Moves msgs into pypit/__init__.py

.travis.yml

@@ -152,6 +152,7 @@ install:
     - git clone git://github.com/astropy/ci-helpers.git
     - source ci-helpers/travis/setup_conda_$TRAVIS_OS_NAME.sh
     - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL git+https://github.com/linetools/linetools.git; fi
+    - if [[ $SETUP_CMD != egg_info ]]; then $PIP_INSTALL git+https://github.com/PYPIT/arclines.git@circular_imports; fi
     - conda install numpy
     - conda install Cython
 

CHANGES.rst

@@ -34,6 +34,10 @@
 * Allowed data sections to be extracted from header information
 * Significant refactor of routines related to pypit_setup
 * Various small improvements, primarly to handle Gemini/GMOS data [not yet fully supported in PYPIT]
+* Removed majority of cython functionality
+* Moved logging to be a package object using the main __init__.py file
+* Begin to adhere to PEP8 (mostly)
+* setup.py rewritten.  Modeled after https://github.com/sdss/marvin/blob/master/setup.py .  Added requirements.txt with the package versions required.
 
 0.7 (2017-02-07)
 ----------------

pypit/__init__.py

@@ -0,0 +1,52 @@
+"""
+pypit package initialization.
+
+The current main purpose of this is to provide package-level globals
+that can be imported by submodules.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+
+# Imports for signal and log handling
+import sys
+import signal
+import warnings
+
+# Set version
+__version__ = '0.8.0.dev0'
+# TODO: Do we need this?  A release should be tied to a date, and the
+# date information could be put in the CHANGES.rst
+__last_updated__ = '23Mar2018'
+
+# Import and instantiate the logger
+from pypit import armsgs
+msgs = armsgs.Messages()
+
+# Import the close_qa method so that it can be called when a hard stop
+# is requested by the user
+# TODO: Is this necessary?  As far as I can tell, close_qa() doesn't
+# actually close any already opened qa files
+
+# TODO: Causes circular imports
+# from pypit.arqa import close_qa
+
+# Send all signals to messages to be dealt with (i.e. someone hits ctrl+c)
+def signal_handler(signalnum, handler):
+    """
+    Handle signals sent by the keyboard during code execution
+    """
+    if signalnum == 2:
+        msgs.info('Ctrl+C was pressed. Ending processes...')
+#         close_qa(msgs.pypit_file)
+        msgs.close()
+        sys.exit()
+
+signal.signal(signal.SIGINT, signal_handler)
+
+# Ignore all warnings given by python
+warnings.resetwarnings()
+warnings.simplefilter('ignore')
+

pypit/ararc.py

@@ -1,21 +1,25 @@
 from __future__ import (print_function, absolute_import, division, unicode_literals)
 
+import os
+import time
+import inspect
+
 import numpy as np
+from matplotlib import pyplot as plt
+from matplotlib import gridspec, font_manager
+
+import arclines
+#from arclines.holy.grail import basic, semi_brute, general
+
 from pypit import arpca
 from pypit import arparse as settings
-from pypit import armsgs
+from pypit import msgs
 from pypit import arsave
 from pypit import arutils
 from pypit import ararclines
 from pypit import arqa
-from matplotlib import pyplot as plt
-import os
-import time
-
 from pypit import ardebug as debugger
-
-# Logging
-msgs = armsgs.get_logger()
+from pypit import arcyarc
 
