Merge pull request #47 from p-slash/0.5.0-dev

0.5.0 merge: + Error method for varlss is configurable. default is regJack. + Adjustable smoothing scale for noise. + Variance fitting auto calculates needed wavelength bins based on 120 A average spacing. + Mean Gaussian sigma is calculated and added to delta headers + Auto calculate quasar redshifts using wavelength ranges
p-slash · Mar 28, 2023 · 82933eb · 82933eb
2 parents 9f54561 + 4cdc2a0
commit 82933eb
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diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -32,7 +32,8 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
-    'sphinxarg.ext'
+    'sphinxarg.ext',
+    "sphinxcontrib.jquery"  # based on https://github.com/readthedocs/readthedocs.org/issues/10159#issuecomment-1478717074
     # 'nbsphinx',
     # 'autoapi.extension'
 ]
@@ -56,7 +57,7 @@
     'numpy': ('https://numpy.org/doc/stable', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/', None)
 }
-intersphinx_disabled_domains = ['std']
+# intersphinx_disabled_domains = ['std']
 # intersphinx_disabled_reftypes = ["*"]
 
 templates_path = ['_templates']
@@ -65,7 +66,6 @@
 
 html_theme = 'sphinx_rtd_theme'
 html_logo = "_static/qsonic-logo.png"
-html_show_sourcelink = False
 
 # -- Options for EPUB output
 epub_show_urls = 'footnote'

diff --git a/docs/source/example.rst b/docs/source/example.rst
@@ -4,7 +4,7 @@ Examples
 Running qsonic-fit
 -------------------------
 
-See :ref:`qsonic-fit arguments <qsonic_fit_arguments_label>` for all options.
+See :ref:`qsonic-fit arguments <qsonic fit arguments>` for all options.
 
 .. code-block:: shell
     :caption: For an imaginary Y5 DESI quickquasars mock

diff --git a/docs/source/generated/catalog.rst b/docs/source/generated/catalog.rst
@@ -1,4 +1,4 @@
-qsonic.catalog module
+qsonic.catalog
 =======================
 
 .. automodule:: qsonic.catalog

diff --git a/docs/source/generated/io.rst b/docs/source/generated/io.rst
@@ -1,4 +1,4 @@
-qsonic.io module
+qsonic.io
 ==================
 
 .. automodule:: qsonic.io

diff --git a/docs/source/generated/masks.rst b/docs/source/generated/masks.rst
@@ -1,4 +1,4 @@
-qsonic.masks module
+qsonic.masks
 =====================
 
 .. automodule:: qsonic.masks

diff --git a/docs/source/generated/mathtools.rst b/docs/source/generated/mathtools.rst
@@ -1,4 +1,4 @@
-qsonic.mathtools module
+qsonic.mathtools
 =========================
 
 .. automodule:: qsonic.mathtools

diff --git a/docs/source/generated/modules.rst b/docs/source/generated/modules.rst
@@ -22,3 +22,4 @@ Scripts
    :maxdepth: 4
 
    scripts.qsonic_fit
+   scripts.qsonic_calib
diff --git a/docs/source/generated/mpi_utils.rst b/docs/source/generated/mpi_utils.rst
@@ -1,7 +1,8 @@
-qsonic.mpi\_utils module
+qsonic.mpi\_utils
 ==========================
 
 .. automodule:: qsonic.mpi_utils
    :members:
    :undoc-members:
    :show-inheritance:
+   :exclude-members: _INVALID_VALUE
diff --git a/docs/source/generated/picca_continuum.rst b/docs/source/generated/picca_continuum.rst
@@ -1,4 +1,4 @@
-qsonic.picca\_continuum module
+qsonic.picca\_continuum
 ================================
 
 .. automodule:: qsonic.picca_continuum

diff --git a/docs/source/generated/scripts.qsonic_calib.rst b/docs/source/generated/scripts.qsonic_calib.rst
@@ -0,0 +1,21 @@
+qsonic.scripts.qsonic_calib
+=========================================
+
+
+.. automodule:: qsonic.scripts.qsonic_calib
+   :members:
+   :undoc-members:
+   :show-inheritance:
+   :exclude-members: get_parser
+
+.. _qsonic calib arguments:
+
+Arguments
+---------
+
+.. autofunction:: qsonic.scripts.qsonic_calib.get_parser
+
+.. argparse::
+   :ref: qsonic.scripts.qsonic_calib.get_parser
+   :prog: qsonic-calib
+
diff --git a/docs/source/generated/scripts.qsonic_fit.rst b/docs/source/generated/scripts.qsonic_fit.rst
@@ -1,4 +1,4 @@
-qsonic.scripts.qsonic_fit script module
+qsonic.scripts.qsonic_fit
 =======================================
 
