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clean up plot routines
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@weaverba137
weaverba137 committed Jun 18, 2024
1 parent 5362786 commit 2edb196
Showing 1 changed file with 50 additions and 57 deletions.
107 changes: 50 additions & 57 deletions pydl/pydlspec2d/spec1d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,6 @@
import numpy as np
from numpy.linalg import solve
try:
import matplotlib
# TODO: Sometimes this interferes with notebooks, other times not.
# Maybe don't set this at import time.
# matplotlib.use('Agg')
matplotlib.rcParams['figure.figsize'] = (16.0, 12.0)
import matplotlib.pyplot as plt
from matplotlib.font_manager import FontProperties
except ImportError:
Expand All @@ -23,6 +18,11 @@
from astropy.io import ascii, fits
from . import Pydlspec2dException, Pydlspec2dUserWarning

#
# Used for automated matplotlib plots.
#
_default_figsize = (16.0, 12.0)

#
# Used by findspec
#
Expand Down Expand Up @@ -782,24 +782,22 @@ def plot_eig(filename, title='Unknown'):
title = 'CV Stars: Eigenspectra'
else:
raise ValueError('Unknown template type!')
base, ext = filename.split('.')
spectrum = fits.open(filename)
newloglam0 = spectrum[0].header['COEFF0']
objdloglam = spectrum[0].header['COEFF1']
spectro_data = spectrum[0].data
spectrum.close()
base, ext = os.path.splitext(filename)
with fits.open(filename, mode='readonly') as hdulist:
newloglam0 = hdulist[0].header['COEFF0']
objdloglam = hdulist[0].header['COEFF1']
spectro_data = hdulist[0].data
(neig, ndata) = spectro_data.shape
newloglam = np.arange(ndata) * objdloglam + newloglam0
lam = 10.0**newloglam
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
colorvec = ['k', 'r', 'g', 'b', 'm', 'c']
for l in range(neig):
_ = ax.plot(lam, spectro_data[l, :],
colorvec[l % len(colorvec)]+'-', linewidth=1)
ax.set_xlabel(r'Wavelength [$\AA$]')
ax.set_ylabel('Flux [Arbitrary Units]')
ax.set_title(title)
_ = ax.set_xlabel(r'Wavelength [$\AA$]')
_ = ax.set_ylabel('Flux [Arbitrary Units]')
_ = ax.set_title(title)
# ax.set_xlim([3500.0,10000.0])
# ax.set_ylim([-400.0,500.0])
# fig.savefig(base+'.zoom.png')
Expand Down Expand Up @@ -1515,47 +1513,44 @@ def template_input(inputfile, dumpfile, flux=False, verbose=False):
for k in range(nplots):
istart = k*nfluxes
iend = min(istart+nfluxes, nspectra) - 1
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
for l in range(istart, iend+1):
_ = ax.plot(10.0**pcaflux['newloglam'],
pcaflux['newflux'][l, :] + separation*(l % nfluxes),
colorvec[l % len(colorvec)]+'-',
linewidth=1)
ax.set_xlabel(r'Wavelength [$\AA$]')
ax.set_ylabel(r'Flux [$\mathsf{10^{-17} erg\, cm^{-2} s^{-1} \AA^{-1}}$] + Constant')
ax.set_title('Input Spectra {0:04d}-{1:04d}'.format(istart+1, iend+1))
ax.set_ylim(pcaflux['newflux'][istart, :].min(), pcaflux['newflux'][iend-1, :].max()+separation*(nfluxes-1))
_ = ax.set_xlabel(r'Wavelength [$\AA$]')
_ = ax.set_ylabel(r'Flux [$\mathsf{10^{-17} erg\, cm^{-2} s^{-1} \AA^{-1}}$] + Constant')
_ = ax.set_title('Input Spectra {0:04d}-{1:04d}'.format(istart+1, iend+1))
_ = ax.set_ylim(pcaflux['newflux'][istart, :].min(), pcaflux['newflux'][iend-1, :].max()+separation*(nfluxes-1))
fig.savefig('{0}.flux.{1:04d}-{2:04d}.png'.format(outfile, istart+1, iend+1))
plt.close(fig)
#
# Missing data diagnostic.
#
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
_ = ax.plot(10.0**pcaflux['newloglam'], (pcaflux['newivar'] == 0).sum(0)/float(nspectra), 'k-')
ax.set_xlabel(r'Wavelength [$\AA$]')
ax.set_ylabel('Fraction of spectra with missing data')
ax.set_title('Missing Data')
ax.grid(True)
_ = ax.set_xlabel(r'Wavelength [$\AA$]')
_ = ax.set_ylabel('Fraction of spectra with missing data')
_ = ax.set_title('Missing Data')
_ = ax.grid(True)
fig.savefig(outfile+'.missing.png')
plt.close(fig)
#
# usemask diagnostic
#
if 'usemask' in pcaflux:
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
_ = ax.semilogy(10.0**pcaflux['newloglam'][pcaflux['usemask'] > 0],
pcaflux['usemask'][pcaflux['usemask'] > 0], 'k-',
