Add filaments postproc, improve units detection, add automatic map rules, add selection
This commit is contained in:
+394
-72
@@ -4,16 +4,16 @@ import pspec_new
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from baseprocessor import *
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import pymses.utils.regions as reg
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from pymses.filters import RegionFilter
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import astropy.units as u
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from fil_finder import FilFinder2D
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import pickle
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from skimage.morphology import medial_axis
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# Getters
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def mass_func(dset):
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try:
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dx = dset["dx"]
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except:
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dx = dset.get_sizes()
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dx = dset["dx"]
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return dset["rho"] * dx ** 3 # Mass function
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@@ -47,7 +47,7 @@ def getter_rho(dset):
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def getter_v_norm(dset):
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v_norm = np.sqrt(np.sum(dset["Br"] ** 2, axis=1))
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v_norm = np.sqrt(np.sum(dset["vel"] ** 2, axis=1))
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return v_norm
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@@ -82,15 +82,6 @@ def mean_by_bins(
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# For each cell, bin_number contains the number of the bins it belongs to
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bin_number = np.zeros(len(y))
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# Go through the min value of x of each bin
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for x_min in x_bins[1:-1]:
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bin_number = bin_number + (x > x_min).astype(int)
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# Compute the mean in each bin
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y_mean = np.zeros(len(x_bins) - 1)
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for i in range(len(y_mean)):
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y_mean[i] = np.mean(y[bin_number == i])
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# Get the center of each bin
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if logbins:
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centers = 10 ** (0.5 * (np.log10(x_bins[1:]) + np.log10(x_bins[:-1])))
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@@ -100,6 +91,39 @@ def mean_by_bins(
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return centers, y_mean
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# Filament helpers
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def find_center(distance, skeleton, i_center, j_center, i, j):
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"""
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Given a distance array, find the cells at a center of a filament at a given postion
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"""
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if skeleton[i, j]:
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i_center[i, j], j_center[i, j] = i, j
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return i, j
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elif i_center[i, j] or j_center[i, j]:
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return i_center[i, j], j_center[i, j]
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else:
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i_neigh = np.array([i - 1, i, i + 1])
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i_neigh = i_neigh[(i_neigh > 0) & (i_neigh < distance.shape[0])]
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j_neigh = np.array([j - 1, j, j + 1])
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j_neigh = j_neigh[(j_neigh > 0) & (j_neigh < distance.shape[1])]
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ii_neigh, jj_neigh = np.meshgrid(i_neigh, j_neigh)
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d_neigh = distance[ii_neigh, jj_neigh]
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ind_max = np.unravel_index(np.argmax(d_neigh), d_neigh.shape)
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i_max, j_max = ii_neigh[ind_max], jj_neigh[ind_max]
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if i_max == i and j_max == j:
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i_center[i, j], j_center[i, j] = i, j
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else:
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i_center[i, j], j_center[i, j] = find_center(
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distance, skeleton, i_center, j_center, i_max, j_max
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)
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return i_center[i, j], j_center[i, j]
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# PostProcessor class
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class PostProcessor(HDF5Container):
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"""
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This class enable to compute and save derived quantities from the raw output
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@@ -110,6 +134,17 @@ class PostProcessor(HDF5Container):
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_axes_h = {"x": "y", "y": "x", "z": "x"} # Associated horizontal axe
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_axes_v = {"x": "z", "y": "z", "z": "y"} # Associated vertical axe
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# Pymses unit key of amr fiels
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unit_key = {
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"rho": "unit_density",
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"vel": "unit_velocity",
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"Br": "unit_mag",
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"Bl": "unit_mag",
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"P": "unit_pressure",
