pz-rail-astro-tools 0.1.2__tar.gz → 0.1.4__tar.gz

{pz-rail-astro-tools-0.1.2 → pz_rail_astro_tools-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 0.1.2
+Version: 0.1.4
 Author-email: "LSST Dark Energy Science Collaboration (DESC)" <lsst-desc-rail-admin@slac.stanford.edu>
 License: MIT License
         
@@ -65,7 +65,7 @@ in [RAIL](https://github.com/LSSTDESC/RAIL).
 
 This code, while public on GitHub, has not yet been released by DESC and is
 still under active development. Our release of v1.0 will be accompanied by a
-journal paper describing the development and validation of RAIL.
+journal paper describing the development and validation of RAIL. 
 
 If you make use of the ideas or software in RAIL, please cite the repository 
 <https://github.com/LSSTDESC/RAIL>. You are welcome to re-use the code, which

{pz-rail-astro-tools-0.1.2 → pz_rail_astro_tools-0.1.4}/README.md

@@ -15,7 +15,7 @@ in [RAIL](https://github.com/LSSTDESC/RAIL).
 
 This code, while public on GitHub, has not yet been released by DESC and is
 still under active development. Our release of v1.0 will be accompanied by a
-journal paper describing the development and validation of RAIL.
+journal paper describing the development and validation of RAIL. 
 
 If you make use of the ideas or software in RAIL, please cite the repository 
 <https://github.com/LSSTDESC/RAIL>. You are welcome to re-use the code, which

{pz-rail-astro-tools-0.1.2 → pz_rail_astro_tools-0.1.4}/src/pz_rail_astro_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 0.1.2
+Version: 0.1.4
 Author-email: "LSST Dark Energy Science Collaboration (DESC)" <lsst-desc-rail-admin@slac.stanford.edu>
 License: MIT License
         
@@ -65,7 +65,7 @@ in [RAIL](https://github.com/LSSTDESC/RAIL).
 
 This code, while public on GitHub, has not yet been released by DESC and is
 still under active development. Our release of v1.0 will be accompanied by a
-journal paper describing the development and validation of RAIL.
+journal paper describing the development and validation of RAIL. 
 
 If you make use of the ideas or software in RAIL, please cite the repository 
 <https://github.com/LSSTDESC/RAIL>. You are welcome to re-use the code, which

{pz-rail-astro-tools-0.1.2 → pz_rail_astro_tools-0.1.4}/src/pz_rail_astro_tools.egg-info/SOURCES.txt

@@ -22,11 +22,12 @@ src/pz_rail_astro_tools.egg-info/requires.txt
 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/degradation/grid_selection.py
-src/rail/creation/degradation/lsst_error_model.py
-src/rail/creation/degradation/observing_condition_degrader.py
-src/rail/creation/degradation/spectroscopic_degraders.py
-src/rail/creation/degradation/spectroscopic_selections.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
+src/rail/creation/degraders/spectroscopic_selections.py
 src/rail/creation/engines/gcr_engine.py
 src/rail/examples_data/creation_data/data/HSC_grid_settings.pkl
 src/rail/examples_data/creation_data/data/hsc_ratios_and_specz.hdf5
@@ -34,7 +35,7 @@ src/rail/examples_data/creation_data/data/survey_conditions/DC2-dr6-galcounts-i2
 src/rail/examples_data/creation_data/data/survey_conditions/DC2-mask-neg-nside-128.fits
 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/tools/util_photometry.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

pz_rail_astro_tools-0.1.4/src/rail/astro_tools/__init__.py

@@ -0,0 +1,8 @@
+from ._version import __version__
+
+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-0.1.2 → pz_rail_astro_tools-0.1.4}/src/rail/astro_tools/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.2'
-__version_tuple__ = version_tuple = (0, 1, 2)
+__version__ = version = '0.1.4'
+__version_tuple__ = version_tuple = (0, 1, 4)

{pz-rail-astro-tools-0.1.2/src/rail/creation/degradation → pz_rail_astro_tools-0.1.4/src/rail/creation/degraders}/grid_selection.py

@@ -1,16 +1,16 @@
-"""Degraders that emulate spectroscopic effects on photometry"""
+"""Selector that emulate spectroscopic effects on photometry"""
 
 import os
 import numpy as np
 import pandas as pd
 import pickle
 import tables_io
-from rail.creation.degrader import Degrader
-from rail.core.utils import find_rail_file
+from rail.creation.selector import Selector
+from rail.utils.path_utils import find_rail_file
 from ceci.config import StageParameter as Param
 
