Rename pytools to analysator

Documentation/components/mayavi/mayavi_usage.tex

@@ -71,7 +71,7 @@
 \section{Plotting the grid}
 
 \begin{python}
-import pytools as pt
+import analysator as pt
 f = pt.vlsvfile.VlsvReader('bulk.0000872.vlsv')
 grid = pt.grid.MayaviGrid(f, 'rho')
 \end{python}

Documentation/examples/example1.py

@@ -21,7 +21,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 # 
 
-import pytools as pt
+import analysator as pt
 
 f = pt.vlsvfile.VlasiatorReader('fullf.0000002.vlsv')
 grid = pt.grid.Particlepusherinterface(f, 'rho')

Documentation/installation/installation.tex

@@ -46,7 +46,7 @@ \section{Testing installation}
 \begin{verbatim}
 cd ~/analysator
 ipython
-import pytools as pt
+import analysator as pt
 \end{verbatim}
 
 The full input/output should look like this (if the installation fails, the import command should 
@@ -63,7 +63,7 @@ \section{Testing installation}
 help -> Python's own help system.
 object? -> Details about 'object', use 'object??' for extra details.
 
-In [1]: import pytools as pt
+In [1]: import analysator as pt
 
 In [2]: 
 

Documentation/particle_pusher/particlepusher.tex

@@ -34,7 +34,7 @@ \section{Using the particle pusher interface}
 \begin{verbatim}
 ipython
 
-In [2]: import pytools as pt
+In [2]: import analysator as pt
 
 In [3]: f = pt.vlsvfile.VlasiatorReader('bulk.0001480.vlsv')
 

Documentation/presentations/analysator.tex

@@ -111,7 +111,7 @@ \section{Introduction}
  \begin{python}[basicstyle=\tiny]
  # We are interested in reading data from the cell whose ID is 75
 
- import pytools as pt # Import Analysator
+ import analysator as pt # Import Analysator
 
  # Open a vlsv file for reading
  vlsvReader = pt.vlsvfile.VlsvReader('bulk.0003710.vlsv')
@@ -163,7 +163,7 @@ \section{Concepts}
 
  \begin{python}[basicstyle=\tiny]
  # Import analysator
- import pytools as pt
+ import analysator as pt
 
  vlsvReader = pt.vlsvfile.VlsvReader('test.vlsv') #What?
 
@@ -189,7 +189,7 @@ \section{Concepts}
  \frametitle{Navigation (the \emph{most} important part)}
  \begin{python}[basicstyle=\tiny]
  # Import analysator
- import pytools as pt
+ import analysator as pt
 
  pt.
  \end{python}
@@ -205,7 +205,7 @@ \section{Concepts}
  \frametitle{Navigation (the \emph{most} important part)}
  \begin{python}[basicstyle=\tiny]
  # Import analysator
- import pytools as pt
+ import analysator as pt
 
  pt.calculations.
  \end{python}
@@ -227,7 +227,7 @@ \section{Concepts}
  \frametitle{Navigation (the \emph{most} important part)}
  \begin{python}[basicstyle=\tiny]
  # Import analysator
- import pytools as pt
+ import analysator as pt
 
  pt.calculations.cut_through?
  \end{python}
@@ -287,7 +287,7 @@ \section{Basics}
  \frametitle{Basic usage}
  \begin{python}[basicstyle=\tiny]
  # Import analysator
- import pytools as pt
+ import analysator as pt
 
  # Open a vlsv file
  vlsvReader = pt.vlsvfile.VlsvReader('test.vlsv')
@@ -384,7 +384,7 @@ \section{Plotting}
  Plotting can be done simply by feeding a vlsv file to the grid class as follows:
  \begin{python}[basicstyle=\tiny]
  # Import Analysator
- import pytools as pt
+ import analysator as pt
 
  # Open a vlsv file
  vlsvReader = pt.vlsvfile.VlsvReader('test.vlsv')
@@ -532,7 +532,7 @@ \section{Hands-on}
  \frametitle{Example from \emph{calculations}}
  \begin{python}[basicstyle=\tiny]
  # Import analysator
- import pytools as pt
+ import analysator as pt
 
  # Open a vlsv file
  vlsvReader = pt.vlsvfile.vlsvReader('testfile.vlsv')

README

@@ -13,7 +13,7 @@ echo "export PYTHONPATH=$PYTHONPATH:$HOME/analysator" >> $HOME/.bashrc
 #################################################
 module load mayavi2 # Load mayavi2 dependencies, if necessary (e.g. CSC system)
 ipython # Start ipython
-import pytools as pt # Import Analysator
+import analysator as pt # Import Analysator
 
 
 # Navigating functions:

examples/generate_panel.py

@@ -31,7 +31,7 @@
 # passed to a job submission system for generating a multitude of frames
 # via e.g. array jobs.
 
