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release version 0.1.5
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Fix respecting bounds bug
Auto plot reference reefs as points or polygons
Config options for point size
Config option for sub-sampling
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@didillysquat
didillysquat committed Jan 11, 2021
1 parent a3b6e56 commit 2c3bded
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Showing 3 changed files with 125 additions and 45 deletions.
2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,5 @@ __pycache__
conda_build
conda_packages
reefMapMaker.egg-info
14_001_WCMC008_CoralReefs2018_v4/
reefMapMaker_Zenodo.org.docx
166 changes: 122 additions & 44 deletions reefmapmaker/reefmapmaker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
warnings.filterwarnings("ignore", category=DownloadWarning)


__version__ = "v0.1.4"
__version__ = "v0.1.5"


class ReefMapMaker:
Expand Down Expand Up @@ -114,7 +114,10 @@ def __init__(self):
self.args = parser.parse_args()
self.root_dir = os.getcwd()
self.date_time = str(datetime.now()).split('.')[0].replace('-', '').replace(' ', 'T').replace(':', '')

if self.args.sub_sample:
self.sub_sample = int(self.args.sub_sample)
else:
self.sub_sample = 1
# User input
# We will allow user configurations through both the command line and a config file
# Prioritise command line input over config sheet input
Expand All @@ -123,6 +126,9 @@ def __init__(self):
'plot_land', 'land_color', 'plot_grid_lines', 'lon_grid_line_pos', 'lat_grid_line_pos',
'lon_grid_lab_pos', 'lat_grid_lab_pos', 'plot_boundaries', 'dpi']
self._set_param_defaults_dict()
# Lat and lon are both set once the bounds are set in config_setup
self.lat = None
self.lon = None
if self.args.config_sheet:
self._config_setup_with_sheet()
else:
Expand All @@ -140,11 +146,13 @@ def __init__(self):
self.large_map_ax = plt.subplot(projection=ccrs.PlateCarree(), zorder=1)
self.large_map_ax.set_extent(extents=(
self.config_dict['bounds'][0], self.config_dict['bounds'][1], self.config_dict['bounds'][2],
self.config_dict['bounds'][3]))
self.config_dict['bounds'][3]), crs=ccrs.PlateCarree())
# Scalar for converting the user inputted coordinate radii to point format for plotting
self.coord_to_point_scaler = self._calc_scaler()

self._setup_fig_output_paths()
self.plot_points = True
self.points = [[],[]]

def _setup_fig_output_paths(self):
if not self.args.fig_out_dir:
Expand Down Expand Up @@ -200,7 +208,8 @@ def _set_param_defaults_dict(self):
'plot_grid_lines': True, 'lon_grid_line_pos': None,
'lat_grid_line_pos': None, 'lon_grid_lab_pos': 'bottom',
'lat_grid_lab_pos': 'left', 'plot_boundaries': True,
'reference_reef_edge_width': None, 'user_site_labels': True, 'dpi': 1200
'reference_reef_edge_width': None, 'reference_reef_point_size': None,
'user_site_labels': True, 'dpi': 1200
}

def _check_site_sheet(self):
Expand Down Expand Up @@ -363,13 +372,12 @@ def _setup_map_figure(self):
Set fig size ratios according to lat lon ratios
"""
big_fig_size = 10
lat = self.config_dict['bounds'][3] - self.config_dict['bounds'][2]
lon = self.config_dict['bounds'][1] - self.config_dict['bounds'][0]

# figsize is w x h
if lat > lon:
fig = plt.figure(figsize=((lon / lat) * big_fig_size, big_fig_size))
if self.lat > self.lon:
fig = plt.figure(figsize=((self.lon / self.lat) * big_fig_size, big_fig_size))
else:
fig = plt.figure(figsize=(big_fig_size, (lat / lon) * big_fig_size))
fig = plt.figure(figsize=(big_fig_size, (self.lat / self.lon) * big_fig_size))
return fig

def _find_shape_path(self):
Expand Down Expand Up @@ -436,21 +444,45 @@ def _setup_config(self):
'bounds', 'plot_sea', 'sea_color', 'plot_reference_reefs',
'reference_reef_color', 'reference_reef_edge_width', 'reference_reef_edge_color',
'plot_land', 'land_color', 'plot_grid_lines', 'lon_grid_line_pos', 'lat_grid_line_pos',
'lon_grid_lab_pos', 'lat_grid_lab_pos', 'plot_boundaries', 'dpi'
'lon_grid_lab_pos', 'lat_grid_lab_pos', 'plot_boundaries', 'dpi', plot_type
"""
self._proper_type_param_val()
self._check_bounds()
self.lat = self.config_dict['bounds'][3] - self.config_dict['bounds'][2]
self.lon = self.config_dict['bounds'][1] - self.config_dict['bounds'][0]
self._check_bool_params()
self._check_ref_reef_edge_width()
self._check_ref_reef_point_size()
self._check_color_params()
self._check_grid_lab_pos()
self._check_grid_line_coords()
self._check_dpi()
if self.lat > 10 or self.lon > 10:
self.param_defaults_dict['plot_type'] = 'point'
else:
self.param_defaults_dict['plot_type'] = 'polygon'
self._check_plot_type()

