astropy:docs

Source code for imexam.connect

# Licensed under a 3-clause BSD style license - see LICENSE.rst

""" This is the main controlling class, it allows the user to connect to (at least) ds9 and the imexamine classes """

from __future__ import print_function, division, absolute_import

import warnings
import logging
import subprocess
import os


from .util import set_logging
from . import xpa
from .ds9_viewer import ds9
try:
    from .ginga_viewer import ginga_mp
    have_ginga = True
except ImportError:
    have_ginga = False


from .imexamine import Imexamine

__all__ = ["Connect"]


[docs]class Connect(object): """ Connect to a display device to look at and examine images that are displayed within The control features below are a basic set that should be available in all display tools. The class for the display tool should override them and add it's own extra features. Parameters ---------- target: string, optional the viewer target name or id (default is to start a new instance of a DS9 window) path : string, optional absolute path to the viewers executable viewer: string, optional The name of the image viewer you want to use, currently only DS9 is supported wait_time: int, optional The time to wait for a connection to be eastablished before quitting Attributes ---------- window: a pointer to an object controls the viewers functions imexam: a pointer to an object controls the imexamine functions and options """ def __init__(self, target=None, path=None, viewer="ds9", wait_time=10, quit_window=True): # better dynamic way so people can add their own viewers? _possible_viewers = ["ds9"] self._viewer = viewer.lower() if have_ginga: _possible_viewers.append('ginga_mp') if self._viewer not in _possible_viewers: warnings.warn("**Unsupported viewer**\n") raise NotImplementedError # init sets empty data array until we can load or check viewer self.exam = Imexamine() if 'ds9' in self._viewer: self.window = ds9( target=target, path=path, wait_time=wait_time, quit_ds9_on_del=quit_window) self._event_driven_exam = False # use the imexam loop elif 'ginga_mp' in self._viewer: self.window = ginga_mp(exam=self.exam, close_on_del=quit_window) # self.window.view.add_callback('key-press',self.window._imexam) # rotate canvas in before this can be used # self.window.canvas.add_callback('key-press',self.start_imexam_ginga) # the viewer will track imexam with callbacks self._event_driven_exam = True # alter the exam.imexam_option_funcs{} here through the viewer code if you want to # change key+function associations # self.window._reassign_keys(imexam_dict) self.logfile = 'imexam_log.txt' self.log = None # points to the package logger self._current_slice = None self._current_frame = None
[docs] def setlog(self, filename=None, on=True, level=logging.DEBUG): """turn on and off imexam logging to the a file""" if filename: self.logfile = filename self.log = set_logging(self.logfile, on, level)
[docs] def close(self): """ close the window and end connection""" self.window.close()
[docs] def imexam(self): """run imexamine with user interaction. At a minimum it requires a copy of the data array""" if self.valid_data_in_viewer(): if self._event_driven_exam: self._run_event_imexam() else: self._run_imexam() else: warnings.warn("No valid image loaded in viewer")
def _run_event_imexam(self): """ let the viewer run an event driven imexam pass the key binding dictionary in for it to attach to? """ if not self._event_driven_exam: warnings.warn("Event driven imexam not implemented for viewer") else: self.exam.print_options() print("\nPress the i key in the graphics window for access to imexam keys, i or q again to exit\n")
[docs] def get_data_filename(self): """return the filename for the data in the current window""" return self.window.get_filename()
[docs] def valid_data_in_viewer(self): """return True if a valid file or array is loaded in the current viewing frame""" return self.window.valid_data_in_viewer()
[docs] def get_frame_info(self): """return more explicit information about the data displayed in the current frame""" return self.window.get_frame_info()
[docs] def get_viewer_info(self): """Return a dictionary which has information about all frames loaded with data""" return self.window.get_viewer_info()
