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Updated the log system to carry on the same version in all scripts
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Bruno Quint committed Sep 13, 2017
1 parent 0c2d121 commit 9bf601c
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76 changes: 18 additions & 58 deletions samfp/mkcube.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
"""

from __future__ import division, print_function
from __future__ import absolute_import, division, print_function

import astropy.io.fits as pyfits
import argparse
Expand All @@ -21,13 +21,15 @@
import numpy as np
import pandas as pd

__author__ = 'Bruno Quint'
from .tools import io, version

log = io.MyLogger(__name__)

log.basicConfig(format='%(levelname)s: %(name)s(%(funcName)s): %(message)s',
level=log.INFO)
__author__ = 'Bruno Quint'


def main():

# Parsing Arguments -------------------------------------------------------
parser = argparse.ArgumentParser(
description="Build a data-cube from image files.")
Expand All @@ -54,10 +56,15 @@ def main():

parsed_args = parser.parse_args()

if parsed_args.quiet:
log.basicConfig(level=log.ERROR)
if parsed_args.debug:
log.basicConfig(level=log.DEBUG)
log.set_verbose(verbose=not parsed_args.quiet)
log.set_debug(debug=parsed_args.debug)

log.info("")
log.info("SAM-FP Tools: mkcube")
log.info("by Bruno Quint ([email protected])")
log.info("version {:s}".format(version.__str__))
log.info("Starting program.")
log.info("")

make_cube(parsed_args.files,
output=parsed_args.output,
Expand Down Expand Up @@ -193,10 +200,10 @@ def make_cube(list_of_files, z_key='FAPEROTZ', combine_algorithm='average',
hdr.add_blank('--- Channels and Files ---', before='CHAN_001')

filename = output
output = safesave(output, verbose=True)
output = io.safe_save(output, verbose=True)

log.info('Writing file to %s' % output)
pyfits.writeto(output, cube, hdr, clobber=True)
log.info('Writing file to {:s}'.format(output))
pyfits.writeto(output, cube, hdr, overwrite=True)

log.debug(pd.DataFrame(data={'x': z,
'y': z_array,
Expand All @@ -207,52 +214,5 @@ def make_cube(list_of_files, z_key='FAPEROTZ', combine_algorithm='average',
return


def safesave(name, overwrite=False, verbose=False):
"""
This is a generic method used to check if a file called 'name'
already exists. If so, it starts some interaction with the user.
Parameters:
name : str
The name of the file that will be written in the future.
overwrite : bool
If False, this method will interact with the user to ask if 'name'
file shall be overwritten or if a new name will be given. If True,
'name' file is automatically overwritten.
verbose : bool
force verbose mode on even when overwrite is automatic.
"""
import os
import sys

v = False if (overwrite is True) else True
if v:
print("\n Writing to output file %s" % name)

while os.path.exists(name):

if overwrite in ['y', 'Y', True]:
if v or verbose:
print(" Overwriting %s file." % name)
os.remove(name)

elif overwrite in ['', 'n', 'N', False]:
name = input(" Please, enter a new filename:\n > ")

elif overwrite in ['q']:
if v:
print(" Exiting program.")
sys.exit()

else:
overwrite = input(" '%s' file exist. Overwrite? (y/[n])" % name)
if v:
print(" Writing data-cube to %s" % name)

return name


if __name__ == '__main__':
main()
145 changes: 53 additions & 92 deletions samfp/phmapply.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,6 @@

from __future__ import division, print_function

from .tools import io

import argparse
import os
import sys
Expand All @@ -20,10 +18,13 @@
import numpy as np
from scipy.interpolate import UnivariateSpline

from .tools import io, version

log = io.MyLogger(__name__)


def main():

# Setting Options ---------------------------------------------------------
parser = argparse.ArgumentParser(
description="Apply a phase-map on a data-cube."
)
Expand Down Expand Up @@ -61,14 +62,16 @@ def main():
)

args = parser.parse_args()
v = not args.quiet
log.set_verbose(verbose=not args.quiet)

# Printing program header --------------------------------------------------
if v:
start = time.time()
print("\n Phase-Map Apply")
print(" by Bruno Quint & Fabricio Ferrari")
print(" version 0.0 - Feb 2014")
start = time.time()
log.info("")
log.info("SAM-FP Tools: PHase-Map Apply")
log.info("by Bruno Quint ([email protected])")
log.info("version {:s}".format(version.__str__))
log.info("Starting program.")
log.info("")

root_dir = os.path.dirname(args.cube_file)
cube_file = args.cube_file
Expand All @@ -79,50 +82,45 @@ def main():
else:
out_file = args.output

if v:
print(" \n Root dir: %s" % root_dir)
print(" Cube to be corrected: %s" % cube_file)
print(" Phase-map to be applied: %s" % map_file)
print(" Output corrected cube: %s" % out_file)
log.info("Root dir: %s" % root_dir)
log.info("Cube to be corrected: %s" % cube_file)
log.info("Phase-map to be applied: %s" % map_file)
log.info("Output corrected cube: %s" % out_file)

# Systemic wavelength ------------------------------------------------------
vel = args.speed
c = 299792 # km/s
wavelength = args.wavelength * np.sqrt((1 + vel / c) / (1 - vel / c))
if v:
print(" Emitted/systemic wavelength: %.2f A" % args.wavelength)
print(" Systemic velocity: %.2f km/s" % vel)
print(" Observed wavelength: %.2f A" % wavelength)

# Reading input data ------------------------------------------------------
if v:
print("\n Reading cube to be corrected.")
log.info("")
log.info("Emitted/systemic wavelength: %.2f A" % args.wavelength)
log.info("Systemic velocity: %.2f km/s" % vel)
log.info("Observed wavelength: %.2f A" % wavelength)

# Reading input data ------------------------------------------------------
log.info("")
log.info("Reading cube to be corrected.")
data_cube = pyfits.open(cube_file)[0]
log.info("Done.")

if v:
print(" Done.")
print("\n Reading phase-map to be applied.")

log.info("Reading phase-map to be applied.")
phase_map = pyfits.open(map_file)[0]

if v:
print(" Done.")
log.info("Done.")