def _check_plot_type(self):
cl_param_set, config_param_set = self._param_set(param='plot_type')
self._set_config_param(param='plot_type', cl_param=cl_param_set,
config_param=config_param_set)

def _check_dpi(self):
cl_param_set, config_param_set = self._param_set(param='dpi')
self._set_config_param(param='dpi', cl_param=cl_param_set,
config_param=config_param_set)

def _check_ref_reef_point_size(self):
"""
Check user provided valid value for reference_reef_point_size or set default
"""
if self.config_dict['plot_reference_reefs']:
cl_param_set, config_param_set = self._param_set(param='reference_reef_point_size')
self._set_config_param(param='reference_reef_point_size', cl_param=cl_param_set,
config_param=config_param_set)


def _check_ref_reef_edge_width(self):
"""
Check user provided valid value for reference_reef_edge_width or set default
Expand Down Expand Up @@ -651,13 +683,21 @@ def _proper_type_param_val(self):
self.config_dict[param] = False
elif self.config_dict[param].lower() in ['none']:
self.config_dict[param] = None
elif self.config_dict[param].lower() in ['points', 'point']:
self.config_dict[param] = 'point'
elif self.config_dict[param].lower() in ['polygons', 'polygon']:
self.config_dict[param] = 'polygon'
if getattr(self.args, param):
if getattr(self.args, param).lower() in ['t', 'true']:
setattr(self.args, param, True)
elif getattr(self.args, param).lower() in ['f', 'false']:
setattr(self.args, param, False)
elif getattr(self.args, param).lower() in ['none']:
setattr(self.args, param, None)
elif getattr(self.args, param).lower() in ['points', 'point']:
setattr(self.args, param, 'point')
elif getattr(self.args, param).lower() in ['polygons', 'polygon']:
setattr(self.args, param, 'polygon')

def _notify_user_set_config_dict_param(self, param):
print(f'{param} set to: {self.config_dict[param]}')
Expand Down Expand Up @@ -707,12 +747,24 @@ def _define_config_args(parser):
parser.add_argument(
'--reference-reef-edge-width',
help='The thickness of the line width for the reference reef polygons in points.\n'
'This will only have an effect when reference reefs are being '
'plotted as polygons rather than points.\n'
'By default this is set to None and the reefs are plotted as only filled polygons with no stroke.\n'
'However, for zoomed out maps, it may be necessary to stroke the reef polygons with a thicker line '
'in order to be able to see the reefs.'
'[None]',
required=False
)
parser.add_argument(
'--reference-reef-point-size',
help='The size of the points used to represent reference reefs when being plotted as points\n'
'Units are given as a fraction of the shortest side of the map.\n'
'This will only have an effect when reference reefs are being plotted as points rather than polygons.'
'E.g. the default is set to 200, which means that the points will be a diameter of '
'1/200 of the shortest side of the map.\n To make points bigger, make this number smaller.'
'[200]',
required=False
)
parser.add_argument(
'--reference-reef-edge-color',
help='The color of the reference reef edge lines.\n'
Expand Down Expand Up @@ -804,6 +856,17 @@ def _define_runtime_args(parser):
'Default is current working directory. The dataset can be downloaded from: '
'https://data.unep-wcmc.org/datasets/1'
)
parser.add_argument('--sub-sample', help="Subsample the reference reef shape file "
"keeping 1 in every <sub-sample> reef record. Subsampling will "
"drastically speed up the time it takes for the code to run, "
"but fewer reefs will be plotted. This is extremely useful for "
"experimenting with your configuration parameters."
"E.g. If sub-sample = 100 only 1 in every 100 reef records from "
"the reference reef shape file will be used. "
"Default = no subsampling.")
parser.add_argument('--plot-type', help='[point|polygon]. How the reference reefs will be '
'represented on the plot. Defaults to "point" when '
'either lat or lon are > 10 degrees. Otherwise, "polygon".')

