Merge pull request #36 from thomaswmorris/multi-layer

Add back multi layer simulations

.github/workflows/release.yml

@@ -0,0 +1,39 @@
+# This workflows will upload a Python Package when a release is created.
+# For more information see:
+# - https://docs.pypi.org/trusted-publishers/adding-a-publisher/
+# - https://github.com/pypa/gh-action-pypi-publish
+
+name: PyPI upload
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish_pypi:
+    name: Publish package to PyPI
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Build package
+        run: |
+          set -vxeuo pipefail
+          python -m pip install --upgrade pip
+          pip install wheel setuptools
+          python setup.py sdist bdist_wheel
+
+      - name: Publish wheels to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: ./dist/

LICENSE

@@ -1,21 +1,29 @@
-MIT License
+BSD 3-Clause License
 
 Copyright (c) 2023 Thomas W. Morris
+All rights reserved.
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -1,7 +1,7 @@
 maria
 =====
 
-.. image:: ./docs/source/_static/cloud_64_b.gif
+.. image:: ./docs/source/_static/cloud_128_a.gif
    :width: 256px
    :alt: StreamPlayer
 

docs/source/index.rst

@@ -6,7 +6,7 @@
 maria
 =====
 
-.. image:: ./_static/cloud_64_b.gif
+.. image:: ./_static/cloud_128_a.gif
    :scale: 30%
    :alt: StreamPlayer
 

docs/source/usage.rst

@@ -21,27 +21,27 @@ A database of supported arrays can be found at::
 
 Supported arrays are customizeable by passing extra keywords to the ``get_array()`` function. We can double the size of the Green Bank Telescope and increase MUSTANG's field of view to one degree with::
 
-   mustang = maria.get_array("MUSTANG-2",
+    mustang = maria.get_array("MUSTANG-2",
                               field_of_view=10, # in degrees
                               primary_size=200 # in meters
                               )
 
 The arrays
 
 - **array** telescope and array design parameters
-  - Predefined configurations: `MUSTANG-2`, `ALMA`, `AtLAST`, `SCUBA-2`
-  - specific keys:
-    - dets (dict): {'float': [number of detectors (int), band_center in Hz (float), band_width in Hz (float)]}
-    - field_of_view (float): in degrees
-    - geometry (string): options are `hex` (defeault), `flower`, `square`
-    - primary_size (float): meters
-    - az_bounds (list): [lower (float), upper (float)] in degrees
-    - el_bounds (list): [lower (float), upper (float)] in degrees
-    - max_az_vel (float): ...
-    - max_el_vel (float): ...
-    - max_az_acc (float): ...
-    - max_el_acc (float): ...
-    - max_baseline (float): meters (only for ALMA)
+    - Predefined configurations: `MUSTANG-2`, `ALMA`, `AtLAST`, `SCUBA-2`
+    - specific keys:
+        - dets (dict): {'float': [number of detectors (int), band_center in Hz (float), band_width in Hz (float)]}
+        - field_of_view (float): in degrees
+        - geometry (string): options are `hex` (defeault), `flower`, `square`
+        - primary_size (float): meters
+        - az_bounds (list): [lower (float), upper (float)] in degrees
+        - el_bounds (list): [lower (float), upper (float)] in degrees
+        - max_az_vel (float): ...
+        - max_el_vel (float): ...
+        - max_az_acc (float): ...
+        - max_el_acc (float): ...
+        - max_baseline (float): meters (only for ALMA)
 
