Merge pull request #129 from achael/dev

Dev updates May - December 2020

ehtim/const_def.py

@@ -143,19 +143,19 @@
           'pvis', 'pamp', 'pphase', 'psnr',
           'evis', 'eamp', 'ephase', 'esnr',
           'bvis', 'bamp', 'bphase', 'bsnr',
-          'm', 'mamp', 'mphase', 'msnr'
+          'm', 'mamp', 'mphase', 'msnr',
           'rrvis', 'rramp', 'rrphase', 'rrsnr', 'rrsigma', 'rrsigma_phase',
-          'llvis', 'llamp', 'llphase', 'llsnr', 'llsigma', 'llsigma_phase'
-          'rlvis', 'rlamp', 'rlphase', 'rlsnr', 'rlsigma', 'rlsigma_phase'
-          'lrvis', 'lramp', 'lrphase', 'lrsnr', 'lrsigma', 'lrsigma_phase'
+          'llvis', 'llamp', 'llphase', 'llsnr', 'llsigma', 'llsigma_phase',
+          'rlvis', 'rlamp', 'rlphase', 'rlsnr', 'rlsigma', 'rlsigma_phase',
+          'lrvis', 'lramp', 'lrphase', 'lrsnr', 'lrsigma', 'lrsigma_phase',
           'rrllvis', 'rrllamp', 'rrllphase', 'rrllsnr', 'rrllsigma', 'rrllsigma_phase']
 
 FIELDS_AMPS = ["amp", "qamp", "uamp", "vamp",
                "pamp", "mamp", "rramp", "llamp", "rlamp", "lramp", "rrllamp"]
 FIELDS_SIGS = ["sigma", "qsigma", "usigma", "vsigma",
                "psigma", "msigma", "rrsigma", "llsigma", "rlsigma", "lrsigma", "rrllsigma"]
 FIELDS_PHASE = ["phase", "qphase", "uphase", "vphase", "pphase", "mphase",
-                "rrphase", "llphase", "lrphase", "rlphase", "rrllphase"]
+                "rrphase", "llphase", "rlphase", "lrphase", "rrllphase"]
 FIELDS_SIGPHASE = ["sigma_phase", "qsigma_phase", "usigma_phase", "vsigma_phase",
                    "psigma_phase", "msigma_phase", "rrsigma_phase", "llsigma_phase",
                    "rlsigma_phase", "lrsigma_phase", "rrllsigma_phase"]

ehtim/imaging/multifreq_imager_utils.py

@@ -199,6 +199,24 @@ def pack_mftuple(mftuple, mf_solve = (1,1,0)):
 
         return vec
 
+def embed(im, mask, clipfloor=0., randomfloor=False):
+    """Embeds a 1d image array into the size of boolean embed mask
+    """
+
+    out = np.zeros(len(mask))
+
+    # Here's a much faster version than before
+    out[mask.nonzero()] = im
+
+    if clipfloor != 0.0:
+        if randomfloor:  # prevent total variation gradient singularities
+            out[(mask-1).nonzero()] = clipfloor * \
+                np.abs(np.random.normal(size=len((mask-1).nonzero())))
+        else:
+            out[(mask-1).nonzero()] = clipfloor
+
+    return out
+
 def embed_mf(imtuple, mask, clipfloor=0., randomfloor=False):
     """Embeds a multifrequency image tuple into the size of boolean embed mask
     """

ehtim/imaging/pol_imager_utils.py

@@ -102,9 +102,7 @@ def pol_imager_func(Obsdata, InitIm, Prior,
 
            ttype (str): The Fourier transform type; options are 'fast' and 'direct'
            fft_pad_factor (float): The FFT will pre-pad the image by this factor x the original size
-           fft_interp (int): Interpolation order for sampling the FFT
-           grid_conv_func (str): The convolving function for gridding; options are 'gaussian', 'pill', and 'spheroidal'
-           grid_prad (float): The pixel radius for the convolving function in gridding for FFTs
+           p_rad (float): The pixel radius for the convolving function in gridding for FFTs
 
            clipfloor (float): The Stokes I Jy/pixel level above which prior image pixels are varied
            grads (bool): If True, analytic gradients are used

ehtim/io/load.py

@@ -772,6 +772,9 @@ def load_array_txt(filename, ephemdir='ephemeris'):
     """
 
     tdata = np.loadtxt(filename, dtype=bytes, comments='#').astype(str)
+    if tdata[0][0].lower() == 'site':
+        tdata = tdata[1:]
+
     path = os.path.dirname(filename)
 
     tdataout = []
@@ -1290,7 +1293,7 @@ def load_obs_uvfits(filename, polrep='stokes', flipbl=False, allow_singlepol=Tru
             endvis = scan['END VIS'] - 1
             scantable.append([scan_start - 0.5 * scan_dur,
                               scan_start + 0.5 * scan_dur])
-        scantable = np.array(scantable * 24)
+        scantable = np.array(scantable) * 24
 
     except BaseException:
         print("No NX table in uvfits!")

ehtim/io/save.py

@@ -856,7 +856,7 @@ def save_obs_oifits(obs, fname, flux=1.0):
 
     # create dictionary
     union = {}
-    union = ehtim.io.writeData.arrayUnion(antennaNames, union)
+    union = ehtim.io.writeoifits.arrayUnion(antennaNames, union)
 
     # extract the integration time
     intTime = data['tint'][0]
@@ -871,8 +871,8 @@ def save_obs_oifits(obs, fname, flux=1.0):
     v = data['v']
 
     # convert antenna name strings to number identifiers
-    ant1 = ehtim.io.writeData.convertStrings(data['t1'], union)
-    ant2 = ehtim.io.writeData.convertStrings(data['t2'], union)
+    ant1 = ehtim.io.writeoifits.convertStrings(data['t1'], union)
+    ant2 = ehtim.io.writeoifits.convertStrings(data['t2'], union)
 
     # convert times to datetime objects
     # TODO: these do not correspond to the acutal times
@@ -896,13 +896,13 @@ def save_obs_oifits(obs, fname, flux=1.0):
                               for x in timeClosure])
 
     # convert antenna name strings to number identifiers
-    biarr_ant1 = ehtim.io.writeData.convertStrings(biarr['t1'], union)
-    biarr_ant2 = ehtim.io.writeData.convertStrings(biarr['t2'], union)
-    biarr_ant3 = ehtim.io.writeData.convertStrings(biarr['t3'], union)
+    biarr_ant1 = ehtim.io.writeoifits.convertStrings(biarr['t1'], union)
+    biarr_ant2 = ehtim.io.writeoifits.convertStrings(biarr['t2'], union)
+    biarr_ant3 = ehtim.io.writeoifits.convertStrings(biarr['t3'], union)
     antOrder = np.transpose(np.array([biarr_ant1, biarr_ant2, biarr_ant3]))
 
     # todo: check that putting the negatives on the phase and t3phi is correct
-    ehtim.io.writeData.writeOIFITS(fname, obs.ra, obs.dec, obs.rf, obs.bw, intTime,
+    ehtim.io.writeoifits.writeOIFITS(fname, obs.ra, obs.dec, obs.rf, obs.bw, intTime,
                                    amp, viserror, phase, viserror, u, v, ant1, ant2, dttime,
                                    t3amp, t3amperr, t3phi, t3phierr, uClosure, vClosure, antOrder,
                                    dttimeClosure, antennaNames, antennaDiam,