BoghdadyJR/codesearch_python · Datasets at Hugging Face

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def extract_flatfield(prihdr, scihdu): """Extract flatfield data from ``PFLTFILE``. Parameters ---------- prihdr : obj FITS primary header HDU. scihdu : obj Extension HDU of the science image. This is only used to extract subarray data. Returns ------- invflat ...
def from_irafpath(irafpath): """Resolve IRAF path like ``jref$`` into actual file path. Parameters ---------- irafpath : str Path containing IRAF syntax. Returns ------- realpath : str Actual file path. If input does not follow ``path$filename`` format, then this is...
def extract_ref(scihdu, refhdu): """Extract section of the reference image that corresponds to the given science image. This only returns a view, not a copy of the reference image's array. Parameters ---------- scihdu, refhdu : obj Extension HDU's of the science and reference image...
def find_line(scihdu, refhdu): """Obtain bin factors and corner location to extract and bin the appropriate subset of a reference image to match a science image. If the science image has zero offset and is the same size and binning as the reference image, ``same_size`` will be set to `True`. Ot...
def get_corner(hdr, rsize=1): """Obtain bin and corner information for a subarray. ``LTV1``, ``LTV2``, ``LTM1_1``, and ``LTM2_2`` keywords are extracted from the given extension header and converted to bin and corner values (0-indexed). ``LTV1`` for the CCD uses the beginning of the illuminated ...
def get_lt(hdr): """Obtain the LTV and LTM keyword values. Note that this returns the values just as read from the header, which means in particular that the LTV values are for one-indexed pixel coordinates. LTM keywords are the diagonal elements of MWCS linear transformation matrix, while LTV...
def from_lt(rsize, ltm, ltv): """Compute the corner location and pixel size in units of unbinned pixels. .. note:: Translated from ``calacs/lib/fromlt.c``. Parameters ---------- rsize : int Reference pixel size. Usually 1. ltm, ltv : tuple of float See :func:`get_lt`. ...
def hdr_vals_for_overscan(root): """Retrieve header keyword values from RAW and SPT FITS files to pass on to :func:`check_oscntab` and :func:`check_overscan`. Parameters ---------- root : str Rootname of the observation. Can be relative path to the file excluding the type of FIT...
def check_oscntab(oscntab, ccdamp, xsize, ysize, leading, trailing): """Check if the supplied parameters are in the ``OSCNTAB`` reference file. .. note:: Even if an entry does not exist in ``OSCNTAB``, as long as the subarray does not have any overscan, it should not be a proble...
def check_overscan(xstart, xsize, total_prescan_pixels=24, total_science_pixels=4096): """Check image for bias columns. Parameters ---------- xstart : int Starting column of the readout in detector coordinates. xsize : int Number of columns in the readout. t...
def process_request(self, request): """ Ignore unnecessary actions for static file requests, posts, or ajax requests. We're only interested in redirecting following a 'natural' request redirection to the `wagtailadmin_explore_root` or `wagtailadmin_explore` views. """ ...
def acs2d(input, exec_path='', time_stamps=False, verbose=False, quiet=False, exe_args=None): r""" Run the acs2d.e executable as from the shell. Output is automatically named based on input suffix: +--------------------+----------------+------------------------------+ \| INPUT ...
def run(configobj=None): """ TEAL interface for the `acs2d` function. """ acs2d(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'] )
def run(configobj=None): """ TEAL interface for the `acscte` function. """ acscte(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'], single_core=config...
def _check_inputs(self): """Check the inputs to ensure they are valid. Returns ------- status : bool True if all inputs are valid, False if one is not. """ valid_detector = True valid_filter = True valid_date = True # Determine the su...
def _check_date(self, fmt='%Y-%m-%d'): """Convenience method for determining if the input date is valid. Parameters ---------- fmt : str The format of the date string. The default is ``%Y-%m-%d``, which corresponds to ``YYYY-MM-DD``. Returns ----...
def _submit_request(self): """Submit a request to the ACS Zeropoint Calculator. If an exception is raised during the request, an error message is given. Otherwise, the response is saved in the corresponding attribute. """ try: self._response = urlopen(self._...
def _parse_and_format(self): """ Parse and format the results returned by the ACS Zeropoint Calculator. Using ``beautifulsoup4``, find all the ``<tb> </tb>`` tags present in the response. Format the results into an astropy.table.QTable with corresponding units and assign it to the zpt_t...
def fetch(self): """Submit the request to the ACS Zeropoints Calculator. This method will: * submit the request * parse the response * format the results into a table with the correct units Returns ------- tab : `astropy.table.QTable` or `None` ...
def get_queryset(self, request): """ Returns a QuerySet of all model instances that can be edited by the admin site. """ qs = self.model._default_manager.get_queryset() ordering = self.get_ordering(request) if ordering: qs = qs.order_by(*ordering) ...
def index_view(self, request): """ Instantiates a class-based view to provide listing functionality for the assigned model. The view class used can be overridden by changing the 'index_view_class' attribute. """ kwargs = {'model_admin': self} view_class = self.ind...
def create_view(self, request): """ Instantiates a class-based view to provide 'creation' functionality for the assigned model, or redirect to Wagtail's create view if the assigned model extends 'Page'. The view class used can be overridden by changing the 'create_view_class' att...
def choose_parent_view(self, request): """ Instantiates a class-based view to provide a view that allows a parent page to be chosen for a new object, where the assigned model extends Wagtail's Page model, and there is more than one potential parent for new instances. The view cla...
def edit_view(self, request, object_id): """ Instantiates a class-based view to provide 'edit' functionality for the assigned model, or redirect to Wagtail's edit view if the assigned model extends 'Page'. The view class used can be overridden by changing the 'edit_view_class' a...