 
@@ -8,7 +8,7 @@ qsonic.scripts.qsonic_fit script module
    :show-inheritance:
    :exclude-members: get_parser
 
-.. _qsonic_fit_arguments_label:
+.. _qsonic fit arguments:
 
 Arguments
 ---------

diff --git a/docs/source/generated/spectrum.rst b/docs/source/generated/spectrum.rst
@@ -1,4 +1,4 @@
-qsonic.spectrum module
+qsonic.spectrum
 ========================
 
 .. automodule:: qsonic.spectrum

diff --git a/docs/source/readme.rst b/docs/source/readme.rst
@@ -2,7 +2,8 @@
 
 Programs
 --------
-+ ``qsonic-fit`` performs picca-like continuum fitting. See :ref:`here <qsonic_fit_arguments_label>` or execute ``srun -n 1 qsonic-fit.py --help`` for help.
++ ``qsonic-fit`` performs picca-like continuum fitting. See :ref:`here <qsonic fit arguments>` or execute ``srun -n 1 qsonic-fit --help`` for help.
++ ``qsonic-calib`` calculates stacked flux and performs variance fitting with noise calibration (eta) enabled.  See :ref:`here <qsonic calib arguments>` ``srun -n 1 qsonic-calib --help`` for help.
 
 Source
 ------

diff --git a/py/qsonic/__init__.py b/py/qsonic/__init__.py
@@ -1,6 +1,6 @@
 __author__ = 'Naim Goksel Karacayli'
 __email__ = '[email protected]'
-__version__ = '0.4.4'
+__version__ = '0.5.0'
 
 
 class QsonicException(Exception):

diff --git a/py/qsonic/catalog.py b/py/qsonic/catalog.py
@@ -8,8 +8,7 @@
 import numpy as np
 from numpy.lib.recfunctions import rename_fields, append_fields
 
-from qsonic import QsonicException
-from qsonic.mpi_utils import logging_mpi, balance_load
+from qsonic.mpi_utils import logging_mpi, balance_load, mpi_fnc_bcast
 
 _accepted_extnames = set(['QSO_CAT', 'ZCATALOG', 'METADATA'])
 """set: Accepted extentions for quasar catalog."""
@@ -53,9 +52,9 @@ def read_quasar_catalog(
         If the catalog is for mocks.
     keep_surveys: None or list(str), default: None
         List of surveys to subselect. None keeps all.
-    zmin: float, default: 2.1
+    zmin: float, default: 0
         Minimum quasar redshift
-    zmax: float, default: 6.0
+    zmax: float, default: 100
         Maximum quasar redshift
 
     Returns
@@ -72,49 +71,47 @@ def read_quasar_catalog(
 
 
 def mpi_read_quasar_catalog(
-        filename, comm, mpi_rank, is_mock,
-        keep_surveys=None, zmin=2.1, zmax=6.0
+        filename, comm=None, mpi_rank=0, is_mock=False,
+        keep_surveys=None, zmin=0, zmax=100
 ):
     """ Returns the same quasar catalog object on all MPI ranks.
 
     It is sorted in the following order: HPXPIXEL, SURVEY (if applicable),
     TARGETID. BAL info included if available. It is required for BAL masking.
 
+    Can be used without MPI by passing ``comm=None`` and ``mpi_rank=0``.
+
     Arguments
     ----------
     filename: str
         Filename to catalog.
-    comm: MPI comm object
+    comm: MPI comm object or None, default: None
         MPI comm object for bcast
-    mpi_rank: int
+    mpi_rank: int, default: 0
         Rank of the MPI process
-    is_mock: bool
+    is_mock: bool, default: False
         If the catalog is for mocks.
     keep_surveys: None or list(str), default: None
         List of surveys to subselect. None keeps all.
-    zmin: float, default: 2.1
+    zmin: float, default: 0
         Minimum quasar redshift
-    zmax: float, default: 6.0
+    zmax: float, default: 100
         Maximum quasar redshift
 
