From 47e3f99f021e6da2348c7518ab21cd45f8f94bd9 Mon Sep 17 00:00:00 2001
From: Tony Wong <tonywong94@gmail.com>
Date: Wed, 23 Dec 2020 21:10:17 -0600
Subject: [PATCH] Deal with astropy and h5py deprecation issues.

---
 astrodendro/flux.py    | 2 +-
 astrodendro/io/hdf5.py | 8 ++++----
 astrodendro/io/util.py | 6 ++++++
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/astrodendro/flux.py b/astrodendro/flux.py
index d780f05..7a27657 100644
--- a/astrodendro/flux.py
+++ b/astrodendro/flux.py
@@ -154,7 +154,7 @@ def compute_flux(input_quantities, output_unit, wavelength=None, spatial_scale=N
         # Convert input quantity to Fnu in Jy
         # Implicitly, this equivalency gives the Janskys in a single beam, so we make this explicit by dividing out a beam
         jansky_per_beam = input_quantities.to(u.Jy, 
-            equivalencies=u.brightness_temperature(omega_beam, nu)) / u.beam
+            equivalencies=u.brightness_temperature(nu, beam_area=omega_beam)) / u.beam
 
         q = jansky_per_beam * beams_per_pixel
 
diff --git a/astrodendro/io/hdf5.py b/astrodendro/io/hdf5.py
index df439b9..8a27f51 100644
--- a/astrodendro/io/hdf5.py
+++ b/astrodendro/io/hdf5.py
@@ -59,9 +59,9 @@ def dendro_import_hdf5(filename):
 
     log.debug('Loading HDF5 file from disk...')
     with h5py.File(filename, 'r') as h5f:
-        newick = h5f['newick'].value
-        data = h5f['data'].value
-        index_map = h5f['index_map'].value
+        newick = h5f['newick'][()]
+        data = h5f['data'][()]
+        index_map = h5f['index_map'][()]
 
         params = {}
         if 'min_value' in h5f.attrs:
@@ -70,7 +70,7 @@ def dendro_import_hdf5(filename):
             params['min_npix'] = h5f.attrs['min_npix']
 
         try:
-            wcs = WCS(h5f['wcs_header'].value)
+            wcs = WCS(h5f['wcs_header'][()])
         except KeyError:
             wcs = None
 
diff --git a/astrodendro/io/util.py b/astrodendro/io/util.py
index 93ee349..b48f330 100644
--- a/astrodendro/io/util.py
+++ b/astrodendro/io/util.py
@@ -7,6 +7,12 @@
 
 def parse_newick(string):
 
+    # Convert bytestring if needed
+    try:
+        string = string.decode('utf-8')
+    except (UnicodeDecodeError, AttributeError):
+        pass
+
     items = {}
 
     # Find maximum level