def confirm_delete_view(self, request, object_id): """ Instantiates a class-based view to provide 'delete confirmation' functionality for the assigned model, or redirect to Wagtail's delete confirmation view if the assigned model extends 'Page'. The view class used can be overrid...
def unpublish_view(self, request, object_id): """ Instantiates a class-based view that redirects to Wagtail's 'unpublish' view for models that extend 'Page' (if the user has sufficient permissions). We do this via our own view so that we can reliably control redirection of the us...
def copy_view(self, request, object_id): """ Instantiates a class-based view that redirects to Wagtail's 'copy' view for models that extend 'Page' (if the user has sufficient permissions). We do this via our own view so that we can reliably control redirection of the user back to...
def get_templates(self, action='index'): """ Utility function that provides a list of templates to try for a given view, when the template isn't overridden by one of the template attributes on the class. """ app = self.opts.app_label model_name = self.opts.model_n...
def get_permissions_for_registration(self): """ Utilised by Wagtail's 'register_permissions' hook to allow permissions for a model to be assigned to groups in settings. This is only required if the model isn't a Page model, and isn't registered as a Snippet """ from wagta...
def get_admin_urls_for_registration(self): """ Utilised by Wagtail's 'register_admin_urls' hook to register urls for our the views that class offers. """ urls = ( url(get_url_pattern(self.opts), self.index_view, name=get_url_name(self.opts)), ...
def get_menu_item(self): """ Utilised by Wagtail's 'register_menu_item' hook to create a menu for this group with a SubMenu linking to listing pages for any associated ModelAdmin instances """ if self.modeladmin_instances: submenu = SubMenu(self.get_submenu_it...
def get_permissions_for_registration(self): """ Utilised by Wagtail's 'register_permissions' hook to allow permissions for a all models grouped by this class to be assigned to Groups in settings. """ qs = Permission.objects.none() for instance in self.modeladmin_i...
def get_admin_urls_for_registration(self): """ Utilised by Wagtail's 'register_admin_urls' hook to register urls for used by any associated ModelAdmin instances """ urls = [] for instance in self.modeladmin_instances: urls.extend(instance.get_admin_urls_for_re...
def is_shown(self, request): """ If there aren't any visible items in the submenu, don't bother to show this menu item """ for menuitem in self.menu._registered_menu_items: if menuitem.is_shown(request): return True return False
def run(configobj=None): """ TEAL interface for the `acscteforwardmodel` function. """ acscteforwardmodel(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], ...
def run(configobj=None): """ TEAL interface for the `acsccd` function. """ acsccd(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'] #, #dqicorr=config...
def destripe_plus(inputfile, suffix='strp', stat='pmode1', maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, scimask1=None, scimask2=None, dqbits=None, rpt_clean=0, atol=0.01, cte_correct=True, clobber=False, verbose=True): r"""Cali...
def run(configobj=None): """TEAL interface for :func:`destripe_plus`.""" destripe_plus( configobj['input'], suffix=configobj['suffix'], stat=configobj['stat'], maxiter=configobj['maxiter'], sigrej=configobj['sigrej'], lower=configobj['lower'], upper=config...
def main(): """Command line driver.""" import argparse # Parse input parameters parser = argparse.ArgumentParser( prog=__taskname__, description=( 'Run CALACS and standalone acs_destripe script on given post-SM4 ' 'ACS/WFC RAW full-frame or supported subarray ima...
def get_search_results(self, request, queryset, search_term): """ Returns a tuple containing a queryset to implement the search, and a boolean indicating if the results may contain duplicates. """ # Apply keyword searches. def construct_search(field_name): if ...
def get_filters_params(self, params=None): """ Returns all params except IGNORED_PARAMS """ if not params: params = self.params lookup_params = params.copy() # a dictionary of the query string # Remove all the parameters that are globally and systematically ...
def get_ordering_field(self, field_name): """ Returns the proper model field name corresponding to the given field_name to use for ordering. field_name may either be the name of a proper model field or the name of a method (on the admin or model) or a callable with the 'admin_ord...
def get_ordering(self, request, queryset): """ Returns the list of ordering fields for the change list. First we check the get_ordering() method in model admin, then we check the object's default ordering. Then, any manually-specified ordering from the query string overrides anyt...
def get_ordering_field_columns(self): """ Returns an OrderedDict of ordering field column numbers and asc/desc """ # We must cope with more than one column having the same underlying # sort field, so we base things on column numbers. ordering = self._get_default_ordering...
def get_field_label(self, field_name, field=None): """ Return a label to display for a field """ label = None if field is not None: label = getattr(field, 'verbose_name', None) if label is None: label = getattr(field, 'name', None) if label is None...
def get_field_display_value(self, field_name, field=None): """ Return a display value for a field """ """ Firstly, check for a 'get_fieldname_display' property/method on the model, and return the value of that, if present. """ val_funct = getattr(self.instance, 'get_%s_d...
def get_image_field_display(self, field_name, field): """ Render an image """ image = getattr(self.instance, field_name) if image: fltr, _ = Filter.objects.get_or_create(spec='max-400x400') rendition = image.get_rendition(fltr) return rendition.img_tag ...
def get_document_field_display(self, field_name, field): """ Render a link to a document """ document = getattr(self.instance, field_name) if document: return mark_safe( '<a href="%s">%s <span class="meta">(%s, %s)</span></a>' % ( document.url, ...
def get_dict_for_field(self, field_name): """ Return a dictionary containing `label` and `value` values to display for a field. """ try: field = self.model._meta.get_field(field_name) except FieldDoesNotExist: field = None return { ...
def get_fields_dict(self): """ Return a list of `label`/`value` dictionaries to represent the fiels named by the model_admin class's `get_inspect_view_fields` method """ fields = [] for field_name in self.model_admin.get_inspect_view_fields(): fields.append(se...
