Merge pull request #171 from achael/dev

merged dev into main for v1.2.6

.gitignore

@@ -20,6 +20,18 @@ build/*
 data/3C279JUN16.UVP
 data/OJ287AUG10B.UVP
 
+examples/*.log
+examples/*.mp4
+examples/old_examples/*
+examples/.ipynb_checkpoints/*
+
+arrays/old_arrays/*
+
+tutorials/tutorial_results/*
+
 # Unit tests should be included
 !ehtim/tests/
 !ehtim/tests/test_*.py
+
+.ipynb_checkpoints
+

CITATION.cff

@@ -1,12 +1,12 @@
-cff-version: 1.2.4
+cff-version: 1.2.6
 message: "If you use this software, please cite it as below."
 authors:
 - family-names: "Chael"
   given-names: "Andrew"
   orcid: "https://orcid.org/0000-0003-2966-6220
 "
 title: "eht-imaging"
-version: 1.2.4
-doi: 10.5281/zenodo.6519440
+version: 1.2.6
+doi: 10.5281/zenodo.7226661
 date-released: 2022-05-04
 url: "https://github.com/achael/eht-imaging"

README.rst

@@ -10,7 +10,7 @@ The package contains several primary classes for loading, simulating, and manipu
 Installation
 ------------
 
-The latest stable version (`1.2.4 <https://github.com/achael/eht-imaging/releases/tag/v1.2.4>`_) is available on `PyPi <https://pypi.org/project/ehtim/>`_. Simply install pip and run
+The latest stable version (`1.2.6 <https://github.com/achael/eht-imaging/releases/tag/v1.2.6>`_) is available on `PyPi <https://pypi.org/project/ehtim/>`_. Simply install pip and run
 
 .. code-block:: bash
 
@@ -33,17 +33,23 @@ Installing with pip will update most of the required libraries automatically (`n
 
 Alternatively, first install NFFT manually following the instructions on the `readme <https://github.com/NFFT/nfft>`_, making sure to use the ``--enable-openmp`` flag in compilation. Then install `pynfft <https://github.com/ghisvail/pyNFFT/>`_, with pip, following the readme instructions to link the installation to where you installed NFFT. Finally, reinstall ehtim.
 
+**For M1 Macs (OS >= v12.0)**, install the M1 Mac version of `pynfft <https://github.com/rohandahale/pyNFFT.git>`_ and follow the instructions on the `readme  <https://github.com/rohandahale/pyNFFT.git>`_. It has the instructions to install `fftw <http://www.fftw.org>`_, `nfft <https://github.com/NFFT/nfft>`_ and then `pynfft <https://github.com/rohandahale/pyNFFT.git>`_.
+
 **Certain eht-imaging functions require other external packages that are not automatically installed.** In addition to pynfft, these include  `networkx <https://networkx.github.io/>`_ (for image comparison functions), `requests <http://docs.python-requests.org/en/master/>`_ (for dynamical imaging), and `scikit-image <https://scikit-image.org/>`_ (for a few image analysis functions). However, the vast majority of the code will work without these dependencies.
 
-Documentation
+Documentation and Tutorials
 -------------
-Documentation is  `here <https://achael.github.io/eht-imaging>`_ .
+Documentation is  `here <https://achael.github.io/eht-imaging>`_.
+
+A intro to imaging tutorial jupyter notebook can be found in the repo at tutorials/ehtim_tutorial.ipynb 
+
+`Slides <https://docs.google.com/presentation/d/1A0y9omYI2ueSUa6_t5reylBhw6eiLwjqDzw-HUOk8Ac/edit?usp=sharing>`_ for the included tutorial walk through the basic steps of reconstructing EHT images with the code
 
-A full tutorial is in progress, but here are some ways to learn to use the code:
+Here are some other ways to learn to use the code:
 
 - Start with the script examples/example.py, which contains a series of sample commands to load an image and array, generate data, and produce an image with various imaging algorithms.
 
