discminer 0.2.29__tar.gz → 0.3.2__tar.gz

{discminer-0.2.29/discminer.egg-info → discminer-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: discminer
-Version: 0.2.29
+Version: 0.3.2
 Summary: Python package for parametric modelling of intensity channel maps from gas discs
 Home-page: https://github.com/andizq/discminer
 Author: Andres F. Izquierdo
@@ -22,7 +22,7 @@ Description: <p align="center">
         
         
         <div align="center">
-          Welcome to the discminer repository! Looking for quick examples and tutorials? Check out the docs.
+          Welcome to the discminer repository! Looking for quick examples and tutorials? Check out the <mark>example/</mark> folder.
           <br />
           <a href="https://github.com/andizq/discminer/issues/new?assignees=&labels=bug&title=bug%3A+">Report a Bug</a>
           ·
@@ -32,12 +32,12 @@ Description: <p align="center">
         </div>
         
         - Model channel maps from molecular line emission of discs by fitting intensity **and** rotation velocity
-        - Study the disc vertical structure by modelling front and back side emission surfaces
+        - Analyse the disc's dynamics by modelling Keplerian motion, and optionally pressure support + self-gravity
+        - Investigate the disc vertical structure by modelling front and back side emission surfaces
         - Compute moment maps that accurately capture complex line profile morphologies
-        - Extract rotation curves, radial and meridional velocities, intensity and line width profiles
-        - Analyse the disc dynamical structure by modelling Keplerian motion + pressure support + self-gravity at once
-        - Identify velocity and intensity substructures; study their coherence and degree of localisation
-        - Non-axisymmetric models are possible; all attributes can be described as a function of $R,\phi,z$ disc coords
+        - Extract rotation curves, radial and meridional velocities, intensity, and line width profiles
+        - Identify velocity and intensity substructures, and examine their coherence and degree of localisation
+        - Support non-axisymmetric models; all attributes can be described in three-dimensional coordinates
         
         
         <img
@@ -47,32 +47,32 @@ Description: <p align="center">
         
         ## Mining tools
         
-        Discminer offers a wide range of analysis and visualisation tools to fully explore the physical and dynamical structure of your disc.
+        Discminer offers a wide range of analysis and visualisation tools to fully explore the physical and dynamical structure of discs.
         
         
         ### cube
         
         - Compute moment maps that accurately capture complex line profile morphologies.
         - Output moment maps include **peak intensity**, **line width**, **line slope**, and **centroid velocity**.
-        - Easily clip, downsample, and convert to brightness temperature units.
+        - Easily clip, downsample, and convert data to brightness temperature units.
         - Quickly visualise model versus data channels and interactively extract spectra.
         
         ### rail
         
-        - Extract azimuthal and radial profiles of intensity, line width and velocity from moment maps.
-        - Compute rotation curves and decompose disc velocity into its three-dimensional components.
-        - Reveal large-scale signatures and quantify their pitch angle, width, extent, and coherence degree.
+        - Extract azimuthal and radial profiles of intensity, line width, and velocity from moment maps.
+        - Compute rotation curves and decompose disc velocities into their three-dimensional components.
+        - Identify large-scale structures and quantify their pitch angle, width, extent, and degree of coherence.
         
         ### pick
         
-        - Identify small-scale velocity and intensity perturbations, and estimate their localisation degree.
+        - Identify small-scale perturbations and estimate their degree of localisation.
         
         ### plottools
         
-        - Customise intensity channels and residual maps, and highlight coherent and localised perturbations.
-        - Use sky or disc projections interchangeably for easier visualisation of features.
-        - Easily overlay the disc geometry (orientation and vertical structure) on any observable product.
-        - Overlay 1D profiles or 2D maps from external data to e.g. highlight the presence of dust substructures.
+        - Customise intensity channels, moments, and residual maps.
+        - Use sky or disc projections interchangeably for improved visualisation of features.
+        - Easily overlay disc geometry (considering orientation and vertical structure) onto any observable product.
+        - Load in 1D profiles or 2D maps from external data e.g. to highlight the presence of dust substructures.
         