 
 def detect_lines(slf, det, msarc, censpec=None, MK_SATMASK=False):
@@ -53,7 +57,6 @@ def detect_lines(slf, det, msarc, censpec=None, MK_SATMASK=False):
       The spectrum used to find detections. This spectrum has
       had any "continuum" emission subtracted off
     """
-    from pypit import arcyarc
     # Extract a rough spectrum of the arc in each order
     msgs.info("Detecting lines")
     msgs.info("Extracting an approximate arc spectrum at the centre of the chip")
@@ -548,7 +551,8 @@ def simple_calib(slf, det, get_poly=False):
         xrej=xrej, yrej=yrej, mask=mask, spec=yprep, nrej=aparm['nsig_rej_final'],
         shift=0., tcent=tcent)
     # QA
-    arqa.arc_fit_qa(slf, final_fit)
+#    arqa.arc_fit_qa(slf, final_fit)
+    arc_fit_qa(slf, final_fit)
     # RMS
     rms_ang = arutils.calc_fit_rms(xfit, yfit, fit, aparm['func'], minv=fmin, maxv=fmax)
     wave = arutils.func_val(fit, np.arange(slf._msarc[det-1].shape[0])/float(slf._msarc[det-1].shape[0]),
@@ -574,22 +578,22 @@ def calib_with_arclines(slf, det, get_poly=False, use_method="general"):
     final_fit : dict
       Dict of fit info
     """
-    from arclines.holy.grail import basic, semi_brute, general
     # Parameters (just for convenience)
     aparm = slf._arcparam[det-1]
     # Extract the arc
     msgs.work("Detecting lines")
     tampl, tcent, twid, w, satsnd, spec = detect_lines(slf, det, slf._msarc[det-1])
 
     if use_method == "semi-brute":
-        best_dict, final_fit = semi_brute(spec, aparm['lamps'], aparm['wv_cen'], aparm['disp'], fit_parm=aparm, min_ampl=aparm['min_ampl'])
+        best_dict, final_fit = arclines.holy.grail.semi_brute(spec, aparm['lamps'], aparm['wv_cen'], aparm['disp'], fit_parm=aparm, min_ampl=aparm['min_ampl'])
     elif use_method == "basic":
-        stuff = basic(spec, aparm['lamps'], aparm['wv_cen'], aparm['disp'])
+        stuff = arclines.holy.grail.basic(spec, aparm['lamps'], aparm['wv_cen'], aparm['disp'])
         status, ngd_match, match_idx, scores, final_fit = stuff
     else:
         # Now preferred
-        best_dict, final_fit = general(spec, aparm['lamps'], fit_parm=aparm, min_ampl=aparm['min_ampl'])
-    arqa.arc_fit_qa(slf, final_fit)
+        best_dict, final_fit = arclines.holy.grail.general(spec, aparm['lamps'], fit_parm=aparm, min_ampl=aparm['min_ampl'])
+#    arqa.arc_fit_qa(slf, final_fit)
+    arc_fit_qa(slf, final_fit)
     #
     return final_fit
 
@@ -661,3 +665,113 @@ def new_saturation_mask(a, satlevel):
 
     return mask.astype(int)
 