 
-class GridSelection(Degrader):
+class GridSelection(Selector):
     """
     Uses the ratio of HSC spectroscpic galaxies to photometric galaxies to portion a sample
     into training and application samples. Option to implement a color-based redshift cut off in each pixel.
@@ -39,12 +39,14 @@ class GridSelection(Degrader):
     Second HSC Data Release, details of which can be found here:
     Aihara, H., AlSayyad, Y., Ando, M., et al. 2019, PASJ, 71, 114
     doi: 10.1093/pasj/psz103
+    
+    Update(Apr 16 2024): Now inherit from selector and implement the _select() instead of run()
     """
     def_ratio_file = find_rail_file("examples_data/creation_data/data/hsc_ratios_and_specz.hdf5")
     def_set_file = find_rail_file("examples_data/creation_data/data/HSC_grid_settings.pkl" )
 
     name = 'GridSelection'
-    config_options = Degrader.config_options.copy()
+    config_options = Selector.config_options.copy()
     config_options.update(color_redshift_cut=Param(bool, True, msg='using color-based redshift cut'),
                           percentile_cut=Param(float, 99.0, msg='percentile cut-off for each pixel in color-based redshift cut off'),
                           redshift_cut=Param(float, 100.0, msg="cut redshifts above this value"),
@@ -57,14 +59,14 @@ class GridSelection(Degrader):
 
     def __init__(self, args, comm=None):
 
-        Degrader.__init__(self, args, comm=comm)
+        Selector.__init__(self, args, comm=comm)
 
         if self.config.redshift_cut < 0:
             raise ValueError("redshift cut must be positive")
         if (self.config.percentile_cut < 0) | (self.config.percentile_cut > 100):
             raise ValueError('percentile cut off must be between 0 and 100')
 
-    def run(self):
+    def _select(self):
         """
         HSC galaxies were binned in color magnitude space with i-band mag from -2 to 6 and g-z color from 13 to 26
         200 bins in each direction. The ratio of of galaxies with spectroscopic redshifts (training galaxies) to
@@ -104,8 +106,9 @@ class GridSelection(Degrader):
             raise ValueError("x limits should have two elements!")
         if len(y_lims) != 2:  # pragma: no cover
             raise ValueError("y limits should have two elements!")
-        data_hsc_like = data[(data['x_vals'] >= x_lims[0]) & (data['x_vals'] <= x_lims[1]) & (data['y_vals'] >= y_lims[0]) & (data['y_vals'] <= y_lims[1])]
-
+        # data_hsc_like = data[(data['x_vals'] >= x_lims[0]) & (data['x_vals'] <= x_lims[1]) & (data['y_vals'] >= y_lims[0]) & (data['y_vals'] <= y_lims[1])]
+        
+        data_hsc_like = data
         x_vals = data_hsc_like['x_vals'].to_numpy()
         y_vals = data_hsc_like['y_vals'].to_numpy()
 
@@ -155,9 +158,15 @@ class GridSelection(Degrader):
 
         ratio_list = []
         max_specz_list = []
+                
         for pix_x, pix_y in zip(pixels_x, pixels_y):
-            ratio_list.append(ratios[pix_y][pix_x])
-            max_specz_list.append(max_specz[pix_y][pix_x])
+            # cover the galaxy outside the grid of ratio
+            if (pix_x in [-1,ratios.shape[0]]) or (pix_y in [-1, ratios.shape[1]]):
+                ratio_list.append(0.0)
+                max_specz_list.append(99.0)
+            else:
+                ratio_list.append(ratios[pix_y][pix_x])
+                max_specz_list.append(max_specz[pix_y][pix_x])
 
         data_hsc_like['ratios'] = ratio_list
         data_hsc_like['max_specz'] = max_specz_list
@@ -204,9 +213,13 @@ class GridSelection(Degrader):
             else:  # pragma: no cover
                 for j in range(int(number_to_keep) + 1):
                     keep_inds.append(indices_to_list[j])
-
-        training_data = data_hsc_like_redshift_cut.loc[keep_inds, :]
-        training_data = training_data[training_data['redshift'] > 0]
-        training_data = training_data.drop(['x_vals', 'y_vals', 'ratios'], axis=1)
-
-        self.add_data('output', training_data)
+        
+        finalcut = data_hsc_like_redshift_cut.loc[keep_inds, :]
+        finalcut = finalcut[finalcut['redshift'] > 0]
+        
+        final_keep_inds = np.array(finalcut.index)
+        
+        total_mask = np.zeros(len(data), dtype=bool)
+        total_mask[final_keep_inds] = True
+
+        return total_mask