def items_for_result(view, result): """ Generates the actual list of data. """ model_admin = view.model_admin for field_name in view.list_display: empty_value_display = model_admin.get_empty_value_display() row_classes = ['field-%s' % field_name] try: f, attr, val...
def result_list(context): """ Displays the headers and data list together """ view = context['view'] object_list = context['object_list'] headers = list(result_headers(view)) num_sorted_fields = 0 for h in headers: if h['sortable'] and h['sorted']: num_sorted_fields +...
def run(configobj=None): """ TEAL interface for the `acssum` function. """ acssum(configobj['input'], configobj['output'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'...
def _detsat_one(filename, ext, sigma=2.0, low_thresh=0.1, h_thresh=0.5, small_edge=60, line_len=200, line_gap=75, percentile=(4.5, 93.0), buf=200, plot=False, verbose=False): """Called by :func:`detsat`.""" if verbose: t_beg = time.time() fname = '{0}[{1}]'.format(fi...
def _get_valid_indices(shape, ix0, ix1, iy0, iy1): """Give array shape and desired indices, return indices that are correctly bounded by the shape.""" ymax, xmax = shape if ix0 < 0: ix0 = 0 if ix1 > xmax: ix1 = xmax if iy0 < 0: iy0 = 0 if iy1 > ymax: iy1 = ym...
def _rotate_point(point, angle, ishape, rshape, reverse=False): """Transform a point from original image coordinates to rotated image coordinates and back. It assumes the rotation point is the center of an image. This works on a simple rotation transformation:: newx = (startx) * np.cos(angle) ...
def make_mask(filename, ext, trail_coords, sublen=75, subwidth=200, order=3, sigma=4, pad=10, plot=False, verbose=False): """Create DQ mask for an image for a given satellite trail. This mask can be added to existing DQ data using :func:`update_dq`. .. note:: Unlike :func:`detsat`, m...
def update_dq(filename, ext, mask, dqval=16384, verbose=True): """Update the given image and DQ extension with the given satellite trails mask and flag. Parameters ---------- filename : str FITS image filename to update. ext : int, str, or tuple DQ extension, as accepted by ``a...
def _satdet_worker(work_queue, done_queue, sigma=2.0, low_thresh=0.1, h_thresh=0.5, small_edge=60, line_len=200, line_gap=75, percentile=(4.5, 93.0), buf=200): """Multiprocessing worker.""" for fil, chip in iter(work_queue.get, 'STOP'): try: result = _de...
def detsat(searchpattern, chips=[1, 4], n_processes=4, sigma=2.0, low_thresh=0.1, h_thresh=0.5, small_edge=60, line_len=200, line_gap=75, percentile=(4.5, 93.0), buf=200, plot=False, verbose=True): """Find satellite trails in the given images and extensions. The trails are calcu...
def on(self, event: str) -> Callable: """ Decorator for subscribing a function to a specific event. :param event: Name of the event to subscribe to. :type event: str :return: The outer function. :rtype: Callable """ def outer(func): self.add_event(f...
def add_event(self, func: Callable, event: str) -> None: """ Adds a function to a event. :param func: The function to call when event is emitted :type func: Callable :param event: Name of the event. :type event: str """ self._events[event].add(func)
def emit(self, event: str, args, *kwargs) -> None: """ Emit an event and run the subscribed functions. :param event: Name of the event. :type event: str .. notes: Passing in threads=True as a kwarg allows to run emitted events as separate threads. This can sig...
def emit_only(self, event: str, func_names: Union[str, List[str]], args, *kwargs) -> None: """ Specifically only emits certain subscribed events. :param event: Name of the event. :type event: str :param func_names: Function(s) to emit. :type func_names: Unio...
def emit_after(self, event: str) -> Callable: """ Decorator that emits events after the function is completed. :param event: Name of the event. :type event: str :return: Callable .. note: This plainly just calls functions without passing params into the ...
def remove_event(self, func_name: str, event: str) -> None: """ Removes a subscribed function from a specific event. :param func_name: The name of the function to be removed. :type func_name: str :param event: The name of the event. :type event: str :raise EventDoesntE...
def _event_funcs(self, event: str) -> Iterable[Callable]: """ Returns an Iterable of the functions subscribed to a event. :param event: Name of the event. :type event: str :return: A iterable to do things with. :rtype: Iterable """ for func in self._events[event...
def _event_func_names(self, event: str) -> List[str]: """ Returns string name of each function subscribed to an event. :param event: Name of the event. :type event: str :return: Names of functions subscribed to a specific event. :rtype: list """ return [func.__n...
def _subscribed_event_count(self) -> int: """ Returns the total amount of subscribed events. :return: Integer amount events. :rtype: int """ event_counter = Counter() # type: Dict[Any, int] for key, values in self._events.items(): event_counter[key] = len(v...
def clean(input, suffix, stat="pmode1", maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, mask1=None, mask2=None, dqbits=None, rpt_clean=0, atol=0.01, clobber=False, verbose=True): r"""Remove horizontal stripes from ACS WFC post-SM4 data. Parameters ---------- ...
def perform_correction(image, output, stat="pmode1", maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, mask=None, dqbits=None, rpt_clean=0, atol=0.01, clobber=False, verbose=True): """ Clean each input image. Parameters --...
def clean_streak(image, stat="pmode1", maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, mask=None, rpt_clean=0, atol=0.01, verbose=True): """ Apply destriping algorithm to input array. Parameters ---------- image : `StripeArray` object Arrays a...
def djs_iterstat(InputArr, MaxIter=10, SigRej=3.0, Max=None, Min=None, Mask=None, lineno=None): """ Iterative sigma-clipping. Parameters ---------- InputArr : `numpy.ndarray` Input image array. MaxIter, SigRej : see `clean` Max, Min : float Max and min val...
def run(configobj=None): """TEAL interface for the `clean` function.""" clean(configobj['input'], suffix=configobj['suffix'], stat=configobj['stat'], maxiter=configobj['maxiter'], sigrej=configobj['sigrej'], lower=configobj['lower'], upper=configobj['u...
def main(): """Command line driver.""" import argparse parser = argparse.ArgumentParser( prog=__taskname__, description='Remove horizontal stripes from ACS WFC post-SM4 data.') parser.add_argument( 'arg0', metavar='input', type=str, help='Input file') parser.add_argument( ...
