Merge pull request #7 from joleroi/region_tests

Add tests for ds9 region parser

.travis.yml

@@ -20,7 +20,7 @@ env:
         # The following versions are the 'default' for tests, unless
         # overidden underneath. They are defined here in order to save having
         # to repeat them for all configurations.
-        - NUMPY_VERSION=1.9
+        - NUMPY_VERSION=1.10
         - ASTROPY_VERSION=stable
         - SETUP_CMD='test'
         - PIP_DEPENDENCIES=''
@@ -54,6 +54,8 @@ matrix:
           env: ASTROPY_VERSION=development
 
         # Try older numpy versions
+        - python: 2.7
+          env: NUMPY_VERSION=1.9
         - python: 2.7
           env: NUMPY_VERSION=1.8
         - python: 2.7

regions/conftest.py

@@ -6,7 +6,7 @@
 
 ## Uncomment the following line to treat all DeprecationWarnings as
 ## exceptions
-enable_deprecations_as_exceptions()
+#enable_deprecations_as_exceptions()
 
 ## Uncomment and customize the following lines to add/remove entries
 ## from the list of packages for which version numbers are displayed

regions/io/__init__.py

@@ -0,0 +1,6 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""I/O
+"""
+from .read_ds9 import *
+from .write_ds9 import *
+

