Rename Loop to Strand (#98)

* infrastructure cleanup

* rename Loop->Strand

* fix circular import

README.md

@@ -1,22 +1,22 @@
-<div align="center">
-  <img src="docs/_static/synthesizar_logo.png" width=55%><br>
-</div>
-
 # synthesizAR
+
 [![Powered by SunPy Badge]( http://img.shields.io/badge/powered%20by-SunPy-orange.svg?style=flat)](http://www.sunpy.org)
-![synthesizAR CI status](https://github.com/wtbarnes/synthesizAR/workflows/Run%20tests/badge.svg)
+[![synthesizAR CI status](https://github.com/wtbarnes/synthesizAR/actions/workflows/ci.yml/badge.svg)](https://github.com/wtbarnes/synthesizAR/actions/workflows/ci.yml)
 [![Documentation Status](http://readthedocs.org/projects/synthesizar/badge/?version=latest)](http://synthesizar.readthedocs.io/en/latest/?badge=latest)
-[![codecov](https://codecov.io/gh/wtbarnes/synthesizAR/branch/master/graph/badge.svg)](https://codecov.io/gh/wtbarnes/synthesizAR)
+[![codecov](https://codecov.io/gh/wtbarnes/synthesizAR/graph/badge.svg?token=QUTQZGWQKB)](https://codecov.io/gh/wtbarnes/synthesizAR)
 
-synthesizAR is a Python package for forward modeling emission from solar active regions using hydrodynamic simulations of coronal loops
+synthesizAR is a Python package for forward modeling optically-thin emission from field-aligned hydrodynamic simulations of astrophysical plasmas.
 
 ## Install
+
 To clone the repository and install the package and all of its needed dependencies,
+
 ```shell
-$ git clone https://github.com/wtbarnes/synthesizAR.git
-$ cd synthesizAR
-$ pip install -e .[all]
+git clone https://github.com/wtbarnes/synthesizAR.git
+cd synthesizAR
+pip install -e .[all]
 ```
 
 ## Help
+
 See the [docs](http://synthesizar.readthedocs.io). To report bugs or request features, create an issue or submit a pull request.

examples/arcade-rtv.py

@@ -6,15 +6,17 @@
 of semi-circular loops who's thermal structure is modeled
 using the RTV scaling laws.
 """
-import astropy.units as u
 import astropy.time
+import astropy.units as u
+
 from astropy.coordinates import SkyCoord
 from sunpy.coordinates import get_earth
 
 import synthesizAR
-from synthesizAR.models import semi_circular_arcade
-from synthesizAR.interfaces import RTVInterface
+
 from synthesizAR.instruments import InstrumentSDOAIA
+from synthesizAR.interfaces import RTVInterface
+from synthesizAR.models import semi_circular_arcade
 
 #########################################################################
 # First, set up the coordinates for loops in the arcade.
@@ -24,7 +26,7 @@
 
 #########################################################################
 # Next, assemble the arcade.
-strands = [synthesizAR.Loop(f'strand{i}', c) for i, c in enumerate(arcade_coords)]
+strands = [synthesizAR.Strand(f'strand{i}', c) for i, c in enumerate(arcade_coords)]
 arcade = synthesizAR.Skeleton(strands)
 
 #########################################################################

examples/loop-bundle-rtv.py

@@ -6,17 +6,20 @@
 bundle of semi-circular strands for two different
 viewpoints.
 """
-import matplotlib.pyplot as plt
 import astropy.time
 import astropy.units as u
-from astropy.visualization import quantity_support
+import matplotlib.pyplot as plt
+
 from astropy.coordinates import SkyCoord
+from astropy.visualization import quantity_support
 from sunpy.map import pixelate_coord_path, sample_at_coords
 
 import synthesizAR
+
 from synthesizAR.instruments import InstrumentSDOAIA
 from synthesizAR.interfaces import RTVInterface
 from synthesizAR.models import semi_circular_bundle
+
 # sphinx_gallery_thumbnail_number = -1
 
