improve format

2020-12-14 16:05:04 +01:00
parent 1a7b33f662
commit 61da2aaa46
13 changed files with 134 additions and 132 deletions
@@ -1,37 +1,42 @@
 # coding: utf-8

-import sys
-import os
-import glob as glob
 import copy
+import glob as glob
+import os
+import subprocess
+import sys
 import time
-import tables
-from tables import HDF5ExtError
+from abc import ABCMeta, abstractmethod
+from functools import partial

-import pymses
 import numpy as np
-from numpy.polynomial.polynomial import polyfit
-from scipy.stats import linregress
-
-from pymses.sources.ramses import output
-from pymses.sources.hop.file_formats import *
-from pymses.analysis import Camera, raytracing, slicing, splatting
-from pymses.filters import CellsToPoints
-from pymses.analysis import ScalarOperator, FractionOperator, MaxLevelOperator
+import pymses
+import tables
 from astrophysix.simdm import SimulationStudy
 from astrophysix.simdm.experiment import (
-    Simulation,
    AppliedAlgorithm,
    ParameterSetting,
    ParameterVisibility,
+    Simulation,
 )
 from astrophysix.simdm.results import GenericResult, Snapshot
+from numpy.polynomial.polynomial import polyfit
+from pymses.analysis import (
+    Camera,
+    FractionOperator,
+    MaxLevelOperator,
+    ScalarOperator,
+    raytracing,
+    slicing,
+    splatting,
+)
+from pymses.filters import CellsToPoints
+from pymses.sources.hop.file_formats import *
+from pymses.sources.ramses import output
+from scipy.stats import linregress
+from tables import HDF5ExtError
+
 from ramses_astrophysix import ramses
-
-import subprocess
-from functools import partial
-from abc import ABCMeta, abstractmethod
-
 from run_selector import *
 from units import *

@@ -429,6 +434,15 @@ class HDF5Container(BaseProcessor):

        name = transform_name + "_" + rule_src_name

+        self.rules[name] = Rule(
+            self,
+            fn,
+            group=group,
+            unit=unit,
+            description=description,
+            dependencies=[rule_src_name],
+        )
+
    def apply(
        self,
        fn,
@@ -26,35 +26,36 @@
 # negotiate a specific contract with a legal representative of CEA.
 #
 from __future__ import print_function, unicode_literals
-import os
-import numpy as N
-import h5py

-from astrophysix.simdm import SimulationStudy, Project, ProjectCategory
+import datetime
+import os
+
+import h5py
+import numpy as N
+from astrophysix import units as U
+from astrophysix.simdm import Project, ProjectCategory, SimulationStudy
+from astrophysix.simdm.datafiles import Datafile, PlotInfo, PlotType
 from astrophysix.simdm.experiment import (
-    Simulation,
    AppliedAlgorithm,
    ParameterSetting,
    ParameterVisibility,
    ResolvedPhysicalProcess,
+    Simulation,
 )
 from astrophysix.simdm.protocol import (
-    SimulationCode,
-    AlgoType,
    Algorithm,
+    AlgoType,
    InputParameter,
    PhysicalProcess,
    Physics,
+    SimulationCode,
 )
 from astrophysix.simdm.results import GenericResult, Snapshot
-from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
 from astrophysix.utils.file import FileType
-from astrophysix import units as U
+from matplotlib import gridspec
+from mpl_toolkits.axes_grid1 import AxesGrid, Grid

 from plotter import *
-import datetime
-from mpl_toolkits.axes_grid1 import AxesGrid, Grid
-from matplotlib import gridspec

 P.rcParams["text.usetex"] = False

@@ -1,14 +1,22 @@
 import matplotlib as mpl
-import matplotlib.pyplot as plt
-from matplotlib.widgets import Slider, Button, RadioButtons, LassoSelector
-from matplotlib.widgets import SpanSelector, PolygonSelector, CheckButtons
 import matplotlib.patches as patches
+import matplotlib.pyplot as plt
 from matplotlib.lines import Line2D
 from matplotlib.path import Path
+from matplotlib.widgets import (
+    Button,
+    CheckButtons,
+    LassoSelector,
+    PolygonSelector,
+    RadioButtons,
+    Slider,
+    SpanSelector,
+)
 from scipy.stats import linregress
-from postprocessor import *
 from skimage.draw import line