 
 Pointings
@@ -102,69 +102,69 @@ Simulation parameters
 ^^^^^^^^^^^^^^^^^^^^^
 
 - **array** telescope and array design parameters
-  - Predefined configurations: `MUSTANG-2`, `ALMA`, `AtLAST`, `SCUBA-2`
-  - specific keys:
-    - dets (Mappable of Mappables): {'float': [number of detectors (int), band_center in Hz (float), band_width in Hz (float)]}
-    - field_of_view (float): in degrees
-    - geometry (string): options are `hex` (defeault), `flower`, `square`
-    - primary_size (float): meters
-    - az_bounds (list): [lower (float), upper (float)] in degrees
-    - el_bounds (list): [lower (float), upper (float)] in degrees
-    - max_az_vel (float): ...
-    - max_el_vel (float): ...
-    - max_az_acc (float): ...
-    - max_el_acc (float): ...
-    - max_baseline (float): meters (only for ALMA)
+    - Predefined configurations: `MUSTANG-2`, `ALMA`, `AtLAST`, `SCUBA-2`
+    - specific keys:
+        - dets (Mappable of Mappables): {'float': [number of detectors (int), band_center in Hz (float), band_width in Hz (float)]}
+        - field_of_view (float): in degrees
+        - geometry (string): options are `hex` (defeault), `flower`, `square`
+        - primary_size (float): meters
+        - az_bounds (list): [lower (float), upper (float)] in degrees
+        - el_bounds (list): [lower (float), upper (float)] in degrees
+        - max_az_vel (float): ...
+        - max_el_vel (float): ...
+        - max_az_acc (float): ...
+        - max_el_acc (float): ...
+        - max_baseline (float): meters (only for ALMA)
 
 - **pointing:** Scanning strategy
-  - Predefined configurations: `stare`, `daisy`, `BAF`,
-  - specific keys:
-    - start_time (string): reference point for generating weather, example: '2022-02-10T06:00:00'
-    - integration_time (float): in seconds
-    - scan_pattern (string):  options are `daisy` or `back-and-forth`
-    - pointing_frame (string): options are `az_el` or `ra_dec`
-    - scan_center (list): [RA (float), Dec (float)] in degree
-    - scan_radius (float): in meters
-    - scan_period (float): in seconds
-    - scan_rate (float): in seconds
+    - Predefined configurations: `stare`, `daisy`, `BAF`,
+    - specific keys:
+        - start_time (string): reference point for generating weather, example: '2022-02-10T06:00:00'
+        - integration_time (float): in seconds
+        - scan_pattern (string):  options are `daisy` or `back-and-forth`
+        - pointing_frame (string): options are `az_el` or `ra_dec`
+        - scan_center (list): [RA (float), Dec (float)] in degree
+        - scan_radius (float): in meters
+        - scan_period (float): in seconds
+        - scan_rate (float): in seconds
 
 - **site:** Site locations
-  - Predefined configurations: `APEX`, `ACT`, `GBT`, `JCMT`, `SPT`, `SRT`
-  - specific keys:
-    - region (string): options are `chajnantor`, `green_bank`, `mauna_kea`, `south_pole`, `sardinia`
-    - latitude (float): in degree
-    - longtitude (float): in degree
-    - altitude (float): in meters
-    - seasonal (bool):
-    - diurnal (bool):
-    - weather_quantiles (dict): keys: `column_water_vapor` (float),  ...
-    - pwv_rms (float): ...
+    - Predefined configurations: `APEX`, `ACT`, `GBT`, `JCMT`, `SPT`, `SRT`
+    - specific keys:
+        - region (string): options are `chajnantor`, `green_bank`, `mauna_kea`, `south_pole`, `sardinia`
+        - latitude (float): in degree
+        - longtitude (float): in degree
+        - altitude (float): in meters
+        - seasonal (bool):
+        - diurnal (bool):
+        - weather_quantiles (dict): keys: `column_water_vapor` (float),  ...
+        - pwv_rms (float): ...
 
 - **atm_model:** Different atmospheric models
-  - Predefined configurations: `single_layer`, None
-  - specific keys:
-    - min_depth (float): in meters
-    - max_depth (float): in meters
-    - n_layers (int): number of atmospheric layers
-    - min_beam_res (int):
+    - Predefined configurations: `single_layer`, None
+    - specific keys:
+        - min_depth (float): in meters
+        - max_depth (float): in meters
+        - n_layers (int): number of atmospheric layers
+        - min_beam_res (int):
 
 - **mapper:** Different mappers
-  - Only one mapper is implemented, the `BinMapper`
-  - specific keys:
-    - map_height (float): radians
-    - map_width (float): radians
-    - map_res (float): radians
-    - map_filter (bool): Fourier filter the time streams before common-mode subtraction
-    - n_modes_to_remove (int): number of eigen modes to remove. Set to 0 for no common-mode subtraction.
+    - Only one mapper is implemented, the `BinMapper`
+    - specific keys:
+        - map_height (float): radians
+        - map_width (float): radians
+        - map_res (float): radians
+        - map_filter (bool): Fourier filter the time streams before common-mode subtraction
+        - n_modes_to_remove (int): number of eigen modes to remove. Set to 0 for no common-mode subtraction.
 
