Add possibility to launch an external rule
+ some plotter improvements + some namelist improvements + add datacube extraction
This commit is contained in:
Noe Brucy
+69
-58
@@ -27,6 +27,7 @@ from pymses.analysis import (
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raytracing,
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slicing,
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splatting,
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cube3d,
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)
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from pymses.filters import CellsToPoints, RegionFilter
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from pymses.sources.hop.hop import HOP
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@@ -41,6 +42,7 @@ from baseprocessor import (
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HDF5Container,
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Rule,
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norm_getter,
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oct_norm_getter,
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simple_getter,
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vect_getter,
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oct_vect_getter,
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@@ -379,6 +381,14 @@ class SnapshotProcessor(HDF5Container):
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else:
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self.fil = None
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# Convert time unit
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if isinstance(unit_time, str):
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factor = self.get_nml(unit_time)
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unit_time = U.Unit(
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name=os.path.basename(unit_time),
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base_unit=self.info["unit_time"],
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coeff=factor)
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time_in_right_unit = self.time * self.info["unit_time"].express(unit_time)
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self.snapshot = Snapshot(
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name=str(self.num),
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@@ -636,6 +646,46 @@ class SnapshotProcessor(HDF5Container):
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""" Azimuthal velocity """
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return self.oct_getter_vect_phi(dset, "vel")
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def datacube(self, getter, level=None, unit=U.none):
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"""
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Return a datacube of the source box.
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Parameters
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----------
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getter : callable
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A callable that extract the wanted data from a pymses dataset
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unit : U.Unit
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Unit of the resulting dataset
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Returns
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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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operator = ScalarOperator(getter, unit)
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extractor = cube3d.CubeExtractor(self._amr, operator)
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if level is None:
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level = self.get_nml("amr_params/levelmin")
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size = 1.0
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cam = Camera(
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center=self.params.pymses.center,
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line_of_sight_axis="z",
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region_size=[size, size],
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distance=size / 2.0,
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far_cut_depth=size / 2.0,
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up_vector="y",
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map_max_size=2 ** level,
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)
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cube = extractor.process(
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cam, cube_size=1.0, resolution=2 ** level
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).data
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return cube
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def slice(self, getter, ax_los="z", z=0.0, unit=U.none):
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"""
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Slice process function.
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@@ -664,7 +714,8 @@ class SnapshotProcessor(HDF5Container):
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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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def ax_avg(self, getter, ax_los, unit=U.none, mass_weighted=True, surf_qty=False):
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def ax_avg(self, oct_getter, ax_los, unit=U.none, mass_weighted=True, surf_qty=False):
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"""
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Map of the average of a quantity (given by getter) along an axis (ax_los)
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Returns 2D array if getter returns a scalar quantity
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@@ -673,12 +724,12 @@ class SnapshotProcessor(HDF5Container):
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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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op = ScalarOperator(oct_getter, unit)
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else:
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if mass_weighted:
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def num(dset):
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value = getter(dset)
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value = oct_getter(dset)
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rho = getter_rho(dset)
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return rho * value
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@@ -688,7 +739,7 @@ class SnapshotProcessor(HDF5Container):
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else: # Volume weighted
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def num(dset):
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value = getter(dset)
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value = oct_getter(dset)
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return value
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def denum(dset):
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@@ -779,9 +830,11 @@ class SnapshotProcessor(HDF5Container):
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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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def vol_pdf(self, getter, bins=100, old_unit=None, unit=None, 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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if old_unit is not None and unit is not None:
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data *= old_unit.express(unit)
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if logbins:
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data = np.log10(data)
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weights = weight_func(self.cells)
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@@ -987,7 +1040,7 @@ class SnapshotProcessor(HDF5Container):
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dmap_omega = rt_omega.process(self._cam[ax_los]).map.T
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return dmap_omega
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def _toomreQ_disk(self, ax_los, omega_approx=True, G1_units=True, coarsen_factor=1):
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def _toomreQ_disk(self, ax_los, omega_approx=False, G1_units=False, coarsen_factor=1):
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"""
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Compute the Toomre Q parameter
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"""
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@@ -1347,6 +1400,8 @@ class SnapshotProcessor(HDF5Container):
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for key in header:
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if units[header.index(key)] == "m":
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df[key] = df[key] * self.info["unit_mass"].express(U.Msun)
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if "M" in df:
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df["msink"] = df["M"]
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else:
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header = [
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"id",
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@@ -1369,6 +1424,7 @@ class SnapshotProcessor(HDF5Container):
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"Teff",
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]
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df = pd.read_csv(csv_name, header=None, names=header)
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return {key: df[key].values for key in df}
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def _pspec(self, overwrite_file=False, **kwargs):
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@@ -1566,7 +1622,7 @@ class SnapshotProcessor(HDF5Container):
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# sort it and apply the sorting to the coordinates
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# this means that the particules of group 1 are written first then of group 2 etc...
