Roll dev fwd

.github/workflows/test_python.yml

@@ -5,9 +5,9 @@ name: Python import test
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, dev ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, dev ]
   schedule:
     - cron: '0 8 * * MON'
   workflow_dispatch:
@@ -60,30 +60,6 @@ jobs:
     - name: Trial imports
       run: python -c 'import analysator as pt'
 
-  turso_system:
-
-        runs-on: carrington
-        strategy:
-          fail-fast: false
-          matrix:
-            extras: ["none", "vtk", "all", "bvtk"]
-
-        steps:
-        - uses: actions/checkout@v4
-        - name: Set up Python 
-          run: |
-            python3 -m venv test_venv
-        - name: Install dependencies
-          run: |
-            source ./test_venv/bin/activate
-            python -m pip install --upgrade pip
-            python -m pip install --editable ../analysator[${{ matrix.extras }}]
-        - name: Trial imports
-          run: |
-            source ./test_venv/bin/activate
-            python -c 'import analysator as pt'
-
-
   lint:
 
     runs-on: ubuntu-latest

.github/workflows/test_python_turso.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Turso import test
+
+on:
+  push:
+    branches: [ master, dev ]
+  pull_request:
+    branches: [ master, dev ]
+  schedule:
+    - cron: '0 8 * * MON'
+  workflow_dispatch:
+
+jobs:
+
+  turso_system:
+        if: github.repository_owner == 'fmihpc'
+        runs-on: carrington
+        strategy:
+          fail-fast: false
+          matrix:
+            extras: ["none", "vtk", "all", "bvtk"]
+        steps:
+        - uses: actions/checkout@v4
+        - name: Set up Python 
+          run: |
+            export TMPDIR=$RUNNER_TEMP
+            python3 -m venv test_venv
+        - name: Install dependencies
+          run: |
+            export TMPDIR=$RUNNER_TEMP
+            source ./test_venv/bin/activate
+            python -m ensurepip
+            python -m pip install --upgrade pip
+            python -m pip install --editable ../analysator[${{ matrix.extras }}]
+        - name: Trial imports
+          run: |
+            export TMPDIR=$RUNNER_TEMP
+            source ./test_venv/bin/activate
+            python -c 'import analysator as pt'
+

CITATION.cff

@@ -68,7 +68,7 @@ authors:
 - family-names: "Reimi"
   given-names: "Johanna"
 title: "Analysator"
-version: 0.9.5
+version: 0.9.6
 doi: 10.5281/zenodo.4462514
 date-released: 2024-11-26
 url: "https://github.com/fmihpc/analysator"

Documentation/sphinx/obliqueshock.rst

@@ -0,0 +1,5 @@
+obliqueshock
+------------
+
+.. automodule:: obliqueshock
+	:members:

Documentation/sphinx/obliqueshock_nif.rst

@@ -0,0 +1,5 @@
+obliqueshock_nif
+----------------
+
+.. automodule:: obliqueshock_nif
+	:members:

Documentation/sphinx/scripts.rst

@@ -39,6 +39,24 @@ magnetopause3d
 
 ------------
 
+obliqueshock
+------------
+:doc:`obliqueshock`
+
+.. automodule:: obliqueshock
+    :no-index:
+
+------------
+
+obliqueshock_nif
+----------------
+:doc:`obliqueshock_nif`
+
+.. automodule:: obliqueshock_nif
+    :no-index:
+
+----------------
+
 shue
 --------------
 :doc:`shue`
@@ -65,6 +83,8 @@ tsyganenko
    gics
    magnetopause2d
    magnetopause3d
+   obliqueshock
+   obliqueshock_nif
    shue
    tsyganenko
 

analysator/pyCalculations/calculations.py

@@ -44,7 +44,7 @@
 from fourier import fourier
 from spectra import get_spectrum_energy, get_spectrum_alongaxis_vel
 from variable import VariableInfo
-from timeevolution import cell_time_evolution
+from timeevolution import cell_time_evolution,point_time_evolution
 from pitchangle import pitch_angles
 #from backstream import extract_velocity_cells_sphere, extract_velocity_cells_non_sphere
 from gyrophaseangle import gyrophase_angles_from_file

