Include params in HDF5 output

astrodendro/dendrogram.py

@@ -87,7 +87,7 @@ def static_warning(self, *args, **kwargs):
         self.load_from = static_warning
 
     @staticmethod
-    def compute(data, min_value=-np.inf, min_delta=0, min_npix=0,
+    def compute(data, min_value="min", min_delta=0, min_npix=0,
                 is_independent=None, verbose=False, neighbours=None, wcs=None):
         """
         Compute a dendrogram from a Numpy array.
@@ -96,9 +96,10 @@ def compute(data, min_value=-np.inf, min_delta=0, min_npix=0,
         ----------
         data : :class:`numpy.ndarray`
             The n-dimensional array to compute the dendrogram for
-        min_value : float, optional
+        min_value : float or "min", optional
             The minimum data value to go down to when computing the
-            dendrogram. Values below this threshold will be ignored.
+            dendrogram. Values below this threshold will be ignored. Defaults
+            to the minimum value in the data.
         min_delta : float, optional
             The minimum height a leaf has to have in order to be considered an
             independent entity.
@@ -128,9 +129,9 @@ def compute(data, min_value=-np.inf, min_delta=0, min_npix=0,
                        that has been padded with one element along each edge.
 
         wcs : WCS object, optional
-            A WCS object that describes `data`. This is used in the 
-            interactive viewer to properly display the data's coordinates 
-            on the image axes. (Requires that `wcsaxes` is installed; see 
+            A WCS object that describes `data`. This is used in the
+            interactive viewer to properly display the data's coordinates
+            on the image axes. (Requires that `wcsaxes` is installed; see
             http://wcsaxes.readthedocs.org/ for install instructions.)
 
 
@@ -160,6 +161,10 @@ def compute(data, min_value=-np.inf, min_delta=0, min_npix=0,
         is_independent = pruning.all_true(tests)
         neighbours = neighbours or Dendrogram.neighbours
 
+        # Default min_val to the minimum in the data
+        if min_value == "min":
+            min_value = np.min(data[np.isfinite(data)]) - 1
+
         self = Dendrogram()
         self.data = data
         self.n_dim = len(data.shape)
@@ -463,6 +468,25 @@ def __eq__(self, other):
         if not (self.data == other.data).all():
             return False
 
+        if self.params['min_value'] != other.params['min_value']:
+            return False
+
+        self_params = self.params.copy()
+        other_params = other.params.copy()
+
+        self_params.pop('min_value')
+        other_params.pop('min_value')
+
+        # Hack for not comparing params that have not been set
+        # There is currently no explicit way to tell if it has not been set
+        # We assume that if it is =0, then it is not set and won't be compared
+        for key in self_params.keys():
+            if self_params[key] == 0 or other_params[key] == 0:
+                continue
+
+            if self_params[key] != other_params[key]:
+                return False
+
         # structures should have the same extent,
         # but idx values need not be identical. This
         # tests the index map for that

astrodendro/io/fits.py

@@ -35,6 +35,13 @@ def dendro_export_fits(d, filename):
     except AttributeError:
         primary_hdu = fits.PrimaryHDU()
 
+    primary_hdu.header["MIN_NPIX"] = (d.params['min_npix'],
+                                      "Minimum number of pixels in a leaf.")
+    primary_hdu.header["MIN_DELT"] = (d.params['min_delta'],
+                                       "Minimum branch height.")
+    primary_hdu.header["MIN_VAL"] = (d.params['min_value'],
+                                       "Minimum intensity value.")
+
     hdus = [primary_hdu,
             fits.ImageHDU(d.data),
             fits.ImageHDU(d.index_map),
@@ -59,7 +66,11 @@ def dendro_import_fits(filename):
         index_map = hdus[2].data
         newick = ''.join(chr(x) for x in hdus[3].data.flat)
 
-    return parse_dendrogram(newick, data, index_map, wcs)
+        params = {"min_npix": hdus[0].header['MIN_NPIX'],
+                  "min_value": hdus[0].header['MIN_VAL'],
+                  "min_delta": hdus[0].header['MIN_DELT']}
+
+    return parse_dendrogram(newick, data, index_map, params, wcs)
 
 
 FITSHandler = IOHandler(identify=is_fits,

astrodendro/io/hdf5.py

@@ -41,6 +41,9 @@ def dendro_export_hdf5(d, filename):
     ds.attrs['IMAGE_VERSION'] = '1.2'
     ds.attrs['IMAGE_MINMAXRANGE'] = [d.data.min(), d.data.max()]
 
+    for key in d.params.keys():
+        f.create_dataset(key, data=d.params[key])
+
     try:
         f.create_dataset('wcs_header', data=d.wcs.to_header_string())
     except AttributeError:
@@ -59,13 +62,18 @@ def dendro_import_hdf5(filename):
         newick = h5f['newick'].value
         data = h5f['data'].value
         index_map = h5f['index_map'].value
+
+        params = {}
+        params['min_value'] = h5f['min_value'].value
+        params['min_delta'] = h5f['min_delta'].value
+        params['min_npix'] = h5f['min_npix'].value
         try:
             wcs = WCS(h5f['wcs_header'].value)
         except KeyError:
             wcs = None
 
     log.debug('Parsing dendrogram...')
-    return parse_dendrogram(newick, data, index_map, wcs)
+    return parse_dendrogram(newick, data, index_map, params, wcs)
 
 
 HDF5Handler = IOHandler(identify=is_hdf5,

astrodendro/io/util.py

@@ -70,7 +70,7 @@ def collect(d):
     return items['trunk']
 
 
-def parse_dendrogram(newick, data, index_map, wcs=None):
+def parse_dendrogram(newick, data, index_map, params, wcs=None):
     from ..dendrogram import Dendrogram
     from ..structure import Structure
 
@@ -80,6 +80,7 @@ def parse_dendrogram(newick, data, index_map, wcs=None):
     d._structures_dict = {}
     d.data = data
     d.index_map = index_map
+    d.params = params
     d.wcs = wcs
 
     try:

astrodendro/tests/test_is_independent.py

@@ -72,7 +72,7 @@ def is_independent_test(structure, index=None, value=None):
 
     d1 = Dendrogram.compute(data,
                             is_independent=is_independent_test,
-                            min_value=p['min_value'] if 'min_value' in p else -np.inf)
+                            min_value=p['min_value'] if 'min_value' in p else "min")
     d2 = Dendrogram.load_from(path)
 
     assert d1 == d2