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"g": {"unit_gravpot": 1, "unit_length": -1},
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"phi": "unit_gravpot",
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}
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G = 1.0 # Gravitational constant
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cells_loaded = False
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@@ -238,6 +273,12 @@ class PostProcessor(HDF5Container):
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self.log_id = "[{}, {}] ".format(self.run, self.num)
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if os.path.exists(self.path_out + "/filaments.pickle"):
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with open(self.path_out + "/filaments.pickle", "rb") as f:
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self.fil = pickle.load(f)
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else:
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self.fil = None
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self.def_rules()
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def load_cells(self):
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@@ -290,22 +331,47 @@ class PostProcessor(HDF5Container):
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"""
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Returns the position in normalized units centered on the position of the star
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"""
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pos = dset.get_cell_centers()
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pos = dset.points
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pos = pos - (np.array(self.pp_params.disk.pos_star) / self.lbox)
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return pos
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def getter_vect_r(self, dset, name_vect):
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""" Radial component of a vector """
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r = self.getter_pos_disk(dset)[:, :, :2]
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r = self.getter_pos_disk(dset)[:, :2]
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ur = np.transpose((np.transpose(r) / np.sqrt(np.sum(r ** 2, axis=1))))
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return np.einsum("ij, ij -> i", dset[name_vect][:, :2], ur)
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def getter_vect_phi(self, dset, name_vect):
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""" Azimuthal component of a vector """
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r = self.getter_pos_disk(dset)[:, :2]
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r_norm = np.sqrt(np.sum(r ** 2, axis=1))
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rot = np.array([[0, -1], [1, 0]])
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uphi = np.transpose(np.einsum("ij, kj -> ik", rot, r) / r_norm)
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vect = dset[name_vect][:, :2]
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return np.einsum("ij,ij -> i", vect, uphi)
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def oct_getter_pos_disk(self, dset):
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"""
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Returns the position in normalized units centered on the position of the star
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"""
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pos = dset.get_cell_centers()
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pos = pos - (np.array(self.pp_params.disk.pos_star) / self.lbox)
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return pos
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def oct_getter_vect_r(self, dset, name_vect):
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""" Radial component of a vector """
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r = self.oct_getter_pos_disk(dset)[:, :, :2]
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ur = np.transpose(
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(np.transpose(r, (2, 0, 1)) / np.sqrt(np.sum(r ** 2, axis=2))), (1, 2, 0)
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)
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return np.einsum("ikj, ikj -> ik", dset[name_vect][:, :, :2], ur)
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def getter_vect_phi(self, dset, name_vect):
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def oct_getter_vect_phi(self, dset, name_vect):
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""" Azimuthal component of a vector """
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r = self.getter_pos_disk(dset)[:, :, :2]
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r = self.oct_getter_pos_disk(dset)[:, :, :2]
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r_norm = np.sqrt(np.sum(r ** 2, axis=2))
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rot = np.array([[0, -1], [1, 0]])
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uphi = np.transpose(np.einsum("ij, klj -> ikl", rot, r) / r_norm, (1, 2, 0))
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@@ -313,14 +379,14 @@ class PostProcessor(HDF5Container):
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return np.einsum("ikj,ikj -> ik", vect, uphi)
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def getter_vr(self, dset):
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return self.getter_vect_r(dset, "vel")
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def oct_getter_vr(self, dset):
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return self.oct_getter_vect_r(dset, "vel")
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def getter_vphi(self, dset):
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def oct_getter_vphi(self, dset):
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""" Azimuthal velocity """
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return self.getter_vect_phi(dset, "vel")
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return self.oct_getter_vect_phi(dset, "vel")
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def _slice(self, getter, ax_los="z", z=0, unit=cst.none):
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def _slice(self, getter, ax_los="z", z=0.0, unit=cst.none):
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"""
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Slice process function.
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Return a slice of the source box.