 ###########################################################################
@@ -32,7 +35,7 @@
 ###########################################################################
 # As in other examples, we then use the coordinates of our strands to
 # construct the `~synthesizAR.Skeleton` object.
-strands = [synthesizAR.Loop(f'strand{i}', c) for i, c in enumerate(bundle_coords)]
+strands = [synthesizAR.Strand(f'strand{i}', c) for i, c in enumerate(bundle_coords)]
 bundle = synthesizAR.Skeleton(strands)
 bundle.peek(observer=pos)
 

examples/multi-instrument.py

@@ -9,16 +9,24 @@
 instrument class.
 """
 import astropy.units as u
-from astropy.coordinates import SkyCoord
-import numpy as np
 import matplotlib.pyplot as plt
-from sunpy.coordinates import get_earth, get_horizons_coord, HeliographicStonyhurst, Helioprojective
+import numpy as np
+
+from astropy.coordinates import SkyCoord
 from astropy.visualization import quantity_support
+from sunpy.coordinates import (
+    get_earth,
+    get_horizons_coord,
+    HeliographicStonyhurst,
+    Helioprojective,
+)
 
 import synthesizAR
-from synthesizAR.models import semi_circular_arcade
+
+from synthesizAR.instruments import InstrumentHinodeXRT, InstrumentSDOAIA
 from synthesizAR.interfaces import MartensInterface
-from synthesizAR.instruments import InstrumentSDOAIA, InstrumentHinodeXRT
+from synthesizAR.models import semi_circular_arcade
+
 # sphinx_gallery_thumbnail_number = -1
 
 ###############################################################################
@@ -27,7 +35,7 @@
 obstime = '2021-10-28T15:00:00'
 loc = SkyCoord(HeliographicStonyhurst(lon=0*u.deg,lat=-30*u.deg, radius=1*u.R_sun, obstime=obstime))
 arcade = semi_circular_arcade(150*u.Mm, 10*u.deg, 50, loc, gamma=90*u.deg, n_points=5000)
-skeleton = synthesizAR.Skeleton([synthesizAR.Loop(f'{i}', c) for i,c in enumerate(arcade)])
+skeleton = synthesizAR.Skeleton([synthesizAR.Strand(f'{i}', c) for i,c in enumerate(arcade)])
 
 ###############################################################################
 # We'll select a few different observer locations for SDO and STERO-A and use
@@ -64,10 +72,10 @@ def get_heating_constant(self, loop):
 with quantity_support():
     plt.figure(figsize=(11, 5))
     ax1 = plt.subplot(121)
-    for l in skeleton.loops:
+    for l in skeleton.strands:
         plt.plot(l.field_aligned_coordinate_center.to('Mm'), l.electron_temperature[0].to('MK'), color='k')
     plt.subplot(122)
-    for l in skeleton.loops:
+    for l in skeleton.strands:
         plt.plot(l.field_aligned_coordinate_center.to('Mm'), l.density[0], color='k')
     plt.yscale('log')
 

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
   {name="Will Barnes", email="[email protected]"}
 ]
 license = {file="LICENSE.rst"}
-description = "A Python package for forward-modeling optically-thin emission from field-aligned coronal loop models"
+description = "A Python package for forward modeling optically-thin emission from field-aligned hydrodynamic simulations of astrophysical plasmas."
 readme = {file="README.md", content-type = "text/markdown"}
 requires-python = ">=3.10"
 dependencies = [

synthesizAR/__init__.py

@@ -3,14 +3,15 @@
 hydrodynamic simulations of coronal loops.
 """
 try:
-    from .version import __version__
+    from synthesizAR.version import __version__
 except ImportError:
     __version__ = "unknown"
 
 
-from .loop import *
-from .skeleton import *
-
 # Set up logger
 from synthesizAR.util.logger import _init_log
+
+from .strand import *  # NOQA
+from .skeleton import *  # NOQA
+
 log = _init_log()

synthesizAR/conftest.py

@@ -1,21 +1,22 @@
 """
 Configure test skeletons here so that they can be used everywhere
 """
+import astropy.units as u
 import pytest
 
-import astropy.units as u
 from sunpy.coordinates import get_earth
 
 import synthesizAR
-from synthesizAR.models import semi_circular_loop, semi_circular_arcade
+
 from synthesizAR.interfaces import MartensInterface
+from synthesizAR.models import semi_circular_arcade, semi_circular_loop
 
 
 @pytest.fixture
 def bare_skeleton():
     observer = get_earth(time='2020-01-01T00:00:00')
     arcade = semi_circular_arcade(100*u.Mm, 20*u.deg, 10, observer)
-    loops = [synthesizAR.Loop(f'{i}', c) for i, c in enumerate(arcade)]
+    loops = [synthesizAR.Strand(f'{i}', c) for i, c in enumerate(arcade)]
     return synthesizAR.Skeleton(loops)
 
