ACID-code 2.0.0a3__py3-none-any.whl → 2.0.0a4__py3-none-any.whl

ACID_code/acid.py

@@ -60,9 +60,9 @@ class Acid:
 
         Important note: All defaults in the signature are None, meaning if any values are input, they will override the default :py:class:`Config` and/or :py:class:`Data` values or
         any values that have already been input. The defaults within the config are written below. The config defaults can also be accessed via 
-        :py:attr:`ACID_code.Config.defaults` (returning a dictionary of defaults for both initialisation and run_acid).
+        :py:attr:`ACID_code.Config.defaults` (returning a dictionary of defaults for both initialisation and the ACID method).
 
-        All parameters below and in run_ACID are stored in the :py:class:`Config` instance, unless explicitly stated to be in the :py:class:`Data` instance.
+        All parameters below and in the ACID method are stored in the :py:class:`Config` instance, unless explicitly stated to be in the :py:class:`Data` instance.
         The :py:class:`Config` instance is for runtime settings and the :py:class:`Data` instance is for storing data and any calculations. 
 
         Parameters
@@ -73,12 +73,11 @@ class Acid:
             choose your own velocity grid, by default None, stored in the Data instance.
         linelist : :py:type:`Array2D | str` | :py:class:`LineList` | dict`, optional
             The linelist to use for LSD. The linelist should have wavelengths in angstroms and relative depths between 0 and 1.
-            This is a required parameter if linelist_wl and linelist_depths are not provided. It can be of the forms:
+            This is a required parameter. It can be of the forms:
             - String: A path to a VALD linelist in string format. Support for other linelists may be added in the future or on request.
             - :py:type:`Array2D`: A 2D array-like object indexed such that 0 is wavelengths and 1 is depths.
             - dict: A dictionary with keys "wavelengths" and "depths", each containing array-like objects for the wavelengths and depths respectively.
             - :py:class:`LineList`: The :py:class:`LineList` class is used to expose the linelist for masking or getting/plotting the linelist. You can input an instance if you have one.
-            - If None, linelist_wl and linelist_depths must be provided (see below), by default None, stored in the Data instance.
         order : :py:type:`IntLike`, optional
             If this ACID instance is intended as a run on a specific order, then you can designate this instance for that order. This will allow
             the resulting Data instance to track of which order the profiles correspond to. Note that orders can be indexed by the correct indexing
@@ -117,7 +116,7 @@ class Acid:
             The path to save the sampler HDF5 backend file to.
             If None, the sampler is not saved and only stored in memory. By default None.
             Note that if your path points to an existing file, it will be overwritten on Acid initialization.
-            If True, we use the emcee HDF5 backend to store and load the sampler.
+            If existing, we use the emcee HDF5 backend to store and load the sampler.
             Should be a valid file path that ends with ".h5". If the directory containing it does not exist, it will be created.
             Note that if you later try and save the sampler through the data class, it is converted to a HD5 backend.
         data : :py:class:`Data` | :py:class:`DataList`, optional
@@ -315,6 +314,9 @@ class Acid:
         skips : :py:type:`IntLike`, optional
             An option to only run acid on one in every n pixels, where n is the integer argument. This is only useful for
             testing to get a quicker result especially for larger wavelength ranges or datasets, by default 1 (no skipping)
+        od : :py:type:`bool`, optional
+            If True, runs ACID in optical depth, otherwise, the LSD methods and ACID fitting is performed in flux. By default None which defaults to True.
+            Note that the whole point of ACID is to run LSD in OD, we highly recommend leaving this unless you specifically want to compare.
         sampler_type : :py:type:`str`, optional
             If you really try to wish to use the dynesty nested sampler, you can set this to "dynesty". It is almost entirely unsupported
             by the rest of the code other than to just get a finished result object, and much slower. We highly recommend using None or "emcee" (default).

ACID_code/data.py

@@ -436,6 +436,7 @@ class Config:
         If return_fig is True, returns a tuple of (fig, ax) where fig is the matplotlib figure object and ax is the axis object.
         Otherwise, returns None and shows the plot.
         """
+        # TODO: SORT out the colours and looks of this and the below continuum fit plot
         fig, ax = plt.subplots(figsize=(10, 6))
         for i, (name, line_data) in enumerate(self.masking_lines):
             for line, width in zip(line_data["lines"], line_data["widths"]):
@@ -646,7 +647,9 @@ class Data:
 