 - **sky:** Input file
-  - specific keys:
-    - map_file (string): `path_to_fits_file.fits`
-    - map_frame (string): options are `az_el` or `ra_dec`
-    - map_center (list): [RA (float), Dec (float)] in degree
-    - map_res (float): in degrees
-    - map_inbright (float): scale the map so the brightest pixel value becomes this value
-    - map_units (string): options are `K_RJ` or `Jy/pixel`
+    - specific keys:
+        - map_file (string): `path_to_fits_file.fits`
+        - map_frame (string): options are `az_el` or `ra_dec`
+        - map_center (list): [RA (float), Dec (float)] in degree
+        - map_res (float): in degrees
+        - map_inbright (float): scale the map so the brightest pixel value becomes this value
+        - map_units (string): options are `K_RJ` or `Jy/pixel`
 
 
 

maria/__init__.py

@@ -8,7 +8,8 @@
 del get_versions
 
 from . import array, pointing, site, utils, weather  # noqa F401
-from .array import get_array  # noqa F401
-from .pointing import get_pointing  # noqa F401
+from .array import all_arrays, get_array  # noqa F401
+from .pointing import all_pointings, get_pointing  # noqa F401
 from .sim import Simulation  # noqa F401
-from .site import get_site  # noqa F401
+from .site import all_sites, get_site  # noqa F401
+from .weather import all_regions  # noqa F401

maria/array.py

@@ -29,14 +29,15 @@
     ARRAY_PARAMS |= set(config.keys())
 
 DISPLAY_COLUMNS = ["description", "field_of_view", "primary_size"]
-supported_arrays = pd.DataFrame(ARRAY_CONFIGS).T
+supported_arrays_table = pd.DataFrame(ARRAY_CONFIGS).T
+all_arrays = supported_arrays_table.index.values
 
 
 class InvalidArrayError(Exception):
     def __init__(self, invalid_array):
         super().__init__(
             f"The array '{invalid_array}' is not supported."
-            f"Supported arrays are:\n\n{supported_arrays.loc[:, DISPLAY_COLUMNS].to_string()}"
+            f"Supported arrays are:\n\n{supported_arrays_table.loc[:, DISPLAY_COLUMNS].to_string()}"
         )
 
 

maria/atmosphere/__init__.py

@@ -1,10 +1,11 @@
+from .linear_angular import LinearAngularSimulation  # noqa F401
 from .single_layer import SingleLayerSimulation  # noqa F401
 
 # how do we do the bands? this is a great question.
 # because all practical telescope instrumentation assume a constant band
 
 # from .kolmogorov_taylor import KolmogorovTaylorSimulation
-# from .linear_angular import LinearAngularSimulation
+
 
 ATMOSPHERE_PARAMS = {
     "min_depth": 500,

maria/atmosphere/base.py

@@ -14,6 +14,29 @@
 here, this_filename = os.path.split(__file__)
 
 
+def extrude(
+    values: np.array,
+    A: np.array,
+    B: np.array,
+    n_steps: int,
+    n_i: int,
+    n_j: int,
+    i_sample_index: int,
+    j_sample_index: int,
+):
+    # muy rapido
+    BUFFER = np.zeros((n_steps + n_i) * n_j)
+    BUFFER[n_steps * n_j :] = values
+
+    # remember that (e, c) -> n_c * e + c
+    for buffer_index in np.arange(n_steps)[::-1]:
+        BUFFER[buffer_index * n_j + np.arange(n_j)] = A @ BUFFER[
+            n_j * (buffer_index + 1 + i_sample_index) + j_sample_index
+        ] + B @ np.random.standard_normal(size=n_j)
+
+    return BUFFER[: n_steps * n_j]
+
+
 class AtmosphericSpectrum:
     def __init__(self, filepath):
         """