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from __future__ import with_statement
import sys
try:
import inspect
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 matplotlib.pyplot import cm
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_combine"
recons_cat = "SCI_RECONSTRUCTED"
recons_cat2 = "SINGLE_CUBES"
combined_cat = "COMBINED_CUBE"
oh_spec_cat = "OH_SPEC"
cores = ['r', 'g', '0.50', 'c', 'm', 'y', 'b']
labels_view=['Display input and output spectra', 'Display output spectra', 'Display input spectra']
vs_state = 0
selected_file_idx = 0
def setCurrentParameterHelper(self, helper):
self.param_helper = helper
def setWindowTitle(self):
return self.recipe_name+"_interactive"
def setInteractiveParameters(self):
return [
reflex.RecipeParameter(recipe=self.recipe_name, displayName="name",
group="Comb.", description="Name of the object to combine. Empty[default] means all."),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="fmethod",
group="Comb.", description="Fitting Method (gauss, moffat)"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="flux",
group="Comb.", description="Apply flux conservation"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="edge_nan",
group="Comb.", description="Set borders of cubes to NaN before combining them"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="cmethod",
group="Comb.", description="Combination Method (average, median, sum, min_max, ksigma)"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="cpos_rej",
group="Comb.", description="The positive rejection threshold"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="cneg_rej",
group="Comb.", description="The negative rejection threshold"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="citer",
group="Comb.", description="The number of iterations"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="cmax",
group="Comb.", description="The number of maximum pixel values"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="cmin",
group="Comb.", description="The number of minimum pixel values"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="skipped_frames",
group="Comb.", description="Comma-separated list of R:I duplets/'labels' indexing the frames to skip. R:I means the Rth RAW frame from the Ith IFU will be ignored. Empty[default] skips none."),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="ifus",
group="Other", description="The indices of the IFUs to combine"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="method",
group="Other", description="The shifting method"),
reflex.RecipeParameter(recipe=self.recipe_name, displayName="filename",
group="Other", description="The path to the file with the shift vectors"),
]
def readFitsData(self, fitsFiles):
# Initialise
self.comb_files = [] # List of Dict (1 per comb. file) - Keys : FILENAME, USEDIFUS, SKIPPEDIFUS, CRPIX3, CRVAL3, CDELT3, UNIT, Spectrum, Collapsed, in_ifus
# in_fus: List of Dict (1 per used IFUS) - Keys : REC_FILENAME, rec_im_nums, ifu_nb, CRPIX3, CRVAL3, CDELT3, UNIT, Spectrum
self.oh_spec = dict() # Dict - Keys : Found, CRVAL1, CDELT1, Spectrum
# Loop on all FITS files
self.oh_spec["Found"] = False
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 COMBINED image
if f.category == self.combined_cat :
combined_file = PipelineProduct(f)
filename = os.path.basename(f.name)
# Create a Dictionary per file
my_file_dict = dict()