-import pytools as pt
+import analysator as pt
 import sys, os, socket
 import numpy as np
 

examples/multi_panel_plot.py

@@ -1,4 +1,4 @@
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 import colormaps as cmaps

miscellaneous/miscellaneous.py

@@ -28,7 +28,7 @@
 
  .. code-block:: python
 
- import pytools as pt
+ import analysator as pt
  pt.miscellaneous.
  #press tab -> get the functions
 

miscellaneous/slams.py

@@ -22,7 +22,7 @@
 # 
 
 import numpy as np
-import pytools as pt
+import analysator as pt
 import os
 import copy
 import matplotlib.pyplot as plt

miscellaneous/vtkwriter.py

@@ -33,7 +33,7 @@ def write_vtk_file( filename, point_data ):
  .. code-block:: python
 
  # Example usage:
- import pytools as pt
+ import analysator as pt
  filename = "test.vtk"
  point_data = [[0.,0.,0.], [1.,1.,1.], [2.,2.,2.], [3.,3.,3.], [4.,4.,4.]]
  pt.miscellaneous.write_vtk_file( filename=filename, point_data=point_data )

pyCalculations/calculations.py

@@ -24,7 +24,7 @@
 ''' This is a module that includes most, if not all, calculations within the analysator. Please type "." and press tab to see which functions this module includes.
 
 Example:
-import pytools as pt
+import analysator as pt
 
 pt.calculations.
 #press tab

pyCalculations/cut3d.py

@@ -45,7 +45,7 @@ def cut3d( vlsvReader, xmin, xmax, ymin, ymax, zmin, zmax, variable, operator="p
  .. code-block:: python
 
  Example:
- import pytools as pt
+ import analysator as pt
  f = pt.vlsvfile.VlsvReader('example.vlsv')
  three_cut = pt.calculations.cut3d( vlsvReader=f, xmin=1e6, xmax=4e6, ymin=1e6, xmax=4e6, zmin=0, zmax=0, variable="rho" )
  import numpy as np

pyCalculations/fieldtracer.py

@@ -23,7 +23,7 @@
 
 import numpy as np
 import scipy as sp
-import pytools as pt
+import analysator as pt
 from scipy import interpolate
 
 def dynamic_field_tracer( vlsvReader_list, x0, max_iterations, dx):

pyCalculations/intpol_file.py

@@ -21,7 +21,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 # 
 
-import pytools as pt
+import analysator as pt
 import numpy as np
 
 def vlsv_intpol_file(file_vlsv,file_orbit,varlist,file_output):
@@ -33,7 +33,7 @@ def vlsv_intpol_file(file_vlsv,file_orbit,varlist,file_output):
  :returns: none
  .. code-block:: python
  # Example:
- import pytools as pt
+ import analysator as pt
  pt.calculations.vlsv_intpol_file("state00040000.vlsv","orbit.dat",["cellB","n_H+sw_ave"],"output.dat")
  '''
  f=pt.vlsvfile.VlsvReader(file_name=file_vlsv)

pyCalculations/intpol_points.py

@@ -35,7 +35,7 @@ def vlsv_intpol_points(vlsvReader,points,varlist,operator="pass",interpolation_o
  :returns: A tuple with output: (coordinates,variable_values,header_string)
  .. code-block:: python
  # Example:
- import pytools as pt
+ import analysator as pt
  import numpy as np
  f=pt.vlsvfile.VlsvReader(file_name="state00040000.vlsv")
  mesh_limits = f.get_spatial_mesh_extent()

pyCalculations/lineout.py

@@ -43,7 +43,7 @@ def lineout( vlsvReader, point1, point2, variable, operator="pass",interpolation
  .. code-block:: python
 
  # Example:
- import pytools as pt # import analysator
+ import analysator as pt # import analysator
 
  vlsvReader = pt.vlsvfile.VlsvReader(\"testfile.vlsv\") # Open a vlsv file
  lineout_rho = pt.calculations.lineout( vlsvReader=vlsvReader, point1=[1.0e5, 1.0e6, 0], point2=[2.0e5, 2.0e6, 0], variable="rho", interpolation_order=1, points=100 )

pyCalculations/timeevolution.py

@@ -37,7 +37,7 @@ def cell_time_evolution( vlsvReader_list, variables, cellids, units="" ):
 