     Returns
     ----------
     catalog: :external+numpy:py:class:`ndarray <numpy.ndarray>`
         Sorted catalog on all MPI ranks.
+
+    Raises
+    ------
+    QsonicException
+        If error occurs while reading the catalog.
     """
-    catalog = None
-
-    if mpi_rank == 0:
-        try:
-            catalog = read_quasar_catalog(
-                filename, is_mock, keep_surveys, zmin, zmax)
-        except Exception as e:
-            logging_mpi(e, 0, "error")
-            catalog = None
-
-    catalog = comm.bcast(catalog, root=0)
-    if catalog is None:
-        raise QsonicException("Error while reading catalog.")
+    catalog = mpi_fnc_bcast(
+        read_quasar_catalog,
+        comm, mpi_rank, "Error while reading catalog.",
+        filename, is_mock, keep_surveys, zmin, zmax)
 
     return catalog
 

diff --git a/py/qsonic/masks.py b/py/qsonic/masks.py
@@ -66,7 +66,7 @@ def __init__(self, fname):
 
             self.mask_rest_frame = mask[mask['frame'] == 'RF']
             self.mask_obs_frame = mask[mask['frame'] == 'OBS']
-        except QsonicException as e:
+        except Exception as e:
             raise QsonicException(
                 f"Error loading SkyMask from mask file {fname}.") from e
 

diff --git a/py/qsonic/mathtools.py b/py/qsonic/mathtools.py
@@ -38,18 +38,16 @@ def mypoly1d(coef, x):
     return results
 
 
-def fft_gaussian_smooth(x, sigma_pix=20, pad_size=25, mode='edge'):
+def fft_gaussian_smooth(x, sigma_pix=20, mode='edge'):
     """ My Gaussian smoother using FFTs. Input array is padded with edge
-    values at the boundary by default.
+    values at the boundary by default. Pad size is ``3*sigma_pix``.
 
     Arguments
     ---------
     x: :external+numpy:py:class:`ndarray <numpy.ndarray>`
         1D array to smooth.
     sigma_pix: float, default: 20
-        Smoothing Gaussian sigma
-    pad_size: int, default: 25
-        Number of pixels to pad the array x at the boundary.
+        Smoothing Gaussian sigma in terms of number of pixels.
     mode: str
         Padding method. See :external+numpy:func:`numpy.pad` for options.
 
@@ -60,6 +58,7 @@ def fft_gaussian_smooth(x, sigma_pix=20, pad_size=25, mode='edge'):
     """
     # Pad the input array to get rid of annoying edge effects
     # Pad values are set to the edge value
+    pad_size = max(1, int(3 * sigma_pix))
     arrsize = x.size + 2 * pad_size
     padded_arr = np.pad(x, pad_size, mode=mode)
 
@@ -71,7 +70,7 @@ def fft_gaussian_smooth(x, sigma_pix=20, pad_size=25, mode='edge'):
     return y
 
 
-def get_smooth_ivar(ivar, sigma_pix=20, pad_size=25, esigma=3.5):
+def get_smooth_ivar(ivar, sigma_pix=20, esigma=3.5):
     """ Smoothing ``ivar`` values to reduce signal-noise coupling.
 
     Smoothing is done on ``error=1/sqrt(ivar)``, while replacing ``ivar=0`` and
@@ -83,9 +82,7 @@ def get_smooth_ivar(ivar, sigma_pix=20, pad_size=25, esigma=3.5):
     ivar: :external+numpy:py:class:`ndarray <numpy.ndarray>`
         Inverse variance array.
     sigma_pix: float, default: 20
-        Smoothing Gaussian sigma.
-    pad_size: int, default: 25
-        Number of pixels to pad the array at the boundary.
+        Smoothing Gaussian sigma in terms of number of pixels.
     esigma: float, default: 3.5
         Sigma to identify outliers via MAD.
 
@@ -107,7 +104,7 @@ def get_smooth_ivar(ivar, sigma_pix=20, pad_size=25, esigma=3.5):
 
     # Replace them with the median
     error[w2] = median_err
-    error = fft_gaussian_smooth(error, sigma_pix, pad_size)
+    error = fft_gaussian_smooth(error, sigma_pix)
 
     # Restore values of bad pixels
     error[w2] = err_org
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,3 +22,4 @@ Scripts
		:maxdepth: 4

		scripts.qsonic_fit
		scripts.qsonic_calib