_degraders.py
@@ -36,9 +35,12 @@ src/rail/examples_data/creation_data/data/survey_conditions/DC2-mask-neg-nside-1
 src/rail/examples_data/creation_data/data/survey_conditions/minion_1016_dc2_Median_airmass_i_and_nightlt1825_HEAL.fits
 src/rail/examples_data/creation_data/data/survey_conditions/minion_1016_dc2_Median_fiveSigmaDepth_i_and_nightlt1825_HEAL.fits
 src/rail/examples_data/testdata/rubin_dm_dc2_example2.pq
+src/rail/pipelines/utility/apply_phot_errors.py
+src/rail/pipelines/utility/spectroscopic_selection_pipeline.py
 src/rail/tools/photometry_tools.py
 tests/astro_tools/test_core.py
 tests/astro_tools/test_degraders.py
 tests/astro_tools/test_gcr_engine.py
+tests/astro_tools/test_pipline.py
 tests/astro_tools/gcr_test_data/schema.yaml
 tests/astro_tools/gcr_test_data/test_object_tract_4850.hdf5

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/rail/astro_tools/__init__.py

@@ -4,5 +4,4 @@ from rail.creation.degraders.grid_selection import *
 from rail.creation.degraders.observing_condition_degrader import *
 from rail.creation.degraders.spectroscopic_degraders import *
 from rail.creation.degraders.spectroscopic_selections import *
-from rail.creation.degraders.lsst_error_model import *
 from rail.tools.photometry_tools import *

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/rail/astro_tools/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.0.3'
-__version_tuple__ = version_tuple = (1, 0, 3)
+__version__ = version = '1.0.4'
+__version_tuple__ = version_tuple = (1, 0, 4)

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/rail/creation/degraders/photometric_errors.py

@@ -4,6 +4,7 @@ error models defined in the package photerr
 
 Author: John Franklin Crenshaw, Tianqing Zhang
 """
+import numpy as np
 from dataclasses import MISSING
 
 from ceci.config import StageParameter as Param
@@ -71,7 +72,11 @@ class PhotoErrorModel(Noisifier):
         data = self.get_data("input")
 
         # Add photometric errors
-        obsData = self.noiseModel(data, random_state=self.config.seed)
+        if self.config.seed is not None:  # pragma: no cover
+            seed = int(self.config.seed)
+        else:
+            seed = np.random.Generator(np.random.PCG64())
+        obsData = self.noiseModel(data, random_state=seed)
         
         # Return the new catalog
         self.add_data("output", obsData)

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/rail/creation/degraders/spectroscopic_selections.py

@@ -36,7 +36,7 @@ class SpecSelection(Selector):
         Random seed for reproducibility
     """
 
-    name = "specselection"
+    name = "SpecSelection"
     config_options = Selector.config_options.copy()
     config_options.update(
         N_tot=Param(int, 10000, msg="Number of selected sources"),
@@ -121,9 +121,9 @@ class SpecSelection(Selector):
             if band not in self.config.colnames.keys():
                 continue
             colname = self.config.colnames[band]
-            self.mask &= (np.abs(data[colname]) < nondetect_val) & (
-                ~np.isnan(data[colname])
-            )
+            self.mask &= data[colname] != nondetect_val
+            self.mask &= ~np.isnan(data[colname])
+            self.mask &= np.isfinite(data[colname])
 
     def downsampling_N_tot(self):
         """Randomly sample down the objects to a given number of data objects.
@@ -180,7 +180,7 @@ class SpecSelection_GAMA(SpecSelection):
     The necessary column is r band.
     """
     
-    name = "specselection_gama"
+    name = "SpecSelection_GAMA"
 
     def selection(self, data):
         """GAMA selection function. """
@@ -208,7 +208,7 @@ class SpecSelection_BOSS(SpecSelection):
     For BOSS selection, the data should at least include gri bands.
     """
 
-    name = "specselection_boss"
+    name = "SpecSelection_BOSS"
 
     def selection(self, data):
         """The BOSS selection function."""
@@ -268,7 +268,7 @@ class SpecSelection_DEEP2(SpecSelection):
     conversion degrader is ready, this subclass will be updated accordingly.
     """
 
-    name = "specselection_deep2"
+    name = "SpecSelection_DEEP2"
 
     def photometryCut(self, data):
         """Applies DEEP2 photometric cut based on Newman+13.
@@ -355,7 +355,7 @@ class SpecSelection_VVDSf02(SpecSelection):
     Necessary columns are i band magnitude and redshift.
     """
 
-    name = "specselection_VVDSf02"
+    name = "SpecSelection_VVDSf02"
 
     def photometryCut(self, data):
         """Photometric cut of VVDS 2h-field based on LeFèvre+05.
@@ -466,7 +466,7 @@ class SpecSelection_zCOSMOS(SpecSelection):
     For zCOSMOS, the data should at least include i band and redshift.
     """
 
-    name = "specselection_zCOSMOS"
+    name = "SpecSelection_zCOSMOS"
 
     def photometryCut(self, data):
         """Photometry cut for zCOSMOS based on Lilly+09.
@@ -527,7 +527,7 @@ class SpecSelection_HSC(SpecSelection):
     For HSC, the data should at least include giz bands and redshift.
     """
 
-    name = "specselection_HSC"
+    name = "SpecSelection_HSC"
 
     def photometryCut(self, data):
         """HSC galaxies were binned in color magnitude space with i-band mag
@@ -604,4 +604,4 @@ class SpecSelection_HSC(SpecSelection):
         # start message
         printMsg = "Applying the HSC selection."
 
