from __future__ import with_statement import sys try: import numpy import os import re import reflex from pipeline_product import PipelineProduct import pipeline_display import reflex_plot_widgets import matplotlib.gridspec as gridspec from matplotlib.text import Text from pylab import * import_success = True except ImportError: import_success = False print "Error importing modules pyfits, wx, matplotlib, numpy" def paragraph(text, width=None): """ wrap text string into paragraph text: text to format, removes leading space and newlines width: if not None, wraps text, not recommended for tooltips as they are wrapped by wxWidgets by default """ import textwrap if width is None: return textwrap.dedent(text).replace('\n', ' ').strip() else: return textwrap.fill(textwrap.dedent(text), width=width) class DataPlotterManager(object): # static members recipe_name = "kmos_sci_red" reconstructed_cat = "SCI_RECONSTRUCTED" oh_spec_cat = "OH_SPEC" IFU_stat_color = {'Active':'summer', 'Locked':'spring', 'NotInPAF':'winter', 'NotInPAF & Locked':'autumn', 'Coll.':'cool', 'Empty':'copper'} def setWindowTitle(self): return self.recipe_name+"_interactive" def setInteractiveParameters(self): return [ reflex.RecipeParameter(recipe=self.recipe_name, displayName="imethod", group="Recons.", description="Interpolation Method (NN, lwNN, swNN, MS, CS)"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="oscan", group="Recons.", description="Apply Overscan Correction"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="xcal_interpolation", group="Recons.", description="Interpolate xcal between rotator angles"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="neighborhoodRange", group="Extr.", description="Range for Neighbors"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="flux", group="Extr.", description="Apply flux conservation"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="obj_sky_table", group="Sky Sub.", description="The path to the file with the modified obj/sky associations."), reflex.RecipeParameter(recipe=self.recipe_name, displayName="background", group="Sky Sub.", description="Apply background removal"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="no_subtract", group="Sky Sub.", description="Don't sky subtract object and references"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="sky_tweak", group="Sky Sub.", description="Use modified sky cube for sky subtraction (TRUE or FALSE)"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="skip_sky_oh_align", group="Sky Sub.", description="Do not align the sky on OH lines - Only is stretch is on (0-no, 1-yes)"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="stretch", group="Sky Sub.", description="Stretch the sky for sky subtraction (0-no, 1-yes)"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="stretch_degree", group="Sky Sub.", description="Stretching polynomial degree."), reflex.RecipeParameter(recipe=self.recipe_name, displayName="stretch_resampling", group="Sky Sub.", description="Stretching interpolation method (linear / spline)"), reflex.RecipeParameter(recipe=self.recipe_name, displayName="velocity_offset", group="Sky Sub.", description="Specify velocity offset correction in km/s for lambda scale."), ] def readFitsData(self, fitsFiles): # Initialise self.files = dict() self.oh_spec = dict() self.oh_spec["Found"] = False # Loop on all FITS files for f in fitsFiles: # Use OH_SPEC if found if f.category == self.oh_spec_cat : oh_spec_file = PipelineProduct(f) self.oh_spec["Found"] = True self.oh_spec["CRVAL1"] = oh_spec_file.all_hdu[1].header["CRVAL1"] self.oh_spec["CDELT1"] = oh_spec_file.all_hdu[1].header["CDELT1"] self.oh_spec["Spectrum"] = oh_spec_file.all_hdu[1].data # For each reconstructed image if f.category == self.reconstructed_cat : recons_file = PipelineProduct(f) filename = os.path.basename(f.name) # Create a Dictionary per file self.files[filename] = dict() # Loop on extensions for recons_ext in recons_file.all_hdu: # EXTNAME is missing in the primary header - Skip it anyway try: extname = recons_ext.header['EXTNAME'] except KeyError: continue # Create Entry for the extension self.files[filename][extname]=dict() # Get the IFU number from extname to get the IFU status m = re.search(r"\d+", extname) ifu_number = m.group() self.files[filename][extname]["IFU_NUMBER"] = int(ifu_number) naxis = recons_ext.header['NAXIS'] # Set the IFU STATUS arm_key = 'ESO OCS ARM'+ifu_number+' NOTUSED' if (arm_key in recons_file.all_hdu[0].header) : self.files[filename][extname]["IFU_STATUS"] = recons_file.all_hdu[0].header[arm_key] else : if (naxis == 3): self.files[filename][extname]["IFU_STATUS"] = 'Active' else : self.files[filename][extname]["IFU_STATUS"] = 'Empty' if (naxis == 3): # Get Keyword infos