Box units conversion (#3)

* linting

* fix long line

* rename nb

* rename import

* add group catalog

* move imports out of functions

* add array_to_structured

* add references

* fix subsampling

* fix coord bug

* add 2M++ dists

* save nb

* fix comment

* add snapshot path

* add snapshot path

* add read_info

* Move transforms

* add import radec

* expand docs

* Move flipcols

* update nb

* add flip_cols

* create file

* add blank line

* Move units transfs

* add blank line

* add units import

* rm imports

* add import

* add box_units

* add comments

galomatch/utils/__init__.py

@@ -13,6 +13,6 @@
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 
-from .recarray_manip import (cols_to_structured, add_columns, rm_columns,
-                             list_to_ndarray)
-from .transforms import cartesian_to_radec
+from .recarray_manip import (cols_to_structured, add_columns, rm_columns,  # noqa
+                             list_to_ndarray, array_to_structured,  # noqa
+                             flip_cols)  # noqa

galomatch/utils/recarray_manip.py

@@ -12,11 +12,14 @@
 # You should have received a copy of the GNU General Public License along
 # with this program; if not, write to the Free Software Foundation, Inc.,
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+"""
+Utilility functions for manipulation structured arrays.
+"""
 
-"""Utilility functions for manipulation structured arrays."""
 
 import numpy
 
+
 def cols_to_structured(N, cols):
     """
     Allocate a structured array from `cols`.
@@ -84,6 +87,7 @@ def add_columns(arr, X, cols):
 
     return out
 
+
 def rm_columns(arr, cols):
     """
     Remove columns `cols` from a record array `arr`. Creates a new array.
@@ -143,7 +147,7 @@ def list_to_ndarray(arrs, cols):
         raise TypeError("`arrs` must be a list of structured arrays.")
     cols = [cols] if isinstance(cols, str) else cols
 
-    Narr  = len(arrs)
+    Narr = len(arrs)
     Nobj_max = max([arr.size for arr in arrs])
     Ncol = len(cols)
     # Preallocate the array and fill it
@@ -153,3 +157,55 @@ def list_to_ndarray(arrs, cols):
         for j in range(Ncol):
             out[i, :Nobj, j] = arrs[i][cols[j]]
     return out
+
+
+def array_to_structured(arr, cols):
+    """
+    Create a structured array from a 2-dimensional array.
+
+    Parameters
+    ----------
+    arr : 2-dimensional array
+        Original array of shape `(n_samples, n_cols)`.
+    cols : list of str
+        Columns of the structured array
+
+    Returns
+    -------
+    out : structured array
+        The output structured array.
+    """
+    cols = [cols] if isinstance(cols, str) else cols
+    if arr.ndim != 2 and arr.shape[1] != len(cols):
+        raise TypeError("`arr` must be a 2-dimensional array of "
+                        "shape `(n_samples, n_cols)`.")
+
+    dtype = {"names": cols, "formats": [arr.dtype] * len(cols)}
+    out = numpy.full(arr.shape[0], numpy.nan, dtype=dtype)
+    for i, col in enumerate(cols):
+        out[col] = arr[:, i]
+
+    return out
+
+
+def flip_cols(arr, col1, col2):
+    """
+    Flip values in columns `col1` and `col2`. `arr` is passed by reference and
+    is not explicitly returned back.
+
+    Parameters
+    ----------
+    arr : structured array
+        The array whose columns are to be converted.
+    col1 : str
+        The first column name.
+    col2 : str
+        The second column name.
+
+    Returns
+    -------
+    nothing
+    """
+    dum = numpy.copy(arr[col1])
+    arr[col1] = arr[col2]
+    arr[col2] = dum

galomatch/utils/transforms.py

@@ -1,56 +0,0 @@
-# Copyright (C) 2022 Richard Stiskalek
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the
-# Free Software Foundation; either version 3 of the License, or (at your
-# option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
-# Public License for more details.
-#
-# You should have received a copy of the GNU General Public License along
-# with this program; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
-
-import numpy
-
-
-def cartesian_to_radec(arr, xpar="peak_x", ypar="peak_y", zpar="peak_z", degrees=True):
-    """
-    Extract `x`, `y`, and `z` coordinates from a record array `arr` and
-    calculate their spherical coordinates representation.
-
-    Parameters
-    ----------
-    arr : record array
-        Record array with the Cartesian coordinates.
-    xpar : str, optional
-        Name of the x coordinate in the record array.
-    ypar : str, optional
-        Name of the y coordinate in the record array.
-    zpar : str, optional
-        Name of the z coordinate in the record array.
-    degrees : bool, optional
-        Whether to return angles in degrees. By default `True`.
-
-    Returns
-    -------
-    dist : 1-dimensional array
-        Radial distance.
-    ra : 1-dimensional array
-        Right ascension.
-    dec : 1-dimensional array
-        Declination.
-    """
-    x, y, z = arr[xpar], arr[ypar], arr[zpar]
-
-    dist = numpy.sqrt(x**2 + y**2 + z**2)
-    dec = numpy.arcsin(z / dist)
-    ra = numpy.arctan2(y, x)
-
-    if degrees:
-        dec = numpy.rad2deg(dec)
-        ra = numpy.rad2deg(ra)
-
-    return dist, ra, dec