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@@ -343,6 +409,7 @@ class PostProcessor(HDF5Container):
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-------
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A numpy array containing the slice
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"""
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unit = self._get_units(unit)
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op = ScalarOperator(getter, unit)
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datamap = slicing.SliceMap(self._amr, self._cam[ax_los], op, z=z)
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return datamap.map.T
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@@ -356,6 +423,7 @@ class PostProcessor(HDF5Container):
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If surf_qty is set (projection mode), mass_weighted is ignored
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"""
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unit = self._get_units(unit)
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if surf_qty:
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op = ScalarOperator(getter, unit)
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else:
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@@ -405,6 +473,7 @@ class PostProcessor(HDF5Container):
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WARNING : This version only works on an uniform grid, need of a box version for AMR
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Returns 1D array if getter returns a scalar quantity
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"""
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unit = self._get_units(unit)
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self.load_cells()
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if isinstance(axis, str):
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axis = self._ax_nb[axis]
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@@ -426,10 +495,10 @@ class PostProcessor(HDF5Container):
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return df.groupby("axis").mean().values[:, 0]
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def _vol_avg(self, getter, mass_weighted=True):
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def _sum(self, getter, mass_weighted=True):
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"""
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Global volumic (or mass_weighted) average of the quantity returned by getter
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Returns a scalar (or a vctor if the quantity returned by getter is a getter, eg. speed)
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Global sum of the quantity returned by getter (variable must be extensive)
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Returns a scalar (or a vector if the quantity returned by getter is a getter, eg. speed)
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"""
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self.load_cells()
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value = getter(self.cells)
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@@ -444,6 +513,24 @@ class PostProcessor(HDF5Container):
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self.unload_cells()
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return data
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def _vol_avg(self, getter, mass_weighted=True):
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"""
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Global volumic (or mass_weighted) average of the quantity returned by getter
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Returns a scalar (or a vector if the quantity returned by getter is a getter, eg. speed)
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"""
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self.load_cells()
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value = getter(self.cells)
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if mass_weighted:
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weight = mass_func(self.cells)
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else:
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weight = vol_func(self.cells)
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# Transpose (.T) is for vectorial values
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data = np.sum((weight * value.T).T, axis=0) / np.sum(weight)
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if self.pp_params.process.unload_cells:
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self.unload_cells()
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return data
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def _vol_pdf(self, getter, bins=100, logbins=False, weight_func=vol_func):
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self.load_cells()
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data = getter(self.cells)
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@@ -656,7 +743,7 @@ class PostProcessor(HDF5Container):