analysator/pyCalculations/timeevolution.py

@@ -60,8 +60,19 @@ def cell_time_evolution( vlsvReader_list, variables, cellids, units="" ):
    vlsvReader_list = np.atleast_1d(vlsvReader_list)
    variables = np.atleast_1d(variables)
    cellids = np.atleast_1d(cellids)
-   parameters = ["t","tstep","fileIndex"]
-   parameter_units=["s","",""]
+   reader_0 = vlsvReader_list[0]
+
+   # Check against legacy files with tstep instead of timestep:
+   if reader_0.check_parameter("tstep"):
+      parameters = ["t","tstep","fileIndex"]
+      parameter_units=["s","",""]
+   elif reader_0.check_parameter("timestep"):
+      parameters = ["t","timestep","fileIndex"]
+      parameter_units=["s","",""]
+   else:
+      logging.warning("Could not obtain tstep or timestep from readers. Returning only t and fileIndex.")
+      parameters = ["t","fileIndex"]
+      parameter_units=["s",""]
    #construct empty units, if none are given
    if (units == "") or (len(units) != len(variables)):
       units=[ "" for i in range(len(variables))]
@@ -86,6 +97,95 @@ def cell_time_evolution( vlsvReader_list, variables, cellids, units="" ):
          # Save the data into the right slot in the data array:
          for i in range(len(cellids)):
             data[len(parameters)+i*len(variables)+j].append(vlsvReader.read_variable( variable, cellids[i] ))
+            #TODO Use vectorization over cellids!
+
+      # For optimization purposes we are now freeing vlsvReader's memory
+      # Note: Upon reading data vlsvReader created an internal hash map that takes a lot of memory
+      vlsvReader.optimize_clear_fileindex_for_cellid()
+      # Close the vlsv reader's file:
+      vlsvReader.optimize_close_file()
+   from output import output_1d
+   return output_1d( data, 
+                     parameters +  [variables[(int)(i)%(int)(len(variables))] for i in range(len(data)-len(parameters))], 
+                     parameter_units + [units[(int)(i)%(int)(len(units))] for i in range(len(data)-len(parameters))] )
+
+
+def point_time_evolution( vlsvReader_list, variables, coordinates, units="", method='nearest'):
+   ''' Returns variable data from a time evolution of some certain cell ids
+
+       :param vlsvReader_list:         List containing VlsvReaders with a file open
+       :type vlsvReader_list:          :class:`vlsvfile.VlsvReader`
+       :param variables:               Name of the variables
+       :param coordinates:             List of coordinates [n,3]
+       :param units:                   List of units for the variables (OPTIONAL)
+       :param method:                  name of interpolation method ['nearest','linear']
+       :returns: an array containing the data for the time evolution for every coordinate
+
+       .. code-block:: python
+
+          import pytools as pt; import pylab as pl
+          # Example of usage:
+          time_data = pt.calculations.point_time_evolution( vlsvReader_list=[VlsvReader("bulk.000.vlsv"), VlsvReader("bulk.001.vlsv"), VlsvReader("bulk.002.vlsv")], variables=["rho", "Pressure", "B"], coordinates=[[1e8,0,0],[1.2e8,0,0]], units=["N", "Pascal", "T"] )
+
+          # Check output
+          logging.info time_data
+
+          # Now plot the results:
+          time = time_data[0]
+          rho = time_data[3]
+          pt.plot.plot_variables(time, rho)
+          pl.show()
+
+          # Do post processing:
+          rho_data = rho.data
+          non_existing_example_function(rho_data)
+
+
+   '''
+   vlsvReader_list = np.atleast_1d(vlsvReader_list)
+   variables = np.atleast_1d(variables)
+   coordinates = np.array(coordinates)
+   if coordinates.ndim == 1:
+      coordinates = coordinates[np.newaxis,:]
+   reader_0 = vlsvReader_list[0]
+
+   # Check against legacy files with tstep instead of timestep:
+   if reader_0.check_parameter("tstep"):
+      parameters = ["t","tstep","fileIndex"]
+      parameter_units=["s","",""]
+   elif reader_0.check_parameter("timestep"):
+      parameters = ["t","timestep","fileIndex"]
+      parameter_units=["s","",""]
+   else:
+      logging.warning("Could not obtain tstep or timestep from readers. Returning only t and fileIndex.")
+      parameters = ["t","fileIndex"]
+      parameter_units=["s",""]
+   #construct empty units, if none are given
+   if (units == "") or (len(units) != len(variables)):
+      units=[ "" for i in range(len(variables))]
+   #construct data 
+   data = [[] for i in range(len(parameters)+coordinates.shape[0]*len(variables))]
+   for t in range(len(vlsvReader_list)):
+      # Get the vlsv reader
+      vlsvReader = vlsvReader_list[t]
+      # Open the vlsv reader's file:
+      vlsvReader.optimize_open_file()
+      #go through parameters
+      for j in range(len(parameters)):
+         # Read the parameter
+         # Save the data into the right slot in the data array:
+         data[j].append(vlsvReader.read_parameter( parameters[j]))
+
+      # Go through variables:
+      for j in range(len(variables)):
+         variable = variables[j]
+         # Read the variable for all cell ids
+         #variables_for_cellids = vlsvReader.read_variables_for_cellids( variable, cellids )
+         # Save the data into the right slot in the data array:
+         for i in range(coordinates.shape[0]):
+            data[len(parameters)+i*len(variables)+j].append(vlsvReader.read_interpolated_variable( variable, coordinates[i,:], method=method ))
+            #TODO Use vectorization over coordinates!
+
       # For optimization purposes we are now freeing vlsvReader's memory
       # Note: Upon reading data vlsvReader created an internal hash map that takes a lot of memory
       vlsvReader.optimize_clear_fileindex_for_cellid()

