[WIP] Implement slice_absolute_position

openpmd_viewer/openpmd_timeseries/data_reader/field_reader.py

@@ -15,7 +15,7 @@
 from ..utilities import construct_3d_from_circ
 
 def read_field_cartesian( filename, field_path, axis_labels,
-  slice_relative_position, slice_across ):
+ slice_relative_position, slice_absolute_position, slice_across ):
  """
  Extract a given field from an HDF5 file in the openPMD format,
  when the geometry is cartesian (1d, 2d or 3d).
@@ -47,6 +47,10 @@ def read_field_cartesian( filename, field_path, axis_labels,
  0 : middle of the simulation box
  1 : upper edge of the simulation box
 
+ slice_absolute_position : list of float, or None
+ Position(s), in meters, where to slice the data, along the
+ directions in `slice_across`s
+
  Returns
  -------
  A tuple with
@@ -74,8 +78,16 @@ def read_field_cartesian( filename, field_path, axis_labels,
  list_slicing_index.append(slicing_index)
  # Number of cells along the slicing direction
  n_cells = shape[ slicing_index ]
- # Index of the slice (prevent stepping out of the array)
- i_cell = int( 0.5 * (slice_relative_position[count] + 1.) * n_cells )
+ # Index of the slice
+ if slice_relative_position is not None:
+ i_cell = int( 0.5 * (slice_relative_position[count] + 1.) * n_cells )
+ elif slice_absolute_position is not None:
+ i_cell = int(
+ (slice_absolute_position[count]-global_offset[slicing_index])/grid_spacing[slicing_index]) )
+ else:
+ raise ValueError( 'slice_relative_position and '
+ 'slice_absolute_position cannot both be None.')
+ # Prevent stepping out of the array
  i_cell = max( i_cell, 0 )
  i_cell = min( i_cell, n_cells - 1)
  list_i_cell.append(i_cell)
@@ -109,7 +121,7 @@ def read_field_cartesian( filename, field_path, axis_labels,
 
 
 def read_field_circ( filename, field_path, slice_relative_position,
- slice_across, m=0, theta=0. ):
+ slice_absolute_position, slice_across, m=0, theta=0. ):
  """
  Extract a given field from an HDF5 file in the openPMD format,
  when the geometry is thetaMode
@@ -144,6 +156,10 @@ def read_field_circ( filename, field_path, slice_relative_position,
  0 : middle of the simulation box
  1 : upper edge of the simulation box
 
+ slice_absolute_position : list of float, or None
+ Position(s), in meters, where to slice the data, along the
+ directions in `slice_across`s
+
  Returns
  -------
  A tuple with
@@ -231,8 +247,15 @@ def read_field_circ( filename, field_path, slice_relative_position,
  coord_array = getattr( info, slice_across_item )
  # Number of cells along the slicing direction
  n_cells = len(coord_array)
- # Index of the slice (prevent stepping out of the array)
- i_cell = int( 0.5 * (slice_relative_position[count] + 1.) * n_cells )
+ # Index of the slice
+ if slice_relative_position is not None:
+ i_cell = int( 0.5 * (slice_relative_position[count] + 1.) * n_cells )
+ elif slice_absolute_position:
+ i_cell = np.argmin( abs(coord_array-slice_absolute_position[count]) )
+ else:
+ raise ValueError( 'slice_relative_position and '
+ 'slice_absolute_position cannot both be None.')
+ # Present stepping out of the array
  i_cell = max( i_cell, 0 )
  i_cell = min( i_cell, n_cells - 1)
  F_total = np.take( F_total, [i_cell], axis=slicing_index )

