Merge pull request #181 from achael/dev

merge dev for 1.2.8

README.rst

@@ -10,7 +10,7 @@ The package contains several primary classes for loading, simulating, and manipu
 Installation
 ------------
 
-The latest stable version (`1.2.7 <https://github.com/achael/eht-imaging/releases/tag/v1.2.7>`_) is available on `PyPi <https://pypi.org/project/ehtim/>`_. Simply install pip and run
+The latest stable version (`1.2.8 <https://github.com/achael/eht-imaging/releases/tag/v1.2.7>`_) is available on `PyPi <https://pypi.org/project/ehtim/>`_. Simply install pip and run
 
 .. code-block:: bash
 
@@ -86,16 +86,8 @@ Let us know if you use ehtim in your publication and we'll list it here!
 
 - First M87 Event Horizon Telescope Results IV: Imaging the Central Supermassive Black Hole, `EHTC et al. 2019 <https://arxiv.org/abs/1906.11241>`_
 
-- VLBI Imaging of black holes via second moment regularization, `Issaoun et al. 2019b <https://arxiv.org/pdf/1908.01296.pdf>`_
-
-- Using evolutionary algorithms to model relativistic jets: Application to NGC 1052, `Fromm et al. 2019 <https://arxiv.org/pdf/1904.00106.pdf>`_
-
 - EHT-HOPS Pipeline for Millimeter VLBI Data Reduction, `Blackburn et al. 2019 <https://arxiv.org/pdf/1903.08832>`_
 
-- Multi-wavelength torus-jet model for Sagittarius A*, `Vincent et al. 2019 <https://arxiv.org/pdf/1902.01175>`_
-
-- How to tell an accreting boson star from a black hole, `Olivares et al. 2020 <https://arxiv.org/abs/1809.08682>`_
-
 - Discriminating Accretion States via Rotational Symmetry in Simulated Polarimetric Images of M87, `Palumbo et al. 2020 <https://arxiv.org/pdf/2004.01751.pdf>`_
 
 - SYMBA: An end-to-end VLBI synthetic data generation pipeline, `Roelofs et al. 2020 <https://arxiv.org/pdf/2004.01161.pdf>`_
@@ -114,8 +106,6 @@ Let us know if you use ehtim in your publication and we'll list it here!
 
 - A D-term Modeling Code (DMC) for Simultaneous Calibration and Full-Stokes Imaging of VLBI Data, `Pesce et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-3881/abe3f8/pdf>`_
 
-- Polarization Images of Accretion Flows around Supermassive BLack Holes: Imprints of Toroidal Field Structure, `Tsunetoe et al. 2021 <https://watermark.silverchair.com/psab054.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsUwggLBBgkqhkiG9w0BBwagggKyMIICrgIBADCCAqcGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMdrsOAaUsDGsDHa2cAgEQgIICeMLAC3MR9Ld7lYRP4iEip8FSTz3TTR4K_yaxhw9kPthLhZLq4Zxs8_b7EyY8BywyYn6jUVlNM1czBskta4icw9YOQf2WX-2SkBGlQo7EdpZmHStribHPOF3ZtF4YA1dWNfzrXMFSR-ZZZW9iAfUFhKhgsyc0AY1O0rJLIAvlYPBE8SEAFUpV4Ck2nV-j-u_lyqe3CZcNO_tNB4fdE1x1HwhVWb_rxyC6n13hJhCJI7U3UJ5Q2u6dNH2BS4SUzet3JZ9RvIr9GkkSRRfdp0EDwNw6aG9TpAf8B-Fu7oW_NI7w_Jvh8kZBGzhnHisZ8acBRoMwbdHMv3cHqEUY5SKcYXVYART-z0QY_MJgxCoa4KDPG6rHl52Vf-eXJaYCmL4Y7xVas_hyPeUNk9TbhPqz4c8kOceb_BTo5oC5AFnwIIKw8kWmvwL7ofkcYmsrTlo0zWtgJ1I6lU7S1wxgD2JzRDg4gtVFdIcapB8q6ZhWWcBEvmwZ9Ad39UbH-hi4VZC8-IvzbvHNqfaifGsw1yvI86uNSu-iMY5ce0vAcZijbkVpAsbkvKGD6wP_T6OczWzayk13gegLvV2wZImleSWNFKO6cOpQSTKy2TbChWuYITc_tW3wUK-QOhjsdoB4V7SvXk_9d-bvjvBflRqDEUN5P8Yj4hpDpJYty4nxGJ4K6IWkyDRt_EZ2k9SOuwgXRZXxWA4tfJvKzvab8sRFqh98EcFNqDyAs_RZt1IVDch9GVl8X1VEbdD7MSzmw04kB-5U0l8HfmgBZyXs_i2hHUKesh1oUShTLUGcx86HApZXjtA4tSJct5CD8fvk_Vim2i5xx1_xGnBt3k7Z>`_
-
 - Using space-VLBI to probe gravity around Sgr A*, `Fromm et al. 2021 <https://www.aanda.org/articles/aa/pdf/2021/05/aa37335-19.pdf>`_
 
 - Persistent Non-Gaussian Structure in the Image of Sagittarius A* at 86 GHz, `Issaoun et al. 2021 <https://iopscience.iop.org/article/10.3847/1538-4357/ac00b0/pdf>`_
@@ -128,6 +118,20 @@ Let us know if you use ehtim in your publication and we'll list it here!
 