def configure_arrays(self): """Get the SCI and ERR data.""" self.science = self.hdulist['sci', 1].data self.err = self.hdulist['err', 1].data self.dq = self.hdulist['dq', 1].data if (self.ampstring == 'ABCD'): self.science = np.concatenate( (self.scien...
def ingest_flatfield(self): """Process flatfield.""" self.invflat = extract_flatfield( self.hdulist[0].header, self.hdulist[1]) # If BIAS or DARK, set flatfield to unity if self.invflat is None: self.invflat = np.ones_like(self.science) return ...
def ingest_flash(self): """Process post-flash.""" self.flash = extract_flash(self.hdulist[0].header, self.hdulist[1]) # Set post-flash to zeros if self.flash is None: self.flash = np.zeros_like(self.science) return # Apply the flash subtraction if neces...
def ingest_dark(self): """Process dark.""" self.dark = extract_dark(self.hdulist[0].header, self.hdulist[1]) # If BIAS or DARK, set dark to zeros if self.dark is None: self.dark = np.zeros_like(self.science) return # Apply the dark subtraction if necess...
def write_corrected(self, output, clobber=False): """Write out the destriped data.""" # un-apply the flatfield if necessary if self.flatcorr != 'COMPLETE': self.science = self.science / self.invflat self.err = self.err / self.invflat # un-apply the post-flash if...
def calacs(input_file, exec_path=None, time_stamps=False, temp_files=False, verbose=False, debug=False, quiet=False, single_core=False, exe_args=None): """ Run the calacs.e executable as from the shell. By default this will run the calacs given by 'calacs.e'. Parameters -----...
def run(configobj=None): """ TEAL interface for the `calacs` function. """ calacs(configobj['input_file'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], temp_files=configobj['temp_files'], verbose=configobj['verbose'], deb...
def has_any_permissions(self, user): """ Return a boolean to indicate whether the supplied user has any permissions at all on the associated model """ for perm in self.get_all_model_permissions(): if self.has_specific_permission(user, perm.codename): r...
def get_valid_parent_pages(self, user): """ Identifies possible parent pages for the current user by first looking at allowed_parent_page_models() on self.model to limit options to the correct type of page, then checking permissions on those individual pages to make sure we have ...
def acsrej(input, output, exec_path='', time_stamps=False, verbose=False, shadcorr=False, crrejtab='', crmask=False, scalense=None, initgues='', skysub='', crsigmas='', crradius=None, crthresh=None, badinpdq=None, newbias=False, readnoise_only=False, exe_args=None): r""" Run the...
def run(configobj=None): """ TEAL interface for the `acsrej` function. """ acsrej(configobj['input'], configobj['output'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], shadcorr=configobj['sha...
def monkeypatch_os_fork_functions(): """ Replace os.fork* with wrappers that use ForkSafeLock to acquire all locks before forking and release them afterwards. """ builtin_function = type(''.join) if hasattr(os, 'fork') and isinstance(os.fork, builtin_function): global _orig_os_fork ...
def atfork(prepare=None, parent=None, child=None): """A Python work-a-like of pthread_atfork. Any time a fork() is called from Python, all 'prepare' callables will be called in the order they were registered using this function. After the fork (successful or not), all 'parent' callables will be ca...
def _call_atfork_list(call_list): """ Given a list of callables in call_list, call them all in order and save and return a list of sys.exc_info() tuples for each exception raised. """ exception_list = [] for func in call_list: try: func() except: exception...
def parent_after_fork_release(): """ Call all parent after fork callables, release the lock and print all prepare and parent callback exceptions. """ prepare_exceptions = list(_prepare_call_exceptions) del _prepare_call_exceptions[:] exceptions = _call_atfork_list(_parent_call_list) _for...
def _print_exception_list(exceptions, message, output_file=None): """ Given a list of sys.exc_info tuples, print them all using the traceback module preceeded by a message and separated by a blank line. """ output_file = output_file or sys.stderr message = 'Exception %s:\n' % message for exc...
def os_forkpty_wrapper(): """Wraps os.forkpty() to run atfork handlers.""" pid = None prepare_to_fork_acquire() try: pid, fd = _orig_os_forkpty() finally: if pid == 0: child_after_fork_release() else: parent_after_fork_release() return pid, fd
def maybe(value): """Wraps an object with a Maybe instance. >>> maybe("I'm a value") Something("I'm a value") >>> maybe(None); Nothing Testing for value: >>> maybe("I'm a value").is_some() True >>> maybe("I'm a value").is_none() False >>> may...
def setup(self): '''Called after instantiation''' TelnetHandlerBase.setup(self) # Spawn a greenlet to handle socket input self.greenlet_ic = eventlet.spawn(self.inputcooker) # Note that inputcooker exits on EOF # Sleep for 0.5 second to allow options negotiation ...
def inputcooker_store_queue(self, char): """Put the cooked data in the input queue (no locking needed)""" if type(char) in [type(()), type([]), type("")]: for v in char: self.cookedq.put(v) else: self.cookedq.put(char)
def setup(self): '''Setup the connection.''' log.debug( 'New request from address %s, port %d', self.client_address ) try: self.transport.load_server_moduli() except: log.exception( '(Failed to load moduli -- gex will be unsupported.)' ) rais...
def streamserver_handle(cls, socket, address): '''Translate this class for use in a StreamServer''' request = cls.dummy_request() request._sock = socket server = None cls(request, address, server)
def check_channel_shell_request(self, channel): '''Request to start a shell on the given channel''' try: self.channels[channel].start() except KeyError: log.error('Requested to start a channel (%r) that was not previously set up.', channel) return False ...
def check_channel_pty_request(self, channel, term, width, height, pixelwidth, pixelheight, modes): '''Request to allocate a PTY terminal.''' #self.sshterm = term #print "term: %r, modes: %r" % (term, modes) log.debug('PTY requested. Setting up %r.', sel...
def download(url, file_name): r = requests.get(url, stream=True) file_size = int(r.headers['Content-length']) ''' if py3: file_size = int(u.getheader("Content-Length")[0]) else: file_size = int(u.info().getheaders("Content-Length")[0]) ''' file_exists = False if...