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ind_sort = np.argsort(group_ids)
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cells_group = val_mat[ind_sort]
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cells_group = cells_group[ind_sort]
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cells_group[6] = group_ids[ind_sort]
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# Make it a pandas' DataFrame
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@@ -1587,14 +1643,12 @@ class SnapshotProcessor(HDF5Container):
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self.rules = {
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# Base rules
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"coldens": Rule(
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self,
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self._coldens,
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"Column density",
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"/maps",
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unit=self.info["unit_density"] * self.info["unit_length"],
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),
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"T_mwavg": Rule(
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self,
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partial(
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self.ax_avg,
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getter_T,
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@@ -1606,7 +1660,6 @@ class SnapshotProcessor(HDF5Container):
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unit=self.info["unit_pressure"] / self.info["unit_density"],
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),
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"omega_mwavg": Rule(
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self,
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partial(self._omega_average),
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"Ax mass-weighted averaged azimuthal of angular frequency",
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"/maps",
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@@ -1614,7 +1667,6 @@ class SnapshotProcessor(HDF5Container):
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/ (self.info["unit_length"] / self.lbox),
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),
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"alpha_disk": Rule(
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self,
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self._alpha_disk,
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"Map of the Shakura&Sunaev alpha parameter for disks",
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"/maps",
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@@ -1627,7 +1679,6 @@ class SnapshotProcessor(HDF5Container):
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],
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),
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"alpha_grav": Rule(
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self,
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self._alpha_grav,
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"Map of the graviational contrib to\
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Shakura&Sunaev alpha parameter for disks",
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@@ -1636,39 +1687,33 @@ class SnapshotProcessor(HDF5Container):
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dependencies=["avg_map_coldens", "avg_map_T_mwavg"],
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),
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"T": Rule(
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self,
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self._temperature,
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"Temperature slice",
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"/maps",
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dependencies=["slice_rho"],
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unit=self.info["unit_pressure"] / self.info["unit_density"],
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),
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"levels": Rule(
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self, self._levels, "Max level within line of sight", "/maps"
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"levels": Rule(self._levels, "Max level within line of sight", "/maps"
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),
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"jeans": Rule(
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self,
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self._jeans,
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"Jeans length slice",
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"/maps",
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dependencies=["slice_rho", "T"],
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),
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"jeans_ratio": Rule(
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self,
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self._jeans_ratio,
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"Jeans' length divided by the max resolution",
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"/maps",
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dependencies=["jeans", "levels"],
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),
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"Q": Rule(
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self,
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self._toomreQ_disk,
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"Toomre Q parameter for a Keplerian disk",
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"/maps",
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dependencies=["coldens", "T_mwavg", "omega_mwavg"],
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),
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"sinks": Rule(
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self,
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self._sinks,
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group="/datasets",
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unit={
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@@ -1702,20 +1747,17 @@ class SnapshotProcessor(HDF5Container):
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"vz_gas": "unit_velocity",
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},
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),
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"pspec": Rule(self, self._pspec, "Power spectrum", "/hdf5"),
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"write_particles": Rule(
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self, self._write_particles, "Particles file", "/hdf5"
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"pspec": Rule(self._pspec, "Power spectrum", "/hdf5"),
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"write_particles": Rule(self._write_particles, "Particles file", "/hdf5"
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),
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"write_cells": Rule(self, self._write_cells, "Cells file", "/hdf5"),
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"write_cells": Rule(self._write_cells, "Cells file", "/hdf5"),
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"filaments": Rule(
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self,
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self._filaments,
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"Filaments",
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"/datasets",
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dependencies={self.params.filaments.datamap: "z"},
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),
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"filaments_forces": Rule(
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self,