self.files[filename][extname]["CRPIX3"] = recons_ext.header['CRPIX3'] self.files[filename][extname]["CRVAL3"] = recons_ext.header['CRVAL3'] self.files[filename][extname]["CDELT3"] = recons_ext.header['CDELT3'] self.files[filename][extname]["UNIT"] = recons_ext.header['ESO QC CUBE_UNIT'] self.files[filename][extname]["NAME"] = recons_ext.header['ESO OCS ARM' + ifu_number +' NAME'] # Fill Spectrum self.files[filename][extname]["Spectrum"] = [] for cube_plane in recons_ext.data: cube_plane_nan_free = cube_plane[~numpy.isnan(cube_plane)] if (len(cube_plane_nan_free) > 0): mean = cube_plane_nan_free.mean() else: mean = numpy.nan self.files[filename][extname]["Spectrum"].append(mean) # Fill Collapsed Image collapsed_frame_ext = self._get_collapsed_ext(fitsFiles, f, extname) if collapsed_frame_ext: self.files[filename][extname]["Collapsed"] = collapsed_frame_ext.data # If proper files are there... if (len(self.files.keys()) > 0): # Set the plotting functions self._add_subplots = self._add_subplots self._plot = self._data_plot else: self._add_subplots = self._add_nodata_subplots self._plot = self._nodata_plot # Inputs : all files, reconstructed file, extension # Returns the corresponding extension in the collapsed corresponding file # The corresponding file must have the same file name as ref_file, prefixed with make_image_ # The corresponding extention must have the same EXTNAME keyword def _get_collapsed_ext(self, fitsFiles, ref_file, extname): ref_file_name = os.path.basename(ref_file.name) # Loop on all FITS files for f in fitsFiles: filename = os.path.basename(f.name) if (filename == "make_image_"+ref_file_name): collapsed_frame = PipelineProduct(f) for collapsed_frame_ext in collapsed_frame.all_hdu: # EXTNAME is missing in the primary header - Skip it anyway try: coll_extname = collapsed_frame_ext.header['EXTNAME'] except KeyError: continue if coll_extname == extname: return collapsed_frame_ext def addSubplots(self, figure): self._add_subplots(figure) def plotProductsGraphics(self): self._plot() def plotWidgets(self) : widgets = list() # Files Selector radiobutton self.radiobutton = reflex_plot_widgets.InteractiveRadioButtons(self.files_selector, self.setFSCallback, sorted(self.files.keys()), 0, title='Files Selection (Left Mouse Button)') widgets.append(self.radiobutton) self.clickable_ifus =reflex_plot_widgets.InteractiveClickableSubplot(self.ifus_selector, self.setIFUSCallback) widgets.append(self.clickable_ifus) return widgets def extension_has_spectrum(self, filename, extname): if ("Spectrum" in self.files[self.selected_file][extname].keys()): return True else: return False def setIFUSCallback(self, point) : if (1 < point.ydata < 3) : extname = "IFU."+str(int((point.xdata/2)+0.5))+".DATA" if (self.extension_has_spectrum(self.selected_file, extname)): # Update selected extension self.selected_extension = extname # Redraw IFUs selection self._plot_ifus_selector(self.selected_file) # Redraw spectrum self._plot_spectrum() # Redisplay image self._disp_image() def setFSCallback(self, filename) : # Keep track of the selected file self.selected_file = filename # Check that the new file currently selected extension is valid if (not self.extension_has_spectrum(self.selected_file, self.selected_extension)): self.selected_extension = self._get_first_valid_extname(self.selected_file) self._plot_ifus_selector(self.selected_file) # Redraw spectrum self._plot_spectrum() # Redisplay image self._disp_image() def _add_subplots(self, figure): gs = gridspec.GridSpec(3, 2) self.files_selector = figure.add_subplot(gs[0,:]) self.ifus_selector = figure.add_subplot(gs[1,:]) self.spec_plot = figure.add_subplot(gs[2,0]) self.collapsed_img = figure.add_subplot(gs[2,1]) def _data_plot_get_tooltip(self): return self.selected_file+" ["+self.selected_extension+"];" +" Object NAME = "+str( self.files[self.selected_file][self.selected_extension]["NAME"] ) def _disp_image(self): extension_dict = self.files[self.selected_file][self.selected_extension] self.collapsed_img.clear() imgdisp = pipeline_display.ImageDisplay() imgdisp.setAspect('equal') # Only if data if 'Collapsed' in extension_dict.keys(): imgdisp.display(self.collapsed_img, "Collapsed image", self._data_plot_get_tooltip(), extension_dict["Collapsed"]) self.collapsed_img.set_xlabel("pixels") # item 6f self.collapsed_img.set_ylabel("pixels") # item 6f def _plot_spectrum(self): extension_dict = self.files[self.selected_file][self.selected_extension] # Plot Spectrum (to be contd.) self.spec_plot.clear() specdisp = pipeline_display.SpectrumDisplay() specdisp.setLabels(r"$\lambda$["+"$\mu$m]" + " (blue: Observed; red: OH[arb. units])", self._process_label(extension_dict["UNIT"]) ) if (self.oh_spec["Found"]): # Placed before spectrum plotting, so it stays in the background # Overplot the OH spectrum pix = numpy.arange(len(self.oh_spec["Spectrum"])) wave = self.oh_spec["CRVAL1"] + pix * self.oh_spec["CDELT1"] oh_flux = self.oh_spec["Spectrum"] / numpy.nanmax(self.oh_spec["Spectrum"]) * 200*numpy.nanmax(extension_dict["Spectrum"]) specdisp.overplot(self.spec_plot, wave, oh_flux, '#ED5D5D') #self.spec_plot.legend(('Observed', 'OH')) self.spec_plot.fill_between(wave, 0, oh_flux, color='#ED5D5D') # Define wave pix = numpy.arange(len(extension_dict["Spectrum"])) wave = extension_dict["CRVAL3"] + pix * extension_dict["CDELT3"] # Plot Spectrum (contd.) specdisp.display(self.spec_plot, "Spectrum", self._data_plot_get_tooltip(), wave, extension_dict["Spectrum"]) def _process_label(self, in_label): # If known, 'pretty print' the label if (in_label == "erg.s**(-1).cm**(-2).angstrom**(-1)"): return "erg sec" + r"$^{-1}$"+"cm" + r"$^{-2}$" + r"$\AA^{-1}$" else: return in_label def _get_ifu_status_from_file(self, filename, extname): cur_status = self.files[filename][extname]["IFU_STATUS"] if cur_status == "NotInPAF/Locked" : return 'NotInPAF & Locked' return cur_status def _plot_ifus_selector(self, filename): self.ifus_selector.clear() # Loop on the different kind of Status to Print the Legend self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(1, 9, 8, 10), cmap='summer') self.ifus_selector.text(2, 8.5, 'Active', fontsize=11,color='white') self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(11, 19, 8, 10), cmap='spring') self.ifus_selector.text(12, 8.5, 'Locked', fontsize=11,color='white') self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(21, 29, 8, 10), cmap='winter') self.ifus_selector.text(22, 8.5, 'NotInPAF', fontsize=11,color='white') self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(31, 39, 8, 10), cmap='autumn') self.ifus_selector.text(32, 8.5, 'NotInPAF & Locked', fontsize=11,color='white') self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(41, 49, 8, 10), cmap='cool') self.ifus_selector.text(42, 8.5, 'Collision', fontsize=11,color='white') self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(1, 9, 4, 6), cmap='copper') self.ifus_selector.text(2, 4.5, 'Empty', fontsize=11,color='white') # Display the IFUs selection squares box_y_start = 1 box_y_stop = 3 box_xwidth = 1.5 for extname in self.files[filename].keys(): # Compute the IFU number ifu_number = self.files[filename][extname]['IFU_NUMBER'] # Draw the little IFU image box_xstart = 2 * ifu_number - 1 box_xstop = box_xstart + box_xwidth ifu_status = self._get_ifu_status_from_file(filename, extname) self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(box_xstart,box_xstop,box_y_start,box_y_stop), cmap=self.IFU_stat_color[ifu_status]) # Write the IFU number in the image self.ifus_selector.text(2 * (ifu_number-1) + 1.2, 1.5, str(ifu_number), fontsize=13,color='white') # Mark the selected IFU if (extname == self.selected_extension): self.ifus_selector.imshow(numpy.zeros((1,1)), extent=(box_xstart,box_xstop,0.5,0.7), cmap=self.IFU_stat_color[ifu_status]) self.ifus_selector.axis([0,50,0,11]) self.ifus_selector.set_title("IFU Selection (Mouse middle button)") self.ifus_selector.get_xaxis().set_ticks([]) self.ifus_selector.get_yaxis().set_ticks([]) # Get the first valid extension name (ie containing a spectrum) in a file - "" if None def _get_first_valid_extname(self, filename): for extname in sorted(self.files[filename].keys()): if (self.extension_has_spectrum(filename, extname)) : return extname return "" def _data_plot(self): # Initial file is the first one self.selected_file = self.files.keys()[0] self.selected_extension = self._get_first_valid_extname(self.selected_file) # Plot the IFUS selection self._plot_ifus_selector(self.selected_file) # Draw Spectrum self._plot_spectrum() # Display image self._disp_image() def _add_nodata_subplots(self, figure): self.img_plot = figure.add_subplot(1,1,1) def _nodata_plot(self): # could be moved to reflex library? self.img_plot.set_axis_off() text_nodata = "Data not found. Input files should contain this" \ " type:\n%s" % self.reconstructed_cat self.img_plot.text(0.1, 0.6, text_nodata, color='#11557c', fontsize=18, ha='left', va='center', alpha=1.0) self.img_plot.tooltip = 'No data found' #This is the 'main' function if __name__ == '__main__': from reflex_interactive_app import PipelineInteractiveApp # Create interactive application interactive_app = PipelineInteractiveApp(enable_init_sop=True) # get inputs from the command line interactive_app.parse_args() #Check if import failed or not if not import_success: interactive_app.setEnableGUI(False) #Open the interactive window if enabled if interactive_app.isGUIEnabled(): #Get the specific functions for this window dataPlotManager = DataPlotterManager() interactive_app.setPlotManager(dataPlotManager) interactive_app.showGUI() else: interactive_app.set_continue_mode() #Print outputs. This is parsed by the Reflex python actor to #get the results. Do not remove interactive_app.print_outputs() sys.exit()