def extract_flatfield(prihdr, scihdu): """Extract flatfield data from ``PFLTFILE``. Parameters ---------- prihdr : obj FITS primary header HDU. scihdu : obj Extension HDU of the science image. This is only used to extract subarray data. Returns ------- invflat ...

def from_irafpath(irafpath): """Resolve IRAF path like ``jref$`` into actual file path. Parameters ---------- irafpath : str Path containing IRAF syntax. Returns ------- realpath : str Actual file path. If input does not follow ``path$filename`` format, then this is...

def extract_ref(scihdu, refhdu): """Extract section of the reference image that corresponds to the given science image. This only returns a view, not a copy of the reference image's array. Parameters ---------- scihdu, refhdu : obj Extension HDU's of the science and reference image...

def find_line(scihdu, refhdu): """Obtain bin factors and corner location to extract and bin the appropriate subset of a reference image to match a science image. If the science image has zero offset and is the same size and binning as the reference image, ``same_size`` will be set to `True`. Ot...

def get_corner(hdr, rsize=1): """Obtain bin and corner information for a subarray. ``LTV1``, ``LTV2``, ``LTM1_1``, and ``LTM2_2`` keywords are extracted from the given extension header and converted to bin and corner values (0-indexed). ``LTV1`` for the CCD uses the beginning of the illuminated ...

def get_lt(hdr): """Obtain the LTV and LTM keyword values. Note that this returns the values just as read from the header, which means in particular that the LTV values are for one-indexed pixel coordinates. LTM keywords are the diagonal elements of MWCS linear transformation matrix, while LTV...

def from_lt(rsize, ltm, ltv): """Compute the corner location and pixel size in units of unbinned pixels. .. note:: Translated from ``calacs/lib/fromlt.c``. Parameters ---------- rsize : int Reference pixel size. Usually 1. ltm, ltv : tuple of float See :func:`get_lt`. ...

def hdr_vals_for_overscan(root): """Retrieve header keyword values from RAW and SPT FITS files to pass on to :func:`check_oscntab` and :func:`check_overscan`. Parameters ---------- root : str Rootname of the observation. Can be relative path to the file excluding the type of FIT...

def check_oscntab(oscntab, ccdamp, xsize, ysize, leading, trailing): """Check if the supplied parameters are in the ``OSCNTAB`` reference file. .. note:: Even if an entry does not exist in ``OSCNTAB``, as long as the subarray does not have any overscan, it should not be a proble...

def check_overscan(xstart, xsize, total_prescan_pixels=24, total_science_pixels=4096): """Check image for bias columns. Parameters ---------- xstart : int Starting column of the readout in detector coordinates. xsize : int Number of columns in the readout. t...

def process_request(self, request): """ Ignore unnecessary actions for static file requests, posts, or ajax requests. We're only interested in redirecting following a 'natural' request redirection to the `wagtailadmin_explore_root` or `wagtailadmin_explore` views. """ ...

def acs2d(input, exec_path='', time_stamps=False, verbose=False, quiet=False, exe_args=None): r""" Run the acs2d.e executable as from the shell. Output is automatically named based on input suffix: +--------------------+----------------+------------------------------+ | INPUT ...

def run(configobj=None): """ TEAL interface for the `acs2d` function. """ acs2d(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'] )

def run(configobj=None): """ TEAL interface for the `acscte` function. """ acscte(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'], single_core=config...

def _check_inputs(self): """Check the inputs to ensure they are valid. Returns ------- status : bool True if all inputs are valid, False if one is not. """ valid_detector = True valid_filter = True valid_date = True # Determine the su...

def _check_date(self, fmt='%Y-%m-%d'): """Convenience method for determining if the input date is valid. Parameters ---------- fmt : str The format of the date string. The default is ``%Y-%m-%d``, which corresponds to ``YYYY-MM-DD``. Returns ----...

def _submit_request(self): """Submit a request to the ACS Zeropoint Calculator. If an exception is raised during the request, an error message is given. Otherwise, the response is saved in the corresponding attribute. """ try: self._response = urlopen(self._...

def _parse_and_format(self): """ Parse and format the results returned by the ACS Zeropoint Calculator. Using ``beautifulsoup4``, find all the ``<tb> </tb>`` tags present in the response. Format the results into an astropy.table.QTable with corresponding units and assign it to the zpt_t...

def fetch(self): """Submit the request to the ACS Zeropoints Calculator. This method will: * submit the request * parse the response * format the results into a table with the correct units Returns ------- tab : `astropy.table.QTable` or `None` ...

def get_queryset(self, request): """ Returns a QuerySet of all model instances that can be edited by the admin site. """ qs = self.model._default_manager.get_queryset() ordering = self.get_ordering(request) if ordering: qs = qs.order_by(*ordering) ...

def index_view(self, request): """ Instantiates a class-based view to provide listing functionality for the assigned model. The view class used can be overridden by changing the 'index_view_class' attribute. """ kwargs = {'model_admin': self} view_class = self.ind...

def create_view(self, request): """ Instantiates a class-based view to provide 'creation' functionality for the assigned model, or redirect to Wagtail's create view if the assigned model extends 'Page'. The view class used can be overridden by changing the 'create_view_class' att...

def choose_parent_view(self, request): """ Instantiates a class-based view to provide a view that allows a parent page to be chosen for a new object, where the assigned model extends Wagtail's Page model, and there is more than one potential parent for new instances. The view cla...

def edit_view(self, request, object_id): """ Instantiates a class-based view to provide 'edit' functionality for the assigned model, or redirect to Wagtail's edit view if the assigned model extends 'Page'. The view class used can be overridden by changing the 'edit_view_class' a...

def confirm_delete_view(self, request, object_id): """ Instantiates a class-based view to provide 'delete confirmation' functionality for the assigned model, or redirect to Wagtail's delete confirmation view if the assigned model extends 'Page'. The view class used can be overrid...

def unpublish_view(self, request, object_id): """ Instantiates a class-based view that redirects to Wagtail's 'unpublish' view for models that extend 'Page' (if the user has sufficient permissions). We do this via our own view so that we can reliably control redirection of the us...