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self._filaments_forces,
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"Filaments",
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"/datasets",
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@@ -1730,14 +1772,12 @@ class SnapshotProcessor(HDF5Container):
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),
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# Helpers
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"radial_bins": Rule(
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self,
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self._radial_bins,
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"Radial bins",
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"/radial",
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unit=self.info["unit_length"] / self.lbox,
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),
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"radial_centers": Rule(
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self,
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self._radial_centers,
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"Centers of radial bins",
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"/radial",
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@@ -1745,21 +1785,18 @@ class SnapshotProcessor(HDF5Container):
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unit=self.info["unit_length"] / self.lbox,
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),
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"rr": Rule(
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self,
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self._rr,
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"Coordinate map",
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"/maps",
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unit=self.info["unit_length"] / self.lbox,
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),
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"bins_on_map": Rule(
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self,
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self._bins_on_map,
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"Convert map coordinates to bins",
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"/maps",
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dependencies=["radial_bins", "rr"],
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),
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"B_int": Rule(
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self,
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self._B_int,
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"Magnetic intensity slice",
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"/maps",
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@@ -1768,14 +1805,12 @@ class SnapshotProcessor(HDF5Container):
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),
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# PDF
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"rho_pdf": Rule(
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self,
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partial(self.vol_pdf, partial(simple_getter, "rho"), logbins=True),
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"Global rho-PDF",
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"/hist",
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unit=self.info["unit_density"],
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),
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"rho_pdf_mw": Rule(
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self,
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partial(
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self.vol_pdf,
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partial(simple_getter, "rho"),
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@@ -1787,14 +1822,12 @@ class SnapshotProcessor(HDF5Container):
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unit=self.info["unit_density"],
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),
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"T_pdf": Rule(
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self,
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partial(self.vol_pdf, getter_T, logbins=True),
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"Global T-PDF",
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"/hist",
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unit=self.info["unit_pressure"] / self.info["unit_density"],
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),
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"cos_pdf": Rule(
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self,
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partial(self.cos_vfluct_B),
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"Global cos fluctuation-PDF",
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"/hist",
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@@ -1802,14 +1835,12 @@ class SnapshotProcessor(HDF5Container):
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unit=U.none,
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),
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"Brho": Rule(
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self,
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self._Brho,
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"Average of B as a function of rho",
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"/datasets",
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unit={"rho": self.info["unit_density"], "B": self.info["unit_mag"]},
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),
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"Ek_Eb_rho": Rule(
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self,
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self._Ek_Eb_rho,
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"Average of Ek/Eb as a function of rho",
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"/datasets",
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@@ -1818,14 +1849,12 @@ class SnapshotProcessor(HDF5Container):
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),
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# Profiles
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"axis": Rule(
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self,
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partial(self._get_axis),
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"Axis",
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"/profile",
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unit=self.info["unit_length"],
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),
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"rho_prof": Rule(
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self,
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partial(self._plane_avg_uniform, partial(simple_getter, "rho")),
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"Rho profile",
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"/profile",
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@@ -1834,28 +1863,24 @@ class SnapshotProcessor(HDF5Container):
|
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),
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# globals
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"time_num": Rule(
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self,
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lambda: self.info["time"],
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"Time",
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"/globals",
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unit=self.info["unit_time"],
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),
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"mass": Rule(
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self,
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partial(self.sum, mass_func, mass_weighted=False),