-        return printMsg
+        return printMsg

pz_rail_astro_tools-1.0.4/src/rail/pipelines/utility/apply_phot_errors.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# Prerquisites, os, and numpy
+import os
+import numpy as np
+
+# Various rail modules
+from rail.tools.photometry_tools import Dereddener, Reddener
+
+from rail.core.stage import RailStage, RailPipeline
+
+import ceci
+
+from rail.core.utils import RAILDIR
+
+if 'PZ_DUSTMAP_DIR' not in os.environ:
+    os.environ['PZ_DUSTMAP_DIR'] = '.'
+
+dustmap_dir = os.path.expandvars("${PZ_DUSTMAP_DIR}")
+
+
+ERROR_MODELS = dict(
+    lsst = dict(
+        ErrorModel='LSSTErrorModel',
+        Module='rail.creation.degraders.photometric_errors',
+    ),
+    roman = dict(
+        ErrorModel='RomanErrorModel',
+        Module='rail.creation.degraders.photometric_errors',
+    ),
+    #euclid = dict(
+    #    ErrorModel='EuclidErrorModel',
+    #    Module='rail.creation.degraders.photometric_errors',
+    #),
+)
+
+
+
+class ApplyPhotErrorsPipeline(RailPipeline):
+
+    default_input_dict = dict(input='dummy.in')
+
+    def __init__(self, error_models=None):
+        RailPipeline.__init__(self)
+
+        DS = RailStage.data_store
+        DS.__class__.allow_overwrite = True
+
+        if error_models is None:
+            error_models = ERROR_MODELS
+
+        self.reddener = Reddener.build(
+            dustmap_dir=dustmap_dir,
+        )
+
+        previous_stage = self.reddener
+        for key, val in error_models.items():
+            error_model_class = ceci.PipelineStage.get_stage(val['ErrorModel'], val['Module'])
+            the_error_model = error_model_class.make_and_connect(
+                name=f'error_model_{key}',
+                connections=dict(input=previous_stage.io.output),
+                hdf5_groupname='',
+            )
+            self.add_stage(the_error_model)
+            previous_stage = the_error_model
+
+        self.dereddener_errors = Dereddener.build(
+            dustmap_dir=dustmap_dir,
+            connections=dict(input=previous_stage.io.output),
+        )

pz_rail_astro_tools-1.0.4/src/rail/pipelines/utility/spectroscopic_selection_pipeline.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# Prerquisites, os, and numpy
+import os
+import numpy as np
+
+# Various rail modules
+
+from rail.core.stage import RailStage, RailPipeline
+
+import ceci
+
+from rail.utils.catalog_utils import CatalogConfigBase
+from rail.core.utils import RAILDIR
+
+SELECTORS = dict(
+    GAMA = dict(
+        Selector='SpecSelection_GAMA',
+        Module='rail.creation.degraders.spectroscopic_selections',
+    ),
+    BOSS = dict(
+        Selector='SpecSelection_BOSS',
+        Module='rail.creation.degraders.spectroscopic_selections',
+    ),
+    VVDSf02 = dict(
+        Selector='SpecSelection_VVDSf02',
+        Module='rail.creation.degraders.spectroscopic_selections',
+    ),
+    zCOSMOS = dict(
+        Selector='SpecSelection_zCOSMOS',
+        Module='rail.creation.degraders.spectroscopic_selections',
+    ),
+    HSC = dict(
+        Selector='SpecSelection_HSC',
+        Module='rail.creation.degraders.spectroscopic_selections',
+    ),
+)
+
+
+CommonConfigParams = dict(
+    N_tot = 100_000,
+    nondetect_val = -np.inf,
+    downsample= False,
+)
+
+
+class SpectroscopicSelectionPipeline(RailPipeline):
+
+    default_input_dict = dict(input='dummy.in')
+    
+    def __init__(self, selectors=None):
+        RailPipeline.__init__(self)
+
+        DS = RailStage.data_store
+        DS.__class__.allow_overwrite = True
+
+        if selectors is None:
+            selectors = SELECTORS.copy()
+
+        config_pars = CommonConfigParams.copy()
+        active_catalog = CatalogConfigBase.active_class()        
+        if active_catalog:
+            colnames = active_catalog.band_name_dict()
+            colnames['redshift'] = active_catalog.redshift_col
+            config_pars['colnames'] = colnames            
+
+        for key, val in selectors.items():
+            the_class = ceci.PipelineStage.get_stage(val['Selector'], val['Module'])
+            the_selector = the_class.make_and_connect(
+                name=f'select_{key}',
+                **config_pars,
+            )
+            
+            self.add_stage(the_selector)

