refactor parser

dev/regions_parse.py

@@ -1,9 +1,13 @@
 import click
 import pyregion
+import logging
 from regions import read_ds9
 from pathlib import Path
+from astropy import log
 
-TEST_FILE_DIR = Path('../regions/io/tests/data')
+log.setLevel('DEBUG')
+
+TEST_FILE_DIR = Path('../regions/io/ds9/tests/data')
 
 @click.group()
 def cli():
@@ -19,13 +23,14 @@ def list_files():
 @cli.command('parse')
 @click.option('--interactive', is_flag=True, default=False)
 @click.option('--parser', default='regions')
+@click.option('--errors', default='strict')
 @click.argument('filename')
-def parse(filename, interactive, parser):
+def parse(filename, interactive, parser, errors):
     readname = TEST_FILE_DIR / filename
     print('Reading {}'.format(readname))
     print('Using parser {}'.format(parser))
     if parser == 'regions':
-        regions = read_ds9(str(readname), errors='warn')
+        regions = read_ds9(str(readname), errors=errors)
     elif parser == 'pyregion':
         regions = pyregion.open(str(readname))
     print(regions)

dev/regions_pyregion_comparison.csv

@@ -1,52 +1,52 @@
 filename,time_regions,time_pyregion,compl_pyregion,compl_regions
-ds9.linear.wcsi.reg,0.005,0.842,100.0%,37.1%
-ds9.mosaic.fk4.hms.reg,0.029,0.747,100.0%,37.1%
-ds9.color.reg,0.005,0.229,100.0%,100.0%
-ds9.fk5.strip.reg,0.010,0.345,100.0%,43.3%
-ds9.fk5.reg,0.011,0.683,100.0%,36.1%
-ds9.physical.strip.reg,0.002,0.368,100.0%,43.3%
-ds9.physical.windows.reg,0.002,0.498,100.0%,37.1%
-ds9.fk5.hms.reg,0.013,0.477,100.0%,36.1%
-ds9.icrs.hms.reg,0.012,0.479,100.0%,36.1%
-ds9.icrs.strip.reg,0.010,0.341,100.0%,43.3%
-ds9.color.spaces.reg,0.005,0.224,100.0%,100.0%
-ds9.mosaic.ecliptic.hms.reg,0.022,0.740,100.0%,37.1%
-ds9.linear.wcs.reg,0.004,0.742,100.0%,37.1%
-ds9.mosaic.ecliptic.reg,0.019,0.734,100.0%,37.1%
-ds9.linear.wcsc.reg,0.004,0.813,100.0%,37.1%
-ds9.fk4.hms.strip.reg,0.016,0.400,100.0%,43.3%
-ds9.mosaic.galactic.reg,0.021,0.794,100.0%,37.1%
-ds9.linear.wcsd.reg,0.004,0.767,100.0%,37.1%
-physical_reference.reg,0.001,0.220,100.0%,100.0%
-ds9.fk4.reg,0.012,0.467,100.0%,36.1%
-ds9.image.strip.reg,0.002,0.321,100.0%,43.3%
-ds9.icrs.hms.strip.reg,0.012,0.351,100.0%,43.3%
-ds9.image.reg,0.002,0.499,100.0%,36.1%
-ds9.mosaic.fk5.hms.reg,0.029,0.777,100.0%,37.1%
-ds9.mosaic.image.reg,0.004,0.727,100.0%,37.1%
-ds9.physical.reg,0.002,0.437,100.0%,36.1%
-ds9.ecliptic.reg,0.010,0.472,100.0%,36.1%
-ds9.ecliptic.strip.reg,0.009,0.342,100.0%,43.3%
-ds9.fits.reg,0.001,0.253,100.0%,100.0%
-ds9.icrs.reg,0.010,0.465,100.0%,36.1%
-ds9.mosaic.fk4.reg,0.023,0.739,100.0%,37.1%
-ds9.mosaic.icrs.hms.reg,0.023,0.824,100.0%,37.1%
-ds9.ecliptic.hms.reg,0.011,0.508,100.0%,36.1%
-ds9.fk4.hms.reg,0.014,0.570,100.0%,36.1%
-ds9.mosaic.galactic.hms.reg,0.038,0.834,100.0%,37.1%
-ds9.mosaic.icrs.reg,0.023,0.820,100.0%,37.1%
+ds9.linear.wcsi.reg,0.009,0.775,100.0%,42.9%
+ds9.mosaic.fk4.hms.reg,0.034,0.749,100.0%,42.9%
