subhaloscript 1.0.7__tar.gz → 1.0.8__tar.gz

{subhaloscript-1.0.7 → subhaloscript-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subhaloscript
-Version: 1.0.7
+Version: 1.0.8
 Summary: Utility functions for analyzing subhalo distributions.
 Author-email: Charles Gannon <cgannon@ucmerced.edu>
 License-File: LICENSE

{subhaloscript-1.0.7 → subhaloscript-1.0.8}/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: subhaloscript
-  version: "1.0.7"
+  version: "1.0.8"
 
 source:
   path: .  # Or use `git_url`/`url` if not building from local files

{subhaloscript-1.0.7 → subhaloscript-1.0.8}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 dependencies = ["numpy","pandas","scipy","h5py", "scikit-learn"]
 name = "subhaloscript"
-version = "1.0.7"
+version = "1.0.8"
 authors = [
   { name="Charles Gannon", email="cgannon@ucmerced.edu" },
 ]

subhaloscript-1.0.8/subscript/defaults.py

@@ -0,0 +1,61 @@
+class Meta():
+    cache = True
+    """If true, use custom code when reading hdf5 to cache read data."""
+    disableDepreciatedWarning = False
+
+class ParamKeys():
+    """Library of default galacticus parameters."""
+    x = 'positionOrbitalX'
+    y = 'positionOrbitalY'
+    z = 'positionOrbitalZ'
+    relx = 'satellitePositionX'
+    rely = 'satellitePositionY'
+    relz = 'satellitePositionZ'
+    mass = 'basicMass'
+    mass_bound = 'satelliteBoundMass'
+    rvir = 'darkMatterOnlyRadiusVirial'
+    mass_basic = 'basicMass'
+    is_isolated = 'nodeIsIsolated'
+    hierarchylevel = 'nodeHierarchyLevel'
+    sphere_radius = 'spheroidRadius'
+    sphere_anglularmomentum = 'spheroidAngularMomentum'
+    sphere_mass_stellar = 'spheroidMassStellar'
+    sphere_mass_gas = 'spheroidMassGas'
+    scale_radius = 'darkMatterProfileScaleRadius'
+    density_profile_radius = 'densityProfileRadius'
+    density_profile = 'densityProfile'
+    z_lastisolated = 'redshiftLastIsolated'
+    tnfw_rt = 'radiusTidalTruncationNFW'
+    tnfw_p0 = 'densityNormalizationTidalTruncationNFW'
+    custom_id = 'custom_id'
+    custom_tree_index = 'custom_node_tree'
+    custom_tree_outputorder = 'custom_node_outputorder'
+    concentration = 'concentration'
+    merger_tree_count = 'mergerTreeCount'
+    merger_tree_index = 'mergerTreeIndex'
+    merger_tree_seed = 'mergerTreeSeed'
+    merger_tree_start_index = 'mergerTreeStartIndex'
+    merger_tree_weight = 'mergerTreeWeight'
+    basic_time_last_isolated = 'basicTimeLastIsolated'
+    dark_matter_temperature_virial = 'darkMatterOnlyTemperatureVirial'
+    dark_matter_velocity_virial = 'darkMatterOnlyVelocityVirial'
+    dark_matter_profile_dmo_radius_velocity_max = 'darkMatterProfileDMORadiusVelocityMaximum'
+    dark_matter_profile_dmo_velocity_max = 'darkMatterProfileDMOVelocityMaximum'
+    dark_matter_profile_scale = 'darkMatterProfileScale'
+    mass_halo_enclosed_current = 'massHaloEnclosedCurrent'
+    hierarchy_level_depth = 'nodeHierarchyLevelDepth'
+    hierarchy_level_maximum = 'nodeHierarchyLevelMaximum'
+    node_index = 'nodeIndex'
+    subsampling_weight = 'nodeSubsamplingWeight'
+    parent_index = 'parentIndex'
+    satellite_index = 'satelliteIndex'
+    satellite_velocity_x = 'satelliteVelocityX'
+    satellite_velocity_y = 'satelliteVelocityY'
+    satellite_velocity_z = 'satelliteVelocityZ'
+    satellite_tidal_field = 'satelliteTidalField'
+    satellite_tidal_heating_normalized = 'satelliteTidalHeatingNormalized'
+    sibling_index = 'siblingIndex'
+    spin_angular_momentum = 'spinAngularMomentum'
+    spin_angular_momentum_vector_x = 'spinAngularMomentumVectorX'
+    spin_angular_momentum_vector_y = 'spinAngularMomentumVectorY'
+    spin_angular_momentum_vector_z = 'spinAngularMomentumVectorZ'