         Parameters
         ----------
-        See :py:class:`Acid` for the accepted linelist formats and parameters.
+        linelist : Array2D, str, LineList, dict[str, Array1D], or None
+             The linelist to be set, which can be in various formats for convenience.
+             See :py:class:`Acid` init for the accepted linelist formats and parameters.
         """
         # Check if linelist already exists, override with new inputs if provided
         if linelist is not None:
@@ -1212,16 +1215,6 @@ class Data:
         """
         Converts the data object to a dictionary payload for saving. This is used internally in the save method, 
         but can also be used for debugging or other purposes.
-
-        Parameters
-        ----------
-        store_sampler : bool, optional
-            Whether to include the MCMC sampler in the dictionary payload, by default True.
-        size_limit : Scalar | None, optional
-            A hard size limit to the sampler in GB.
-            If the sampler exceeds this size, it will not be stored regardless of the store_sampler flag.
-            This is to avoid accidentally storing very large samplers. If None, no limit is set. Default is 1GB.
-            A warning will be printed if this size_limit forces the store_sampler to be False if store_sampler was set to True.
         """
         if self.sampler is not None and self.config.sampler_type == "dynesty":
             raise ValueError("Storing the sampler is not currently supported for dynesty samplers.\n" \
@@ -1322,10 +1315,6 @@ class LineList:
         ----------
         linelist : str, dict, LineList, list, or np.ndarray
             See :py:class:`Acid`.
-        linelist_wl : array-like, optional
-            See :py:class:`Acid`.
-        linelist_depths : array-like, optional
-            See :py:class:`Acid`.
 
         Returns
         -------
@@ -1356,8 +1345,6 @@ class LineList:
                 raise ValueError("If 'linelist' is a list or array, it must have length 2, with index 0 being wavelengths and index 1 being depths")
             linelist_wl = linelist[0]
             linelist_depths = linelist[1]
-        elif linelist_wl is not None and linelist_depths is not None:
-            pass # linelist_wl and linelist_depths already set, will be processed below
         else:
             raise ValueError(f"'linelist' must be a string path to a VALD linelist, a dictionary with keys 'wavelengths' and 'depths', \n" \
             "a LineList object, or a list/array indexed such that 0 is wavelengths and 1 is depths.")
@@ -1429,8 +1416,7 @@ class DataList:
     strictly necessary to run ACID over multiple orders, you can handle the multiple instances yourself.
 
     The DataList class works with a required root directory specified by the user to access to the same data across parallel processes, 
-    and also to save intermediate results and figures per order. It also can save the whole sampler if you specify save_sampler=True in the run_ACID method,
-    which will save the sampler with Data in result to the save_dir after running ACID for each order but take up much more disk space.
+    and also to save intermediate results and figures per order.
     """
 
     def __init__(
@@ -1524,11 +1510,6 @@ class DataList:
                                       f"The idea is that you can input a Load object which has its own tools to pull s2d data from common "\
                                       f"instruments such as ESPRESSO, HARPS, etc. \nIf you want to use this feature, please open an issue or "\
                                       f"contribute a pull request with the implementation.")
-            from .load import Load
-            if not isinstance(load, Load):
-                raise ValueError("load must be an instance of the Load class. Got: {load!r}")
-            wavelengths, flux, errors, sn = load.get_data()
-            order_range = load.order_range
 
         # Configure verbosity
         self.verbose = Config(verbose=verbose).verbose
@@ -1864,6 +1845,10 @@ class DataList:
         if nworkers > 1:
             orders = np.array_split(orders, nworkers)[worker]
 
+        # Check if linelist or velocities were in kwargs and remove them now once if so
+        ll = kwargs.pop("linelist", None)
+        vel = kwargs.pop("velocities", None)
+
         iterable = tqdm(orders, "Running ACID on orders", unit="order") if self.verbose > 1 else orders
         for order in iterable:
 
@@ -1884,11 +1869,9 @@ class DataList:
 
             # Handling if any kwargs were input
             # Only overwrite if overwrite_kwargs is True, otherwise keep the existing linelist/velocities in the Data instance
-            if "linelist" in kwargs:
-                ll = kwargs.pop("linelist")
+            if ll is not None:
                 data.linelist = ll if overwrite_kwargs else data.linelist
-            if "velocities" in kwargs:
-                vel = kwargs.pop("velocities")
+            if vel is not None:
                 data.velocities = vel if overwrite_kwargs else data.velocities
             if overwrite_kwargs:
                 data.config.update_hipri(**kwargs)

