timewise 0.5.4__py3-none-any.whl → 1.0.0a1__py3-none-any.whl

timewise/point_source_utils.py

@@ -1,68 +0,0 @@
-import logging
-import pandas as pd
-
-from timewise.parent_sample_base import ParentSampleBase
-from timewise.wise_data_by_visit import WiseDataByVisit
-
-
-logger = logging.getLogger(__name__)
-
-
-###########################################################################################################
-#            START POINT SOURCE  UTILS              #
-#####################################################
-
-
-def get_point_source_parent_sample(base_name, ra, dec):
-
-    class PointSourceParentSample(ParentSampleBase):
-        default_keymap = {
-            'ra': 'ra',
-            'dec': 'dec',
-            'id': 'id'
-        }
-
-        def __init__(self):
-
-            super().__init__(base_name=base_name)
-
-            self.base_name = base_name
-            self.df = pd.DataFrame({'ra': [ra], 'dec': [dec], 'id': [base_name]})
-
-        def save_local(self):
-            logger.debug(f"not saving")
-
-    return PointSourceParentSample
-
-
-def get_point_source_wise_data(base_name, ra, dec, min_sep_arcsec=10, match=False, **kwargs):
-    """
-    Get a WISEData instance for a point source
-
-    :param base_name: base name for storage in the data directory
-    :type base_name: str
-    :param ra: right ascencion
-    :type ra: float
-    :param dec: declination
-    :type dec: float
-    :param min_sep_arcsec: search radius in arcsec
-    :type min_sep_arcsec: float
-    :param match: match to AllWISE Source Catalogue
-    :type match: bool
-    :param kwargs: keyword arguments passed to WISEData.get_photometric_data()
-    :type kwargs: dict
-    :return: WISEData
-    """
-    ps = get_point_source_parent_sample(base_name, ra, dec)
-    wd = WiseDataByVisit(n_chunks=1, base_name=base_name, parent_sample_class=ps, min_sep_arcsec=min_sep_arcsec)
-    if match:
-        wd.match_all_chunks()
-    service = kwargs.pop('service', 'gator')
-    wd.get_photometric_data(service=service, **kwargs)
-    wd.plot_lc(parent_sample_idx=0, service=service)
-    return wd
-
-
-#####################################################
-#            END POINT SOURCE  UTILS                #
-###########################################################################################################

timewise/utils.py

@@ -1,558 +0,0 @@
-import requests
-import os
-import getpass
-import logging
-import pandas as pd
-import matplotlib.pyplot as plt
-import pyvo as vo
-import backoff
-import numpy
-from scipy.stats import chi2
-from functools import cache
-from astropy.table import Table
-from PIL import Image
-from io import BytesIO
-import hashlib
-from threading import Thread
-from queue import Queue
-import sys
-
-from timewise.general import backoff_hndlr, get_directories
-
-
-logger = logging.getLogger(__name__)
-mirong_url = 'http://staff.ustc.edu.cn/~jnac/data_public/wisevar.txt'
-
-
-def get_mirong_path():
-    return get_directories()['cache_dir'] / 'mirong_sample.csv'
-
-
-@cache
-def get_2d_gaussian_correction(cl):
-    return numpy.sqrt(chi2.ppf(cl, 2))
-
-
-def get_mirong_sample():
-
-    mirong_path = get_mirong_path()
-    if not mirong_path.is_file():
-
-        logger.info(f'getting MIRONG sample from {mirong_url}')
-        r = requests.get(mirong_url)
-        lll = list()
-        for l in r.text.split('\n')[1:]:
-            illl = list()
-            for ll in l.split(' '):
-                if ll and '#' not in ll:
-                    illl.append(ll)
-            lll.append(illl)
-
-        mirong_sample = pd.DataFrame(lll[1:-1], columns=lll[0])
-        mirong_sample['ra'] = mirong_sample['RA']
-        mirong_sample['dec'] = mirong_sample['DEC']
-        logger.info(f'found {len(mirong_sample)} objects in MIRONG Sample')
-
-        mirong_sample.drop(columns=['ra', 'dec'], inplace=True)
-        logger.debug(f'saving to {mirong_path}')
-        mirong_path.parent.mkdir(parents=True, exist_ok=True)
-        mirong_sample.to_csv(mirong_path, index=False)
-
-    else:
-        logger.debug(f'loading {mirong_path}')
-        mirong_sample = pd.read_csv(mirong_path)
-
-    return mirong_sample
-
-
-###########################################################################################################
-#            START SDSS UTILS                       #
-#####################################################
-
-
-def get_sdss_credentials():
-    if not os.environ.get('SDSS_USERID'):
-        os.environ['SDSS_USERID'] = input('Enter SDSS user ID:')
-    if not os.environ.get('SDSS_USERPW'):
-        os.environ['SDSS_USERPW'] = getpass.getpass('Enter SDSS password:')
-    return os.environ['SDSS_USERID'], os.environ['SDSS_USERPW']
-
-
-def login_to_sciserver():
-    try:
-        from SciServer import Authentication
-    except ModuleNotFoundError:
-        raise ModuleNotFoundError("Please install SciServer (https://github.com/sciserver/SciScript-Python) "
-                                  "if you want to see SDSS cutouts!")