-- `Slides <https://www.dropbox.com/s/7533ucj8bt54yh7/Bouman_Chael.pdf?dl=0>`_ from the EHT2016 data generation and imaging workshop contain a tutorial on generating data with the VLBI imaging `website <http://vlbiimaging.csail.mit.edu>`_, loading into the library, and producing an image.
+- Older `Slides <https://www.dropbox.com/s/7533ucj8bt54yh7/Bouman_Chael.pdf?dl=0>`_ from the EHT2016 data generation and imaging workshop contain a tutorial on generating data with the VLBI imaging `website <http://vlbiimaging.csail.mit.edu>`_, loading into the library, and producing an image.
 
 Citation
 --------------------------------
@@ -122,7 +128,7 @@ 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>`_
 
-Documentation
+oifits Documentation
 ----------------
 
 The oifits_new.py file used for reading/writing .oifits files is a slightly modified version of Paul Boley's package `oifits <http://astro.ins.urfu.ru/pages/~pboley/oifits/>`_.  

arrays/EHT2025wTESS.txt

@@ -0,0 +1,16 @@
+#NAME X             Y             Z             SEFDR SEFDL FR_PAR_ANGLE FR_ELEV_ANGLE FR_OFFSET[d] DR_RE   DR_IM   DL_RE    DL_IM 
+PDB   4523998.40    468045.240    4460309.760   1500  1500  0            0             0            0       0       0        0
+PV    5088967.9000 -301681.6000   3825015.8000  1400  1400  1            -1            0            0       0       0        0
+SMT   -1828796.200 -5054406.800   3427865.200   5000  5000  1            1             0            0.012   0.106   -0.007   0.093
+SMA   -5464523.400 -2493147.080   2150611.750   4900  4900  1            -1            45           0.022   0.009   0.008    0.010
+LMT   -768713.9637 -5988541.7982  2063275.9472  600   600   1            -1            0            0       0       0        0
+ALMA  2225061.164  -5440057.37   -2481681.15    90    90    1            0             0            0       0       0        0
+SPT   0.01          0.01         -6359609.7     5000  5000  1            0             0            0       0       0        0
+APEX  2225039.53   -5441197.63   -2479303.36    3500  3500  1            1             0            0       0       0        0
+JCMT  -5464584.68  -2493001.17    2150653.98    6000  6000  1            0             0            0       0       0        0
+CARMA -2397431.300 -4482018.900   3843524.500   10000 10000 0            0             0            0       0       0        0
+KP    -1995678.840  -5037317.697  3357328.025   10000 10000 0            0             0            0       0       0        0
+GLT    1500692.0     -1191735.0    6066409.0    10000 10000 0            0             0            0       0       0        0
+TESS   0.0           0.0           0.0          10000 10000 0            0             0            0       0       0        0
+
+

arrays/ephemeris/ISS

@@ -1,4 +1,4 @@
 ISS
-1 25544U 98067A   22125.65004684  .00007804  00000-0  14483-3 0  9997
-2 25544  51.6425 187.2553 0006711  69.7320  66.5837 15.49943763338581
+1 25544U 98067A   23109.53559294  .00019257  00000-0  34454-3 0  9994
+2 25544  51.6389 259.1975 0006157 210.6524 231.6170 15.49989360392694
 

arrays/ephemeris/TESS

@@ -0,0 +1,3 @@
+TESS
+1 43435U 18038A   23096.90060626 -.00000924  00000-0  00000-0 0  9994
+2 43435  37.5590  76.7615 4777727 169.3023   2.8332  0.07302504   994

docs/source/index.rst

@@ -60,6 +60,7 @@ Documentation
    plotting
    scattering
    statistics
+   survey
    vex
 
 

docs/source/model.rst

@@ -2,7 +2,7 @@
 
 .. _model:
 
-Image
+Model
 =====
 
 .. automodule:: ehtim.model

docs/source/survey.rst

@@ -0,0 +1,11 @@
+.. module:: survey
+
+.. _survey:
+
+Survey
+===============
+
+.. automodule:: ehtim.survey
+    :members:
+
+

ehtim/__init__.py

@@ -42,6 +42,7 @@
 import ehtim.movie
 import ehtim.image
 import ehtim.model
+import ehtim.survey
 
 
 import warnings