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/src/rail/tools/photometry_tools.py

@@ -453,7 +453,10 @@ class DustMapBase(RailStage):
     def run(self):
         data = self.get_data('input', allow_missing=True)
         out_data = {}
-        coords = SkyCoord(data[self.config.ra_name], data[self.config.dec_name], unit = 'deg',frame='fk5')
+        coords = SkyCoord(
+            np.array(data[self.config.ra_name]),
+            np.array(data[self.config.dec_name]),
+            unit = 'deg',frame='fk5')
         dust_map_dict = dict(sfd=dustmaps_sfd.SFDQuery)
         try:
             dust_map_class = dust_map_dict[self.config.dustmap_name]

{pz_rail_astro_tools-1.0.3 → pz_rail_astro_tools-1.0.4}/tests/astro_tools/test_degraders.py

@@ -13,7 +13,7 @@ from rail.creation.degraders.spectroscopic_degraders import InvRedshiftIncomplet
 from rail.creation.degraders.spectroscopic_selections import *
 from rail.creation.degraders.observing_condition_degrader import ObsCondition
 from rail.creation.degraders.grid_selection import GridSelection
-from rail.creation.degraders.lsst_error_model import LSSTErrorModel
+from rail.creation.degraders.photometric_errors import EuclidErrorModel, LSSTErrorModel
 
 
 @pytest.fixture
@@ -391,3 +391,9 @@ def test_LSSTErrorModel_returns_correct_columns(data):
         assert f"{band}_err" in degraded_data.columns
     os.remove(degrader.get_output(degrader.get_aliased_tag("output"), final_name=True))
 
+
+def test_EucliErrorModel(data):
+    # Setup the stage
+    degrader = EuclidErrorModel.make_stage()
+
+    

pz_rail_astro_tools-1.0.4/tests/astro_tools/test_pipline.py

@@ -0,0 +1,15 @@
+import os
+from rail.utils.testing_utils import build_and_read_pipeline
+
+import pytest
+
+@pytest.mark.parametrize(
+    "pipeline_class",
+    [
+        'rail.pipelines.utility.apply_phot_errors.ApplyPhotErrorsPipeline',
+        'rail.pipelines.utility.spectroscopic_selection_pipeline.SpectroscopicSelectionPipeline',
+    ]
+)
+def test_build_and_read_pipeline(pipeline_class):
+    build_and_read_pipeline(pipeline_class)
+

pz_rail_astro_tools-1.0.3/src/rail/creation/degraders/lsst_error_model.py

@@ -1,61 +0,0 @@
-"""The LSST Model for photometric errors."""
-from dataclasses import MISSING
-
-from ceci.config import StageParameter as Param
-from photerr import LsstErrorModel as PhotErrErrorModel
-from photerr import LsstErrorParams as PhotErrErrorParams
-from rail.creation.degrader import Degrader
-
-
-class LSSTErrorModel(Degrader):
-    """The LSST Model for photometric errors.
-
-    This is a wrapper around the error model from PhotErr. The parameter
-    docstring below is dynamically added by the installed version of PhotErr:
-
-    """
-
-    # Dynamically add the parameter docstring from PhotErr
-    __doc__ += PhotErrErrorParams.__doc__
-
-    name = "LSSTErrorModel"
-    config_options = Degrader.config_options.copy()
-
-    # Dynamically add all parameters from PhotErr
-    _photerr_params = PhotErrErrorParams.__dataclass_fields__
-    for key, val in _photerr_params.items():
-        # Get the default value
-        if val.default is MISSING:
-            default = val.default_factory()
-        else:
-            default = val.default
-
-        # Add this param to config_options
-        config_options[key] = Param(
-            None,  # Let PhotErr handle type checking
-            default,  
-            msg="See the main docstring for details about this parameter.",
-            required=False,
-        )
-
-    def __init__(self, args, **kwargs):
-        """
-        Constructor
-
-        Does standard Degrader initialization and sets up the error model.
-        """
-        super().__init__(args, **kwargs)
-        self.error_model = PhotErrErrorModel(
-            **{key: self.config[key] for key in self._photerr_params}
-        )
-
-    def run(self):
-        """Return pandas DataFrame with photometric errors."""
-        # Load the input catalog
-        data = self.get_data("input")
-
-        # Add photometric errors
-        obsData = self.error_model(data, random_state=self.config.seed)
-
-        # Return the new catalog
-        self.add_data("output", obsData)