# STORE the combined file name
my_file_dict["FILENAME"] = filename
# STORE the Used reconstructed files IFUS : "1:3,2:5,..."
combined_primary = combined_file.all_hdu[0]
# Support case where keyword is missing
if 'ESO PRO USEDIFUS' in combined_primary.header :
my_file_dict["USEDIFUS"] = combined_primary.header['ESO PRO USEDIFUS']
else :
my_file_dict["USEDIFUS"] = ""
if 'ESO PRO SKIPPEDIFUS' in combined_primary.header :
my_file_dict["SKIPPEDIFUS"] = combined_primary.header['ESO PRO SKIPPEDIFUS']
else :
my_file_dict["SKIPPEDIFUS"] = ""
# Store the COMBINE Spectrum and Image
combined_ext = combined_file.all_hdu[1]
naxis = combined_ext.header['NAXIS']
if (naxis == 3):
# Get Keyword infos
my_file_dict["CRPIX3"] = combined_ext.header['CRPIX3']
my_file_dict["CRVAL3"] = combined_ext.header['CRVAL3']
my_file_dict["CDELT3"] = combined_ext.header['CDELT3']
my_file_dict["UNIT"] = combined_ext.header['ESO QC CUBE_UNIT']
# Fill Spectrum
my_file_dict["Spectrum"] = []
for cube_plane in combined_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
my_file_dict["Spectrum"].append(mean)
# Fill Collapsed Image
collapsed_frame_ext = self._get_collapsed_ext(fitsFiles, f)
if collapsed_frame_ext:
my_file_dict["Collapsed"] = collapsed_frame_ext.data
### Parse R:I from CSV string ##################
rec_im_nums = dict()
ifu_nums = dict()
skipped = dict()
# Store used IFUs from the FITS keyword
duplet_seq = my_file_dict["USEDIFUS"]
duplet_seq.strip()
if len(duplet_seq) > 1 :
duplet_seq = duplet_seq.split(",")
for kindx in range(0, len(duplet_seq)):
xpto = duplet_seq[kindx]
aux = xpto.split(":")
rec_im_nums[kindx] = int( aux[0] )
ifu_nums[kindx] = int( aux[1] )
skipped[kindx] = 0
# Store Skipped IFUs
next_idx = len(duplet_seq)
duplet_seq = my_file_dict["SKIPPEDIFUS"]
duplet_seq.strip()
if len(duplet_seq) > 1 :
duplet_seq = duplet_seq.split(",")
for skipped_idx in range(0, len(duplet_seq)):
xpto = duplet_seq[skipped_idx]
aux = xpto.split(":")
rec_im_nums[next_idx+skipped_idx] = int( aux[0] )
ifu_nums[next_idx+skipped_idx] = int( aux[1] )
skipped[next_idx+skipped_idx] = 1
### end ########################################
# Get the Input IFUs for this combined image
my_file_dict["in_ifus"] = []
# Loop on all input fitsfiles
countr = 0
for frec in fitsFiles:
if frec.category == self.recons_cat or frec.category == self.recons_cat2 :
reconstructed_file = PipelineProduct(frec)
reconstructed_filename = os.path.basename(frec.name)
# countr is the id of the current REC file amongst the REC files
countr += 1
# Loop on the used IFUS to get the ones from the current REC file
for duplet_num in range(0, len(rec_im_nums) ) :
r = rec_im_nums[duplet_num]
# Check if the current REC file is specified here
if r == countr :
# Create a dictionary per used IFU
my_used_ifus_dict = dict()
# STORE RECONSTRUCTED filename
my_used_ifus_dict["REC_FILENAME"] = reconstructed_filename
i = ifu_nums[duplet_num]
# STORE the ifu nb / rec file idx / skipped info
my_used_ifus_dict["ifu_nb"] = i
my_used_ifus_dict["rec_im_nums"] = r
my_used_ifus_dict["skipped"] = skipped[duplet_num]
# Store the spectrum in a dictionary
# TODO : ith IFU in ith extension ??
rec_ext = reconstructed_file.all_hdu[i]
rec_naxis = rec_ext.header['NAXIS']
if (rec_naxis == 3):
# Get Keyword infos
my_used_ifus_dict["CRPIX3"] = rec_ext.header['CRPIX3']
my_used_ifus_dict["CRVAL3"] = rec_ext.header['CRVAL3']
my_used_ifus_dict["CDELT3"] = rec_ext.header['CDELT3']
my_used_ifus_dict["UNIT"] = rec_ext.header['ESO QC CUBE_UNIT']
# Fill Spectrum
my_used_ifus_dict["Spectrum"] = []
for cube_plane in rec_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
my_used_ifus_dict["Spectrum"].append(mean)
# add this dictionary my_file_dict["in_ifus"]
my_file_dict["in_ifus"].append(my_used_ifus_dict)
# Append the dictionary to the files list
self.comb_files.append(my_file_dict)