10.0**pcaflux['newloglam'],
np.zeros(pcaflux['newloglam'].shape,
dtype=pcaflux['newloglam'].dtype) + metadata['minuse'],
'k--')
ax.set_xlabel(r'Wavelength [$\AA$]')
ax.set_ylabel('Usemask')
ax.set_title('UseMask')
ax.grid(True)
_ = ax.set_xlabel(r'Wavelength [$\AA$]')
_ = ax.set_ylabel('Usemask')
_ = ax.set_title('UseMask')
_ = ax.grid(True)
fig.savefig(outfile+'.usemask.png')
plt.close(fig)
#
Expand All @@ -1565,36 +1560,34 @@ def template_input(inputfile, dumpfile, flux=False, verbose=False):
aratio10 = pcaflux['acoeff'][:, 1]/pcaflux['acoeff'][:, 0]
aratio20 = pcaflux['acoeff'][:, 2]/pcaflux['acoeff'][:, 0]
aratio30 = pcaflux['acoeff'][:, 3]/pcaflux['acoeff'][:, 0]
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
_ = ax.plot(aratio10, aratio20, marker='None', linestyle='None')
for k in range(len(aratio10)):
_ = ax.text(aratio10[k], aratio20[k],
'{0:04d}-{1:04d}'.format(slist.plate[k], slist.fiberid[k]),
horizontalalignment='center', verticalalignment='center',
color=colorvec[k % len(colorvec)],
fontproperties=smallfont)
# ax.set_xlim([aratio10.min(), aratio10.max])
# ax.set_xlim([aratio20.min(), aratio20.max])
ax.set_xlabel('Eigenvalue Ratio, $a_1/a_0$')
ax.set_ylabel('Eigenvalue Ratio, $a_2/a_0$')
ax.set_title('Eigenvalue Ratios')
# _ = ax.set_xlim([aratio10.min(), aratio10.max])
# _ = ax.set_xlim([aratio20.min(), aratio20.max])
_ = ax.set_xlabel('Eigenvalue Ratio, $a_1/a_0$')
_ = ax.set_ylabel('Eigenvalue Ratio, $a_2/a_0$')
_ = ax.set_title('Eigenvalue Ratios')
fig.savefig(outfile+'.a2_v_a1.png')
plt.close(fig)
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
_ = ax.plot(aratio20, aratio30, marker='None', linestyle='None')
for k in range(len(aratio10)):
_ = ax.text(aratio20[k], aratio30[k],
'{0:04d}-{1:04d}'.format(slist.plate[k], slist.fiberid[k]),
horizontalalignment='center', verticalalignment='center',
color=colorvec[k % len(colorvec)],
fontproperties=smallfont)
# ax.set_xlim([aratio10.min(), aratio10.max])
# ax.set_xlim([aratio20.min(), aratio20.max])
ax.set_xlabel('Eigenvalue Ratio, $a_2/a_0$')
ax.set_ylabel('Eigenvalue Ratio, $a_3/a_0$')
ax.set_title('Eigenvalue Ratios')
# _ = ax.set_xlim([aratio10.min(), aratio10.max])
# _ = ax.set_xlim([aratio20.min(), aratio20.max])
_ = ax.set_xlabel('Eigenvalue Ratio, $a_2/a_0$')
_ = ax.set_ylabel('Eigenvalue Ratio, $a_3/a_0$')
_ = ax.set_title('Eigenvalue Ratios')
fig.savefig(outfile+'.a3_v_a2.png')
plt.close(fig)
#
Expand Down Expand Up @@ -1862,8 +1855,7 @@ def template_star(metadata, newloglam, newflux, newivar, slist, outfile,
thesesubclassnum = np.zeros(thesesubclass.size, dtype='i4')
colorvec = ['k', 'r', 'g', 'b', 'm', 'c']
smallfont = FontProperties(size='xx-small')
fig = plt.figure(dpi=100)
ax = fig.add_subplot(111)
fig, ax = plt.subplots(1, 1, figsize=_default_figsize, dpi=100)
for isub in range(nsubclass):
ii = (thesesubclass == subclasslist[isub]).nonzero()[0]
thesesubclassnum[ii] = isub
Expand All @@ -1881,13 +1873,13 @@ def template_star(metadata, newloglam, newflux, newivar, slist, outfile,
# Plot spectra
#
plotflux = thisflux/thisflux.max()
ax.plot(10.0**newloglam, plotflux,
"{0}-".format(colorvec[isub % len(colorvec)]),
linewidth=1)
_ = ax.plot(10.0**newloglam, plotflux,
"{0}-".format(colorvec[isub % len(colorvec)]),
linewidth=1)
if isub == 0:
ax.set_xlabel(r'Wavelength [$\AA$]')
ax.set_ylabel('Flux [arbitrary units]')
ax.set_title('STAR {0}: Eigenspectra Reconstructions'.format(c))
_ = ax.set_xlabel(r'Wavelength [$\AA$]')
_ = ax.set_ylabel('Flux [arbitrary units]')
_ = ax.set_title('STAR {0}: Eigenspectra Reconstructions'.format(c))
_ = ax.text(10.0**newloglam[-1], plotflux[-1],
subclasslist[isub],
horizontalalignment='right', verticalalignment='center',
Expand Down Expand Up @@ -1919,7 +1911,8 @@ def template_input_main(): # pragma: no cover
#
import sys
from argparse import ArgumentParser

import matplotlib
matplotlib.use("Agg")
# Get home directory in platform-independent way
home_dir = os.path.expanduser('~')
#
Expand Down

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