regions/io/read_ds9.py

@@ -0,0 +1,263 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+
+import string
+import itertools
+import re
+from astropy import units as u
+from astropy import coordinates
+from ..shapes import circle, rectangle, polygon, ellipse
+from ..core import PixCoord
+
+
+def read_ds9(filename):
+    region_list = ds9_parser(filename)
+    return region_list_to_objects(region_list)
+
+
+def coordinate(string_rep, unit):
+    # Any ds9 coordinate representation (sexagesimal or degrees)
+    if 'd' in string_rep or 'h' in string_rep:
+        return coordinates.Angle(string_rep)
+    elif unit is 'hour_or_deg':
+        if ':' in string_rep:
+            return coordinates.Angle(string_rep, unit=u.hour)
+        else:
+            return coordinates.Angle(string_rep, unit=u.deg)
+    elif unit.is_equivalent(u.deg):
+        return coordinates.Angle(string_rep, unit=unit)
+    else:
+        return u.Quantity(float(string_rep), unit)
+
+unit_mapping = {'"': u.arcsec,
+                "'": u.arcmin,
+                'r': u.rad,
+                'i': u.dimensionless_unscaled,
+               }
+
+
+def angular_length_quantity(string_rep):
+    has_unit = string_rep[-1] not in string.digits
+    if has_unit:
+        unit = unit_mapping[string_rep[-1]]
+        return u.Quantity(float(string_rep[:-1]), unit=unit)
+    else:
+        return u.Quantity(float(string_rep), unit=u.deg)
+
+# these are the same function, just different names
+radius = angular_length_quantity
+width = angular_length_quantity
+height = angular_length_quantity
+angle = angular_length_quantity
+
+language_spec = {'point': (coordinate, coordinate),
+                 'circle': (coordinate, coordinate, radius),
+                 # This is a special case to deal with n elliptical annuli
+                 'ellipse': itertools.chain((coordinate, coordinate), itertools.cycle((radius, ))),
+                 'box': (coordinate, coordinate, width, height, angle),
+                 'polygon': itertools.cycle((coordinate, )),
+                }
+
+coordinate_systems = ['fk5', 'fk4', 'icrs', 'galactic', 'wcs', 'physical', 'image', 'ecliptic']
+coordinate_systems += ['wcs{0}'.format(letter) for letter in string.ascii_lowercase]
+
+coordsys_name_mapping = dict(zip(coordinates.frame_transform_graph.get_names(),
+                                 coordinates.frame_transform_graph.get_names()))
+coordsys_name_mapping['ecliptic'] = 'geocentrictrueecliptic' # needs expert attention TODO
+
+hour_or_deg = 'hour_or_deg'
+coordinate_units = {'fk5': (hour_or_deg, u.deg),
+                    'fk4': (hour_or_deg, u.deg),
+                    'icrs': (hour_or_deg, u.deg),
+                    'geocentrictrueecliptic': (u.deg, u.deg),
+                    'galactic': (u.deg, u.deg),
+                    'physical': (u.dimensionless_unscaled, u.dimensionless_unscaled),
+                    'image': (u.dimensionless_unscaled, u.dimensionless_unscaled),
+                    'wcs': (u.dimensionless_unscaled, u.dimensionless_unscaled),
+                   }
+for letter in string.ascii_lowercase:
+    coordinate_units['wcs{0}'.format(letter)] = (u.dimensionless_unscaled, u.dimensionless_unscaled)
+
+region_type_or_coordsys_re = re.compile("^#? *(-?)([a-zA-Z0-9]+)")
+
+paren = re.compile("[()]")
+
+def strip_paren(string_rep):
+    return paren.sub("", string_rep)
+
+
+def region_list_to_objects(region_list):
+    viz_keywords = ['color', 'dashed', 'width', 'point', 'font', 'text']
+
+    output_list = []
+    for region_type, coord_list, meta in region_list:
+        #print("region_type, region_type is 'circle', type(region_type), type('circle'), id(region_type), id('circle'), id(str(region_type))")
+        #print(region_type, region_type is 'circle', type(region_type), type('circle'), id(region_type), id('circle'), id(str(region_type)))
+        if region_type == 'circle':
+            if isinstance(coord_list[0], coordinates.SkyCoord):
+                reg = circle.CircleSkyRegion(coord_list[0], coord_list[1])
+            elif isinstance(coord_list[0], PixCoord):
+                reg = circle.CirclePixelRegion(coord_list[0], coord_list[1])
+            else:
+                raise ValueError("No central coordinate")
+        elif region_type == 'ellipse':
+            # Do not read elliptical annuli for now
+            if len(coord_list) > 4:
+                continue
+            if isinstance(coord_list[0], coordinates.SkyCoord):
+                reg = ellipse.EllipseSkyRegion(coord_list[0], coord_list[1], coord_list[2], coord_list[3])
+            elif isinstance(coord_list[0], PixCoord):
+                reg = ellipse.EllipsePixelRegion(coord_list[0], coord_list[1], coord_list[2], coord_list[3])
+            else:
+                raise ValueError("No central coordinate")
+        elif region_type == 'polygon':
+            if isinstance(coord_list[0], coordinates.SkyCoord):
+                reg = polygon.PolygonSkyRegion(coord_list[0])
+            elif isinstance(coord_list[0], PixCoord):
+                reg = polygon.PolygonPixelRegion(coord_list[0])
+            else:
+                raise ValueError("No central coordinate")
+        elif region_type == 'rectangle':
+            if isinstance(coord_list[0], coordinates.SkyCoord):
+                reg = rectangle.RectangleSkyRegion(coord_list[0], coord_list[1], coord_list[2], coord_list[3])
+            elif isinstance(coord_list[0], PixCoord):
+                reg = rectangle.RectanglePixelRegion(coord_list[0], coord_list[1], coord_list[2], coord_list[3])
+            else:
+                raise ValueError("No central coordinate")
+        else:
+            continue
+        reg.vizmeta = {key: meta[key] for key in meta.keys() if key in viz_keywords}
+        reg.meta = {key: meta[key] for key in meta.keys() if key not in viz_keywords}
+        output_list.append(reg)
+    return output_list
+
+
+def ds9_parser(filename):
+    """
+    Parse a complete ds9 .reg file
+
+    Returns
+    -------
+    list of (region type, coord_list, meta) tuples
+    """
+    coordsys = None
+    regions = []
+    composite_region = None
+
+    with open(filename,'r') as fh:
+        for line_ in fh:
+            # ds9 regions can be split on \n or ;
+            for line in line_.split(";"):
+                parsed = line_parser(line, coordsys)
+                if parsed in coordinate_systems:
+                    coordsys = parsed
+                elif parsed:
+                    region_type, coordlist, meta, composite = parsed
+                    if composite and composite_region is None:
+                        composite_region = [(region_type, coordlist)]
+                    elif composite:
+                        composite_region.append((region_type, coordlist))
+                    elif composite_region is not None:
+                        composite_region.append((region_type, coordlist))
+                        regions.append(composite_region)
+                        composite_region = None
+                    else:
+                        regions.append((region_type, coordlist, meta))
+
+    return regions
+
+
+def line_parser(line, coordsys=None):
+    region_type_search = region_type_or_coordsys_re.search(line)
+    if region_type_search:
+        include = region_type_search.groups()[0]
+        region_type = region_type_search.groups()[1]
+    else:
+        return
+
+    if region_type in coordinate_systems:
+        return region_type # outer loop has to do something with the coordinate system information
+    elif region_type in language_spec:
+        if coordsys is None:
+            raise ValueError("No coordinate system specified and a region has been found.")
+
+        if "||" in line:
+            composite = True
+        else:
+            composite = False
+
+        # end_of_region_name is the coordinate of the end of the region's name, e.g.:
+        # circle would be 6 because circle is 6 characters
+        end_of_region_name = region_type_search.span()[1]
+        # coordinate of the # symbol or end of the line (-1) if not found
+        hash_or_end = line.find("#")
+        coords_etc = strip_paren(line[end_of_region_name:hash_or_end].strip(" |"))
+        meta_str = line[hash_or_end:]
+
+        parsed_meta = meta_parser(meta_str)
+
+        if coordsys in coordsys_name_mapping:
+            parsed = type_parser(coords_etc, language_spec[region_type],
+                                 coordsys_name_mapping[coordsys])
+
+            # Reset iterator for ellipse annulus
+            if region_type == 'ellipse':
+                language_spec[region_type] = itertools.chain((coordinate, coordinate), itertools.cycle((radius, )))
+
+            coords = coordinates.SkyCoord([(x, y)
+                                           for x, y in zip(parsed[:-1:2], parsed[1::2])
+                                           if isinstance(x, coordinates.Angle) and
+                                           isinstance(x, coordinates.Angle)], frame=coordsys_name_mapping[coordsys])
+
+            return region_type, [coords] + parsed[len(coords)*2:], parsed_meta, composite
+        else:
+            parsed = type_parser(coords_etc, language_spec[region_type],
+                                 coordsys)
+            if region_type == 'polygon':
+                # have to special-case polygon in the phys coord case b/c can't typecheck when iterating as in sky coord case
+                coord = PixCoord(parsed[0::2], parsed[1::2])
+                parsed_return = [coord]
+            else:
+                parsed = [_.value for _ in parsed]
+                coord = PixCoord(parsed[0], parsed[1])
+                parsed_return = [coord]+parsed[2:]
+
+            # Reset iterator for ellipse annulus
+            if region_type == 'ellipse':
+                language_spec[region_type] = itertools.chain((coordinate, coordinate), itertools.cycle((radius, )))
+
+            return region_type, parsed_return, parsed_meta, composite
+
+
+def type_parser(string_rep, specification, coordsys):
+    coord_list = []
+    splitter = re.compile("[, ]")
+    for ii, (element, element_parser) in enumerate(zip(splitter.split(string_rep), specification)):
+        if element_parser is coordinate:
+            unit = coordinate_units[coordsys][ii % 2]
+            coord_list.append(element_parser(element, unit))
+        else:
+            coord_list.append(element_parser(element))
+
+    return coord_list
+
+
+# match an x=y pair (where y can be any set of characters) that may or may not
+# be followed by another one
+meta_token = re.compile("([a-zA-Z]+)(=)([^= ]+) ?")
+
+#meta_spec = {'color': color,
+#            }
+# global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
+# ruler(+175:07:14.900,+50:56:21.236,+175:06:52.643,+50:56:11.190) ruler=physical physical color=white font="helvetica 12 normal roman" text={Ruler}
+
+
+
+def meta_parser(meta_str):
+    meta_token_split = [x for x in meta_token.split(meta_str.strip()) if x]
+    equals_inds = [i for i, x in enumerate(meta_token_split) if x is '=']
+    result = {meta_token_split[ii-1]:
+              " ".join(meta_token_split[ii+1:jj-1 if jj is not None else None])
+              for ii,jj in zip(equals_inds, equals_inds[1:]+[None])}
+
+    return result
+