 
@@ -29,4 +30,4 @@ def skeleton_with_model(bare_skeleton):
 @pytest.fixture
 def semi_circle_strand(bare_skeleton):
     coords = semi_circular_loop(length=100*u.Mm)
-    return synthesizAR.Loop('test', coords)
+    return synthesizAR.Strand('test', coords)

synthesizAR/instruments/base.py

@@ -1,21 +1,21 @@
 """
 Base class for instrument objects.
 """
+import astropy.units as u
 import copy
-import tempfile
+import numpy as np
 import pathlib
-from dataclasses import dataclass
+import tempfile
+import zarr
 
-import numpy as np
+from astropy.coordinates import SkyCoord
+from dataclasses import dataclass
 from scipy.interpolate import interp1d
 from scipy.ndimage import gaussian_filter
-import astropy.units as u
-from astropy.coordinates import SkyCoord
-from sunpy.coordinates.frames import Helioprojective, HeliographicStonyhurst
+from sunpy.coordinates.frames import HeliographicStonyhurst, Helioprojective
 from sunpy.map import make_fitswcs_header, Map
-import zarr
 
-from synthesizAR.util import is_visible, find_minimum_fov
+from synthesizAR.util import find_minimum_fov, is_visible
 from synthesizAR.util.decorators import return_quantity_as_tuple
 
 __all__ = ['ChannelBase', 'InstrumentBase']
@@ -27,7 +27,7 @@ class ChannelBase:
     channel: u.Quantity = None
 
 
-class InstrumentBase(object):
+class InstrumentBase:
     """
     Base class for instruments. This object is not meant to be instantiated directly. Instead,
     specific instruments should subclass this base object and implement a
@@ -170,17 +170,17 @@ def observe(self, skeleton, save_directory=None, channels=None, **kwargs):
             if client:
                 # Parallel
                 kernel_futures = client.map(self.calculate_intensity_kernel,
-                                            skeleton.loops,
+                                            skeleton.strands,
                                             channel=channel,
                                             **kwargs)
                 kernel_interp_futures = client.map(self.interpolate_to_instrument_time,
                                                    kernel_futures,
-                                                   skeleton.loops,
+                                                   skeleton.strands,
                                                    observing_time=(self.observing_time.value, self.observing_time.unit.to_string()))
             else:
                 # Serial
                 kernels_interp = []
-                for l in skeleton.loops:
+                for l in skeleton.strands:
                     k = self.calculate_intensity_kernel(l, channel=channel, **kwargs)
                     k = self.interpolate_to_instrument_time(
                         k, l, observing_time=(self.observing_time.value, self.observing_time.unit.to_string()),
@@ -189,22 +189,22 @@ def observe(self, skeleton, save_directory=None, channels=None, **kwargs):
 
             if kwargs.get('save_kernels_to_disk', False):
                 with tempfile.TemporaryDirectory() as tmpdir:
-                    self._make_stacked_kernel_array(tmpdir, skeleton.loops, channel)
-                    indices = self._find_loop_array_bounds(skeleton.loops)
+                    self._make_stacked_kernel_array(tmpdir, skeleton.strands, channel)
+                    indices = self._find_loop_array_bounds(skeleton.strands)
                     if client:
                         files = client.map(self.write_kernel_to_file,
                                            kernel_interp_futures,
-                                           skeleton.loops,
+                                           skeleton.strands,
                                            indices,
                                            channel=channel,
                                            name=self.name,
                                            tmp_store=tmpdir)
                         # NOTE: block here to avoid pileup of tasks that can overwhelm the scheduler
                         distributed.wait(files)
                     else:
-                        for k, l, i in zip(kernels_interp, skeleton.loops, indices):
+                        for k, l, i in zip(kernels_interp, skeleton.strands, indices):
                             self.write_kernel_to_file(k, l, i, channel, self.name, tmpdir)
-                    self._rechunk_stacked_kernels(tmpdir, skeleton.loops[0].model_results_filename, channel)
+                    self._rechunk_stacked_kernels(tmpdir, skeleton.strands[0].model_results_filename, channel)
                     kernels = self.observing_time.shape[0]*[None]  # placeholder so we know to read from a file
             else:
                 # NOTE: this can really blow up your memory if you are not careful
@@ -336,7 +336,7 @@ def integrate_los(self, time, channel, skeleton, coordinates_centers, bins, bin_
         # Compute weights
         if kernels is None:
             i_time = np.where(time == self.observing_time)[0][0]
-            root = skeleton.loops[0].zarr_root
+            root = skeleton.strands[0].zarr_root
             ds = root[f'{self.name}/{channel.name}_stacked_kernels']
             kernels = u.Quantity(ds[i_time, :], ds.attrs['unit'])
         # If a volumetric quantity, integrate over the cell and normalize by pixel area.