# If proper files are there...
if (len(self.comb_files) > 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
# 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_
def _get_collapsed_ext(self, fitsFiles, comb_file):
comb_file_name = os.path.basename(comb_file.name)
# Loop on all FITS files
for f in fitsFiles:
make_image_filename = os.path.basename(f.name)
if (make_image_filename == "make_image_"+comb_file_name):
collapsed_frame = PipelineProduct(f)
return collapsed_frame.all_hdu[1]
def addSubplots(self, figure):
self._add_subplots(figure)
#def addSubplots_SS(self, figure):
#self._add_subplots_SS(figure)
def plotProductsGraphics(self):
# print self.param_helper("skipped_frames")
self._plot()
def plotWidgets(self) :
#self.radiobutton.clear()
widgets = list()
labels=[]
for idx in range(0, len(self.comb_files)):
labels.append(self.comb_files[idx]["FILENAME"])
#labels_view=['Combined', 'Classic', 'Spectra Stack']
# Files Selector radiobutton
self.radiobutton = reflex_plot_widgets.InteractiveRadioButtons(self.comb_files_selector, self.setFSCallback, labels, self.selected_file_idx, title='Files Selection (double-click Left Mouse Button)')
widgets.append(self.radiobutton)
self.plotVS_Widget()
return widgets
def plotVS_Widget(self) :
self.view_select.clear()
widgets = list()
# View Selector radiobutton
self.radiobutton_VS = reflex_plot_widgets.InteractiveRadioButtons(self.view_select, self.setVSCallback, self.labels_view, self.vs_state)
self.view_select.text(0.5, 0.0, 'View Selection (Left Mouse Button)', verticalalignment='bottom', horizontalalignment='center',
fontsize=12, fontweight='semibold')
widgets.append(self.radiobutton_VS)
return widgets
#def setCurrentParameterHelper(self, helper) :
#print helper('skipped_frames')
def setFSCallback(self, filename) :
for idx in range(0, len(self.comb_files)):
if (self.comb_files[idx]["FILENAME"] == filename):
self.selected_file_idx = idx
# Redraw spectrum
self._plot_spectrum()
# Redisplay image
self._disp_image()
# Redraw spectra stack
self._disp_spectra_stack()
def setVSCallback(self, chosen_view) :
#print(chosen_view)
if(chosen_view == self.labels_view[0]): #if(chosen_view == 'Combined'):
self.vs_state = 0
self.addSubplots(self.my_figure)
# Redraw spectrum
self._plot_spectrum()
# Redisplay image
self._disp_image()
# Redraw spectra stack
self._disp_spectra_stack()
# Redraw View Selection radiobutton panel
self.plotWidgets()
if(chosen_view == self.labels_view[1]): #if(chosen_view == 'Classic'):
self.vs_state = 1
self._add_subplots_Clssc(self.my_figure)
# Redraw spectrum
self._plot_spectrum()
# Redisplay image
self._disp_image()
# Redraw View Selection radiobutton panel
self.plotWidgets()
if(chosen_view == self.labels_view[2]): #if(chosen_view == 'Spectra Stack'):
self.vs_state = 2
self._add_subplots_SS(self.my_figure)
# Redraw spectra stack
self._disp_spectra_stack()
# Redraw View Selection radiobutton panel
self.plotVS_Widget()
self.my_figure.canvas.draw()
def _add_subplots_Clssc(self, figure):
self.my_figure = figure
self.my_figure.clear()
figure.clear()
gs = gridspec.GridSpec(4, 3)
self.comb_files_selector = figure.add_subplot(gs[0:2, :])
self.spec_plot = figure.add_subplot( gs[2, 0:2])
self.collapsed_img = figure.add_subplot( gs[2, 2])
self.view_select = figure.add_subplot( gs[3, :])
def _add_subplots_SS(self, figure):
self.my_figure = figure
self.my_figure.clear()
figure.clear()
gs = gridspec.GridSpec(4, 3)
self.spec_stack = figure.add_subplot( gs[0:3, :])
self.view_select = figure.add_subplot( gs[3, :])
def _add_subplots(self, figure):
self.my_figure = figure
self.my_figure.clear()
figure.clear()
#stop_here()
gs = gridspec.GridSpec(4, 3)
self.comb_files_selector = figure.add_subplot(gs[0:2, 0:2])