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# Operator to compute the angular speed times rho
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def omega_rho_func(dset):
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pos = self.getter_pos_disk(dset)
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pos = self.oct_getter_pos_disk(dset)
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xx = pos[:, :, 0]
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yy = pos[:, :, 1]
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rc = np.sqrt(xx ** 2 + yy ** 2) # cylindrical radius
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@@ -743,9 +830,17 @@ class PostProcessor(HDF5Container):
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map_size = self.pp_params.pymses.map_size
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pos_star = self.pp_params.disk.pos_star
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x = np.linspace(im_extent[0], im_extent[1], map_size)
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y = np.linspace(im_extent[2], im_extent[3], map_size)
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# Physical size of cells
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dx = (im_extent[1] - im_extent[0]) / map_size
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dy = (im_extent[3] - im_extent[2]) / map_size
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# Physical coordinates of the center of the cells
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x = np.linspace(im_extent[0], im_extent[1], map_size) + 0.5 * dx
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y = np.linspace(im_extent[2], im_extent[3], map_size) + 0.5 * dy
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xx, yy = np.meshgrid(x, y)
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# Physical radius
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rr = np.sqrt((xx - pos_star[0]) ** 2 + (yy - pos_star[1]) ** 2)
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return rr
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@@ -810,14 +905,17 @@ class PostProcessor(HDF5Container):
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fluct_map = self.save.get_node("/maps/fluct_" + name + "_" + ax_los).read()
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rr = self.save.get_node("/maps/rr_" + ax_los).read()
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mask_pdf = (rr > self.pp_params.disk.rmin_pdf) & (
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rr < self.pp_params.disk.rmax_pdf
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mask_pdf = (
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(rr > self.pp_params.disk.rmin_pdf)
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& (rr < self.pp_params.disk.rmax_pdf)
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& (fluct_map > 0)
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)
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nb_cells = np.sum(mask_pdf.flatten())
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values, edges = np.histogram(
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np.log10(fluct_map[mask_pdf].flatten()),
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self.pp_params.pdf.nb_bin,
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range=self.pp_params.pdf.range,
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weights=np.ones(nb_cells) / nb_cells,
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)
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centers = 0.5 * (edges[1:] + edges[:-1])
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@@ -848,7 +946,7 @@ class PostProcessor(HDF5Container):
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# Mean part
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T_avg = self.save.get_node("/maps/avg_map_T_avg_z").read()
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T_avg = self.save.get_node("/maps/avg_map_T_mwavg_z").read()
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radial_bins = self.save.get_node("/radial/radial_bins_" + ax_los).read()
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mean_bin_vr = self.save.get_node(
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@@ -862,7 +960,9 @@ class PostProcessor(HDF5Container):
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# Fluct part
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def getter_alpha_num(dset):
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r = np.sqrt(np.sum((self.lbox * self.getter_pos_disk(dset)) ** 2, axis=2))
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r = np.sqrt(
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np.sum((self.lbox * self.oct_getter_pos_disk(dset)) ** 2, axis=2)
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)
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bins = np.zeros(r.shape, dtype=int)
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for r0 in radial_bins[1:]:
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@@ -871,8 +971,8 @@ class PostProcessor(HDF5Container):
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vr_mean = mean_bin_vr[bins]