+from postprocessor import *
+

 class DraggablePoint:

@@ -26,29 +26,30 @@
 # negotiate a specific contract with a legal representative of CEA.
 #
 from __future__ import print_function, unicode_literals
-import os
-import numpy as N

-from astrophysix.simdm import SimulationStudy, Project, ProjectCategory
+import os
+
+import numpy as N
+from astrophysix import units as U
+from astrophysix.simdm import Project, ProjectCategory, SimulationStudy
+from astrophysix.simdm.datafiles import Datafile, PlotInfo, PlotType
 from astrophysix.simdm.experiment import (
-    Simulation,
    AppliedAlgorithm,
    ParameterSetting,
    ParameterVisibility,
    ResolvedPhysicalProcess,
+    Simulation,
 )
 from astrophysix.simdm.protocol import (
-    SimulationCode,
-    AlgoType,
    Algorithm,
+    AlgoType,
    InputParameter,
    PhysicalProcess,
    Physics,
+    SimulationCode,
 )
 from astrophysix.simdm.results import GenericResult, Snapshot
-from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
 from astrophysix.utils.file import FileType
-from astrophysix import units as U

 # ----------------------------------------------- Project creation --------------------------------------------------- #
 # Available project categories are :
@@ -7,7 +7,6 @@ import multiprocessing
 # multiprocessing module.
 import multiprocessing.pool
 import time
-
 from random import randint


@@ -1,16 +1,17 @@
 # coding: utf-8

-import os
-import glob
-from shutil import copy
 import argparse
+import glob
+import os
 import time
-import numpy as np
 from functools import reduce
+from shutil import copy
+
+import numpy as np

-from pp_params import *
 from plotter import *
 from postprocessor import *
+from pp_params import *

 fake_pp = PostProcessor()

@@ -8,27 +8,30 @@ This is the plotter module.
@author Noé Brucy 2019-2020
 """

-import sys
 import os
+import sys
 from functools import partial
-import tables
-import numpy as np
-from scipy.stats import linregress
-from numpy.polynomial.polynomial import polyfit
-from scipy.ndimage.filters import gaussian_filter1d
-from scipy import optimize
-from astrophysix.simdm.datafiles import Datafile, PlotType, PlotInfo
-from astrophysix.utils.file import FileType
+
 import matplotlib as mpl
+import numpy as np
+import tables
+from astrophysix.simdm.datafiles import Datafile, PlotInfo, PlotType
+from astrophysix.utils.file import FileType
+from numpy.polynomial.polynomial import polyfit
+from scipy import optimize
+from scipy.ndimage.filters import gaussian_filter1d
+from scipy.stats import linregress

 if os.environ.get("DISPLAY", "") == "":
    print("No display found. Using non-interactive Agg backend")
    mpl.use("Agg")
-import pylab as P
-from comparator import *
-import pspec_read
 import datetime

+import pylab as P
+
+import pspec_read
+from comparator import *
+
 filetype_from_ext = {ext: ft for ft in FileType for ext in ft.extension_list}


@@ -1,13 +1,15 @@
 # coding: utf-8
+import pickle
+
+import astropy.units as u
 import pandas as pd
+import pymses.utils.regions as reg
+from fil_finder import FilFinder2D
+from pymses.filters import RegionFilter
+from skimage.morphology import medial_axis
+
 import pspec_new
 from baseprocessor import *
-import pymses.utils.regions as reg
-from pymses.filters import RegionFilter
-import astropy.units as u
-from fil_finder import FilFinder2D
-import pickle
-from skimage.morphology import medial_axis

 # Getters

@@ -82,6 +84,15 @@ def mean_by_bins(
    # For each cell, bin_number contains the number of the bins it belongs to
    bin_number = np.zeros(len(y))

+    # Go through the min value of x of each bin
+    for x_min in x_bins[1:-1]:
+        bin_number = bin_number + (x > x_min).astype(int)
+
+    # Compute the mean in each bin
+    y_mean = np.zeros(len(x_bins) - 1)
+    for i in range(len(y_mean)):
+        y_mean[i] = np.mean(y[bin_number == i])
+
    # Get the center of each bin
    if logbins:
        centers = 10 ** (0.5 * (np.log10(x_bins[1:]) + np.log10(x_bins[:-1])))
@@ -1044,14 +1055,6 @@ class PostProcessor(HDF5Container):
        alpha_g = (2.0 / 3) * alpha_g
        return alpha_g