+ds9.color.reg,0.005,0.227,100.0%,100.0%
+ds9.fk5.strip.reg,0.011,0.350,100.0%,50.0%
+ds9.fk5.reg,0.011,0.476,100.0%,41.7%
+ds9.physical.strip.reg,0.003,0.338,100.0%,50.0%
+ds9.physical.windows.reg,0.003,0.437,100.0%,42.9%
+ds9.fk5.hms.reg,0.013,0.506,100.0%,41.7%
+ds9.icrs.hms.reg,0.014,0.478,100.0%,41.7%
+ds9.icrs.strip.reg,0.010,0.362,100.0%,50.0%
+ds9.color.spaces.reg,0.005,0.235,100.0%,100.0%
+ds9.mosaic.ecliptic.hms.reg,0.024,0.753,100.0%,42.9%
+ds9.linear.wcs.reg,0.008,0.742,100.0%,42.9%
+ds9.mosaic.ecliptic.reg,0.021,0.775,100.0%,42.9%
+ds9.linear.wcsc.reg,0.007,0.784,100.0%,42.9%
+ds9.fk4.hms.strip.reg,0.014,0.346,100.0%,50.0%
+ds9.mosaic.galactic.reg,0.022,0.745,100.0%,42.9%
+ds9.linear.wcsd.reg,0.007,0.773,100.0%,42.9%
+physical_reference.reg,0.001,0.219,100.0%,100.0%
+ds9.fk4.reg,0.012,0.484,100.0%,41.7%
+ds9.image.strip.reg,0.003,0.324,100.0%,50.0%
+ds9.icrs.hms.strip.reg,0.012,0.350,100.0%,50.0%
+ds9.image.reg,0.003,0.458,100.0%,41.7%
+ds9.mosaic.fk5.hms.reg,0.029,0.771,100.0%,42.9%
+ds9.mosaic.image.reg,0.007,0.753,100.0%,42.9%
+ds9.physical.reg,0.003,0.446,100.0%,41.7%
+ds9.ecliptic.reg,0.011,0.473,100.0%,41.7%
+ds9.ecliptic.strip.reg,0.010,0.363,100.0%,50.0%
+ds9.fits.reg,0.002,0.262,100.0%,100.0%
+ds9.icrs.reg,0.011,0.473,100.0%,41.7%
+ds9.mosaic.fk4.reg,0.024,0.768,100.0%,42.9%
+ds9.mosaic.icrs.hms.reg,0.025,0.779,100.0%,42.9%
+ds9.ecliptic.hms.reg,0.012,0.487,100.0%,41.7%
+ds9.fk4.hms.reg,0.014,0.486,100.0%,41.7%
+ds9.mosaic.galactic.hms.reg,0.026,0.761,100.0%,42.9%
+ds9.mosaic.icrs.reg,0.022,0.764,100.0%,42.9%
 ds9.comment.reg,0.000,-1.000,0.0%,nan%
-fk5_reference.reg,0.002,0.217,100.0%,100.0%
-ds9.mosaic.fk5.reg,0.024,0.847,100.0%,37.1%
-ds9.fk4.strip.reg,0.011,0.356,100.0%,43.3%
-ds9.galactic.strip.reg,0.013,0.390,100.0%,43.3%
-ds9.galactic.reg,0.010,0.543,100.0%,36.1%
-ds9.composite.reg,0.011,0.485,100.0%,0.0%
-ds9.linear.wcsa.reg,0.005,0.765,100.0%,37.1%
-ds9.linear.wcsp.reg,0.005,0.757,100.0%,37.1%
-ds9.fk5.hms.strip.reg,0.013,0.342,100.0%,43.3%
-ds9.galactic.hms.reg,0.012,0.467,100.0%,36.1%
-galactic_reference.reg,0.002,0.219,100.0%,100.0%
-ds9.galactic.hms.strip.reg,0.012,0.342,100.0%,43.3%
-ds9.mosaic.physical.reg,0.004,0.765,100.0%,37.1%
-ds9.ecliptic.hms.strip.reg,0.011,0.343,100.0%,43.3%
+fk5_reference.reg,0.003,0.220,100.0%,100.0%
+ds9.mosaic.fk5.reg,0.023,0.749,100.0%,42.9%
+ds9.fk4.strip.reg,0.012,0.351,100.0%,50.0%
+ds9.galactic.strip.reg,0.011,0.349,100.0%,50.0%
+ds9.galactic.reg,0.011,0.493,100.0%,41.7%
+ds9.composite.reg,0.012,0.474,100.0%,41.7%
+ds9.linear.wcsa.reg,0.007,0.775,100.0%,42.9%
+ds9.linear.wcsp.reg,0.007,0.760,100.0%,42.9%
+ds9.fk5.hms.strip.reg,0.013,0.347,100.0%,50.0%
+ds9.galactic.hms.reg,0.013,0.473,100.0%,41.7%
+galactic_reference.reg,0.002,0.220,100.0%,100.0%
+ds9.galactic.hms.strip.reg,0.013,0.346,100.0%,50.0%
+ds9.mosaic.physical.reg,0.007,0.735,100.0%,42.9%
+ds9.ecliptic.hms.strip.reg,0.012,0.345,100.0%,50.0%

