ACID-code 2.0.0a1__py3-none-any.whl → 2.0.0a2__py3-none-any.whl

ACID_code/result.py

@@ -544,15 +544,21 @@ class Result:
 
         # Get flat_samples which are the same samples used to calculate the final profile, alpha is OD, 
         # so convert profile back to OD and reconvert to flux for forward model
-        profile = utils.flux_to_od(self.data.combined_profile[0])
+        profile = utils.flux_to_od(self[0])
         model_flux = utils.od_to_flux(self.data.alpha @ profile) * self.data.continuum_model
 
+        # Due to distortion at the edges of the profile, we drop the last 2 pixels
+        wavelengths = utils.drop_edges(wavelengths)
+        flux = utils.drop_edges(flux)
+        model_flux = utils.drop_edges(model_flux)
+        continuum_model = utils.drop_edges(self.data.continuum_model)
+
         # Plotting
         fig, ax = plt.subplots(2, 1, **subplot_kwargs)
         ax[0].plot(wavelengths, flux, color='black', linewidth=1, label='Observed Spectrum')
         ax[0].plot(wavelengths, model_flux, color='C0', linewidth=1, label='Forward Model Fit')
-        ax[0].plot(wavelengths, self.data.continuum_model, color='C1', linewidth=1, label='Fitted Continuum', linestyle='--')
-        ax[1].plot(wavelengths, model_flux - flux, color='C0', linewidth=1, label='Residuals')
+        ax[0].plot(wavelengths, continuum_model, color='C1', linewidth=1, label='Fitted Continuum', linestyle='--')
+        ax[1].plot(wavelengths, model_flux-flux, color='C0', linewidth=1, label='Residuals')
         ax[1].axhline(0, color='black', linestyle='--', linewidth=1)
         ax[0].set_title(labels["title"])
         ax[1].set_xlabel(labels["xlabel"])

ACID_code/utils.py

@@ -153,8 +153,11 @@ def drop_invalid(wavelengths, flux, errors=None, return_mask=False, verbose=2):
     output = output + (mask,) if return_mask else output
     return output
 
-def clip_wavelengths(wavelengths, wavelengths_linelist, depths_linelist):
-    """Clips the linelist to only include lines within the wavelength range of the observed spectrum.
+def clip_wavelengths(wavelengths, wavelengths_linelist, depths_linelist, pad=5):
+    """
+    Clips the linelist to only include lines within the wavelength range of the observed spectrum.
+    Includes a pad either side of the wavelength range so that the wings of lines outside
+    the range can also contribute to the fit.
 
     Parameters
     ----------
@@ -164,6 +167,8 @@ def clip_wavelengths(wavelengths, wavelengths_linelist, depths_linelist):
         Wavelengths from the linelist
     depths_linelist : np.ndarray
         Depths from the linelist
+    pad : float, optional
+        Number of angstroms to pad on either side of the wavelength range. By default, 5.
 
     Returns
     -------
@@ -172,10 +177,28 @@ def clip_wavelengths(wavelengths, wavelengths_linelist, depths_linelist):
     depths_linelist : np.ndarray
         Clipped depths from the linelist
     """
-    lower, upper = np.nanmin(wavelengths), np.nanmax(wavelengths)
+    lower, upper = np.nanmin(wavelengths)-pad, np.nanmax(wavelengths)+pad
     idx = (wavelengths_linelist >= lower) & (wavelengths_linelist <= upper)
     return wavelengths_linelist[idx], depths_linelist[idx]
 
+def drop_edges(array, n_pix=2):
+    """
+    Drops the edges of an array by a specified number of pixels.
+    
+    Parameters
+    ----------
+    array : np.ndarray
+        The input array.
+    n_pix : int, optional
+        Number of pixels to drop from each edge. Default is 2.
+
+    Returns
+    -------
+    np.ndarray
+        The array with edges dropped.
+    """
+    return array[n_pix:-n_pix]
+
 @beartype
 def calc_deltav(wavelengths:Array1D)->Scalar:
     """Calculates velocity pixel size

{acid_code-2.0.0a1.dist-info → acid_code-2.0.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ACID_code
-Version: 2.0.0a1
+Version: 2.0.0a2
 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-2.0.0a1.dist-info → acid_code-2.0.0a2.dist-info}/RECORD

@@ -6,10 +6,10 @@ ACID_code/load.py,sha256=3gzIZpAv7flgX5ekWdRDI95hkPTxvtp2F1liygpivOQ,5453
 ACID_code/lsd.py,sha256=iSNjxga-ic1tDCEpEOr5ISSxOsg6GLL_BYqTJi58MTA,20814
 ACID_code/mcmc.py,sha256=kNW1Aj5jfWb5xa95yKJU4NBOp1hnGV3KzHV5DrCtKU8,11434
 ACID_code/profiles.py,sha256=KkVsJjCLXx_wjRBialfmnlGwjWsROy0GkggdPPYLelc,17103
-ACID_code/result.py,sha256=MjLk43Q7P7nCnvE2y38Bg5ektJ_hNgVTQhlOIFKfEaQ,39559
-ACID_code/utils.py,sha256=MBO_DouultP-j3GrKCa3PnZpEUetT91lPeX0_ZGT0Rs,26656
-acid_code-2.0.0a1.dist-info/licenses/LICENSE,sha256=L6dUgqjvHmRoobrBCPSHKC4UtRM5Ldp1DJBC4bnLk3w,1070
-acid_code-2.0.0a1.dist-info/METADATA,sha256=HI4YBBrChQgiGbZ6Mu1iiafpfxgOxlAFjZMJo3iERWg,2999
-acid_code-2.0.0a1.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
-acid_code-2.0.0a1.dist-info/top_level.txt,sha256=O4OaSabv1ebFYQmHgftr1PGAv6BvC2l81Y3HjgNehQI,10
-acid_code-2.0.0a1.dist-info/RECORD,,
+ACID_code/result.py,sha256=9VXQkovQflDSUIYjwHCAo_cFMs7981IOuKDwlFv8_9w,39819
+ACID_code/utils.py,sha256=SY7qlIM15h8yYz7G_-DqXpYhralFbE0ycpOPvnw6DZw,27323
+acid_code-2.0.0a2.dist-info/licenses/LICENSE,sha256=L6dUgqjvHmRoobrBCPSHKC4UtRM5Ldp1DJBC4bnLk3w,1070
+acid_code-2.0.0a2.dist-info/METADATA,sha256=qVMgFV_XyFpmUQgGZ6zG3gSZXZR4aT7Lbhfdp6mIabA,2999
+acid_code-2.0.0a2.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+acid_code-2.0.0a2.dist-info/top_level.txt,sha256=O4OaSabv1ebFYQmHgftr1PGAv6BvC2l81Y3HjgNehQI,10
+acid_code-2.0.0a2.dist-info/RECORD,,