# Checking data -----------------------------------------------------------
if data_cube.data[0].shape != phase_map.shape:
print("[!] Cube and map does not have matching width and height.")
print("[!] Leaving now.\n")
log.error("Cube and map does not have matching width and height.")
log.error("[!] Leaving now.\n")
sys.exit()

if data_cube.data.ndim != 3:
print("[!] Cube file is not really a cube.")
print("[!] Leaving now.\n")
log.error("[!] Cube file is not really a cube.")
log.error("[!] Leaving now.\n")
sys.exit()

if phase_map.data.ndim != 2:
print("[!] Map file is not really an image.")
print("[!] Leaving now.\n")
log.error("[!] Map file is not really an image.")
log.error("[!] Leaving now.\n")
sys.exit()

m = data_cube.header['NAXIS1']
Expand All @@ -137,36 +135,33 @@ def main():

# Reading the Free-Spectral-Range --------------------------------------
try:
if v:
print(" Reading free-spectral-range from cube header.")
log.info("")
log.info("Reading free-spectral-range from cube header.")
# TODO add an option to use the FSR found while extracting
# TODO the phase-map or while fitting it.
# TODO or even to give the option for the user to enter it.
cal_fsr = phase_map.header['PHM_FSR']
cal_wavelength = phase_map.header['PHMWCAL']
f_s_r = cal_fsr / cal_wavelength * wavelength
if v:
print(" Free Spectral Range = %.2f %s" % (f_s_r, units))
log.info(" Free Spectral Range = %.2f %s" % (f_s_r, units))

except KeyError:
print(" Please, enter the free-spectral-range in %s units" % units)
f_s_r = io.input(" > ")
log.info("Please, enter the free-spectral-range in %s units" % units)
f_s_r = io.input(" >")

f_s_r = round(f_s_r / abs(sample)) # From BCV to Channels
if v:
print(" Free-Spectral-Range is %d channels" % f_s_r)
log.info("Free-Spectral-Range is %d channels" % f_s_r)

fsr = f_s_r * args.npoints # From Channels to nPoints
fsr = int(round(fsr))
if v:
print(" Free-Spectral-Range is %d points" % fsr)
log.info("Free-Spectral-Range is %d points" % fsr)

# Assure that the reference spectrum will not be moved ----------------
try:
phase_map.data = phase_map.data - phase_map.data[ref_y, ref_x]
except IndexError:
print("[!] Reference pixel out of field.")
print("[!] Skipping reference pixel map subtraction.")
log.warn("Reference pixel out of field.")
log.warn("Skipping reference pixel map subtraction.")
pass
phase_map.data *= -1

Expand All @@ -177,8 +172,8 @@ def main():
phase_map.data = phase_map.data * args.npoints

# Applying phase-map --------------------------------------------------
if v:
print("\n Applying phase-map:")
log.info("")
log.info("Applying phase-map:")

n_channels = data_cube.header['NAXIS3']
z = np.arange(3 * n_channels) - n_channels
Expand Down Expand Up @@ -211,15 +206,14 @@ def main():
data_cube.data[:, j, i] = spec[n_channels:2 * n_channels]

# Giving a feedback to the user
if v:
if not args.quiet:
temp = ((i + 1) * 100.00 / m)
sys.stdout.write('\r %2.2f%% ' % temp)
sys.stdout.write('\r %2.2f%% ' % temp)
sys.stdout.flush()

end_of_cube = min(int(round(f_s_r)), data_cube.data.shape[0])
data_cube.data = data_cube.data[0:end_of_cube, :, :]
if v:
print(" Done.")
log.info(" Done.")

if args.center:
collapsed_cube = data_cube.data.sum(axis=2).sum(axis=1)
Expand Down Expand Up @@ -252,21 +246,20 @@ def main():
# data_cube.header.add_blank(after='PHMFIT_C')

# Saving corrected data-cube ----------------------------------------------
if v:
print("\n Writing output to file %s." % out_file)
log.info("Writing output to file %s." % out_file)

try:
data_cube.writeto(out_file, overwrite=True)
except TypeError:
data_cube.writeto(out_file, clobber=True)

if v:
print(" Done.")
# noinspection PyUnboundLocalVariable
end = time.time() - start
print("\n Total time ellapsed: {0:02d}:{1:02d}:{2:02d}".format(
log.info("Done.")

end = time.time() - start
log.info("")
log.info("Total time ellapsed: {0:02d}:{1:02d}:{2:02d}".format(
int(end // 3600), int(end % 3600 // 60), int(end % 60)))
print(" All done!\n")
log.info(" All done!\n")


# Method shift_spectrum ========================================================
Expand Down Expand Up @@ -318,35 +311,3 @@ def shift_spectrum(spec, dz, fsr=-1, sample=1.0, n_points=100):
spec = spline(z)

return spec


def error(my_string):
s = BColors.FAIL + '[ERROR] ' + BColors.ENDC
s = s + my_string
print(s)
return


def warning(my_string):
s = BColors.WARNING + '[WARNING] ' + BColors.ENDC
s = s + my_string
print(s)
return


# noinspection PyClassHasNoInit
class BColors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL = '\033[91m'
ENDC = '\033[0m'

def disable(self):
self.HEADER = ''
self.OKBLUE = ''
self.OKGREEN = ''
self.WARNING = ''
self.FAIL = ''
self.ENDC = ''
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