-
-    uid, pw = get_sdss_credentials()
-    logger.debug(f"logging in to SciServer with username {uid}")
-    Authentication.login(uid, pw)
-
-
-@backoff.on_exception(
-        backoff.expo,
-        requests.RequestException,
-        max_tries=50,
-        on_backoff=backoff_hndlr
-    )
-def get_cutout(*args, **kwargs):
-    login_to_sciserver()
-    from SciServer import SkyServer
-    return SkyServer.getJpegImgCutout(*args, **kwargs)
-
-
-def plot_sdss_cutout(ra, dec, arcsec=20, arcsec_per_px=0.1, interactive=False, fn=None, title=None, save=False, ax=False,
-                height=2.5):
-
-    ang_px = int(arcsec / arcsec_per_px)
-    ang_deg = arcsec / 3600
-
-    if not ax:
-        fig, ax = plt.subplots(figsize=(height, height))
-    else:
-        fig = plt.gcf()
-
-    try:
-        im = get_cutout(ra, dec, scale=arcsec_per_px, height=ang_px, width=ang_px)
-        ax.imshow(im, origin='upper',
-                  extent=([ra + ang_deg / 2, ra - ang_deg / 2,
-                           dec - ang_deg / 2, dec + ang_deg / 2]),
-                  cmap='gray')
-        ax.scatter(ra, dec, marker='x', color='red')
-
-    except Exception as e:
-        if "outside the SDSS footprint" in str(e):
-            xlim = ax.get_xlim()
-            ylim = ax.get_ylim()
-            x = sum(xlim) / 2
-            y = sum(ylim) / 2
-            ax.annotate("Outside SDSS Footprint", (x, y), color='red', ha='center', va='center', fontsize=20)
-        else:
-            raise Exception(e)
-
-    if title:
-        ax.set_title(title)
-
-    if save:
-        logger.debug(f"saving under {fn}")
-        fig.savefig(fn)
-
-    if interactive:
-        return fig, ax
-
-    plt.close()
-
-
-#####################################################
-#            END SDSS UTILS                         #
-###########################################################################################################
-
-###########################################################################################################
-#            START PANSTARRS UTILS                  #
-#####################################################
-
-
-class PanSTARRSQueryError(Exception):
-    pass
-
-
-def load_cache_or_download(url):
-    logger.debug(f"loading or downloading {url}")
-    h = hashlib.md5(url.encode()).hexdigest()
-    cache_dir = get_directories()['cache_dir']
-    cache_file = cache_dir / (h + ".cache")
-    logger.debug(f"cache file is {cache_file}")
-    if not cache_file.is_file():
-        logger.debug(f"downloading {url}")
-        r = requests.get(url)
-        with open(cache_file, 'wb') as f:
-            f.write(r.content)
-        return r.content
-    else:
-        logger.debug(f"loading {cache_file}")
-        with open(cache_file, 'rb') as f:
-            return f.read()
-
-
-def annotate_not_available(ax):
-    xlim = ax.get_xlim()
-    ylim = ax.get_ylim()
-    x = sum(xlim) / 2
-    y = sum(ylim) / 2
-    logger.debug(f"annotate_not_available at {x}, {y}")
-    ax.annotate("Outside\nPanSTARRS\nFootprint", (x, y), color='red', ha='center', va='center', fontsize=10)
-
-
-def getimages(ra, dec, filters="grizy"):
-    """Query ps1filenames.py service to get a list of images
-
-    ra, dec = position in degrees
-    size = image size in pixels (0.25 arcsec/pixel)
-    filters = string with filters to include
-    Returns a table with the results
-    """
-
-    service = "https://ps1images.stsci.edu/cgi-bin/ps1filenames.py"
-    url = f"{service}?ra={ra}&dec={dec}&filters={filters}"
-    content = load_cache_or_download(url)
-    table = Table.read(content.decode(), format='ascii')
-    return table
-
-
-def geturl(ra, dec, size=240, output_size=None, filters="grizy", format="jpg", color=False):
-    """Get URL for images in the table
-
-    ra, dec = position in degrees
-    size = extracted image size in pixels (0.25 arcsec/pixel)
-    output_size = output (display) image size in pixels (default = size).