         
         ## Installation
@@ -89,7 +89,6 @@ Description: <p align="center">
         
         #### Optional dependencies
         
-        - [termtables](https://pypi.org/project/termtables)
         - [termplotlib](https://pypi.org/project/termplotlib)
         - [FilFinder](https://pypi.org/project/fil-finder)
         - [schwimmbad](https://pypi.org/project/schwimmbad)
@@ -97,10 +96,9 @@ Description: <p align="center">
         
         ## How to use
         
-        The package documentation is still under construction, but you can find practical examples demonstrating the main
-        functionality of the code in the `./template` folder of this repository.
+        You can find practical examples demonstrating the main functionality of the code in the `./example` folder of this repository.
         
-        To run the examples on your local machine you can clone this repository and follow the instructions provided in the readme file,
+        To run the examples on your local machine, clone this repository and follow the instructions provided in the README file,
         
         ```bash
         git clone https://github.com/andizq/discminer.git

{discminer-0.2.29 → discminer-0.3.2}/README.md

@@ -12,7 +12,7 @@
 
 
 <div align="center">
-  Welcome to the discminer repository! Looking for quick examples and tutorials? Check out the docs.
+  Welcome to the discminer repository! Looking for quick examples and tutorials? Check out the <mark>example/</mark> folder.
   <br />
   <a href="https://github.com/andizq/discminer/issues/new?assignees=&labels=bug&title=bug%3A+">Report a Bug</a>
   ·
@@ -22,12 +22,12 @@
 </div>
 
 - Model channel maps from molecular line emission of discs by fitting intensity **and** rotation velocity
-- Study the disc vertical structure by modelling front and back side emission surfaces
+- Analyse the disc's dynamics by modelling Keplerian motion, and optionally pressure support + self-gravity
+- Investigate the disc vertical structure by modelling front and back side emission surfaces
 - Compute moment maps that accurately capture complex line profile morphologies
-- Extract rotation curves, radial and meridional velocities, intensity and line width profiles
-- Analyse the disc dynamical structure by modelling Keplerian motion + pressure support + self-gravity at once
-- Identify velocity and intensity substructures; study their coherence and degree of localisation
-- Non-axisymmetric models are possible; all attributes can be described as a function of $R,\phi,z$ disc coords
+- Extract rotation curves, radial and meridional velocities, intensity, and line width profiles
+- Identify velocity and intensity substructures, and examine their coherence and degree of localisation
+- Support non-axisymmetric models; all attributes can be described in three-dimensional coordinates
 
 
 <img
@@ -37,32 +37,32 @@
 
 ## Mining tools
 
-Discminer offers a wide range of analysis and visualisation tools to fully explore the physical and dynamical structure of your disc.
+Discminer offers a wide range of analysis and visualisation tools to fully explore the physical and dynamical structure of discs.
 
 
 ### cube
 
 - Compute moment maps that accurately capture complex line profile morphologies.
 - Output moment maps include **peak intensity**, **line width**, **line slope**, and **centroid velocity**.
-- Easily clip, downsample, and convert to brightness temperature units.
+- Easily clip, downsample, and convert data to brightness temperature units.
 - Quickly visualise model versus data channels and interactively extract spectra.
 
 ### rail
 
-- Extract azimuthal and radial profiles of intensity, line width and velocity from moment maps.
-- Compute rotation curves and decompose disc velocity into its three-dimensional components.
-- Reveal large-scale signatures and quantify their pitch angle, width, extent, and coherence degree.
+- Extract azimuthal and radial profiles of intensity, line width, and velocity from moment maps.
+- Compute rotation curves and decompose disc velocities into their three-dimensional components.
+- Identify large-scale structures and quantify their pitch angle, width, extent, and degree of coherence.
 
 ### pick
 
-- Identify small-scale velocity and intensity perturbations, and estimate their localisation degree.
+- Identify small-scale perturbations and estimate their degree of localisation.
 