def copy_view(self, request, object_id): """ Instantiates a class-based view that redirects to Wagtail's 'copy' view for models that extend 'Page' (if the user has sufficient permissions). We do this via our own view so that we can reliably control redirection of the user back to...

def get_templates(self, action='index'): """ Utility function that provides a list of templates to try for a given view, when the template isn't overridden by one of the template attributes on the class. """ app = self.opts.app_label model_name = self.opts.model_n...

def get_permissions_for_registration(self): """ Utilised by Wagtail's 'register_permissions' hook to allow permissions for a model to be assigned to groups in settings. This is only required if the model isn't a Page model, and isn't registered as a Snippet """ from wagta...

def get_admin_urls_for_registration(self): """ Utilised by Wagtail's 'register_admin_urls' hook to register urls for our the views that class offers. """ urls = ( url(get_url_pattern(self.opts), self.index_view, name=get_url_name(self.opts)), ...

def get_menu_item(self): """ Utilised by Wagtail's 'register_menu_item' hook to create a menu for this group with a SubMenu linking to listing pages for any associated ModelAdmin instances """ if self.modeladmin_instances: submenu = SubMenu(self.get_submenu_it...

def get_permissions_for_registration(self): """ Utilised by Wagtail's 'register_permissions' hook to allow permissions for a all models grouped by this class to be assigned to Groups in settings. """ qs = Permission.objects.none() for instance in self.modeladmin_i...

def get_admin_urls_for_registration(self): """ Utilised by Wagtail's 'register_admin_urls' hook to register urls for used by any associated ModelAdmin instances """ urls = [] for instance in self.modeladmin_instances: urls.extend(instance.get_admin_urls_for_re...

def is_shown(self, request): """ If there aren't any visible items in the submenu, don't bother to show this menu item """ for menuitem in self.menu._registered_menu_items: if menuitem.is_shown(request): return True return False

def run(configobj=None): """ TEAL interface for the `acscteforwardmodel` function. """ acscteforwardmodel(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], ...

def run(configobj=None): """ TEAL interface for the `acsccd` function. """ acsccd(configobj['input'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'] #, #dqicorr=config...

def destripe_plus(inputfile, suffix='strp', stat='pmode1', maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, scimask1=None, scimask2=None, dqbits=None, rpt_clean=0, atol=0.01, cte_correct=True, clobber=False, verbose=True): r"""Cali...

def run(configobj=None): """TEAL interface for :func:`destripe_plus`.""" destripe_plus( configobj['input'], suffix=configobj['suffix'], stat=configobj['stat'], maxiter=configobj['maxiter'], sigrej=configobj['sigrej'], lower=configobj['lower'], upper=config...

def main(): """Command line driver.""" import argparse # Parse input parameters parser = argparse.ArgumentParser( prog=__taskname__, description=( 'Run CALACS and standalone acs_destripe script on given post-SM4 ' 'ACS/WFC RAW full-frame or supported subarray ima...

def get_search_results(self, request, queryset, search_term): """ Returns a tuple containing a queryset to implement the search, and a boolean indicating if the results may contain duplicates. """ # Apply keyword searches. def construct_search(field_name): if ...

def get_filters_params(self, params=None): """ Returns all params except IGNORED_PARAMS """ if not params: params = self.params lookup_params = params.copy() # a dictionary of the query string # Remove all the parameters that are globally and systematically ...

def get_ordering_field(self, field_name): """ Returns the proper model field name corresponding to the given field_name to use for ordering. field_name may either be the name of a proper model field or the name of a method (on the admin or model) or a callable with the 'admin_ord...

def get_ordering(self, request, queryset): """ Returns the list of ordering fields for the change list. First we check the get_ordering() method in model admin, then we check the object's default ordering. Then, any manually-specified ordering from the query string overrides anyt...

def get_ordering_field_columns(self): """ Returns an OrderedDict of ordering field column numbers and asc/desc """ # We must cope with more than one column having the same underlying # sort field, so we base things on column numbers. ordering = self._get_default_ordering...

def get_field_label(self, field_name, field=None): """ Return a label to display for a field """ label = None if field is not None: label = getattr(field, 'verbose_name', None) if label is None: label = getattr(field, 'name', None) if label is None...

def get_field_display_value(self, field_name, field=None): """ Return a display value for a field """ """ Firstly, check for a 'get_fieldname_display' property/method on the model, and return the value of that, if present. """ val_funct = getattr(self.instance, 'get_%s_d...

def get_image_field_display(self, field_name, field): """ Render an image """ image = getattr(self.instance, field_name) if image: fltr, _ = Filter.objects.get_or_create(spec='max-400x400') rendition = image.get_rendition(fltr) return rendition.img_tag ...

def get_document_field_display(self, field_name, field): """ Render a link to a document """ document = getattr(self.instance, field_name) if document: return mark_safe( '<a href="%s">%s <span class="meta">(%s, %s)</span></a>' % ( document.url, ...

def get_dict_for_field(self, field_name): """ Return a dictionary containing `label` and `value` values to display for a field. """ try: field = self.model._meta.get_field(field_name) except FieldDoesNotExist: field = None return { ...

def get_fields_dict(self): """ Return a list of `label`/`value` dictionaries to represent the fiels named by the model_admin class's `get_inspect_view_fields` method """ fields = [] for field_name in self.model_admin.get_inspect_view_fields(): fields.append(se...

def items_for_result(view, result): """ Generates the actual list of data. """ model_admin = view.model_admin for field_name in view.list_display: empty_value_display = model_admin.get_empty_value_display() row_classes = ['field-%s' % field_name] try: f, attr, val...

def result_list(context): """ Displays the headers and data list together """ view = context['view'] object_list = context['object_list'] headers = list(result_headers(view)) num_sorted_fields = 0 for h in headers: if h['sortable'] and h['sorted']: num_sorted_fields +...

def run(configobj=None): """ TEAL interface for the `acssum` function. """ acssum(configobj['input'], configobj['output'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], quiet=configobj['quiet'...