-                  output_size has no effect for fits format images.
-    filters = string with filters to include
-    format = data format (options are "jpg", "png" or "fits")
-    color = if True, creates a color image (only for jpg or png format).
-            Default is return a list of URLs for single-filter grayscale images.
-    Returns a string with the URL
-    """
-
-    if color and format == "fits":
-        raise ValueError("color images are available only for jpg or png formats")
-    if format not in ("jpg", "png", "fits"):
-        raise ValueError("format must be one of jpg, png, fits")
-    table = getimages(ra, dec, filters=filters)
-    if len(table) == 0:
-        raise PanSTARRSQueryError("No images available")
-    url = (f"https://ps1images.stsci.edu/cgi-bin/fitscut.cgi?"
-           f"ra={ra}&dec={dec}&size={size}&format={format}")
-    if output_size:
-        url = url + "&output_size={}".format(output_size)
-    # sort filters from red to blue
-    flist = ["yzirg".find(x) for x in table['filter']]
-    table = table[numpy.argsort(flist)]
-    if color:
-        if len(table) > 3:
-            # pick 3 filters
-            table = table[[0, len(table) // 2, len(table) - 1]]
-        for i, param in enumerate(["red", "green", "blue"]):
-            url = url + "&{}={}".format(param, table['filename'][i])
-    else:
-        urlbase = url + "&red="
-        url = []
-        for filename in table['filename']:
-            url.append(urlbase + filename)
-    return url
-
-
-def getcolorim(ra, dec, size=240, output_size=None, filters="grizy", format="jpg"):
-    """Get color image at a sky position
-
-    ra, dec = position in degrees
-    size = extracted image size in pixels (0.25 arcsec/pixel)
-    output_size = output (display) image size in pixels (default = size).
-                  output_size has no effect for fits format images.
-    filters = string with filters to include
-    format = data format (options are "jpg", "png")
-    Returns the image
-    """
-
-    if format not in ("jpg", "png"):
-        raise ValueError("format must be jpg or png")
-    url = geturl(ra, dec, size=size, filters=filters, output_size=output_size, format=format, color=True)
-    content = load_cache_or_download(url)
-    im = Image.open(BytesIO(content))
-    return im
-
-
-def getgrayim(ra, dec, size=240, output_size=None, filter="g", format="jpg"):
-    """Get grayscale image at a sky position
-
-    ra, dec = position in degrees
-    size = extracted image size in pixels (0.25 arcsec/pixel)
-    output_size = output (display) image size in pixels (default = size).
-                  output_size has no effect for fits format images.
