improve format

baseprocessor.py

@@ -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 abc import ABCMeta, abstractmethod
-from tables import HDF5ExtError
+from functools import partial
 
-import pymses
 import numpy as np
-from numpy.polynomial.polynomial import polyfit
+import pymses
-from scipy.stats import linregress
+import tables
-
-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
 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,

fragdisk_galactica.py

@@ -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
 

gui.py

@@ -1,20 +1,28 @@
 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:
 
     # http://stackoverflow.com/questions/21654008/matplotlib-drag-overlapping-points-interactively
 
-    lock = None  #  only one can be animated at a time
+    lock = None  # only one can be animated at a time
 
     def __init__(self, parent, x=0.1, y=0.1, size=0.1):
 

ismfeed_galactica.py

@@ -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 :

mypool.py

@@ -7,7 +7,6 @@ import multiprocessing
 # multiprocessing module.
 import multiprocessing.pool
 import time
-
 from random import randint
 
 

pipeline.py

@@ -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()
 

plotter.py

@@ -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}
 
 

postprocessor.py

@@ -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

pp_params.py

@@ -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__))
 

pspec_new.py

@@ -1,25 +1,19 @@
 """Compute power spectra"""
 
-from __future__ import division
+from __future__ import division, print_function
-from __future__ import 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, tools
-from i_utils import args
+from numpy.fft import fftn, ifft
-from i_utils import tools
+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")

pspec_read.py

@@ -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

ramses_astrophysix.py

@@ -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)",

run_selector.py

@@ -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,