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vphi_mean = mean_bin_vphi[bins]
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vr = self.getter_vr(dset)
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vphi = self.getter_vphi(dset)
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vr = self.oct_getter_vr(dset)
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vphi = self.oct_getter_vphi(dset)
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alpha = (vphi - vphi_mean) * (vr - vr_mean)
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return alpha
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@@ -889,15 +989,15 @@ class PostProcessor(HDF5Container):
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"Map of the gravitational contribution to the Shakura&Sunaev alpha parameter for disks"
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assert ax_los == "z"
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T_avg = self.save.get_node("/maps/avg_map_T_avg_z").read()
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T_avg = self.save.get_node("/maps/avg_map_T_mwavg_z").read()
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coldens = self.save.get_node("/maps/avg_map_coldens_z").read()
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def getter_alpha_grav(dset):
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r2 = np.sum((self.lbox * self.getter_pos_disk(dset)) ** 2, axis=2)
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r2 = np.sum((self.lbox * self.oct_getter_pos_disk(dset)) ** 2, axis=2)
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e2 = (1.0 / 256.0) ** 2
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gstar = -self.G * self.pp_params.disk.mass_star / (e2 + r2)
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gr = self.getter_vect_r(dset, "g") - gstar
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gphi = self.getter_vect_phi(dset, "g")
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gr = self.oct_getter_vect_r(dset, "g") - gstar
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gphi = self.oct_getter_vect_phi(dset, "g")
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return gr * gphi / (4 * np.pi * self.G)
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alpha_g = self._ax_avg(getter_alpha_grav, "z", unit=cst.none, surf_qty=True) / (
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@@ -908,6 +1008,14 @@ class PostProcessor(HDF5Container):
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alpha_g = (2.0 / 3) * alpha_g
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return alpha_g
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alpha_g = self._ax_avg(getter_alpha_grav, "z", unit=cst.none, surf_qty=True) / (
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coldens * T_avg
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)
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# alpha
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alpha_g = (2.0 / 3) * alpha_g
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return alpha_g
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def _sinks(self):
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csv_name = (
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self.path
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@@ -950,7 +1058,139 @@ class PostProcessor(HDF5Container):
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def _pspec(self):
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outfile = self.path_out + "/pspec.h5"
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pspec_new.pspec(repo=self.path, iouts=[self.num], outfile=outfile)
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return outfile
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return True
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def _filaments(self):
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datamap_name = self.pp_params.filaments.datamap
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verbose = self.pp_params.filaments.verbose
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rmin_frac = self.pp_params.filaments.rmin
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rmax_frac = self.pp_params.filaments.rmax
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size_thresh = self.pp_params.filaments.size_thresh
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skel_thresh = self.pp_params.filaments.skel_thresh
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branch_thresh = self.pp_params.filaments.branch_thresh
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glob_thresh = self.pp_params.filaments.glob_thresh
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datamap = self.save.get_node("/maps/" + datamap_name + "_z").read()
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shape = datamap.shape
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x = np.arange(shape[0]) - shape[0] / 2
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y = np.arange(shape[1]) - shape[1] / 2
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xx, yy = np.meshgrid(x, y)
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rr = np.sqrt(xx ** 2 + yy ** 2)