def _detsat_one(filename, ext, sigma=2.0, low_thresh=0.1, h_thresh=0.5, small_edge=60, line_len=200, line_gap=75, percentile=(4.5, 93.0), buf=200, plot=False, verbose=False): """Called by :func:`detsat`.""" if verbose: t_beg = time.time() fname = '{0}[{1}]'.format(fi...

def _get_valid_indices(shape, ix0, ix1, iy0, iy1): """Give array shape and desired indices, return indices that are correctly bounded by the shape.""" ymax, xmax = shape if ix0 < 0: ix0 = 0 if ix1 > xmax: ix1 = xmax if iy0 < 0: iy0 = 0 if iy1 > ymax: iy1 = ym...

def _rotate_point(point, angle, ishape, rshape, reverse=False): """Transform a point from original image coordinates to rotated image coordinates and back. It assumes the rotation point is the center of an image. This works on a simple rotation transformation:: newx = (startx) * np.cos(angle) ...

def make_mask(filename, ext, trail_coords, sublen=75, subwidth=200, order=3, sigma=4, pad=10, plot=False, verbose=False): """Create DQ mask for an image for a given satellite trail. This mask can be added to existing DQ data using :func:`update_dq`. .. note:: Unlike :func:`detsat`, m...

def update_dq(filename, ext, mask, dqval=16384, verbose=True): """Update the given image and DQ extension with the given satellite trails mask and flag. Parameters ---------- filename : str FITS image filename to update. ext : int, str, or tuple DQ extension, as accepted by ``a...

def _satdet_worker(work_queue, done_queue, sigma=2.0, low_thresh=0.1, h_thresh=0.5, small_edge=60, line_len=200, line_gap=75, percentile=(4.5, 93.0), buf=200): """Multiprocessing worker.""" for fil, chip in iter(work_queue.get, 'STOP'): try: result = _de...

def detsat(searchpattern, chips=[1, 4], n_processes=4, sigma=2.0, low_thresh=0.1, h_thresh=0.5, small_edge=60, line_len=200, line_gap=75, percentile=(4.5, 93.0), buf=200, plot=False, verbose=True): """Find satellite trails in the given images and extensions. The trails are calcu...

def on(self, event: str) -> Callable: """ Decorator for subscribing a function to a specific event. :param event: Name of the event to subscribe to. :type event: str :return: The outer function. :rtype: Callable """ def outer(func): self.add_event(f...

def add_event(self, func: Callable, event: str) -> None: """ Adds a function to a event. :param func: The function to call when event is emitted :type func: Callable :param event: Name of the event. :type event: str """ self._events[event].add(func)

def emit(self, event: str, *args, **kwargs) -> None: """ Emit an event and run the subscribed functions. :param event: Name of the event. :type event: str .. notes: Passing in threads=True as a kwarg allows to run emitted events as separate threads. This can sig...

def emit_only(self, event: str, func_names: Union[str, List[str]], *args, **kwargs) -> None: """ Specifically only emits certain subscribed events. :param event: Name of the event. :type event: str :param func_names: Function(s) to emit. :type func_names: Unio...

def emit_after(self, event: str) -> Callable: """ Decorator that emits events after the function is completed. :param event: Name of the event. :type event: str :return: Callable .. note: This plainly just calls functions without passing params into the ...

def remove_event(self, func_name: str, event: str) -> None: """ Removes a subscribed function from a specific event. :param func_name: The name of the function to be removed. :type func_name: str :param event: The name of the event. :type event: str :raise EventDoesntE...

def _event_funcs(self, event: str) -> Iterable[Callable]: """ Returns an Iterable of the functions subscribed to a event. :param event: Name of the event. :type event: str :return: A iterable to do things with. :rtype: Iterable """ for func in self._events[event...

def _event_func_names(self, event: str) -> List[str]: """ Returns string name of each function subscribed to an event. :param event: Name of the event. :type event: str :return: Names of functions subscribed to a specific event. :rtype: list """ return [func.__n...

def _subscribed_event_count(self) -> int: """ Returns the total amount of subscribed events. :return: Integer amount events. :rtype: int """ event_counter = Counter() # type: Dict[Any, int] for key, values in self._events.items(): event_counter[key] = len(v...

def clean(input, suffix, stat="pmode1", maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, mask1=None, mask2=None, dqbits=None, rpt_clean=0, atol=0.01, clobber=False, verbose=True): r"""Remove horizontal stripes from ACS WFC post-SM4 data. Parameters ---------- ...

def perform_correction(image, output, stat="pmode1", maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, mask=None, dqbits=None, rpt_clean=0, atol=0.01, clobber=False, verbose=True): """ Clean each input image. Parameters --...

def clean_streak(image, stat="pmode1", maxiter=15, sigrej=2.0, lower=None, upper=None, binwidth=0.3, mask=None, rpt_clean=0, atol=0.01, verbose=True): """ Apply destriping algorithm to input array. Parameters ---------- image : `StripeArray` object Arrays a...

def djs_iterstat(InputArr, MaxIter=10, SigRej=3.0, Max=None, Min=None, Mask=None, lineno=None): """ Iterative sigma-clipping. Parameters ---------- InputArr : `numpy.ndarray` Input image array. MaxIter, SigRej : see `clean` Max, Min : float Max and min val...

def run(configobj=None): """TEAL interface for the `clean` function.""" clean(configobj['input'], suffix=configobj['suffix'], stat=configobj['stat'], maxiter=configobj['maxiter'], sigrej=configobj['sigrej'], lower=configobj['lower'], upper=configobj['u...

def main(): """Command line driver.""" import argparse parser = argparse.ArgumentParser( prog=__taskname__, description='Remove horizontal stripes from ACS WFC post-SM4 data.') parser.add_argument( 'arg0', metavar='input', type=str, help='Input file') parser.add_argument( ...

def configure_arrays(self): """Get the SCI and ERR data.""" self.science = self.hdulist['sci', 1].data self.err = self.hdulist['err', 1].data self.dq = self.hdulist['dq', 1].data if (self.ampstring == 'ABCD'): self.science = np.concatenate( (self.scien...