+
+def arc_fit_qa(slf, fit, outfile=None, ids_only=False, title=None):
+    """
+    QA for Arc spectrum
+
+    Parameters
+    ----------
+    fit : Wavelength fit
+    arc_spec : ndarray
+      Arc spectrum
+    outfile : str, optional
+      Name of output file
+    """
+
+    plt.rcdefaults()
+    plt.rcParams['font.family']= 'times new roman'
+
+    # Grab the named of the method
+    method = inspect.stack()[0][3]
+    # Outfil
+    if outfile is None:
+        outfile = arqa.set_qa_filename(slf.setup, method)
+    #
+    arc_spec = fit['spec']
+
+    # Begin
+    if not ids_only:
+        plt.figure(figsize=(8, 4.0))
+        plt.clf()
+        gs = gridspec.GridSpec(2, 2)
+        idfont = 'xx-small'
+    else:
+        plt.figure(figsize=(11, 8.5))
+        plt.clf()
+        gs = gridspec.GridSpec(1, 1)
+        idfont = 'small'
+
+    # Simple spectrum plot
+    ax_spec = plt.subplot(gs[:,0])
+    ax_spec.plot(np.arange(len(arc_spec)), arc_spec)
+    ymin, ymax = 0., np.max(arc_spec)
+    ysep = ymax*0.03
+    for kk, x in enumerate(fit['xfit']*fit['xnorm']):
+        yline = np.max(arc_spec[int(x)-2:int(x)+2])
+        # Tick mark
+        ax_spec.plot([x,x], [yline+ysep*0.25, yline+ysep], 'g-')
+        # label
+        ax_spec.text(x, yline+ysep*1.3,
+            '{:s} {:g}'.format(fit['ions'][kk], fit['yfit'][kk]), ha='center', va='bottom',
+            size=idfont, rotation=90., color='green')
+    ax_spec.set_xlim(0., len(arc_spec))
+    ax_spec.set_ylim(ymin, ymax*1.2)
+    ax_spec.set_xlabel('Pixel')
+    ax_spec.set_ylabel('Flux')
+    if title is not None:
+        ax_spec.text(0.04, 0.93, title, transform=ax_spec.transAxes,
+                     size='x-large', ha='left')#, bbox={'facecolor':'white'})
+    if ids_only:
+        plt.tight_layout(pad=0.2, h_pad=0.0, w_pad=0.0)
+        plt.savefig(outfile, dpi=800)
+        plt.close()
+        return
+
+    # Arc Fit
+    ax_fit = plt.subplot(gs[0, 1])
+    # Points
+    ax_fit.scatter(fit['xfit']*fit['xnorm'], fit['yfit'], marker='x')
+    if len(fit['xrej']) > 0:
+        ax_fit.scatter(fit['xrej']*fit['xnorm'], fit['yrej'], marker='o',
+            edgecolor='gray', facecolor='none')
+    # Solution
+    xval = np.arange(len(arc_spec))
+    wave = arutils.func_val(fit['fitc'], xval/fit['xnorm'], 'legendre',
+        minv=fit['fmin'], maxv=fit['fmax'])
+    ax_fit.plot(xval, wave, 'r-')
+    xmin, xmax = 0., len(arc_spec)
+    ax_fit.set_xlim(xmin, xmax)
+    ymin,ymax = np.min(wave)*.95,  np.max(wave)*1.05
+    ax_fit.set_ylim(np.min(wave)*.95,  np.max(wave)*1.05)
+    ax_fit.set_ylabel('Wavelength')
+    ax_fit.get_xaxis().set_ticks([]) # Suppress labeling
+    # Stats
+    wave_fit = arutils.func_val(fit['fitc'], fit['xfit'], 'legendre',
+        minv=fit['fmin'], maxv=fit['fmax'])
+    rms = np.sqrt(np.sum((fit['yfit']-wave_fit)**2)/len(fit['xfit'])) # Ang
+    dwv_pix = np.median(np.abs(wave-np.roll(wave,1)))
+    ax_fit.text(0.1*len(arc_spec), 0.90*ymin+(ymax-ymin),
+        r'$\Delta\lambda$={:.3f}$\AA$ (per pix)'.format(dwv_pix), size='small')
+    ax_fit.text(0.1*len(arc_spec), 0.80*ymin+(ymax-ymin),
+        'RMS={:.3f} (pixels)'.format(rms/dwv_pix), size='small')
+    # Arc Residuals
+    ax_res = plt.subplot(gs[1,1])
+    res = fit['yfit']-wave_fit
+    ax_res.scatter(fit['xfit']*fit['xnorm'], res/dwv_pix, marker='x')
+    ax_res.plot([xmin,xmax], [0.,0], 'k--')
+    ax_res.set_xlim(xmin, xmax)
+    ax_res.set_xlabel('Pixel')
+    ax_res.set_ylabel('Residuals (Pix)')
+
+    # Finish
+    plt.tight_layout(pad=0.2, h_pad=0.0, w_pad=0.0)
+    plt.savefig(outfile, dpi=800)
+    plt.close()
+
+    plt.rcdefaults()
+
+    return
+
+
+

pypit/ararclines.py

@@ -4,14 +4,18 @@
 from astropy.table import Table, Column, vstack
 import glob, copy
 import yaml
+from pkg_resources import resource_filename
 
