pz-rail-astro-tools 0.1.3__tar.gz → 1.0.0__tar.gz

{pz_rail_astro_tools-0.1.3 → pz_rail_astro_tools-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 0.1.3
+Version: 1.0.0
 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-0.1.3 → pz_rail_astro_tools-1.0.0}/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-0.1.3 → pz_rail_astro_tools-1.0.0}/src/pz_rail_astro_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pz-rail-astro-tools
-Version: 0.1.3
+Version: 1.0.0
 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-0.1.3 → pz_rail_astro_tools-1.0.0}/src/pz_rail_astro_tools.egg-info/SOURCES.txt

@@ -22,13 +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/photerr_demo.ipynb
-src/rail/creation/degradation/photometric_errors.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
@@ -36,7 +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-1.0.0/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-0.1.3 → pz_rail_astro_tools-1.0.0}/src/rail/astro_tools/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.3'
-__version_tuple__ = version_tuple = (0, 1, 3)
+__version__ = version = '1.0.0'
+__version_tuple__ = version_tuple = (1, 0, 0)

{pz_rail_astro_tools-0.1.3/src/rail/creation/degradation → pz_rail_astro_tools-1.0.0/src/rail/creation/degraders}/grid_selection.py

@@ -6,7 +6,7 @@ import pandas as pd
 import pickle
 import tables_io
 from rail.creation.selector import Selector
-from rail.core.utils import find_rail_file
+from rail.utils.path_utils import find_rail_file
 from ceci.config import StageParameter as Param
 
 

{pz_rail_astro_tools-0.1.3/src/rail/creation/degradation → pz_rail_astro_tools-1.0.0/src/rail/creation/degraders}/spectroscopic_selections.py

@@ -6,7 +6,7 @@ import numpy as np
 from ceci.config import StageParameter as Param
 from rail.creation.selector import Selector
 from scipy.interpolate import interp1d
-from rail.core.utils import RAILDIR
+from rail.utils.path_utils import RAILDIR
 
 
 class SpecSelection(Selector):

pz_rail_astro_tools-0.1.3/src/rail/tools/util_photometry.py → pz_rail_astro_tools-1.0.0/src/rail/tools/photometry_tools.py

@@ -68,7 +68,7 @@ def _compute_flux_error(flux, magnitude_error):
     return flux_error
 
 
-class PhotormetryManipulator(RailStage, ABC):
+class PhotometryManipulator(RailStage, ABC):
     """
     Base class to perform opertations on magnitudes. A table with input magnitudes and errors is
     processed and transformed into an output table with new magnitudes and errors.
@@ -76,7 +76,7 @@ class PhotormetryManipulator(RailStage, ABC):
     Subclasses must implement the run() and compute() method.
     """
 
-    name = 'PhotormetryManipulator'
+    name = 'PhotometryManipulator'
     config_options = RailStage.config_options.copy()
     config_options.update(
         value_columns=Param(
@@ -171,7 +171,7 @@ class PhotormetryManipulator(RailStage, ABC):
         return self.get_handle('output')
 
 
-class HyperbolicSmoothing(PhotormetryManipulator):
+class HyperbolicSmoothing(PhotometryManipulator):
     """
     Initial stage to compute hyperbolic magnitudes (Lupton et al. 1999). Estimates the smoothing
     parameter b that is used by the second stage (`HyperbolicMagnitudes`) to convert classical to
@@ -179,7 +179,7 @@ class HyperbolicSmoothing(PhotormetryManipulator):
     """
 
     name = 'HyperbolicSmoothing'
-    config_options = PhotormetryManipulator.config_options.copy()
+    config_options = PhotometryManipulator.config_options.copy()
     inputs = [('input', PqHandle)]
     outputs = [('parameters', PqHandle)]
 
@@ -240,7 +240,7 @@ class HyperbolicSmoothing(PhotormetryManipulator):
         return self.get_handle('parameters')
 
