Commit edcf2dd8 authored by Ambra Di Piano's avatar Ambra Di Piano
Browse files

save maps in npy option

parent c5cfd1a8

astrort/configure/test.yml

+1 −0
Original line number Original line Diff line number Diff line
@@ -18,6 +18,7 @@ mapper: 
  plot: true

  plot: true

  region: false

  region: false

  output: /data01/homes/dipiano/astroRT/astrort/testing/tmp

  output: /data01/homes/dipiano/astroRT/astrort/testing/tmp

  save: npy





visibility:

visibility:

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

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

astrort/simulator/base_mapper.py

+1 −1
Original line number Original line Diff line number Diff line
@@ -37,7 +37,7 @@ def base_mapper(configuration_file, seeds=None): 
        fitsmap = execute_mapper_no_visibility(configuration, log)

        fitsmap = execute_mapper_no_visibility(configuration, log)

        log.info(f"Mapping (seed = {seed}) complete, took {time() - clock_map} s")

        log.info(f"Mapping (seed = {seed}) complete, took {time() - clock_map} s")

        # make plot

        # make plot

        if configuration['mapper']['plot']:

        if configuration['mapper']['plot'] and configuration['mapper']['save'] == 'fits':

            clock_plot = time()

            clock_plot = time()

            plotmap = plot_map(fitsmap, log)

            plotmap = plot_map(fitsmap, log)

            log.info(f"Plotting (seed = {seed}) complete, took {time() - clock_plot} s")

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




import pytest

import pytest

import numpy as np

import numpy as np

from yaml import dump

from shutil import rmtree

from shutil import rmtree

from os import listdir

from os import listdir

from os.path import isfile, join

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.test_conf_file

@pytest.mark.parametrize('seeds', [None, list()])

@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

    # clean output

    conf = load_yaml_conf(test_conf_file)

    conf = load_yaml_conf(test_conf_file)

    conf['mapper']['save'] = save

    rmtree(conf['mapper']['output'], ignore_errors=True)

    rmtree(conf['mapper']['output'], ignore_errors=True)





    # run simulator

    # run simulator

    base_simulator(test_conf_file)

    base_simulator(test_conf_file)

    if type(seeds) == list:

    if type(seeds) == list:

        seeds = np.arange(conf['simulator']['samples'])

        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

    # check output

    expected_maps = conf['simulator']['samples']

    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}"

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

    assert isfile(fitsmap)





@pytest.mark.test_conf_file

@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

    # clean output

    conf = load_yaml_conf(test_conf_file)

    conf = load_yaml_conf(test_conf_file)

    conf['mapper']['save'] = save

    rmtree(conf['mapper']['output'], ignore_errors=True)

    rmtree(conf['mapper']['output'], ignore_errors=True)

    conf['simulator']['samples'] = 1

    conf['simulator']['samples'] = 1

    log = set_logger(logging.CRITICAL)

    log = set_logger(logging.CRITICAL)
@@ -162,5 +164,6 @@ def test_plot_map(test_conf_file): 
    # run simulator

    # run simulator

    base_simulator(test_conf_file)

    base_simulator(test_conf_file)

    fitsmap = execute_mapper_no_visibility(conf, log)

    fitsmap = execute_mapper_no_visibility(conf, log)

    if save == 'fits':

        plotmap = plot_map(fitsmap, log)

        plotmap = plot_map(fitsmap, log)

        assert isfile(plotmap)
 
        assert isfile(plotmap)
 
 No newline at end of file

astrort/utils/mapping.py

+17 −12
Original line number Original line Diff line number Diff line
@@ -191,26 +191,19 @@ class Mapper(): 
        extent = [pointing['ra']-roi, pointing['ra']+roi, pointing['dec']-roi, pointing['dec']+roi]

        extent = [pointing['ra']-roi, pointing['ra']+roi, pointing['dec']-roi, pointing['dec']+roi]

        return extent

        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]]]

        r = [[extent[0], extent[1]], [extent[2], extent[3]]]

        heatmap, xedges, yedges = np.histogram2d(x, y, bins=bins)

        heatmap, xedges, yedges = np.histogram2d(x, y, bins=bins)

        if sigma != 0:

            heatmap = gaussian_filter(heatmap, sigma=sigma)

            heatmap = gaussian_filter(heatmap, sigma=sigma)

        return heatmap.T

        return heatmap.T





    def heatmap(self, x, y, extent, bins=1000):

    def from_dl3_to_dl4(self, dl3_data, pointing, maproi=5, pixelsize=0.02, sigma=0):

        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):

        ra = np.array(dl3_data.field('RA')).flatten()

        ra = np.array(dl3_data.field('RA')).flatten()

        dec = np.array(dl3_data.field('DEC')).flatten()

        dec = np.array(dl3_data.field('DEC')).flatten()

        nbins = self.get_binning_size(maproi=maproi, pixelsize=pixelsize)

        nbins = self.get_binning_size(maproi=maproi, pixelsize=pixelsize)

        extent = self.get_extent(pointing=pointing, roi=maproi)

        extent = self.get_extent(pointing=pointing, roi=maproi)

        if sigma != 0:

        dl4_data = self.get_heatmap(ra, dec, extent=extent, bins=nbins, sigma=sigma)

            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)

        return dl4_data

        return dl4_data





    def selection_cuts(self, dl3_data, pointing, trange=None, erange=None, maproi=None):

    def selection_cuts(self, dl3_data, pointing, trange=None, erange=None, maproi=None):
@@ -224,3 +217,15 @@ class Mapper(): 
        if len(dl3_data) == 0:

        if len(dl3_data) == 0:

            self.log.warning("Empty photon list selection.")

            self.log.warning("Empty photon list selection.")

        return dl3_data

        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