dev/regions_pyregion_comparison.py

@@ -20,7 +20,7 @@
 import numpy as np
 import re
 
-TEST_FILE_DIR = Path('../regions/io/tests/data')
+TEST_FILE_DIR = Path('../regions/io/ds9/tests/data')
 REPETITIONS = 1
 
 p_region_count = re.compile(r"[^=\)]\(")

regions/io/__init__.py

@@ -1,5 +1 @@
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
-"""Region I/O.
-"""
-from .read_ds9 import *
-from .write_ds9 import *
+from .ds9 import *

regions/io/ds9/__init__.py

@@ -0,0 +1,2 @@
+from .read import *
+from .write import *

regions/io/ds9/core.py

@@ -0,0 +1,160 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from __future__ import absolute_import, division, print_function
+import string
+import itertools
+import re
+import copy
+from astropy import units as u
+from astropy import coordinates
+from astropy.coordinates import BaseCoordinateFrame
+from astropy import log
+from astropy.utils.exceptions import AstropyUserWarning
+from warnings import warn
+from ... import shapes
+from ...core import PixCoord
+
+__all__ = [
+    'Shape',
+    'ShapeList',
+]
+
+class ShapeList(list):
+    """List of Shape
+    """
+    def to_region(self):
+        regions = list()
+        for shape in self:
+            log.debug(shape)
+            region = shape.to_region()
+            log.debug(region)
+            regions.append(region)
+        return regions
+
+class Shape(object):
+    """Helper class to represent a DS9
+    
+    This serves as intermediate step in the parsing process.
+
+    Parameters
+    ---------
+    coordsys : str
+        Coordinate system
+    region_type : str
+        Region type
+    coord : list of `~astropy.coordinates.Angle` or `~astropy.units.Quantity`
+        Coordinates
+    meta : dict
+        Meta attributed
+    composite : bool
+        Composite region
+    include : bool
+        Include/exclude region
+    """
+    shape_to_sky_region = dict(
+        circle=shapes.CircleSkyRegion,
+        ellipse=shapes.EllipseSkyRegion,
+        box=shapes.RectangleSkyRegion,
+        polygon=shapes.PolygonSkyRegion,
+        annulus=shapes.CircleAnnulusSkyRegion,
+        line=shapes.LineSkyRegion,
+        point=shapes.PointSkyRegion,
+    )
+    shape_to_pixel_region = dict(
+        circle=shapes.CirclePixelRegion,
+        ellipse=shapes.EllipsePixelRegion,
+        box=shapes.RectanglePixelRegion,
+        polygon=shapes.PolygonPixelRegion,
+        annulus=shapes.CircleAnnulusPixelRegion,
+        line=shapes.LinePixelRegion,
+        point=shapes.PointPixelRegion,
+    )
+
+    def __init__(self, coordsys, region_type, coord, meta, composite, include):
+        self.coordsys = coordsys
+        self.region_type=region_type
+        self.coord=coord
+        self.meta=meta
+        self.composite=composite
+        self.include=include
+
+    def __str__(self):
+        ss = self.__class__.__name__
+        ss += '\nCoord sys : {}'.format(self.coordsys)
+        ss += '\nRegion type : {}'.format(self.region_type)
+        ss += '\nCoord: {}'.format(self.coord)