 
-class HyperbolicMagnitudes(PhotormetryManipulator):
+class HyperbolicMagnitudes(PhotometryManipulator):
     """
     Convert a set of classical magnitudes to hyperbolic magnitudes  (Lupton et al. 1999). Requires
     input from the initial stage (`HyperbolicSmoothing`) to supply optimal values for the smoothing
@@ -248,7 +248,7 @@ class HyperbolicMagnitudes(PhotormetryManipulator):
     """
 
     name = 'HyperbolicMagnitudes'
-    config_options = PhotormetryManipulator.config_options.copy()
+    config_options = PhotometryManipulator.config_options.copy()
     inputs = [('input', PqHandle),
               ('parameters', PqHandle)]
     outputs = [('output', PqHandle)]

{pz_rail_astro_tools-0.1.3 → pz_rail_astro_tools-1.0.0}/tests/astro_tools/test_core.py

@@ -20,8 +20,8 @@ from rail.core.data import (
     TableHandle,
 )
 from rail.core.stage import RailStage
-from rail.tools.util_photometry import HyperbolicMagnitudes, HyperbolicSmoothing, PhotormetryManipulator, LSSTFluxToMagConverter, Dereddener
-from rail.core.utils import RAILDIR
+from rail.tools.photometry_tools import HyperbolicMagnitudes, HyperbolicSmoothing, PhotometryManipulator, LSSTFluxToMagConverter, Dereddener
+from rail.utils.path_utils import RAILDIR
 #from rail.tools.util_stages import (
 #    LSSTFluxToMagConverter,
 #    Dereddener,
@@ -98,38 +98,38 @@ def load_result_smoothing():
     return DS.read_file("test_data", TableHandle, testFile).data
 
 
-def test_PhotormetryManipulator(hyperbolic_configuration):
+def test_PhotometryManipulator(hyperbolic_configuration):
     DS = RailStage.data_store
     DS.clear()
     DS.__class__.allow_overwrite = False
 
-    # NOTE: the __init__ machinery of HyperbolicSmoothing is identical to PhotormetryManipulator
-    # and is used as substitute since PhotormetryManipulator cannot be instantiated.
+    # NOTE: the __init__ machinery of HyperbolicSmoothing is identical to PhotometryManipulator
+    # and is used as substitute since PhotometryManipulator cannot be instantiated.
     n_filters = len(hyperbolic_configuration["value_columns"])
 
     # wrong number of "error_columns"
     config = hyperbolic_configuration.copy()
     config["error_columns"] = hyperbolic_configuration["error_columns"][:-1]
     with pytest.raises(IndexError):
-        inst = HyperbolicSmoothing.make_stage(name="photormetry_manipulator", **config)
+        inst = HyperbolicSmoothing.make_stage(name="photometry_manipulator", **config)
 
     # wrong number of "zeropoints"
     config = hyperbolic_configuration.copy()
     config["zeropoints"] = np.arange(0, n_filters - 1)
     with pytest.raises(IndexError):
-        inst = HyperbolicSmoothing.make_stage(name="photormetry_manipulator", **config)
+        inst = HyperbolicSmoothing.make_stage(name="photometry_manipulator", **config)
 
     # default values for "zeropoints"
     config = hyperbolic_configuration.copy()
     config.pop("zeropoints")  # should resort to default of 0.0
-    inst = HyperbolicSmoothing.make_stage(name="photormetry_manipulator", **config)
+    inst = HyperbolicSmoothing.make_stage(name="photometry_manipulator", **config)
     assert len(inst.zeropoints) == n_filters
     assert all(zp == 0.0 for zp in inst.zeropoints)
 
     # if_flux preserves the values
     dummy_data = pd.DataFrame(dict(val=[1, 2, 3], err=[1, 2, 3]))
     config = dict(value_columns=["val"], error_columns=["err"], zeropoints=[0.0])
-    inst = HyperbolicSmoothing.make_stage(name="photormetry_manipulator", **config, is_flux=True)
+    inst = HyperbolicSmoothing.make_stage(name="photometry_manipulator", **config, is_flux=True)
     inst.set_data("input", dummy_data)
     data = inst.get_as_fluxes()
     assert np.allclose(data, dummy_data)