-    filter = string with filter to extract (one of grizy)
-    format = data format (options are "jpg", "png")
-    Returns the image
-    """
-
-    if format not in ("jpg", "png"):
-        raise ValueError("format must be jpg or png")
-    if filter not in list("grizy"):
-        raise ValueError("filter must be one of grizy")
-    url = geturl(ra, dec, size=size, filters=filter, output_size=output_size, format=format)
-    content = load_cache_or_download(url[0])
-    im = Image.open(BytesIO(content))
-    return im
-
-
-def plot_panstarrs_cutout(
-        ra,
-        dec,
-        arcsec,
-        interactive=False,
-        fn=None,
-        title=None,
-        save=False,
-        ax=False,
-        plot_color_image=False,
-        height=2.5
-):
-    arcsec_per_px = 0.25
-    ang_px = int(arcsec / arcsec_per_px)
-
-    imshow_kwargs = {
-        'origin': 'upper',
-        "extent": ([arcsec / 2, -arcsec / 2, -arcsec / 2, arcsec / 2])
-    }
-    scatter_args = [0, 0]
-    scatter_kwargs = {'marker': 'x', 'color': 'red'}
-
-    if not plot_color_image:
-        filters = 'grizy'
-        if not ax:
-            fig, axss = plt.subplots(2, len(filters), sharex='all', sharey='all',
-                                     gridspec_kw={'wspace': 0, 'hspace': 0, 'height_ratios': [1, 8]},
-                                     figsize=(height * 5, height))
-        else:
-            fig = plt.gcf()
-            axss = ax
-
-        for j, fil in enumerate(list(filters)):
-            axs = axss[1]
-            try:
-                im = getgrayim(ra, dec, size=ang_px, filter=fil)
-                axs[j].imshow(im, cmap='gray', **imshow_kwargs)
-            except PanSTARRSQueryError:
-                axs[j].set_xlim(-arcsec / 2, arcsec / 2)
-                axs[j].set_ylim(-arcsec / 2, arcsec / 2)
-                annotate_not_available(axs[j])
-
-            axs[j].scatter(*scatter_args, **scatter_kwargs)
-            axs[j].set_title(fil)
-            axss[0][j].axis('off')
-
-    else:
-        logger.debug('plotting color image')
-        if not ax:
-            fig, axss = plt.subplots(figsize=(height, height))
-        else:
-            fig = plt.gcf()
-            axss = ax
-
-        try:
-            im = getcolorim(ra, dec, size=ang_px)
-            axss.imshow(im, **imshow_kwargs)
-        except PanSTARRSQueryError:
-            axss.set_xlim(-arcsec / 2, arcsec / 2)
-            axss.set_ylim(-arcsec / 2, arcsec / 2)
-            annotate_not_available(axss)
-        axss.scatter(*scatter_args, **scatter_kwargs)
-
-    _this_title = title if title else f"{ra}_{dec}"
-    si = "-" if dec > 0 else "+"
-    ylabel = f"Dec {si} {abs(dec):.2f} [arcsec]"
-    xlabel = f"RA - {ra:.2f} [arcsec]"
-    try:
-        axss.set_title(_this_title)
-        axss.set_xlabel(xlabel)
-        axss.set_ylabel(ylabel)
-        axss.grid(ls=":", alpha=0.5)
-    except AttributeError:  # in this case axss is an array
-        fig.supylabel(ylabel)
-        fig.supxlabel(xlabel)
-        fig.suptitle(_this_title)
-        for a in axss.flatten():
-            a.grid(ls=":", alpha=0.5)
-
-    if save:
-        logger.info(f'saving under {fn}')
-        fig.savefig(fn)
-
-    if interactive:
-        return fig, axss
-
-    plt.close()
-
-
-#####################################################
-#            END PANSTARRS UTILS                    #
-###########################################################################################################
-
-###########################################################################################################
-#            START EXCESS VARIANCE UTILS            #
-#####################################################
-
-# calculate excess variance as done in section 7.3.4 of (Boller et al)
-# https://www.aanda.org/articles/aa/full_html/2016/04/aa25648-15/aa25648-15.html#S26
-
-
-def calc_Expectation(a):
-     
-    # variable prb is for probability
-    # of each element which is same for
-    # each element
-    n = len(a)
-    prb = 1 / n
-    # calculating expectation overall
-    sum = 0
-    for i in range(0, n):
-        sum += (a[i] * prb)
-    # returning expectation as sum
-    return float(sum)
-
-
-def get_excess_variance(y, y_err, mu):
-    import numpy as np
-    N = len(y)
-    sum_variance = 0
-    for i, (X, sig) in enumerate(zip(y, y_err)):
-        sum_variance += np.power(X-mu,2) - np.power(sig,2)
-       
-    excess_variance = (sum_variance)/(N*mu**2)
-    
-    # calculate the uncertainty
-    F_var = np.sqrt(np.abs(excess_variance))/mu
-    std_exp = calc_Expectation(y_err**2)
-    term1 = np.sqrt(2/N)*std_exp/(np.power(mu,2))
-    term2 = np.sqrt((std_exp*2*F_var)/(N*mu))
-    
-    uncertainty = np.sqrt(term1**2 + term2**2)
-    return excess_variance, uncertainty
-
-
-#####################################################
-#              END EXCESS VARIANCE UTILS            #
-###########################################################################################################
-
-
-###########################################################################################################
-#            START CUSTOM TAP Service                 #
-#######################################################
-
-
-class StableAsyncTAPJob(vo.dal.AsyncTAPJob):
-    """
-    Implements backoff for call of phase which otherwise breaks the code if there are connection issues.
