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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()
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