def draw_map(self):
land_110m, ocean_110m, boundary_110m = self._get_naural_earth_features_big_map()
Expand Down Expand Up @@ -874,23 +937,29 @@ def _add_reference_reefs(self):
reef_count = 0
checked_count = 0
start_time = time.time()
for r in reader.records(): # reader.records() produces a generator
try:
if r.geometry.geom_type.lower() == 'multipolygon':
checked_count, reef_count = self._handle_multipolygon(
checked_count, r, reef_count, start_time
)
elif r.geometry.geom_type.lower() == 'polygon':
checked_count, reef_count = self._handle_polygon(
checked_count, r, reef_count, start_time
)
except Exception:
# The common error that occurs is Unexpected Error: unable to find ring point
# We've given up trying to catch this is a more elegant way
# The class of exception raised is Exception in shapefile.py
error_count += 1
continue

for n, r in enumerate(reader.records()): # reader.records() produces a generator
if n % self.sub_sample == 0:
try:
if r.geometry.geom_type.lower() == 'multipolygon':
checked_count, reef_count = self._handle_multipolygon(
checked_count, r, reef_count, start_time
)
elif r.geometry.geom_type.lower() == 'polygon':
checked_count, reef_count = self._handle_polygon(
checked_count, r, reef_count, start_time
)
except Exception:
# The common error that occurs is Unexpected Error: unable to find ring point
# We've given up trying to catch this is a more elegant way
# The class of exception raised is Exception in shapefile.py
error_count += 1
continue
if self.config_dict['plot_type'] == 'point':
self._plot_ref_scatter(coords_x=self.points[0], coords_y=self.points[1])
else:
# We are plotting polygons and they have already been added to the plot.
pass
self._report_on_ref_reef_plotting(error_count, reef_count)

@staticmethod
Expand Down Expand Up @@ -935,9 +1004,11 @@ def _report_checked_reef_number(self, checked_count, start_time):
def _make_and_add_ref_reef_patches(self, coords):
self._make_and_add_poly(coords)

def _plot_ref_scatter(self, coords):
coords_x, coords_y = self._concat_input_coord_arrays(coords)
def _plot_ref_scatter(self, coords_x, coords_y):
# coords_x, coords_y = self._concat_input_coord_arrays(coords)

point_size = self._calc_ref_point_size()
# point_size = 10
self.large_map_ax.scatter(x=coords_x, y=coords_y, s=point_size ** 2, zorder=2,
facecolors=self.config_dict['reference_reef_color'], edgecolors='none')
return coords_x
Expand All @@ -949,28 +1020,35 @@ def _concat_input_coord_arrays(self, coords):

def _calc_ref_point_size(self):
# A sensible size is perhaps 1/500th of the shortest size
lat = self.config_dict['bounds'][3] - self.config_dict['bounds'][2]
lon = self.config_dict['bounds'][1] - self.config_dict['bounds'][0]
if lat > lon:
deg_size = lon / 500
if self.config_dict['reference_reef_point_size']:
div = int(self.config_dict['reference_reef_point_size'])
else:
div = 200
if self.lat > self.lon:
deg_size = self.lon / div
else:
deg_size = lat / 500
deg_size = self.lat / div
point_size = self.coord_to_point_scaler * deg_size
return point_size

def _make_and_add_poly(self, coords):
if self.config_dict['reference_reef_edge_width']:
reef_poly = Polygon([(x, y) for x, y in zip(list(coords[0]), list(coords[1]))],
closed=True, fill=True, edgecolor=self.config_dict['reference_reef_edge_color'],
facecolor=self.config_dict['reference_reef_color'],
linewidth=float(self.config_dict['reference_reef_edge_width']),
alpha=1, zorder=2)
if self.config_dict['plot_type'] == 'point':
self.points[0].append(sum(list(coords[0]))/len(list(coords[0])))
self.points[1].append(sum(list(coords[1])) / len(list(coords[1])))
else:
reef_poly = Polygon([(x, y) for x, y in zip(list(coords[0]), list(coords[1]))],
closed=True, fill=True, edgecolor=None,
facecolor=self.config_dict['reference_reef_color'],
alpha=1, zorder=2)
self.large_map_ax.add_patch(reef_poly)
# Plotting polygons
if self.config_dict['reference_reef_edge_width']:
reef_poly = Polygon([(x, y) for x, y in zip(list(coords[0]), list(coords[1]))],
closed=True, fill=True, edgecolor=self.config_dict['reference_reef_edge_color'],
facecolor=self.config_dict['reference_reef_color'],
linewidth=float(self.config_dict['reference_reef_edge_width']),
alpha=1, zorder=2)
else:
reef_poly = Polygon([(x, y) for x, y in zip(list(coords[0]), list(coords[1]))],
closed=True, fill=True, edgecolor=None,
facecolor=self.config_dict['reference_reef_color'],
alpha=1, zorder=2)
self.large_map_ax.add_patch(reef_poly)

def _if_within_bounds(self, bounds):
"""
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@

setuptools.setup(
name="reefmapmaker", # Replace with your own username
version='0.1.4',
version='0.1.5',
author="Benjamin C C Hume",
author_email="[email protected]",
description="Script to plot maps with reference coral reefs annotated.",
Expand Down

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