def ingest_flatfield(self): """Process flatfield.""" self.invflat = extract_flatfield( self.hdulist[0].header, self.hdulist[1]) # If BIAS or DARK, set flatfield to unity if self.invflat is None: self.invflat = np.ones_like(self.science) return ...

def ingest_flash(self): """Process post-flash.""" self.flash = extract_flash(self.hdulist[0].header, self.hdulist[1]) # Set post-flash to zeros if self.flash is None: self.flash = np.zeros_like(self.science) return # Apply the flash subtraction if neces...

def ingest_dark(self): """Process dark.""" self.dark = extract_dark(self.hdulist[0].header, self.hdulist[1]) # If BIAS or DARK, set dark to zeros if self.dark is None: self.dark = np.zeros_like(self.science) return # Apply the dark subtraction if necess...

def write_corrected(self, output, clobber=False): """Write out the destriped data.""" # un-apply the flatfield if necessary if self.flatcorr != 'COMPLETE': self.science = self.science / self.invflat self.err = self.err / self.invflat # un-apply the post-flash if...

def calacs(input_file, exec_path=None, time_stamps=False, temp_files=False, verbose=False, debug=False, quiet=False, single_core=False, exe_args=None): """ Run the calacs.e executable as from the shell. By default this will run the calacs given by 'calacs.e'. Parameters -----...

def run(configobj=None): """ TEAL interface for the `calacs` function. """ calacs(configobj['input_file'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], temp_files=configobj['temp_files'], verbose=configobj['verbose'], deb...

def has_any_permissions(self, user): """ Return a boolean to indicate whether the supplied user has any permissions at all on the associated model """ for perm in self.get_all_model_permissions(): if self.has_specific_permission(user, perm.codename): r...

def get_valid_parent_pages(self, user): """ Identifies possible parent pages for the current user by first looking at allowed_parent_page_models() on self.model to limit options to the correct type of page, then checking permissions on those individual pages to make sure we have ...

def acsrej(input, output, exec_path='', time_stamps=False, verbose=False, shadcorr=False, crrejtab='', crmask=False, scalense=None, initgues='', skysub='', crsigmas='', crradius=None, crthresh=None, badinpdq=None, newbias=False, readnoise_only=False, exe_args=None): r""" Run the...

def run(configobj=None): """ TEAL interface for the `acsrej` function. """ acsrej(configobj['input'], configobj['output'], exec_path=configobj['exec_path'], time_stamps=configobj['time_stamps'], verbose=configobj['verbose'], shadcorr=configobj['sha...

def monkeypatch_os_fork_functions(): """ Replace os.fork* with wrappers that use ForkSafeLock to acquire all locks before forking and release them afterwards. """ builtin_function = type(''.join) if hasattr(os, 'fork') and isinstance(os.fork, builtin_function): global _orig_os_fork ...

def atfork(prepare=None, parent=None, child=None): """A Python work-a-like of pthread_atfork. Any time a fork() is called from Python, all 'prepare' callables will be called in the order they were registered using this function. After the fork (successful or not), all 'parent' callables will be ca...

def _call_atfork_list(call_list): """ Given a list of callables in call_list, call them all in order and save and return a list of sys.exc_info() tuples for each exception raised. """ exception_list = [] for func in call_list: try: func() except: exception...

def parent_after_fork_release(): """ Call all parent after fork callables, release the lock and print all prepare and parent callback exceptions. """ prepare_exceptions = list(_prepare_call_exceptions) del _prepare_call_exceptions[:] exceptions = _call_atfork_list(_parent_call_list) _for...

def _print_exception_list(exceptions, message, output_file=None): """ Given a list of sys.exc_info tuples, print them all using the traceback module preceeded by a message and separated by a blank line. """ output_file = output_file or sys.stderr message = 'Exception %s:\n' % message for exc...

def os_forkpty_wrapper(): """Wraps os.forkpty() to run atfork handlers.""" pid = None prepare_to_fork_acquire() try: pid, fd = _orig_os_forkpty() finally: if pid == 0: child_after_fork_release() else: parent_after_fork_release() return pid, fd

def maybe(value): """Wraps an object with a Maybe instance. >>> maybe("I'm a value") Something("I'm a value") >>> maybe(None); Nothing Testing for value: >>> maybe("I'm a value").is_some() True >>> maybe("I'm a value").is_none() False >>> may...

def setup(self): '''Called after instantiation''' TelnetHandlerBase.setup(self) # Spawn a greenlet to handle socket input self.greenlet_ic = eventlet.spawn(self.inputcooker) # Note that inputcooker exits on EOF # Sleep for 0.5 second to allow options negotiation ...

def inputcooker_store_queue(self, char): """Put the cooked data in the input queue (no locking needed)""" if type(char) in [type(()), type([]), type("")]: for v in char: self.cookedq.put(v) else: self.cookedq.put(char)

def setup(self): '''Setup the connection.''' log.debug( 'New request from address %s, port %d', self.client_address ) try: self.transport.load_server_moduli() except: log.exception( '(Failed to load moduli -- gex will be unsupported.)' ) rais...

def streamserver_handle(cls, socket, address): '''Translate this class for use in a StreamServer''' request = cls.dummy_request() request._sock = socket server = None cls(request, address, server)

def check_channel_shell_request(self, channel): '''Request to start a shell on the given channel''' try: self.channels[channel].start() except KeyError: log.error('Requested to start a channel (%r) that was not previously set up.', channel) return False ...

def check_channel_pty_request(self, channel, term, width, height, pixelwidth, pixelheight, modes): '''Request to allocate a PTY terminal.''' #self.sshterm = term #print "term: %r, modes: %r" % (term, modes) log.debug('PTY requested. Setting up %r.', sel...

def download(url, file_name): r = requests.get(url, stream=True) file_size = int(r.headers['Content-length']) ''' if py3: file_size = int(u.getheader("Content-Length")[0]) else: file_size = int(u.info().getheaders("Content-Length")[0]) ''' file_exists = False if...