self.spec_plot = figure.add_subplot( gs[2, 0])
self.collapsed_img = figure.add_subplot( gs[2, 1])
self.spec_stack = figure.add_subplot( gs[0:3, 2])
self.view_select = figure.add_subplot( gs[3, :])
def _data_plot_get_tooltip(self):
return self.comb_files[self.selected_file_idx]["FILENAME"]
def _disp_image(self):
extension_dict = self.comb_files[self.selected_file_idx]
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.comb_files[self.selected_file_idx]
# 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 _disp_spectra_stack(self):
comb_dict = self.comb_files[self.selected_file_idx]
spec_list = []
ifus_list = []
rec_idx_list = []
skipped = []
for ind in range( 0, len(comb_dict["in_ifus"]) ) :
spec_list.append( comb_dict["in_ifus"][ind]["Spectrum"] )
ifus_list.append( comb_dict["in_ifus"][ind]["ifu_nb"] )
rec_idx_list.append( comb_dict["in_ifus"][ind]["rec_im_nums"] )
skipped.append( comb_dict["in_ifus"][ind]["skipped"] )
# Define wave
pix = numpy.arange(len(comb_dict["Spectrum"]))
wave = comb_dict["CRVAL3"] + pix * comb_dict["CDELT3"]
lower_xbound = np.nanmin(wave)
upper_xbound = np.nanmax(wave)
#debug
#print("\n" + "np.nanmin(wave) = " + str(np.nanmin(wave)) + "\n")
#print("\n" + "np.nanmax(wave) = " + str(np.nanmax(wave)) + "\n")
# Plot Spectrum
self.spec_stack.clear()
sstackdisp = pipeline_display.SpectrumDisplay()
sstackdisp.setLabels(r"$\lambda$ ["+"$\mu$m] ", self._process_label(comb_dict["UNIT"]) )
v_offset = 0.
lower_ybound = 0.
upper_ybound = 0.
for indx in range(0, len(spec_list) ):
c = self.cores[mod(indx, len(self.cores))]
spectrum = spec_list[indx]
spec_ = [x for x in spectrum if (np.isnan(x) == False)]
#os_factor = 1.0e-16; v_offset = os_factor * (indx+0) #<-fixed step
med = np.median(spec_) if not np.isnan(np.median(spec_)) else 0
mad = np.median(np.abs(spec_ - med)) if not np.isnan(np.median(spec_)) else 0.1 #Once NaN always NaN assumption forced because of isnan()
os_factor = med
v_offset += mad*10 # cumulative version
if lower_ybound == 0 :
lower_ybound = v_offset
# Skipped Spectra in Black
if (skipped[indx]) :
c = 'black' ;
spectrum_str = str(rec_idx_list[indx])+':'+str(ifus_list[indx])
sstackdisp.overplot(self.spec_stack, wave, np.add(spectrum, v_offset), c )
self.spec_stack.text(upper_xbound*1.01211366512 if self.vs_state==2 else upper_xbound*1.04411725927,
v_offset +os_factor, spectrum_str, verticalalignment='top', horizontalalignment='right', color=c, fontsize=10)
upper_ybound = v_offset + mad*10
if (lower_ybound != 0 and upper_ybound != 0) :
self.spec_stack.set_ybound(lower=lower_ybound*1.15, upper=upper_ybound*1.02)
self.spec_stack.set_xbound(lower=lower_xbound*1.00259742743, upper=upper_xbound)
if self.vs_state == 2 :
self.spec_stack.set_title("IFUs for '"+comb_dict["FILENAME"]+"' (skipped in black)", fontsize=12, fontweight='semibold')
self.spec_stack.set_xlabel(r"$\lambda$ ["+"$\mu$m]" + " (duplet label syntax, <Recons. Image #> : <IFU #>)")
else :
self.spec_stack.set_title("IFUs (skipped in black)\n", fontsize=12, fontweight='semibold')
self.spec_stack.set_xlabel(r"$\lambda$ ["+"$\mu$m]")
self.spec_stack.set_ylabel( self._process_label(comb_dict["UNIT"]) )
if len(spec_list) == 0 :
self.spec_stack.set_title("Missing USEDIFUS", fontsize=12, fontweight='semibold')
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 _data_plot(self):
#~ # Initial file is the first one
#~ self.selected_file_idx = 0
# Draw Spectrum
self._plot_spectrum()
# Display image
self._disp_image()
# Display spectra stack
self._disp_spectra_stack()
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.combined_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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