subhaloscript-1.0.8/subscript/tracking.py

@@ -0,0 +1,81 @@
+import numpy as np
+import subscript.scripts.nfilters as nf
+from subscript.tabulatehdf5 import get_galacticus_outputs, tabulate_trees
+from subscript.scripts.nodes import nodedata
+from subscript.defaults import ParamKeys
+
+def track_subhalos(galacticus_out, nodeIndices, treeIndex,  param_keys = None):
+    """Extract time-series data for specified subhalo nodes across all Galacticus snapshots.
+    NOTE: To use this function, galacticus must be run with the nodeOperator indexShift.
+    Ie  
+    ```
+    <nodeOperator value="indexShift" />
+    ```
+
+    
+    Parameters
+    ----------
+    galacticus_out : h5py.File
+        Opened HDF5 file object containing Galacticus simulation output
+    nodeIndices : array-like
+        Array of node indices for subhalos to track
+    treeIndex : int
+        Index of the merger tree to extract data from
+    param_keys : list of str, optional
+        List of parameter keys to extract for each subhalo. If None, extracts all available keys
+        from the tree at the first snapshot
+    
+    Returns
+    -------
+    subhalo_data : dict
+        Nested dictionary with structure {node_id: {param_key: time_series_array, 'zsnap': redshift_array}}
+    zsnaps : ndarray
+        Array of redshifts at each snapshot (averaged over host halos)
+    """
+    snaps = np.flip(np.asarray(get_galacticus_outputs(galacticus_out)))
+
+    param_keys = param_keys if param_keys is not None else [_key for _key in tabulate_trees(galacticus_out, snaps[0])[treeIndex].keys()]
+
+    subhalo_data = {id : {key: np.zeros(len(snaps)) for key in param_keys} | {'zsnap' : np.zeros(len(snaps))} for id in nodeIndices}
+
+    zsnaps = np.zeros(len(snaps))
+
+    for j, isnap in enumerate(snaps):
+        snap = tabulate_trees(galacticus_out, isnap)[treeIndex]  
+        nd = nodedata(snap, key=param_keys)    
+
+        ids = nodedata(snap, 'nodeIndex')
+
+        zsnaps[j] = np.mean(nodedata(snap, ParamKeys.z_lastisolated, nfilter=nf.hosthalos))
+
+        for n, id in enumerate(ids):
+            if id not in nodeIndices:
+                continue 
+            for i, key in enumerate(param_keys):
+                subhalo_data[id][key][j] = nd[i][n]
+                        
+    return subhalo_data, zsnaps
+ 
+def track_subalo(subhalos_over_time, zsnaps, nodeindex, param_keys):
+    """Filter subhalo time-series data to retain only non-isolated, bound snapshots. 
+    Parameters
+    ----------
+    subhalos_over_time : dict
+        Nested dictionary output from track_subhalos containing time-series for each subhalo
+    zsnaps : ndarray
+        Array of redshifts at each snapshot
+    nodeindex : int
+        Node index of the subhalo to filter
+    param_keys : list of str
+        List of parameter keys to include in filtered output
+    
+    Returns
+    -------
+    filtered_data : dict
+        Dictionary with structure {param_key: filtered_time_series_array} where filtering removes
+        snapshots where the subhalo is isolated (is_isolated == 1) or has no bound mass (mass_bound <= 0)
+    filtered_zsnaps : ndarray
+        Filtered array of redshifts corresponding to non-isolated, bound snapshots
+    """
+    _filter = (subhalos_over_time[nodeindex][ParamKeys.is_isolated] == 0) & (subhalos_over_time[nodeindex][ParamKeys.mass_bound] > 0)
+    return {key: subhalos_over_time[nodeindex][key][_filter] for key in param_keys}, zsnaps[_filter]

{subhaloscript-1.0.7 → subhaloscript-1.0.8}/subscript/wrappers.py

@@ -169,7 +169,7 @@ def gscript(func):
             elif is_arraylike(nfilter):
                 _nodefilter = np.asarray(nfilter, dtype=bool)
             else:
-                TypeError("Unrecognized type provided to nodefilter")
+                raise TypeError("Unrecognized type provided to nodefilter")
 
             _nodestree_filtered = _nodestree.filter(_nodefilter)
 

subhaloscript-1.0.7/subscript/defaults.py

@@ -1,32 +0,0 @@
-class Meta():
-    cache = True
-    """If true, use custom code when reading hdf5 to cache read data."""
-    disableDepreciatedWarning = False
-
-class ParamKeys():
-    """Library of default galacticus parameters."""
-    x = 'positionOrbitalX'
-    y = 'positionOrbitalY'
-    z = 'positionOrbitalZ'
-    relx = 'satellitePositionX'
-    rely = 'satellitePositionY'
-    relz = 'satellitePositionZ'
-    mass = 'basicMass'
-    mass_bound = 'satelliteBoundMass'
-    rvir = 'darkMatterOnlyRadiusVirial'
-    mass_basic = 'basicMass'
-    is_isolated = 'nodeIsIsolated'
-    hierarchylevel = 'nodeHierarchyLevel'
-    sphere_radius = 'spheroidRadius'
-    sphere_anglularmomentum = 'spheroidAngularMomentum'
-    sphere_mass_stellar = 'spheroidMassStellar'
-    sphere_mass_gas = 'spheroidMassGas'
-    scale_radius = 'darkMatterProfileScaleRadius'
-    density_profile_radius = 'densityProfileRadius'
-    density_profile = 'densityProfile'
-    z_lastisolated = 'redshiftLastIsolated'
-    tnfw_rt = 'radiusTidalTruncationNFW'
-    tnfw_p0 = 'densityNormalizationTidalTruncationNFW'
-    custom_id = 'custom_id'
-    custom_tree_index = 'custom_node_tree'
-    custom_tree_outputorder = 'custom_node_outputorder'