-    Also stores the response of TapQuery.submit() under self.submit_response for debugging
-    """
-
-    def __init__(self, url, *, session=None, delete=True):
-        super(StableAsyncTAPJob, self).__init__(url, session=session, delete=delete)
-        self.submit_response = None
-
-    @classmethod
-    def create(
-            cls, baseurl, query, *, language="ADQL", maxrec=None, uploads=None,
-            session=None, **keywords):
-        """
-        creates a async tap job on the server under ``baseurl``
-        Raises requests.HTTPError if TAPQuery.submit() failes.
-
-        Parameters
-        ----------
-        baseurl : str
-            the TAP baseurl
-        query : str
-            the query string
-        language : str
-            specifies the query language, default ADQL.
-            useful for services which allow to use the backend query language.
-        maxrec : int
-            the maximum records to return. defaults to the service default
-        uploads : dict
-            a mapping from table names to objects containing a votable
-        session : object
-           optional session to use for network requests
-        """
-        tapquery = vo.dal.TAPQuery(
-            baseurl, query, mode="async", language=language, maxrec=maxrec,
-            uploads=uploads, session=session, **keywords)
-        response = tapquery.submit()
-        response.raise_for_status()
-        job = cls(response.url, session=session)
-        job._client_set_maxrec = maxrec
-        job.submit_response = response
-        return job
-
-    @property
-    @backoff.on_exception(
-        backoff.expo,
-        (vo.dal.DALServiceError, AttributeError),
-        max_tries=50,
-        on_backoff=backoff_hndlr
-    )
-    def phase(self):
-        return super(StableAsyncTAPJob, self).phase
-
-
-class StableTAPService(vo.dal.TAPService):
-    """
-    Implements the StableAsyncTAPJob for job submission
-    """
-
-    def submit_job(
-            self,
-            query,
-            *,
-            language="ADQL",
-            maxrec=None,
-            uploads=None,
-            **keywords
-    ):
-        return StableAsyncTAPJob.create(
-            self.baseurl,
-            query,
-            language=language,
-            maxrec=maxrec,
-            uploads=uploads,
-            session=self._session,
-            **keywords
-        )
-
-
-#######################################################
-#            END CUSTOM TAP Service                   #
-###########################################################################################################
-
-
-###########################################################################################################
-#            START CUSTOM TAP Service                 #
-#######################################################
-
-
-class ErrorQueue(Queue):
-    """Queue subclass whose join() re-raises exceptions from worker threads."""
-
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.error_queue = Queue()
-
-    def report_error(self, exc_info):
-        """Called by workers to push an exception into the error queue."""
-        self.error_queue.put(exc_info)
-        # Also decrement unfinished_tasks, so join() won't block forever
-        with self.all_tasks_done:
-            self.unfinished_tasks = max(0, self.unfinished_tasks - 1)
-            self.all_tasks_done.notify_all()
-
-    def join(self):
-        """Wait until all tasks are done, or raise if a worker failed."""
-        with self.all_tasks_done:
-            while self.unfinished_tasks:
-                if not self.error_queue.empty():
-                    exc_info = self.error_queue.get()
-                    raise exc_info[1].with_traceback(exc_info[2])
-                self.all_tasks_done.wait()
-
-
-class ExceptionSafeThread(Thread):
-    """Thread subclass that reports uncaught exceptions to the ErrorQueue."""
-
-    def __init__(self, error_queue: ErrorQueue, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.error_queue = error_queue
-
-    def run(self):
-        try:
-            super().run()
-        except Exception:
-            self.error_queue.report_error(sys.exc_info())