save maps in npy option (edcf2dd8) · Commits · Ambra Di Piano / astroRT

astrort/configure/test.yml

+1 −0

Original line number	Diff line number	Diff line
		@@ -18,6 +18,7 @@ mapper:
		plot: true
		region: false
		output: /data01/homes/dipiano/astroRT/astrort/testing/tmp
		save: npy

		visibility:
		start_time: '2030-01-01T00:00:00'

astrort/simulator/base_mapper.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -37,7 +37,7 @@ def base_mapper(configuration_file, seeds=None):
		fitsmap = execute_mapper_no_visibility(configuration, log)
		log.info(f"Mapping (seed = {seed}) complete, took {time() - clock_map} s")
		# make plot
		if configuration['mapper']['plot']:
		if configuration['mapper']['plot'] and configuration['mapper']['save'] == 'fits':
		clock_plot = time()
		plotmap = plot_map(fitsmap, log)
		log.info(f"Plotting (seed = {seed}) complete, took {time() - clock_plot} s")

astrort/testing/test_simulator/test_base_mapper.py

+11 −3

Original line number	Diff line number	Diff line
		@@ -8,6 +8,7 @@

		import pytest
		import numpy as np
		from yaml import dump
		from shutil import rmtree
		from os import listdir
		from os.path import isfile, join
		@@ -17,21 +18,28 @@ from astrort.utils.wrap import load_yaml_conf

		@pytest.mark.test_conf_file
		@pytest.mark.parametrize('seeds', [None, list()])
		def test_base_mapper(test_conf_file, seeds):
		@pytest.mark.parametrize('save', ['fits', 'npy'])
		def test_base_mapper(test_conf_file, seeds, save):

		# clean output
		conf = load_yaml_conf(test_conf_file)
		conf['mapper']['save'] = save
		rmtree(conf['mapper']['output'], ignore_errors=True)

		# run simulator
		base_simulator(test_conf_file)
		if type(seeds) == list:
		seeds = np.arange(conf['simulator']['samples'])
		base_mapper(test_conf_file, seeds)

		# write new mapper configuration
		update_conf_file = join(conf['mapper']['output'], 'tmp.yml')
		with open(update_conf_file, 'w+') as f:
		dump(conf, f, default_flow_style=False)
		base_mapper(update_conf_file, seeds)

		# check output
		expected_maps = conf['simulator']['samples']
		found_maps = len([f for f in listdir(conf['mapper']['output']) if isfile(join(conf['mapper']['output'], f)) and '.fits' in f and conf['simulator']['name'] in f and 'map' in f])
		found_maps = len([f for f in listdir(conf['mapper']['output']) if isfile(join(conf['mapper']['output'], f)) and conf['mapper']['save'] in f and conf['simulator']['name'] in f and 'map' in f])
		assert found_maps == expected_maps, f"Expected {expected_maps} maps, found {found_maps}"

astrort/testing/test_utils/test_wrap.py

+6 −3

Original line number	Diff line number	Diff line
		@@ -152,9 +152,11 @@ def test_execute_mapper_no_visibility(test_conf_file):
		assert isfile(fitsmap)

		@pytest.mark.test_conf_file
		def test_plot_map(test_conf_file):
		@pytest.mark.parametrize('save', ['fits', 'npy'])
		def test_plot_map(test_conf_file, save):
		# clean output
		conf = load_yaml_conf(test_conf_file)
		conf['mapper']['save'] = save
		rmtree(conf['mapper']['output'], ignore_errors=True)
		conf['simulator']['samples'] = 1
		log = set_logger(logging.CRITICAL)
		@@ -162,5 +164,6 @@ def test_plot_map(test_conf_file):
		# run simulator
		base_simulator(test_conf_file)
		fitsmap = execute_mapper_no_visibility(conf, log)
		if save == 'fits':
		plotmap = plot_map(fitsmap, log)
		assert isfile(plotmap)
		No newline at end of file

astrort/utils/mapping.py

+17 −12

Original line number	Diff line number	Diff line
		@@ -191,26 +191,19 @@ class Mapper():
		extent = [pointing['ra']-roi, pointing['ra']+roi, pointing['dec']-roi, pointing['dec']+roi]
		return extent

		def heatmap_with_smoothing(self, x, y, extent, sigma=1, bins=1000):
		def get_heatmap(self, x, y, extent, sigma=0, bins=1000):
		r = [[extent[0], extent[1]], [extent[2], extent[3]]]
		heatmap, xedges, yedges = np.histogram2d(x, y, bins=bins)
		if sigma != 0:
		heatmap = gaussian_filter(heatmap, sigma=sigma)
		return heatmap.T

		def heatmap(self, x, y, extent, bins=1000):
		r = [[extent[0], extent[1]], [extent[2], extent[3]]]
		heatmap, xedges, yedges = np.histogram2d(x, y, bins=bins)
		return heatmap.T

		def from_dl3_to_dl4(self, dl3_data, pointing, maproi=5, pixelsize=0.02, sigma=1):
		def from_dl3_to_dl4(self, dl3_data, pointing, maproi=5, pixelsize=0.02, sigma=0):
		ra = np.array(dl3_data.field('RA')).flatten()
		dec = np.array(dl3_data.field('DEC')).flatten()
		nbins = self.get_binning_size(maproi=maproi, pixelsize=pixelsize)
		extent = self.get_extent(pointing=pointing, roi=maproi)
		if sigma != 0:
		dl4_data = self.heatmap_with_smoothing(ra, dec, extent=extent, bins=nbins, sigma=sigma)
		else:
		dl4_data = self.heatmap(ra, dec, extent=extent, bins=nbins)
		dl4_data = self.get_heatmap(ra, dec, extent=extent, bins=nbins, sigma=sigma)
		return dl4_data

		def selection_cuts(self, dl3_data, pointing, trange=None, erange=None, maproi=None):
		@@ -224,3 +217,15 @@ class Mapper():
		if len(dl3_data) == 0:
		self.log.warning("Empty photon list selection.")
		return dl3_data

		def get_countmap_in_npy(self, dl3_file, pixelsize=0.02, maproi=5, trange=None, erange=None, sigma=1, npyname='heatmap.npy'):
		dl3_hdr = self.get_dl3_hdr(dl3_file=dl3_file)
		pointing = {'ra': float(dl3_hdr['RA_PNT']), 'dec': float(dl3_hdr['DEC_PNT'])}
		dl3_data = self.get_dl3_data(dl3_file=dl3_file)
		dl3_data = self.selection_cuts(dl3_data=dl3_data, pointing=pointing, trange=trange, erange=erange, maproi=maproi)
		if sigma != 0:
		dl4_data = self.from_dl3_to_dl4(dl3_data=dl3_data, pointing=pointing, maproi=maproi, pixelsize=0.02, sigma=sigma)
		else:
		dl4_data = self.from_dl3_to_dl4(dl3_data=dl3_data, pointing=pointing, maproi=maproi, pixelsize=pixelsize)
		np.save(npyname, dl4_data, allow_pickle=True, fix_imports=True)
		return