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"Total mass",
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"/globals",
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unit=self.info["unit_density"] * self.info["unit_length"] ** 3,
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),
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"mwa_speed": Rule(
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self,
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partial(self.vol_avg, partial(simple_getter, "vel")),
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"Mass weighted speed average",
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"/globals",
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unit=self.info["unit_velocity"],
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),
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"mwa_sigma": Rule(
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self,
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self._mwa_sigma,
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"Mass weighted speed average",
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"/globals",
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@@ -1863,7 +1888,6 @@ class SnapshotProcessor(HDF5Container):
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unit=self.info["unit_velocity"],
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),
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"mwa_B_int": Rule(
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self,
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partial(self.vol_avg, getter_B_int),
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"Mass weighted Magnetic intensity average",
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"/globals",
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@@ -1888,7 +1912,6 @@ class SnapshotProcessor(HDF5Container):
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oct_getter = getter
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self.rules["slice_" + name] = Rule(
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self,
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partial(self.slice, getter, z=0.0, unit=unit),
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"{} slice".format(name),
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"/maps",
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@@ -1896,7 +1919,6 @@ class SnapshotProcessor(HDF5Container):
|
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)
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self.rules[name + "_mwavg"] = Rule(
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self,
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partial(self.ax_avg, oct_getter, mass_weighted=True, unit=unit),
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"Ax mass-weighted averaged {}".format(name),
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"/maps",
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@@ -1904,7 +1926,6 @@ class SnapshotProcessor(HDF5Container):
|
||||
)
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self.rules[name + "_avg"] = Rule(
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self,
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partial(self.ax_avg, oct_getter, mass_weighted=False, unit=unit),
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"Ax averaged {}".format(name),
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"/maps",
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@@ -1944,7 +1965,8 @@ class SnapshotProcessor(HDF5Container):
|
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# Norm
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generic_rule(
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field + "_norm", partial(norm_getter, field), self.unit_key[field]
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field + "_norm", partial(norm_getter, field), self.unit_key[field],
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oct_getter=partial(oct_norm_getter, field)
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)
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else:
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@@ -1958,7 +1980,6 @@ class SnapshotProcessor(HDF5Container):
|
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|
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self.rules["rad_avg_" + name] = Rule(
|
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self,
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partial(self._rad_avg, name),
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"Azimuthal average of {}".format(name),
|
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"/radial",
|
||||
@@ -1966,7 +1987,6 @@ class SnapshotProcessor(HDF5Container):
|
||||
unit=unit,
|
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)
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self.rules["rad_mwavg_" + name] = Rule(
|
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self,
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partial(self._rad_avg, name, mass_weighted=True),
|
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"Mass weighted azimuthal average of {}".format(name),
|
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"/radial",
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@@ -1974,7 +1994,6 @@ class SnapshotProcessor(HDF5Container):
|
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unit=unit,
|
||||
)
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self.rules["rad_avg_map_" + name] = Rule(
|
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self,
|
||||
partial(self._rad_avg_map, name),
|
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"Interpolated map of azimuthal average of {}".format(name),
|
||||
"/maps",
|
||||
@@ -1982,7 +2001,6 @@ class SnapshotProcessor(HDF5Container):
|
||||
unit=unit,
|
||||
)
|
||||
self.rules["rad_mwavg_map_" + name] = Rule(
|
||||
self,
|
||||
partial(self._rad_avg_map, name, mass_weighted=True),
|
||||
"Interpolated map of azimuthal average of {}".format(name),
|
||||
"/maps",
|
||||
@@ -1990,14 +2008,12 @@ class SnapshotProcessor(HDF5Container):
|
||||
unit=unit,
|
||||
)
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self.rules["fluct_" + name] = Rule(
|
||||
self,
|
||||
partial(self._fluct_map, name),
|
||||
"Fluctuation wrt to average of {}".format(name),
|
||||
"/maps",
|
||||
dependencies=[name, "rad_avg_map_" + name],
|
||||
)
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||||
self.rules["dispersion_rad_" + name] = Rule(
|
||||
self,
|
||||
partial(self._dispersion_rad, name),
|
||||
"radial RMS of {}".format(name),
|
||||
"/radial",
|
||||
@@ -2005,21 +2021,18 @@ class SnapshotProcessor(HDF5Container):
|
||||
unit=unit,
|
||||
)
|
||||
self.rules["mwfluct_" + name] = Rule(
|
||||
self,
|
||||
partial(self._fluct_map, name, mass_weigthed=True),
|
||||
"Fluctuation wrt to mass weighted average of {}".format(name),
|
||||
"/maps",
|
||||
dependencies=[name, "rad_mwavg_map_" + name],
|
||||
)
|
||||
self.rules["fluct_pdf_" + name] = Rule(
|
||||
self,
|
||||
partial(self._rad_fluct_pdf, name),
|
||||
"Probability density function of {} fluctuations".format(name),
|
||||
"/hist",
|
||||
dependencies=["rr", "fluct_" + name],
|
||||
)
|
||||
self.rules["fluct_mwpdf_" + name] = Rule(
|
||||
self,
|
||||
partial(self._rad_fluct_pdf, name, mass_weigthed=True),
|
||||
"Probability density function of {} mass weighted fluctuations".format(
|
||||
name
|
||||
@@ -2028,7 +2041,6 @@ class SnapshotProcessor(HDF5Container):
|
||||
dependencies=["rr", "mwfluct_" + name],
|
||||
)
|
||||
self.rules["fit_fluct_pdf_" + name] = Rule(
|
||||
self,
|
||||
partial(self._fit_pdf, name),
|
||||
"Fit the PDF of {} fluctuations".format(name),
|
||||
"/hist",
|
||||
@@ -2038,7 +2050,6 @@ class SnapshotProcessor(HDF5Container):
|
||||
unit_bin = self.rules[name_bin].unit
|
||||
if name_bin is not name:
|
||||
self.rules["mbb_" + name + "_" + name_bin] = Rule(
|
||||
self,
|
||||
partial(self.mean_by_bins, name_bin, name),
|
||||
"Mean of {} by bins of {}".format(name, name_bin),
|
||||
"/hist",
|
||||
|
||||
Reference in New Issue
Block a user