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rmin = int(rmin_frac * shape[0])
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rmax = int(rmax_frac * shape[0])
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mask = (rr >= rmin) & (rr <= rmax)
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datamap[np.logical_not(mask)] = np.nan
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self.fil = FilFinder2D(datamap, distance=1 * u.cm, beamwidth=1 * u.pix)
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self.fil.preprocess_image(flatten_percent=95)
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self.fil.create_mask(
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verbose=verbose,
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||||
smooth_size=1 * u.pix,
|
||||
adapt_thresh=2 * u.pix,
|
||||
size_thresh=size_thresh * u.pix ** 2,
|
||||
glob_thresh=glob_thresh,
|
||||
)
|
||||
self.fil.medskel(verbose=verbose)
|
||||
self.fil.analyze_skeletons(
|
||||
skel_thresh=skel_thresh * u.pix,
|
||||
branch_thresh=branch_thresh * u.pix,
|
||||
relintens_thresh=0.1,
|
||||
)
|
||||
self.fil.exec_rht()
|
||||
self.fil.find_widths()
|
||||
|
||||
outfile = self.path_out + "/filaments.pickle"
|
||||
with open(outfile, "wb") as f:
|
||||
pickle.dump(self.fil, f, pickle.HIGHEST_PROTOCOL)
|
||||
return True
|
||||
|
||||
def _filaments_center(self):
|
||||
"""
|
||||
Fill an array with center postion for each cell in a filament
|
||||
"""
|
||||
fil = self.fil
|
||||
mask = fil.mask.copy()
|
||||
_, distance = medial_axis(mask, return_distance=True)
|
||||
skel = fil.skeleton
|
||||
i_center = np.zeros(distance.shape, dtype=int)
|
||||
j_center = np.zeros(distance.shape, dtype=int)
|
||||
x_mask, y_mask = np.where(mask)
|
||||
for k in range(len(x_mask)):
|
||||
find_center(distance, skel, i_center, j_center, x_mask[k], y_mask[k])
|
||||
return np.stack([i_center, j_center])
|
||||
|
||||
def _filaments_forces(self):
|
||||
"""
|
||||
Compute forces within a filament (for disks)
|
||||
"""
|
||||
|
||||
GM = self.G * self.pp_params.disk.mass_star # Mass parameter
|
||||
|
||||
# Get mask for filaments
|
||||
fil = self.fil
|
||||
mask_fil = np.asarray(fil.mask.copy(), dtype=bool)
|
||||
|
||||
# Find center of filaments
|
||||
i_center, j_center = self._filaments_center()
|
||||
|
||||
# Get slices and projections at z = 0
|
||||
vphi = self.save.get_node("/maps/slice_velphi_z").read()
|
||||
gr = self.save.get_node("/maps/slice_gr_z").read()
|
||||
Pz = self.save.get_node("/maps/slice_P_z").read()
|
||||
coldens = self.save.get_node("/maps/coldens_z").read()
|
||||
vr = self.save.get_node("/maps/slice_velr_z").read()
|
||||
|
||||
# Get coordinates
|
||||
im_extent = np.array(self.save.root.maps._v_attrs.im_extent) * self.lbox
|
||||
map_size = self.pp_params.pymses.map_size
|
||||
pos_star = self.pp_params.disk.pos_star
|
||||
|
||||
# Physical size of cells
|
||||
dx = (im_extent[1] - im_extent[0]) / map_size
|
||||
dy = (im_extent[3] - im_extent[2]) / map_size
|
||||
|
||||
# Physical coordinates of the center of the cells
|
||||
x = np.linspace(im_extent[0], im_extent[1], map_size) + 0.5 * dx
|
||||
y = np.linspace(im_extent[2], im_extent[3], map_size) + 0.5 * dy
|
||||
|
||||
xx, yy = np.meshgrid(x, y)
|
||||
rr = np.sqrt((xx - pos_star[0]) ** 2 + (yy - pos_star[1]) ** 2)
|
||||
|
||||
# Rotational support
|
||||
R = vphi ** 2 / rr
|
||||
|
||||
# Equilibrium
|
||||
Gvrx, Gvry = np.gradient(vr)
|
||||
gradvr = (xx * Gvrx + yy * Gvry) / rr
|
||||
dvr = gradvr + vr * gradvr # Complete derivative
|
||||
|
||||
# Thermal support
|
||||
GPx, GPy = np.gradient(Pz)
|
||||
gradPr = (xx * GPx + yy * GPy) / rr
|
||||
fP = gradPr / coldens
|
||||
|
||||
# Gravitational field
|
||||
e2 = (1.0 / 512) ** 2
|
||||
gstar = -GM / (rr ** 2 + e2)
|
||||
|
||||
# Substract gravitational field from the star
|
||||
Rdisk = R + gstar
|
||||
gdisk = gr - gstar
|
||||
|
||||
# Forces at the center of filaments
|
||||
Rdisk_center = Rdisk[i_center, j_center]
|
||||
gr_center = gdisk[i_center, j_center]
|
||||
fP_center = fP[i_center, j_center]
|
||||
dvr_center = dvr[i_center, j_center]
|
||||
|
||||
# Forces for the filaments equilibrium
|
||||
Rfil = Rdisk - Rdisk_center
|
||||
gfil = gdisk - gr_center
|
||||
fPfil = fP - fP_center
|
||||
dvr_fil = dvr - dvr_center
|
||||
|
||||
return {"gfil": gfil, "Rfil": Rfil, "fPfil": fPfil, "dvr": dvr_fil}
|
||||
|
||||
def def_rules(self):
|
||||
|
||||
@@ -967,7 +1207,7 @@ class PostProcessor(HDF5Container):
|
||||
self,
|
||||
partial(
|
||||
self._ax_avg,
|
||||
self.getter_vr,
|
||||
self.oct_getter_vr,
|
||||
mass_weighted=True,
|
||||
unit=self.info["unit_velocity"],
|
||||
),
|
||||
@@ -979,7 +1219,7 @@ class PostProcessor(HDF5Container):
|
||||
self,
|
||||
partial(
|
||||
self._ax_avg,
|
||||
self.getter_vphi,
|
||||
self.oct_getter_vphi,
|
||||
mass_weighted=True,
|
||||
unit=self.info["unit_velocity"],
|
||||
),
|
||||
@@ -987,31 +1227,7 @@ class PostProcessor(HDF5Container):
|
||||
"/maps",
|
||||
unit=self.info["unit_velocity"],
|
||||
),
|
||||
"rho_avg": Rule(
|
||||
self,
|
||||
partial(
|
||||
self._ax_avg,
|
||||
getter_rho,
|
||||
mass_weighted=False,