 ### plottools
 
-- Customise intensity channels and residual maps, and highlight coherent and localised perturbations.
-- Use sky or disc projections interchangeably for easier visualisation of features.
-- Easily overlay the disc geometry (orientation and vertical structure) on any observable product.
-- Overlay 1D profiles or 2D maps from external data to e.g. highlight the presence of dust substructures.
+- Customise intensity channels, moments, and residual maps.
+- Use sky or disc projections interchangeably for improved visualisation of features.
+- Easily overlay disc geometry (considering orientation and vertical structure) onto any observable product.
+- Load in 1D profiles or 2D maps from external data e.g. to highlight the presence of dust substructures.
 
 
 ## Installation
@@ -79,7 +79,6 @@ pip install -U discminer
 
 #### Optional dependencies
 
-- [termtables](https://pypi.org/project/termtables)
 - [termplotlib](https://pypi.org/project/termplotlib)
 - [FilFinder](https://pypi.org/project/fil-finder)
 - [schwimmbad](https://pypi.org/project/schwimmbad)
@@ -87,10 +86,9 @@ pip install -U discminer
 
 ## How to use
 
-The package documentation is still under construction, but you can find practical examples demonstrating the main
-functionality of the code in the `./template` folder of this repository.
+You can find practical examples demonstrating the main functionality of the code in the `./example` folder of this repository.
 