def _run_imexam(self): """start imexam analysis loop for non event driven viewers Notes ----- The data displayed in the current frame is grabbed .The catch is that the user can change the data that is displayed using the gui menus in DS9, so during the imexam loop the display needs to be checked after each key stroke. This function will track the user changing the frame number using the gui display for images and update the data array. TODO ds9 returns 1-based, figure out how to deal with this better so that other viewers can be implemented, the problem comes with printing the coordinates and visual comparison with what's displayed in the gui. The gui display seems to round up integer pixels at some zoom factors. Verify this to some level by looking at the pixel returned and using the pixel table window in DS9 to look at surrounding values. imexamine() returns the value at the integer pixel location. """ print("\nPress 'q' to quit\n") keys = self.exam.get_options() # possible commands self.exam.print_options() cstring = "Current image {0}".format(self.get_data_filename(),) logging.info(cstring) print(cstring) # set defaults self._current_frame = self.frame() if self.window.iscube(): self._current_slice = self.window.get_slice_info() self.exam.set_data(self.window.get_data()) current_key = keys[0] # q is not in the list of keys while current_key: self._check_frame() if self.window.iscube(): self._check_slice() try: x, y, current_key = self.readcursor() self._check_frame() if self.window.iscube(): self._check_slice() if current_key not in keys and 'q' not in current_key: print("Invalid key") else: if 'q' in current_key: current_key = None else: self.exam.do_option( x - 1, y - 1, current_key) # ds9 returns 1 based array except KeyError: print( "Invalid key, use\n: {0}".format( self.exam.print_options())) def _check_frame(self): """check if the user switched frames""" frame = self.frame() if self._current_frame != frame: # the user has changed window frames self.exam.set_data(self.window.get_data()) self._current_frame = frame cstring = "\nCurrent image {0:s}".format( self.get_frame_info()['filename'],) logging.info(cstring) print(cstring) def _check_slice(self): """ check if the user switched slice images """ this_slice = self.window.get_slice_info() if self._current_slice != this_slice: self.exam.set_data(self.window.get_data()) self._current_slice = this_slice cstring = "\nCurrent slice {0:s}".format( self.get_frame_info()['naxis'],) logging.info(cstring) print(cstring) """Implement the following functions in your viewer class"""
[docs] def readcursor(self): """returns image coordinate postion and key pressed, in the form of x,y,str with 0arrar offset""" return self.window.readcursor()
[docs] def alignwcs(self, **kwargs): """align frames with wcs""" self.window.alignwcs(**kwargs)
[docs] def clear_contour(self): self.window.clear_contour()
[docs] def cmap(self, **kwargs): """Set the color map table to something else, in a defined list of options""" self.window.cmap(**kwargs)
[docs] def colorbar(self, **kwargs): """turn the colorbar on the screen on and off""" self.window.colorbar(**kwargs)
[docs] def contour(self, **kwargs): """show contours on the window""" self.window.contour(**kwargs)
[docs] def contour_load(self, *args): """load contours from a file""" self.window.contour_load(*args)
[docs] def crosshair(self, **kwargs): """Control the current position of the crosshair in the current frame, crosshair mode is turned on""" self.window.crosshair(**kwargs)
[docs] def cursor(self, **kwargs): """move the cursor in the current frame to the specified image pixel, it will also move selected regions""" self.window.cursor(**kwargs)
[docs] def disp_header(self, **kwargs): """Display the header of the current image to a window""" self.window.disp_header()
[docs] def frame(self, *args, **kwargs): """ move to a frame """ return self.window.frame(*args, **kwargs)
[docs] def get_data(self): """ return a numpy array of the data in the current window""" return self.window.get_data()
[docs] def get_header(self): """return the current fits header as a string, or None if there's a problem""" return self.window.get_header()
[docs] def grid(self, *args, **kwargs): """convenience to turn the grid on and off, grid can be flushed with many more options""" self.window.grid(*args, **kwargs)
[docs] def hideme(self): """lower the display window""" self.window.hideme()
[docs] def load_fits(self, *args, **kwargs): """convenience function to load fits image to current frame""" self.window.load_fits(*args, **kwargs)
[docs] def load_region(self, *args, **kwargs): """Load regions from a file which uses ds9 standard formatting""" self.window.load_region(*args, **kwargs)
[docs] def load_mef_as_cube(self, *args, **kwargs): """Load a Mult-Extension-Fits image one frame as a cube""" self.window.load_mef_as_cube(*args, **kwargs)
[docs] def load_mef_as_multi(self, *args, **kwargs): """Load a Mult-Extension-Fits image into multiple frames""" self.window.load_mef_as_multi(*args, **kwargs)