ACID_code/result.py

@@ -87,7 +87,7 @@ class Result:
             the Result object for methods that do not require the profiles attribute, such as 
             continue_sampling() or plot_walkers(). This requires a Data object with the necessary attributes, 
             and a sampler object in the initialisation, or an Acid object with the necessary attributes already set.
-            By default, None.
+            By default, True.
         verbose : :py:type:`IntLike | bool | str`, optional
             Verbosity level, works exactly the same as :py:class:`Acid`, if not provided
             defaults to provided :py:class:`Acid`/:py:class:`Data` class verbosity (which itself defaults to 2).
@@ -112,7 +112,10 @@ class Result:
         # Handle the sampler if input, initiate if one exists
         self.sampler = sampler if sampler is not None else self.sampler # update sampler if provided, otherwise keep the same
         if self.sampler is not None:
-            self.dynesty = isinstance(self.sampler, Sampler)
+            if Sampler is not None: # ie, only if dynesty is installed do this cheeck
+                self.dynesty = isinstance(self.sampler, Sampler)
+            else:
+                self.dynesty = False
             self.initiate_sampler(self.sampler) # set internal variables based on sampler, sets sampler_initialiated to True
 
         if not self.data.complete:
@@ -259,7 +262,7 @@ class Result:
             # Tuples allow for array-like indexing of the list
             if len(item) == 3:
                 _order, frame, velocity = item
-                return self.data.alphaprofiles[frame][velocity]
+                return self.data.profiles[frame][velocity]
             elif len(item) == 2:
                 return self.data.profiles[item[0]][item[1]]
             elif len(item) == 1:

{acid_code-2.0.0a3.dist-info → acid_code-2.0.0a4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code
-Version: 2.0.0a3
+Version: 2.0.0a4
 Summary: Returns line profiles from input spectra by fitting the stellar continuum and performing LSD
 Author: Lucy Dolan
 Author-email: Benjamin Cadell <bcadell01@qub.ac.uk>

{acid_code-2.0.0a3.dist-info → acid_code-2.0.0a4.dist-info}/RECORD

@@ -1,15 +1,15 @@
 ACID_code/__init__.py,sha256=-cmUx-kDheDBhk8ZlleWVRrWZyXZRVe-dwciVV9ZxLg,655
-ACID_code/acid.py,sha256=hibDm91O0_HLO3d50I2Q137rXi_xmXdcJSb9KcDNLCs,75532
-ACID_code/data.py,sha256=qaLGYFDPyK7XlXg09b1AZO4xGMZCmrYd7t04SU3LknA,114575
+ACID_code/acid.py,sha256=oRc5JrJlaWkjSl4eldnoKalInsoyZySRnj8R6k9CZ5o,75702
+ACID_code/data.py,sha256=xXms6yzpdtRwKyv-M1qGqcr468DGNQc7iQGkXBuqotY,113469
 ACID_code/errors.py,sha256=qqG44x_rVpi5njLIoRkwvw_6owy33wejvsFuAZ-XKKM,525
 ACID_code/load.py,sha256=3gzIZpAv7flgX5ekWdRDI95hkPTxvtp2F1liygpivOQ,5453
 ACID_code/lsd.py,sha256=VfdB-mN2uH20N6jT6lGKhEaepOwB2bJQepyZfIpqM9U,21521
 ACID_code/mcmc.py,sha256=PjGuxUhq-oFRkKKQmQPdSp82NyueG9FPwr7kpLgLk0U,14314
 ACID_code/profiles.py,sha256=KkVsJjCLXx_wjRBialfmnlGwjWsROy0GkggdPPYLelc,17103
-ACID_code/result.py,sha256=itDNK0zxgtNH8-Igqip-zFi6StK5ZyuMS47UYVooSq8,42141
+ACID_code/result.py,sha256=tMumOLz4wwG62uvUoh1owuKQDEcaGzHTcgapJ3-hJnY,42281
 ACID_code/utils.py,sha256=Xt24WrhV6bKW-NiNl1FsNiJ2krntCJeCUL-hzIQAdLA,27637
-acid_code-2.0.0a3.dist-info/licenses/LICENSE,sha256=L6dUgqjvHmRoobrBCPSHKC4UtRM5Ldp1DJBC4bnLk3w,1070
-acid_code-2.0.0a3.dist-info/METADATA,sha256=XFBGmLrD4od1XTRY4SRGN3Cg-RAvM21VUEClyV6paIQ,2999
-acid_code-2.0.0a3.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-acid_code-2.0.0a3.dist-info/top_level.txt,sha256=O4OaSabv1ebFYQmHgftr1PGAv6BvC2l81Y3HjgNehQI,10
-acid_code-2.0.0a3.dist-info/RECORD,,
+acid_code-2.0.0a4.dist-info/licenses/LICENSE,sha256=L6dUgqjvHmRoobrBCPSHKC4UtRM5Ldp1DJBC4bnLk3w,1070
+acid_code-2.0.0a4.dist-info/METADATA,sha256=ehz0pcO49ONL8_XkLyj5k_K0ft_oi5i6BXkMuyGrrg4,2999
+acid_code-2.0.0a4.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+acid_code-2.0.0a4.dist-info/top_level.txt,sha256=O4OaSabv1ebFYQmHgftr1PGAv6BvC2l81Y3HjgNehQI,10
+acid_code-2.0.0a4.dist-info/RECORD,,