|
||||
unit=self.info["unit_density"],
|
||||
),
|
||||
"Ax mass-weighted averaged azimuthal density",
|
||||
"/maps",
|
||||
unit=self.info["unit_density"],
|
||||
),
|
||||
"P_avg": Rule(
|
||||
self,
|
||||
partial(
|
||||
self._ax_avg,
|
||||
getter_P,
|
||||
mass_weighted=True,
|
||||
unit=self.info["unit_pressure"],
|
||||
),
|
||||
"Ax mass-weighted averaged azimuthal pressure",
|
||||
"/maps",
|
||||
unit=self.info["unit_pressure"],
|
||||
),
|
||||
"T_avg": Rule(
|
||||
"T_mwavg": Rule(
|
||||
self,
|
||||
partial(
|
||||
self._ax_avg,
|
||||
@@ -1031,7 +1247,7 @@ class PostProcessor(HDF5Container):
|
||||
unit=cst.none,
|
||||
dependencies=[
|
||||
"avg_map_rho_avg",
|
||||
"avg_map_T_avg",
|
||||
"avg_map_T_mwavg",
|
||||
"avg_map_vr",
|
||||
"avg_map_vphi",
|
||||
],
|
||||
@@ -1043,7 +1259,7 @@ class PostProcessor(HDF5Container):
|
||||
Shakura&Sunaev alpha parameter for disks",
|
||||
"/maps",
|
||||
unit=cst.none,
|
||||
dependencies=["avg_map_coldens", "avg_map_T_avg"],
|
||||
dependencies=["avg_map_coldens", "avg_map_T_mwavg"],
|
||||
),
|
||||
"rho": Rule(
|
||||
self,
|
||||
@@ -1139,6 +1355,27 @@ class PostProcessor(HDF5Container):
|
||||
},
|
||||
),
|
||||
"pspec": Rule(self, self._pspec, "Power spectrum", "/hdf5"),
|
||||
"filaments": Rule(
|
||||
self,
|
||||
self._filaments,
|
||||
"Filaments",
|
||||
"/datasets",
|
||||
dependencies={self.pp_params.filaments.datamap: "z"},
|
||||
),
|
||||
"filaments_forces": Rule(
|
||||
self,
|
||||
self._filaments_forces,
|
||||
"Filaments",
|
||||
"/datasets",
|
||||
dependencies={
|
||||
"filaments": None,
|
||||
"slice_velphi": "z",
|
||||
"slice_gr": "z",
|
||||
"slice_P": "z",
|
||||
"coldens": "z",
|
||||
"slice_velr": "z",
|
||||
},
|
||||
),
|
||||
# Helpers
|
||||
"radial_bins": Rule(self, self._radial_bins, "Radial bins", "/radial"),
|
||||
"rr": Rule(self, self._rr, "Coordinate map", "/maps"),
|
||||
@@ -1165,6 +1402,18 @@ class PostProcessor(HDF5Container):
|
||||
"/hist",
|
||||
unit=self.info["unit_density"],
|
||||
),
|
||||
"rho_pdf_mw": Rule(
|
||||
self,
|
||||
partial(
|
||||
self._vol_pdf,
|
||||
partial(simple_getter, "rho"),
|
||||
weight_func=mass_func,
|
||||
logbins=True,
|
||||
),
|
||||
"Global rho-PDF",
|
||||
"/hist",
|
||||
unit=self.info["unit_density"],
|
||||
),
|
||||
"T_pdf": Rule(
|
||||
self,
|
||||
partial(self._vol_pdf, getter_T, logbins=True),
|
||||
@@ -1226,6 +1475,13 @@ class PostProcessor(HDF5Container):
|
||||
"/globals",
|
||||
unit=self.info["unit_time"],
|
||||
),
|
||||
"mass": Rule(
|
||||
self,
|
||||
partial(self._sum, mass_func),
|
||||
"Total mass",
|
||||
"/globals",
|
||||
unit=self.info["unit_density"] * self.info["unit_length"] ** 3,
|
||||
),
|
||||
"mwa_speed": Rule(
|
||||
self,
|
||||
partial(self._vol_avg, partial(simple_getter, "vel")),
|
||||
@@ -1261,7 +1517,8 @@ class PostProcessor(HDF5Container):
|
||||
"rho_avg",
|
||||
"P_avg",
|
||||
"T_avg",
|
||||
"alpha_disk",
|
||||
"P_mwavg",
|
||||
"T_mwavg" "alpha_disk",
|
||||
"alpha_grav",
|
||||
]
|
||||
for name in averageables:
|
||||
@@ -1312,7 +1569,72 @@ class PostProcessor(HDF5Container):
|
||||
dependencies=[name, name_bin],
|
||||
)
|
||||
|
||||
self._gen_rule_transform("fluct_coldens", np.max, "max", group="/globals")
|
||||
self._gen_rule_transform("fluct_coldens", np.nanmax, "max", group="/globals")
|
||||
|
||||
# Generic rules directly from Ramses fields
|
||||
for field in self.pp_params.pymses.variables:
|
||||
|
||||
def generic_rule(name, getter, unit, oct_getter=None):
|
||||
if oct_getter is None:
|
||||
oct_getter = getter
|
||||
|
||||
self.rules["slice_" + name] = Rule(
|
||||
self,
|
||||
partial(self._slice, getter, z=0.0, unit=unit),
|
||||
"{} slice".format(name),
|
||||
"/maps",
|
||||
unit=unit,
|
||||
)
|
||||
|
||||
self.rules[name + "_mwavg"] = Rule(
|
||||
self,
|
||||
partial(self._ax_avg, oct_getter, mass_weighted=True, unit=unit),
|
||||
"Ax mass-weighted averaged {}".format(name),
|
||||
"/maps",
|
||||
unit=unit,
|
||||
)
|
||||
|
||||
self.rules[name + "_avg"] = Rule(
|
||||
self,
|
||||
partial(self._ax_avg, oct_getter, mass_weighted=False, unit=unit),
|
||||
"Ax averaged {}".format(name),
|
||||
"/maps",
|
||||
unit=unit,
|
||||
)
|
||||
|
||||
# special for vectors
|
||||
if field in ["g", "vel"]:
|
||||
# Components
|
||||
for i, dir in enumerate(["x", "y", "z"]):
|
||||
generic_rule(
|
||||
field + dir,
|
||||
partial(vect_getter, field, i),
|
||||
self.unit_key[field],
|
||||
)
|
||||
|
||||
# Radial
|
||||
generic_rule(
|
||||
field + "r",
|
||||
partial(self.getter_vect_r, name_vect=field),
|
||||
self.unit_key[field],
|
||||
oct_getter=self.oct_getter_vect_r,
|
||||
)
|
||||
|
||||
# Othoradial
|
||||
generic_rule(
|
||||
field + "phi",
|
||||
partial(self.getter_vect_phi, name_vect=field),
|
||||
self.unit_key[field],
|
||||
oct_getter=self.oct_getter_vect_phi,
|
||||
)
|
||||
|
||||
# Norm
|
||||
generic_rule(
|
||||
field + "_norm", partial(norm_getter, field), self.unit_key[field]
|
||||
)
|
||||
|
||||
else:
|
||||
generic_rule(field, partial(simple_getter, field), self.unit_key[field])
|
||||
|
||||
super(PostProcessor, self).def_rules()
|
||||
|
||||
|
||||
Reference in New Issue
Block a user