{pz-rail-astro-tools-0.1.2/src/rail/creation/degradation → pz_rail_astro_tools-0.1.4/src/rail/creation/degraders}/observing_condition_degrader.py

@@ -9,10 +9,10 @@ import pandas as pd
 from ceci.config import StageParameter as Param
 from photerr import LsstErrorModel, LsstErrorParams
 
-from rail.creation.degrader import Degrader
+from rail.creation.noisifier import Noisifier
 
 
-class ObsCondition(Degrader):
+class ObsCondition(Noisifier):
     """Photometric errors based on observation conditions
 
     This degrader calculates spatially-varying photometric errors
@@ -60,7 +60,7 @@ class ObsCondition(Degrader):
     """
 
     name = "ObsCondition"
-    config_options = Degrader.config_options.copy()
+    config_options = Noisifier.config_options.copy()
     config_options.update(
         nside=Param(
             int,
@@ -117,7 +117,7 @@ class ObsCondition(Degrader):
     
 
     def __init__(self, args, comm=None):
-        Degrader.__init__(self, args, comm=comm)
+        Noisifier.__init__(self, args, comm=comm)
 
         # store a list of keys relevant for
         # survey conditions;
@@ -407,10 +407,17 @@ class ObsCondition(Degrader):
 
         return pixel_cat
 
+    
+    def _initNoiseModel(self):
+        """
+        Initialise the error model: LSSTerrorModel
+        """
+        self.default_errorModel = LsstErrorModel()
 
-    def run(self):
+        
+    def _addNoise(self):
         """
-        Run the degrader.
+        Run the noisifier.
         """
         self.rng = np.random.default_rng(seed=self.config["random_seed"])
 
@@ -437,8 +444,8 @@ class ObsCondition(Degrader):
                 
                 # first, check if pixel is -99 - these objects have default obs_conditions:
                 if pixel==-99:
-                    # creating the error model for this pixel
-                    errorModel = LsstErrorModel()
+                    # use the default error model for this pixel
+                    errorModel = self.default_errorModel
                 
                 else:            
                     # get the observing conditions for this pixel

pz_rail_astro_tools-0.1.4/src/rail/creation/degraders/photometric_errors.py

@@ -0,0 +1,136 @@
+"""
+The Photometric error Model LSST, Roman, and Euclid. Based on photometric 
+error models defined in the package photerr
+
+Author: John Franklin Crenshaw, Tianqing Zhang
+"""
+from dataclasses import MISSING
+
+from ceci.config import StageParameter as Param
+from photerr import LsstErrorModel as peLsstErrorModel
+from photerr import LsstErrorParams as peLsstErrorParams
+from photerr import RomanErrorModel as peRomanErrorModel
+from photerr import RomanErrorParams as peRomanErrorParams
+from photerr import EuclidErrorModel as peEuclidErrorModel
+from photerr import EuclidErrorParams as peEuclidErrorParams
+from rail.creation.noisifier import Noisifier
+
+class PhotoErrorModel(Noisifier):
+    """The Base 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:
+    
+    
+    """
+    
+    name = "PhotoErrorModel"
+    
+    def set_params(self, peparams):
+        """
+        Set the photometric error parameters from photerr to 
+        the ceci config
+        """
+        PhotErrErrorParams = peparams
+                
+        config_options = Noisifier.config_options.copy()
+
+        # Dynamically add all parameters from PhotErr
+        _photerr_params = PhotErrErrorParams.__dataclass_fields__
+        self._photerr_params = _photerr_params
+        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
+            self.config[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, comm=None):
+        """
+        Constructor
+
+        Does standard Degrader initialization and sets up the error model.
+        """
+        Noisifier.__init__(self, args, comm=comm)
+        
+    def _initNoiseModel(self):
+        """
+        Initialize the noise model by the peNoiseModel
+        """
+        self.noiseModel = self.peNoiseModel(
+            **{key: self.config[key] for key in self._photerr_params}
+        )
+        
+    def _addNoise(self):
+        
+        """
+        Add noise to the input catalog
+        """
+        
+        # Load the input catalog
+        data = self.get_data("input")
+
+        # Add photometric errors
+        obsData = self.noiseModel(data, random_state=self.config.seed)
+        
+        # Return the new catalog
+        self.add_data("output", obsData)
+ 
+        
+class LSSTErrorModel(PhotoErrorModel):
+
+    """
+    The LSST Error model, defined by peLsstErrorParams and peLsstErrorModel
+    """
+    
+    name = "LSSTErrorModel"
+    
+    def __init__(self, args, comm=None):
+
+        PhotoErrorModel.__init__(self, args, comm=comm)
+        
+        self.set_params(peLsstErrorParams)   
+        self.peNoiseModel = peLsstErrorModel
+        
+
+        
+        
+class RomanErrorModel(PhotoErrorModel):
+    
+    """
+    The Roman Error model, defined by peRomanErrorParams and peRomanErrorModel
+    """
+    
+    name = "RomanErrorModel"
+    
+    def __init__(self, args, comm=None):
+
+        PhotoErrorModel.__init__(self, args, comm=comm)
+        
+        self.set_params(peRomanErrorParams)    
+        self.peNoiseModel = peRomanErrorModel
+
+                
+        
+class EuclidErrorModel(PhotoErrorModel):
+    
+    """
+    The Roman Error model, defined by peRomanErrorParams and peRomanErrorModel
+    """
+    
+    name = "EuclidErrorModel"
+    
+    def __init__(self, args, comm=None):
+
+        PhotoErrorModel.__init__(self, args, comm=comm)
+        
+        self.set_params(peEuclidErrorParams)    
+        self.peNoiseModel = peEuclidErrorModel