openpmd_viewer/openpmd_timeseries/main.py

@@ -409,8 +409,16 @@ def get_field(self, field=None, coord=None, t=None, iteration=None,
  -1 : lower edge of the simulation box
  0 : middle of the simulation box
  1 : upper edge of the simulation box
- Default: None, which results in slicing at 0 in all direction
- of `slice_across`.
+ Default: None, which results in slicing at the middle of the box,
+ in each direction of `slice_across
+ (unless `slice_absolute_position` is set)
+
+ slice_absolute_position : float or list of float, optional
+ Position(s), in meters, where to slice the data, along the
+ directions in `slice_across`
+ Default: None, which results in slicing at the middle of the box,
+ in each direction of `slice_across`
+ (unless `slice_relative_position` is set)
 
  plot : bool, optional
  Whether to plot the requested quantity
@@ -442,8 +450,9 @@ def get_field(self, field=None, coord=None, t=None, iteration=None,
  "The available fields are: \n - %s\nPlease set the `field` "
  "argument accordingly." % field_list)
  # Check slicing
- slice_across, slice_relative_position = \
- sanitize_slicing(slice_across, slice_relative_position)
+ slice_across, slice_relative_position, slice_absolute_position = \
+ sanitize_slicing( slice_across, slice_relative_position,
+ slice_absolute_position )
  if slice_across is not None:
  # Check that the elements are valid
  axis_labels = self.fields_metadata[field]['axis_labels']
@@ -495,21 +504,25 @@ def get_field(self, field=None, coord=None, t=None, iteration=None,
  # - For cartesian
  if geometry in ["1dcartesian", "2dcartesian", "3dcartesian"]:
  F, info = read_field_cartesian( filename, field_path,
- axis_labels, slice_relative_position, slice_across)
+ axis_labels, slice_relative_position, slice_absolute_position,
+ slice_across)
  # - For thetaMode
  elif geometry == "thetaMode":
  if (coord in ['x', 'y']) and \
  (self.fields_metadata[field]['type'] == 'vector'):
  # For Cartesian components, combine r and t components
  Fr, info = read_field_circ(filename, field + '/r',
- slice_relative_position, slice_across, m, theta)
+ slice_relative_position, slice_absolute_position,
+ slice_across, m, theta)
  Ft, info = read_field_circ(filename, field + '/t',
- slice_relative_position, slice_across, m, theta)
+ slice_relative_position, slice_absolute_position,
+ slice_across, m, theta)
  F = combine_cylindrical_components(Fr, Ft, theta, coord, info)
  else:
  # For cylindrical or scalar components, no special treatment
  F, info = read_field_circ(filename, field_path,
- slice_relative_position, slice_across, m, theta)
+ slice_relative_position, slice_absolute_position,
+ slice_across, m, theta)
 
  # Plot the resulting field
  # Deactivate plotting when there is no slice selection

openpmd_viewer/openpmd_timeseries/utilities.py

@@ -16,7 +16,8 @@
 from .data_reader.particle_reader import read_species_data
 from .numba_wrapper import jit
 
-def sanitize_slicing(slice_across, slice_relative_position):
+def sanitize_slicing(slice_across, slice_relative_position,
+ slice_absolute_position):
  """
  Return standardized format for `slice_across` and `slice_relative_position`:
  - either `slice_across` and `slice_relative_position` are both `None` (no slicing)
@@ -27,13 +28,23 @@ def sanitize_slicing(slice_across, slice_relative_position):
  ----------
  slice_relative_position : float, or list of float, or None
 
+ slice_absolute_position : float, or list of float, or None
+
  slice_across : str, or list of str, or None
  Direction(s) across which the data should be sliced
  """
  # Skip None and empty lists
  if slice_across is None or slice_across == []:
  return None, None
 
+ # Check that `slice_relative_position` and `slice_absolute_position`
+ # are not simultaneously provided:
+ if (slice_relative_position is not None) and \
+ (slice_absolute_position is not None):
+ raise ValueError(
+ 'The arguments `slice_relative_position` and `slice_absolute_position` '
+ 'cannot be used simultaneously.')
+
  # Convert to lists
  if not isinstance(slice_across, list):
  slice_across = [slice_across]