-        alpha_g = self._ax_avg(getter_alpha_grav, "z", unit=cst.none, surf_qty=True) / (
-            coldens * T_avg
-        )
-
-        # alpha
-        alpha_g = (2.0 / 3) * alpha_g
-        return alpha_g
-
    def _sinks(self):
        csv_name = (
            self.path
@@ -1,10 +1,11 @@
 # coding: utf-8

-import numpy as np
-import re
-import munch
-import yaml
 import os
+import re
+
+import munch
+import numpy as np
+import yaml

 _dir_path = os.path.dirname(os.path.realpath(__file__))

@@ -1,25 +1,19 @@
 """Compute power spectra"""

-from __future__ import division
-from __future__ import print_function
+from __future__ import division, print_function

-from builtins import range
 import argparse
 import sys
 import textwrap
+from builtins import range

 import numpy as np
-from numpy.fft import fftn, ifft
-
 import pymses
-from pymses.analysis import ScalarOperator, Camera
-from pymses.analysis import cube3d
 import pymses.utils.misc
-
 import tables as T
-
-from i_utils import args
-from i_utils import tools
+from i_utils import args, tools
+from numpy.fft import fftn, ifft
+from pymses.analysis import Camera, ScalarOperator, cube3d

 __generator__ = "pspec_new.py"
 __version__ = "0.2"
@@ -434,37 +428,6 @@ parser = argparse.ArgumentParser(
            """
    ),
 )
-parser.add_argument("repo", help="RAMSES output repository", type=str, default=".")
-parser.add_argument("iouts", help="output numbers", type=args.selection, default=":")
-parser.add_argument(
-    "outfile", help="output file format (see below for fields)", type=str
-)
-parser.add_argument(
-    "-n",
-    "--nodename",
-    help="node name format (see below for fields)",
-    type=str,
-    default="/out_%(iout)05d/d%(dim)d/%(varname)s",
-)
-parser.add_argument(
-    "-O",
-    "--order",
-    help="byte order (= for native)",
-    type=str,
-    default="=",
-    choices=["<", ">", "="],
-)
-parser.add_argument(
-    "-c",
-    "--center",
-    help="coordinates of the center",
-    type=args.center,
-    default=[0.5, 0.5, 0.5],
-)
-parser.add_argument("-s", "--size", help="cube size", type=float, default=1.0)
-parser.add_argument(
-    "-l", "--level", help="cube level (default: levelMIN)", type=int, default=0
-)
 parser.add_argument(
    "repo", help="RAMSES output repository", type=str, default=".", nargs="?"
 )
@@ -617,6 +580,7 @@ def main(arg):
                % (clvl, read_lvl)
            )
            clvl = read_lvl
+
        # Degrade cubes ----------------------------------------------------------------
        if clvl < read_lvl:
            print("Degrade cubes")
@@ -1,8 +1,8 @@
 from builtins import str
-import tables as T
-import numpy as np
-import matplotlib.pyplot as P

+import matplotlib.pyplot as P
+import numpy as np
+import tables as T

 ################################################################
 # 3D
@@ -2,15 +2,14 @@


 from astrophysix.simdm.protocol import (
-    SimulationCode,
-    AlgoType,
    Algorithm,
+    AlgoType,
    InputParameter,
    PhysicalProcess,
    Physics,
+    SimulationCode,
 )

-
 # Simulation code definition  #
 ramses = SimulationCode(
    name="Ramses 3 (MHD)",
@@ -2,12 +2,14 @@
 # coding: utf-8


-import os
 import glob
+import os
 from functools import partial
-from pp_params import *
+
 import f90nml

+from pp_params import *
+

 class NamelistRecursive:
    def __init__(self, namelist):
@@ -107,7 +109,13 @@ class RunSelector:
                in_nums[run] = nums_temp

        for i, run in enumerate(self.runs):
-            self.nums[run] = self.get_nums(run, in_nums[run], time_min, time_max, time)
+            self.nums[run] = self.get_nums(
+                run,
+                in_nums[run],
+                time_min,
+                time_max,
+                time,
+            )

    def select(
        self,