{pz-rail-astro-tools-0.1.2/src/rail/creation/degradation → pz_rail_astro_tools-0.1.4/src/rail/creation/degraders}/spectroscopic_degraders.py

@@ -2,10 +2,12 @@
 
 import numpy as np
 import pandas as pd
-from rail.creation.degrader import Degrader
+from rail.creation.selector import Selector
+from rail.creation.noisifier import Noisifier
 
 
-class LineConfusion(Degrader):
+
+class LineConfusion(Noisifier):
     """Degrader that simulates emission line confusion.
 
     .. code-block:: python
@@ -37,7 +39,7 @@ class LineConfusion(Degrader):
     """
 
     name = 'LineConfusion'
-    config_options = Degrader.config_options.copy()
+    config_options = Noisifier.config_options.copy()
     config_options.update(true_wavelen=float,
                           wrong_wavelen=float,
                           frac_wrong=float)
@@ -45,7 +47,7 @@ class LineConfusion(Degrader):
     def __init__(self, args, comm=None):
         """
         """
-        Degrader.__init__(self, args, comm=comm)
+        Noisifier.__init__(self, args, comm=comm)
         # validate parameters
         if self.config.true_wavelen < 0:
             raise ValueError("true_wavelen must be positive, not {self.config.true_wavelen}")
@@ -53,8 +55,12 @@ class LineConfusion(Degrader):
             raise ValueError("wrong_wavelen must be positive, not {self.config.wrong_wavelen}")
         if self.config.frac_wrong < 0 or self.config.frac_wrong > 1:
             raise ValueError("frac_wrong must be between 0 and 1., not {self.config.wrong_wavelen}")
+            
+            
+    def _initNoiseModel(self):
+        self.rng = np.random.default_rng(self.config.seed)
 
-    def run(self):
+    def _addNoise(self):
         """ Run method
 
         Applies line confusion
@@ -75,8 +81,7 @@ class LineConfusion(Degrader):
         zmin = self.config.wrong_wavelen / self.config.true_wavelen - 1
 
         # select the random fraction of galaxies whose lines are confused
-        rng = np.random.default_rng(self.config.seed)
-        idx = rng.choice(
+        idx = self.rng.choice(
             np.where(values[:, 0] > zmin)[0],
             size=int(self.config.frac_wrong * values.shape[0]),
             replace=False,
@@ -92,7 +97,7 @@ class LineConfusion(Degrader):
         self.add_data('output', outData)
 
 
-class InvRedshiftIncompleteness(Degrader):
+class InvRedshiftIncompleteness(Selector):
     """Degrader that simulates incompleteness with a selection function
     inversely proportional to redshift.
 
@@ -107,17 +112,17 @@ class InvRedshiftIncompleteness(Degrader):
     """
 
     name = 'InvRedshiftIncompleteness'
-    config_options = Degrader.config_options.copy()
+    config_options = Selector.config_options.copy()
     config_options.update(pivot_redshift=float)
 
     def __init__(self, args, comm=None):
         """
         """
-        Degrader.__init__(self, args, comm=comm)
+        Selector.__init__(self, args, comm=comm)
         if self.config.pivot_redshift < 0:
             raise ValueError("pivot redshift must be positive, not {self.config.pivot_redshift}")
 
-    def run(self):
+    def _select(self):
         """ Run method
 
         Applies incompleteness
@@ -136,4 +141,4 @@ class InvRedshiftIncompleteness(Degrader):
         rng = np.random.default_rng(self.config.seed)
         mask = rng.random(size=data.shape[0]) <= survival_prob
 
-        self.add_data('output', data[mask])
+        return mask