-from pypit import armsgs
+from arclines.io import load_line_list
+
+#from pypit import armsgs
+from pypit import msgs
 from pypit import arparse as settings
 
 from pypit import ardebug as debugger
 
 # Logging
-msgs = armsgs.get_logger()
+#msgs = armsgs.get_logger()
 
 
 def parse_nist(slf,ion):
@@ -23,47 +27,10 @@ def parse_nist(slf,ion):
     ion : str
       Name of ion
     """
-    # Root (for development only)
-    if slf is None:
-        from pypit import arutils as arut
-        msgs.warn("Using arutils.dummy_self.  Better know what you are doing.")
-        slf = arut.dummy_self()
-    root = settings.argflag['run']['pypitdir']
-    # Find file
-    srch_file = root + '/data/arc_lines/NIST/'+ion+'_vacuum.ascii'
-    nist_file = glob.glob(srch_file)
-    if len(nist_file) == 0:
-        msgs.error("Cannot find NIST file {:s}".format(srch_file))
-    elif len(nist_file) != 1:
-        msgs.error("Multiple NIST files for {:s}".format(srch_file))
-    # Read
-    nist_tbl = Table.read(nist_file[0], format='ascii.fixed_width', comment='#')
-    gdrow = nist_tbl['Observed'] > 0.  # Eliminate dummy lines
-    nist_tbl = nist_tbl[gdrow]
-    # Now unique values only (no duplicates)
-    uniq, indices = np.unique(nist_tbl['Observed'],return_index=True)
-    nist_tbl = nist_tbl[indices]
-    # Deal with Rel
-    agdrel = []
-    for row in nist_tbl:
-        try:
-            gdrel = int(row['Rel.'])
-        except:
-            try:
-                gdrel = int(row['Rel.'][:-1])
-            except: 
-                gdrel = 0
-        agdrel.append(gdrel) 
-    agdrel = np.array(agdrel)
-    # Remove and add
-    nist_tbl.remove_column('Rel.')
-    nist_tbl.remove_column('Ritz')
-    nist_tbl.add_column(Column(agdrel,name='RelInt'))
-    nist_tbl.remove_column('Acc.')
-    nist_tbl.remove_column('Type')
-    #nist_tbl.add_column(Column([ion]*len(nist_tbl), name='Ion', dtype='S5'))
-    nist_tbl.add_column(Column([ion]*len(nist_tbl), name='Ion', dtype='U5'))
-    nist_tbl.rename_column('Observed','wave')
+    nist_path = resource_filename('arclines', 'data/NIST/')
+    line_file = nist_path+'{:s}_vacuum.ascii'.format(ion)
+    nist_tbl = load_line_list(line_file, NIST=True)
+
     # Return
     return nist_tbl
 

pypit/archeck.py

@@ -4,6 +4,23 @@
 
 from __future__ import absolute_import, division, print_function
 
+import pkg_resources
+
+requirements_file = pkg_resources.resource_filename('pypit', 'requirements.txt')
+install_requires = [line.strip().replace('==', '>=') for line in open(requirements_file)
+                    if not line.strip().startswith('#') and line.strip() != '']
+for requirement in install_requires:
+    pkg, version = requirement.split('>=')
+    try:
+        pv = pkg_resources.get_distribution(pkg).version
+    except pkg_resources.DistributionNotFound:
+        raise ImportError("Package: {:s} not installed!".format(pkg))
+    else:
+        if pkg_resources.parse_version(pv) < pkg_resources.parse_version(version):
+            print("Version of package {:s} = {:s}".format(pkg, pv))
+            raise ImportError("You need version >= {:s}".format(version))
+
+'''
 from distutils.version import LooseVersion
 
 import warnings
@@ -42,3 +59,4 @@ def version_check():
     for dep, ver in minimum_versions.items():
         if LooseVersion(globals()[dep].__version__) < LooseVersion(ver):
             raise VersionError('Update ' + dep + ' to at least version ' + ver + '!')
+'''