 - Unravelling the Innermost Jet Structure of OJ 287 with the First GMVA+ALMA Observations, `Zhao et al. 2022 <https://arxiv.org/pdf/2205.00554.pdf>`_
 
+- First Sagittarius A* Event Horizon Telescope Results. III: Imaging of the Galactic Center Supermassive Black Hole, `EHTC et al. 2022 <https://arxiv.org/pdf/2311.09479.pdf>`_
+
+- Resolving the Inner Parsec of the Blazar J1924-2914 with the Event Horizon Telescope, `Issaoun et al. 2022 <https://arxiv.org/pdf/2208.01662.pdf>`_
+
+- The Event Horizon Telescope Image of the Quasar NRAO 530, `Jorstad et al. 2023 <https://arxiv.org/pdf/2302.04622.pdf>`_
+
+- First M87 Event Horizon Telescope Results. IX. Detection of Near-horizon Circular Polarization, `EHTC et al. 2023 <https://arxiv.org/pdf/2311.10976.pdf>`_
+
+- Filamentary structures as the origin of blazar jet radio variability, `Fuentes et al. 2023 <https://arxiv.org/pdf/2311.01861.pdf>`_
+
+- The persistent shadow of the supermassive black hole of M 87. I. Observations, calibration, imaging, and analysis, `EHTC et al. 2023 <https://ui.adsabs.harvard.edu/abs/2024A%26A...681A..79E/abstract>`_
+
+- Parsec-scale evolution of the gigahertz-peaked spectrum quasar PKS 0858-279, `Kosogorov et al. 2024 <https://arxiv.org/pdf/2401.03603.pdf>`_
+
 oifits Documentation
 --------------------
 

ehtim/__init__.py

@@ -29,6 +29,7 @@
 from ehtim.calibrating.network_cal import network_cal as netcal
 from ehtim.calibrating.self_cal import self_cal as selfcal
 from ehtim.calibrating.pol_cal import *
+from ehtim.calibrating.pol_cal_new import *
 from ehtim.calibrating import pol_cal
 from ehtim.calibrating import network_cal
 from ehtim.calibrating import self_cal

ehtim/calibrating/__init__.py

@@ -9,6 +9,7 @@
 from . import self_cal
 from . import network_cal
 from . import pol_cal
+from . import pol_cal_new
 from . import polgains_cal
 
 from ..const_def import *

ehtim/calibrating/network_cal.py

@@ -124,13 +124,12 @@ def network_cal(obs, zbl, sites=[], zbl_uvdist_max=ZBLCUTOFF, method="amp", mini
     # loop over scans and calibrate
     tstart = time.time()
     if processes > 0:  # with multiprocessing
-        scans_cal = pool.map(get_network_scan_cal,
-                             [[i, len(scans), scans[i],
-                               zbl, sites, cluster_data, obs.polrep, pol,
-                               method, pad_amp, gain_tol,
-                               caltable, show_solution, debias, msgtype]
-                              for i in range(len(scans))
-                              ])
+        scans_cal = np.array(pool.map(get_network_scan_cal, [[i, len(scans), scans[i],
+                                                              zbl, sites, cluster_data, obs.polrep, pol,
+                                                              method, pad_amp, gain_tol,
+                                                              caltable, show_solution, debias, msgtype
+                                                             ] for i in range(len(scans))]),
+                                                             dtype=object)
     else:  # without multiprocessing
         for i in range(len(scans)):
             obsh.prog_msg(i, len(scans), msgtype=msgtype, nscan_last=i - 1)

ehtim/calibrating/pol_cal.py

@@ -65,7 +65,7 @@ def leakage_cal(obs, im=None, sites=[], leakage_tol=.1, pol_fit=['RL', 'LR'], dt
            fft_pad_factor (float): zero pad the image to fft_pad_factor * image size in FFT
 
            show_solution (bool): if True, display the solution as it is calculated
-
+           obs_apply (Obsdata): apply the solution to another observation
        Returns:
            (Obsdata): the calibrated observation, with computed leakage values added to the obs.tarr
     """