[docs] def make_region(self, *args, **kwargs): """make an input reg file with [x,y,comment] to a DS9 reg file, the input file should contains lines with x,y,comment""" self.window.make_region(*args, **kwargs)
[docs] def mark_region_from_array(self, *args, **kwargs): """mark regions on the viewer with a list of tuples as input""" self.window.mark_region_from_array(*args, **kwargs)
[docs] def match(self, **kwargs): """match all other frames to the current frame""" self.window.match(**kwargs)
[docs] def nancolor(self, **kwargs): """set the not-a-number color, default is red""" self.window.nancolor(**kwargs)
[docs] def panto_image(self, *args, **kwargs): """convenience function to change to x,y images coordinates using ra,dec x, y in image coord""" self.window.panto_image(*args, **kwargs)
[docs] def panto_wcs(self, *args, **kwargs): """pan to wcs coordinates in image""" self.window.panto_wcs(*args, **kwargs)
[docs] def load_rgb(self, *args, **kwargs): """load three images into a frame, each one for a different color""" self.window.load_rgb(*args, **kwargs)
[docs] def rotate(self, *args, **kwargs): """rotate the current frame (in degrees)""" self.window.rotate(*args, **kwargs)
[docs] def save_rgb(self, *args, **kwargs): """save an rgb image frame that is displayed as an MEF fits file""" self.window.save_rgb(*args, **kwargs)
[docs] def save_header(self, *args, **kwargs): """save the header of the current image to a file""" self.window.save_header(*args, **kwargs)
[docs] def save_regions(self, *args, **kwargs): """save the regions on the current window to a file""" self.window.save_regions(*args, **kwargs)
[docs] def scale(self, *args, **kwargs): """ Scale the image on display.The default zscale is the most widely used option""" self.window.scale(*args, **kwargs)
[docs] def set_region(self, *args, **kwargs): """display a region using the specifications in region_string""" self.window.set_region(*args, **kwargs)
[docs] def showme(self): """raise the display window""" self.window.showme()
[docs] def showpix(self, *args, **kwargs): """display the pixel value table, close window when done""" self.window.showpix(*args, **kwargs)
[docs] def show_window_commands(self): """print the available commands for the selected display application""" self.window.show_commands()
[docs] def snapsave(self, *args, **kwargs): """create a snap shot of the current window and save in specified format. If no format is specified the filename extension is used """ self.window.snapsave(*args, **kwargs)
[docs] def view(self, *args, **kwargs): """ Display numpy image array """ self.window.view(*args, **kwargs)
[docs] def zoom(self, *args, **kwargs): """zoom to parameter which can be any recognized string""" self.window.zoom(*args, **kwargs)
[docs] def zoomtofit(self): """zoom the image to fit the display""" self.window.zoomtofit()
""" These are imexam parameters that the user can change for plotting """ # seems easiest to return the parameter dictionaries here, then the user can catch it, edit it # and reset the pars with self.set in the exam link or directly into the # imexamine object.
[docs] def aimexam(self): """show current parameters for aperture photometry""" return(self.exam.aperphot_pars)
[docs] def cimexam(self): """show current parameters for column plots""" return(self.exam.colplot_pars)
[docs] def eimexam(self): """show current parameters for contour plots""" return(self.exam.contour_pars)
[docs] def himexam(self): """show current parameters for histogram plots""" return(self.exam.histogram_pars)
[docs] def jimexam(self): """show current parameters for 1D fit line plots""" return(self.exam.line_fit_pars)
[docs] def kimexam(self): """show current parameters for 1D fit column plots""" return(self.exam.column_fit_pars)
[docs] def limexam(self): """show current parameters for line plots""" return(self.exam.lineplot_pars)
[docs] def mimexam(self): """show the current parameters for statistical regions""" return(self.exam.report_stat_pars)
[docs] def rimexam(self): """show current parameters for curve of growth plots""" return(self.exam.curve_of_growth_pars)
[docs] def wimexam(self): """show current parameters for surface plots""" return(self.exam.surface_pars)
[docs] def unlearn(self): """unlearn all the imexam parameters and reset to default""" self.exam.unlearn_all()
[docs] def plotname(self, filename=None): """change or show the default save plotname for imexamine""" if not filename: self.exam.get_plot_name() # show the current default else: if os.access(filename, os.F_OK): warnings.warn( "File with that name already exists:{0s}".format(filename)) else: self.exam.set_plot_name(filename)

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