-To run the examples on your local machine you can clone this repository and follow the instructions provided in the readme file,
+To run the examples on your local machine, clone this repository and follow the instructions provided in the README file,
 
 ```bash
 git clone https://github.com/andizq/discminer.git

discminer-0.3.2/discminer/_version.py

@@ -0,0 +1 @@
+__version__ = "0.3.2"

{discminer-0.2.29 → discminer-0.3.2}/discminer/cart.py

@@ -2,6 +2,8 @@ import numpy as np
 from astropy import units as u
 from astropy import constants as ct
 from scipy.interpolate import interp1d, RectBivariateSpline
+
+from .grid import GridTools
 from .tools.utils import hypot_func
 
 au_to_m = u.au.to('m')
@@ -9,6 +11,12 @@ au_to_m = u.au.to('m')
 #*******************
 #VELOCITY FUNCTIONS
 #*******************
+def keplerian(coord, Mstar=1.0, vel_sign=1, vsys=0):
+    Mstar *= u.M_sun.to('kg')
+    if 'R' not in coord.keys(): R = hypot_func(coord['x'], coord['y'])
+    else: R = coord['R'] 
+    return vel_sign*np.sqrt(ct.G.value*Mstar/R) * 1e-3
+
 def keplerian_vertical(coord, Mstar=1.0, vel_sign=1, vsys=0):
     Mstar *= u.M_sun.to('kg')
     if 'R' not in coord.keys():
@@ -21,25 +29,33 @@ def keplerian_vertical(coord, Mstar=1.0, vel_sign=1, vsys=0):
         r = coord['r']
     return vel_sign*np.sqrt(ct.G.value*Mstar/r**3)*R * 1e-3 
 
-def velocity_hydro2d(coord, func_interp_R=None, func_interp_phi=None, Mstar=1.0, vel_sign=1, vsys=0, **dummies):
+def velocity_hydro2d(coord, func_interp_R=None, func_interp_phi=None, Mstar=1.0, vel_sign=1, vsys=0, phip=0.0, **dummies):
     Mstar *= u.M_sun.to('kg')
-    y = coord['x'] #switch for 90 deg shift on planet azimuth
+    y = coord['x'] #90 deg shift so that phip=0 aligns with disc major axis
     x = coord['y']
     R = coord['R']
 
+    if phip != 0.0:
+        phip = np.radians(phip)
+        x, y = GridTools._rotate_sky_plane(x, y, phip)
+        
     if 'r' not in coord.keys():
         r = hypot_func(R, coord['z'])
+        
     else:
         r = coord['r']
 
     if func_interp_R is None and func_interp_phi is not None:
         vphi = func_interp_phi(x,y, grid=False)                    
         vR = np.zeros_like(vphi)
+
     elif func_interp_R is not None and func_interp_phi is None:
         vR = func_interp_R(x,y, grid=False)        
         vphi = np.zeros_like(vR)
+
     elif func_interp_R is None and func_interp_phi is None:
         return [0, 0, 0]    
+
     else:
         vR = func_interp_R(x,y, grid=False)
         vphi = func_interp_phi(x,y, grid=False)
@@ -136,6 +152,64 @@ def intensity_powerlaw_rbreak_nosurf(coord, I0=1.0, p0=-2.5, p1=-1.5,
     Ieff_rout = np.where(R<=Rout, Ieff, 0.0)
     return Ieff_rout
 
+def intensity_powerlaw_rout_hydro(coord, I0=30.0, R0=100, p=-0.4, z0=100, q=0.3, Rout=500, func_interp_sigma=None, phip=0.0, weight=1.0):
+    
+    y = coord['x'] 
+    x = coord['y']
+
+    if phip != 0.0:
+        phip = np.radians(phip)
+        x, y = GridTools._rotate_sky_plane(x, y, phip)
+
+    if 'R' not in coord.keys():
+        R = hypot_func(coord['x'], coord['y'])
+    else:
+        R = coord['R']
+
+    if func_interp_sigma is None:
+        sigma = np.zeros_like(R)
+    else:
+        sigma = func_interp_sigma(x,y, grid=False)
+        
+    z = coord['z']
+    R0*=au_to_m
+    z0*=au_to_m
+    Rout*=au_to_m
+    A = I0*R0**-p*z0**-q
+    Ieff = np.where(R<=Rout, A*R**p*np.abs(z)**q, 0.0) * sigma**weight
+
+    return Ieff
+
+def intensity_powerlaw_rbreak_hydro(coord, I0=30.0, p0=-0.4, p1=-0.4, z0=100, q=0.3, Rbreak=20, Rout=500, p=0, func_interp_sigma=None, phip=0.0, weight=1.0):
+    
+    y = coord['x'] 
+    x = coord['y']
+
+    if phip != 0.0:
+        phip = np.radians(phip)
+        x, y = GridTools._rotate_sky_plane(x, y, phip)
+
+    if 'R' not in coord.keys():
+        R = hypot_func(coord['x'], coord['y'])
+    else:
+        R = coord['R']
+
+    if func_interp_sigma is None:
+        sigma = np.zeros_like(R)
+    else:
+        sigma = func_interp_sigma(x,y, grid=False)
+
+    z = coord['z']
+    z0*=au_to_m
+    Rout*=au_to_m
+    Rbreak*=au_to_m
+    A = I0*Rbreak**-p0*z0**-q
+    B = I0*Rbreak**-p1*z0**-q
+    Ieff = np.where(R<=Rbreak, A*R**p0*np.abs(z)**q, B*R**p1*np.abs(z)**q)
+    ind = R>Rout
+    Ieff[ind] = 0.0
+    return Ieff
+
 #***********
 #LINE WIDTH 
 #***********

{discminer-0.2.29 → discminer-0.3.2}/discminer/core.py

@@ -15,7 +15,7 @@ import warnings
 import json
 
 class Data(Cube):
-    def __init__(self, filename, dpc, twodim=False):
+    def __init__(self, filename, dpc, twodim=False, disc=None, mol='12co', kind=['mask']):
         """
         Initialise Data object. Inherits `~discminer.disc2d.Cube` properties and methods.
         
@@ -95,13 +95,14 @@ class Data(Cube):
                 raise InputError(cube_vel,
                                  'The input datacube is not valid. Only the following spectral_cube instances are supported: SpectralCube, VaryingResolutionSpectralCube.')
             
-        super().__init__(data, header, vchannels, dpc, beam=beam, filename=filename)
+        super().__init__(data, header, vchannels, dpc, beam=beam, filename=filename, disc=disc, mol=mol, kind=kind)
 
     def _init_cube(self):
         super().__init__(
             self.data,
             self.header,
             self.vchannels,
+            self.dpc,
             beam = self.beam,
             filename = self.filename            
         )