regions/io/setup_package.py

@@ -0,0 +1,6 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+import os
+
+def get_package_data():
+    parser_test = ['data/*.reg']
+    return {'regions.io.tests': parser_test}

regions/io/tests/__init__.py

@@ -0,0 +1,4 @@
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+"""
+This packages contains affiliated package tests.
+"""

regions/io/tests/data/ds9.color.reg

@@ -0,0 +1,10 @@
+# Region file format: DS9 version 4.1
+global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
+fk5
+circle(13:29:52.675,+47:11:45.02,1") # color=blue
+circle(13:29:52.675,+47:11:45.02,2") # color=#800
+circle(13:29:52.675,+47:11:45.02,3") # color=#0a0
+circle(13:29:52.675,+47:11:45.02,4") # color=#880000
+circle(13:29:52.675,+47:11:45.02,5") # color=#00aa00
+circle(13:29:52.675,+47:11:45.02,6") # color=#888800000000
+circle(13:29:52.675,+47:11:45.02,7") # color=#0000aaaa0000

regions/io/tests/data/ds9.comment.reg

@@ -0,0 +1,10 @@
+# Region file format: DS9 version 4.0
+#
+# foobar
+# foobar+
+# foo+bar
+## foobar
+### foobar
+#. foobar
+##. foobar
+