{pz_rail_astro_tools-0.1.3 → pz_rail_astro_tools-1.0.0}/tests/astro_tools/test_degraders.py

@@ -7,13 +7,13 @@ import pytest
 from photerr import LsstErrorModel as PhoterrErrorModel
 
 from rail.core.data import DATA_STORE, TableHandle
-from rail.core.utils import find_rail_file
-from rail.core.util_stages import ColumnMapper
-from rail.creation.degradation.spectroscopic_degraders import InvRedshiftIncompleteness, LineConfusion
-from rail.creation.degradation.spectroscopic_selections import *
-from rail.creation.degradation.observing_condition_degrader import ObsCondition
-from rail.creation.degradation.grid_selection import GridSelection
-from rail.creation.degradation.lsst_error_model import LSSTErrorModel
+from rail.utils.path_utils import find_rail_file
+from rail.tools.table_tools import ColumnMapper
+from rail.creation.degraders.spectroscopic_degraders import InvRedshiftIncompleteness, LineConfusion
+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
 
 
 @pytest.fixture

pz_rail_astro_tools-0.1.3/src/rail/astro_tools/__init__.py

@@ -1,8 +0,0 @@
-from ._version import __version__
-
-from rail.creation.degradation.grid_selection import *
-from rail.creation.degradation.observing_condition_degrader import *
-from rail.creation.degradation.spectroscopic_degraders import *
-from rail.creation.degradation.spectroscopic_selections import *
-from rail.creation.degradation.lsst_error_model import *
-from rail.tools.util_photometry import *

