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Support reading of 'rt' lasy files #371

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merged 3 commits into from
Oct 12, 2023
Merged

Support reading of 'rt' lasy files #371

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0a14180
Support time axes in RZ
RemiLehe May 17, 2023
eb4e5a8
Support complex files
RemiLehe May 17, 2023
dbd1cd5
Merge branch 'dev' into prepare_v2
RemiLehe Oct 11, 2023
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23 changes: 11 additions & 12 deletions openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/field_reader.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -188,18 +188,17 @@ def read_field_circ( filename, iteration, field, coord,
# Extract the metainformation
coord_labels = {ii: coord.decode() for (ii,coord) in
enumerate(group.attrs['axisLabels'])}
coord_label_str = ''.join(coord_labels.values())
coord_label_str = 'm' + coord_label_str
coord_order = RZorder[coord_label_str]

if coord_order == RZorder.mrz:
if coord_labels[0] == 'r':
coord_order = RZorder.mrz
Nm, Nr, Nz = get_shape( dset )
N_pair = (Nr, Nz)
elif coord_order == RZorder.mzr:
elif coord_labels[1] == 'r':
Nm, Nz, Nr = get_shape( dset )
N_pair = (Nz, Nr)
coord_order = RZorder.mzr
else:
raise Exception(order_error_msg)

info = FieldMetaInformation( coord_labels, N_pair,
group.attrs['gridSpacing'], group.attrs['gridGlobalOffset'],
group.attrs['gridUnitSI'], dset.attrs['position'], thetaMode=True )
Expand Down Expand Up @@ -269,12 +268,6 @@ def read_field_circ( filename, iteration, field, coord,
else:

# Extract the modes and recombine them properly
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ) )
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ) )
else:
raise Exception(order_error_msg)
if m == 'all':
# Sum of all the modes
# - Prepare the multiplier arrays
Expand All @@ -290,11 +283,13 @@ def read_field_circ( filename, iteration, field, coord,
# - Sum the modes
F = get_data( dset ) # (Extracts all modes)
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ), dtype=F.dtype )
F_total[Nr:, :] = np.tensordot( mult_above_axis,
F, axes=(0, 0) )[:, :]
F_total[:Nr, :] = np.tensordot( mult_below_axis,
F, axes=(0, 0) )[::-1, :]
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ), dtype=F.dtype )
F_total[:, Nr:] = np.tensordot( mult_above_axis,
F, axes=(0, 0) )[:, :]
F_total[:, :Nr] = np.tensordot( mult_below_axis,
Expand All @@ -303,9 +298,11 @@ def read_field_circ( filename, iteration, field, coord,
# Extract mode 0
F = get_data( dset, 0, 0 )
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ), dtype=F.dtype )
F_total[Nr:, :] = F[:, :]
F_total[:Nr, :] = F[::-1, :]
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ), dtype=F.dtype )
F_total[:, Nr:] = F[:, :]
F_total[:, :Nr] = F[:, ::-1]
else:
Expand All @@ -319,9 +316,11 @@ def read_field_circ( filename, iteration, field, coord,
F_sin = get_data( dset, 2 * m, 0 )
F = cos * F_cos + sin * F_sin
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ), dtype=F.dtype )
F_total[Nr:, :] = F[:, :]
F_total[:Nr, :] = (-1) ** m * F[::-1, :]
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ), dtype=F.dtype )
F_total[:, Nr:] = F[:, :]
F_total[:, :Nr] = (-1) ** m * F[:, ::-1]
else:
Expand Down
22 changes: 11 additions & 11 deletions openpmd_viewer/openpmd_timeseries/data_reader/io_reader/field_reader.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -192,15 +192,15 @@ def read_field_circ( series, iteration, field_name, component_name,
# grid spacing/offset/position

coord_labels = {ii: coord for (ii, coord) in enumerate(field.axis_labels)}
coord_label_str = ''.join(coord_labels.values())
coord_label_str = 'm' + coord_label_str
coord_order = RZorder[coord_label_str]
if coord_order is RZorder.mrz:

if coord_labels[0] == 'r':
coord_order = RZorder.mrz
Nm, Nr, Nz = component.shape
N_pair = (Nr, Nz)
elif coord_order is RZorder.mzr:
elif coord_labels[1] == 'r':
Nm, Nz, Nr = component.shape
N_pair = (Nz, Nr)
coord_order = RZorder.mzr
else:
raise Exception(order_error_msg)

Expand Down Expand Up @@ -271,12 +271,6 @@ def read_field_circ( series, iteration, field_name, component_name,
else:

# Extract the modes and recombine them properly
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ) )
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ) )
else:
raise Exception(order_error_msg)
if m == 'all':
# Sum of all the modes
# - Prepare the multiplier arrays
Expand All @@ -292,11 +286,13 @@ def read_field_circ( series, iteration, field_name, component_name,
# - Sum the modes
F = get_data( series, component ) # (Extracts all modes)
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ), dtype=F.dtype )
F_total[Nr:, :] = np.tensordot( mult_above_axis,
F, axes=(0, 0) )[:, :]
F_total[:Nr, :] = np.tensordot( mult_below_axis,
F, axes=(0, 0) )[::-1, :]
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ), dtype=F.dtype )
F_total[:, Nr:] = np.tensordot( mult_above_axis,
F, axes=(0, 0) )[:, :]
F_total[:, :Nr] = np.tensordot( mult_below_axis,
Expand All @@ -307,9 +303,11 @@ def read_field_circ( series, iteration, field_name, component_name,
# Extract mode 0
F = get_data( series, component, 0, 0 )
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ), dtype=F.dtype )
F_total[Nr:, :] = F[:, :]
F_total[:Nr, :] = F[::-1, :]
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ), dtype=F.dtype )
F_total[:, Nr:] = F[:, :]
F_total[:, :Nr] = F[:, ::-1]
else:
Expand All @@ -322,9 +320,11 @@ def read_field_circ( series, iteration, field_name, component_name,
F_sin = get_data( series, component, 2 * m, 0 )
F = cos * F_cos + sin * F_sin
if coord_order is RZorder.mrz:
F_total = np.zeros( (2 * Nr, Nz ), dtype=F.dtype )
F_total[Nr:, :] = F[:, :]
F_total[:Nr, :] = (-1) ** m * F[::-1, :]
elif coord_order is RZorder.mzr:
F_total = np.zeros( (Nz, 2 * Nr ), dtype=F.dtype )
F_total[:, Nr:] = F[:, :]
F_total[:, :Nr] = (-1) ** m * F[:, ::-1]
else:
Expand Down