regions/io/tests/data/ds9.composite.reg

@@ -0,0 +1,39 @@
+# Region file format: DS9 version 4.1
+global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1
+fk5
+# composite(202.48165,47.1931,317.39831) || composite=1
+circle(202.48705,47.208237,3.9640007") || # color=pink width=3 font="times 10 normal roman" text={Circle} tag={foo} tag={foo bar} This is a Comment
+-ellipse(202.48309,47.204492,7.9280014",3.9640007",2.3983109) || # color=#0ff font="helvetica 10 normal italic" text={Ellipse} background
+-box(202.47783,47.201057,15.856003",7.9280014",2.3983109) || # color=yellow font="helvetica 10 bold roman" text={Box}
+polygon(202.47309,47.198922,202.46877,47.199044,202.46859,47.196108,202.47291,47.195985) || # font="courier 10 normal roman" text={Polygon} edit=0 rotate=0
+-line(202.4684,47.194116,202.46202,47.193946) || # line=1 1 color=cyan text={Line}
+# vector(202.46159,47.191504,7.9280014",2.3983109) || vector=1 color=red text={Vector}
+# text(202.45907,47.188886) || color=magenta font="helvetica 14 bold roman" text={Region}
+# ruler(202.48176,47.194165,202.47471,47.194171) || ruler=physical physical color=white font="helvetica 12 normal roman" text={Ruler}
+annulus(202.49319,47.203697,1.9820003",3.9640007",5.946001") || # color=magenta font="helvetica 10 bold roman" text={Annulus}
+ellipse(202.48834,47.200368,2.9730005",1.4865003",5.946001",2.9730005",2.3983109) || # color=red width=3 font="helvetica 10 bold roman" text={Ellipse Annulus}
+box(202.4832,47.197085,7.9280014",3.9640007",11.892002",5.946001",2.3983109) || # font="helvetica 10 bold roman" text={Box Annulus}
+point(202.49871,47.200189) || # point=circle text={Circle Point}
+point(202.49351,47.196791) || # point=box color=red width=3 text={Box Point}
+point(202.48857,47.193854) || # point=diamond text={Diamond Point}
+point(202.5005,47.197643) || # point=cross color=blue text={Cross Point}
+point(202.49591,47.194852) || # point=x text={X Point}
+point(202.49148,47.191862) || # point=arrow color=magenta text={Arrow Point}
+point(202.49864,47.19267) || # point=boxcircle text={BoxCircle Point}
+# projection(202.47611,47.189884,202.46694,47.189092,3.9640007") || text={Projection}
+panda(202.48266,47.190165,317.39831,587.39831,3,0",5.946001",2) || # text={Panda}
+panda(202.48753,47.186403,8.9802109,47.398311,1,0",2.9730005",1) || # panda=(8.9802109 47.398311 137.39831 227.39831)(0" 2.9730005" 5.946001") text={Panda 2}
+panda(202.48753,47.186403,8.9802109,47.398311,1,2.9730005",5.946001",1) || # panda=ignore
+panda(202.48753,47.186403,47.398311,137.39831,1,0",2.9730005",1) || # panda=ignore
+panda(202.48753,47.186403,47.398311,137.39831,1,2.9730005",5.946001",1) || # panda=ignore
+panda(202.48753,47.186403,137.39831,227.39831,1,0",2.9730005",1) || # panda=ignore
+panda(202.48753,47.186403,137.39831,227.39831,1,2.9730005",5.946001",1) || # panda=ignore
+# compass(202.46768,47.186188,7.9280014") || compass=physical {N} {E} 1 1 text={Compass}
+epanda(202.47821,47.186785,317.39831,587.39831,3,2.9730005",1.4865003",5.946001",2.9730005",1,2.3983109) || # text={Epanda}
+epanda(202.48291,47.183066,2.3983109,47.398311,1,2.9730005",1.4865003",5.946001",2.9730005",1,2.3983109) || # epanda=(2.3983109 47.398311 137.39831 227.39831)(2.9730005" 1.4865003" 5.946001" 2.9730005")(2.3983109) text={Epanda 2}
+epanda(202.48291,47.183066,47.398311,137.39831,1,2.9730005",1.4865003",5.946001",2.9730005",1,2.3983109) || # epanda=ignore
+epanda(202.48291,47.183066,137.39831,227.39831,1,2.9730005",1.4865003",5.946001",2.9730005",1,2.3983109) || # epanda=ignore
+bpanda(202.47302,47.183543,317.39831,587.39831,3,7.9280014",3.9640007",11.892002",5.946001",1,2.3983109) || # text={Bpanda}
+bpanda(202.47809,47.180126,2.3983109,47.398311,1,7.9280014",3.9640007",11.892002",5.946001",1,2.3983109) # bpanda=(2.3983109 47.398311 137.39831 227.39831)(7.9280014" 3.9640007" 11.892002" 5.946001")(2.3983109) text={Bpanda 2}
+bpanda(202.47809,47.180126,47.398311,137.39831,1,7.9280014",3.9640007",11.892002",5.946001",1,2.3983109) # bpanda=ignore
+bpanda(202.47809,47.180126,137.39831,227.39831,1,7.9280014",3.9640007",11.892002",5.946001",1,2.3983109) # bpanda=ignore