+        ss += '\nMeta: {}'.format(self.meta)
+        ss += '\nComposite: {}'.format(self.composite)
+        ss += '\nInclude: {}'.format(self.include)
+        ss += '\n'
+        return ss
+
+    def convert_coords(self):
+        """Process list of coordinates
+
+        This mainly seaches for tuple of coordinates in the coordinate list and
+        creates a SkyCoord or PixCoord object from them if appropriate for a
+        given region type. This involves again some coordinate transformation,
+        so this step could be moved to the parsing process
+        """
+        from .read import DS9Parser
+        if self.coordsys in DS9Parser.coordsys_mapping:
+            coords = self._convert_sky_coords()
+        else:
+            coords = self._convert_pix_coords()
+
+        if self.region_type == 'line':
+            coords = [coords[0][0], coords[0][1]]
+
+        return coords
+
+    def _convert_sky_coords(self):
+        """Convert to sky coords"""
+        parsed_angles = [(x, y)
+                         for x, y in zip(self.coord[:-1:2], self.coord[1::2])
+                         if (isinstance(x, coordinates.Angle) and
+                             isinstance(y, coordinates.Angle))
+                        ]
+        frame = coordinates.frame_transform_graph.lookup_name(self.coordsys)
+
+        lon, lat = zip(*parsed_angles)
+        if hasattr(lon, '__len__') and hasattr(lon, '__lat__') and len(lon) == 1 and len(lat==1):
+            # force entries to be scalar if they are length-1
+            lon, lat = u.Quantity(lon[0]), u.Quantity(lat[0])
+        else:
+            # otherwise, they are vector quantitites
+            lon, lat = u.Quantity(lon), u.Quantity(lat)
+        sphcoords = coordinates.UnitSphericalRepresentation(lon, lat)
+        coords = [frame(sphcoords)]
+
+        if self.region_type != 'polygon':
+            coords += self.coord[len(coords * 2):]
+
+        return coords
+
+    def _convert_pix_coords(self):
+        """Convert to pix coords"""
+        if self.region_type in ['polygon', 'line']:
+            # have to special-case polygon in the phys coord case
+            # b/c can't typecheck when iterating as in sky coord case
+            coords = [PixCoord(self.coord[0::2], self.coord[1::2])]
+        else:
+            temp = [_.value for _ in self.coord]
+            coord = PixCoord(temp[0], temp[1])
+            coords = [coord] + temp[2:]
+
+        return coords
+
+    def to_region(self):
+        """Convert to region object
+        """
+        coords = self.convert_coords()
+        log.debug(coords)
+        viz_keywords = ['color', 'dashed', 'width', 'point', 'font']
+
+        if isinstance(coords[0], BaseCoordinateFrame):
+            reg = self.shape_to_sky_region[self.region_type](*coords)
+        elif isinstance(coords[0], PixCoord):
+            reg = self.shape_to_pixel_region[self.region_type](*coords)
+        else:
+            raise DS9RegionParserError("No central coordinate")
+        return reg