Merge branch 'master' of https://github.com/teuben/nemo

src/scripts/mknemo.d/hdf4

@@ -24,6 +24,7 @@
 version=4.2.14    # 2018-06-26
 version=4.2.15    # 2020-03-03
 version=4.2.16    # 2023-03-06   (this fixed missing xdr problems on ubuntu22)
+version=4.2.16-2  # 2023-03-06
 
 wget=wgetc
 

src/scripts/mknemo.d/valkey

@@ -1,10 +1,13 @@
-#
+#! /usr/bin/env bash
 
 url=https://github.com/valkey-io/valkey
+version=git
 
 cd $NEMO/local
 git clone $url
 cd valkey
 
 make distclean
 make PROG_SUFFIX="_nemo" PREFIX=$NEMO/opt  install
+
+echo valkey $version `date` >> $NEMO/opt/mknemo.log

src/scripts/python/fitsplot.py

@@ -5,35 +5,132 @@
 import os
 import sys
 import aplpy
+import argparse
+import numpy as np
+import matplotlib.pyplot as plt
+from astropy.io import fits
 
-#   dims for an [ra,dec,vel] cube
-dims = [0,1]   # ra-dec
-#dims = [1,2]   # dec-vel
-#dims = [0,2]   # ra-vel
 
-fitsfile = sys.argv[1]
-if len(sys.argv) > 2:
-    plane = int(sys.argv[2])
+help_main = ["Simple color plot of a FITS image",
+             "with options to pick a plane (if a cube) or slicing method",
+             "colormaps and plot file extension can also be changed",
+             "plot file name is derived from input FITS file",
+             ]
+
+help_color =  ['Popular colors: viridis, gist_heat gist_ncar (default)',
+               '                rainbow, jet, nipy_spectral', 
+               'https://matplotlib.org/stable/tutorials/colors/colormaps.html']
+
+
+parser = argparse.ArgumentParser(description="\n".join(help_main),
+                                 formatter_class=argparse.RawTextHelpFormatter)
+                                 # formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+
+
+parser.add_argument('fitsfile',    help="input FITS file",        default=None)
+parser.add_argument('--plane',     help="plane (if cube) [-1]",   default=-1,            type=int)
+parser.add_argument('--pvar',      help="plane var (x,y,[z])",    default='z')
+parser.add_argument('--color',     help="\n".join(help_color),    default='gist_ncar')
+parser.add_argument('--ext',       help="plot type ([png],pdf)",  default='png')
+parser.add_argument('--hist',      help="add histogram",          action="store_true")
+parser.add_argument('--size',      help="plot size (inch)",       default=8,             type=float)
+
+args  = parser.parse_args()
+
+
+fitsfile = args.fitsfile
+plane    = args.plane
+color    = args.color
+ext      = args.ext
+pvar     = args.pvar
+size     = args.size
+
+if pvar == 'z':
+    dims = [0,1]   # ra-dec
+elif pvar == 'y':
+    dims = [0,2]   # ra-vel
+elif pvar == 'x':
+    dims = [1,2]   # dec-vel
 else:
-    plane = -1
-
+    dims = [0,1]
+
+hdu = fits.open(fitsfile)
 if plane < 0:
-    f = aplpy.FITSFigure(fitsfile)
+    data = hdu[0].data
 else:
-    f = aplpy.FITSFigure(fitsfile, slices=[plane], dimensions=dims)
+    data = hdu[0].data[plane]
+
+data = data[~np.isnan(data)]
+data = data[data != 0]
+
+dmin = np.min(data)
+dmax = np.max(data)
+dmean = np.mean(data)
+dstd  = np.std(data)
+print("Data min/max/mean/sig: %g %g %g %g" % (dmin,dmax,dmean,dstd))
+dmin = dmean - 3*dstd;
+dmax = dmean + 3*dstd;
+print("Data min/max: %g %g" % (dmin,dmax))
+bins = np.linspace(dmin, dmax, 32)
+if args.hist:
+    print("BINS: ",bins)
+
+if args.hist:
+    # side by side
+    f=0.7
+    #box1 = [0.1,0.1,0.8,0.8]   # full size, image
+    box2 = [0.05,0.1,0.5/f,0.5/f]   # left side, image
+    box3 = [0.55/f,0.1,0.2,f]  # right side, histo
+else:
+    # just a square image
+    box1 = [0.1,0.1,0.8,0.8]   # full size, image
+    #box2 = [0.1,0.1,0.5,0.5]   # left side, image
+    #box3 = [0.7,0.15,0.2,0.4]  # right side, histo
+
+try:
+    if args.hist:
+        fig = plt.figure(figsize=(size, f*size))
+    else:
+        fig = plt.figure(figsize=(size, size))
 
-f.show_grayscale()
-f.show_colorscale(cmap='gist_heat')
-f.add_colorbar()
-# Cannot show beam when WCS is not celestial
-# perhaps doesn't like VRAD, but our fits files are not good enough
-# for 2D maps, ccdfits ndim=2 will help
+    if plane < 0:
+        if args.hist:
+            f1 = aplpy.FITSFigure(fitsfile, figure=fig, subplot=box2)
+            ax_hist = fig.add_axes(box3)
+            ax_hist.hist(data, bins=bins, orientation='horizontal', facecolor='blue',log=True)
+        else:
+            f1 = aplpy.FITSFigure(fitsfile, figure=fig, subplot=box1)
+    else:
+        if args.hist:
+            f1 = aplpy.FITSFigure(fitsfile, slices=[plane], dimensions=dims, figure=fig, subplot=box2)
+            ax_hist = fig.add_axes(box3)
+            ax_hist.hist(data, bins=bins, orientation='horizontal', facecolor='blue',log=True)
+        else:
+            f1 = aplpy.FITSFigure(fitsfile, slices=[plane], dimensions=dims, figure=fig, subplot=box1)
+except:
+    print("problem processing %s in %s" % (fitsfile,os.getcwd()))
+    sys.exit(0)
+
+f1.show_grayscale()
+f1.show_colorscale(cmap=color)
+f1.add_colorbar()
 
 try:
-    f.add_beam()
+    f1.add_beam()
 except:
     pass
 
 # f.show_contour(fitsfile, levels=10)
-f.add_grid()
-f.save(fitsfile + ".pdf")
+f1.add_grid()
+fig.canvas.draw()
+
+idx = fitsfile.rfind('.fits')
+if plane < 0:
+    pfile = fitsfile[:idx] + ".%s" % ext
+else:
+    pfile = fitsfile[:idx] + ".%04d.%s" % (plane,ext)
+# fig.subplots_adjust(right=0.15)   
+fig.savefig(pfile)
+print("Writing ",pfile)
+# plt.show()