  .. code-block:: python
 
- import pytools as pt; import pylab as pl
+ import analysator as pt; import pylab as pl
  # Example of usage:
  time_data = pt.calculations.cell_time_evolution( vlsvReader_list=[VlsvReader("bulk.000.vlsv"), VlsvReader("bulk.001.vlsv"), VlsvReader("bulk.002.vlsv")], variables=["rho", "Pressure", "B"], cellids=[2,4], units=["N", "Pascal", "T"] )
 

pyMayaVi/grid.py

@@ -27,7 +27,7 @@
  .. code-block:: python
 
  # Example:
- import pytools as pt
+ import analysator as pt
  pt.grid.
  #press [tab] -> get the functions
 

pyMayaVi/velocityspace.py

@@ -37,7 +37,7 @@ def generate_custom_velocity_grid( vlsvReader, blocks_and_values, iso_surface=Fa
 
  # Example usage:
 
- import pytools as pt
+ import analysator as pt
 
  #vlsvReader = pt.vlsvfile.VlsvReader("example.vlsv")
 

pyPlots/plot.py

@@ -26,7 +26,7 @@
  .. code-block:: python
 
  # Example:
- import pytools as pt
+ import analysator as pt
  pt.pt.
  #press [tab] -> get the functions
 

pyPlots/plot_colormap.py

@@ -22,7 +22,7 @@
 # 
 
 import matplotlib
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 import scipy
@@ -139,7 +139,7 @@ def plot_colormap(filename=None,
  :kword nooverwrite: Set to only perform actions if the target output file does not yet exist 
 
  :kword var: variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
- E, B, v, V or others. Accepts any variable known by analysator/pytools.
+ E, B, v, V or others. Accepts any variable known by analysator.
  Per-population variables are simply given as "proton/rho" etc
  :kword operator: Operator to apply to variable: None, x, y, or z. Vector variables return either
  the queried component, or otherwise the magnitude. 

pyPlots/plot_colormap3dslice.py

@@ -22,7 +22,7 @@
 # 
 
 import matplotlib
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 import scipy
@@ -137,7 +137,7 @@ def plot_colormap3dslice(filename=None,
  :kword nooverwrite: Set to only perform actions if the target output file does not yet exist 
 
  :kword var: variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
- E, B, v, V or others. Accepts any variable known by analysator/pytools.
+ E, B, v, V or others. Accepts any variable known by analysator.
  Per-population variables are simply given as "proton/rho" etc
  :kword operator: Operator to apply to variable: None, x, y, or z. Vector variables return either
  the queried component, or otherwise the magnitude. 

pyPlots/plot_helpers.py

@@ -21,7 +21,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 # 
 
-import pytools as pt
+import analysator as pt
 import numpy as np
 from rotation import rotateTensorToVector
 

pyPlots/plot_isosurface.py

@@ -22,7 +22,7 @@
 # 
 
 import matplotlib
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 

pyPlots/plot_threeslice.py

@@ -1,5 +1,5 @@
 import matplotlib
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 import scipy
@@ -158,7 +158,7 @@ def plot_threeslice(filename=None,
  :kword step: output step index, used for constructing output (and possibly input) filename 
 
  :kword var: variable to plot, e.g. rho, RhoBackstream, beta, Temperature, MA, Mms, va, vms,
- E, B, v, V or others. Accepts any variable known by analysator/pytools.
+ E, B, v, V or others. Accepts any variable known by analysator.
  Per-population variables are simply given as "proton/rho" etc
  :kword operator: Operator to apply to variable: None, x, y, or z. Vector variables return either
  the queried component, or otherwise the magnitude. 

pyPlots/plot_vdf.py

@@ -22,7 +22,7 @@
 # 
 
 import matplotlib
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 import scipy

pyPlots/plot_vdf_profiles.py

@@ -22,7 +22,7 @@
 # 
 
 import matplotlib
-import pytools as pt
+import analysator as pt
 import numpy as np
 import matplotlib.pyplot as plt
 import scipy

pyVlsv/vlsvfile.py

@@ -27,7 +27,7 @@
  .. code-block:: python
 
  # Example:
- import pytools as pt
+ import analysator as pt
  pt.vlsvfile.
  #press [tab] -> get the functions
 

scripts/create_time_energy_spectrogram.py

@@ -72,7 +72,7 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import matplotlib.colors as colors
-import pytools as pt
+import analysator as pt
 import numpy as np
 import operator as oper
 

scripts/estimate_AMR6D_FRODO.py

@@ -1,4 +1,4 @@
-import pytools as pt
+import analysator as pt
 import sys, os, socket
 import numpy as np
 import math

scripts/plot_jet_criteria.py

@@ -21,7 +21,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 # 
 
-import pytools as pt
+import analysator as pt
 import sys, os, socket
 import numpy as np
 

scripts/plot_time_energy_spectrogram.py

@@ -35,7 +35,7 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import matplotlib.colors as colors
-import pytools as pt
+import analysator as pt
 import numpy as np
 
 # font size and linewidth