analysator/pyPlots/plot_ionosphere.py

@@ -142,7 +142,12 @@ def plot_ionosphere(filename=None,
     fontsize3=8*scale # Colour bar ticks and title
 
     # Plot title with time
-    timeval=f.read_parameter("time")
+    try:
+        timeval=f.read_parameter("time")
+    except:
+        # The ionosphere solver miniApp writes outputfiles without a valid
+        # time value.
+        timeval=None
 
     # Plot title with time
     if title is None or title=="msec" or title=="musec":        

analysator/pyPlots/plot_vdf.py

@@ -269,6 +269,8 @@ def vSpaceReducer(vlsvReader, cid, slicetype, normvect, VXBins, VYBins, pop="pro
          Vpeak = V[peakindex,:]
          V = V - Vpeak
          logging.info(peakindex)
+         VXBins -= 0.5*inputcellsize
+         VYBins -= 0.5*inputcellsize
          logging.info("Transforming to frame of peak f-value, travelling at speed "+str(Vpeak))
     elif not center is None:
         # assumes it's a vector, either provided or extracted from bulk velocity
@@ -689,7 +691,7 @@ def plot_vdf(filename=None,
     vysize = int(vysize)
     vzsize = int(vzsize)
     [vxmin, vymin, vzmin, vxmax, vymax, vzmax] = vlsvReader.get_velocity_mesh_extent(pop=pop)
-    inputcellsize=(vxmax-vxmin)/vxsize
+
 
     # Account for WID3 cells per block
     widval=4 #default WID=4
@@ -699,6 +701,9 @@ def plot_vdf(filename=None,
     vysize = widval*vysize
     vzsize = widval*vzsize
 
+    inputcellsize=(vxmax-vxmin)/(vxsize)
+    # print(inputcellsize)
+
     Re = 6.371e+6 # Earth radius in m
     # unit of velocity
     velUnit = 1e3