pz_rail_astro_tools-0.1.3/src/rail/creation/degradation/photerr_demo.ipynb

@@ -1,238 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "id": "2610a0f0-0c71-4401-896f-734442bcd66d",
-   "metadata": {},
-   "source": [
-    "## Photometric error stage demo\n",
-    "\n",
-    "author: Tianqing Zhang, John-Franklin Crenshaw\n",
-    "\n",
-    "This notebook demonstrate the use of `rail.creation.degradation.photometric_errors`, which adds column for the  photometric noise to the catalog based on the package PhotErr developed by John-Franklin Crenshaw. The RAIL stage PhotoErrorModel inherit from the Noisifier base classes, and the LSST, Roman, Euclid child classes inherit from the PhotoErrorModel"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f7a6adc3-68e8-4a1d-842f-bfb0960a1c4a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "from rail.creation.degradation.photometric_errors import LSSTErrorModel\n",
-    "from rail.creation.degradation.photometric_errors import RomanErrorModel\n",
-    "from rail.creation.degradation.photometric_errors import EuclidErrorModel\n",
-    "\n",
-    "from rail.core.data import PqHandle\n",
-    "from rail.core.stage import RailStage\n",
-    "\n",
-    "import matplotlib.pyplot as plt\n",
-    "import pandas as pd\n",
-    "import numpy as np\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6912a740-31ea-4987-b06d-81ff17cd895a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "DS = RailStage.data_store\n",
-    "DS.__class__.allow_overwrite = True\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "a282c2ed-141b-4507-8254-dc8fbc9864dc",
-   "metadata": {},
-   "source": [
-    "### Create a random catalog with ugrizy+YJHF bands as the the true input"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "1078bc2a-fc54-41c3-bd30-6c447bb971d4",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "data = np.random.normal(23, 3, size = (1000,10))\n",
-    "\n",
-    "data_df = pd.DataFrame(data=data,    # values\n",
-    "            columns=['u', 'g', 'r', 'i', 'z', 'y', 'Y', 'J', 'H', 'F'])\n",
-    "data_truth = PqHandle('input')\n",
-    "data_truth.set_data(data_df)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "1da27deb-d167-4f38-8c59-f270184d6ab3",
-   "metadata": {},
-   "source": [
-    "### The LSST error model adds noise to the optical bands"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "e5f4862a-0621-46d4-8901-7e84b461c424",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "errorModel_lsst = LSSTErrorModel.make_stage(name=\"error_model\")\n",
-    "\n",
-    "samples_w_errs = errorModel_lsst(data_truth)\n",
-    "samples_w_errs()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "6282c42e-1a6f-480a-aa2b-817bd30d372f",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fig, ax = plt.subplots(figsize=(5, 4), dpi=100)\n",
-    "\n",
-    "for band in \"ugrizy\":\n",
-    "    # pull out the magnitudes and errors\n",
-    "    mags = samples_w_errs.data[band].to_numpy()\n",
-    "    errs = samples_w_errs.data[band + \"_err\"].to_numpy()\n",
-    "\n",
-    "    # sort them by magnitude\n",
-    "    mags, errs = mags[mags.argsort()], errs[mags.argsort()]\n",
-    "\n",
-    "    # plot errs vs mags\n",
-    "    ax.plot(mags, errs, label=band)\n",
-    "\n",
-    "ax.legend()\n",
-    "ax.set(xlabel=\"Magnitude (AB)\", ylabel=\"Error (mags)\")\n",
-    "plt.show()\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "50927ccb-4492-4bdd-a29b-0907704b2c59",
-   "metadata": {},
-   "source": [
-    "### The Roman error model adds noise to the infrared bands"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "d484a34b-cf10-45bd-8571-b78dc1818180",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "errorModel_Roman = RomanErrorModel.make_stage(name=\"error_model\")\n",
-    "\n",
-    "samples_w_errs_roman = errorModel_Roman(data_truth)\n",
-    "samples_w_errs_roman()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a12362dc-0689-43f3-b990-edff734010bb",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fig, ax = plt.subplots(figsize=(5, 4), dpi=100)\n",
-    "\n",
-    "for band in \"YJHF\":\n",
-    "    # pull out the magnitudes and errors\n",
-    "    mags = samples_w_errs_roman.data[band].to_numpy()\n",
-    "    errs = samples_w_errs_roman.data[band + \"_err\"].to_numpy()\n",
-    "\n",
-    "    # sort them by magnitude\n",
-    "    mags, errs = mags[mags.argsort()], errs[mags.argsort()]\n",
-    "\n",
-    "    # plot errs vs mags\n",
-    "    ax.plot(mags, errs, label=band)\n",
-    "\n",
-    "ax.legend()\n",
-    "ax.set(xlabel=\"Magnitude (AB)\", ylabel=\"Error (mags)\")\n",
-    "plt.show()\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "359de4ad-a47c-4dc5-8c81-53aeb92bdf42",
-   "metadata": {},
-   "source": [
-    "### The Euclid error model adds noise to YJH bands"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "775d0a23-7435-4b01-83db-2234c3d24f57",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "errorModel_Euclid = EuclidErrorModel.make_stage(name=\"error_model\")\n",
-    "\n",
-    "samples_w_errs_Euclid = errorModel_Euclid(data_truth)\n",
-    "samples_w_errs_Euclid()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "7fcfe07a-5571-4dd3-8ad0-358964c1d493",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fig, ax = plt.subplots(figsize=(5, 4), dpi=100)\n",
-    "\n",
-    "for band in \"YJH\":\n",
-    "    # pull out the magnitudes and errors\n",
-    "    mags = samples_w_errs_Euclid.data[band].to_numpy()\n",
-    "    errs = samples_w_errs_Euclid.data[band + \"_err\"].to_numpy()\n",
-    "\n",
-    "    # sort them by magnitude\n",
-    "    mags, errs = mags[mags.argsort()], errs[mags.argsort()]\n",
-    "\n",
-    "    # plot errs vs mags\n",
-    "    ax.plot(mags, errs, label=band)\n",
-    "\n",
-    "ax.legend()\n",
-    "ax.set(xlabel=\"Magnitude (AB)\", ylabel=\"Error (mags)\")\n",
-    "plt.show()\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "268b3d37-b7fd-4ac1-8457-2104a87c9e6d",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "rail_env",
-   "language": "python",
-   "name": "rail_env"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.4"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}